116 results on '"Gengyun Zhang"'
Search Results
2. Gapless Genome Assembly of Puccinia triticina Provides Insights into Chromosome Evolution in Pucciniales
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Chuang Li, Liuhui Qiao, Yanan Lu, Guozhen Xing, Xiaodong Wang, Gengyun Zhang, Huimin Qian, Yilin Shen, Yibo Zhang, Wen Yao, Kun Cheng, Zhenling Ma, Na Liu, Daowen Wang, and Wenming Zheng
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HiFi sequencing ,gapless genome ,rust fungi ,chromosomal rearrangement ,evolutionary radiation ,Microbiology ,QR1-502 - Abstract
ABSTRACT Chromosome evolution drives species evolution, speciation, and adaptive radiation. Accurate genome assembly is crucial to understanding chromosome evolution of species, such as dikaryotic fungi. Rust fungi (Pucciniales) in dikaryons represent the largest group of plant pathogens, but the evolutionary process of adaptive radiation in Pucciniales remains poorly understood. Here, we report a gapless genome for the wheat leaf rust fungus Puccinia triticina determined using PacBio high-fidelity (HiFi) sequencing. This gapless assembly contains two sets of chromosomes, showing that one contig represents one chromosome. Comparisons of homologous chromosomes between the phased haplotypes revealed that highly frequent small-scale sequence divergence shapes haplotypic variation. Genome analyses of Puccinia triticina along with other rusts revealed that recent transposable element bursts and extensive segmental gene duplications synergistically highlight the evolution of chromosome structures. Comparative analysis of chromosomes indicated that frequent chromosomal rearrangements may act as a major contributor to rapid radiation of Pucciniales. This study presents the first gapless, phased assembly for a dikaryotic rust fungus and provides insights into adaptive evolution and species radiation in Pucciniales. IMPORTANCE Rust fungi (Pucciniales) are the largest group of plant pathogens. Adaptive radiation is a predominant feature in Pucciniales evolution. Chromosome evolution plays an important role in adaptive evolution. Accurate chromosome-scale assembly is required to understand the role of chromosome evolution in Pucciniales. We took advantage of HiFi sequencing to construct a gapless, phased genome for Puccinia triticina. Further analyses revealed that the evolution of chromosome structures in rust lineage is shaped by the combination of transposable element bursts and segmental gene duplications. Chromosome comparisons of Puccinia triticina and other rusts suggested that frequent chromosomal arrangements may make remarkable contributions to high species diversity of rust fungi. Our results present the first gapless genome for Pucciniales and shed light on the feature of chromosome evolution in Pucciniales.
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- 2023
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3. Draft genome of the famous ornamental plant Paeonia suffruticosa
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Shuzuo Lv, Shu Cheng, Zhanying Wang, Shiming Li, Xin Jin, Lei Lan, Bing Yang, Kang Yu, Xuemei Ni, Ning Li, Xiaogai Hou, Gang Huang, Jie Wang, Yang Dong, Erqiang Wang, Jiangtao Huang, Gengyun Zhang, and Canjun Zhang
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Comparative genomics ,draft genome ,MADS‐box ,Paeonia suffruticosa ,Tree peony ,Ecology ,QH540-549.5 - Abstract
Abstract Tree peony (Paeonia Sect. Moutan) is a famous ornamental plant, with huge historical, cultural, and economic significance worldwide. In this study, we reported the ~13.79 Gb draft genome of a wide‐grown Paeonia suffruticosa cultivar “Luo shen xiao chun,” representing the largest sequenced genome in dicots to date. Phylogenetic analyses based on genome sequences demonstrated that P. suffruticosa was placed as sister to Vitales, and they together formed a clade that was sister to Rosids, weakly supporting a relationship of ((Saxifragales and Vitales) and Rosids). The identification and expression analysis of MADS‐box genes based on the genome assembly and de novo transcriptome assembly of P. suffruticosa revealed that the function of C class genes was restricted in flower development, which might be responsible for the stamen petalody in tree peony cultivars. Overall, the first sequenced genome in the family Paeoniaceae provides an important resource for the origin, domestication, and evolutionary study as well as cultivar breeding in tree peony.
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- 2020
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4. QTL fine-mapping of soybean (Glycine max L.) leaf type associated traits in two RILs populations
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Liang Wang, Yanbo Cheng, Qibin Ma, Yinghui Mu, Zhifeng Huang, Qiuju Xia, Gengyun Zhang, and Hai Nian
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Soybean ,Leaf type traits ,QTL ,Fine mapping ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background The different leaf type associated traits of soybean (Glycine max L.) including leaf area, leaf length, leaf width, leaf shape and petiole length are considered to be associated with seed yield. In order to identify quantitative trait loci (QTLs) affecting leaf type traits, two advanced recombinant inbred line (RIL, ZH, Zhonghuang 24 × Huaxia 3; GB, Guizao 1 × Brazil 13) populations were introduced to score phenotypic values in plants across nine different environments (years, seasons, locations and soybean growth stages). Two restriction site-associated DNA sequencing (RAD-seq) based high-density genetic linkage maps with an average distance of 1.00 centimorgan (cM) between adjacent bin markers were utilized for QTL fine mapping. Results Correlation analysis showed that most of the traits were correlated with each other and regulated both by hereditary and environmental factors. A total of 190 QTLs were identified for leaf type associated traits in the two populations, of which 14 loci were found to be environmentally stable. Moreover, these detected QTLs were categorized into 34 QTL hotspots, and four important QTL hotspots with phenotypic variance ranging from 3.89–23.13% were highlighted. Furthermore, Glyma04g05840, Glyma19g37820, Glyma14g07140 and Glyma19g39340 were predicted in the intervals of the stable loci and important QTL hotspots for leaf type traits by adopting Gene Ontology (GO) enrichment analysis. Conclusions Our findings of the QTLs and the putative genes will be beneficial to gain new insights into the genetic basis for soybean leaf type traits and may further accelerate the breeding process for reasonable leaf type soybean.
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- 2019
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5. The Chromosome Level Genome and Genome-wide Association Study for the Agronomic Traits of Panax Notoginseng
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Guangyi Fan, Xiaochuan Liu, Shuai Sun, Chengcheng Shi, Xiao Du, Kai Han, Binrui Yang, Yuanyuan Fu, Minghua Liu, Inge Seim, He Zhang, Qiwu Xu, Jiahao Wang, Xiaoshan Su, Libin Shao, Yuanfang Zhu, Yunchang Shao, Yunpeng Zhao, Andrew KC. Wong, Dennis Zhuang, Wenbin Chen, Gengyun Zhang, Huanming Yang, Xun Xu, Stephen Kwok-Wing Tsui, Xin Liu, and Simon Ming-Yue Lee
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Biological Sciences ,Plant Biology ,Genomics ,Transcriptomics ,Science - Abstract
Summary: The Chinese ginseng Panax notoginseng is a domesticated herb with significant medicinal and economic value. Here we report a chromosome-level P. notoginseng genome assembly with a high (∼79%) repetitive sequence content. The juxtaposition with the widely distributed, closely related Korean ginseng (Panax ginseng) genome revealed contraction of plant defense genes (in particular R-genes) in the P. notoginseng genome. We also investigated the reasons for the larger genome size of Panax species, revealing contributions from two Panax-specific whole-genome duplication events and transposable element expansion. Transcriptome data and comparative genome analysis revealed the candidate genes involved in the ginsenoside synthesis pathway. We also performed a genome-wide association study on 240 cultivated P. notoginseng individuals and identified the associated genes with dry root weight (63 genes) and stem thickness (168 genes). The P. notoginseng genome represents a critical step toward harnessing the full potential of an economically important and enigmatic plant.
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- 2020
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6. IterCluster: a barcode clustering algorithm for long fragment read analysis
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Jiancong Weng, Tian Chen, Yinlong Xie, Xun Xu, Gengyun Zhang, Brock A. Peters, and Radoje Drmanac
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Next-generation sequencing ,Long fragment read ,De novo assembly ,Barcode cluster ,kmer ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
Recent advances in long fragment read (LFR, also known as linked-read technologies or read-cloud) technologies, such as single tube long fragment reads (stLFR), 10X Genomics Chromium reads, and TruSeq synthetic long-reads, have enabled efficient haplotyping and genome assembly. However, in the case of stLFR and 10X Genomics Chromium reads, the long fragments of a genome are covered sparsely by reads in each barcode and most barcodes are contained in multiple long fragments from different regions, which results in inefficient assembly when using long-range information. Thus, methods to address these shortcomings are vital for capitalizing on the additional information obtained using these technologies. We therefore designed IterCluster, a novel, alignment-free clustering algorithm that can cluster barcodes from the same target region of a genome, using -mer frequency-based features and a Markov Cluster (MCL) approach to identify enough reads in a target region of a genome to ensure sufficient target genome sequence depth. The IterCluster method was validated using BGI stLFR and 10X Genomics chromium reads datasets. IterCluster had a higher precision and recall rate on BGI stLFR data compared to 10X Genomics Chromium read data. In addition, we demonstrated how IterCluster improves the de novo assembly results when using a divide-and-conquer strategy on a human genome data set (scaffold/contig N50 = 13.2 kbp/7.1 kbp vs. 17.1 kbp/11.9 kbp before and after IterCluster, respectively). IterCluster provides a new way for determining LFR barcode enrichment and a novel approach for de novo assembly using LFR data. IterCluster is OpenSource and available on https://github.com/JianCong-WENG/IterCluster.
