34 results on '"QUANWEI LU"'
Search Results
2. Flow cytometry-based cell cycle synchronization and transcriptome analysis in cotton (Gossypium arboretum L.)
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Yangyang Wei, Zilin Zhao, Sumei Wan, Yi Li, Jiajia Feng, Qiankun Liu, Jingjing Zhai, Jianyu Wang, Yongqing Zhao, Xingyan Li, Yuling Liu, Tao Wang, Pengtao Li, Quanwei Lu, Baohong Zhang, Shoulin Hu, and Renhai Peng
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Agronomy and Crop Science - Published
- 2023
3. Genome-wide identification, characterization, and expression analysis of aluminum-activated malate transporter genes (ALMTs) in Gossypium hirsutum L
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QUANWEI LU, YUZHEN SHI, RUILI CHEN, XIANGHUI XIAO, PENGTAO LI, JUWU GONG, RENHAI PENG, and YOULU YUAN
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General Medicine - Published
- 2022
4. Linkage and association analyses reveal that hub genes in energy-flow and lipid biosynthesis pathways form a cluster in upland cotton
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Juwu Gong, Yan Peng, Jiwen Yu, Wenfeng Pei, Zhen Zhang, Daoran Fan, Linjie Liu, Xianghui Xiao, Ruixian Liu, Quanwei Lu, Pengtao Li, Haihong Shang, Yuzhen Shi, Junwen Li, Qun Ge, Aiying Liu, Xiaoying Deng, Senmiao Fan, Jingtao Pan, Quanjia Chen, Youlu Yuan, and Wankui Gong
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Structural Biology ,Genetics ,Biophysics ,Biochemistry ,Computer Science Applications ,Biotechnology - Abstract
Upland cotton is an important allotetraploid crop that provides both natural fiber for the textile industry and edible vegetable oil for the food or feed industry. To better understand the genetic mechanism that regulates the biosynthesis of storage oil in cottonseed, we identified the genes harbored in the major quantitative trait loci/nucleotides (QTLs/QTNs) of kernel oil content (KOC) in cottonseed via both multiple linkage analyses and genome-wide association studies (GWAS). In 'CCRI70' RILs, six stable QTLs were simultaneously identified by linkage analysis of CHIP and SLAF-seq strategies. In '0-153' RILs, eight stable QTLs were detected by consensus linkage analysis integrating multiple strategies. In the natural panel, thirteen and eight loci were associated across multiple environments with two algorithms of GWAS. Within the confidence interval of a major common QTL on chromosome 3, six genes were identified as participating in the interaction network highly correlated with cottonseed KOC. Further observations of gene differential expression showed that four of the genes
- Published
- 2022
5. Trends in grain quality of starch, protein, fat and lysine content for normal maize varieties in China since the 1960s
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Xiaoliang Qin, Kadambot H. M. Siddique, Quanwei Lu, Jiquan Xue, Chen Lu, and Zhenxing Zhou
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Protein content ,chemistry.chemical_compound ,Chemistry ,Starch ,Fat content ,Organic Chemistry ,Lysine ,Grain quality ,Food science ,Food Science - Published
- 2021
6. Large-scale metabolome analysis reveals dynamic changes of metabolites during foxtail millet grain filling
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Tao Wang, Lu Xing, Hui Song, Yangyang Wei, Pengtao Li, Quanwei Lu, Nan Hu, Yuling Liu, Yongqing Zhao, Jinrong Liu, Baohong Zhang, and Renhai Peng
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Food Science - Published
- 2023
7. Genome-Wide Identification and Characterization of the PPO Gene Family in Cotton (Gossypium) and Their Expression Variations Responding to Verticillium Wilt Infection
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Shuhan Yang, Qun Ge, Sumei Wan, Zhihao Sun, Yu Chen, Yanfang Li, Qiankun Liu, Juwu Gong, Xianghui Xiao, Quanwei Lu, Yuzhen Shi, Renhai Peng, Haihong Shang, Guodong Chen, and Pengtao Li
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bioinformatics analysis ,Gossypium ,Genetics ,qRT-PCR ,PPO gene family ,Verticillium wilt ,Genetics (clinical) - Abstract
Polyphenol oxidases (PPOs) are copper-binding metalloproteinases encoded by nuclear genes, ubiquitously existing in the plastids of microorganisms, plants, and animals. As one of the important defense enzymes, PPOs have been reported to participate in the resistant processes that respond to diseases and insect pests in multiple plant species. However, PPO gene identification and characterization in cotton and their expression patterns under Verticillium wilt (VW) treatment have not been clearly studied. In this study, 7, 8, 14, and 16 PPO genes were separately identified from Gossypium arboreum, G. raimondii, G. hirsutum, and G. barbadense, respectively, which were distributed within 23 chromosomes, though mainly gathered in chromosome 6. The phylogenetic tree manifested that all the PPOs from four cotton species and 14 other plants were divided into seven groups, and the analyses of the conserved motifs and nucleotide sequences showed highly similar characteristics of the gene structure and domains in the cotton PPO genes. The dramatically expressed differences were observed among the different organs at various stages of growth and development or under the diverse stresses referred to in the published RNA-seq data. Quantitative real-time PCR (qRT-PCR) experiments were also performed on the GhPPO genes in the roots, stems, and leaves of VW-resistant MBI8255 and VW-susceptible CCRI36 infected with Verticillium dahliae V991, proving the strong correlation between PPO activity and VW resistance. A comprehensive analysis conducted on cotton PPO genes contributes to the screening of the candidate genes for subsequent biological function studies, which is also of great significance for the in-depth understanding of the molecular genetic basis of cotton resistance to VW.
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- 2023
8. Genome-wide artificial introgressions of Gossypium barbadense into G. hirsutum reveal superior loci for simultaneous improvement of cotton fiber quality and yield traits
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Shaoqi Li, Linglei Kong, Xianghui Xiao, Pengtao Li, Aiying Liu, Junwen Li, Juwu Gong, Wankui Gong, Qun Ge, Haihong Shang, Jingtao Pan, Hong Chen, Yan Peng, Yuanming Zhang, Quanwei Lu, Yuzhen Shi, and Youlu Yuan
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Multidisciplinary - Abstract
The simultaneous improvement of fiber quality and yield for cotton is strongly limited by the narrow genetic backgrounds of Gossypium hirsutum (Gh) and the negative genetic correlations among traits. An effective way to overcome the bottlenecks is to introgress the favorable alleles of Gossypium barbadense (Gb) for fiber quality into Gh with high yield.This study was to identify superior loci for the improvement of fiber quality and yield.Two sets of chromosome segment substitution lines (CSSLs) were generated by crossing Hai1 (Gb, donor-parent) with cultivar CCRI36 (Gh) and CCRI45 (Gh) as genetic backgrounds, and cultivated in 6 and 8 environments, respectively. The kmer genotyping strategy was improved and applied to the population genetic analysis of 743 genomic sequencing data. A progeny segregating population was constructed to validate genetic effects of the candidate loci.A total of 68,912 and 83,352 genome-wide introgressed kmers were identified in the CCRI36 and CCRI45 populations, respectively. Over 90 % introgressions were homologous exchanges and about 21 % were reverse insertions. In total, 291 major introgressed segments were identified with stable genetic effects, of which 66(22.98 %), 64(21.99 %), 35(12.03 %), 31(10.65 %) and 18(6.19 %) were beneficial for the improvement of fiber length (FL), strength (FS), micronaire, lint-percentage (LP) and boll-weight, respectively. Thirty-nine introgression segments were detected with stable favorable additive effects for simultaneous improvement of 2 or more traits in Gh genetic background, including 6 could increase FL/FS and LP. The pyramiding effects of 3 pleiotropic segments (A07:C45Clu-081, D06:C45Clu-218, D02:C45Clu-193) were further validated in the segregating population.The combining of genome-wide introgressions and kmer genotyping strategy showed significant advantages in exploring genetic resources. Through the genome-wide comprehensive mining, a total of 11 clusters (segments) were discovered for the stable simultaneous improvement of FL/FS and LP, which should be paid more attention in the future.
