133 results on '"Tingzhao Rong"'
Search Results
2. A teosinte-derived allele of ZmSC improves salt tolerance in maize
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Xiaofeng Li, Qiangqiang Ma, Xingyu Wang, Yunfeng Zhong, Yibo Zhang, Ping Zhang, Yiyang Du, Hanyu Luo, Yu Chen, Xiangyuan Li, Yingzheng Li, Ruyu He, Yang Zhou, Yang Li, Mingjun Cheng, Jianmei He, Tingzhao Rong, and Qilin Tang
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salt stress ,maize ,wild relatives ,transgenic Arabidopsis ,CDPK ,Plant culture ,SB1-1110 - Abstract
Maize, a salt-sensitive crop, frequently suffers severe yield losses due to soil salinization. Enhancing salt tolerance in maize is crucial for maintaining yield stability. To address this, we developed an introgression line (IL76) through introgressive hybridization between maize wild relatives Zea perennis, Tripsacum dactyloides, and inbred Zheng58, utilizing the tri-species hybrid MTP as a genetic bridge. Previously, genetic variation analysis identified a polymorphic marker on Zm00001eb244520 (designated as ZmSC), which encodes a vesicle-sorting protein described as a salt-tolerant protein in the NCBI database. To characterize the identified polymorphic marker, we employed gene cloning and homologous cloning techniques. Gene cloning analysis revealed a non-synonymous mutation at the 1847th base of ZmSCIL76, where a guanine-to-cytosine substitution resulted in the mutation of serine to threonine at the 119th amino acid sequence (using ZmSCZ58 as the reference sequence). Moreover, homologous cloning demonstrated that the variation site derived from Z. perennis. Functional analyses showed that transgenic Arabidopsis lines overexpressing ZmSCZ58 exhibited significant reductions in leaf number, root length, and pod number, alongside suppression of the expression of genes in the SOS and CDPK pathways associated with Ca2+ signaling. Similarly, fission yeast strains expressing ZmSCZ58 displayed inhibited growth. In contrast, the ZmSCIL76 allele from Z. perennis alleviated these negative effects in both Arabidopsis and yeast, with the lines overexpressing ZmSCIL76 exhibiting significantly higher abscisic acid (ABA) content compared to those overexpressing ZmSCZ58. Our findings suggest that ZmSC negatively regulates salt tolerance in maize by suppressing downstream gene expression associated with Ca2+ signaling in the CDPK and SOS pathways. The ZmSCIL76 allele from Z. perennis, however, can mitigate this negative regulatory effect. These results provide valuable insights and genetic resources for future maize salt tolerance breeding programs.
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- 2024
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3. ZmMS39 encodes a callose synthase essential for male fertility in maize (Zea mays L.)
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Qunkai Niu, Ziwen Shi, Peng Zhang, Shuai Su, Bin Jiang, Xiaowei Liu, Zhuofan Zhao, Suzhi Zhang, Qiang Huang, Chuan Li, Tao Yu, Hongyang Yi, Tingzhao Rong, and Moju Cao
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Maize ,Genic male sterility ,Callose synthase ,Tapetal PCD ,Anther and pollen development ,Autophagy ,Agriculture ,Agriculture (General) ,S1-972 - Abstract
Callose contributes to many biological processes of higher plants including pollen development, cell plate and vascular tissue formation, as well as regulating the transport function of plasmodesmata. The functions of callose synthase genes in maize have been little studied. We describe a maize male-sterile mutant 39 (ms39) characterized by reduced plant height. In this study, we confirmed using CRISPR/Cas9 technology that a mutation in Zm00001d043909 (ZmCals12), encoding a callose synthase, is responsible for the male sterility of the ms39 mutant. Compared with male-fertile plants, callose deposition around the dyads and tetrads in ms39 anthers was significantly reduced. Increased cell autophagy observed in ms39 anthers may have been due to the premature programmed cell death of tapetal cells, leading to collapse of the anther wall structure. Disordered glucose metabolism in ms39 may have intensified autophagy in anthers. Evaluation of the ms39 gene on maize heterosis by paired-crossed experiment with 11 maize inbred lines indicated that ms39 can be used for maize hybrid seed production.
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- 2023
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4. Integrated single-molecule real-time sequencing and RNA sequencing reveal the molecular mechanisms of salt tolerance in a novel synthesized polyploid genetic bridge between maize and its wild relatives
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Xiaofeng Li, Xingyu Wang, Qiangqiang Ma, Yunfeng Zhong, Yibo Zhang, Ping Zhang, Yingzheng Li, Ruyu He, Yang Zhou, Yang Li, Mingjun Cheng, Xu Yan, Yan Li, Jianmei He, Muhammad Zafar Iqbal, Tingzhao Rong, and Qilin Tang
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SMRT-sequencing ,RNA-sequencing ,Zea mays ,Tripsacum dactyloides ,Zea perennis ,Genetic bridge ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Tripsacum dactyloides (2n = 4x = 72) and Zea perennis (2n = 4x = 40) are tertiary gene pools of Zea mays L. and exhibit many abiotic adaptations absent in modern maize, especially salt tolerance. A previously reported allopolyploid (hereafter referred to as MTP, 2n = 74) synthesized using Zea mays, Tripsacum dactyloides, and Zea perennis has even stronger salt tolerance than Z. perennis and T. dactyloides. This allopolyploid will be a powerful genetic bridge for the genetic improvement of maize. However, the molecular mechanisms underlying its salt tolerance, as well as the key genes involved in regulating its salt tolerance, remain unclear. Results Single-molecule real-time sequencing and RNA sequencing were used to identify the genes involved in salt tolerance and reveal the underlying molecular mechanisms. Based on the SMRT-seq results, we obtained 227,375 reference unigenes with an average length of 2300 bp; most of the unigenes were annotated to Z. mays sequences (76.5%) in the NR database. Moreover, a total of 484 and 1053 differentially expressed genes (DEGs) were identified in the leaves and roots, respectively. Functional enrichment analysis of DEGs revealed that multiple pathways responded to salt stress, including “Flavonoid biosynthesis,” “Oxidoreductase activity,” and “Plant hormone signal transduction” in the leaves and roots, and “Iron ion binding,” “Acetyl-CoA carboxylase activity,” and “Serine-type carboxypeptidase activity” in the roots. Transcription factors, such as those in the WRKY, B3-ARF, and bHLH families, and cytokinin negatively regulators negatively regulated the salt stress response. According to the results of the short time series-expression miner analysis, proteins involved in “Spliceosome” and “MAPK signal pathway” dynamically responded to salt stress as salinity changed. Protein–protein interaction analysis revealed that heat shock proteins play a role in the large interaction network regulating salt tolerance. Conclusions Our results reveal the molecular mechanism underlying the regulation of MTP in the response to salt stress and abundant salt-tolerance-related unigenes. These findings will aid the retrieval of lost alleles in modern maize and provide a new approach for using T. dactyloides and Z. perennis to improve maize.
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- 2023
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5. Combining QTL-seq and linkage mapping to uncover the genetic basis of single vs. paired spikelets in the advanced populations of two-ranked maize×teosinte
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Zhengjie Chen, Dengguo Tang, Kun Hu, Lei Zhang, Yong Yin, Jixing Ni, Peng Li, Le Wang, Tingzhao Rong, and Jian Liu
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Maize domestication ,Single vs. paired spikelets ,QTL-seq ,Major QTL ,Epistasis ,Photoperiod ,Botany ,QK1-989 - Abstract
Abstract Background Teosinte ear bears single spikelet, whereas maize ear bears paired spikelets, doubling the number of grains in each cupulate during maize domestication. In the past 20 years, genetic analysis of single vs. paired spikelets (PEDS) has been stagnant. A better understanding of genetic basis of PEDS could help fine mapping of quantitative trait loci (QTL) and cloning of genes. Results In this study, the advanced mapping populations (BC3F2 and BC4F2) of maize × teosinte were developed by phenotypic recurrent selection. Four genomic regions associated with PEDS were detected using QTL-seq, located on 194.64–299.52 Mb, 0–162.80 Mb, 12.82–97.17 Mb, and 125.06–157.01 Mb of chromosomes 1, 3, 6, and 8, respectively. Five QTL for PEDS were identified in the regions of QTL-seq using traditional QTL mapping. Each QTL explained 1.12–38.05% of the phenotypic variance (PVE); notably, QTL qPEDS3.1 with the average PVE of 35.29% was identified in all tests. Moreover, 14 epistatic QTL were detected, with the total PVE of 47.57–66.81% in each test. The QTL qPEDS3.1 overlapped with, or was close to, one locus of 7 epistatic QTL. Near-isogenic lines (NILs) of QTL qPEDS1.1, qPEDS3.1, qPEDS6.1, and qPEDS8.1 were constructed. All individuals of NIL-qPEDS6.1(MT1) and NIL-qPEDS8.1(MT1) showed paired spikelets (PEDS = 0), but the flowering time was 7 days shorter in the NIL-qPEDS8.1(MT1). The ratio of plants with PEDS > 0 was low (1/18 to 3/18) in the NIL-qPEDS1.1(MT1) and NIL-qPEDS3.1(MT1), maybe due to the epistatic effect. Conclusion Our results suggested that major QTL, minor QTL, epistasis and photoperiod were associated with the variation of PEDS, which help us better understand the genetic basis of PEDS and provide a genetic resource for fine mapping of QTL.
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- 2021
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6. qRf8-1, a Novel QTL for the Fertility Restoration of Maize CMS-C Identified by QTL-seq
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Mingmin Zheng, Tian Yang, Xiaowei Liu, Guihua Lü, Peng Zhang, Bin Jiang, Shufeng Zhou, Yanli Lu, Hai Lan, Suzhi Zhang, Chuan Li, Tingzhao Rong, and Moju Cao
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maize ,cytoplasmic male sterility ,fertility restoration ,restorer gene ,qtl-seq ,Genetics ,QH426-470 - Abstract
C-type cytoplasmic male sterility (CMS-C), one of the three major CMS types in maize, has a promising application prospect in hybrid seed production. However, the complex genetic mechanism underlying the fertility restoration of CMS-C remains poorly understood. The maize inbred line A619 is one of the rare strong restorer lines carrying the restorer gene Rf4, but different fertility segregation ratios are found in several F2 populations derived from crosses between isocytoplasmic allonucleus CMS-C lines and A619. In the present study, the segregation ratios of fertile to sterile plants in the (CHuangzaosi × A619) F2 and BC1F1 populations (36.77:1 and 2.36:1, respectively) did not follow a typical monogenic model of inheritance, which suggested that some F2 and BC1F1 plants displayed restored fertility even without Rf4. To determine the hidden locus affecting fertility restoration, next-generation sequencing-based QTL-seq was performed with two specific extreme bulks consisting of 30 fertile and 30 sterile rf4rf4 individuals from the F2 population. A major QTL related to fertility restoration, designated qRf8-1, was detected on the long arm of chromosome 8 in A619. Subsequently, qRf8-1 was further validated and narrowed down to a 17.93-Mb genomic interval by insertion and deletion (InDel) and simple sequence repeat (SSR) marker-based traditional QTL mapping, explaining 12.59% (LOD = 25.06) of the phenotypic variation. Thus, using genetic analyses and molecular markers, we revealed another fertility restoration system acting in parallel with Rf4 in A619 that could rescue the male sterility of CHuangzaosi. This study not only expands the original fertility restoration system but also provides valuable insights into the complex genetic mechanisms underlying the fertility restoration of CMS-C.
