The Experts below are selected from a list of 5868 Experts worldwide ranked by ideXlab platform
Qiang Zhao - One of the best experts on this subject based on the ideXlab platform.
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genetic discovery for oil production and quality in sesame
2015Co-Authors: Yanxin Zhang, Yiqi Lu, Wenjun Li, Qiang Zhao, Yan Zhao, Qi Feng, Linhai Wang, Donghua Li, Xianmei Zhang, Xiumei TangAbstract:Oilseed crops are used to produce vegetable oil. Sesame (Sesamum indicum), an oilseed crop grown worldwide, has high oil content and a small diploid genome, but the genetic basis of oil production and quality is unclear. Here we sequence 705 diverse sesame varieties to construct a Haplotype Map of the sesame genome and de novo assemble two representative varieties to identify sequence variations. We investigate 56 agronomic traits in four environments and identify 549 associated loci. Examination of the major loci identifies 46 candidate causative genes, including genes related to oil content, fatty acid biosynthesis and yield. Several of the candidate genes for oil content encode enzymes involved in oil metabolism. Two major genes associated with lignification and black pigmentation in the seed coat are also associated with large variation in oil content. These findings may inform breeding and improvement strategies for a broad range of oilseed crops.
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a Haplotype Map of genomic variations and genome wide association studies of agronomic traits in foxtail millet setaria italica
2013Co-Authors: Xuehui Huang, Hengyun Lu, Yiqi Lu, Congcong Zhou, Lifang Yang, Wenjun Li, Yang Chai, Qiang Zhao, Yan Zhao, Qijun WengAbstract:Foxtail millet (Setaria italica) is an important grain crop that is grown in arid regions. Here we sequenced 916 diverse foxtail millet varieties, identified 2.58 million SNPs and used 0.8 million common SNPs to construct a Haplotype Map of the foxtail millet genome. We classified the foxtail millet varieties into two divergent groups that are strongly correlated with early and late flowering times. We phenotyped the 916 varieties under five different environments and identified 512 loci associated with 47 agronomic traits by genome-wide association studies. We performed a de novo assembly of deeply sequenced genomes of a Setaria viridis accession (the wild progenitor of S. italica) and an S. italica variety and identified complex interspecies and intraspecies variants. We also identified 36 selective sweeps that seem to have occurred during modern breeding. This study provides fundamental resources for genetics research and genetic improvement in foxtail millet.
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Genome-wide association studies of 14 agronomic traits in rice landraces
2010Co-Authors: Xuehui Huang, Qiang Zhao, Yan Zhao, Xinghua Wei, Tao Sang, Qi Feng, Chuanrang Zhu, Zhiwu ZhangAbstract:Uncovering the genetic basis of agronomic traits in crop landraces that have adapted to various agro-climatic conditions is important to world food security. Here we have identified ∼ 3.6 million SNPs by sequencing 517 rice landraces and constructed a high-density Haplotype Map of the rice genome using a novel data-imputation method. We performed genome-wide association studies (GWAS) for 14 agronomic traits in the population of Oryza sativa indica subspecies. The loci identified through GWAS explained ∼ 36% of the phenotypic variance, on average. The peak signals at six loci were tied closely to previously identified genes. This study provides a fundamental resource for rice genetics research and breeding, and demonstrates that an approach integrating second-generation genome sequencing and GWAS can be used as a powerful complementary strategy to classical biparental cross-Mapping for dissecting complex traits in rice.
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seg Map a novel software for genotype calling and genetic Map construction from next generation sequencing
2010Co-Authors: Xuehui Huang, Qiang Zhao, Zhixin Lin, Bin HanAbstract:The advent of next-generation sequencing tech- nologies opens a new era for discovering genome diversity and genetic Mapping. A sequencing-based method was recently developed to genotype recombinant populations with considerably improved resolution and reduced time and cost. To effectively implement this method, here we report the development of an analytic pipeline, sequencing enabled genotyping for Mapping recombination populations (SEG-Map), for genotype calling and constructing genetic Maps from next-generation sequencing data. SEG-Map was designed to interface with the commonly used tools for Mapping next-generation short reads. The output data of SEG-Map would then allow constructing genetic Maps and subsequent quantitative trait loci analyses directly. The package is available at http://www.ncgr.ac.cn/software/ SEG. Moreover, directly sequencing over 500 rice land- races enabled a construction of a high-density rice Haplotype Map. This data set with an average of 2-3 SNPs per kilobyte between indica and japonica could be effectively used in the sequencing-based genotyping of their recombinant Mapping populations.