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- 2022
9. Multi-environment Evaluations Across Ecological Regions Reveal That the Kernel Oil Content of Cottonseed Is Equally Determined by Genotype and Environment
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Juwu Gong, Depei Kong, Changwen Liu, Pengtao Li, Ping Liu, Xianghui Xiao, Ruixian Liu, Quanwei Lu, Haihong Shang, Yuzhen Shi, Junwen Li, Qun Ge, Aiying Liu, Xiaoying Deng, Senmiao Fan, Jingtao Pan, Quanjia Chen, Youlu Yuan, and Wankui Gong
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Gossypium ,Phenotype ,Cottonseed Oil ,Genotype ,General Chemistry ,General Agricultural and Biological Sciences - Abstract
Cotton is the fifth-largest oil crop in the world. A high kernel oil content (KOC) and high stability are important cottonseed attributes for food security. In this study, the phenotype of KOC and the genotype-by-environment interaction factors were collectively dissected using 250 recombinant inbred lines, their parental cultivars sGK156 and 901-001, and CCRI70 across multi-environments. ANOVA and correlation analysis showed that both genotype and environment contributed significantly to KOC accumulation. Analyses of additive main effect multiplicative interaction and genotype-by-environment interaction biplot models presented the effects of genotype, environment, and genotype by environment on KOC performance and the stability of the experimental materials. Interaction network analysis revealed that meteorological and geographical factors explained 38% of the total KOC variance, with average daily rainfall contributing the largest positive impact and cumulative rainfall having the largest negative impact on KOC accumulation. This study provides insight into KOC accumulation and could direct selection strategies for improved KOC and field management of cottonseed in the future.
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- 2022
10. Current advances in pathogen-plant interaction between Verticillium dahliae and cotton provide new insight in the disease management
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Gong Wankui, Ruixian Liu, Li Junwen, Youlu Yuan, Koffi Kibalou Palanga, Juwu Gong, Qun Ge, Quanwei Lu, and Pengtao Li
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Molecular breeding ,business.industry ,Verticillium wilt ,fungi ,Callose ,Plant culture ,food and beverages ,Virulence ,Biology ,biology.organism_classification ,Agricultural and Biological Sciences (miscellaneous) ,Biochemistry, Genetics and Molecular Biology (miscellaneous) ,SB1-1110 ,Biotechnology ,chemistry.chemical_compound ,Upland cotton ,chemistry ,RNA interference ,Disease management (agriculture) ,Disease management ,Verticillium dahliae ,business ,Pathogen ,Plant-pathogen interaction - Abstract
Verticillium wilt is the second serious vascular wilt caused by the phytopathogenic fungus Verticillium dahliae Kleb. It has distributed worldwide, causing serious yield losses and fiber quality reduction in cotton production. The pathogen has developed different mechanisms like the production of cell wall degrading enzymes, activation of virulence genes and protein effectors to succeed in its infection. Cotton plant has also evolved multiple mechanisms in response to the fungus infection, including a strong production of lignin and callose deposition to strengthen the cell wall, burst of reactive oxygen species, accumulation of defene hormones, expression of defense-related genes, and target-directed strategies like cross-kingdom RNAi for specific virulent gene silencing. This review summarizes the recent progress made over the past two decades in understanding the interactions between cotton plant and the pathogen Verticillium dahliae during the infection process. The review also discusses the achievements in the control practices of cotton verticillium wilt in recent years, including cultivation practices, biological control, and molecular breeding strategies. These studies reveal that effective management strategies are needed to control the disease, while cultural practices and biological control approaches show promising results in the future. Furthermore, the biological control approaches developed in recent years, including antagonistic fungi, endophytic bacteria, and host induced gene silencing strategies provide efficient choices for integrated disease management.
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- 2021
11. QTL mapping and candidate gene prediction for fiber yield and quality traits in a high-generation cotton chromosome substitution line with Gossypium barbadense segments
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Quanwei Lu, Pengtao Li, Rui Yang, Xianghui Xiao, Ziyin Li, Qiuyu Wu, Juwu Gong, Qun Ge, Aiying Liu, Shengli Du, Jundi Wang, Yuzhen Shi, and Youlu Yuan
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Gossypium ,Phenotype ,Quantitative Trait Loci ,Genetics ,Chromosome Mapping ,Humans ,General Medicine ,Cotton Fiber ,Molecular Biology ,Chromosomes, Plant - Abstract
Gossypium provides the foremost natural fiber for supporting the rapid development of the textile industry. Quantitative trait locus (QTL) mapping of fiber yield and quality traits is, thus, of great significance for providing a foundation for the genetic improvement of key target traits in cotton production. In this study, a superior chromosome segment substitution line (CSSL), MBI8255, with high yield and premium fiber quality characteristics was cultivated from the BC
- Published
- 2021
12. Genome‐wide quantitative trait loci reveal the genetic basis of cotton fibre quality and yield‐related traits in a Gossypium hirsutum recombinant inbred line population
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Xiao Jiang, Nijiang Ai, Chuanyun Zhang, Fan Senmiao, Yanling Wang, Gong Wankui, Shi Yuzhen, Li Junwen, Shilin Li, Aixia Xu, Zhang Zhibin, Wenming Lian, Chaojun Zhang, Youlu Yuan, Ruixian Liu, Fuding Sun, Qin Tian, Pengtao Li, Jinping Hua, Zhen Zhang, Xiaoying Deng, Xianyan Zou, Ping Liu, Quanwei Lu, Ge Qun, Yumei Wang, Fan Liqiang, Muhammad Jamshed, Baoqin Wang, Mei Hong, Fei Jia, Juan Zou, Shufang Wang, Jinyong Huang, Muhammad Sajid Iqbal, Xinhe Jia, Jianhong Zhang, Liu Aiying, Juwu Gong, Guoli Feng, Bo Wu, Haihong Shang, Pan Jingtao, and Hong Chen
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Genetic Markers ,0106 biological sciences ,0301 basic medicine ,Quantitative Trait Loci ,Population ,Plant Science ,Biology ,Quantitative trait locus ,01 natural sciences ,Genetic correlation ,Genome ,fibre yield ,03 medical and health sciences ,Centimorgan ,Cotton Fiber ,RNA-Seq ,education ,Gene ,Research Articles ,Chromosome 13 ,Genetics ,Gossypium ,education.field_of_study ,consensus genetic map ,Chromosome Mapping ,QTL clusters ,genetic correlation ,fibre quality ,Plant Breeding ,Phenotype ,030104 developmental biology ,upland cotton ,Natural population growth ,Agronomy and Crop Science ,gene expression level ,Research Article ,010606 plant biology & botany ,Biotechnology - Abstract
Summary Cotton is widely cultivated globally because it provides natural fibre for the textile industry and human use. To identify quantitative trait loci (QTLs)/genes associated with fibre quality and yield, a recombinant inbred line (RIL) population was developed in upland cotton. A consensus map covering the whole genome was constructed with three types of markers (8295 markers, 5197.17 centimorgans (cM)). Six fibre yield and quality traits were evaluated in 17 environments, and 983 QTLs were identified, 198 of which were stable and mainly distributed on chromosomes 4, 6, 7, 13, 21 and 25. Thirty‐seven QTL clusters were identified, in which 92.8% of paired traits with significant medium or high positive correlations had the same QTL additive effect directions, and all of the paired traits with significant medium or high negative correlations had opposite additive effect directions. In total, 1297 genes were discovered in the QTL clusters, 414 of which were expressed in two RNA‐Seq data sets. Many genes were discovered, 23 of which were promising candidates. Six important QTL clusters that included both fibre quality and yield traits were identified with opposite additive effect directions, and those on chromosome 13 (qClu‐chr13‐2) could increase fibre quality but reduce yield; this result was validated in a natural population using three markers. These data could provide information about the genetic basis of cotton fibre quality and yield and help cotton breeders to improve fibre quality and yield simultaneously.