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- 2020
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7. Dissection of complicate genetic architecture and breeding perspective of cottonseed traits by genome-wide association study
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Xiongming Du, Shouye Liu, Junling Sun, Gengyun Zhang, Yinhua Jia, Zhaoe Pan, Haitao Xiang, Shoupu He, Qiuju Xia, Songhua Xiao, Weijun Shi, Zhiwu Quan, Jianguang Liu, Jun Ma, Baoyin Pang, Liru Wang, Gaofei Sun, Wenfang Gong, Johnie N. Jenkins, Xiangyang Lou, Jun Zhu, and Haiming Xu
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Complex traits ,Cottonseed traits ,Association mapping ,GWAS ,Gene by environment interaction ,Epistasis ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Cottonseed is one of the most important raw materials for plant protein, oil and alternative biofuel for diesel engines. Understanding the complex genetic basis of cottonseed traits is requisite for achieving efficient genetic improvement of the traits. However, it is not yet clear about their genetic architecture in genomic level. GWAS has been an effective way to explore genetic basis of quantitative traits in human and many crops. This study aims to dissect genetic mechanism seven cottonseed traits by a GWAS for genetic improvement. Results A genome-wide association study (GWAS) based on a full gene model with gene effects as fixed and gene-environment interaction as random, was conducted for protein, oil and 5 fatty acids using 316 accessions and ~ 390 K SNPs. Totally, 124 significant quantitative trait SNPs (QTSs), consisting of 16, 21, 87 for protein, oil and fatty acids (palmitic, linoleic, oleic, myristic, stearic), respectively, were identified and the broad-sense heritability was estimated from 71.62 to 93.43%; no QTS-environment interaction was detected for the protein, the palmitic and the oleic contents; the protein content was predominantly controlled by epistatic effects accounting for 65.18% of the total variation, but the oil content and the fatty acids except the palmitic were mainly determined by gene main effects and no epistasis was detected for the myristic and the stearic. Prediction of superior pure line and hybrid revealed the potential of the QTSs in the improvement of cottonseed traits, and the hybrid could achieve higher or lower genetic values compared with pure lines. Conclusions This study revealed complex genetic architecture of seven cottonseed traits at whole genome-wide by mixed linear model approach; the identified genetic variants and estimated genetic component effects of gene, gene-gene and gene-environment interaction provide cotton geneticist or breeders new knowledge on the genetic mechanism of the traits and the potential molecular breeding design strategy.
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- 2018
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8. 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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9. Construction of high-density genetic map and QTL mapping of yield-related and two quality traits in soybean RILs population by RAD-sequencing
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Nianxi Liu, Mu Li, Xiangbao Hu, Qibin Ma, Yinghui Mu, Zhiyuan Tan, Qiuju Xia, Gengyun Zhang, and Hai Nian
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QTL ,Yield-related traits ,Quality traits ,RAD-sequencing ,Soybean ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background One of the overarching goals of soybean breeding is to develop lines that combine increased yield with improved quality characteristics. High-density-marker QTL mapping can serve as an effective strategy to identify novel genomic information to facilitate crop improvement. In this study, we genotyped a recombinant inbred line (RIL) population (Zhonghuang 24 × Huaxia 3) using a restriction-site associated DNA sequencing (RAD-seq) approach. A high-density soybean genetic map was constructed and used to identify several QTLs that were shown to influence six yield-related and two quality traits. Results A total of 47,472 single-nucleotide polymorphisms (SNPs) were detected for the RILs that were integrated into 2639 recombination bin units, with an average distance of 1.00 cM between adjacent markers. Forty seven QTLs for yield-related traits and 13 QTLs for grain quality traits were found to be distributed on 16 chromosomes in the 2 year studies. Among them, 18 QTLs were stable, and were identified in both analyses. Twenty six QTLs were identified for the first time, with a single QTL (qNN19a) in a 56 kb region explaining 32.56% of phenotypic variation, and an additional 10 of these were novel, stable QTLs. Moreover, 8 QTL hotpots on four different chromosomes were identified for the correlated traits. Conclusions With RAD-sequencing, some novel QTLs and important QTL clusters for both yield-related and quality traits were identified based on a new, high-density bin linkage map. Three predicted genes were selected as candidates that likely have a direct or indirect influence on both yield and quality in soybean. Our findings will be helpful for understanding common genetic control mechanisms of co-localized traits and to select cultivars for further analysis to predictably modulate soybean yield and quality simultaneously.
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- 2017
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10. Identification of QTLs for 14 Agronomically Important Traits in Setaria italica Based on SNPs Generated from High-Throughput Sequencing
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Kai Zhang, Guangyu Fan, Xinxin Zhang, Fang Zhao, Wei Wei, Guohua Du, Xiaolei Feng, Xiaoming Wang, Feng Wang, Guoliang Song, Hongfeng Zou, Xiaolei Zhang, Shuangdong Li, Xuemei Ni, Gengyun Zhang, and Zhihai Zhao
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foxtail millet ,SNP map ,agronomic traits ,photoperiod ,QTL mapping ,Genetics ,QH426-470 - Abstract
Foxtail millet (Setaria italica) is an important crop possessing C4 photosynthesis capability. The S. italica genome was de novo sequenced in 2012, but the sequence lacked high-density genetic maps with agronomic and yield trait linkages. In the present study, we resequenced a foxtail millet population of 439 recombinant inbred lines (RILs) and developed high-resolution bin map and high-density SNP markers, which could provide an effective approach for gene identification. A total of 59 QTL for 14 agronomic traits in plants grown under long- and short-day photoperiods were identified. The phenotypic variation explained ranged from 4.9 to 43.94%. In addition, we suggested that there may be segregation distortion on chromosome 6 that is significantly distorted toward Zhang gu. The newly identified QTL will provide a platform for sequence-based research on the S. italica genome, and for molecular marker-assisted breeding.
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- 2017
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11. Rapid Characterization of the Genetic Loci Controlling Commodity Traits of Chinese Hami Melon (Cucumis melo var. Saccharinensis Naud.) through Multiplexed Shotgun Genotyping
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Shiming Li, Xuemei Ni, Qiuju Xia, Yunfei Li, Xiao Dong, Junliang Hou, Zehua Li, Shu Cheng, Dong Cao, Zhenyu Zhang, Gengyun Zhang, Shancen Zhao, Baolong Liu, and Yong Chen
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genetic architecture ,QTL ,commondity ,trait ,Chinese ,Hami melon ,multiplexed shotgun genotyping ,Agriculture - Abstract
The genetic architecture and the genetic loci controlling commodity traits in this Hami melon have not been characterized. Multiplexed shotgun genotyping (MSG) was used to genotype an F2 population of 370 Chinese Hami melon progeny. A total of 47,609 single nucleotide polymorphism (SNP) markers were obtained after strict filtering. Thebins were used to construct a genetic linkage map with a total length of 1572.954 cM. Quantitative trait locus (QTL) analysis revealed that fruit color was controlled by one major gene about 2 Mb region on chr09, while exocarp color (EC) was controlled by one major gene about 1.9 Mb on chr04, and skin spotting was controlled by two dominant genes, one in the same region of chr04as the EC QTL and the other in the 1031.05 kb region on chr02. Two major QTLs on chr03 and chr05 were related pleiotropically to several quantitative fruit traits, namely, edge sugar content (ES), center sugar content (CS), fruit weight (FW), and fruit length (FL). A further QTL on chr09 also influenced ES, while five other QTLs affected FL. This study was the first to conduct genetic architecture analysis and QTL mapping in Chinese Hami melon with high-density markers and a large target population.
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- 2019
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12. Phylogenomics Provides New Insights into Gains and Losses of Selenoproteins among Archaeplastida
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Hongping Liang, Tong Wei, Yan Xu, Linzhou Li, Sunil Kumar Sahu, Hongli Wang, Haoyuan Li, Xian Fu, Gengyun Zhang, Michael Melkonian, Xin Liu, Sibo Wang, and Huan Liu
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evolution ,horizontal gene transfer ,phylogenomics ,selenoproteins ,selenocysteine ,Sec machinery ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Selenoproteins that contain selenocysteine (Sec) are found in all kingdoms of life. Although they constitute a small proportion of the proteome, selenoproteins play essential roles in many organisms. In photosynthetic eukaryotes, selenoproteins have been found in algae but are missing in land plants (embryophytes). In this study, we explored the evolutionary dynamics of Sec incorporation by conveying a genomic search for the Sec machinery and selenoproteins across Archaeplastida. We identified a complete Sec machinery and variable sizes of selenoproteomes in the main algal lineages. However, the entire Sec machinery was missing in the Bangiophyceae-Florideophyceae clade (BV) of Rhodoplantae (red algae) and only partial machinery was found in three species of Archaeplastida, indicating parallel loss of Sec incorporation in different groups of algae. Further analysis of genome and transcriptome data suggests that all major lineages of streptophyte algae display a complete Sec machinery, although the number of selenoproteins is low in this group, especially in subaerial taxa. We conclude that selenoproteins tend to be lost in Archaeplastida upon adaptation to a subaerial or acidic environment. The high number of redox-active selenoproteins found in some bloom-forming marine microalgae may be related to defense against viral infections. Some of the selenoproteins in these organisms may have been gained by horizontal gene transfer from bacteria.
