Soybean seed isoflavones are a type of secondary metabolites that can provide health and nutrition benefits for humans. In our previous study, a stable quantitative trait locus(QTL) qIF05-1 controlling the seed isofla...Soybean seed isoflavones are a type of secondary metabolites that can provide health and nutrition benefits for humans. In our previous study, a stable quantitative trait locus(QTL) qIF05-1 controlling the seed isoflavone content in soybean was detected on chromosome(Chr.) 05 in a recombinant inbred line(RIL) population from a cross of Huachun 2×Wayao. In this study, the parental lines were re-sequenced using the Illumina Solexa System with deep coverage. A total of 63,099 polymorphic long insertions and deletions(InDels)(≥15 bp)were identified between the parents Huachun 2 and Wayao. The InDels were unevenly distributed on 20chromosomes of soybean, varying from 1,826 in Chr. 12 to 4,544 in Chr. 18. A total of 10,002 long InDels(15.85% of total) were located in genic regions, including 1,139 large-effect long InDels which resulted in truncated or elongated protein sequences. In the qIF05-1 region, 68 long InDels were detected between the two parents. Using a progeny recombination experiment and genotype analysis, the qIF05-1 locus was mapped into a 102.2 kb genomic region, and this region contained 12 genes. By RNA-seq data analysis, genome sequence comparison and functional validation through ectopic expression in Arabidopsis thaliana, Glyma.05G208300(described as GmEGL3), which is a basic helix-loop-helix(bHLH) transcription factor in plants, emerged as the most likely confirmed gene in qIF05-1. These long InDels can be used as a type of complementary genetic method for QTL fine mapping, and they can facilitate genetic studies and molecular-assisted selection breeding in soybean.展开更多
Somatic mutations accumulate with age in human tissues.Clonal amplifi-cation of some mutations causes cancers and other diseases.However,it is unclear if random mutation accumulation affects cellular function without ...Somatic mutations accumulate with age in human tissues.Clonal amplifi-cation of some mutations causes cancers and other diseases.However,it is unclear if random mutation accumulation affects cellular function without clonal amplification.We tested this in cell culture,avoiding the lim-itation that mutation accumulation in vivo leads to cancer.展开更多
陕北白绒山羊是我国特色绒肉兼用型山羊品种,其生长性状遗传改良进程相对滞后且表型稳定性不足,亟待筛选与生长性状关联的高效分子标记以加速陕北白绒山羊高效选育。成纤维细胞生长因子受体1(FGFR1)作为调控细胞增殖与分化的关键基因,...陕北白绒山羊是我国特色绒肉兼用型山羊品种,其生长性状遗传改良进程相对滞后且表型稳定性不足,亟待筛选与生长性状关联的高效分子标记以加速陕北白绒山羊高效选育。成纤维细胞生长因子受体1(FGFR1)作为调控细胞增殖与分化的关键基因,其遗传变异可能影响山羊生长性能。因此,本研究旨在探究FGFR1在陕北白绒山羊各组织中的表达水平,分析FGFR1 Indel变异与陕北白绒山羊生长性状的相关性。以1332只成年陕北白绒山羊为对象,采集耳组织与14种组织样本,通过PCR扩增和琼脂糖凝胶电泳检测FGFR1基因InDel分型,利用qRT-PCR分析组织表达谱,并通过一般线性模型分析基因型与生长性状的关联性。结果显示,FGFR1基因在各组织中广泛表达,其中睾丸和大脑表达水平显著高于其它组织(P<0.05);群体遗传变异检测到P5位点存在22 bp InDel多态性,形成纯合插入型(Ⅱ,220 bp)、杂合型(ID,220/198 bp)及纯合缺失型(DD,198 bp)三种基因型,等位基因频率分别为0.822(I)和0.178(D),群体多态信息含量(PIC)为0.25,属中度多态(0.25≤PIC≤0.5);关联分析结果显示,II和ID基因型个体的胸围显著大于DD型(P<0.05),而ID型绒细度显著低于其他基因型(P<0.05)。综上所述,FGFR1基因22 bp InDel变异可作为陕北白绒山羊胸围与绒细度的候选分子标记。本研究为山羊分子标记辅助选择提供了理论依据,对加快绒山羊遗传改良进程具有重要意义。展开更多
Soybean(Glycine max L.)is a globally vital crop for oil production and food security.High-quality genomic resources are instrumental for both functional genomics and breeding.Here,we report a near-complete,high-qualit...Soybean(Glycine max L.)is a globally vital crop for oil production and food security.High-quality genomic resources are instrumental for both functional genomics and breeding.Here,we report a near-complete,high-quality genome assembly of the elite cultivar Tianlong 1(TL1),featuring fully resolved telomeres and centromeres,as well as a gap-free assembly of 14 of its 20 chromosomes.On the basis of the genome assembly,we generate an ethyl methanesulfonate(EMS)-mutagenized population comprising 2555 M7 plants.Whole-genome resequencing of 288 EMS mutants uncovers 1,163,869 high-confidence single-nucleotide polymorphisms(SNPs)and 542,709 insertions/deletions(InDels),achieving 91.89%coverage of predicted protein-coding genes.Phenotypic screening demonstrates robust genotype–phenotype associations,with two nonsynonymous mutants displaying pronounced defects in seed and leaf development.Collectively,the chromosome-scale TL1 genome assembly and the extensively characterized mutant population establish valuable resources for functional genomics and precision breeding in soybean and related legume species.展开更多