S S Moore - One of the best experts on this subject based on the ideXlab platform.
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a high resolution radiation hybrid Map of bovine chromosome 14 identifies scaffold rearrangement in the latest bovine assembly
2007Co-Authors: E Marques, Simon De Givry, Paul Stothard, B Murdoch, Zhiquan Wang, J E Womack, S S MooreAbstract:Background: Radiation hybrid (RH) Maps are considered to be a tool of choice for fine Mapping closely linked loci, considering that the resolution of linkage Maps is determined by the number of informative meiosis and recombination events which may require very large Mapping populations. Accurately defining the marker order on chromosomes is crucial for correct identification of quantitative trait loci (QTL), Haplotype Map construction and refinement of candidate gene searches. Results: A 12 k Radiation hybrid Map of bovine chromosome 14 was constructed using 843 single nucleotide polymorphism markers. The resulting Map was aligned with the latest version of the bovine assembly (Btau_3.1) as well as other previously published RH Maps. The resulting Map identified distinct regions on Bovine chromosome 14 where discrepancies between this RH Map and the bovine assembly occur. A major region of discrepancy was found near the centromere involving the arrangement and order of the scaffolds from the assembly. The Map further confirms previously published conserved synteny blocks with human chromosome 8. As well, it identifies an extra breakpoint and conserved synteny block previously undetected due to lower marker density. This conserved synteny block is in a region where markers between the RH Map presented here and the latest sequence assembly are in very good agreement. Conclusion: The increase of publicly available markers shifts the rate limiting step from marker discovery to the correct identification of their order for further use by the research community. This high resolution Map of bovine chromosome 14 will facilitate identification of regions in the sequence assembly where additional information is required to resolve marker ordering.
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a high resolution radiation hybrid Map of bovine chromosome 14 identifies scaffold rearrangement in the latest bovine assembly
2007Co-Authors: E Marques, Simon De Givry, Paul Stothard, B Murdoch, Zhiquan Wang, J E Womack, S S MooreAbstract:Radiation hybrid (RH) Maps are considered to be a tool of choice for fine Mapping closely linked loci, considering that the resolution of linkage Maps is determined by the number of informative meiosis and recombination events which may require very large Mapping populations. Accurately defining the marker order on chromosomes is crucial for correct identification of quantitative trait loci (QTL), Haplotype Map construction and refinement of candidate gene searches. A 12 k Radiation hybrid Map of bovine chromosome 14 was constructed using 843 single nucleotide polymorphism markers. The resulting Map was aligned with the latest version of the bovine assembly (Btau_3.1) as well as other previously published RH Maps. The resulting Map identified distinct regions on Bovine chromosome 14 where discrepancies between this RH Map and the bovine assembly occur. A major region of discrepancy was found near the centromere involving the arrangement and order of the scaffolds from the assembly. The Map further confirms previously published conserved synteny blocks with human chromosome 8. As well, it identifies an extra breakpoint and conserved synteny block previously undetected due to lower marker density. This conserved synteny block is in a region where markers between the RH Map presented here and the latest sequence assembly are in very good agreement. The increase of publicly available markers shifts the rate limiting step from marker discovery to the correct identification of their order for further use by the research community. This high resolution Map of bovine chromosome 14 will facilitate identification of regions in the sequence assembly where additional information is required to resolve marker ordering.
Xuehui Huang - One of the best experts on this subject based on the ideXlab platform.