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- 2019
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13. Zea mays (L.) P1 locus for cob glume color identified as a post-domestication selection target with an effect on temperate maize genomes
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Chuanxiao Xie, Jianfeng Weng, Wenguo Liu, Cheng Zou, Zhuanfang Hao, Wenxue Li, Minshun Li, Xiaosen Guo, Gengyun Zhang, Yunbi Xu, Xinhai Li, and Shihuang Zhang
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Genome-wide association studym ,Artificial selection ,Linkage disequilibrium ,Crop genome evolution ,Agriculture ,Agriculture (General) ,S1-972 - Abstract
Artificial selection during domestication and post-domestication improvement results in loss of genetic diversity near target loci. However, the genetic locus associated with cob glume color and the nature of the genomic pattern surrounding it was elusive and the selection effect in that region was not clear. An association mapping panel consisting of 283 diverse modern temperate maize elite lines was genotyped by a chip containing over 55,000 evenly distributed SNPs. Ten-fold resequencing at the target region on 40 of the panel lines and 47 tropical lines was also undertaken. A genome-wide association study (GWAS) for cob glume color confirmed the P1 locus, which is located on the short arm of chromosome 1, with a − log10P value for surrounding SNPs higher than the Bonferroni threshold (α/n, α
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- 2013
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14. A Comprehensive Genome Survey Provides Novel Insights into Bile Salt Hydrolase (BSH) in Lactobacillaceae
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Lifeng Liang, Yunhai Yi, Yunyun Lv, Junwei Qian, Xuejing Lei, and Gengyun Zhang
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bile salt hydrolase (BSH) ,Lactobacillaceae ,genome survey ,BSH classification ,cholesterol-lowering probiotics ,Organic chemistry ,QD241-441 - Abstract
Bile salt hydrolase (BSH) is a well-known enzyme that has been commonly characterized in probiotic bacteria, as it has cholesterol-lowering effects. However, its molecular investigations are scarce. Here, we build a local database of BSH sequences from Lactobacillaceae (BSH–SDL), and phylogenetic analysis and homology searches were employed to elucidate their comparability and distinctiveness among species. Evolutionary study demonstrates that BSH sequences in BSH–SDL are divided into five groups, named BSH A, B, C, D and E here, which can be the genetic basis for BSH classification and nomenclature. Sequence analysis suggests the differences between BSH-active and BSH-inactive proteins clearly, especially on site 82. In addition, a total of 551 BSHs from 107 species are identified from 451 genomes of 158 Lactobacillaceae species. Interestingly, those bacteria carrying various copies of BSH A or B can be predicted to be potential cholesterol-lowering probiotics, based on the results of phylogenetic analysis and the subtypes that those previously reported BSH-active probiotics possess. In summary, this study elaborates the molecular basis of BSH in Lactobacillaceae systematically, and provides a novel methodology as well as a consistent standard for the identification of the BSH subtype. We believe that high-throughput screening can be efficiently applied to the selection of promising candidate BSH-active probiotics, which will advance the development of healthcare products in cholesterol metabolism.
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- 2018
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15. SOAPMetaS: profiling large metagenome datasets efficiently on distributed clusters.
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Shixu He, Zhibo Huang, Xiaohan Wang, Lin Fang, Shengkang Li, Yong Zhang 0036, and Gengyun Zhang
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- 2021
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16. SNP-Seek database of SNPs derived from 3000 rice genomes.
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Nickolai Alexandrov, Shuaishuai Tai, Wensheng Wang, Locedie Mansueto, Kevin Palis, Roven Rommel Fuentes, Victor Jun M. Ulat, Dmytro Chebotarov, Gengyun Zhang, Zhikang Li, Ramil Mauleon, Ruaraidh Sackville Hamilton, and Kenneth L. McNally
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- 2015
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17. Draft genome of the famous ornamental plant Paeonia suffruticosa
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Gengyun Zhang, Xuemei Ni, Kang Yu, Canjun Zhang, Lei Lan, Huang Jiangtao, Gang Huang, Zhanying Wang, Ning Li, Bing Yang, Erqiang Wang, Shuzuo Lv, Dong Yang, Jie Wang, Xin Jin, Shiming Li, Xiaogai Hou, and Shu Cheng
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0106 biological sciences ,De novo transcriptome assembly ,010603 evolutionary biology ,01 natural sciences ,Genome ,03 medical and health sciences ,lcsh:QH540-549.5 ,Botany ,Clade ,Ecology, Evolution, Behavior and Systematics ,MADS-box ,030304 developmental biology ,Nature and Landscape Conservation ,Saxifragales ,Comparative genomics ,0303 health sciences ,Ecology ,Phylogenetic tree ,biology ,draft genome ,Tree peony ,Paeonia suffruticosa ,food and beverages ,biology.organism_classification ,MADS‐box ,lcsh:Ecology - Abstract
Tree peony (Paeonia Sect. Moutan) is a famous ornamental plant, with huge historical, cultural, and economic significance worldwide. In this study, we reported the ~13.79 Gb draft genome of a wide‐grown Paeonia suffruticosa cultivar “Luo shen xiao chun,” representing the largest sequenced genome in dicots to date. Phylogenetic analyses based on genome sequences demonstrated that P. suffruticosa was placed as sister to Vitales, and they together formed a clade that was sister to Rosids, weakly supporting a relationship of ((Saxifragales and Vitales) and Rosids). The identification and expression analysis of MADS‐box genes based on the genome assembly and de novo transcriptome assembly of P. suffruticosa revealed that the function of C class genes was restricted in flower development, which might be responsible for the stamen petalody in tree peony cultivars. Overall, the first sequenced genome in the family Paeoniaceae provides an important resource for the origin, domestication, and evolutionary study as well as cultivar breeding in tree peony.
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- 2020
18. Selective and comparative genome architecture of Asian cultivated rice (Oryza sativa L.) attributed to domestication and modern breeding
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Xueqiang Wang, Wensheng Wang, Shuaishuai Tai, Min Li, Qiang Gao, Zhiqiang Hu, Wushu Hu, Zhichao Wu, Xiaoyang Zhu, Jianyin Xie, Fengmei Li, Zhifang Zhang, Linran Zhi, Fan Zhang, Xiaoqian Ma, Ming Yang, Jiabao Xu, Yanhong Li, Wenzhuo Zhang, Xiyu Yang, Ying Chen, Yan Zhao, Binying Fu, Xiuqin Zhao, Jinjie Li, Miao Wang, Zhen Yue, Xiaodong Fang, Wei Zeng, Ye Yin, Gengyun Zhang, Jianlong Xu, Hongliang Zhang, Zichao Li, and Zhikang Li
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Multidisciplinary - Abstract
Rice, Oryza sativa L. (Os), is one of the oldest domesticated cereals that has also gone through extensive improvement in modern breeding.How rice was domesticated and impacted by modern breeding.We performed comprehensive analyses of genomic sequences of 504 accessions of Os and 456 accessions of O. rufipogon/O. nivara (Or).The natural selection on Or before domestication and the natural and artificial selection during domestication together shaped the well-differentiated genomes of two subspecies, geng(j) (japonica) and xian(i) (indica), while breeding has made apparent genomic imprints between landrace and modern varieties of each subspecies, and also between primary modern and advanced modern varieties of xian(i). Selection during domestication and breeding left genome-wide selective signals covering ∼ 22.8 % and ∼ 8.6 % of the Os genome, significantly reduced within-population genomic diversity by ∼ 22 % in xian(i) and ∼ 53 % in geng(j) plus more pronounced subspecific differentiation. Only ∼ 10 % reduction in the total genomic diversity was observed between the Os and Or populations, indicating domestication did not suffer severe genetic bottleneck.Our results revealed clear differentiation of the Or accessions into three large populations, two of which correspond to the well-differentiated Os subspecies, geng(j) and xian(i). Improved productivity and common changes in the same suit of adaptive traits in xian(i) and geng(j) during domestication and breeding resulted apparently from compensatory and convergent selections for different genes/alleles acting in the common KEGG terms and/or same gene families, and thus maintaining or even increasing the within population diversity and subspecific differentiation of Os, while more genes/alleles of novel function were selected during domestication than modern breeding. Our results supported the multiple independent domestication of Os in Asia and suggest the more efficient utilization of the rich diversity within Os by exploiting inter-subspecific and among population diversity in future rice improvement.
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- 2022
19. SOAPMetaS: profiling large metagenome datasets efficiently on distributed clusters
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Xiaohan Wang, Lin Fang, Gengyun Zhang, Huang Zhibo, Li Shengkang, Shixu He, and Yong Zhang
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Big Data ,Statistics and Probability ,FASTQ format ,Computer science ,Big data ,computer.software_genre ,Biochemistry ,Marker gene ,03 medical and health sciences ,0302 clinical medicine ,Spark (mathematics) ,Profiling (information science) ,Molecular Biology ,030304 developmental biology ,0303 health sciences ,business.industry ,Computer Science Applications ,Computational Mathematics ,Computational Theory and Mathematics ,Metagenomics ,Metagenome ,Data mining ,business ,computer ,Algorithms ,Software ,030217 neurology & neurosurgery - Abstract
Summary Rapid increase of the data size in metagenome researches has raised the demand for new tools to process large datasets efficiently. To accelerate the metagenome profiling process in the scenario of big data, we developed SOAPMetaS, a marker gene-based multiple-sample metagenome profiling tool built on Apache Spark. SOAPMetaS demonstrates high performance and scalability to process large datasets. It can process 80 samples of FASTQ data, summing up to 416 GiB, in around half an hour; and the accuracy of species profiling results of SOAPMetaS is similar to that of MetaPhlAn2. SOAPMetaS can deal with a large volume of metagenome data more efficiently than common-used single-machine tools. Availability and implementation Source code is implemented in Java and freely available at https://github.com/BGI-flexlab/SOAPMetaS. Supplementary information Supplementary data are available at Bioinformatics online.
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- 2020
20. Molecular evidence for origin, diversification and ancient gene duplication of plant subtilases (SBTs)
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Morten Petersen, Huan Liu, Sibo Wang, Gengyun Zhang, Yan Xu, Sunil Kumar Sahu, Linzhou Li, Xin Liu, and Michael Melkonian
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0301 basic medicine ,Gene Transfer, Horizontal ,lcsh:Medicine ,Biology ,Genes, Plant ,Article ,Evolutionary genetics ,Subtilase ,Evolution, Molecular ,Plant evolution ,03 medical and health sciences ,0302 clinical medicine ,Phylogenetics ,Gene Duplication ,Gene duplication ,lcsh:Science ,Phylogeny ,Multidisciplinary ,Phylogenetic tree ,Phylum ,lcsh:R ,Zygnematophyceae ,Plants ,biology.organism_classification ,030104 developmental biology ,Sister group ,Evolutionary biology ,Horizontal gene transfer ,lcsh:Q ,030217 neurology & neurosurgery - Abstract
Plant subtilases (SBTs) are a widely distributed family of serine proteases which participates in plant developmental processes and immune responses. Although SBTs are divided into seven subgroups in plants, their origin and evolution, particularly in green algae remain elusive. Here, we present a comprehensive large-scale evolutionary analysis of all subtilases. The plant subtilases SBT1-5 were found to be monophyletic, nested within a larger radiation of bacteria suggesting that they originated from bacteria by a single horizontal gene transfer (HGT) event. A group of bacterial subtilases comprising representatives from four phyla was identified as a sister group to SBT1-5. The phylogenetic analyses, based on evaluation of novel streptophyte algal genomes, suggested that the recipient of the HGT of bacterial subtilases was the common ancestor of Coleochaetophyceae, Zygnematophyceae and embryophytes. Following the HGT, the subtilase gene duplicated in the common ancestor and the two genes diversified into SBT2 and SBT1, 3–5 respectively. Comparative structural analysis of homology-modeled SBT2 proteins also showed their conservation from bacteria to embryophytes. Our study provides the first molecular evidence about the evolution of plant subtilases via HGT followed by a first gene duplication in the common ancestor of Coleochaetophyceae, Zygnematophyceae, and embryophytes, and subsequent expansion in embryophytes.