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- 2020
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7. Tripsazea, a Novel Trihybrid of Zea mays, Tripsacum dactyloides, and Zea perennis
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Xu Yan, Mingjun Cheng, Yingzheng Li, Zizhou Wu, Yang Li, Xiaofeng Li, Ruyu He, Chunyan Yang, Yanli Zhao, Huaxiong Li, Xiaodong Wen, Ping Zhang, Ebenezer Sam, Tingzhao Rong, Jianmei He, and Qilin Tang
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zea mays ,tripsacum dactyloides ,zea perennis ,trihybrid ,maize improvement ,forage breeding ,Genetics ,QH426-470 - Abstract
A trispecific hybrid, MTP (hereafter called tripsazea), was developed from intergeneric crosses involving tetraploid Zea mays (2n = 4x = 40, genome: MMMM), tetraploid Tripsacum dactyloides (2n = 4x = 72, TTTT), and tetraploid Z. perennis (2n = 4x = 40, PPPP). On crossing maize-Tripsacum (2n = 4x = 56, MMTT) with Z. perennis, 37 progenies with varying chromosome numbers (36-74) were obtained, and a special one (i.e., tripsazea) possessing 2n = 74 chromosomes was generated. Tripsazea is perennial and expresses phenotypic characteristics affected by its progenitor parent. Flow cytometry analysis of tripsazea and its parents showed that tripsazea underwent DNA sequence elimination during allohexaploidization. Of all the chromosomes in diakinesis I, 18.42% participated in heterogenetic pairing, including 16.43% between the M- and P-genomes, 1.59% between the M- and T-genomes, and 0.39% in T- and P-genome pairing. Tripsazea is male sterile and partly female fertile. In comparison with previously synthesized trihybrids containing maize, Tripsacum and teosinte, tripsazea has a higher chromosome number, higher seed setting rate, and vegetative propagation ability of stand and stem. However, few trihybrids possess these valuable traits at the same time. The potential of tripsazea is discussed with respect to the deployment of the genetic bridge for maize improvement and forage breeding.
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- 2020
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8. Mysterious meiotic behavior of autopolyploid and allopolyploid maize
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Muhammad Zafar Iqbal, Mingjun Cheng, Yanli Zhao, Xiaodong Wen, Ping Zhang, Lei Zhang, Asif Ali, Tingzhao Rong, and Qi Lin Tang
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Genetics ,QH426-470 - Abstract
This study was aimed to investigate the stability of chromosomes during meiosis in autopolyploid and allopolyploid maize, as well as to determine an association of chromosomes between maize (Zea mays ssp. mays Linnaeus, 1753) and Z. perennis (Hitchcock, 1922) Reeves & Mangelsdor, 1942, by producing a series of autopolyploid and allopolyploid maize hybrids. The intra-genomic and inter-genomic meiotic pairings in these polyploids were quantified and compared using dual-color genomic in-situ hybridization. The results demonstrated higher level of chromosome stability in allopolyploid maize during meiosis as compared to autopolyploid maize. In addition, the meiotic behavior of Z. perennis was relatively more stable as compared to the allopolyploid maize. Moreover, ten chromosomes of "A” subgenome in maize were homologous to twenty chromosomes of Z. perennis genome with a higher pairing frequency and little evolutionary differentiation. At the same time, little evolutionary differentiation has been shown by chromosomes of "A” subgenome in maize, while chromosomes of "B” subgenome, had a lower pairing frequency and higher evolutionary differentiation. Furthermore, 5IM + 5IIPP + 5IIIMPP and 5IIMM + 5IIPP + 5IVMMPP were observed in allotriploids and allotetraploids respectively, whereas homoeologous chromosomes were found between the "A” and "B” genome of maize and Z. perennis.
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- 2018
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9. Transcriptomic Analysis Reveals Candidate Genes Responding Maize Gray Leaf Spot Caused by Cercospora zeina
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Wenzhu He, Yonghui Zhu, Yifeng Leng, Lin Yang, Biao Zhang, Junpin Yang, Xiao Zhang, Hai Lan, Haitao Tang, Jie Chen, Shibin Gao, Jun Tan, Jiwei Kang, Luchang Deng, Yan Li, Yuanyuan He, Tingzhao Rong, and Moju Cao
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maize ,RNA-Seq ,gray leaf spot ,WGCNA ,disease resistance ,Botany ,QK1-989 - Abstract
Gray leaf spot (GLS), caused by the fungal pathogen Cercospora zeina (C. zeina), is one of the most destructive soil-borne diseases in maize (Zea mays L.), and severely reduces maize production in Southwest China. However, the mechanism of resistance to GLS is not clear and few resistant alleles have been identified. Two maize inbred lines, which were shown to be resistant (R6) and susceptible (S8) to GLS, were injected by C. zeina spore suspensions. Transcriptome analysis was carried out with leaf tissue at 0, 6, 24, 144, and 240 h after inoculation. Compared with 0 h of inoculation, a total of 667 and 419 stable common differentially expressed genes (DEGs) were found in the resistant and susceptible lines across the four timepoints, respectively. The DEGs were usually enriched in ‘response to stimulus’ and ‘response to stress’ in GO term analysis, and ‘plant–pathogen interaction’, ‘MAPK signaling pathways’, and ‘plant hormone signal transduction’ pathways, which were related to maize’s response to GLS, were enriched in KEGG analysis. Weighted-Genes Co-expression Network Analysis (WGCNA) identified two modules, while twenty hub genes identified from these indicated that plant hormone signaling, calcium signaling pathways, and transcription factors played a central role in GLS sensing and response. Combing DEGs and QTL mapping, five genes were identified as the consensus genes for the resistance of GLS. Two genes, were both putative Leucine-rich repeat protein kinase family proteins, specifically expressed in R6. In summary, our results can provide resources for gene mining and exploring the mechanism of resistance to GLS in maize.
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- 2021
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10. Genome-wide characterization of non-reference transposable element insertion polymorphisms reveals genetic diversity in tropical and temperate maize
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Xianjun Lai, James C. Schnable, Zhengqiao Liao, Jie Xu, Gengyun Zhang, Chuan Li, Erliang Hu, Tingzhao Rong, Yunbi Xu, and Yanli Lu
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Adaptation ,Genetic recombination ,GWAS ,Maize ,Transposable elements ,Non-redundant TEs (NRTE) ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Maize was originally domesticated in a tropical environment but is now widely cultivated at temperate latitudes. Temperate and tropical maize populations have diverged both genotypically and phenotypically. Tropical maize lines grown in temperate environments usually exhibit delayed flowering, pollination, and seed set, which reduces their grain yield relative to temperate adapted maize lines. One potential mechanism by which temperate maize may have adapted to a new environment is novel transposable element insertions, which can influence gene regulation. Recent advances in sequencing technology have made it possible to study variation in transposon content and insertion location in large sets of maize lines. Results In total, 274,408 non-redundant TEs (NRTEs) were identified using resequencing data generated from 83 maize inbred lines. The locations of DNA TEs and copia-superfamily retrotransposons showed significant positive correlations with gene density and genetic recombination rates, whereas gypsy-superfamily retrotransposons showed a negative correlation with these two parameters. Compared to tropical maize, temperate maize had fewer unique NRTEs but higher insertion frequency, lower background recombination rates, and higher linkage disequilibrium, with more NRTEs close to flowering and stress-related genes in the genome. Association mapping demonstrated that the presence/absence of 48 NRTEs was associated with flowering time and that expression of neighboring genes differed between haplotypes where a NRTE was present or absent. Conclusions This study suggests that NRTEs may have played an important role in creating the variation in gene regulation that enabled the rapid adaptation of maize to diverse environments.
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- 2017
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11. Validation of potential reference genes for qPCR in maize across abiotic stresses, hormone treatments, and tissue types.
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Yueai Lin, Chenlu Zhang, Hai Lan, Shibin Gao, Hailan Liu, Jian Liu, Moju Cao, Guangtang Pan, Tingzhao Rong, and Suzhi Zhang
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Medicine ,Science - Abstract
The reverse transcription quantitative polymerase chain reaction (RT-qPCR) is a powerful and widely used technique for the measurement of gene expression. Reference genes, which serve as endogenous controls ensure that the results are accurate and reproducible, are vital for data normalization. To bolster the literature on reference gene selection in maize, ten candidate reference genes, including eight traditionally used internal control genes and two potential candidate genes from our microarray datasets, were evaluated for expression level in maize across abiotic stresses (cold, heat, salinity, and PEG), phytohormone treatments (abscisic acid, salicylic acid, jasmonic acid, ethylene, and gibberellins), and different tissue types. Three analytical software packages, geNorm, NormFinder, and Bestkeeper, were used to assess the stability of reference gene expression. The results revealed that elongation factor 1 alpha (EF1α), tubulin beta (β-TUB), cyclophilin (CYP), and eukaryotic initiation factor 4A (EIF4A) were the most reliable reference genes for overall gene expression normalization in maize, while GRP (Glycine-rich RNA-binding protein), GLU1(beta-glucosidase), and UBQ9 (ubiquitin 9) were the least stable and most unsuitable genes. In addition, the suitability of EF1α, β-TUB, and their combination as reference genes was confirmed by validating the expression of WRKY50 in various samples. The current study indicates the appropriate reference genes for the urgent requirement of gene expression normalization in maize across certain abiotic stresses, hormones, and tissue types.
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- 2014
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12. Revisiting the hetero-fertilization phenomenon in maize.
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Shibin Gao, Raman Babu, Yanli Lu, Carlos Martinez, Zhuanfang Hao, Alan F Krivanek, Jiankang Wang, Tingzhao Rong, Jonathan Crouch, and Yunbi Xu
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Medicine ,Science - Abstract
Development of a seed DNA-based genotyping system for marker-assisted selection (MAS) has provided a novel opportunity for understanding aberrant reproductive phenomena such as hetero-fertilization (HF) by observing the mismatch of endosperm and leaf genotypes in monocot species. In contrast to conventional approaches using specific morphological markers, this approach can be used for any population derived from diverse parental genotypes. A large-scale experiment was implemented using seven F(2) populations and four three-way cross populations, each with 534 to 1024 individuals. The frequency of HF within these populations ranged from 0.14% to 3.12%, with an average of 1.46%. The highest frequency of HF in both types of population was contributed by the pollen gametes. Using three-way crosses allowed, for the first time, detection of the HF contributed by maternal gametes, albeit at very low frequency (0.14%-0.65%). Four HF events identified from each of two F(2) populations were tested and confirmed using 1032 single nucleotide polymorphic markers. This analysis indicated that only 50% of polymorphic markers can detect a known HF event, and thus the real HF frequency can be inferred by doubling the estimate obtained from using only one polymorphic marker. As expected, 99% of the HF events can be detected by using seven independent markers in combination. Although seed DNA-based analysis may wrongly predict plant genotypes due to the mismatch of endosperm and leaf DNA caused by HF, the relatively low HF frequencies revealed with diverse germplasm in this study indicates that the effect on the accuracy of MAS is limited. In addition, comparative endosperm and leaf DNA analysis of specific genetic stocks could be useful for revealing the relationships among various aberrant fertilization phenomena including haploidy and apomixis.
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- 2011
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13. Comparative SNP and haplotype analysis reveals a higher genetic diversity and rapider LD decay in tropical than temperate germplasm in maize.
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Yanli Lu, Trushar Shah, Zhuanfang Hao, Suketoshi Taba, Shihuang Zhang, Shibin Gao, Jian Liu, Moju Cao, Jing Wang, A Bhanu Prakash, Tingzhao Rong, and Yunbi Xu
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Medicine ,Science - Abstract
Understanding of genetic diversity and linkage disequilibrium (LD) decay in diverse maize germplasm is fundamentally important for maize improvement. A total of 287 tropical and 160 temperate inbred lines were genotyped with 1943 single nucleotide polymorphism (SNP) markers of high quality and compared for genetic diversity and LD decay using the SNPs and their haplotypes developed from genic and intergenic regions. Intronic SNPs revealed a substantial higher variation than exonic SNPs. The big window size haplotypes (3-SNP slide-window covering 2160 kb on average) revealed much higher genetic diversity than the 10 kb-window and gene-window haplotypes. The polymorphic information content values revealed by the haplotypes (0.436-0.566) were generally much higher than individual SNPs (0.247-0.259). Cluster analysis classified the 447 maize lines into two major groups, corresponding to temperate and tropical types. The level of genetic diversity and subpopulation structure were associated with the germplasm origin and post-domestication selection. Compared to temperate lines, the tropical lines had a much higher level of genetic diversity with no significant subpopulation structure identified. Significant variation in LD decay distance (2-100 kb) was found across the genome, chromosomal regions and germplasm groups. The average of LD decay distance (10-100 kb) in the temperate germplasm was two to ten times larger than that in the tropical germplasm (5-10 kb). In conclusion, tropical maize not only host high genetic diversity that can be exploited for future plant breeding, but also show rapid LD decay that provides more opportunity for selection.