Genetic improvement of meat production traits has always been the primary goal of pig breeding.Geographical isolation,natural and artificial selection led to significant differences in the phenotypes of meat productio...Genetic improvement of meat production traits has always been the primary goal of pig breeding.Geographical isolation,natural and artificial selection led to significant differences in the phenotypes of meat production traits between Chinese local pigs and Western commercial pigs.Comparative genomics and transcriptomics analysis provided powerful tools to identify genetic variants and genes associated with skeletal muscle growth.However,the number of available genetic variants and genes are still limited.In this study,a comprehensive comparison of transcriptomes showed that ribosomal protein S27-like(RPS27L)gene was highly expressed in skeletal muscle and up-regulated in Chinese local pigs when compared with Western commercial pigs.Functional analysis revealed that overexpression of RPS27L promoted myoblast proliferation and repressed differentiation in pig skeletal muscle cells.Conversely,the knockdown of RPS27L led to the inhibition of myoblast proliferation and the promotion of differentiation.Notably,a 13-bp insertion-deletion(InDel)mutation was identified within the RPS27L promoter,inserted in Chinese local breeds and predominantly deleted in Western commercial breeds.Luciferase reporter assay suggested this InDel modulated RPS27L expression by influencing transcription factor 3(TCF3)and myogenic differentiation antigen(MYOD)binding to the promoter.Furthermore,a positive correlation was observed between RPS27L expression and backfat thickness.Association studies demonstrated this InDel was significantly associated with the body weight of pigs at the age of 240 d.Together,our results suggested that RPS27L was a regulator of skeletal muscle development and growth,and was a candidate marker for improving meat production traits in pigs.This study not only provided a biomarker for animal breeding,but also was helpful for understanding skeletal muscle development and muscular disease in humans.展开更多
基金supported by the China Agriculture Research System of MOF and MARA(CARS-04-PS12)the Research and Development Program in the Key-Areas of Guangdong Province,China(2020B020220008)the Guangdong Agricultural Research System,China(2023KJ136-03).
文摘Soybean seed isoflavones are a type of secondary metabolites that can provide health and nutrition benefits for humans. In our previous study, a stable quantitative trait locus(QTL) qIF05-1 controlling the seed isoflavone content in soybean was detected on chromosome(Chr.) 05 in a recombinant inbred line(RIL) population from a cross of Huachun 2×Wayao. In this study, the parental lines were re-sequenced using the Illumina Solexa System with deep coverage. A total of 63,099 polymorphic long insertions and deletions(InDels)(≥15 bp)were identified between the parents Huachun 2 and Wayao. The InDels were unevenly distributed on 20chromosomes of soybean, varying from 1,826 in Chr. 12 to 4,544 in Chr. 18. A total of 10,002 long InDels(15.85% of total) were located in genic regions, including 1,139 large-effect long InDels which resulted in truncated or elongated protein sequences. In the qIF05-1 region, 68 long InDels were detected between the two parents. Using a progeny recombination experiment and genotype analysis, the qIF05-1 locus was mapped into a 102.2 kb genomic region, and this region contained 12 genes. By RNA-seq data analysis, genome sequence comparison and functional validation through ectopic expression in Arabidopsis thaliana, Glyma.05G208300(described as GmEGL3), which is a basic helix-loop-helix(bHLH) transcription factor in plants, emerged as the most likely confirmed gene in qIF05-1. These long InDels can be used as a type of complementary genetic method for QTL fine mapping, and they can facilitate genetic studies and molecular-assisted selection breeding in soybean.
基金supported by the American Federation for Aging Research(the Sagol Network GerOmic Award for Junior Faculty)the US National Institutes of Health(P01AG017242,P01 AG047200,P01 AI172501,P01HL132825,P01 HL160476,P30 AG038072,R00 AG056656,U01 ES029519,U01 HL145560,and U19 AG056278)+2 种基金the University of Minnesota(Fesler-Lampert Chair for Aging Studies)the Veteran’s Affairs Medical Center of Boston(36C24122N0769)the European Union’s Horizon 2020 Research and Innovation Programme(810115-DYNASNET).
文摘Somatic mutations accumulate with age in human tissues.Clonal amplifi-cation of some mutations causes cancers and other diseases.However,it is unclear if random mutation accumulation affects cellular function without clonal amplification.We tested this in cell culture,avoiding the lim-itation that mutation accumulation in vivo leads to cancer.