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- 2019
21. QTL fine-mapping of soybean (Glycine max L.) leaf type associated traits in two RILs populations
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Qibin Ma, Yinghui Mu, Gengyun Zhang, Yanbo Cheng, Zhifeng Huang, Hai Nian, Liang Wang, and Qiuju Xia
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0106 biological sciences ,Fine mapping ,Genotype ,lcsh:QH426-470 ,QTL ,lcsh:Biotechnology ,Quantitative Trait Loci ,Leaf type traits ,Quantitative trait locus ,Biology ,Polymorphism, Single Nucleotide ,01 natural sciences ,Chromosomes, Plant ,Petiole (botany) ,DNA sequencing ,03 medical and health sciences ,Centimorgan ,Genetic linkage ,lcsh:TP248.13-248.65 ,Genetics ,Gene ,030304 developmental biology ,0303 health sciences ,fungi ,Chromosome Mapping ,food and beverages ,Sequence Analysis, DNA ,Phenotype ,Plant Leaves ,Horticulture ,lcsh:Genetics ,Glycine ,Soybeans ,Soybean ,Research Article ,010606 plant biology & botany ,Biotechnology - Abstract
Background The different leaf type associated traits of soybean (Glycine max L.) including leaf area, leaf length, leaf width, leaf shape and petiole length are considered to be associated with seed yield. In order to identify quantitative trait loci (QTLs) affecting leaf type traits, two advanced recombinant inbred line (RIL, ZH, Zhonghuang 24 × Huaxia 3; GB, Guizao 1 × Brazil 13) populations were introduced to score phenotypic values in plants across nine different environments (years, seasons, locations and soybean growth stages). Two restriction site-associated DNA sequencing (RAD-seq) based high-density genetic linkage maps with an average distance of 1.00 centimorgan (cM) between adjacent bin markers were utilized for QTL fine mapping. Results Correlation analysis showed that most of the traits were correlated with each other and regulated both by hereditary and environmental factors. A total of 190 QTLs were identified for leaf type associated traits in the two populations, of which 14 loci were found to be environmentally stable. Moreover, these detected QTLs were categorized into 34 QTL hotspots, and four important QTL hotspots with phenotypic variance ranging from 3.89–23.13% were highlighted. Furthermore, Glyma04g05840, Glyma19g37820, Glyma14g07140 and Glyma19g39340 were predicted in the intervals of the stable loci and important QTL hotspots for leaf type traits by adopting Gene Ontology (GO) enrichment analysis. Conclusions Our findings of the QTLs and the putative genes will be beneficial to gain new insights into the genetic basis for soybean leaf type traits and may further accelerate the breeding process for reasonable leaf type soybean. Electronic supplementary material The online version of this article (10.1186/s12864-019-5610-8) contains supplementary material, which is available to authorized users.
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- 2019
22. IterCluster: a barcode clustering algorithm for long fragment read analysis
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Gengyun Zhang, Brock A. Peters, Xun Xu, Jiancong Weng, Yinlong Xie, Radoje Drmanac, and Tian Chen
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Barcode cluster ,Computer science ,Bioinformatics ,Sequence assembly ,lcsh:Medicine ,Genomics ,Computational biology ,Barcode ,Genome ,General Biochemistry, Genetics and Molecular Biology ,law.invention ,03 medical and health sciences ,0302 clinical medicine ,law ,De novo assembly ,Cluster analysis ,kmer ,Long fragment read ,030304 developmental biology ,Whole genome sequencing ,0303 health sciences ,Contig ,General Neuroscience ,lcsh:R ,Computational Biology ,General Medicine ,Next-generation sequencing ,Human genome ,General Agricultural and Biological Sciences ,030217 neurology & neurosurgery - Abstract
Recent advances in long fragment read (LFR, also known as linked-read technologies or read-cloud) technologies, such as single tube long fragment reads (stLFR), 10X Genomics Chromium reads, and TruSeq synthetic long-reads, have enabled efficient haplotyping and genome assembly. However, in the case of stLFR and 10X Genomics Chromium reads, the long fragments of a genome are covered sparsely by reads in each barcode and most barcodes are contained in multiple long fragments from different regions, which results in inefficient assembly when using long-range information. Thus, methods to address these shortcomings are vital for capitalizing on the additional information obtained using these technologies. We therefore designed IterCluster, a novel, alignment-free clustering algorithm that can cluster barcodes from the same target region of a genome, using -mer frequency-based features and a Markov Cluster (MCL) approach to identify enough reads in a target region of a genome to ensure sufficient target genome sequence depth. The IterCluster method was validated using BGI stLFR and 10X Genomics chromium reads datasets. IterCluster had a higher precision and recall rate on BGI stLFR data compared to 10X Genomics Chromium read data. In addition, we demonstrated how IterCluster improves the de novo assembly results when using a divide-and-conquer strategy on a human genome data set (scaffold/contig N50 = 13.2 kbp/7.1 kbp vs. 17.1 kbp/11.9 kbp before and after IterCluster, respectively). IterCluster provides a new way for determining LFR barcode enrichment and a novel approach for de novo assembly using LFR data. IterCluster is OpenSource and available on https://github.com/JianCong-WENG/IterCluster.
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- 2020
23. Genotyping by sequencing of 270 Indica rice varieties revealed genetic markers probably related to heavy metal accumulation
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Yuhu Liang, Qi Wang, Xuemei Ni, Junliang Hou, Xiao Dong, Gengyun Zhang, Sunil Kumar Sahu, Manzhong Liang, and Liangbi Chen
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0301 basic medicine ,Genotyping by sequencing ,Genetics ,Single-nucleotide polymorphism ,Heavy metals ,Plant Science ,Biology ,03 medical and health sciences ,030104 developmental biology ,Genetic marker ,Identification (biology) ,Plant breeding ,Agronomy and Crop Science - Published
- 2018
24. Taxonomic structure and functional association of foxtail millet root microbiome
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Yuzhen Li, Yunzeng Zhang, Yayu Wang, Suisha Liang, Guohua Du, Yang Bai, Jian Wang, Zhang Haifeng, Jingwang Wan, Yueying Huang, Jin Xu, Guang Liu, Pengfan Zhang, Tao Jin, Xun Xu, Guangyi Fan, Huijue Jia, Xin Liu, Liang Xiao, Dechun Lin, Honggang Jiang, Karsten Kristiansen, Jing Xu, Houbao Zhang, Hongfeng Zou, Zhuye Jie, Jinying Li, Nian Wang, Huanming Yang, Haiyan Chu, and Gengyun Zhang
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0106 biological sciences ,0301 basic medicine ,Setaria ,productivity ,Setaria italica ,Biofertilizer ,microbiome ,Health Informatics ,Biology ,Plant disease resistance ,01 natural sciences ,03 medical and health sciences ,RNA, Ribosomal, 16S ,Botany ,DNA Barcoding, Taxonomic ,Microbiome ,16S rRNA ,Millets ,Rhizosphere ,Bacteria ,Research ,Microbiota ,Root microbiome ,food and beverages ,root ,biology.organism_classification ,Computer Science Applications ,030104 developmental biology ,Agronomy ,Metagenomics ,Foxtail ,Erratum ,Genome, Bacterial ,Rhizome ,010606 plant biology & botany - Abstract
The root microbes play pivotal roles in plant productivity, nutrient uptakes, and disease resistance. The root microbial community structure has been extensively investigated by 16S/18S/ITS amplicons and metagenomic sequencing in crops and model plants. However, the functional associations between root microbes and host plant growth are poorly understood. This work investigates the root bacterial community of foxtail millet (Setaria italica) and its potential effects on host plant productivity. We determined the bacterial composition of 2882 samples from foxtail millet rhizoplane, rhizosphere and corresponding bulk soils from 2 well-separated geographic locations by 16S rRNA gene amplicon sequencing. We identified 16 109 operational taxonomic units (OTUs), and defined 187 OTUs as shared rhizoplane core OTUs. The β-diversity analysis revealed that microhabitat was the major factor shaping foxtail millet root bacterial community, followed by geographic locations. Large-scale association analysis identified the potential beneficial bacteria correlated with plant high productivity. Besides, the functional prediction revealed specific pathways enriched in foxtail millet rhizoplane bacterial community. We systematically described the root bacterial community structure of foxtail millet and found its core rhizoplane bacterial members. Our results demonstrated that host plants enrich specific bacteria and functions in the rhizoplane. The potentially beneficial bacteria may serve as a valuable knowledge foundation for bio-fertilizer development in agriculture.