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- 2011
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14. RAPD and internal transcribed spacer sequence analyses reveal Zea nicaraguensis as a section Luxuriantes species close to Zea luxurians.
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Pei Wang, Yanli Lu, Mingmin Zheng, Tingzhao Rong, and Qilin Tang
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Medicine ,Science - Abstract
Genetic relationship of a newly discovered teosinte from Nicaragua, Zea nicaraguensis with waterlogging tolerance, was determined based on randomly amplified polymorphic DNA (RAPD) markers and the internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA using 14 accessions from Zea species. RAPD analysis showed that a total of 5,303 fragments were produced by 136 random decamer primers, of which 84.86% bands were polymorphic. RAPD-based UPGMA analysis demonstrated that the genus Zea can be divided into section Luxuriantes including Zea diploperennis, Zea luxurians, Zea perennis and Zea nicaraguensis, and section Zea including Zea mays ssp. mexicana, Zea mays ssp. parviglumis, Zea mays ssp. huehuetenangensis and Zea mays ssp. mays. ITS sequence analysis showed the lengths of the entire ITS region of the 14 taxa in Zea varied from 597 to 605 bp. The average GC content was 67.8%. In addition to the insertion/deletions, 78 variable sites were recorded in the total ITS region with 47 in ITS1, 5 in 5.8S, and 26 in ITS2. Sequences of these taxa were analyzed with neighbor-joining (NJ) and maximum parsimony (MP) methods to construct the phylogenetic trees, selecting Tripsacum dactyloides L. as the outgroup. The phylogenetic relationships of Zea species inferred from the ITS sequences are highly concordant with the RAPD evidence that resolved two major subgenus clades. Both RAPD and ITS sequence analyses indicate that Zea nicaraguensis is more closely related to Zea luxurians than the other teosintes and cultivated maize, which should be regarded as a section Luxuriantes species.
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- 2011
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15. Advances in research and utilization of maize wild relatives
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Yingzheng Li, Xu Yan, Xiaofeng Li, Yulin Cheng, Wansong Li, Lulu Xu, Jianmei He, Tingzhao Rong, and Qilin Tang
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Multidisciplinary - Published
- 2022
16. Multispecies polyploidization, chromosome shuffling, and genome extraction in Zea/Tripsacum hybrids
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Muhammad Zafar Iqbal, Xiaodong Wen, Lulu Xu, Yanli Zhao, Jing Li, Weiming Jiang, Mingjun Cheng, Huaxiong Li, Yingzheng Li, Xiaofeng Li, Ruyu He, Jianmei He, Yuegui Su, Asif Ali, Yan Peng, Tingzhao Rong, and Qilin Tang
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Genetics - Abstract
By hybridization and special sexual reproduction, we sequentially aggregated Zea mays, Zea perennis, and Tripsacum dactyloides in an allohexaploid, backcrossed it with maize, derived self-fertile allotetraploids of maize and Z. perennis by natural genome extraction, extended their first six selfed generations, and finally constructed amphitetraploid maize using nascent allotetraploids as a genetic bridge. Transgenerational chromosome inheritance, subgenome stability, chromosome pairings and rearrangements, and their impacts on an organism's fitness were investigated by fertility phenotyping and molecular cytogenetic techniques genomic in situ hybridization (GISH) and fluorescence in situ hybridization (FISH). Results showed that diversified sexual reproductive methods produced highly differentiated progenies (2n = 35–84) with varying proportions of subgenomic chromosomes, of which one individual (2n = 54, MMMPT) overcame self-incompatibility barriers and produced a self-fertile nascent near-allotetraploid by preferentially eliminating Tripsacum chromosomes. Nascent near-allotetraploid progenies showed persistent chromosome changes, intergenomic translocations, and rDNA variations for at least up to the first six selfed generations; however, the mean chromosome number preferably maintained at the near-tetraploid level (2n = 40) with full integrity of 45S rDNA pairs, and a trend of decreasing variations by advancing generations with an average of 25.53, 14.14, and 0.37 for maize, Z. perennis, and T. dactyloides chromosomes, respectively. The mechanisms for three genome stabilities and karyotype evolution for formatting new polyploid species were discussed.
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- 2023
17. Multi-species polyploidization, chromosome shuffling, and genome extraction inZea/Tripsacumhybrids
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Muhammad Zafar Iqbal, Xiaodong Wen, Lulu Xu, Yanli Zhao, Jing Li, Weiming Jiang, Mingjun Cheng, Huaxiong Li, Yinzheng Li, Xiaofeng Li, Ruyu He, Jianmei He, Asif Ali, Yan Peng, Tingzhao Rong, and Qilin Tang
- Abstract
By hybridization and special sexual reproduction, we sequentially aggregatedZea mays, Zea perennis,andTripsacum dactyloidesin an allohexaploid, backcrossed it with maize, derived self-fertile allotetraploids of maize andZ. perennisby natural genome extraction, extended their first six selfed generations, and finally constructed amphitetraploid maize using nascent allotetraploids as a genetic bridge. Transgenerational chromosome inheritance, subgenomes stability, chromosome pairings and rearrangements, and their impacts on an organism’s fitness were investigated by fertility phenotyping and molecular cytogenetics techniques GISH and FISH. Results showed that diversified sexual reproductive methods produced highly differentiated progenies (2n=35-84) with varying proportions of subgenomic chromosomes, of which one individual (2n=54, MMMPT) overcame self-incompatibility barriers and produced self-fertile nascent near-allotetraploid by preferentially eliminatingTripsacumchromosomes. Nascent near-allotetraploid progenies showed persistent chromosome changes, intergenomic translocations, and rDNA variations for at least up to the first six selfed generations; however, ploidy tended to stabilize at near-tetraploid level (2n=40) with full integrity of 45SrDNA pairs, and a trend of decreasing variations by advancing generations with an average of 25.53, 14.14, and 0.37 maize,Z. perennis,andT. dactyloideschromosomes, respectively. The mechanisms for three genome stabilities and karyotype evolution for formatting new polyploid species were discussed.
- Published
- 2023
18. Map-based cloning and WGCNA uncover the key genes controlling cold tolerance in maize introgression lines seedlings
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Ruyu He, Junjun Zheng, Tao Yang, Zeyang Pan, Yang Zhou, Mingjun Cheng, Xiaofeng Li, Yingzheng Li, Chunyan Yang, Muhammad Zafar Iqba, Jianmei He, Tingzhao Rong, and Qilin Tang
- Abstract
Summary Low-temperature chilling injury in early spring or late spring severely restricts maize production. Therefore, improving its temperature tolerance is one of the important goals of maize breeding. The wild maize relatives such as Z. perennis and T. dactyloides have strong cold tolerance and thus can be used to improve the cold tolerance of cultivated maize. In the previous study, the allohexaploid MTP ( Zea . Z. perennis and T. dactyloides ) was created as a genetic bridge material and the introgressed cross of the backbone maize inbred line to obtain the MTP-maize introgression line with strong cold tolerance. In this study, F 2:3 populations was developed of the cold-tolerant maize introgression line IB030 and the cold-sensitive maize introgression line IB021. A high-density genetic linkage map was constructed using SSR genetic markers and performed QTL mapping for related traits at 2°C, RNA-seq was performed using cold-tolerant introgression line IB030 and recurrent parent B73 (cold-sensitive) after low temperature stress at seedling stage. The key genes controlling REC, SDW and SFW of maize introgression line seedlings were located by forward genetics combined with WGCNA analysis strategy. Key genes function verification results showed that, Zm00001d037590 REC and Zm00001d012321 REC have the highest expression levels in introgression line IB030, followed by the wild type B73, and finally the EMS mutant after low temperature stress, these results initially concluded that key genes positively regulate the cold tolerance of maize, and also laid a theoretical and practical foundation for improvement of cultivated maize against low-temperature stress.
- Published
- 2022
19. Identification of a major QTL and genome-wide epistatic interactions for single vs. paired spikelets in a maize-teosinte F(2) population
- Author
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Zhengjie Chen, Kun Hu, Yong Yin, Dengguo Tang, Jixing Ni, Peng Li, Le Wang, Tingzhao Rong, and Jian Liu
- Subjects
Genetics ,Plant Science ,Agronomy and Crop Science ,Molecular Biology ,Article ,Biotechnology - Abstract
Maize ear carries paired spikelets, whereas the ear of its wild ancestor, teosinte, bears single spikelets. However, little is known about the genetic basis of the processes of transformation of single spikelets in teosinte ear to paired spikelets in maize ear. In this study, a two-ranked, paired-spikelets primitive maize and a two-ranked, single-spikelet teosinte were utilized to develop an F(2) population, and quantitative trait locus (loci) (QTL) mapping for single vs. paired spikelets (PEDS) was performed. One major QTL (qPEDS3.1) for PEDS located on chromosome 3S was identified in the 162 F(2) plants using the inclusive composite interval mapping of additive (ICIM-ADD) module, explaining 23.79% of the phenotypic variance. Out of the 409 F(2) plants, 43 plants with PEDS = 0% and 43 plants with PEDS > 20% were selected for selective genotyping, and the QTL (qPEDS3.1) was detected again. Moreover, the QTL (qPEDS3.1) was validated in three environments, which explained 31.05%, 38.94%, and 23.16% of the phenotypic variance, respectively. In addition, 50 epistatic QTLs were detected in the 162 F(2) plants using the two-locus epistatic QTL (ICIM-EPI) module; they were distributed on all 10 chromosomes and explained 94.40% of the total phenotypic variance. The results contribute to a better understanding of the genetic basis of domestication of paired spikelets and provide a genetic resource for future map-based cloning; in addition, the systematic dissection of epistatic interactions underlies a theoretical framework for overcoming epistatic effects on QTL fine mapping. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11032-022-01276-x.
- Published
- 2022
20. qRf8-1, a Novel QTL for the Fertility Restoration of Maize CMS-C Identified by QTL-seq
- Author
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Shufeng Zhou, Bin Jiang, Shuzhi Zhang, Peng Zhang, Tingzhao Rong, Guihua Lü, Mingmin Zheng, Yanli Lu, Moju Cao, Liu Xiaowei, Chuan Li, Hai Lan, and Tian Yang
- Subjects
Genetics ,Sterility ,media_common.quotation_subject ,Cytoplasmic male sterility ,Locus (genetics) ,Fertility ,QH426-470 ,Investigations ,Quantitative trait locus ,Biology ,Hybrid seed ,Maize ,QTL-seq ,Restorer gene ,Fertility restoration ,Indel ,Molecular Biology ,Gene ,Genetics (clinical) ,media_common - Abstract
C-type cytoplasmic male sterility (CMS-C), one of the three major CMS types in maize, has a promising application prospect in hybrid seed production. However, the complex genetic mechanism underlying the fertility restoration of CMS-C remains poorly understood. The maize inbred line A619 is one of the rare strong restorer lines carrying the restorer gene Rf4, but different fertility segregation ratios are found in several F2 populations derived from crosses between isocytoplasmic allonucleus CMS-C lines and A619. In the present study, the segregation ratios of fertile to sterile plants in the (CHuangzaosi × A619) F2 and BC1F1 populations (36.77:1 and 2.36:1, respectively) did not follow a typical monogenic model of inheritance, which suggested that some F2 and BC1F1 plants displayed restored fertility even without Rf4. To determine the hidden locus affecting fertility restoration, next-generation sequencing-based QTL-seq was performed with two specific extreme bulks consisting of 30 fertile and 30 sterile rf4rf4 individuals from the F2 population. A major QTL related to fertility restoration, designated qRf8-1, was detected on the long arm of chromosome 8 in A619. Subsequently, qRf8-1 was further validated and narrowed down to a 17.93-Mb genomic interval by insertion and deletion (InDel) and simple sequence repeat (SSR) marker-based traditional QTL mapping, explaining 12.59% (LOD = 25.06) of the phenotypic variation. Thus, using genetic analyses and molecular markers, we revealed another fertility restoration system acting in parallel with Rf4 in A619 that could rescue the male sterility of CHuangzaosi. This study not only expands the original fertility restoration system but also provides valuable insights into the complex genetic mechanisms underlying the fertility restoration of CMS-C.
