谷子(Setaria italica L.)是我国北方地区重要的粮食作物,籽粒营养丰富,且富含多种类黄酮物质,对生长发育和品质形成发挥着重要作用。目前谷子籽粒类黄酮合成及粒色形成相关调控机制研究较少。分析谷子类黄酮含量及粒色性状相关的QTL,...谷子(Setaria italica L.)是我国北方地区重要的粮食作物,籽粒营养丰富,且富含多种类黄酮物质,对生长发育和品质形成发挥着重要作用。目前谷子籽粒类黄酮合成及粒色形成相关调控机制研究较少。分析谷子类黄酮含量及粒色性状相关的QTL,为类黄酮合成关键基因的精细定位、克隆及功能研究奠定基础,同时,也为揭示谷子类黄酮合成及代谢机制和培育富含类黄酮谷子品种提供技术支撑。本研究以红粒色高类黄酮品种金苗红酒谷和黄粒色低类黄酮品种豫谷28为亲本构建的包含150个家系的重组自交系(RIL)群体为试验材料,在谷子成熟期对籽粒粒色和类黄酮含量相关性状进行分析。同时,采用复合区间作图法(composite interval mapping,CIM)对粒色和类黄酮含量进行QTL定位与分析,并对QTL置信区间内的候选基因进行预测。相关性分析表明,类黄酮含量与粒色呈显著正相关。共定位到4个与类黄酮含量相关和11个与粒色相关的QTL,分别位于1号、2号、5号、6号、7号、8号和9号染色体上,单个QTL的表型贡献率为2.01%~29.25%,6个为主效QTL,其中,qSC1-2和qFLA1-1、qSC7-1和qFLA7-1、qSC9-3和qFLA9-1为2个性状下共同定位到的QTL。通过基因预测与功能注释,筛选出QTL置信区间内5个与类黄酮物质合成及代谢相关的候选基因,表明类黄酮物质的合成、代谢及利用相关基因极有可能控制了这些基因的表达。15个QTL分别聚集于7条染色体上,基于基因功能注释,共筛选了5个与谷子类黄酮合成及代谢相关的候选基因,表明不同QTL位点参与到了共同遗传机制,并可通过分子标记辅助选择进行类黄酮合成及代谢等有利基因的聚合育种。展开更多
With increasing demand for high-quality cotton,it is desirable to identify genes involved in fiber development for molecular improvement of cotton.In this study,780 differentially expressed genes(DEGs)were identified ...With increasing demand for high-quality cotton,it is desirable to identify genes involved in fiber development for molecular improvement of cotton.In this study,780 differentially expressed genes(DEGs)were identified in developing fibers at 10 days post-anthesis(DPA)in Gossypium hirsutum acc.DH962 and G.hirsutum cv.Jimian 5 using RNA-seq.Of 15 stable QTL for fiber quality identified in the same two parents in previous studies,4,3,6,1,and 1 QTL were associated with fiber length(FL),fiber strength(FS),micronaire(MIC),fiber elongation(FE)and fiber length uniformity ratio(FU),respectively.Integration of DEGs and QTL allowed the identification of 31 genes in 9 QTL regions,of which 25 were highly expressed in fibers based on the transcriptome datasets and 9 were preferentially expressed in different stages of fiber development.Gh_A01G0453(GhDTX19),Gh_D07G1581 and Gh_D04G0942 were expressed specifically in 5 and 10 DPA fibers,with Gh_D04G0942 showing low expression in other tissues except pistil.Gh_D07G1799(GhGAUT9),Gh_D11G0326(GhVPS29),Gh_D11G0333(GhTCP14),and Gh_D11G0334(GhNRP2)were preferentially expressed in 5 or 10 DPA fibers;Gh_A01G0397(GhABCG10)and Gh_D07G1744 were expressed specifically in 20 and 25 DPA fibers.These results suggest candidate genes for molecular improvement of cotton fiber quality.展开更多
Diseases caused by fungal pathogens account for approximately 50% of all soybean disease losses around the world. Conflicting results of fungal disease resistance QTLs from different populations often occurred. The ob...Diseases caused by fungal pathogens account for approximately 50% of all soybean disease losses around the world. Conflicting results of fungal disease resistance QTLs from different populations often occurred. The objectives of this study were to： （i） evaluate evidence for reported fungal disease resistance QTLs associations in soybean and （ii） extract relatively reliable and useful information from the ＂real＂ QTLs and mine putative genes in soybean. An integrated map of fungal disease resistance QTLs in soybean was established with soymap 2 published in 2004 as a reference map. QTLs of fungal disease resistance developed from each of separate populations in recent 10 years were integrated into a combinative map for gene cloning and marker assisted selection in soybean. 