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- 2017
25. Identification of QTLs for 14 Agronomically Important Traits in Setaria italica Based on SNPs Generated from High-Throughput Sequencing
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Li Shuangdong, Wei Wei, Wang Xiaoming, Fan Guangyu, Zhaihai Zhao, Feng Xiaolei, Guohua Du, Xuemei Ni, Zhang Xiaolei, Zhao Fang, Xinxin Zhang, Wang Feng, Zou Hongfeng, Song Guoliang, Gengyun Zhang, and Kai Zhang
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0301 basic medicine ,QTL mapping ,Setaria ,Population ,agronomic traits ,Genomics ,Quantitative trait locus ,QH426-470 ,photoperiod ,Genome ,DNA sequencing ,03 medical and health sciences ,Botany ,Genetics ,education ,Molecular Biology ,Gene ,Genetics (clinical) ,SNP map ,education.field_of_study ,biology ,food and beverages ,biology.organism_classification ,030104 developmental biology ,Genetic marker ,foxtail millet - Abstract
Foxtail millet (Setaria italica) is an important crop possessing C4 photosynthesis capability. The S. italica genome was de novo sequenced in 2012, but the sequence lacked high-density genetic maps with agronomic and yield trait linkages. In the present study, we resequenced a foxtail millet population of 439 recombinant inbred lines (RILs) and developed high-resolution bin map and high-density SNP markers, which could provide an effective approach for gene identification. A total of 59 QTL for 14 agronomic traits in plants grown under long- and short-day photoperiods were identified. The phenotypic variation explained ranged from 4.9 to 43.94%. In addition, we suggested that there may be segregation distortion on chromosome 6 that is significantly distorted toward Zhang gu. The newly identified QTL will provide a platform for sequence-based research on the S. italica genome, and for molecular marker-assisted breeding.
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- 2017
26. Probiotic strains improve high-fat diet-induced hypercholesterolemia through modulating gut microbiota in ways different from atorvastatin
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Lifeng Liang, Xiao Chen, Songling Liu, Dun Su, Xiaofen He, Can Peng, Shancen Zhao, and Gengyun Zhang
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Male ,0301 basic medicine ,Atorvastatin ,Hypercholesterolemia ,Inflammation ,Gut flora ,Pharmacology ,Diet, High-Fat ,Weight Gain ,medicine.disease_cause ,law.invention ,Feces ,03 medical and health sciences ,Probiotic ,law ,Cricetinae ,Prevotella ,Animals ,Medicine ,Pediococcus ,Pediococcus acidilactici ,Pediococcus pentosaceus ,030109 nutrition & dietetics ,Bacteria ,Mesocricetus ,biology ,business.industry ,Anticholesteremic Agents ,Probiotics ,nutritional and metabolic diseases ,General Medicine ,biology.organism_classification ,medicine.disease ,Gastrointestinal Microbiome ,Hypocholesterolemia ,Glucose ,030104 developmental biology ,Cytokines ,Dysbiosis ,lipids (amino acids, peptides, and proteins) ,medicine.symptom ,business ,Oxidative stress ,Lactobacillus plantarum ,Food Science ,medicine.drug - Abstract
Hypercholesterolemia is a major risk factor for cardiovascular disease (CVD). Probiotics are one of the most popular dietary supplements for hypercholesterolemia, but there are questions as to whether there are differences between probiotics and cholesterol-lowering drugs like atorvastatin (ATO) both in effectiveness and in the underlying mechanisms. In this study, the hypocholesterolemia effects of 4 probiotic strains were investigated and compared with ATO, focusing on their impacts on the gut microbiota. A hypercholesterolemia model was established via high-fat diet (HFD) in golden hamsters after which ATO and the 4 probiotics were orally administered individually for 8 weeks. All probiotics were effective, but less than ATO, on body weight, serum parameters (TG, TC, LDL, INS, HbA1c) and expression of inflammatory factors (INF-α, IL-1β, CRP), with strain JQII-5 being most significant. Besides, these effects were associated with restoration of microbiota dysbiosis induced by HFD. It was worth noting that ATO and probiotics induced different shifts of the gut microbiota in both structure and key phylotypes. Most interestingly, Allobaculum, a HFD-suppressed genus, reported to be involved in alleviating oxidative stress, was enriched by all tested probiotic strains, but not by ATO. Furthermore, Prevotella, also a HFD-suppressed genus, was uniquely reversed by JQII-5. Importantly, most of the alerted genera and reversed genera were found to be correlated with the inflammatory state and serum lipid level. Compared with ATO, the probiotic strains were less effective on body weight, hypercholesterolemia, and inflammation. However, probiotics exert additional favorable effects on the gut microbiota, making them excellent potential complements to cholesterol-lowering drugs like ATO.
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- 2019
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27. Construction of a high-density genetic map of tree peony (Paeonia suffruticosa Andr. Moutan) using restriction site associated DNA sequencing (RADseq) approach
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Huang Jiangtao, Shu Cheng, Gang Huang, Shuzuo Lv, Zhanying Wang, Erqiang Wang, Jie Wang, Yunfei Li, Kang Yu, Shiming Li, Xuemei Ni, Xin Jin, and Gengyun Zhang
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0106 biological sciences ,0301 basic medicine ,Molecular breeding ,education.field_of_study ,biology ,Population ,Paeonia suffruticosa ,Forestry ,Horticulture ,biology.organism_classification ,01 natural sciences ,DNA sequencing ,03 medical and health sciences ,Restriction site ,Tree (data structure) ,030104 developmental biology ,Evolutionary biology ,Genetic linkage ,Genetics ,education ,Molecular Biology ,Selection (genetic algorithm) ,010606 plant biology & botany - Abstract
High-density genetic maps play a vital role in dissecting genetic components of biologically or agronomically important traits and molecular marker-assisted selection breeding, especially for a species with limited genomic information. Tree Peony (Paeonia suffruticosa Andr. Moutan DC.) is a traditional flowering plant in China, with important ornamental value, which have been spread around the world. However, less genetic and genomic information is available for the tree peony molecular studies. Here, we performed restriction site-associated DNA sequencing (RADseq) of an F1 population, derived from a traditional variety “Qing Long Wo Mo Chi (QL)” and a variety “Mo Zi Lian (MZL)”. High-density genetic maps were developed using RADseq markers for female (1471 markers) and male (793 markers) parents. They covered 965.69 and 870.21 cM, with the average marker intervals of 0.66 and 1.10 cM along the seven and five linkage groups (LGs), respectively. Furthermore, the identified markers were assigned to 1671 bins, representing the unique genetic positions in LGs, and inter-marker distances smaller than 5 cM covered 97.93% of genetic maps. This study suggests that rapid de novo construction of genetic maps in peony could be conducted through RADseq approach, which provides an important tool for further linkage mapping and genomic structure analysis, and enable development of molecular markers for molecular breeding in tree peony.
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- 2019
28. Phylogenomics provides new insights into gains and losses of selenoproteins among Archaeplastida
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Xian Fu, Sunil Kumar Sahu, Michael Melkonian, Huan Liu, Hongping Liang, Sibo Wang, Hongli Wang, Linzhou Li, Gengyun Zhang, Haoyuan Li, Xin Liu, Tong Wei, and Yan Xu
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0301 basic medicine ,Gene Transfer, Horizontal ,selenocysteine ,Red algae ,Genome ,Article ,Catalysis ,Evolution, Molecular ,Inorganic Chemistry ,lcsh:Chemistry ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Algae ,Chlorophyta ,Phylogenetics ,Phylogenomics ,evolution ,Sec machinery ,Physical and Theoretical Chemistry ,Molecular Biology ,lcsh:QH301-705.5 ,Phylogeny ,Spectroscopy ,Plant Proteins ,integumentary system ,biology ,Selenocysteine ,Archaeplastida ,Streptophyta ,Organic Chemistry ,phylogenomics ,Genomics ,General Medicine ,biology.organism_classification ,Computer Science Applications ,030104 developmental biology ,lcsh:Biology (General) ,lcsh:QD1-999 ,chemistry ,Evolutionary biology ,Rhodophyta ,Horizontal gene transfer ,selenoproteins ,horizontal gene transfer ,Adaptation ,Transcriptome ,030217 neurology & neurosurgery - Abstract
Selenoproteins that contain selenocysteine (Sec) are found in all kingdoms of life. Although they constitute a small proportion of the proteome, selenoproteins play essential roles in many organisms. In photosynthetic eukaryotes, selenoproteins have been found in algae but are missing in land plants (embryophytes). In this study, we explored the evolutionary dynamics of Sec incorporation by conveying a genomic search for the Sec machinery and selenoproteins across Archaeplastida. We identified a complete Sec machinery and variable sizes of selenoproteomes in the main algal lineages. However, the entire Sec machinery was missing in the BV clade (Bangiophyceae-Florideophyceae) of Rhodoplantae (red algae) and only partial machinery was found in three species of Archaeplastida, indicating parallel loss of Sec incorporation in different groups of algae. Further analysis of genome and transcriptome data suggests that all major lineages of streptophyte algae display a complete Sec machinery, although the number of selenoproteins is low in this group, especially in subaerial taxa. We conclude that selenoproteins tend to be lost in Archaeplastida upon adaptation to a subaerial or acidic environment. The high number of redox-active selenoproteins found in some bloom-forming marine microalgae may be related to defense against viral infections. Some of the selenoproteins in these organisms may have been gained by horizontal gene transfer from bacteria.
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- 2019
29. Draft genome of the famous ornamental plant
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Shuzuo, Lv, Shu, Cheng, Zhanying, Wang, Shiming, Li, Xin, Jin, Lei, Lan, Bing, Yang, Kang, Yu, Xuemei, Ni, Ning, Li, Xiaogai, Hou, Gang, Huang, Jie, Wang, Yang, Dong, Erqiang, Wang, Jiangtao, Huang, Gengyun, Zhang, and Canjun, Zhang
- Subjects
draft genome ,Tree peony ,Comparative genomics ,MADS‐box ,food and beverages ,Paeonia suffruticosa ,Original Research - Abstract
Tree peony (Paeonia Sect. Moutan) is a famous ornamental plant, with huge historical, cultural, and economic significance worldwide. In this study, we reported the ~13.79 Gb draft genome of a wide‐grown Paeonia suffruticosa cultivar “Luo shen xiao chun,” representing the largest sequenced genome in dicots to date. Phylogenetic analyses based on genome sequences demonstrated that P. suffruticosa was placed as sister to Vitales, and they together formed a clade that was sister to Rosids, weakly supporting a relationship of ((Saxifragales and Vitales) and Rosids). The identification and expression analysis of MADS‐box genes based on the genome assembly and de novo transcriptome assembly of P. suffruticosa revealed that the function of C class genes was restricted in flower development, which might be responsible for the stamen petalody in tree peony cultivars. Overall, the first sequenced genome in the family Paeoniaceae provides an important resource for the origin, domestication, and evolutionary study as well as cultivar breeding in tree peony., Tree peony (Paeonia Sect. Moutan) is a famous ornamental plant, with huge historical, cultural, and economic significance worldwide. The presented genome assembly in this study would serve as an important resource for functional genomic and genetic studies on tree peony, which would be useful for the conservation of endangered wild paeonia species and exploring the mechanisms of plant diversification and adaption under domestication in various environments.