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- 2019
13. QTL mapping and genetic effect of chromosome segment substitution lines with excellent fiber quality from Gossypium hirsutum × Gossypium barbadense
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Shaoqi Li, Gong Juwu, Pengtao Li, Shi Yuzhen, Shang Haihong, Gong Wankui, Li Junwen, Ge Qun, Ruixian Liu, Qi Zhang, Ling-lei Kong, Liu Aiying, Xianghui Xiao, Quanwei Lu, and Youlu Yuan
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0106 biological sciences ,0301 basic medicine ,Quantitative Trait Loci ,Molecular cloning ,Biology ,Quantitative trait locus ,01 natural sciences ,Genome ,Chromosomes, Plant ,03 medical and health sciences ,Chromosome regions ,Genetics ,Cotton Fiber ,Molecular Biology ,Crosses, Genetic ,Gossypium ,Chromosome Mapping ,Chromosome ,General Medicine ,Gossypium barbadense ,Human genetics ,Phenotype ,030104 developmental biology ,Genetic marker ,Genome, Plant ,010606 plant biology & botany - Abstract
Chromosome segment substitution lines (CSSLs) are ideal materials for identifying genetic effects. In this study, CSSL MBI7561 with excellent fiber quality that was selected from BC4F3:5 of CCRI45 (Gossypium hirsutum) × Hai1 (Gossypium barbadense) was used to construct 3 secondary segregating populations with 2 generations (BC5F2 and BC5F2:3). Eighty-one polymorphic markers related to 33 chromosome introgressive segments on 18 chromosomes were finally screened using 2292 SSR markers which covered the whole tetraploid cotton genome. A total of 129 quantitative trait loci (QTL) associated with fiber quality (103) and yield-related traits (26) were detected on 17 chromosomes, explaining 0.85-30.35% of the phenotypic variation; 39 were stable (30.2%), 53 were common (41.1%), 76 were new (58.9%), and 86 had favorable effects on the related traits. More QTL were distributed in the Dt subgenome than in the At subgenome. Twenty-five stable QTL clusters (with stable or common QTL) were detected on 22 chromosome introgressed segments. Finally, the 6 important chromosome introgressed segments (Seg-A02-1, Seg-A06-1, Seg-A07-2, Seg-A07-3, Seg-D07-3, and Seg-D06-2) were identified as candidate chromosome regions for fiber quality, which should be given more attention in future QTL fine mapping, gene cloning, and marker-assisted selection (MAS) breeding.
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- 2019
14. Micro-FTIR combined with curve fitting method to study cellulose crystallinity of developing cotton fibers
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Quanwei Lu, Renhai Peng, Shiding Zhang, Youlu Yuan, Huawen Zou, Peng Xu, Xianchang Li, Haihong Shang, Lipeng Zhang, and Qianqian Gao
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Diffraction ,Coefficient of determination ,Materials science ,02 engineering and technology ,01 natural sciences ,Biochemistry ,Analytical Chemistry ,Crystallinity ,chemistry.chemical_compound ,X-Ray Diffraction ,Spectroscopy, Fourier Transform Infrared ,Cotton Fiber ,Composite material ,Fourier transform infrared spectroscopy ,Cellulose ,Cellulose crystallinity ,Wax ,010401 analytical chemistry ,021001 nanoscience & nanotechnology ,0104 chemical sciences ,chemistry ,visual_art ,visual_art.visual_art_medium ,Curve fitting ,0210 nano-technology ,Crystallization - Abstract
This study aimed to use micro-FTIR with transmission mode to investigate cellulose crystallinity of developing cotton fibers. Compared with ATR-FTIR method, we found that micro-FTIR can obtain more information of cellulose inside of the developing cotton fibers, especially in high wavenumber of 2800–3000 cm−1 region. Combined with curve fitting method, a new IR crystallinity index (CI) method named wax crystallinity index (WCI) was introduced to evaluate the cellulose crystallinity in the development of cotton fibers based on the peak and area ratios of 2900 cm−1/2850 cm−1 and 2900 cm−1/2920 cm−1. The obtained WCI values demonstrated an excellent coefficient of determination with X-ray diffraction (XRD) CI method with the value up to 0.99. This study suggested that micro-FTIR was an effective technique to qualitatively analyze the crystallinity in developing cotton fibers combined with curve fitting method.
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- 2020
15. Chromosome Painting Based on Bulked Oligonucleotides in Cotton
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Renhai Peng, Fang Liu, Zhen Liu, Yuling Liu, Tao Zhang, Yangyang Wei, Xiuyuan Wang, and Quanwei Lu
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oligonucleotide ,0106 biological sciences ,0301 basic medicine ,Plant Science ,lcsh:Plant culture ,Biology ,Gossypium raimondii ,01 natural sciences ,Genome ,45S rDNA ,03 medical and health sciences ,Chromosome regions ,medicine ,lcsh:SB1-1110 ,fluorescence in situ hybridization ,Ribosomal DNA ,Original Research ,Whole genome sequencing ,Genetics ,medicine.diagnostic_test ,Oligonucleotide ,Chromosome ,030104 developmental biology ,chromosome painting ,010606 plant biology & botany ,Fluorescence in situ hybridization - Abstract
Chromosome painting is one of the key technologies in cytogenetic research, which can accurately identify chromosomes or chromosome regions. Oligonucleotide (oligo) probes designed based on genome sequences have both flexibility and specificity, which would be ideal probes for fluorescence in situ hybridization (FISH) analysis of genome structure. In this study, the bulked oligos of the two arms of chromosome seven of cotton were developed based on the genome sequence of Gossypium raimondii (DD, 2n = 2× = 26), and each arm contains 12,544 oligos. Chromosome seven was easily identified in both D genome and AD genome cotton species using the bulked chromosome-specific painting probes. Together with 45S ribosomal DNA (rDNA) probe, the chromosome-specific painting probe was also successfully used to correct the chromosomal localization of 45S rDNA in G. raimondii. The study reveals that bulked oligos specific to a chromosome is a useful tool for chromosome painting in cotton.
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- 2020
16. Lengthened flowering season under climate warming: Evidence from manipulative experiments
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Shilin Wang, Yupeng Cui, Yuanchen Zhang, Hu Mengjun, Zhaolin Sun, Yuan Miao, Dong Wang, Lingjie Lei, Quanwei Lu, Kunpeng Zhang, Yinzhan Liu, Zhenxing Zhou, Ying Li, Shijie Han, and Mingxing Zhong
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Atmospheric Science ,Global and Planetary Change ,Phenology ,ved/biology ,ved/biology.organism_classification_rank.species ,Global warming ,Forestry ,Biology ,Herbaceous plant ,Latitude ,Flowering season ,Agronomy ,Terrestrial plant ,Forb ,Precipitation ,Agronomy and Crop Science - Abstract
Climate warming potentially changes the flowering seasons of terrestrial plants, and thus species interaction, with consequently substantial impacts on ecosystem structure and function. However, the general response patterns of flowering seasons to warming and the underlying mechanisms remain poorly understood. Here, a meta-analysis of data from 26 experimental studies examining 168 species was conducted to quantify the responses of the flowering seasons of terrestrial plants to experimental warming. The results showed that experimental warming prolonged the flowering season by 2.08% across all species included in this study. In addition, flowering season responses were dependent on plant functional types, with a significant extension in herbaceous species (+2.18%) but no change in woody species. The warming impacts on the flowering season of wind-pollinated (-4.53%) and insect-pollinated species (+4.21%) were opposite. Among herbaceous species, the flowering seasons of forb (+4.47%) and specifically legume species (+15.06%) were positive, whereas grass species (-4.53%) showed negative responses to experimental warming. Moreover, experimental warming effects on the flowering season showed quadratic relationships with the latitude and the mean annual temperature but did not change with the mean annual precipitation. The responses of the flowering season to experimental warming also differed in terms of the warming magnitude. These diverse findings indicate the need for additional experimental warming experiments, especially for underrepresented plant functional groups, to better understand the mechanistic relationships between phenology and temperature under future climate warming scenarios.
