Gene expression profiling at early stages(0～2 DPA) of fiber development in Gossypium hirsutum identified a number of transcription factors which were down regulated in fiberless mutants relative to wild type controls...Gene expression profiling at early stages(0～2 DPA) of fiber development in Gossypium hirsutum identified a number of transcription factors which were down regulated in fiberless mutants relative to wild type controls and which could play a role in controlling early fiber development.Chief among these was GhMYB25,a Mixta-like MYB gene.Transgenic GhMYB25-silenced cotton展开更多
Background:Meta-analysis of quantitative trait locus(QTL)is a computational technique to identify consensus QTL and refine QTL positions on the consensus map from multiple mapping studies.The combination of meta-QTL i...Background:Meta-analysis of quantitative trait locus(QTL)is a computational technique to identify consensus QTL and refine QTL positions on the consensus map from multiple mapping studies.The combination of meta-QTL intervals,significant SNPs and transcriptome analysis has been widely used to identify candidate genes in various plants.Results:In our study,884 QTLs associated with cotton fiber quality traits from 12 studies were used for meta-QTL analysis based on reference genome TM-1,as a result,74 meta-QTLs were identified,including 19 meta-QTLs for fiber length;18 meta-QTLs for fiber strength;11 meta-QTLs for fiber uniformity;11 meta-QTLs for fiber elongation;and 15 meta-QTLs for micronaire.Combined with 8589 significant single nucleotide polymorphisms associated with fiber quality traits collected from 15 studies,297 candidate genes were identified in the meta-QTL intervals,20 of which showed high expression levels specifically in the developing fibers.According to the function annotations,some of the 20 key candidate genes are associated with the fiber development.Conclusions:This study provides not only stable QTLs used for marker-assisted selection,but also candidate genes to uncover the molecular mechanisms for cotton fiber development.展开更多
Previous study indicated that the thermo-sensitive genic malesterile(TGMS) gene in rice was regulated by temperature.TGMS rice plays an important role in hybrid rice production,because the application of the TGMS syst...Previous study indicated that the thermo-sensitive genic malesterile(TGMS) gene in rice was regulated by temperature.TGMS rice plays an important role in hybrid rice production,because the application of the TGMS system in two-line breeding is laborsaving,timesaving,simple,inexpensive,efficient,and eliminating the limitations of the cytoplasmic male sterility(CMS) system.'AnnongS' is the first discovered and deeply studied TGMS rice lines in China.'AnnongS-1' and 'Y58S',two derivatives of TGMS line AnnongS,were both controlled by a single recessive gene named tms5,which was genetically mapped on chromosome 2.In this study,three populations('AnnongS-1' × 'Nanjing11','Y58S' × 'Q611',and 'Y58S' × 'Guanghui122') were developed and used for the molecular fine mapping of the tms5 gene.By analyzing recombination events in the sterile individuals using a total of 125 probes covering the tms5 region,the tms5 gene was physically mapped to a 19-kb DNA fragment between two markers 4039-1 and 4039-2,which were located on the BAC clone AP004039.After the construction of the physical map between two markers 4039-1 and 4039-2,a member(ONAC023) of the NAC(NAM-ATAF-CUC-related) gene family was identified as the candidate gene of the tms5 gene.展开更多