- Published
- 2020
21. Tripsazea, a Novel Trihybrid of Zea mays, Tripsacum dactyloides, and Zea perennis
- Author
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Tingzhao Rong, Li Yang, Yang Chunyan, He Jianmei, Mingjun Cheng, Ebenezer Kofi Sam, Wen Xiaodong, Yan Xu, He Ruyu, Li Huaxiong, Ping Zhang, Zhao Yanli, Wu Zizhou, Li Xiaofeng, Qilin Tang, and Li Yingzheng
- Subjects
0106 biological sciences ,Perennial plant ,forage breeding ,Vegetative reproduction ,Karyotype ,trihybrid ,Investigations ,QH426-470 ,Poaceae ,01 natural sciences ,Genome ,Chromosomes, Plant ,DNA sequencing ,Polyploidy ,zea mays ,03 medical and health sciences ,maize improvement ,Botany ,Tripsacum dactyloides ,Genetics ,zea perennis ,Molecular Biology ,Tripsacum ,Crosses, Genetic ,Genetics (clinical) ,030304 developmental biology ,0303 health sciences ,biology ,Reproduction ,Chromosome ,biology.organism_classification ,tripsacum dactyloides ,Plant Breeding ,Phenotype ,Zea perennis ,Hybridization, Genetic ,Genome, Plant ,010606 plant biology & botany - Abstract
A trispecific hybrid, MTP (hereafter called tripsazea), was developed from intergeneric crosses involving tetraploid Zea mays (2n = 4x = 40, genome: MMMM), tetraploid Tripsacum dactyloides (2n = 4x = 72, TTTT), and tetraploid Z. perennis (2n = 4x = 40, PPPP). On crossing maize-Tripsacum (2n = 4x = 56, MMTT) with Z. perennis, 37 progenies with varying chromosome numbers (36-74) were obtained, and a special one (i.e., tripsazea) possessing 2n = 74 chromosomes was generated. Tripsazea is perennial and expresses phenotypic characteristics affected by its progenitor parent. Flow cytometry analysis of tripsazea and its parents showed that tripsazea underwent DNA sequence elimination during allohexaploidization. Of all the chromosomes in diakinesis I, 18.42% participated in heterogenetic pairing, including 16.43% between the M- and P-genomes, 1.59% between the M- and T-genomes, and 0.39% in T- and P-genome pairing. Tripsazea is male sterile and partly female fertile. In comparison with previously synthesized trihybrids containing maize, Tripsacum and teosinte, tripsazea has a higher chromosome number, higher seed setting rate, and vegetative propagation ability of stand and stem. However, few trihybrids possess these valuable traits at the same time. The potential of tripsazea is discussed with respect to the deployment of the genetic bridge for maize improvement and forage breeding.
- Published
- 2020
22. Analysis of the genitor origin of an intergeneric hybrid clone between Zea and Tripsacum for forage production by McGISH
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Tingzhao Rong, He Jianmei, Wu Zizhou, Zhao Yanli, Ebenezer Kofi Sam, Yang Chunyan, Li Yang, Qilin Tang, He Ruyu, Ping Zhang, Mingjun Cheng, Yan Xu, Wen Xiaodong, Li Xiaofeng, and Li Yingzheng
- Subjects
clone (Java method) ,Perennial plant ,biology ,Chromosome ,Forage ,Plant Science ,medicine.disease_cause ,biology.organism_classification ,Pollen ,Botany ,Tripsacum dactyloides ,Genetics ,medicine ,Ploidy ,Agronomy and Crop Science ,Tripsacum - Abstract
In this study, the chromosome number and composition of a novel perennial forage crop, 'Yucao No. 6' (Yu6), was revealed by chromosome spread and McGISH (multicolor genomic in situ hybridization) techniques to clarify its genitor origin. Cytogenetic analysis showed that Yu6, which has 56 chromosomes, is an aneuploid representing 12, 17 and 27 chromosomes from Zea mays ssp. mays L. (Zm, 2n = 2x = 20), Tripsacum dactyloides L. (Td, 2n = 4x = 72), and Z. perennis (Hitchc.) Reeves & Mangelsd. (Zp, 2n = 4x = 40), respectively. This finding indicates that Yu6 is the product of a reduced egg (n = 36 = 12Zm + 17Td + 7Zp) of MTP (a near-allohexaploid hybrid, 2n = 74 = 20Zm + 34Td + 20Zp) fertilized by a haploid sperm nucleus (n = 20Zp) of Z. perennis. Moreover, 3 translocated chromosomes consisting of the maize-genome chromosome with the segment of Z. perennis were observed. These results suggest that it is practical to develop perennial forage maize by remodeling the chromosomal architecture of MTP offspring with Z. perennis as a pollen parent. Finally, the overview of forage breeding in the Zea and Tripsacum genera was discussed.
- Published
- 2020
23. Characterization of a major QTL and Genome-Wide Epistatic Interactions for the Transformation of Single Spikelet in Teosinte Ears into Paired Spikelets in Maize Ears During Maize Domestication
- Author
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Peng Li, Yong Yin, Jixing Ni, Zhengjie Chen, Tingzhao Rong, Dengguo Tang, Jian Liu, Le Wang, and Kun Hu
- Subjects
Genetics ,Transformation (genetics) ,Epistasis ,Biology ,Quantitative trait locus ,Domestication ,Genome - Abstract
Maize ear carries paired spikelets, whereas the ear of its wild ancestor, teosinte, bears single spikelets. However, little is known about the genetic basis of the processes of transformation of single spikelets in teosinte ear to paired spikelets in maize ear. In this study, a two-ranked, paired-spikelets primitive maize and a two-ranked, single-spikelet teosinte were utilized to develop an F2 population, and QTL mapping for single vs. paired spikelets (PEDS) was performed. Two QTL (qPEDS1.1 and qPEDS3.1) for PEDS located on chromosomes 1L and 3S were identified in the 162 F2 plants using the inclusive composite interval mapping of additive (ICIM-ADD) module, explaining 1.93% and 23.79% of the phenotypic variance, respectively. Out of the 409 F2 plants, 43 plants with PEDS = 0% and 43 plants with PEDS > 20% were selected for selective genotyping; the QTL (qPEDS3.1) accounting for 64.01% of the phenotypic variance for PEDS was also detected. Moreover, the QTL (qPEDS3.1) was validated in three environments, which explained 31.05%, 38.94% and 23.16% of the phenotypic variance, respectively. In addition, 50 epistatic QTLs were detected in 162 F2 plants using the two-locus epistatic QTL (ICIM-EPI) module; they were distributed on all 10 chromosomes and explained 94.40% of the total phenotypic variance. The results contribute to a better understanding of the genetic basis of domestication of paired spikelets and provide a genetic resource for future map-based cloning; in addition, the systematic dissection of epistatic interactions underlies a theoretical framework for overcoming epistatic effects on QTL fine mapping.
- Published
- 2021
24. Metabolite profiling and genome‐wide association studies reveal response mechanisms of phosphorus deficiency in maize seedling
- Author
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Zhang Suzhi, Zhi Nie, Ling Wu, Lu Quanxiao, Wu Yuanqi, Xuan He, Yaou Shen, Feng Xing, Tingzhao Rong, Haijian Lin, Ma Peng, Ding Xin, Zhiyong Ren, Dan Liu, Shibin Gao, Xiao Zhang, Bowen Luo, and Guangtang Pan
- Subjects
0106 biological sciences ,0301 basic medicine ,Resource ,Metabolite ,Population ,Plant Science ,Biology ,maize ,01 natural sciences ,Plant Roots ,Zea mays ,consensus genes ,03 medical and health sciences ,chemistry.chemical_compound ,Biosynthesis ,Inbred strain ,Gene Expression Regulation, Plant ,Stress, Physiological ,Genetics ,Metabolomics ,Phosphorus deficiency ,education ,Gene ,Plant Proteins ,chemistry.chemical_classification ,phosphorus‐use efficiency ,education.field_of_study ,Phosphorus ,Cell Biology ,Amino acid ,Plant Leaves ,Metabolic pathway ,genome‐wide association study (GWAS) ,030104 developmental biology ,Phenotype ,Biochemistry ,chemistry ,Seedlings ,metabolite profiling ,plant immunity ,010606 plant biology & botany ,Genome-Wide Association Study - Abstract
SUMMARY Inorganic phosphorus (Pi) is an essential element in numerous metabolic reactions and signaling pathways, but the molecular details of these pathways remain largely unknown. In this study, metabolite profiles of maize (Zea mays L.) leaves and roots were compared between six low‐Pi‐sensitive lines and six low‐Pi‐tolerant lines under Pi‐sufficient and Pi‐deficient conditions to identify pathways and genes associated with the low‐Pi stress response. Results showed that under Pi deprivation the concentrations of nucleic acids, organic acids and sugars were increased, but that the concentrations of phosphorylated metabolites, certain amino acids, lipid metabolites and nitrogenous compounds were decreased. The levels of secondary metabolites involved in plant immune reactions, including benzoxazinoids and flavonoids, were significantly different in plants grown under Pi‐deficient conditions. Among them, the 11 most stable metabolites showed significant differences under low‐ and normal‐Pi conditions based on the coefficient of variation (CV). Isoleucine and alanine were the most stable metabolites for the identification of Pi‐sensitive and Pi‐resistant maize inbred lines. With the significant correlation between morphological traits and metabolites, five low‐Pi‐responding consensus genes associated with morphological traits and simultaneously involved in metabolic pathways were mined by combining metabolites profiles and genome‐wide association study (GWAS). The consensus genes induced by Pi deficiency in maize seedlings were also validated by reverse‐transcription quantitative polymerase chain reaction (RT‐qPCR). Moreover, these genes were further validated in a recombinant inbred line (RIL) population, in which the glucose‐6‐phosphate‐1‐epimerase encoding gene mediated yield and correlated traits to phosphorus availability. Together, our results provide a framework for understanding the metabolic processes underlying Pi‐deficient responses and give multiple insights into improving the efficiency of Pi use in maize., Significance statement Metabolite profiling and GWAS were applied to reveal maize low‐Pi response mechanisms.
- Published
- 2019
25. QTL mapping for resistance of maize to grey leaf spot
- Author
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Yifeng Leng, Moju Cao, Li Lujiang, Jiwei Kang, Haitao Tang, Yang Lin, Luchang Deng, Biao Zhang, Junpin Yang, He Wenzhu, Yuanqi Wu, Yunping Chen, and Tingzhao Rong
- Subjects
0106 biological sciences ,0301 basic medicine ,Resistance (ecology) ,biology ,Physiology ,Plant Science ,Quantitative trait locus ,biology.organism_classification ,01 natural sciences ,03 medical and health sciences ,030104 developmental biology ,Agronomy ,Genetics ,Leaf spot ,Agronomy and Crop Science ,010606 plant biology & botany - Published
- 2017
26. Natural antisense transcripts are significantly involved in regulation of drought stress in maize
- Author
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Hai Lan, Yunbi Xu, M Freeling, Fengkai Wu, Xuecai Zhang, Jie Xu, Damon Lisch, Yan Mao, Xin Tang, Moju Cao, Tingzhao Rong, Qi Wang, and Yanli Lu
- Subjects
0301 basic medicine ,Transposable element ,endocrine system ,DNA, Plant ,Acclimatization ,Mutant ,Zea mays ,Histones ,03 medical and health sciences ,Stress, Physiological ,Sense (molecular biology) ,Genetics ,RNA, Antisense ,Gene ,2. Zero hunger ,biology ,Gene regulation, Chromatin and Epigenetics ,fungi ,RNA ,DNA Methylation ,Chromatin ,Droughts ,Antisense RNA ,body regions ,030104 developmental biology ,Histone ,RNA, Plant ,Nat ,DNA Transposable Elements ,biology.protein - Abstract
Natural antisense transcripts (NATs) are a prominent and complex class of regulatory RNAs. Using strand-specific RNA sequencing, we identified 1769 sense and antisense transcript pairs (NAT pairs) in two maize inbreds with different sensitivity to drought, as well as in two derivative recombination inbred lines (RILs). A significantly higher proportion of NATs relative to non-NATs are specifically expressed under water stress (WS). Surprisingly, expression of sense and antisense transcripts produced by NAT pairs is significantly correlated, particularly under WS. We found an unexpected large proportion of NATs with protein coding potential, as estimated by ribosome release scores. Small RNAs significantly accumulate within NAT pairs, with 21 nt smRNA particularly enriched in overlapping regions of these pairs of genes. The abundance of these smRNAs is significantly altered in the leafbladeless1 mutant, suggesting that these genes may be regulated by the tasiRNA pathway. Further, NATs are significantly hypomethylated and include fewer transposable element sequences relative to non-NAT genes. NAT gene regions also exhibit higher levels of H3K36me3, H3K9ac, and H3K4me3, but lower levels of H3K27me3, indicating that NAT gene pairs generally exhibit an open chromatin configuration. Finally, NAT pairs in 368 diverse maize inbreds and 19 segregating populations were specifically enriched for polymorphisms associated with drought tolerance. Taken together, the data highlight the potential impact of that small RNAs and histone modifications have in regulation of NAT expression, and the significance of NATs in response to WS.