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- 2019
30. RAPD tagging of a salt tolerant gene in rice
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Haiyuan, Ding, Gengyun, Zhang, Yan, Guo, Shaolin, Chen, and Shouyi, Chen
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- 1998
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31. Genetic mapping of powdery mildew resistance genes in soybean by high-throughput genome-wide sequencing
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Ruirui Ma, Qibin Ma, Qiuju Xia, Ze Jiang, Zhandong Cai, Bingzhi Jiang, Gengyun Zhang, Mu Li, Yanbo Cheng, and Hai Nian
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Candidate gene ,Locus (genetics) ,Plant disease resistance ,Genome ,Polymorphism, Single Nucleotide ,Chromosomes, Plant ,Linkage Disequilibrium ,Gene mapping ,Actinomycetales ,Genetics ,Gene ,Disease Resistance ,Plant Diseases ,Plant Proteins ,biology ,food and beverages ,Chromosome Mapping ,General Medicine ,biology.organism_classification ,Phenotype ,Microsphaera diffusa ,Soybeans ,Agronomy and Crop Science ,Powdery mildew ,Genome, Plant ,Biotechnology ,Genome-Wide Association Study ,Microsatellite Repeats - Abstract
The Mendelian locus conferring resistance to powdery mildew in soybean was precisely mapped using a combination of phenotypic screening, genetic analyses, and high-throughput genome-wide sequencing. Powdery mildew (PMD), caused by the fungus Microsphaera diffusa Cooke & Peck, leads to considerable yield losses in soybean [Glycine max (L.) Merr.] under favourable environmental conditions and can be controlled by identifying germplasm resources with resistance genes. In this study, resistance to M. diffusa among resistant varieties B3, Fudou234, and B13 is mapped as a single Mendelian locus using three mapping populations derived from crossing susceptible with resistant cultivars. The position of the PMD resistance locus in B3 is located between simple sequence repeat (SSR) markers GMES6959 and Satt_393 on chromosome 16, at genetic distances of 7.1 cM and 4.6 cM, respectively. To more finely map the PMD resistance gene, a high-density genetic map was constructed using 248 F8 recombinant inbred lines derived from a cross of Guizao1 × B13. The final map includes 3748 bins and is 3031.9 cM in length, with an average distance of 0.81 cM between adjacent markers. This genotypic analysis resulted in the precise delineation of the B13 PMD resistance locus to a 188.06-kb genomic region on chromosome 16 that harbours 28 genes, including 17 disease resistance (R)-like genes in the reference Williams 82 genome. Quantitative real-time PCR assays of possible candidate genes revealed differences in the expression levels of 9 R-like genes between the resistant and susceptible parents. These results provide useful information for marker-assisted breeding and gene cloning for PMD resistance.
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- 2018
32. Dissection of complicate genetic architecture and breeding perspective of cottonseed traits by genome-wide association study
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Johnie N. Jenkins, Gaofei Sun, Wenfang Gong, Jianguang Liu, Shouye Liu, Liru Wang, Qiuju Xia, Junling Sun, Songhua Xiao, Shoupu He, Weijun Shi, Gengyun Zhang, Zhaoe Pan, Haiming Xu, Haitao Xiang, Zhiwu Quan, Baoyin Pang, Xiongming Du, Yinhua Jia, Jun Ma, Jun Zhu, and Xiang-Yang Lou
- Subjects
0301 basic medicine ,lcsh:QH426-470 ,Genotype ,lcsh:Biotechnology ,Molecular breeding by design ,Genome-wide association study ,Biology ,Quantitative trait locus ,Cottonseed traits ,Genes, Plant ,Cottonseed ,03 medical and health sciences ,Quantitative Trait, Heritable ,lcsh:TP248.13-248.65 ,Genetics ,GWAS ,Gene by environment interaction ,Association mapping ,Plant Proteins ,2. Zero hunger ,Gossypium ,Fatty Acids ,Heritability ,Complex traits ,Mixed linear model ,Genetic architecture ,lcsh:Genetics ,Plant Breeding ,030104 developmental biology ,Plant protein ,Seeds ,Epistasis ,Biotechnology ,Research Article ,Genome-Wide Association Study - Abstract
Background Cottonseed is one of the most important raw materials for plant protein, oil and alternative biofuel for diesel engines. Understanding the complex genetic basis of cottonseed traits is requisite for achieving efficient genetic improvement of the traits. However, it is not yet clear about their genetic architecture in genomic level. GWAS has been an effective way to explore genetic basis of quantitative traits in human and many crops. This study aims to dissect genetic mechanism seven cottonseed traits by a GWAS for genetic improvement. Results A genome-wide association study (GWAS) based on a full gene model with gene effects as fixed and gene-environment interaction as random, was conducted for protein, oil and 5 fatty acids using 316 accessions and ~ 390 K SNPs. Totally, 124 significant quantitative trait SNPs (QTSs), consisting of 16, 21, 87 for protein, oil and fatty acids (palmitic, linoleic, oleic, myristic, stearic), respectively, were identified and the broad-sense heritability was estimated from 71.62 to 93.43%; no QTS-environment interaction was detected for the protein, the palmitic and the oleic contents; the protein content was predominantly controlled by epistatic effects accounting for 65.18% of the total variation, but the oil content and the fatty acids except the palmitic were mainly determined by gene main effects and no epistasis was detected for the myristic and the stearic. Prediction of superior pure line and hybrid revealed the potential of the QTSs in the improvement of cottonseed traits, and the hybrid could achieve higher or lower genetic values compared with pure lines. Conclusions This study revealed complex genetic architecture of seven cottonseed traits at whole genome-wide by mixed linear model approach; the identified genetic variants and estimated genetic component effects of gene, gene-gene and gene-environment interaction provide cotton geneticist or breeders new knowledge on the genetic mechanism of the traits and the potential molecular breeding design strategy. Electronic supplementary material The online version of this article (10.1186/s12864-018-4837-0) contains supplementary material, which is available to authorized users.
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- 2018
33. A Comprehensive Genome Survey Provides Novel Insights into Bile Salt Hydrolase (BSH) in Lactobacillaceae
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Yunhai Yi, Yunyun Lv, Xuejing Lei, Lifeng Liang, Junwei Qian, and Gengyun Zhang
- Subjects
0301 basic medicine ,Sequence analysis ,Pharmaceutical Science ,Genomics ,Computational biology ,Genome ,Article ,Homology (biology) ,Amidohydrolases ,Analytical Chemistry ,lcsh:QD241-441 ,cholesterol-lowering probiotics ,03 medical and health sciences ,0302 clinical medicine ,Bacterial Proteins ,lcsh:Organic chemistry ,Phylogenetics ,Catalytic Domain ,Drug Discovery ,Amino Acid Sequence ,Physical and Theoretical Chemistry ,Peptide sequence ,Phylogeny ,biology ,Phylogenetic tree ,Organic Chemistry ,Lactobacillaceae ,bile salt hydrolase (BSH) ,biology.organism_classification ,Enzyme Activation ,030104 developmental biology ,genome survey ,Chemistry (miscellaneous) ,030220 oncology & carcinogenesis ,Molecular Medicine ,Genome, Bacterial ,BSH classification - Abstract
Bile salt hydrolase (BSH) is a well-known enzyme that has been commonly characterized in probiotic bacteria, as it has cholesterol-lowering effects. However, its molecular investigations are scarce. Here, we build a local database of BSH sequences from Lactobacillaceae (BSH–SDL), and phylogenetic analysis and homology searches were employed to elucidate their comparability and distinctiveness among species. Evolutionary study demonstrates that BSH sequences in BSH–SDL are divided into five groups, named BSH A, B, C, D and E here, which can be the genetic basis for BSH classification and nomenclature. Sequence analysis suggests the differences between BSH-active and BSH-inactive proteins clearly, especially on site 82. In addition, a total of 551 BSHs from 107 species are identified from 451 genomes of 158 Lactobacillaceae species. Interestingly, those bacteria carrying various copies of BSH A or B can be predicted to be potential cholesterol-lowering probiotics, based on the results of phylogenetic analysis and the subtypes that those previously reported BSH-active probiotics possess. In summary, this study elaborates the molecular basis of BSH in Lactobacillaceae systematically, and provides a novel methodology as well as a consistent standard for the identification of the BSH subtype. We believe that high-throughput screening can be efficiently applied to the selection of promising candidate BSH-active probiotics, which will advance the development of healthcare products in cholesterol metabolism.