【目的】对金定鸭与台湾褐色菜鸭进行选择信号分析,挖掘这2个蛋鸭品种在长期进化过程中受到强烈选择的重要经济性状相关候选基因,为揭示优异性状形成的遗传差异奠定基础。【方法】选取金定鸭和台湾褐色菜鸭各30只进行全基因组重测序,经...【目的】对金定鸭与台湾褐色菜鸭进行选择信号分析,挖掘这2个蛋鸭品种在长期进化过程中受到强烈选择的重要经济性状相关候选基因,为揭示优异性状形成的遗传差异奠定基础。【方法】选取金定鸭和台湾褐色菜鸭各30只进行全基因组重测序,经过滤获取高质量单核苷酸多态性位点(SNPs)后,对其进行主成分分析(PCA),确定其遗传分化情况;然后采用群体遗传分化指数(Fst)和群体核酸多样性比值(πratio)2种方法综合筛选金定鸭和台湾褐色菜鸭的受选择信号,分析其遗传差异。【结果】金定鸭和台湾褐色菜鸭重测序分别获得5.68和5.59 Gb高质量数据,分别检测到152238286和155009562个SNPs,其SNP位点分布相似。主成分分析结果显示,金定鸭和台湾褐色菜鸭显著分化;以100 kb为窗口、10 kb为步长分别计算Fst与πratio值,将Fst top 5%(Fst>0.482)与πratio top 5%&bottom 5%(0<πratio≤0.47&πratio≥3.00)作为信号重叠区域,共注释到208个候选基因。对这208个候选基因进行GO与KEGG富集分析,发现金定鸭在免疫、脂质代谢、肌肉生长发育等方面受到更强烈的选择,筛选到IL15、CCL3、CD180、AKT1、PPARGC1A、PRKAA1、FASN、PIK3R1等功能基因。【结论】金定鸭和台湾褐色菜鸭显著分化,金定鸭在免疫、脂质代谢、肌肉生长发育等方面受到强烈选择。展开更多
旨在探究影响猪达100 kg体重日龄(age at 100 kg,AGE)和达100 kg体重平均日增重(average daily gain at 100 kg,ADG)的候选基因。本研究采集了来自大白、长白和杜洛克3个品种的共计4593头健康成年猪的耳组织作为试验材料,其中公猪2563头...旨在探究影响猪达100 kg体重日龄(age at 100 kg,AGE)和达100 kg体重平均日增重(average daily gain at 100 kg,ADG)的候选基因。本研究采集了来自大白、长白和杜洛克3个品种的共计4593头健康成年猪的耳组织作为试验材料,其中公猪2563头,母猪2030头。通过记录猪只的日龄和体重,计算校正AGE和ADG。通过酚氯仿法提取样品DNA,利用“中芯一号”50K SNP芯片对样本进行基因分型,并对质控后的SNPs进行基因型填充,将SNPs位点数从4万填充至800万。随后,利用GEMMA混合线性模型对AGE和ADG性状进行填充前后的全基因组关联分析,使用BEDTools在显著位点上、下游1 Mb范围查找候选基因。同时,结合PigGTEx中的34个组织的表达量数量性状位点数据,使用R软件进行共定位分析,挖掘与GWAS信号共享同一因果变异的基因,通过GWAS和共定位分析,确定AGE和ADG性状的候选基因。GWAS分析结果显示,AGE与ADG性状的显著SNP为1号染色体上的1_270827213。在该位点上、下游1 Mb范围内,共鉴定到32个基因。共定位分析结果显示,对于AGE性状,有10个基因的eQTL信号与GWAS信号共定位。对于ADG性状,有11个基因的eQTL信号与GWAS信号共定位。最终,确定了CRAT、GPR 107和USP 20这3个基因作为AGE的候选基因,确定了CRAT、GPR107、USP20、FNBP1、PTGES和HMCN 2这6个基因作为ADG的候选基因。本研究为猪品种改良提供了分子标记,对猪生长相关性状功能基因挖掘奠定基础。展开更多
适当降低株高可以提高植物的养分利用效率和抗倒伏性,对高粱的高产和稳产具有重要意义。为揭示高粱株高遗传机制,本研究以242份中国高粱为研究对象,利用2,015,850个单核苷酸多态性(SNP)标记,在7个不同环境条件下对株高、节间数及节间长...适当降低株高可以提高植物的养分利用效率和抗倒伏性,对高粱的高产和稳产具有重要意义。为揭示高粱株高遗传机制,本研究以242份中国高粱为研究对象,利用2,015,850个单核苷酸多态性(SNP)标记,在7个不同环境条件下对株高、节间数及节间长度进行全基因组关联分析(Genome-wide association study,GWAS)。表型调查表明,株高、节间数和节间长度的表型变异系数在13.47%~30.06%之间,在所有环境下的偏度和峰度的绝对值均小于1。利用2种不同的关联模型(Blink和FarmCPU)对株高、节间数及节间长度进行GWAS分析,在10条染色体上共鉴定出118个与这3个性状显著相关的数量性状核苷酸(QTN)。其中,与株高、节间数及节间长度显著相关的QTN分别为60个、37个和32个,株高与节间数、节间长度共定位QTN分别有8个和3个。通过对候选基因的序列分析和功能注释,在12个QTN置信区间或附近鉴定出14个候选基因,它们与水稻和玉米中参与糖代谢、激素合成与信号传递以及细胞分裂的基因同源。选择性消除分析揭示,位于1号染色体的候选基因Sobic.001G510400在中国南北高粱群体中受到强烈选择,形成了以北方矮秆高粱为主的单倍型Hap1和以南方高秆高粱为主的单倍型Hap2。携有Hap1的北方种质871255和携有Hap2的南方种质红缨子之间,该基因表达存在显著差异。本研究结果为中国高粱品种株高遗传改良提供了理论依据。展开更多
文摘Gene expression profiling at early stages(0～2 DPA) of fiber development in Gossypium hirsutum identified a number of transcription factors which were down regulated in fiberless mutants relative to wild type controls and which could play a role in controlling early fiber development.Chief among these was GhMYB25,a Mixta-like MYB gene.Transgenic GhMYB25-silenced cotton
基金This work was supported by the National Natural Science Foundation of China(31760402)Public Welfare Research Projects in the Autonomous Region(KY2019002)Special Programs for New Varieties Cultivation of Shihezi University(YZZX201701).