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- 2022
17. Rapid identification of a candidate gene related to fiber strength using a superior chromosome segment substitution line from Gossypium hirsutum ×Gossypium barbadense via bulked segregant RNA-sequencing
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Qi Zhang, Pengtao Li, Aiying Liu, Quanwei Lu, Juwu Gong, Qun Ge, Junwen Li, Wankui Gong, Haihong Shang, Yuzhen Shi, and Youlu Yuan
- Abstract
Gossypium is the most widely cultivated commercial crop producing natural fiber around the world, and fiber strength principally determined during the secondary wall thickening period is a critical trait for fiber quality. Based on the developed BC 5 F 3:5 CSSLs (chromosome segment substitution lines) from G. hisutum CCRI36 × G. barbadense Hai1, the superior MBI9915 was chosen to construct the secondary segregated population BC 7 F 2 with its recurrent parent CCRI36, which was subjected to Bulk segregant RNA-sequencing (BSR-seq) for rapid identification of candidate genes related to fiber strength. Four fiber-transcriptome libraries were separately constructed and sequenced, including two parents (CCRI36 and MBI9915) and two extreme pools at 20 DPA (days post anathesis). Through multiple comparisons, 3742 DEGs (differentially expressed genes) and 3252 DEGs were separately identified between two parents and between two extreme pools, while 536 DEGs were overlapped between parent and extreme pool groups. A total of 831high-probability SNPs (single nucleotide polymorphism) were identified relevant to fiber strength between two extreme pools through allelic-polymorphism comparison in mRNA sequences, and 18 correlated regions with 1981 annotation genes were finally screened by linkage analysis with SNP-index method, of which including only 12 common genes differentially expressed both between two parents and two pools. Interesting, there was one correlated region consistent with the previous study with the same parents on chromosome A07 with 13-14 Mb, and one common DEG ( Gh_A07G0837 ) in the candidate region was identified in both parents and extreme pools, which has been reported to be involved in fiber strength development through regulating reactive oxygen species (ROS) activity. The reliability of BSR-seq results was validated by the quantitative real-time PCR (qRT-PCR) experiments on 5 DEGs at 20 DPA. This study focuses on bulked segregant analysis of the extreme pools from segregation population developed by superior CSSL and its recurrent parent, indicating that BSR-seq can be efficiently applied on rapid identification for candidate genes related to the significant quantitative traits, which provides valuable contributions for comprehension of fiber strength formation in cotton.
- Published
- 2019
18. Genome-wide identification of the MIOX gene family and their expression profile in cotton development and response to abiotic stress
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Yuling Liu, Pengtao Li, Renhai Peng, Mengjie Liu, Zhaoguo Li, Quanwei Lu, Yangyang Wei, Linxue Xing, and Zhen Liu
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0106 biological sciences ,Physiology ,Arabidopsis ,Gene Expression ,Cotton ,Plant Science ,Sodium Chloride ,Plant Genetics ,Gossypium ,01 natural sciences ,Genome ,Polyethylene Glycols ,Gene Expression Regulation, Plant ,Gene Duplication ,Plant Resistance to Abiotic Stress ,Plant Genomics ,Promoter Regions, Genetic ,Gossypium darwinii ,Phylogeny ,Flowering Plants ,Data Management ,Genetics ,0303 health sciences ,Multidisciplinary ,Ecology ,biology ,Eukaryota ,Agriculture ,Phylogenetic Analysis ,Exons ,Genomics ,Plants ,Cold Temperature ,Phylogenetics ,Organ Specificity ,Multigene Family ,Plant Physiology ,Engineering and Technology ,Medicine ,Genome, Plant ,Research Article ,Biotechnology ,Computer and Information Sciences ,Science ,Bioengineering ,Crops ,Gossypium raimondii ,Chromosomes, Plant ,Polyploidy ,Gossypium herbaceum ,03 medical and health sciences ,Stress, Physiological ,Plant-Environment Interactions ,Gene family ,Evolutionary Systematics ,Plant Defenses ,Selection, Genetic ,Gene ,Taxonomy ,030304 developmental biology ,Evolutionary Biology ,Gene Expression Profiling ,Plant Ecology ,Ecology and Environmental Sciences ,Organisms ,Biology and Life Sciences ,Fiber Crops ,Gossypium barbadense ,Plant Pathology ,biology.organism_classification ,Introns ,Tetraploidy ,Plant Biotechnology ,Departures from Diploidy ,Crop Science ,010606 plant biology & botany - Abstract
The enzyme myo-inositol oxygenase (MIOX) catalyzes the myo-inositol into glucuronic acid. In this study, 6 MIOX genes were identified from all of the three diploid cotton species (Gossypium arboretum, Gossypium herbaceum and Gossypium raimondii) and Gossypioides kirkii, 12 MIOX genes were identified from two domesticated tetraploid cottons Gossypium hirsutum, Gossypium barbadense, and 11 MIOX genes were identified from three wild tetraploid cottons Gossypium tomentosum, Gossypium mustelinum and Gossypium darwinii. The number of MIOX genes in tetraploid cotton genome is roughly twice that of diploid cotton genome. Members of MIOX family were classified into six groups based on the phylogenetic analysis. Integrated analysis of collinearity events and chromosome locations suggested that both whole genome duplication and segmental duplication events contributed to the expansion of MIOX genes during cotton evolution. The ratios of non-synonymous (Ka) and synonymous (Ks) substitution rates revealed that purifying selection was the main force driving the evolution of MIOX genes. Numerous cis-acting elements related to light responsive element, defense and stress responsive element were identified in the promoter of the MIOX genes. Expression analyses of MIOX genes based on RNA-seq data and quantitative real time PCR showed that MIOX genes within the same group shared similar expression patterns with each other. All of these results provide the foundation for further study of the biological functions of MIOX genes in cotton environmental adaptability.
- Published
- 2021
19. Transcriptome Analysis Suggests That Chromosome Introgression Fragments from Sea Island Cotton (Gossypium barbadense) Increase Fiber Strength in Upland Cotton (Gossypium hirsutum)
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Shi Yuzhen, Youlu Yuan, Zhen Zhang, Quanwei Lu, Renhai Peng, Xianghui Xiao, Weiwu Song, Pengtao Li, Liu Aiying, Junwen Li, Gong Wankui, Ge Qun, Haihong Shang, Harun or Rashid, Shaoqi Li, Juwu Gong, and Jinling Huang
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0106 biological sciences ,0301 basic medicine ,Genotype ,Population ,Introgression ,QH426-470 ,Biology ,cotton ,01 natural sciences ,Chromosomes, Plant ,fiber strength ,Shared Data Resources ,03 medical and health sciences ,Gene Expression Regulation, Plant ,secondary cell wall synthesis ,Botany ,Genetics ,DEG ,Cotton Fiber ,Cultivar ,Fiber ,education ,Molecular Biology ,Crosses, Genetic ,Genetics (clinical) ,Hybrid ,Molecular breeding ,Gossypium ,education.field_of_study ,Gene Expression Profiling ,Gossypium barbadense ,Genomic Selection ,GenPred ,Phenotype ,030104 developmental biology ,Cell wall organization ,transcriptome ,010606 plant biology & botany - Abstract
As high-strength cotton fibers are critical components of high quality cotton, developing cotton cultivars with high-strength fibers as well as high yield is a top priority for cotton development. Recently, chromosome segment substitution lines (CSSLs) have been developed from high-yield Upland cotton (Gossypium hirsutum) crossed with high-quality Sea Island cotton (G. barbadense). Here, we constructed a CSSL population by crossing CCRI45, a high-yield Upland cotton cultivar, with Hai1, a Sea Island cotton cultivar with superior fiber quality. We then selected two CSSLs with significantly higher fiber strength than CCRI45 (MBI7747 and MBI7561), and one CSSL with lower fiber strength than CCRI45 (MBI7285), for further analysis. We sequenced all four transcriptomes at four different time points postanthesis, and clustered the 44,678 identified genes by function. We identified 2200 common differentially-expressed genes (DEGs): those that were found in both high quality CSSLs (MBI7747 and MBI7561), but not in the low quality CSSL (MBI7285). Many of these genes were associated with various metabolic pathways that affect fiber strength. Upregulated DEGs were associated with polysaccharide metabolic regulation, single-organism localization, cell wall organization, and biogenesis, while the downregulated DEGs were associated with microtubule regulation, the cellular response to stress, and the cell cycle. Further analyses indicated that three genes, XLOC_036333 [mannosyl-oligosaccharide-α-mannosidase (MNS1)], XLOC_029945 (FLA8), and XLOC_075372 (snakin-1), were potentially important for the regulation of cotton fiber strength. Our results suggest that these genes may be good candidates for future investigation of the molecular mechanisms of fiber strength formation and for the improvement of cotton fiber quality through molecular breeding.