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- 2018
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34. Acid phosphatase gene GmHAD1 linked to low phosphorus tolerance in soybean, through fine mapping
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Ke Wen, Hai Nian, Zhandong Cai, Peiqi Xian, Yanbo Cheng, Qibin Ma, Qiuju Xia, and Gengyun Zhang
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0106 biological sciences ,0301 basic medicine ,Population ,Phosphatase ,Acid Phosphatase ,Quantitative Trait Loci ,Arabidopsis ,Locus (genetics) ,Quantitative trait locus ,Genes, Plant ,01 natural sciences ,Plant Roots ,Phosphorus metabolism ,03 medical and health sciences ,Genetics ,Biomass ,Cloning, Molecular ,education ,Gene ,education.field_of_study ,biology ,Acid phosphatase ,food and beverages ,Chromosome Mapping ,Phosphorus ,General Medicine ,biology.organism_classification ,Plants, Genetically Modified ,030104 developmental biology ,Phenotype ,biology.protein ,Soybeans ,Agronomy and Crop Science ,010606 plant biology & botany ,Biotechnology - Abstract
Map-based cloning identified GmHAD1, a gene which encodes a HAD-like acid phosphatase, associated with soybean tolerance to low phosphorus stress. Phosphorus (P) deficiency in soils is a major limiting factor for crop growth worldwide. Plants may adapt to low phosphorus (LP) conditions via changes to root morphology, including the number, length, orientation, and branching of the principal root classes. To elucidate the genetic mechanisms for LP tolerance in soybean, quantitative trait loci (QTL) related to root morphology responses to LP were identified via hydroponic experiments. In total, we identified 14 major loci associated with these traits in a RIL population. The log-likelihood scores ranged from 2.81 to 7.43, explaining 4.23–13.98% of phenotypic variance. A major locus on chromosome 08, named qP8-2, was co-localized with an important P efficiency QTL (qPE8), containing phosphatase genes GmACP1 and GmACP2. Another major locus on chromosome 10 named qP10-2 explained 4.80–13.98% of the total phenotypic variance in root morphology. The qP10-2 contains GmHAD1, a gene which encodes an acid phosphatase. In the transgenic soybean hairy roots, GmHAD1 overexpression increased P efficiency by 8.4–16.5% relative to the control. Transgenic Arabidopsis plants had higher biomass than wild-type plants across both short- and long-term P reduction. These results suggest that GmHAD1, an acid phosphatase gene, improved the utilization of organic phosphate by soybean and Arabidopsis plants.
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- 2018
35. Additional file 6: of Dissection of complicate genetic architecture and breeding perspective of cottonseed traits by genome-wide association study
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Xiongming Du, Shouye Liu, Junling Sun, Gengyun Zhang, Yinhua Jia, Zhaoe Pan, Haitao Xiang, Shoupu He, Qiuju Xia, Songhua Xiao, Weijun Shi, Zhiwu Quan, Jianguang Liu, Ma, Jun, Baoyin Pang, Liru Wang, Gaofei Sun, Wenfang Gong, Jenkins, Johnie, Xiangyang Lou, Zhu, Jun, and Haiming Xu
- Abstract
Table S5. The SNP genotypes achieving the maximum genetic value of seed traits in designed superior homozygous lines and hybrids at the QTSs absent in the Table 5. (DOC 168 kb)
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- 2018
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36. Additional file 2: of Dissection of complicate genetic architecture and breeding perspective of cottonseed traits by genome-wide association study
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Xiongming Du, Shouye Liu, Junling Sun, Gengyun Zhang, Yinhua Jia, Zhaoe Pan, Haitao Xiang, Shoupu He, Qiuju Xia, Songhua Xiao, Weijun Shi, Zhiwu Quan, Jianguang Liu, Ma, Jun, Baoyin Pang, Liru Wang, Gaofei Sun, Wenfang Gong, Jenkins, Johnie, Xiangyang Lou, Zhu, Jun, and Haiming Xu
- Abstract
Figure S3. Genome-wide average LD decay estimated based on the population of 316 cotton accessions. (DOC 58 kb)
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- 2018
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37. Additional file 9: of Dissection of complicate genetic architecture and breeding perspective of cottonseed traits by genome-wide association study
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Xiongming Du, Shouye Liu, Junling Sun, Gengyun Zhang, Yinhua Jia, Zhaoe Pan, Haitao Xiang, Shoupu He, Qiuju Xia, Songhua Xiao, Weijun Shi, Zhiwu Quan, Jianguang Liu, Ma, Jun, Baoyin Pang, Liru Wang, Gaofei Sun, Wenfang Gong, Jenkins, Johnie, Xiangyang Lou, Zhu, Jun, and Haiming Xu
- Abstract
Table S1. The information of 316 accessions and the summary statistics of seven seed traits (DOC 321 kb)
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- 2018
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38. Additional file 1: of Dissection of complicate genetic architecture and breeding perspective of cottonseed traits by genome-wide association study
- Author
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Xiongming Du, Shouye Liu, Junling Sun, Gengyun Zhang, Yinhua Jia, Zhaoe Pan, Haitao Xiang, Shoupu He, Qiuju Xia, Songhua Xiao, Weijun Shi, Zhiwu Quan, Jianguang Liu, Ma, Jun, Baoyin Pang, Liru Wang, Gaofei Sun, Wenfang Gong, Jenkins, Johnie, Xiangyang Lou, Zhu, Jun, and Haiming Xu
- Subjects
nervous system ,fungi - Abstract
Figure S2. Population structure of 316 cotton accessions based on pruned unlinked SNPs. (DOC 69 kb)
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- 2018
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39. Additional file 5: of Dissection of complicate genetic architecture and breeding perspective of cottonseed traits by genome-wide association study
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Xiongming Du, Shouye Liu, Junling Sun, Gengyun Zhang, Yinhua Jia, Zhaoe Pan, Haitao Xiang, Shoupu He, Qiuju Xia, Songhua Xiao, Weijun Shi, Zhiwu Quan, Jianguang Liu, Ma, Jun, Baoyin Pang, Liru Wang, Gaofei Sun, Wenfang Gong, Jenkins, Johnie, Xiangyang Lou, Zhu, Jun, and Haiming Xu
- Abstract
Table S4. Predicted genetic values (G) for QQ, qq, Qq, superior homozygous line (SL), and superior hybrids (SH) of seven cottonseed traits. (DOC 114 kb)
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- 2018
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40. Additional file 7: of Dissection of complicate genetic architecture and breeding perspective of cottonseed traits by genome-wide association study
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Xiongming Du, Shouye Liu, Junling Sun, Gengyun Zhang, Yinhua Jia, Zhaoe Pan, Haitao Xiang, Shoupu He, Qiuju Xia, Songhua Xiao, Weijun Shi, Zhiwu Quan, Jianguang Liu, Ma, Jun, Baoyin Pang, Liru Wang, Gaofei Sun, Wenfang Gong, Jenkins, Johnie, Xiangyang Lou, Zhu, Jun, and Haiming Xu
- Abstract
Table S6. The SNP genotypes achieving the minimum genetic value of seed traits in designed lines for QTSs (DOC 210 kb)
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- 2018
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41. Additional file 3: of Dissection of complicate genetic architecture and breeding perspective of cottonseed traits by genome-wide association study
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Xiongming Du, Shouye Liu, Junling Sun, Gengyun Zhang, Yinhua Jia, Zhaoe Pan, Haitao Xiang, Shoupu He, Qiuju Xia, Songhua Xiao, Weijun Shi, Zhiwu Quan, Jianguang Liu, Ma, Jun, Baoyin Pang, Liru Wang, Gaofei Sun, Wenfang Gong, Jenkins, Johnie, Xiangyang Lou, Zhu, Jun, and Haiming Xu
- Abstract
Table S3. The other genome-wide significant QTSs associated with five fatty acids. (DOC 185 kb)
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- 2018
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42. Additional file 8: of Dissection of complicate genetic architecture and breeding perspective of cottonseed traits by genome-wide association study
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Xiongming Du, Shouye Liu, Junling Sun, Gengyun Zhang, Yinhua Jia, Zhaoe Pan, Haitao Xiang, Shoupu He, Qiuju Xia, Songhua Xiao, Weijun Shi, Zhiwu Quan, Jianguang Liu, Ma, Jun, Baoyin Pang, Liru Wang, Gaofei Sun, Wenfang Gong, Jenkins, Johnie, Xiangyang Lou, Zhu, Jun, and Haiming Xu
- Abstract
Figure S1. The observed phenotype distribution of seven traits. (DOC 83 kb)
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- 2018
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43. Additional file 4: of Dissection of complicate genetic architecture and breeding perspective of cottonseed traits by genome-wide association study
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Xiongming Du, Shouye Liu, Junling Sun, Gengyun Zhang, Yinhua Jia, Zhaoe Pan, Haitao Xiang, Shoupu He, Qiuju Xia, Songhua Xiao, Weijun Shi, Zhiwu Quan, Jianguang Liu, Ma, Jun, Baoyin Pang, Liru Wang, Gaofei Sun, Wenfang Gong, Jenkins, Johnie, Xiangyang Lou, Zhu, Jun, and Haiming Xu
- Abstract
Table S2. Phenotypic and genotypic correlation between seven cottonseed traits. (DOC 58 kb)
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- 2018
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44. Rice functional genomics and breeding database (RFGB)-3K-rice SNP and InDel sub-database
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Li Jiayang, Jue Ruan, Tianqing Zheng, Fan Zhang, Dabing Zhang, Yiguang Hong, Chaochun Wei, Lu Chi, Zhi-kang Li, Wensheng Wang, Yongli Zhou, Shuaishuai Tai, ZiChao Li, Hongliang Zhang, Yongming Gao, Gengyun Zhang, ZhiChao Wu, Xiuqin Zhao, Jianxin Shi, Kenneth L. McNally, Xu JianLong, and Bin-Ying Fu
- Subjects
Germplasm ,Molecular breeding ,Genetics ,Multidisciplinary ,Database ,food and beverages ,Single-nucleotide polymorphism ,Genome project ,Genome browser ,Biology ,computer.software_genre ,Genome ,Indel ,Functional genomics ,computer - Abstract
Rice is an important food crop worldwide. Genomic research on global germplasm has theoretical and practical significances in the mining of favorable alleles and on genome-based molecular breeding, which are related to Chinese and global food security. Through the 3000 (3K) Rice Genome Project, we collected single nucleotide polymorphism (SNP) and insertion and deletion (InDel) genomic variation data for the 2859 rice genomes, and establish a comprehensive SNP and InDel sub-database for the Rice Functional Genomics-based Breeding (RFGB) Database. This sub-database is a global resource containing a polymorphism information retrieval function, a genome browser visualization system and a data export system for specific genomic regions, along with other tools. This study establishes an important platform for rice gene functional research and rice molecular breeding by genomic selection.