- Published
- 2017
27. Genome-wide analysis of Gro/Tup1 family corepressors and their responses to hormones and abiotic stresses in maize
- Author
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Wang Hongling, Hailan Liu, Zhang Suzhi, Huang Kaifeng, Yanli Lu, Du Hanmei, Hongyou Li, Xin Chen, Tingzhao Rong, Moju Cao, and Shibin Gao
- Subjects
0301 basic medicine ,Genetics ,Abiotic component ,biology ,Abiotic stress ,Plant Science ,Meristem ,biology.organism_classification ,03 medical and health sciences ,030104 developmental biology ,WD40 repeat ,Arabidopsis ,lipids (amino acids, peptides, and proteins) ,Gene ,Transcription factor ,Segmental duplication - Abstract
Gro/Tup1 proteins act as negative transcriptional regulators and play crucial roles in many growth and developmental processes in a wide range of organisms. However, our understanding of Gro/Tup1 protein functions in plants is confined to the model plant Arabidopsis. Here, 11 Gro/Tup1 genes, which were characterized by the typical LisH and WD40 repeat domains, were identified in maize through a genome-wide survey. A phylogenetic analysis revealed that maize Gro/Tup1 proteins could be divided into three subfamilies, in which members shared similar protein and gene structures. The predicted maize Gro/Tup1 genes were distributed on seven chromosomes and segmental duplication contributed to their expansion. Many predicted cis-elements associated with hormones, biotic- or abioticstress responses, meristem and seed development, and circadian rhythms, were found in their putative promoter regions. A potential associated protein analysis identified a large number of candidates, including transcription factors, chromatin-modifying enzymes, protein kinases, and ubiquitinconjugating enzymes. An expression profile derived from the RNA-seq data indicated that Gro/Tup1 genes in maize were widely expressed in various organs and tissues. Quantitative real-time PCR revealed that these genes responded to at least one hormone or abiotic stress, either in roots or in shoots. Our study provides useful information on the Gro/Tup1 genes in maize and will facilitate the further functional validation of these genes in growth and development, hormone responses, and biotic- or abiotic-stress resistance.
- Published
- 2016
28. Analysis of the genitor origin of an intergeneric hybrid clone between
- Author
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Xu, Yan, Yingzheng, Li, Zizhou, Wu, Yang, Li, Xiaodong, Wen, Xiaofeng, Li, Ruyu, He, Chunyan, Yang, Yanli, Zhao, Mingjun, Cheng, Ping, Zhang, Ebenezer Kofi, Sam, Tingzhao, Rong, Jianmei, He, and Qilin, Tang
- Subjects
Tripsacum ,forage breeding ,McGISH ,Zea ,perennial forage maize ,Note - Abstract
In this study, the chromosome number and composition of a novel perennial forage crop, ‘Yucao No. 6’ (Yu6), was revealed by chromosome spread and McGISH (multicolor genomic in situ hybridization) techniques to clarify its genitor origin. Cytogenetic analysis showed that Yu6, which has 56 chromosomes, is an aneuploid representing 12, 17 and 27 chromosomes from Zea mays ssp. mays L. (Zm, 2n = 2x = 20), Tripsacum dactyloides L. (Td, 2n = 4x = 72), and Z. perennis (Hitchc.) Reeves & Mangelsd. (Zp, 2n = 4x = 40), respectively. This finding indicates that Yu6 is the product of a reduced egg (n = 36 = 12Zm + 17Td + 7Zp) of MTP (a near-allohexaploid hybrid, 2n = 74 = 20Zm + 34Td + 20Zp) fertilized by a haploid sperm nucleus (n = 20Zp) of Z. perennis. Moreover, 3 translocated chromosomes consisting of the maize-genome chromosome with the segment of Z. perennis were observed. These results suggest that it is practical to develop perennial forage maize by remodeling the chromosomal architecture of MTP offspring with Z. perennis as a pollen parent. Finally, the overview of forage breeding in the Zea and Tripsacum genera was discussed.
- Published
- 2019
29. QTL analysis of delayed maize flowering in response to low phosphate across multi-environments
- Author
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Su Shunzong, Xiao Zhang, Bowen Luo, Haixu Zhong, Zhi Nie, Ling Wu, Duojiang Gao, Tingzhao Rong, Zhiyong Ren, Hailan Liu, Haijian Lin, Ma Peng, Liu Wenjun, Shibin Gao, and Dan Liu
- Subjects
education.field_of_study ,Phosphorus ,fungi ,Population ,food and beverages ,chemistry.chemical_element ,Plant physiology ,Plant Science ,Horticulture ,Quantitative trait locus ,Biology ,Phosphate ,chemistry.chemical_compound ,Agronomy ,chemistry ,Inbred strain ,Genetics ,Plant breeding ,Adaptation ,education ,Agronomy and Crop Science - Abstract
Phosphorus (P) is required for numerous developmental processes, such as flowering and reproduction, in maize (Zea mays L.). It is also an essential nutrient in fertilizers to sustain high yields in farmlands with insufficient available phosphate, particularly in acid soils in China. Flowering time is a key factor influencing the adaptation of maize to the local environment and is associated with high yields. However, few studies have focused on the genetic characteristics of flowering time under low phosphate conditions. In this study, a recombinant inbred line (RIL) population derived from a cross between X178 and 9782 was evaluated for three flowering time traits under two phosphates (Pi) levels at four locations. We found that low phosphate significantly delayed the flowering stage of maize and proposed the hypothesis of “Phosphorus Accumulation Effect”. Mixed-model-based composite interval mapping was used to dissect the genetic basis of the flowering time traits. A total of 41 quantitative trait loci (QTL) was identified for the three flowering time traits through four procedures. Among these 41 QTL, 38 focused on four hot regions, including bin 2.02, bin 2.03, bin 5.04, and bin 6.01. These regions and linked markers should be the targets for fine mapping, map-based cloning, and marker-assisted selection of flowering time and phosphate utilization efficiency.
- Published
- 2019
30. Heterotic grouping based on genetic variation and population structure of maize inbred lines from current breeding program in Sichuan province, Southwest China using genotyping by sequencing (GBS)
- Author
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Hai Lan, Tingzhao Rong, Yong Xiang, Yifeng Leng, Chao Xia, Li Lujiang, Chenxi Lv, and Ru-jun Wei
- Subjects
0106 biological sciences ,0301 basic medicine ,Germplasm ,Genetics ,Genetic diversity ,Breeding program ,Plant Science ,Biology ,01 natural sciences ,Analysis of molecular variance ,03 medical and health sciences ,030104 developmental biology ,Genetic distance ,Backcrossing ,Genetic variation ,Agronomy and Crop Science ,Molecular Biology ,010606 plant biology & botany ,Biotechnology ,Hybrid - Abstract
Maize (Zea mays L.), which is an important food crop in the word, displays large genetic diversity. Knowledge of the relationships among maize inbred lines is essential to the maize breeder because it directs the exploitation of germplasm in hybrid production. In this study, the genetic diversity, population structure, and relatedness between pairs of 157 elite maize inbred lines from the current breeding program of Sichuan province in Southwest China were assessed with 4976 polymorphic single-nucleotide polymorphisms (SNPs) developed by genotyping by sequencing (GBS). A total of 91.1% of the inbred lines were considered pure with
- Published
- 2019
31. Genetic dissection of stalk lodging-related traits using an IBM Syn10 DH population in maize across three environments (Zea mays L.)
- Author
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Guangtang Pan, Peng Liu, Thomas Lübberstedt, Yanling Zhang, Tianhu Liang, Tingzhao Rong, Chaoying Zou, Tao Wang, Haijian Lin, Yaou Shen, Min Chen, Yinchao Zhang, and Michael D. Lee
- Subjects
0106 biological sciences ,0301 basic medicine ,Candidate gene ,Genetic Linkage ,Population ,Quantitative Trait Loci ,Single-nucleotide polymorphism ,Biology ,Quantitative trait locus ,Genes, Plant ,01 natural sciences ,Polymorphism, Single Nucleotide ,Zea mays ,03 medical and health sciences ,Genetics ,education ,Molecular Biology ,Crosses, Genetic ,Genetic dissection ,education.field_of_study ,Chromosome Mapping ,General Medicine ,Heritability ,Horticulture ,030104 developmental biology ,Phenotype ,Stalk ,Edible Grain ,010606 plant biology & botany - Abstract
Stalk lodging severely limits the grain yield of maize (Zea mays L.). Mechanical stalk strength can be reflected by the traits of stalk diameter (SD), stalk bending strength (SBS), and lodging rind penetrometer resistance (RPR). To determine the genetic basis of maize stalk lodging, quantitative trait loci (QTLs) were mapped for these three traits using the IBM Syn10 DH population in three environments. The results indicated that there were strong genetic correlations among the three traits, and the analyses of phenotypic variations for SD, SBS, and RPR across the three environments showed high broad-sense heritability (0.6843, 0.5175, and 0.7379, respectively). In total, 44 significant QTLs were identified control the above traits across the 3 environments. A total of 14, 14, and 16 QTLs were identified for SD, SBS, and RPR across single-environment mapping, respectively. Notably, ten QTLs were stably expressed across multiple-environments, including two QTLs for SD, three for SBS, and five for RPR. Three major QTLs each accounting for over 10% of the phenotypic variation were qSD6-2 (10.03%), qSD8-2 (13.73%), and qSBS1-2 (11.89%). Comprehensive analysis of all QTLs in this study revealed that 5 QTL clusters including 12 QTLs were located on chromosomes 1, 3, 7, and 8, respectively. Among these 44 QTLs, 9 harbored 13 stalk lodging-associated SNPs that were detected by our recently published work, with 1 SNP successfully validated in the IBM Syn10 DH population. These chromosomal regions will be useful for marker-assisted selection and fine mapping of stalk lodging-related traits in maize.
- Published
- 2019
32. De novo assembly of Zea nicaraguensis root transcriptome identified 5 261 full-length transcripts
- Author
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Hailan Liu, Jiang Wei, Tingzhao Rong, Zhang Suzhi, Yan-li Lu, Yuan-qi Wu, Jian Liu, and Qilin Tang
- Subjects
0106 biological sciences ,0301 basic medicine ,Germplasm ,Agriculture (General) ,Sequence assembly ,RNA-Seq ,Plant Science ,teosinte ,01 natural sciences ,Biochemistry ,S1-972 ,Transcriptome ,03 medical and health sciences ,Food Animals ,KEGG ,Gene ,Zea nicaraguensis ,Genetics ,Ecology ,biology ,Contig ,full-length transcript ,biology.organism_classification ,030104 developmental biology ,Animal Science and Zoology ,Agronomy and Crop Science ,010606 plant biology & botany ,Food Science - Abstract
Zea nicaraguensis , a wild relative of cultivated maize ( Zea mays subsp. mays ), is considered to be a valuable germplasm to improve the waterlogging tolerance of cultivated maize. Use of reverse genetic-based gene cloning and function verification to discover waterlogging tolerance genes in Z. nicaraguensis is currently impractical, because little gene sequence information for Z. nicaraguensis is available in public databases. In this study, Z. nicaraguensis seedlings were subjected to simulated waterlogging stress and total RNAs were isolated from roots stressed and non-stressed controls. In total, 80 mol L −1 Illumina 100-bp paired-end reads were generated. De novo assembly of the reads generated 81 002 final non-redundant contigs, from which 5 261 full-length transcripts were identified. Among these full-length transcripts, 3 169 had at least one Gene Ontology (GO) annotation, 2 354 received cluster of orthologous groups (COG) terms, and 1 992 were assigned a Kyoto encyclopedia of genes and genomes (KEGG) Orthology number. These sequence data represent a valuable resource for identification of Z. nicaraguensis genes involved in waterlogging response.