- Published
- 2017
20. Construction of a High‐Density Genetic Map and Its Application to QTL Identification for Fiber Strength in Upland Cotton
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Yunna Tan, Jamshed Muhammad, Gong Wankui, Junwen Li, Liu Aiying, Youlu Yuan, Shi Yuzhen, Koffi Kibalou Palanga, Haihong Shang, Chen Tingting, Yanling Wang, Ruixian Liu, Juwu Gong, Zhen Zhang, Xiaoying Deng, Ge Qun, Quanwei Lu, Muhammad Sajid Iqbal, Harun or Rashid, and Xianyan Zou
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0106 biological sciences ,0301 basic medicine ,03 medical and health sciences ,030104 developmental biology ,Agronomy ,Fiber strength ,Identification (biology) ,Biology ,Quantitative trait locus ,01 natural sciences ,Agronomy and Crop Science ,010606 plant biology & botany - Published
- 2017
21. Genome-wide characterization of the UDP-glycosyltransferase gene family in upland cotton
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Liu Aiying, Xiaoying Deng, Doudou Niu, Shi Yuzhen, Ruixian Liu, Pengtao Li, Youlu Yuan, Haihong Shang, Xianghui Xiao, Juwu Gong, Quanjia Chen, Quanwei Lu, Hua Zhang, Ge Qun, Shaoqi Li, Junwen Li, Qi Zhang, and Gong Wankui
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Genetics ,Subfamily ,Chromosome localization ,Intron ,Environmental Science (miscellaneous) ,Biology ,Quantitative trait locus ,Agricultural and Biological Sciences (miscellaneous) ,Genome ,digestive system ,Phylogenetics ,Gene family ,Original Article ,Gene ,Biotechnology - Abstract
Uridine diphosphate (UDP)-glycosyltransferases (UGTs) involved in many metabolic processes are ubiquitous in plants, animals, microorganisms and other organisms and are essential for their growth and development. Upland cotton contains a large number of UGT genes. In this study, we aimed to identify UGT family members in the genome of upland cotton (Gossypium hirsutum L.) and analyze their expression patterns. Bioinformatics methods were used to identify UGT genes from the whole genome of upland cotton (Gossypium hirsutum L. acc. TM-1). Phylogenetic analysis was conducted based on alignment of UGT proteins from upland cotton, and the gene structure, motif and chromosome localization were analyzed for the H subgroup of the UGT family. And the physical and chemical properties and expressions of the genes in the H subgroup of this family were also analyzed. A total of 274 UGT genes were identified from the whole genome of upland cotton and were divided into nine subgroups based on phylogenetic analyses. In subgroup H, 36 genes were distributed on 18 chromosomes. The subfamily genes were simple in the structure, 19 of its members contained two introns, and the others contained only one intron. The qRT-PCR results and transcriptomic data indicated that most of the genes had a wide range of tissue expression characteristics. And the phylogenetic analysis results and expression profiles of these genes revealed tissues and different UGT genes from this crop. Taking RNA-seq, RT-qPCR, and quantitative trait locus (QTL) mapping together, our results suggested that GhUGT6 and GhUGT105 in subgroup H of the GhUGT gene family could be potential candidate genes for cotton yield, and GhUGT16, GhUGT103 might play a vital role in fiber development. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13205-019-1984-1) contains supplementary material, which is available to authorized users.
- Published
- 2019
22. Transcriptomic and biochemical analysis of upland cotton (Gossypium hirsutum) and a chromosome segment substitution line from G. hirsutum × G. barbadense in response to Verticillium dahliae infection
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Pengtao Li, Ruixian Liu, Liu Aiying, Shaoqi Li, Li Duan, Gong Wankui, Xianyan Zou, Juwu Gong, Md. Harun or Rashid, Junwen Li, Ya Zhang, Qi Zhang, Ge Qun, Shi Yuzhen, Xiao Jiang, Xiaoying Deng, Haihong Shang, Ting-ting Chen, Zhen Zhang, Quanwei Lu, Renhai Peng, Xianghui Xiao, and Youlu Yuan
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0106 biological sciences ,0301 basic medicine ,Candidate gene ,Gossypium hirsutum ,Plant Science ,Verticillium ,Biochemical tests ,01 natural sciences ,Chromosomes, Plant ,Transcriptome ,03 medical and health sciences ,Gene Expression Regulation, Plant ,lcsh:Botany ,Verticillium dahliae ,KEGG ,Gene ,Genetics ,Gossypium ,Phenylpropanoid ,biology ,Verticillium wilt ,biology.organism_classification ,lcsh:QK1-989 ,030104 developmental biology ,Chromosome segment substitution lines ,Plant hormone ,Transcriptome analysis ,Research Article ,010606 plant biology & botany - Abstract
Background Verticillium wilt (VW), also known as “cotton cancer,” is one of the most destructive diseases in global cotton production that seriously impacts fiber yield and quality. Despite numerous attempts, little significant progress has been made in improving the VW resistance of upland cotton. The development of chromosome segment substitution lines (CSSLs) from Gossypium hirsutum × G. barbadense has emerged as a means of simultaneously developing new cotton varieties with high-yield, superior fiber, and resistance to VW. Results In this study, VW-resistant investigations were first conducted in an artificial greenhouse, a natural field, and diseased nursery conditions, resulting in the identification of one stably VW-resistant CSSL, MBI8255, and one VW-susceptible G. hirsutum, CCRI36, which were subsequently subjected to biochemical tests and transcriptome sequencing during V991 infection (0, 1, and 2 days after inoculation). Eighteen root samples with three replications were collected to perform multiple comparisons of enzyme activity and biochemical substance contents. The findings indicated that VW resistance was positively correlated with peroxidase and polyphenol oxidase activity, but negatively correlated with malondialdehyde content. Additionally, RNA sequencing was used for the same root samples, resulting in a total of 77,412 genes, of which 23,180 differentially expressed genes were identified from multiple comparisons between samples. After Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis on the expression profiles identified using Short Time-series Expression Miner, we found that the metabolic process in the biological process, as well as the pathways of phenylpropanoid biosynthesis and plant hormone signal transduction, participated significantly in the response to VW. Gene functional annotation and expression quantity analysis indicated the important roles of the phenylpropanoid metabolic pathway and oxidation-reduction process in response to VW, which also provided plenty of candidate genes related to plant resistance. Conclusions This study concentrates on the preliminary response to V991 infection by comparing the VW-resistant CSSL and its VW-susceptible recurrent parent. Not only do our findings facilitate the culturing of new resistant varieties with high yield and superior performance, but they also broaden our understanding of the mechanisms of cotton resistance to VW. Electronic supplementary material The online version of this article (10.1186/s12870-018-1619-4) contains supplementary material, which is available to authorized users.