107 QTLs from different maps were integrated and projected to the reference map with the software BioMercator 2.1. A method of meta-analysis was used to narrow down the confidence interval, and 23 ＂real＂ QTLs and their corresponding markers were obtained from 12 linkage groups （LG）, respectively. Two published R genes were found in these ＂real＂ QTLs intervals. Sequences in the ＂real＂ QTLs intervals were predicted by GENSCAN, and these predicted genes were annotated in Goblet. 228 resistance gene analogs （RGAs） in 12 different terms were mined. The results will lay the foundation for a bioinformatics platform combining abundant QTLs, and offer the basis for marker assisted selection and gene cloning in soybean.展开更多
Soybean is a global principal source of edible plant oil. As more soybean oil-related quantitative trait loci(QTLs) have been located in the collective genome, it is urgent to establish a classification system for the...Soybean is a global principal source of edible plant oil. As more soybean oil-related quantitative trait loci(QTLs) have been located in the collective genome, it is urgent to establish a classification system for these distributed QTLs. A collinear platform may be useful to characterize and identify relationships among QTLs as well as aid in novel gene discovery. In this study, the collinearity MCScan X algorithm and collective soybean genomic information were used to construct collinearity blocks, to which soybean oil-related QTLs were mapped. The results demonstrated that 666 collinearity blocks were detected in the soybean genome across 20 chromosomes, and 521 collinearity relationships existed in 231 of the 242 effective soybean oil-related QTLs. This included 214 inclusion relationships and 307 intersecting relationships. Among them, the collinearity among QTLs that are related to soybean oil content was shown on a maximum of seven chromosomes and minimum of one chromosome, with the majority of QTLs having collinearity on two chromosomes. Using overlapping hotspot regions in the soybean oil QTLs with collinearity, we mined for novel oil content-related genes. Overall, we identified 23 putatively functional genes associated with oil content in soybean and annotated them using a number of annotation databases. Our findings provide a valuable framework for elucidating evolutionary relationships between soybean oil-related QTLs and lay a foundation for functional marker-assisted breeding relating to soybean oil content.展开更多
Drought is becoming an increasingly important constraint limiting world's rice production (Bennett, 2003). About half of the world's rice is grown in rainfed environments where the rainfall is the major source...Drought is becoming an increasingly important constraint limiting world's rice production (Bennett, 2003). About half of the world's rice is grown in rainfed environments where the rainfall is the major source of water sup-展开更多