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- 2015
45. SNP-Seek database of SNPs derived from 3000 rice genomes
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Locedie Mansueto, Roven Rommel Fuentes, Dmytro Chebotarov, Victor Jun Ulat, Gengyun Zhang, Kenneth L. McNally, Ruaraidh Sackville Hamilton, Nickolai Alexandrov, Kevin Palis, Ramil Mauleon, Shuaishuai Tai, Wensheng Wang, and Zhikang Li
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Genetics ,Database ,food and beverages ,Single-nucleotide polymorphism ,Oryza ,Biology ,computer.software_genre ,Genome ,Polymorphism, Single Nucleotide ,SNP genotyping ,Genotype ,SNP ,Database Issue ,Allele ,Databases, Nucleic Acid ,computer ,Gene ,Oracle database ,Genome, Plant - Abstract
We have identified about 20 million rice SNPs by aligning reads from the 3000 rice genomes project with the Nipponbare genome. The SNPs and allele information are organized into a SNP-Seek system (http://www.oryzasnp.org/iric-portal/), which consists of Oracle database having a total number of rows with SNP genotypes close to 60 billion (20 M SNPs × 3 K rice lines) and web interface for convenient querying. The database allows quick retrieving of SNP alleles for all varieties in a given genome region, finding different alleles from predefined varieties and querying basic passport and morphological phenotypic information about sequenced rice lines. SNPs can be visualized together with the gene structures in JBrowse genome browser. Evolutionary relationships between rice varieties can be explored using phylogenetic trees or multidimensional scaling plots.
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- 2014
46. Genome-wide characterization of non-reference transposable element insertion polymorphisms reveals genetic diversity in tropical and temperate maize
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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
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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.
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- 2017
47. Construction of high-density genetic map and QTL mapping of yield-related and two quality traits in soybean RILs population by RAD-sequencing
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Yinghui Mu, Nianxi Liu, Gengyun Zhang, Hai Nian, Mu Li, Zhiyuan Tan, Qibin Ma, Xiangbao Hu, and Qiuju Xia
- Subjects
0106 biological sciences ,0301 basic medicine ,lcsh:QH426-470 ,QTL ,lcsh:Biotechnology ,Population ,Quantitative Trait Loci ,Single-nucleotide polymorphism ,Quantitative trait locus ,Biology ,01 natural sciences ,Polymorphism, Single Nucleotide ,DNA sequencing ,03 medical and health sciences ,Family-based QTL mapping ,Genetic linkage ,lcsh:TP248.13-248.65 ,Genetics ,Grain quality ,education ,Yield-related traits ,Gene ,education.field_of_study ,fungi ,Quality traits ,food and beverages ,Chromosome Mapping ,RAD-sequencing ,DNA Restriction Enzymes ,Sequence Analysis, DNA ,lcsh:Genetics ,030104 developmental biology ,Gene Ontology ,Phenotype ,Soybeans ,Soybean ,010606 plant biology & botany ,Biotechnology ,Research Article - Abstract
Background One of the overarching goals of soybean breeding is to develop lines that combine increased yield with improved quality characteristics. High-density-marker QTL mapping can serve as an effective strategy to identify novel genomic information to facilitate crop improvement. In this study, we genotyped a recombinant inbred line (RIL) population (Zhonghuang 24 × Huaxia 3) using a restriction-site associated DNA sequencing (RAD-seq) approach. A high-density soybean genetic map was constructed and used to identify several QTLs that were shown to influence six yield-related and two quality traits. Results A total of 47,472 single-nucleotide polymorphisms (SNPs) were detected for the RILs that were integrated into 2639 recombination bin units, with an average distance of 1.00 cM between adjacent markers. Forty seven QTLs for yield-related traits and 13 QTLs for grain quality traits were found to be distributed on 16 chromosomes in the 2 year studies. Among them, 18 QTLs were stable, and were identified in both analyses. Twenty six QTLs were identified for the first time, with a single QTL (qNN19a) in a 56 kb region explaining 32.56% of phenotypic variation, and an additional 10 of these were novel, stable QTLs. Moreover, 8 QTL hotpots on four different chromosomes were identified for the correlated traits. Conclusions With RAD-sequencing, some novel QTLs and important QTL clusters for both yield-related and quality traits were identified based on a new, high-density bin linkage map. Three predicted genes were selected as candidates that likely have a direct or indirect influence on both yield and quality in soybean. Our findings will be helpful for understanding common genetic control mechanisms of co-localized traits and to select cultivars for further analysis to predictably modulate soybean yield and quality simultaneously. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3854-8) contains supplementary material, which is available to authorized users.
- Published
- 2017
48. Fine-mapping of QTLs for individual and total isoflavone content in soybean (Glycine max L.) using a high-density genetic map
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Qibin Ma, Hai Nian, Qiuju Xia, Yanbo Cheng, Zhandong Cai, Zhuwen Ma, Yinghui Mu, Xinguo Liu, and Gengyun Zhang
- Subjects
0106 biological sciences ,0301 basic medicine ,Genotype ,Genetic Linkage ,Population ,Quantitative Trait Loci ,Quantitative trait locus ,Biology ,01 natural sciences ,Polymorphism, Single Nucleotide ,03 medical and health sciences ,Gene mapping ,Inbred strain ,Genetic linkage ,Botany ,Genetics ,Plant breeding ,education ,education.field_of_study ,Chromosome Mapping ,General Medicine ,Sequence Analysis, DNA ,Isoflavones ,030104 developmental biology ,Phenotype ,Genetic marker ,Seeds ,Soybeans ,Agronomy and Crop Science ,010606 plant biology & botany ,Biotechnology - Abstract
Fifteen stable QTLs were identified using a high-density soybean genetic map across multiple environments. One major QTL, qIF5-1, contributing to total isoflavone content explained phenotypic variance 49.38, 43.27, 46.59, 45.15 and 52.50%, respectively. Soybeans (Glycine max L.) are a major source of dietary isoflavones. To identify novel quantitative trait loci (QTL) underlying isoflavone content, and to improve the accuracy of marker-assisted breeding in soybean, a valuable mapping population comprised of 196 F7:8–10 recombinant inbred lines (RILs, Huachun 2 × Wayao) was utilized to evaluate individual and total isoflavone content in plants grown in four different environments in Guangdong. A high-density genetic linkage map containing 3469 recombination bin markers based on 0.2 × restriction site-associated DNA tag sequencing (RAD-seq) technology was used to finely map QTLs for both individual and total isoflavone contents. Correlation analyses showed that total isoflavone content, and that of five individual isoflavone, was significantly correlated across the four environments. Based on the high-density genetic linkage map, a total of 15 stable quantitative trait loci (QTLs) associated with isoflavone content across multiple environments were mapped onto chromosomes 02, 05, 07, 09, 10, 11, 13, 16, 17, and 19. Further, one of them, qIF5-1, localized to chromosomes 05 (38,434,171–39,045,620 bp) contributed to almost all isoflavone components across all environments, and explained 6.37–59.95% of the phenotypic variance, especially explained 49.38, 43.27, 46.59, 45.15 and 52.50% for total isoflavone. The results obtained in the present study will pave the way for a better understanding of the genetics of isoflavone accumulation and reveals the scope available for improvement of isoflavone content through marker-assisted selection.
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- 2017
49. Updated foxtail millet genome assembly and gene mapping of nine key agronomic traits by resequencing a RIL population
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Qingchun Chen, Houbao Zhang, Ning Li, Guohua Du, Hui Li, Gengyun Zhang, Shu Cheng, Xuemei Cai, Wang Xiaoming, Haitao Xiang, Ping Huang, Cai Wei, Xuemei Ni, Zhiwu Quan, Fan Guangyu, Xuejing Lei, Qiuju Xia, Zhao Zhihai, Hongfeng Zou, Tao Guo, and Zhou Chengshu
- Subjects
Genetic Markers ,0106 biological sciences ,0301 basic medicine ,Setaria ,Candidate gene ,Quantitative Trait Loci ,Setaria Plant ,Population ,Health Informatics ,Single-nucleotide polymorphism ,Quantitative trait locus ,Data Note ,Polymorphism, Single Nucleotide ,01 natural sciences ,Genome ,Chromosomes, Plant ,Chromosome Breakpoints ,03 medical and health sciences ,Quantitative Trait, Heritable ,Gene mapping ,Inbreeding ,education ,Recombination, Genetic ,Genetics ,education.field_of_study ,biology ,Chromosome Mapping ,High-Throughput Nucleotide Sequencing ,Genomics ,biology.organism_classification ,Computer Science Applications ,030104 developmental biology ,Foxtail ,Genome, Plant ,010606 plant biology & botany - Abstract
Foxtail millet (Setaria italica) provides food and fodder in semi-arid regions and infertile land. Resequencing of 184 foxtail millet recombinant inbred lines (RILs) was carried out to aid essential research on foxtail millet improvement. A total 483 414 single nucleotide polymorphisms were determined. Bin maps were constructed based on the RILs’ recombination data. Based on the high-density bin map, we updated Zhanggu reference with 416 Mb after adding 16 Mb unanchored scaffolds and Yugu reference with some assembly error correction and 3158 gaps filled. Quantitative trait loci (QTL) mapping of nine agronomic traits was done based on this RIL population, five of which were controlled by a single gene. Meanwhile, two QTLs were found for plant height, and a candidate gene showed 89% identity to the known rice gibberellin-synthesis gene sd1. Three QTLs were found for the trait of heading date. The whole genome resequencing and QTL mapping provided important tools for foxtail millet research and breeding. Resequencing of the RILs could also provide an effective way for high-quality genome assembly and gene identification.
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- 2017
50. Additional file 4: of Construction of high-density genetic map and QTL mapping of yield-related and two quality traits in soybean RILs population by RAD-sequencing
- Author
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Nianxi Liu, Li, Mu, Xiangbao Hu, Qibin Ma, Yinghui Mu, Zhiyuan Tan, Qiuju Xia, Gengyun Zhang, and Nian, Hai
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food and beverages - Abstract
8 QTL hotspots detected in Zhonghuang24 × Huaxia3 RIL population in 2 years. **marked by QTL name indicates a new, stable QTL that was detected in both years; aChr indicates chromosome; bLOD indicates the logarithm of odds score; cPercentage of phenotypic variation explained. (PDF 62 kb)
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- 2017
- Full Text
- View/download PDF
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