- Published
- 2019
23. Dissecting the genetic basis of fiber quality and yield traits in interspecific backcross populations of Gossypium hirsutum × Gossypium barbadense
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Zhang Baocai, Pan Jingtao, Shi Yuzhen, Haihong Shang, Muhammad Jamshed, Juwu Gong, Xiaoying Deng, Liu Aiying, Shaoqi Li, Junwen Li, Xianghui Xiang, Jinfa Zhang, Quanwei Lu, Ge Qun, Youlu Yuan, and Gong Wankui
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0106 biological sciences ,0301 basic medicine ,Population ,Quantitative Trait Loci ,Biology ,Quantitative trait locus ,01 natural sciences ,03 medical and health sciences ,Centimorgan ,Genetics ,Cotton Fiber ,education ,Molecular Biology ,Selection (genetic algorithm) ,Crosses, Genetic ,education.field_of_study ,Gossypium ,fungi ,food and beverages ,General Medicine ,Interspecific competition ,Phenotypic trait ,Gossypium barbadense ,Phenotype ,030104 developmental biology ,Seeds ,010606 plant biology & botany - Abstract
Fiber quality and yield are important traits of cotton. Quantitative trait locus (QTL) mapping is a prerequisite for marker-assisted selection (MAS) in cotton breeding. To identify QTLs for fiber quality and yield traits, 4 backcross-generation populations (BC1F1, BC1S1, BC2F1, and BC3F0) were developed from an interspecific cross between CCRI36 (Gossypium hirsutum L.) and Hai1 (G. barbadense L.). A total of 153 QTLs for fiber quality and yield traits were identified based on data from the BC1F1, BC1S1, BC2F1 and BC3F0 populations in the field and from the BC2F1 population in an artificial disease nursery using a high-density genetic linkage map with 2292 marker loci covering 5115.16 centimorgans (cM) from the BC1F1 population. These QTLs were located on 24 chromosomes, and each could explain 4.98–19.80% of the observed phenotypic variations. Among the 153 QTLs, 30 were consistent with those identified previously. Specifically, 23 QTLs were stably detected in 2 or 3 environments or generations, 6 of which were consistent with those identified previously and the other 17 of which were stable and novel. Ten QTL clusters for different traits were found and 9 of them were novel, which explained the significant correlations among some phenotypic traits in the populations. The results including these stable or consensus QTLs provide valuable information for marker-assisted selection (MAS) in cotton breeding and will help better understand the genetic basis of fiber quality and yield traits, which can then be used in QTL cloning.
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- 2018
24. Genome-wide identification, characterization, and expression analysis of superoxide dismutase (SOD) genes in foxtail millet (Setaria italica L.)
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Baohong Zhang, Tao Wang, Hui Song, Renhai Peng, Shulin Zhang, Ruilin Guo, Zilin Zhao, Zhen Liu, Jinrong Liu, Cong Wang, and Quanwei Lu
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0106 biological sciences ,0301 basic medicine ,Genetics ,Setaria ,Oryza sativa ,biology ,Setaria viridis ,Abiotic stress ,food and beverages ,Environmental Science (miscellaneous) ,biology.organism_classification ,01 natural sciences ,Agricultural and Biological Sciences (miscellaneous) ,Superoxide dismutase ,03 medical and health sciences ,030104 developmental biology ,Foxtail ,biology.protein ,Gene family ,Gene ,010606 plant biology & botany ,Biotechnology - Abstract
Superoxide dismutases (SODs) play important roles in plant growth, development, and response to abiotic stresses. Despite SOD gene families have been identified in various plant species, little is known in foxtail millet (Setaria italica L.). In this study, a systematic analysis of SOD gene family was performed in foxtail millet and the expression pattern of SOD genes in response to abiotic stressors was analyzed at the whole-genomic level. Eight SOD genes were identified in foxtail millet, including 4 Cu/ZnSODs, 3 FeSODs, and 1 MnSOD. These SiSODs are unevenly distributed across 5 of the 9 chromosomes. Phylogenetic analysis showed that SOD proteins could be divided into two major categories (Cu/ZnSODs and Fe-MnSODs), containing seven subgroups, from foxtail millet and other plant species. SOD genes have conserved motif and exon/intron composition in the same subgroup among Setaria italica, Setaria viridis, and Oryza sativa. Additionally, many cis-elements that respond to different stressors were distributed at different densities in the promoters of 8 SiSODs. The expression patterns of SiSODs in different tissues and different abiotic stressors indicated that the SiSODs may play important roles in reactive oxygen species scavenging, caused by various stressors in foxtail millet. This study provides a foundation for the further cloning and functional verification of the SOD gene family response to environmental stimuli in foxtail millet.
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- 2018
25. Genome-wide identification, characterization, and expression analysis of superoxide dismutase (SOD) genes in foxtail millet (
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Tao, Wang, Hui, Song, Baohong, Zhang, Quanwei, Lu, Zhen, Liu, Shulin, Zhang, Ruilin, Guo, Cong, Wang, Zilin, Zhao, Jinrong, Liu, and Renhai, Peng
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food and beverages ,Original Article - Abstract
Superoxide dismutases (SODs) play important roles in plant growth, development, and response to abiotic stresses. Despite SOD gene families have been identified in various plant species, little is known in foxtail millet (Setaria italica L.). In this study, a systematic analysis of SOD gene family was performed in foxtail millet and the expression pattern of SOD genes in response to abiotic stressors was analyzed at the whole-genomic level. Eight SOD genes were identified in foxtail millet, including 4 Cu/ZnSODs, 3 FeSODs, and 1 MnSOD. These SiSODs are unevenly distributed across 5 of the 9 chromosomes. Phylogenetic analysis showed that SOD proteins could be divided into two major categories (Cu/ZnSODs and Fe-MnSODs), containing seven subgroups, from foxtail millet and other plant species. SOD genes have conserved motif and exon/intron composition in the same subgroup among Setaria italica, Setaria viridis, and Oryza sativa. Additionally, many cis-elements that respond to different stressors were distributed at different densities in the promoters of 8 SiSODs. The expression patterns of SiSODs in different tissues and different abiotic stressors indicated that the SiSODs may play important roles in reactive oxygen species scavenging, caused by various stressors in foxtail millet. This study provides a foundation for the further cloning and functional verification of the SOD gene family response to environmental stimuli in foxtail millet. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13205-018-1502-x) contains supplementary material, which is available to authorized users.
- Published
- 2018
26. Genetic analysis of the fiber quality and yield traits in G. hirsutum background using chromosome segments substitution lines (CSSLs) from Gossypium barbadense
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Gong Wankui, Youlu Yuan, Liu Aiying, Lixue Guo, Yunna Tan, Junwen Li, Jie Sun, Haihong Shang, Shi Yuzhen, Juwu Gong, Chen Tingting, Ge Qun, and Quanwei Lu
- Subjects
0106 biological sciences ,0301 basic medicine ,Genetics ,Germplasm ,food and beverages ,Selfing ,Introgression ,Plant Science ,Gossypium barbadense ,Horticulture ,Biology ,Quantitative trait locus ,01 natural sciences ,Genetic analysis ,03 medical and health sciences ,030104 developmental biology ,Backcrossing ,Allele ,Agronomy and Crop Science ,010606 plant biology & botany - Abstract
Developing chromosome segments substitution lines (CSSLs) is an effective method for broadening the cotton germplasm resource, and improving the fiber quality and yield traits. In this study, the 1054 F2 individual plants and 116 F2:3 lineages were generated from the two parents of MBI9749 and MBI9915 selected from BC5F3:5 lines which originated from hybridization of CCRI36 and Hai1, and advanced backcrossing and repeated selfing. Genotypes of the parents and F2 population were analyzed. The results showed that 19 segments were introgressed for MBI9749 and 12 segments were introgressed for MBI9915, distributing on 17 linkage groups. The average background recovery rate to the recurrent parent CCRI36 was 96.70% for the two parents. An average of 16.46 segments was introgressed in F2 population. The average recovery rate of 1054 individual plants was 96.85%, and the mean length of sea island introgression segments was 157.18 cM, accounting for 3.15% of detection length. QTL mapping analysis detected 22 QTLs associated with fiber quality and yield traits in the F2 and F2:3 populations. These QTLs distributed on seven chromosomes, and the phenotypic variation was explained ranging from 1.20 to 14.61%. Four stable QTLs were detected in F2 and F2:3 populations, simultaneously. We found that eight QTLs were in agreement with the previous research. Six QTL-clusters were identified for fiber quality and yield traits, in which five QTL-clusters were on chromosome20. The results indicated that most of QTL-clusters always improve the fiber quality and have negative additive effect for yield related traits. This study demonstrated that CSSLs provide basis for fine mapping of the fiber quality and yield traits in future, and could be efficiently used for pyramiding favourable alleles to develop the new germplasms for breeding by molecular marker-assisted selection.