- Published
- 2016
33. Identification, and Functional and Expression Analyses of the CorA/MRS2/MGT-Type Magnesium Transporter Family in Maize
- Author
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Hongyou Li, Du Hanmei, Huang Kaifeng, Qilin Tang, Hailan Liu, Zhang Suzhi, Liu Tianyu, Xin Chen, Shibin Gao, and Tingzhao Rong
- Subjects
0106 biological sciences ,0301 basic medicine ,Genotype ,Physiology ,Magnesium transporter ,Arabidopsis ,Plant Science ,Genes, Plant ,Zea mays ,01 natural sciences ,Chromosomes, Plant ,03 medical and health sciences ,Inbred strain ,Gene Expression Regulation, Plant ,Stress, Physiological ,Protein-fragment complementation assay ,Gene Duplication ,Gene family ,Inbreeding ,Magnesium ,Amino Acid Sequence ,Gene ,Phylogeny ,Plant Proteins ,biology ,Membrane transport protein ,Gene Expression Profiling ,Genetic Complementation Test ,Membrane Transport Proteins ,Oryza ,Cell Biology ,General Medicine ,biology.organism_classification ,Adaptation, Physiological ,030104 developmental biology ,Biochemistry ,Multigene Family ,Mutation ,biology.protein ,Sequence Alignment ,Aluminum ,010606 plant biology & botany - Abstract
Magnesium (Mg(2+)) is an essential macronutrient for plant growth and development, and the CorA/MRS2/MGT-type Mg(2+) transporters play important roles in maintaining Mg(2+) homeostasis in plants. Although the MRS2/MGT genes have been identified in two model plant species, Arabidopsis and rice, a comprehensive analysis of the MRS2/MGT gene family in other plants is lacking. In this work, 12 putative MRS2/MGT genes (ZmMGT1- ZmMGT12) were identified in maize and all of them were classified into five distinct subfamilies by phylogenetic analysis. A complementation assay in the Salmonella typhimurium MM281 strain showed that five representatives of the 12 members possess Mg(2+) transport abilities. Inhibition of ZmMGT protein activity using the hexaamminecobalt (III) (Co-Hex) inhibitor indicated that the ZmMGT protein mediated both low-affinity and high-affinity Mg(2+) transport in maize. A semi-quantitative reverse transcription-PCR (RT-PCR) analysis revealed that eight genes were constitutively expressed in all of the detected tissues, with one being specifically expressed in roots and three having no detectable expression signals. A quantitative RT-PCR analysis showed that some ZmMGT members displayed differential responses to Mg(2+) deficiency and aluminum (Al) stress. Furthermore, root growth inhibition and Mg(2+) accumulation analyses in two maize inbred lines, which conferred different levels of Al tolerance, revealed that ZmMGT proteins contributed to the Al resistance of the Al tolerance genotype. We hypothesize that ZmMGT family members function as Mg(2+) transporters and may play a role in linking Mg(2+) deficiency and Al stress responses. Our results will be valuable in a further analysis of the important biological functions of ZmMGT members in maize.
- Published
- 2016
34. Fine mapping of the novel male-sterile mutant gene ms39 in maize originated from outer space flight
- Author
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Shizhao Li, Yonghui Zhu, Shi Ziwen, Fu-Xia Liu, Moju Cao, Hongyang Yi, Jing Wang, Chuan Li, He-Yang Liu, Tingzhao Rong, and Niu Qunkai
- Subjects
0106 biological sciences ,0301 basic medicine ,Genetics ,education.field_of_study ,Candidate gene ,Nuclear gene ,Callose ,Population ,Mutant ,Plant Science ,Biology ,01 natural sciences ,Frameshift mutation ,03 medical and health sciences ,chemistry.chemical_compound ,Exon ,030104 developmental biology ,chemistry ,Chromosome 3 ,education ,Agronomy and Crop Science ,Molecular Biology ,010606 plant biology & botany ,Biotechnology - Abstract
A novel male-sterile maize mutant male sterility 39 (ms39) was obtained from offspring of the commercial hybrid Chuandan No. 9 that had been carried into outer space. A previous study demonstrated that ms39 is controlled by a single recessive nuclear gene, located on the long arm of chromosome 3. Here, we used 1073 mutant individuals derived from the (ms39 × Mo17) F2 population and sequentially developed new primers to identify markers supporting the fine mapping of ms39. A 365-kb region on chromosome 3 flanked by markers L8 and M30 at a genetic distance of 0.18 and 0.47 cM, respectively, was identified. According to the reference sequence of ZmB73_Ref-Gen_v4, 12 candidate genes were identified within the 365-kb mapping region. Based on cloning and sequence BLAST analysis of the 12 candidate genes, a four-base-pair deletion was found within the exon of Zm00001d043909, which encoded callose synthase12. This four-base-pair deletion resulted in a frameshift mutation in ms39, leading to the earlier termination of the coding protein, and ultimately caused abnormal performance of the callose synthase. Additionally, cytological observation was conducted on a sister cross population (ms39/ms39 × ms39/Ms39). These observations showed that the tapetum cells of the ms39 mutant appeared abnormal from the dyad stage, and aborted microspores were observed during pollen development. These results lay the foundation for the cloning of ms39 and exploration of the molecular mechanism underlying aborted pollen development in ms39 maize.
- Published
- 2018
35. Allopolyploidization facilitates gene flow and speciation among corn, Zea perennis and Tripsacum dactyloides
- Author
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Zhao Yanli, Asif Ali, Wen Xiaodong, Jiang Weiming, Li Huaxiong, Mingjun Cheng, Muhammad Zafar Iqbal, Su Yuegui, Li Yang, Zhang Lei, Tingzhao Rong, and Qilin Tang
- Subjects
0106 biological sciences ,0301 basic medicine ,Germplasm ,Gene Flow ,Genetic Speciation ,Plant Science ,Biology ,Poaceae ,01 natural sciences ,Zea mays ,Chromosomes, Plant ,Translocation, Genetic ,Polyploidy ,03 medical and health sciences ,Apomixis ,Chromosome Segregation ,Botany ,Tripsacum dactyloides ,Genetics ,Plant breeding ,In Situ Hybridization ,Hybrid ,Chimera ,Reproduction ,food and beverages ,biology.organism_classification ,Sexual reproduction ,Plant Breeding ,030104 developmental biology ,Phenotype ,Zea perennis ,Backcrossing ,Genome, Plant ,010606 plant biology & botany - Abstract
Tripsacum dactyloides is closely related to Zea mays since Zea perennis and the MTP tri- species hybrid have four possible reproductive modes. Eastern gamagrass (Tripsacum dactyloides L.) and tetraploid perennial teosinte (Zea perennis) are well known to possess genes conferring resistance against biotic and abiotic stresses as well as adaptation to flood and aluminum toxic soils. However, plant breeders have been hampered to utilize these and other beneficial traits for maize improvement due to sterility in their hybrids. By crossing a tetraploid maize-inbred line × T. dactyloides, a female fertile hybrid was produced that was crossed with Z. perennis to yield a tri-genomic female fertile hybrid, which was backcrossed with diploid maize to produce BC1 and BC2. The tri-genomic hybrid provided a new way to transfer genetic material from both species into maize by utilizing conventional plant breeding methods. On the basis of cytogenetic observations using multi-color genomic in situ hybridization, the progenies were classified into four groups, in which chromosomes could be scaled both up and down with ease to produce material for varying breeding and genetic purposes via apomixis or sexual reproduction. In the present study, pathways were found to recover maize and to obtain specific translocations as well as a speedy recovery of the T. dactyloides–maize addition line in a second backcross generation. However, phenotypes of the recovered maize were in most cases far from maize as a result of genetic load from T. dactyloides and Z. perennis, and could not be directly used as a maize-inbred line but could serve as an intermediate material for maize improvement. A series of hybrids was produced (having varying chromosome number, constitution, and translocations) with agronomic traits from all three parental species. The present study provides an application of overcoming the initial interspecific barriers among these species. Moreover, T. dactyloides is closely related to Z. mays L. ssp. mays since Z. perennis and the MTP tri- species hybrid have four possible reproductive modes.
- Published
- 2018
36. Mysterious meiotic behavior of autopolyploid and allopolyploid maize
- Author
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Zhao Yanli, Ping Zhang, Mingjun Cheng, Muhammad Zafar Iqbal, Wen Xiaodong, Zhang Lei, Asif Ali, Qi Lin Tang, and Tingzhao Rong
- Subjects
0106 biological sciences ,0301 basic medicine ,Genome evolution ,Asia ,lcsh:QH426-470 ,Plant Science ,Biology ,genome evolution ,01 natural sciences ,Genome ,03 medical and health sciences ,Meiosis ,Chromosome Stability ,Homologous chromosome ,Genetics ,meiosis ,Plantae ,polyploidy ,Hybrid ,Evolutionary Biology ,Reproductive Biology ,World ,Zea mays ,Maize ,lcsh:Genetics ,chromosome stability ,030104 developmental biology ,GISH ,Animal Science and Zoology ,010606 plant biology & botany ,Biotechnology ,Research Article - Abstract
This study was aimed to investigate the stability of chromosomes during meiosis in autopolyploid and allopolyploid maize, as well as to determine an association of chromosomes between maize (Zeamaysssp.mays Linnaeus, 1753) andZ.perennis(Hitchcock, 1922) Reeves & Mangelsdor, 1942, by producing a series of autopolyploid and allopolyploid maize hybrids. The intra-genomic and inter-genomic meiotic pairings in these polyploids were quantified and compared using dual-color genomic in-situ hybridization. The results demonstrated higher level of chromosome stability in allopolyploid maize during meiosis as compared to autopolyploid maize. In addition, the meiotic behavior ofZ.perenniswas relatively more stable as compared to the allopolyploid maize. Moreover, ten chromosomes of "A” subgenome in maize were homologous to twenty chromosomes ofZ.perennisgenome with a higher pairing frequency and little evolutionary differentiation. At the same time, little evolutionary differentiation has been shown by chromosomes of "A” subgenome in maize, while chromosomes of "B” subgenome, had a lower pairing frequency and higher evolutionary differentiation. Furthermore, 5IM+ 5IIPP+ 5IIIMPPand 5IIMM+ 5IIPP+ 5IVMMPPwere observed in allotriploids and allotetraploids respectively, whereas homoeologous chromosomes were found between the "A” and "B” genome of maize andZ.perennis.
- Published
- 2018
37. The effect of different genome and cytoplasm on meiotic pairing in maize newly synthetic polyploids
- Author
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Shipeng Yang, Mingjun Cheng, Li Yang, Tingzhao Rong, Li Jing, Wu Yuanqi, Li Huaxiong, Xingchun Dong, Qilin Tang, Mingmin Zheng, Zhou Shufeng, and Sun Rulong
- Subjects
0301 basic medicine ,Genetics ,Genome evolution ,Chromosome ,Plant Science ,Horticulture ,Biology ,biology.organism_classification ,Genetic recombination ,Genome ,03 medical and health sciences ,030104 developmental biology ,Meiosis ,Zea perennis ,Ploidy ,Agronomy and Crop Science ,Genomic organization - Abstract
Allopolyploidization plays the special role in the evolution of many crops. Moreover, the evolution in early stage of some allopolyploidization events is predicted to be effected by nuclear-cytoplasmic interactions. Maize and teosintes are well model system for study of genetic recombination in allopolyploidization. In order to investigate the effects of genome organization and cytoplasm on genome evolution in newly synthesized allopolyploids (neoallopolyploids), a series of neoallopolyploids were produced by reciprocal crosses of maize and Zea perennis. By using dual-color genomic in situ hybridization, intra- and intergenomic meiosis pairing of these polyploids were quantified and compared with regard to its genome organization and cytoplasm background. In the four neoallopolyploids, the stability of maize genome is consistently lower than that of Z. perennis genome. Additional, the stability of maize genome is affected by genome ploidy. The cytoplasm, genome composition and their interaction do have the special role in chromosome paring and the meiosis behaviors in Zea allopolyploids vary significantly and showed non-diploidization. Z. perennis cytoplasm may give a relatively relaxed environment for maize genome.