This is an in silico analysis of quantitative trait loci (QTLs), genes, polymorphisms, and chromosomal regions regulating hypertension in the rat genome. Utilizing PGmapper, a program that matches phenoltypes to genes...This is an in silico analysis of quantitative trait loci (QTLs), genes, polymorphisms, and chromosomal regions regulating hypertension in the rat genome. Utilizing PGmapper, a program that matches phenoltypes to genes, we identified 266 essential hypertension-associated genes (HyperA), and 83 of these genes contain known hypertension-associated polymorphisms (HyperAP). The majority of HyperAP have been reported in recent years. Surprisingly, only a few of these HyperAP genes have been investigated for their candidacy as the QTL for hypertension. The frequency of candidate genes within peak regions of the QTL is higher than the rest of the QTL region. We also found that QTL located in both gene-rich regions and gene-rich chromosomes contained the most candidate genes. However, the number of candidate genes within a peak region is not associated with the number of total genes in a QTL region. This data could not only facilitate a more rapid and comprehensive identification for the causal genes underlying hypertension in rats, but also provides new insights into genomic structure in regulation of hypertension.展开更多
文摘谷子(Setaria italica L.)是我国北方地区重要的粮食作物,籽粒营养丰富,且富含多种类黄酮物质,对生长发育和品质形成发挥着重要作用。目前谷子籽粒类黄酮合成及粒色形成相关调控机制研究较少。分析谷子类黄酮含量及粒色性状相关的QTL,为类黄酮合成关键基因的精细定位、克隆及功能研究奠定基础,同时,也为揭示谷子类黄酮合成及代谢机制和培育富含类黄酮谷子品种提供技术支撑。本研究以红粒色高类黄酮品种金苗红酒谷和黄粒色低类黄酮品种豫谷28为亲本构建的包含150个家系的重组自交系(RIL)群体为试验材料,在谷子成熟期对籽粒粒色和类黄酮含量相关性状进行分析。同时,采用复合区间作图法(composite interval mapping,CIM)对粒色和类黄酮含量进行QTL定位与分析,并对QTL置信区间内的候选基因进行预测。相关性分析表明,类黄酮含量与粒色呈显著正相关。共定位到4个与类黄酮含量相关和11个与粒色相关的QTL,分别位于1号、2号、5号、6号、7号、8号和9号染色体上,单个QTL的表型贡献率为2.01%~29.25%,6个为主效QTL,其中,qSC1-2和qFLA1-1、qSC7-1和qFLA7-1、qSC9-3和qFLA9-1为2个性状下共同定位到的QTL。通过基因预测与功能注释,筛选出QTL置信区间内5个与类黄酮物质合成及代谢相关的候选基因,表明类黄酮物质的合成、代谢及利用相关基因极有可能控制了这些基因的表达。15个QTL分别聚集于7条染色体上,基于基因功能注释,共筛选了5个与谷子类黄酮合成及代谢相关的候选基因,表明不同QTL位点参与到了共同遗传机制,并可通过分子标记辅助选择进行类黄酮合成及代谢等有利基因的聚合育种。
基金supported by the National Natural Science Foundation of China(31871669)
文摘With increasing demand for high-quality cotton,it is desirable to identify genes involved in fiber development for molecular improvement of cotton.In this study,780 differentially expressed genes(DEGs)were identified in developing fibers at 10 days post-anthesis(DPA)in Gossypium hirsutum acc.DH962 and G.hirsutum cv.Jimian 5 using RNA-seq.Of 15 stable QTL for fiber quality identified in the same two parents in previous studies,4,3,6,1,and 1 QTL were associated with fiber length(FL),fiber strength(FS),micronaire(MIC),fiber elongation(FE)and fiber length uniformity ratio(FU),respectively.Integration of DEGs and QTL allowed the identification of 31 genes in 9 QTL regions,of which 25 were highly expressed in fibers based on the transcriptome datasets and 9 were preferentially expressed in different stages of fiber development.Gh_A01G0453(GhDTX19),Gh_D07G1581 and Gh_D04G0942 were expressed specifically in 5 and 10 DPA fibers,with Gh_D04G0942 showing low expression in other tissues except pistil.Gh_D07G1799(GhGAUT9),Gh_D11G0326(GhVPS29),Gh_D11G0333(GhTCP14),and Gh_D11G0334(GhNRP2)were preferentially expressed in 5 or 10 DPA fibers;Gh_A01G0397(GhABCG10)and Gh_D07G1744 were expressed specifically in 20 and 25 DPA fibers.These results suggest candidate genes for molecular improvement of cotton fiber quality.