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- 2018
27. Genetic and Phenotypic Effects of Chromosome Segments Introgressed From Gossypium barbadense into Gossypium hirsutum v1
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Weiwu Song, Mi Wang, Wei Su, Quanwei Lu, Xianghui Xiao, Juan Cai, Zhen Zhang, Shaoqi Li, Juwu Gong, Wankui Gong, Haihong Shang, Aiying Liu, Junwen Li, Tingting Chen, Qun Ge, Yuzhen Shi, Youlu Yuan, and Pengtao Li
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- 2017
28. Genome-wide identification, phylogeny, and expression analysis of pectin methylesterases reveal their major role in cotton fiber development
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Changsong Zou, Gong Wankui, Pengtao Li, Palanga Kibalou Koffi, Weijie Li, Fan Senmiao, Xiaoying Deng, Juwu Gong, Zhen Zhang, Weiwu Song, Muhammad Jamshed, Juan Cai, Chen Tingting, Shi Yuzhen, Junwen Li, Ge Qun, Daojie Wang, Liu Aiying, Haihong Shang, Quanwei Lu, Youlu Yuan, and Yunna Tan
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0106 biological sciences ,0301 basic medicine ,Protein domain ,Cotton ,Expression patterns ,Biology ,Gossypium ,01 natural sciences ,Genome ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Botany ,Gene duplication ,Genetics ,Cluster Analysis ,Gene family ,Cotton Fiber ,Pectin methylesterases (PMEs) ,Gene ,Phylogeny ,Gene Expression Profiling ,Reproducibility of Results ,biology.organism_classification ,Pectinesterase ,Enzyme Activation ,Gene structure ,Gene expression profiling ,030104 developmental biology ,Multigene Family ,Transcriptome ,Carboxylic Ester Hydrolases ,Genome, Plant ,Genome-Wide Association Study ,Research Article ,010606 plant biology & botany ,Biotechnology - Abstract
Background Pectin methylesterase (PME, EC 3.1.1.11) is a hydrolytic enzyme that utilizes pectin as substrates, and plays a significant role in regulating pectin reconstruction thereby regulating plant growth. Pectin is one of the important components of the plant cell wall, which forms the main structural material of cotton fiber. In this research, cotton genome information was used to identify PMEs. Results We identified 80 (GaPME01-GaPME80) PME genes from diploid G. arboreum (A genome), 78 (GrPME01-GrPME78) PME genes from G. raimondii (D genome), and 135 (GhPME001-GhPME135) PME genes from tetraploid cotton G. hirsutum (AD genome). We further analyzed their gene structure, conserved domain, gene expression, and systematic evolution to lay the foundation for deeper research on the function of PMEs. Phylogenetic data indicated that members from the same species demonstrated relatively high sequence identities and genetic similarities. Analysis of gene structures showed that most of the PMEs genes had 2–3 exons, with a few having a variable number of exons from 4 to 6. There are nearly no differences in the gene structure of PMEs among the three (two diploid and one tetraploid) cotton species. Selective pressure analysis showed that the Ka/Ks value for each of the three cotton species PME families was less than one. Conclusion Conserved domain analysis showed that PMEs members had a relatively conserved C-terminal pectinesterase domain (PME) while the N-terminus was less conserved. Moreover, some of the family members contained a pectin methylesterase inhibitor (PMEI) domain. The Ka/Ks ratios suggested that the duplicated PMEs underwent purifying selection after the duplication events. This study provided an important basis for further research on the functions of cotton PMEs. Results from qRT-PCR indicated that the expression level of different PMEs at various fiber developmental stages was different. Moreover, some of the PMEs showed fiber predominant expression in secondary wall thickening indicating tissue-specific expression patterns. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3365-z) contains supplementary material, which is available to authorized users.
- Published
- 2016
29. Transcriptome analysis revealed the possible contribution of chromosome introgression fragments from Sea Island cotton (Gossypium barbadense) to fiber strength in Upland cotton (Gossypium hirsutum)
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Juwu Gong, Jian Huang, Gong Wankui, Ying-Jin Yuan, Shi Yuzhen, Liu Aiying, Zhuohua Zhang, W Su, Quanwei Lu, Peng Li, S Li, Xiangming Xiao, Chen Tingting, Jiyao Li, Ge Qun, and H Shang
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Transcriptome ,Cell wall organization ,Backcrossing ,Botany ,Cell cycle process ,Polysaccharide metabolic process ,Introgression ,Gossypium barbadense ,Biology ,Secondary cell wall - Abstract
Cotton fiber strength is a critical property determining fiber qualities, and determined by the secondary cell wall development. Understanding the mechanism of fiber development will provide a way to improvement of fiber strength. In this study, the introgression lines of upland and sea island cotton, and have experience of four generations of backcross with upland parent, and have significant higher fiber strength than their upland parent, and the transcriptome were analyzed and compared between the introgression lines and their upland parent. There were 2201 differentially expressed genes (DEG) identified by comparing two introgression lines with their recurrent parent CCRI45, in different development stages from 15 days post-anthesis (DPA) to 28 DPA. The up-regulated genes regulated the polysaccharide metabolic process, single-organism localization, cell wall organization or biogenesis and so on. The down-regulated genes involved in the microtubule-based process, cellular response to stress, cell cycle process and so on. Further functional analysis revealed three significant functional genes, XLOC_036333 (mannosyl-oligosaccharide-alpha-mannosidase mns1), XLOC_029945 (FLA8) and XLOC_075372 (snakin-1), playing important roles in the regulation of cotton fiber strength. Our results provide important candidates genes and inspirations for the future investigation of the molecular mechanism of fiber quality formation, and improvement of cotton fiber quality in breeding.
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- 2016
30. Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.)