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a Haplotype Map of genomic variations and genome wide association studies of agronomic traits in foxtail millet setaria italica
2013Co-Authors: Xuehui Huang, Hengyun Lu, Yiqi Lu, Congcong Zhou, Lifang Yang, Wenjun Li, Yang Chai, Qiang Zhao, Yan Zhao, Qijun WengAbstract:Foxtail millet (Setaria italica) is an important grain crop that is grown in arid regions. Here we sequenced 916 diverse foxtail millet varieties, identified 2.58 million SNPs and used 0.8 million common SNPs to construct a Haplotype Map of the foxtail millet genome. We classified the foxtail millet varieties into two divergent groups that are strongly correlated with early and late flowering times. We phenotyped the 916 varieties under five different environments and identified 512 loci associated with 47 agronomic traits by genome-wide association studies. We performed a de novo assembly of deeply sequenced genomes of a Setaria viridis accession (the wild progenitor of S. italica) and an S. italica variety and identified complex interspecies and intraspecies variants. We also identified 36 selective sweeps that seem to have occurred during modern breeding. This study provides fundamental resources for genetics research and genetic improvement in foxtail millet.
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Genome-wide association studies of 14 agronomic traits in rice landraces
2010Co-Authors: Xuehui Huang, Qiang Zhao, Yan Zhao, Xinghua Wei, Tao Sang, Qi Feng, Chuanrang Zhu, Zhiwu ZhangAbstract:Uncovering the genetic basis of agronomic traits in crop landraces that have adapted to various agro-climatic conditions is important to world food security. Here we have identified ∼ 3.6 million SNPs by sequencing 517 rice landraces and constructed a high-density Haplotype Map of the rice genome using a novel data-imputation method. We performed genome-wide association studies (GWAS) for 14 agronomic traits in the population of Oryza sativa indica subspecies. The loci identified through GWAS explained ∼ 36% of the phenotypic variance, on average. The peak signals at six loci were tied closely to previously identified genes. This study provides a fundamental resource for rice genetics research and breeding, and demonstrates that an approach integrating second-generation genome sequencing and GWAS can be used as a powerful complementary strategy to classical biparental cross-Mapping for dissecting complex traits in rice.
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seg Map a novel software for genotype calling and genetic Map construction from next generation sequencing
2010Co-Authors: Xuehui Huang, Qiang Zhao, Zhixin Lin, Bin HanAbstract:The advent of next-generation sequencing tech- nologies opens a new era for discovering genome diversity and genetic Mapping. A sequencing-based method was recently developed to genotype recombinant populations with considerably improved resolution and reduced time and cost. To effectively implement this method, here we report the development of an analytic pipeline, sequencing enabled genotyping for Mapping recombination populations (SEG-Map), for genotype calling and constructing genetic Maps from next-generation sequencing data. SEG-Map was designed to interface with the commonly used tools for Mapping next-generation short reads. The output data of SEG-Map would then allow constructing genetic Maps and subsequent quantitative trait loci analyses directly. The package is available at http://www.ncgr.ac.cn/software/ SEG. Moreover, directly sequencing over 500 rice land- races enabled a construction of a high-density rice Haplotype Map. This data set with an average of 2-3 SNPs per kilobyte between indica and japonica could be effectively used in the sequencing-based genotyping of their recombinant Mapping populations.
E Marques - One of the best experts on this subject based on the ideXlab platform.
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a high resolution radiation hybrid Map of bovine chromosome 14 identifies scaffold rearrangement in the latest bovine assembly
2007Co-Authors: E Marques, Simon De Givry, Paul Stothard, B Murdoch, Zhiquan Wang, J E Womack, S S MooreAbstract:Background: Radiation hybrid (RH) Maps are considered to be a tool of choice for fine Mapping closely linked loci, considering that the resolution of linkage Maps is determined by the number of informative meiosis and recombination events which may require very large Mapping populations. Accurately defining the marker order on chromosomes is crucial for correct identification of quantitative trait loci (QTL), Haplotype Map construction and refinement of candidate gene searches. Results: A 12 k Radiation hybrid Map of bovine chromosome 14 was constructed using 843 single nucleotide polymorphism markers. The resulting Map was aligned with the latest version of the bovine assembly (Btau_3.1) as well as other previously published RH Maps. The resulting Map identified distinct regions on Bovine chromosome 14 where discrepancies between this RH Map and the bovine assembly occur. A major region of discrepancy was found near the centromere involving the arrangement and order of the scaffolds from the assembly. The Map further confirms previously published conserved synteny blocks with human chromosome 8. As well, it identifies an extra breakpoint and conserved synteny block previously undetected due to lower marker density. This conserved synteny block is in a region where markers between the RH Map presented here and the latest sequence assembly are in very good agreement. Conclusion: The increase of publicly available markers shifts the rate limiting step from marker discovery to the correct identification of their order for further use by the research community. This high resolution Map of bovine chromosome 14 will facilitate identification of regions in the sequence assembly where additional information is required to resolve marker ordering.