文摘陕北白绒山羊是我国特色绒肉兼用型山羊品种,其生长性状遗传改良进程相对滞后且表型稳定性不足,亟待筛选与生长性状关联的高效分子标记以加速陕北白绒山羊高效选育。成纤维细胞生长因子受体1(FGFR1)作为调控细胞增殖与分化的关键基因,其遗传变异可能影响山羊生长性能。因此,本研究旨在探究FGFR1在陕北白绒山羊各组织中的表达水平,分析FGFR1 Indel变异与陕北白绒山羊生长性状的相关性。以1332只成年陕北白绒山羊为对象,采集耳组织与14种组织样本,通过PCR扩增和琼脂糖凝胶电泳检测FGFR1基因InDel分型,利用qRT-PCR分析组织表达谱,并通过一般线性模型分析基因型与生长性状的关联性。结果显示,FGFR1基因在各组织中广泛表达,其中睾丸和大脑表达水平显著高于其它组织(P<0.05);群体遗传变异检测到P5位点存在22 bp InDel多态性,形成纯合插入型(Ⅱ,220 bp)、杂合型(ID,220/198 bp)及纯合缺失型(DD,198 bp)三种基因型,等位基因频率分别为0.822(I)和0.178(D),群体多态信息含量(PIC)为0.25,属中度多态(0.25≤PIC≤0.5);关联分析结果显示,II和ID基因型个体的胸围显著大于DD型(P<0.05),而ID型绒细度显著低于其他基因型(P<0.05)。综上所述,FGFR1基因22 bp InDel变异可作为陕北白绒山羊胸围与绒细度的候选分子标记。本研究为山羊分子标记辅助选择提供了理论依据,对加快绒山羊遗传改良进程具有重要意义。
基金supported by the National Natural Science Foundation of China(31970344)Joint Funds of the Natural Science Foundation of Hainan Province,China(2021JJLH0065).
文摘Soybean(Glycine max L.)is a globally vital crop for oil production and food security.High-quality genomic resources are instrumental for both functional genomics and breeding.Here,we report a near-complete,high-quality genome assembly of the elite cultivar Tianlong 1(TL1),featuring fully resolved telomeres and centromeres,as well as a gap-free assembly of 14 of its 20 chromosomes.On the basis of the genome assembly,we generate an ethyl methanesulfonate(EMS)-mutagenized population comprising 2555 M7 plants.Whole-genome resequencing of 288 EMS mutants uncovers 1,163,869 high-confidence single-nucleotide polymorphisms(SNPs)and 542,709 insertions/deletions(InDels),achieving 91.89%coverage of predicted protein-coding genes.Phenotypic screening demonstrates robust genotype–phenotype associations,with two nonsynonymous mutants displaying pronounced defects in seed and leaf development.Collectively,the chromosome-scale TL1 genome assembly and the extensively characterized mutant population establish valuable resources for functional genomics and precision breeding in soybean and related legume species.
基金supported by the Sustainable Development Special Project from Shenzhen,China(KCXFZ20201221173213037)the National Natural Science Foundation of China(32172697 and U23A20229)+1 种基金the Guangdong Provincial Natural Science Foundation(2021A1515011336)the Agricultural Science and Technology Innovation Program,China(CAASZDRW202406)。
文摘Genetic improvement of meat production traits has always been the primary goal of pig breeding.Geographical isolation,natural and artificial selection led to significant differences in the phenotypes of meat production traits between Chinese local pigs and Western commercial pigs.Comparative genomics and transcriptomics analysis provided powerful tools to identify genetic variants and genes associated with skeletal muscle growth.However,the number of available genetic variants and genes are still limited.In this study,a comprehensive comparison of transcriptomes showed that ribosomal protein S27-like(RPS27L)gene was highly expressed in skeletal muscle and up-regulated in Chinese local pigs when compared with Western commercial pigs.Functional analysis revealed that overexpression of RPS27L promoted myoblast proliferation and repressed differentiation in pig skeletal muscle cells.Conversely,the knockdown of RPS27L led to the inhibition of myoblast proliferation and the promotion of differentiation.Notably,a 13-bp insertion-deletion(InDel)mutation was identified within the RPS27L promoter,inserted in Chinese local breeds and predominantly deleted in Western commercial breeds.Luciferase reporter assay suggested this InDel modulated RPS27L expression by influencing transcription factor 3(TCF3)and myogenic differentiation antigen(MYOD)binding to the promoter.Furthermore,a positive correlation was observed between RPS27L expression and backfat thickness.Association studies demonstrated this InDel was significantly associated with the body weight of pigs at the age of 240 d.Together,our results suggested that RPS27L was a regulator of skeletal muscle development and growth,and was a candidate marker for improving meat production traits in pigs.This study not only provided a biomarker for animal breeding,but also was helpful for understanding skeletal muscle development and muscular disease in humans.