- Published
- 2015
38. Identification of QTL for ear row number and two-ranked versus many-ranked ear in maize across four environments
- Author
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Cong Yang, Tingzhao Rong, Lei Zhang, Jian Liu, and Dengguo Tang
- Subjects
Genetics ,Inbred strain ,Trait ,Grain yield ,Epistasis ,Plant Science ,Horticulture ,Quantitative trait locus ,Biology ,Joint analysis ,Agronomy and Crop Science ,Zea mays - Abstract
Ear row number (ERN) is not only a key trait involved in maize (Zea mays L.) evolution but also an important component directly related to grain yield. In this report, 325 recombinant inbred lines (RILs, F6:7) derived from a cross between B73 with 16 rows and SICAU1212 with four rows (two-ranked with two rows per rank) were utilized to detect quantitative trait loci (QTL) associated with ERN and two-ranked versus many-ranked ears (TR). Compared to modern maize that formed approximately 8–20 rows, SICAU1212 with four rows was the extreme case. A total of 12 and 8 QTLs were associated with ERN and TR across four environments through single-environment mapping, respectively. Each QTL responsible for ERN explained 2.33–21.28 % of the phenotypic variation. And the TR variation contributed by individual TR QTL ranged from 2.09 to 12.99 %. Notably, only three QTLs, qERN2-1 (bin 2.02), qERN8-1 (bin 8.02) and qERN8-2 (bin 8.04), were consistently detected in each environment and by joint analysis among all environments, which simultaneously influenced ERN and TR. One of the three QTLs, qERN8-1 was also identified as interacting with environment. In addition, nine pairs of significant epistatic interactions (two for ERN and seven for TR) were detected among all QTLs. The epistasis between qTR2-1 and qTR8-1 was consistent in most environments. This present study may provide the understanding of the genetic basis of ERN and TR and a foundation for further fine-mapping of these common QTLs.
- Published
- 2015
39. DNA methylation analysis of sterile and fertile CMS-C hybrids and their parents in maize
- Author
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Tingzhao Rong, Bo Chen, Yan Zhang, Zhang Suzhi, Jing Wang, Moju Cao, Hai Lan, and Yanli Lu
- Subjects
0106 biological sciences ,0301 basic medicine ,Genetics ,Sterility ,media_common.quotation_subject ,Fertility ,Plant Science ,Methylation ,Biology ,medicine.disease_cause ,01 natural sciences ,03 medical and health sciences ,030104 developmental biology ,Pollen ,DNA methylation ,medicine ,Epigenetics ,Agronomy and Crop Science ,Gene ,010606 plant biology & botany ,Biotechnology ,media_common ,Hybrid - Abstract
C-type cytoplasmic male sterile (CMS-C) line plays an important role in hybrid seed production in maize. However, mechanisms of pollen abortion and fertility restoration remain unclear. This study aimed to investigate the mechanisms of CMS-C pollen abortion and fertility restoration, particularly based on epigenetics, and to understand the relationship between male fertility performance and DNA methylation status. Methylation-sensitive amplification polymorphism (MSAP) technique was conducted to analyze DNA methylation levels and patterns of tassels at pollen-mother cell, tetrad, mononuclear, and binuclear stages among four half-sib hybrids and their parents with different fertility. Results showed that DNA methylation levels in fertility restored hybrids were higher than those in sterility maintained hybrids. Nine CCGG sites, which displayed methylation polymorphism between male-fertile and male-sterile hybrids, were screened. To validate MSAP results, we performed methylation-sensitive PCR (MS-PCR) and found consistent observations in cloned methylation sites. Interestingly, a specific site named 16–1 was discovered in the region of Rf5 gene, which is one of the restorer genes of CMS-C. Thus, DNA methylation may participate in regulating the expression of fertility restorer genes of maize CMS-C.
- Published
- 2015
40. Perennial aneuploidy as a potential material for gene introgression between maize and Zea perennis
- Author
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Zhou Shufeng, Qilin Tang, Yuan-qi Wu, Xiu-yan Yang, Jie Fu, Pei Wang, Mingjun Cheng, Gui-hua Lü, Mingmin Zheng, and Tingzhao Rong
- Subjects
Agriculture (General) ,Introgression ,Aneuploidy ,Plant Science ,Biology ,maize ,Biochemistry ,Gene flow ,S1-972 ,Food Animals ,Botany ,medicine ,aneuploidy ,Hybrid ,Genetics ,Ecology ,Chromosome ,food and beverages ,chromosome constitution ,medicine.disease ,biology.organism_classification ,Plant morphology ,Z. perennis ,Zea perennis ,Backcrossing ,Animal Science and Zoology ,gene flow ,Agronomy and Crop Science ,Food Science - Abstract
Hybridization, which allows for gene flow between crops, is difficult between maize and Zea perennis. In this study, we aim to initiate and study gene flow between maize and Z. perennis via a special aneuploid plant (MDT) derived from an interspecific hybrid of the two species. The chromosome constitution and morphological characters of MDT as well as certain backcross progenies were examined. Results from genomic in situ hybridization (GISH) indicate that aneuploid MDT consisted of nine maize chromosomes and 30 Z. perennis chromosomes. The backcross progenies of MDT×maize displayed significant diversity of vegetative and ear morphology; several unusual plants with specific chromosome constitution were founded in its progenies. Some special perennial progeny with several maize chromosomes were obtained by backcrossing MDT with Z. perennis , and the first whole chromosome introgression from maize to Z. perennis was detected in this study. With this novel material and method, a number of maize-tetraploid teosinte addition or substitution lines can be generated for further study, which has great significance to maize and Z. perennis genetic research, especially for promoting introgression and transferring desirable traits.
- Published
- 2015
41. Detection of quantitative trait loci for ear row number in F2 populations of maize
- Author
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Junying Liu, Cong Yang, and Tingzhao Rong
- Subjects
Genetics ,Genetic Linkage ,Quantitative Trait Loci ,Chromosome Mapping ,General Medicine ,Biology ,Quantitative trait locus ,Zea mays ,Chromosomes, Plant ,Epistatic interaction ,Agronomy ,Genetic linkage ,Trait ,Grain yield ,Plant traits ,Molecular Biology ,Genetic Association Studies - Abstract
Ear row number (ERN) is not only a key trait involved in maize (Zea mays L.) evolution but is also an important component that is directly related to grain yield. In this study, quantitative trait loci (QTLs) for ERN were detected across two F2 populations that were derived from a same cross between B73 with 16 rows (N = 233) and SICAU1212 with four rows (N = 231). As a result, 33 QTLs were associated with 12 agronomic traits: three plant traits, four ear-related traits, and five kernel-related traits. The total phenotypic variation explained by the QTLs for each trait ranged from 8.60 to 72.67%, and four QTLs were identified for ERN in the two populations. Each QTL explained between 6.78 and 36.76% of the ERN variation. Notably, three of the four QTLs (qERN2-1, qERN4-2, and qERN8-1) were associated with ERN, and qERN8-1 simultaneously influenced grain yield, plant diameter, ear diameter, and kernel length. In addition, only one significant epistatic interaction was detected in all 33 QTLs. This study should provide a foundation for further fine-mapping and map-based cloning of these consistent QTLs, and for controlling maize ERN by marker-assisted breeding.
- Published
- 2015
42. Genome-wide identification of candidate phosphate starvation responsive genes and the development of intron length polymorphism markers in maize
- Author
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Bowen Luo, Su Shunzong, Yanli Lu, Hailan Liu, Ling Wu, Xiao Zhang, Shibin Gao, Tingzhao Rong, He Chunmeng, Dan Liu, and Zhi Nie
- Subjects
Genetics ,Genetic diversity ,medicine.medical_specialty ,Intron ,Plant Science ,Biology ,Marker-assisted selection ,Genome ,Inbred strain ,Genetic marker ,Molecular genetics ,medicine ,Agronomy and Crop Science ,Gene - Abstract
To develop genetic markers associated with tolerance to low phosphorus, we identified candidate phosphate starvation responsive (PSR) genes and developed their intron length polymorphism (ILP) markers in maize on a genome-wide scale. Based on the known plant PSR genes, 161 candidate PSR genes were identified. Of these genes, 138 genes contained at least one intron and were then used to develop 606 PSR-ILP markers by designing PCR primers to the intron-flanking exonic regions. PCR evaluation was performed on 43 randomly selected PSR-ILP markers in 30 maize inbred lines. Of the primers, 88.4% amplified stable and pure products in all maize inbred lines, and 53.5% of the markers showed ILP, with PIC values ranging from 0.06 to 0.80. The result of clustering analysis of the 30 maize inbred lines, based on the polymorphism of 23 ILP markers, suggests that the ILP markers developed in this study are not only efficient for genetic diversity analysis but also potentially useful for marker assisted selection for tolerance to low phosphorus.
- Published
- 2014
43. Genome-wide characterization of non-reference transposable element insertion polymorphisms reveals genetic diversity in tropical and temperate maize
- Author
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Chuan Li, Erliang Hu, Gengyun Zhang, Yanli Lu, James C. Schnable, Tingzhao Rong, Jie Xu, Yunbi Xu, Xianjun Lai, and Zhengqiao Liao
- Subjects
0301 basic medicine ,Transposable element ,lcsh:QH426-470 ,lcsh:Biotechnology ,Retrotransposon ,Biology ,Zea mays ,Genome ,03 medical and health sciences ,lcsh:TP248.13-248.65 ,Gene density ,Genetics ,Temperate climate ,GWAS ,Non-redundant TEs (NRTE) ,Adaptation ,Association mapping ,Gene ,Ecosystem ,Recombination, Genetic ,Tropical Climate ,Genetic diversity ,Polymorphism, Genetic ,Genetic recombination ,fungi ,food and beverages ,Genomics ,Adaptation, Physiological ,Maize ,lcsh:Genetics ,030104 developmental biology ,DNA Transposable Elements ,Transposable elements ,Research Article ,Biotechnology - Abstract
Background Maize was originally domesticated in a tropical environment but is now widely cultivated at temperate latitudes. Temperate and tropical maize populations have diverged both genotypically and phenotypically. Tropical maize lines grown in temperate environments usually exhibit delayed flowering, pollination, and seed set, which reduces their grain yield relative to temperate adapted maize lines. One potential mechanism by which temperate maize may have adapted to a new environment is novel transposable element insertions, which can influence gene regulation. Recent advances in sequencing technology have made it possible to study variation in transposon content and insertion location in large sets of maize lines. Results In total, 274,408 non-redundant TEs (NRTEs) were identified using resequencing data generated from 83 maize inbred lines. The locations of DNA TEs and copia-superfamily retrotransposons showed significant positive correlations with gene density and genetic recombination rates, whereas gypsy-superfamily retrotransposons showed a negative correlation with these two parameters. Compared to tropical maize, temperate maize had fewer unique NRTEs but higher insertion frequency, lower background recombination rates, and higher linkage disequilibrium, with more NRTEs close to flowering and stress-related genes in the genome. Association mapping demonstrated that the presence/absence of 48 NRTEs was associated with flowering time and that expression of neighboring genes differed between haplotypes where a NRTE was present or absent. Conclusions This study suggests that NRTEs may have played an important role in creating the variation in gene regulation that enabled the rapid adaptation of maize to diverse environments. Electronic supplementary material The online version of this article (10.1186/s12864-017-4103-x) contains supplementary material, which is available to authorized users.
- Published
- 2017
44. Molecular characterization of global maize breeding germplasm based on genome-wide single nucleotide polymorphisms
- Author
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Jonathan H. Crouch, Dan Makumbi, Stephen Mugo, Jianbing Yan, Trushar Shah, Shibin Gao, Suketoshi Taba, Yanli Lu, Tingzhao Rong, Sidney Netto Parentoni, Shaojiang Chen, Shihuang Zhang, Bindiganavile S. Vivek, Jiansheng Li, Zhuanfang Hao, Cosmos Magorokosho, Claudia Teixeira Guimarães, Yunbi Xu, Yanli Lu, CIMMYT, Jianbing Yan, CIMMYT, CLAUDIA TEIXEIRA GUIMARAES, CNPMS, Suketoshi Taba, CIMMYT, Zhuanfang Hao, CIMMYT, Shibin Gao, Schuan Agricultural University, Shaojiang Chen, National Maize Improvement Center of China, Jiansheng Li, National Maize Improvement Center of China, Shihuang Zang, Institute of Crop Science, Bindiganavile S. Vivek, CIMMYT, Cosmos Magorokosho, CIMMYT, Stephen Mugo, CIMMYT, Dan Makaumbi, CIMMYT, SIDNEY NETTO PARENTONI, CNPMS, Trushar Shah, CIMMYT, Tingzhao Rong, Schuan Agricultural University, Jonatham H. Crouch, CIMMYT, and Yunbi Xu, CIMMYT.