基金supported by the funding from the National Natural Science Foundation of China(30971809)the National 973 Program of China(2004CB 117203-5)+2 种基金the National 948 Project of China[(2006-G1(A)]the National High-Tech R&D Program of China(863 Program, 2006AA100104-3)the Heilongjiang Foundation for University Key Teachers,China(1152G007)
文摘Diseases caused by fungal pathogens account for approximately 50% of all soybean disease losses around the world. Conflicting results of fungal disease resistance QTLs from different populations often occurred. The objectives of this study were to： （i） evaluate evidence for reported fungal disease resistance QTLs associations in soybean and （ii） extract relatively reliable and useful information from the ＂real＂ QTLs and mine putative genes in soybean. An integrated map of fungal disease resistance QTLs in soybean was established with soymap 2 published in 2004 as a reference map. QTLs of fungal disease resistance developed from each of separate populations in recent 10 years were integrated into a combinative map for gene cloning and marker assisted selection in soybean. 107 QTLs from different maps were integrated and projected to the reference map with the software BioMercator 2.1. A method of meta-analysis was used to narrow down the confidence interval, and 23 ＂real＂ QTLs and their corresponding markers were obtained from 12 linkage groups （LG）, respectively. Two published R genes were found in these ＂real＂ QTLs intervals. Sequences in the ＂real＂ QTLs intervals were predicted by GENSCAN, and these predicted genes were annotated in Goblet. 228 resistance gene analogs （RGAs） in 12 different terms were mined. The results will lay the foundation for a bioinformatics platform combining abundant QTLs, and offer the basis for marker assisted selection and gene cloning in soybean.
基金financially supported by the National Key R&D Program of China (2016YFD0100500, 2016YFD0100300, 2016YFD0100201-21)the National Natural Science Foundation of China (31701449, 31471516, 31401465, 31400074, 31501332)+7 种基金the Natural Science Foundation of Heilongjiang Province, China (QC2017013)the Young Innovative Talent Training Plan of Undergraduate Colleges and Universities in Heilongjiang Province, China (UNPYSCT-2016144)the Special Financial Aid to Postdoctor Research Fellow in Heilongjiang, China (To Qi Zhaoming)the Heilongjiang Funds for Distinguished Young Scientists, China (JC2016004)the Outstanding Academic Leaders Projects of Harbin, China (2015RQXXJ018)the China Post Doctoral Project (2015M581419)the Dongnongxuezhe Project, China (to Chen Qingshan)the Young Talent Project of Northeast Agricultural University, China (to Qi Zhaoming, 518062)
文摘Soybean is a global principal source of edible plant oil. As more soybean oil-related quantitative trait loci(QTLs) have been located in the collective genome, it is urgent to establish a classification system for these distributed QTLs. A collinear platform may be useful to characterize and identify relationships among QTLs as well as aid in novel gene discovery. In this study, the collinearity MCScan X algorithm and collective soybean genomic information were used to construct collinearity blocks, to which soybean oil-related QTLs were mapped. The results demonstrated that 666 collinearity blocks were detected in the soybean genome across 20 chromosomes, and 521 collinearity relationships existed in 231 of the 242 effective soybean oil-related QTLs. This included 214 inclusion relationships and 307 intersecting relationships. Among them, the collinearity among QTLs that are related to soybean oil content was shown on a maximum of seven chromosomes and minimum of one chromosome, with the majority of QTLs having collinearity on two chromosomes. Using overlapping hotspot regions in the soybean oil QTLs with collinearity, we mined for novel oil content-related genes. Overall, we identified 23 putatively functional genes associated with oil content in soybean and annotated them using a number of annotation databases. Our findings provide a valuable framework for elucidating evolutionary relationships between soybean oil-related QTLs and lay a foundation for functional marker-assisted breeding relating to soybean oil content.
文摘Drought is becoming an increasingly important constraint limiting world's rice production (Bennett, 2003). About half of the world's rice is grown in rainfed environments where the rainfall is the major source of water sup-
文摘This is an in silico analysis of quantitative trait loci (QTLs), genes, polymorphisms, and chromosomal regions regulating hypertension in the rat genome. Utilizing PGmapper, a program that matches phenoltypes to genes, we identified 266 essential hypertension-associated genes (HyperA), and 83 of these genes contain known hypertension-associated polymorphisms (HyperAP). The majority of HyperAP have been reported in recent years. Surprisingly, only a few of these HyperAP genes have been investigated for their candidacy as the QTL for hypertension. The frequency of candidate genes within peak regions of the QTL is higher than the rest of the QTL region. We also found that QTL located in both gene-rich regions and gene-rich chromosomes contained the most candidate genes. However, the number of candidate genes within a peak region is not associated with the number of total genes in a QTL region. This data could not only facilitate a more rapid and comprehensive identification for the causal genes underlying hypertension in rats, but also provides new insights into genomic structure in regulation of hypertension.