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Harun or Rashid, Jamshed Muhammad, Junwen Li, Yanling Wang, Yunna Tan, Shi Yuzhen, Long Huang, Youlu Yuan, Liu Aiying, Weiwu Song, Pengtao Li, Zhen Zhang, Juan Cai, Gong Wankui, Quanwei Lu, Xiaoying Deng, Juwu Gong, Chen Tingting, Haihong Shang, Koffi Kibalou Palanga, Dan Wang, Weijie Li, and Ge Qun
- Subjects
Genetic Markers ,0106 biological sciences ,0301 basic medicine ,Candidate gene ,DNA, Plant ,Genotype ,Genetic Linkage ,Quantitative Trait Loci ,Single nucleotide polymorphism marker ,Population ,Single-nucleotide polymorphism ,Locus (genetics) ,Plant Science ,Quantitative trait locus ,Biology ,Genes, Plant ,Polymorphism, Single Nucleotide ,01 natural sciences ,Chromosomes, Plant ,03 medical and health sciences ,Species Specificity ,Specific locus amplified fragment sequencing ,Genetic linkage ,Boll weight ,education ,Whole genome sequencing ,Genetics ,Analysis of Variance ,Gossypium ,education.field_of_study ,Chromosome Mapping ,High-Throughput Nucleotide Sequencing ,Phenotype ,030104 developmental biology ,Genetic marker ,Upland cotton (Gossypium hirsutum L.) ,Quantitative trait loci mapping ,Genome, Plant ,Research Article ,010606 plant biology & botany - Abstract
Background Upland Cotton (Gossypium hirsutum) is one of the most important worldwide crops it provides natural high-quality fiber for the industrial production and everyday use. Next-generation sequencing is a powerful method to identify single nucleotide polymorphism markers on a large scale for the construction of a high-density genetic map for quantitative trait loci mapping. Results In this research, a recombinant inbred lines population developed from two upland cotton cultivars 0–153 and sGK9708 was used to construct a high-density genetic map through the specific locus amplified fragment sequencing method. The high-density genetic map harbored 5521 single nucleotide polymorphism markers which covered a total distance of 3259.37 cM with an average marker interval of 0.78 cM without gaps larger than 10 cM. In total 18 quantitative trait loci of boll weight were identified as stable quantitative trait loci and were detected in at least three out of 11 environments and explained 4.15–16.70 % of the observed phenotypic variation. In total, 344 candidate genes were identified within the confidence intervals of these stable quantitative trait loci based on the cotton genome sequence. These genes were categorized based on their function through gene ontology analysis, Kyoto Encyclopedia of Genes and Genomes analysis and eukaryotic orthologous groups analysis. Conclusions This research reported the first high-density genetic map for Upland Cotton (Gossypium hirsutum) with a recombinant inbred line population using single nucleotide polymorphism markers developed by specific locus amplified fragment sequencing. We also identified quantitative trait loci of boll weight across 11 environments and identified candidate genes within the quantitative trait loci confidence intervals. The results of this research would provide useful information for the next-step work including fine mapping, gene functional analysis, pyramiding breeding of functional genes as well as marker-assisted selection. Electronic supplementary material The online version of this article (doi:10.1186/s12870-016-0741-4) contains supplementary material, which is available to authorized users.
- Published
- 2016
31. Additional file 9: Table S5. of Genome-wide identification, phylogeny, and expression analysis of pectin methylesterases reveal their major role in cotton fiber development
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Weijie Li, Haihong Shang, Ge, Qun, Changsong Zou, Cai, Juan, Daojie Wang, Senmiao Fan, Zhang, Zhen, Xiaoying Deng, Yunna Tan, Weiwu Song, Pengtao Li, Palanga Koffi, Jamshed, Muhammad, Quanwei Lu, Wankui Gong, Junwen Li, Yuzhen Shi, Tingting Chen, Juwu Gong, Aiying Liu, and Youlu Yuan
- Abstract
Primer pairs used in quantitative real-time PCR analysis. (DOCX 12 kb)
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- 2016
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32. Additional file 7: of Identification of stable quantitative trait loci (QTLs) for fiber quality traits across multiple environments in Gossypium hirsutum recombinant inbred line population
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Jamshed, Muhammad, Jia, Fei, Juwu Gong, Koffi Palanga, Yuzhen Shi, Junwen Li, Haihong Shang, Aiying Liu, Tingting Chen, Zhang, Zhen, Cai, Juan, Ge, Qun, Liu, Zhi, Quanwei Lu, Xiaoying Deng, Yunna Tan, Rashid, Harun Or, Zareen Sarfraz, Hassan, Murtaza, Wankui Gong, and Youlu Yuan
- Abstract
Meta-analysis results of the remaining chromosomes. (DOCX 672 kb)
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- 2016
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33. Additional file 9: Table S5. of Genome-wide identification, phylogeny, and expression analysis of pectin methylesterases reveal their major role in cotton fiber development
- Author
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Weijie Li, Haihong Shang, Ge, Qun, Changsong Zou, Cai, Juan, Daojie Wang, Senmiao Fan, Zhang, Zhen, Xiaoying Deng, Yunna Tan, Weiwu Song, Pengtao Li, Palanga Koffi, Jamshed, Muhammad, Quanwei Lu, Wankui Gong, Junwen Li, Yuzhen Shi, Tingting Chen, Juwu Gong, Aiying Liu, and Youlu Yuan
- Abstract
Primer pairs used in quantitative real-time PCR analysis. (DOCX 12 kb)
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- 2016
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34. Identification of stable quantitative trait loci (QTLs) for fiber quality traits across multiple environments in Gossypium hirsutum recombinant inbred line population
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Harun or Rashid, Liu Aiying, Shi Yuzhen, Gong Wankui, Koffi Kibalou Palanga, Youlu Yuan, Zhen Zhang, Junwen Li, Xiaoying Deng, Quanwei Lu, Juwu Gong, Juan Cai, Fei Jia, Zareen Sarfraz, Muhammad Jamshed, Chen Tingting, Ge Qun, Haihong Shang, Murtaza Hassan, Zhi Liu, and Yunna Tan
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0106 biological sciences ,0301 basic medicine ,Genetic Markers ,Breeding program ,DNA, Plant ,Genetic Linkage ,Population ,Quantitative Trait Loci ,Multiple environments ,Meta-QTL analyses ,Quantitative trait locus ,Environment ,Gossypium raimondii ,Gossypium ,01 natural sciences ,03 medical and health sciences ,Inbred strain ,Genetics ,Cotton Fiber ,education ,education.field_of_study ,SSR markers ,biology ,fungi ,Recombinant inbred line ,food and beverages ,Chromosome Mapping ,Sequence Analysis, DNA ,Heritability ,biology.organism_classification ,Stable QTLs ,Plant Breeding ,030104 developmental biology ,Phenotype ,Upland cotton ,Chromosomal region ,010606 plant biology & botany ,Biotechnology ,Microsatellite Repeats ,Research Article - Abstract
Background The identification of quantitative trait loci (QTLs) that are stable and consistent across multiple environments and populations plays an essential role in marker-assisted selection (MAS). In the present study, we used 28,861 simple sequence repeat (SSR) markers, which included 12,560 Gossypium raimondii (D genome) sequence-based SSR markers to identify polymorphism between two upland cotton strains 0–153 and sGK9708. A total of 851 polymorphic primers were finally selected and used to genotype 196 recombinant inbred lines (RIL) derived from a cross between 0 and 153 and sGK9708 and used to construct a linkage map. The RIL population was evaluated for fiber quality traits in six locations in China for five years. Stable QTLs identified in this intraspecific cross could be used in future cotton breeding program and with fewer obstacles. Results The map covered a distance of 4,110 cM, which represents about 93.2 % of the upland cotton genome, and with an average distance of 5.2 cM between adjacent markers. We identified 165 QTLs for fiber quality traits, of which 47 QTLs were determined to be stable across multiple environments. Most of these QTLs aggregated into clusters with two or more traits. A total of 30 QTL clusters were identified which consisted of 103 QTLs. Sixteen clusters in the At sub-genome comprised 44 QTLs, whereas 14 clusters in the Dt sub-genome that included 59 QTLs for fiber quality were identified. Four chromosomes, including chromosome 4 (c4), c7, c14, and c25 were rich in clusters harboring 5, 4, 5, and 6 clusters respectively. A meta-analysis was performed using Biomercator V4.2 to integrate QTLs from 11 environmental datasets on the RIL populations of the above mentioned parents and previous QTL reports. Among the 165 identified QTLs, 90 were identified as common QTLs, whereas the remaining 75 QTLs were determined to be novel QTLs. The broad sense heritability estimates of fiber quality traits were high for fiber length (0.93), fiber strength (0.92), fiber micronaire (0.85), and fiber uniformity (0.80), but low for fiber elongation (0.27). Meta-clusters on c4, c7, c14 and c25 were identified as stable QTL clusters and were considered more valuable in MAS for the improvement of fiber quality of upland cotton. Conclusion Multiple environmental evaluations of an intraspecific RIL population were conducted to identify stable QTLs. Meta-QTL analyses identified a common chromosomal region that plays an important role in fiber development. Therefore, QTLs identified in the present study are an ideal candidate for MAS in cotton breeding programs to improve fiber quality. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2560-2) contains supplementary material, which is available to authorized users.
- Published
- 2015
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