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a high resolution radiation hybrid Map of bovine chromosome 14 identifies scaffold rearrangement in the latest bovine assembly
2007Co-Authors: E Marques, Simon De Givry, Paul Stothard, B Murdoch, Zhiquan Wang, J E Womack, S S MooreAbstract:Radiation hybrid (RH) Maps are considered to be a tool of choice for fine Mapping closely linked loci, considering that the resolution of linkage Maps is determined by the number of informative meiosis and recombination events which may require very large Mapping populations. Accurately defining the marker order on chromosomes is crucial for correct identification of quantitative trait loci (QTL), Haplotype Map construction and refinement of candidate gene searches. A 12 k Radiation hybrid Map of bovine chromosome 14 was constructed using 843 single nucleotide polymorphism markers. The resulting Map was aligned with the latest version of the bovine assembly (Btau_3.1) as well as other previously published RH Maps. The resulting Map identified distinct regions on Bovine chromosome 14 where discrepancies between this RH Map and the bovine assembly occur. A major region of discrepancy was found near the centromere involving the arrangement and order of the scaffolds from the assembly. The Map further confirms previously published conserved synteny blocks with human chromosome 8. As well, it identifies an extra breakpoint and conserved synteny block previously undetected due to lower marker density. This conserved synteny block is in a region where markers between the RH Map presented here and the latest sequence assembly are in very good agreement. The increase of publicly available markers shifts the rate limiting step from marker discovery to the correct identification of their order for further use by the research community. This high resolution Map of bovine chromosome 14 will facilitate identification of regions in the sequence assembly where additional information is required to resolve marker ordering.
Kenshi Hayashi - One of the best experts on this subject based on the ideXlab platform.
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A definitive Haplotype Map of structural variations determined by microarray analysis of duplicated haploid genomes
2014Co-Authors: Tomoko Tahira, Yoji Kukita, Koji Yahara, Koichiro Higasa, Kiyoko Kato, Norio Wake, Kenshi HayashiAbstract:Complete hydatidiform moles (CHMs) are tissues carrying duplicated haploid genomes derived from single sperms, and detecting copy number variations (CNVs) in CHMs is assumed to be sensitive and straightforward methods. We genotyped 108 CHM genomes using Affymetrix SNP 6.0 (GEO#: GSE18642) and Illumina 1 M-duo (GEO#: GSE54948). After quality control, we obtained 84 definitive Haplotype consisting of 1.7 million SNPs and 2339 CNV regions. The results are presented in the database of our web site (http://orca.gen.kyushu-u.ac.jp/cgi-bin/gbrowse/humanBuild37D4_1/).
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A Definitive Haplotype Map as Determined by Genotyping Duplicated Haploid Genomes Finds a Predominant Haplotype Preference at Copy-Number Variation Events
2010Co-Authors: Yoji Kukita, Koji Yahara, Tomoko Tahira, Koichiro Higasa, Miki Sonoda, Ken Yamamoto, Kiyoko Kato, Norio Wake, Kenshi HayashiAbstract:The majority of complete hydatidiform moles (CHMs) harbor duplicated haploid genomes that originate from sperm. This makes CHMs more advantageous than conventional diploid cells for determining Haplotypes of SNPs and copy-number variations (CNVs), because all of the genetic variants in a CHM genome are homozygous. Here we report SNP and CNV Haplotype structures determined by analysis of 100 CHMs from Japanese subjects via high-density DNA arrays. The obtained Haplotype Map should be useful as a reference for the Haplotype structure of Asian populations. We resolved common CNV regions (merged CNV segments across the examined samples) into CNV events (clusters of CNV segments) on the basis of mutual overlap and found that the Haplotype backgrounds of different CNV events within the same CNV region were predominantly similar, perhaps because of inherent structural instability.