文摘Background:Meta-analysis of quantitative trait locus(QTL)is a computational technique to identify consensus QTL and refine QTL positions on the consensus map from multiple mapping studies.The combination of meta-QTL intervals,significant SNPs and transcriptome analysis has been widely used to identify candidate genes in various plants.Results:In our study,884 QTLs associated with cotton fiber quality traits from 12 studies were used for meta-QTL analysis based on reference genome TM-1,as a result,74 meta-QTLs were identified,including 19 meta-QTLs for fiber length;18 meta-QTLs for fiber strength;11 meta-QTLs for fiber uniformity;11 meta-QTLs for fiber elongation;and 15 meta-QTLs for micronaire.Combined with 8589 significant single nucleotide polymorphisms associated with fiber quality traits collected from 15 studies,297 candidate genes were identified in the meta-QTL intervals,20 of which showed high expression levels specifically in the developing fibers.According to the function annotations,some of the 20 key candidate genes are associated with the fiber development.Conclusions:This study provides not only stable QTLs used for marker-assisted selection,but also candidate genes to uncover the molecular mechanisms for cotton fiber development.
文摘Previous study indicated that the thermo-sensitive genic malesterile(TGMS) gene in rice was regulated by temperature.TGMS rice plays an important role in hybrid rice production,because the application of the TGMS system in two-line breeding is laborsaving,timesaving,simple,inexpensive,efficient,and eliminating the limitations of the cytoplasmic male sterility(CMS) system.'AnnongS' is the first discovered and deeply studied TGMS rice lines in China.'AnnongS-1' and 'Y58S',two derivatives of TGMS line AnnongS,were both controlled by a single recessive gene named tms5,which was genetically mapped on chromosome 2.In this study,three populations('AnnongS-1' × 'Nanjing11','Y58S' × 'Q611',and 'Y58S' × 'Guanghui122') were developed and used for the molecular fine mapping of the tms5 gene.By analyzing recombination events in the sterile individuals using a total of 125 probes covering the tms5 region,the tms5 gene was physically mapped to a 19-kb DNA fragment between two markers 4039-1 and 4039-2,which were located on the BAC clone AP004039.After the construction of the physical map between two markers 4039-1 and 4039-2,a member(ONAC023) of the NAC(NAM-ATAF-CUC-related) gene family was identified as the candidate gene of the tms5 gene.
文摘【目的】对金定鸭与台湾褐色菜鸭进行选择信号分析,挖掘这2个蛋鸭品种在长期进化过程中受到强烈选择的重要经济性状相关候选基因,为揭示优异性状形成的遗传差异奠定基础。【方法】选取金定鸭和台湾褐色菜鸭各30只进行全基因组重测序,经过滤获取高质量单核苷酸多态性位点(SNPs)后,对其进行主成分分析(PCA),确定其遗传分化情况;然后采用群体遗传分化指数(Fst)和群体核酸多样性比值(πratio)2种方法综合筛选金定鸭和台湾褐色菜鸭的受选择信号,分析其遗传差异。【结果】金定鸭和台湾褐色菜鸭重测序分别获得5.68和5.59 Gb高质量数据,分别检测到152238286和155009562个SNPs,其SNP位点分布相似。主成分分析结果显示,金定鸭和台湾褐色菜鸭显著分化;以100 kb为窗口、10 kb为步长分别计算Fst与πratio值,将Fst top 5%(Fst>0.482)与πratio top 5%&bottom 5%(0<πratio≤0.47&πratio≥3.00)作为信号重叠区域,共注释到208个候选基因。对这208个候选基因进行GO与KEGG富集分析,发现金定鸭在免疫、脂质代谢、肌肉生长发育等方面受到更强烈的选择,筛选到IL15、CCL3、CD180、AKT1、PPARGC1A、PRKAA1、FASN、PIK3R1等功能基因。【结论】金定鸭和台湾褐色菜鸭显著分化,金定鸭在免疫、脂质代谢、肌肉生长发育等方面受到强烈选择。
文摘适当降低株高可以提高植物的养分利用效率和抗倒伏性,对高粱的高产和稳产具有重要意义。为揭示高粱株高遗传机制,本研究以242份中国高粱为研究对象,利用2,015,850个单核苷酸多态性(SNP)标记,在7个不同环境条件下对株高、节间数及节间长度进行全基因组关联分析(Genome-wide association study,GWAS)。表型调查表明,株高、节间数和节间长度的表型变异系数在13.47%~30.06%之间,在所有环境下的偏度和峰度的绝对值均小于1。利用2种不同的关联模型(Blink和FarmCPU)对株高、节间数及节间长度进行GWAS分析,在10条染色体上共鉴定出118个与这3个性状显著相关的数量性状核苷酸(QTN)。其中,与株高、节间数及节间长度显著相关的QTN分别为60个、37个和32个,株高与节间数、节间长度共定位QTN分别有8个和3个。通过对候选基因的序列分析和功能注释,在12个QTN置信区间或附近鉴定出14个候选基因,它们与水稻和玉米中参与糖代谢、激素合成与信号传递以及细胞分裂的基因同源。选择性消除分析揭示,位于1号染色体的候选基因Sobic.001G510400在中国南北高粱群体中受到强烈选择,形成了以北方矮秆高粱为主的单倍型Hap1和以南方高秆高粱为主的单倍型Hap2。携有Hap1的北方种质871255和携有Hap2的南方种质红缨子之间,该基因表达存在显著差异。本研究结果为中国高粱品种株高遗传改良提供了理论依据。