- Subjects
Germplasm ,Linkage disequilibrium ,Genotype ,Melhoramento genético vegetal ,Molecular Sequence Data ,Single-nucleotide polymorphism ,Biology ,Polymorphism, Single Nucleotide ,Zea mays ,Milho ,Gene Frequency ,Genetic variation ,Genetics ,Cluster Analysis ,Allele ,Allele frequency ,Alleles ,Oligonucleotide Array Sequence Analysis ,Principal Component Analysis ,Genetic diversity ,General Medicine ,Genetic divergence ,Phenotype ,Agronomy and Crop Science ,Genome, Plant ,Biotechnology - Abstract
Characterization of genetic diversity is of great value to assist breeders in parental line selection and breeding system design. We screened 770 maize inbred lines with 1,034 single nucleotide polymorphism (SNP) markers and identified 449 high-quality markers with no germplasm-specific biasing effects. Pairwise comparisons across three distinct sets of germplasm, CIMMYT (394), China (282), and Brazil (94), showed that the elite lines from these diverse breeding pools have been developed with only limited utilization of genetic diversity existing in the center of origin. Temperate and tropical/subtropical germplasm clearly clustered into two separate groups. The temperate germplasm could be further divided into six groups consistent with known heterotic patterns. The greatest genetic divergence was observed between temperate and tropical/subtropical lines, followed by the divergence between yellow and white kernel lines, whereas the least divergence was observed between dent and flint lines. Long-term selection for hybrid performance has contributed to significant allele differentiation between heterotic groups at 20% of the SNP loci. There appeared to be substantial levels of genetic variation between different breeding pools as revealed by missing and unique alleles. Two SNPs developed from the same candidate gene were associated with the divergence between two opposite Chinese heterotic groups. Associated allele frequency change at two SNPs and their allele missing in Brazilian germplasm indicated a linkage disequilibrium block of 142 kb. These results confirm the power of SNP markers for diversity analysis and provide a feasible approach to unique allele discovery and use in maize breeding programs.
- Published
- 2009
45. Genome-Wide Expression Profile of Maize Root Response to Phosphorus Deficiency Revealed by Deep Sequencing
- Author
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Hailan Liu, Xiao Zhang, Shun-zhong Su, Haijian Lin, Tingzhao Rong, Yan-li Lu, Zhiming Zhang, Yue-hui Tian, Shibin Gao, Dan Liu, Zhi Nie, Yaou Shen, Shu-zhi Zhang, and Ling Wu
- Subjects
Agriculture (General) ,chemistry.chemical_element ,Plant Science ,Biology ,Carbohydrate metabolism ,maize ,Biochemistry ,Deep sequencing ,S1-972 ,Food Animals ,Gene expression ,Botany ,Phosphorus deficiency ,Gene ,Genetics ,Molecular breeding ,Ecology ,Phosphorus ,root ,phosphorus efficiency ,chemistry ,Animal Science and Zoology ,digital gene expression ,Adaptation ,Agronomy and Crop Science ,Food Science - Abstract
Phosphorus (P) is one of the three primary macronutrients that are required in large amounts for plant growth and development. To better understand molecular mechanism of maize and identify relevant genes in response to phosphorus deficiency, we used Solexa/Illumina's digital gene expression (DGE) technology to investigate six genome-wide expression profiles of seedling roots of the low-P tolerant maize inbred line 178. DGE studies were conducted at 6, 24 and 72 h under both phosphorus deficient and sufficient conditions. Approximately 3.93 million raw reads for each sample were sequenced and 6 816 genes exhibited significant levels of differential expressions in at least one of three time points in response to P starvation. The number of genes with increased expression increased over time from 6 to 24 h, whereas genes with decreased expression were more abundant at 72 h, suggesting a gradual response process for P deficiency at different stages. Gene annotations illustrated that most of differentially expressed genes (DEGs) are involved in different cellular and molecular processes such as environmental adaptation and carbohydrate metabolism. The expression of some known genes identified in other plants, such as those involved in root architecture, P metabolism and transport were found to be altered at least two folds, indicating that the mechanisms of molecular and morphological adaptation to P starvation are conserved in plants. This study provides insight into the general molecular mechanisms underlying plant adaptation to low-P stress and thus may facilitate molecular breeding for improving P utilization in maize.
- Published
- 2014
46. Large-scale screening maize germplasm for low-phosphorus tolerance using multiple selection criteria
- Author
-
Jie Xu, Yaxi Liu, Erliang Hu, Jing Wang, Menglu Li, Fengkai Wu, Jia Li, Li-tian Zhang, Moju Cao, Yanli Lu, Shibin Gao, and Tingzhao Rong
- Subjects
Germplasm ,Phosphorus ,chemistry.chemical_element ,Regression analysis ,Plant Science ,Horticulture ,Heritability ,Biology ,Agronomy ,chemistry ,Dry weight ,Genetic variation ,Shoot ,Genetics ,Agronomy and Crop Science ,Selection (genetic algorithm) - Abstract
Phosphorus (P) deficiency is one of the major limiting factors in maize production in many developing countries. This experiment was conducted to evaluate multiple low-P tolerance criteria and identify the suitable maize germplasm for our future low-P tolerance breeding. A total of 456 diverse maize inbreds were evaluated for low-P tolerance at seedling stage using four shoot-related traits and six root-related traits measured under applied phosphorus (AP) and non-applied phosphorus (NAP) conditions. Analysis of variance revealed significant genetic variation among genotypes for all tested traits. Medium-to-high heritability estimates were obtained for most traits. Total dry weight (DW) was highly inheritable while the widely used root/shoot ratio had only an intermediate level of heritability. Based on the synthetic index (SI), the tested inbreds were classified into three groups representing low, moderate and high tolerance to low-P stress. Regression model built based on selection criteria for low-P tolerance explained 67.8 and 76.8 % of variation for DW under NAP and AP conditions, respectively. Using low-P tolerance index for DW and SI as selection criteria, 23 and 109 maize inbreds were identified as germplasm resources that were extremely tolerant and sensitive to low-P stress, respectively, which could be further used for genetic improvement of low-P tolerance.
- Published
- 2014
47. Challenges and Suggestions for Sustainable Development of Food Security in Southwest China
- Author
-
Kaixian Wu, Tingzhao Rong, Zhuo Chen, Daiwen Chen, Bing Yu, Shibin Gao, and Song Yang
- Subjects
Sustainable development ,Food security ,General Earth and Planetary Sciences ,Business ,China ,Environmental planning ,General Environmental Science - Published
- 2019
48. Analysis on breeding potential of eight synthetic populations to improve a Chinese maize hybrid Zhengdan 958
- Author
-
Degui Zhang, Hongjun Yong, Guangtang Pan, Tingzhao Rong, Xinhai Li, Mingshun Li, and Shihuang Zhang
- Subjects
Germplasm ,business.industry ,Heterosis ,General Medicine ,Biology ,Zea mays ,Biotechnology ,Test weight ,Agronomy ,Inbred strain ,Trait ,Grain yield ,business ,Hybrid - Abstract
Maize (Zea mays L.) populations are potential sources of favorable alleles absent in parental inbred lines to improve elite hybrids. The maize hybrid Zhengdan 958 has been hampered by the lack of favorable new alleles for improving yield and commodity quality. In the present study, 16 testcrosses made by using eight synthetic populations as the donors and the two parental lines of Zhengdan 958 as the receptors were evaluated in 2009 and 2010 at Shunyi, Beijing and Xinxiang, Henan Province for grain yield and test weight. Four genetic parameters were used to determine the breeding potential of eight synthetic populations as the donors to improve the target hybrid. Several synthetic populations were identified as the potential sources of favorable alleles absent in the target hybrid for each trait evaluated. The two most promising germplasms, WBMC-4 and Shanxi Syn3, had the potential for simultaneously improving grain yield and test weight of the target hybrid, which could be used to improve the parental lines Zheng 58 and Chang 7-2, respectively, and further broaden the germplasm base of Chinese heterotic groups PA and Sipingtou.
- Published
- 2013
49. Combining Ability and Parent-Offspring Correlation of Maize (Zea may L.) Grain β-Carotene Content with a Complete Diallel
- Author
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Hai Lan, Yan-li Lu, Qilin Tang, Moju Cao, Guangtang Pan, Jing Wang, Run Li, Yuan-qi Wu, Lan-hai Xiao, and Tingzhao Rong
- Subjects
Agriculture (General) ,Reciprocal cross ,medicine.medical_treatment ,Plant Science ,Biology ,maize ,Biochemistry ,S1-972 ,β-carotene content ,Correlation ,Diallel cross ,Animal science ,Food Animals ,Inbred strain ,Botany ,medicine ,combining ability ,Ecology ,Mean value ,Carotene ,food and beverages ,complete diallel cross ,Parent offspring ,medicine.disease ,Vitamin A deficiency ,Animal Science and Zoology ,Agronomy and Crop Science ,Food Science - Abstract
Vitamin A deficiency has become a worldwide problem. Biofortified foods can potentially be an inexpensive, locally adaptable, and long-term solution to dietary-nutrient deficiency. In order to improve the β-carotene content in maize grain by breeding and minimize vitamin A deficiency, a complete diallel cross was designed with eight inbred lines of maize, and 64 combinations were obtained in this study. The experimental combinations were planted in Yunnan and Sichuan provinces, respectively, with a random complete block design. The β-carotene contents in the grains of the experimental materials were analyzed by high-performance liquid chromatography. Among the tested materials, the effect difference of general combining ability of the β-carotene content was significant; however, the effect difference of the special combining ability and the reciprocal effect were not significant. The β-carotene content of maize grain was not influenced significantly by the cross and the reciprocal cross. There was a significant correlation about the β-carotene content in the maize grains between the F1 and their parents. The combinations with high β-carotene content were obviously influenced by the environment, and the mean value of β-carotene content for the experimental materials planted in Ya'an of Sichuan was higher than that planted in Yuanjiang of Yunnan, with the results being significant at the 0.01 level.
- Published
- 2013
50. Root-lodging resistance in maize as an example for high-throughput genetic mapping via single nucleotide polymorphism-based selective genotyping
- Author
-
Yunbi Xu, Bahman Yazdi Samadi, Mohammad Farkhari, Mohammad Reza Naghavi, Yanli Lu, Alan F. Krivanek, and Tingzhao Rong
- Subjects
Genetics ,food and beverages ,Single-nucleotide polymorphism ,Plant Science ,Quantitative trait locus ,Biology ,SNP genotyping ,Chromosome 4 ,Family-based QTL mapping ,Gene mapping ,Agronomy and Crop Science ,Allele frequency ,Selection (genetic algorithm) - Abstract
Large-scale selective genotyping and high-throughput analysis are two important strategies for low-cost and high-effective genetic mapping. In this study, selective genotyping was applied to four maize F2 populations. Thirty plants were selected from each of the two tails of the original F2 populations to represent extreme resistant and susceptible plants to root lodging, and genotyped individually with 1536 single nucleotide polymorphisms (SNPs). A quantitative trait locus (QTL) was declared when at least three closely linked SNPs showed significant allele frequency difference between the two tails. Nine QTL were identified for root lodging across the four populations, which were located on chromosomes 2, 4, 5, 7, 8 and 10 and one of them was shared between two populations. A total of 20 segregation distortion regions (SDRs) were identified across the four populations, one of which was co-localized with a QTL on chromosome 4. The tightly linked SNPs identified in this study can be used for marker-assisted selection for root lodging. Selective genotyping, when combined with pooled DNA analysis, can be used to develop strategies for high-throughput genetic mapping for all crops.
- Published
- 2012
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