High-throughput single nucleotide polymorphism(SNP) arrays have emerged as essential genotyping tools,significantly accelerating breeding programs and advancing basic research.In this study,a high-throughput 10K SNP g...High-throughput single nucleotide polymorphism(SNP) arrays have emerged as essential genotyping tools,significantly accelerating breeding programs and advancing basic research.In this study,a high-throughput 10K SNP genotyping array for wax gourd was developed using genotyping by target sequencing(GBTS),featuring 10,722 SNPs evenly distributed across all 12 chromosomes,including 278 functional loci associated with key economic traits.To demonstrate its utility,genetic distances among 19 elite inbred lines were calculated from SNP data and correlated with heterosis for single fruit weight.The results revealed that greater genetic distance was associated with higher middle parent heterosis(MPH) for single fruit weight.Furthermore,56 commercial wax gourd cultivars collected from eight regions were selected and genotyped.Population structure analysis,phylogenetic analysis,and principal component analysis(PCA) collectively indicated that these cultivars fall into two major groups.Group I,comprising black or dark green skinned wax gourds,exhibited lower genetic diversity than Group II,which includes green or light green skinned varieties,reflecting shorter genetic distances within Group I.Finally,60 polymorphic SNPs were used to construct DNA fingerprints for distinguishing the 56 cultivars.As the first high-throughput genotyping platform for wax gourd,this SNP array provides an effective and powerful tool for genetic analysis.展开更多
为更好地保护、开发和利用乌饭树资源,采用基因分型测序(GBS,genotyping by sequencing)技术对采集于5个地区的70份乌饭树野生种质进行了SNP分子标记开发,利用开发的标记研究了乌饭树种质的遗传多样性和群体遗传结构。结果显示,通过测...为更好地保护、开发和利用乌饭树资源,采用基因分型测序(GBS,genotyping by sequencing)技术对采集于5个地区的70份乌饭树野生种质进行了SNP分子标记开发,利用开发的标记研究了乌饭树种质的遗传多样性和群体遗传结构。结果显示,通过测序数据分析共筛选得到9752个高质量SNP标记用于后续研究;乌饭树5个群体均具有丰富的遗传多样性,平均有效等位基因数为1.523,平均期望杂合度为0.219,平均观测杂合度为0.231,其中江苏溧阳群体的遗传多样性最高。分子方差分析显示整个群体的遗传变异主要来自个体间(65.45%)。群体间遗传分化系数显示5个群体间遗传分化程度高,其中江苏溧阳与江西上犹群体间的遗传分化系数最高,为0.406。系统进化树(邻接法)显示乌饭树种质聚类为3个进化分支,种质的聚集与其地理来源无确定性关系;群体结构分析将乌饭树种质分为3个亚群,主成分分析结果与群体结构的结果类似,不同地区的乌饭树种质在3个亚群中均有分布,显示了乌饭树资源存在着广泛的基因交流。本研究可为今后乌饭树良种选育和资源保护提供参考。展开更多
【目的】对广西玉米种质材料进行类群结构分析和核心种质构建,为广西玉米种质资源的高效利用、多样性保护及品种改良提供参考依据。【方法】利用SNP分子标记对523份具有重要育种价值的玉米种质材料进行遗传多样性分析,基于主成分判别分...【目的】对广西玉米种质材料进行类群结构分析和核心种质构建,为广西玉米种质资源的高效利用、多样性保护及品种改良提供参考依据。【方法】利用SNP分子标记对523份具有重要育种价值的玉米种质材料进行遗传多样性分析,基于主成分判别分析(Discriminant analysis of principal components,DAPC)法、K-means聚类法和系谱关系分析材料的群体结构和遗传差异;采用模拟退火算法,在30.00%~10.00%取样范围内,以5.00%梯度取样比例逐级探索构建广西玉米核心种质。【结果】通过7888个SNP分子标记分析发现,523份玉米种质材料的基因多样性(Genetic diversity,GD)平均值为0.391,多态信息含量(Polymorphism information content,PIC)平均值为0.309,遗传多样性总体上处于中度多态。基于DAPC法和K-means聚类法,可将523份玉米种质材料划分为4个类群,分别为Suwan群、墨黄群、Reid群和Non-Reid群,其遗传多态性排序为Suwan群<墨黄群<Non-Reid群<Reid群,其中,Reid群的遗传多样性最高(GD=0.398,PIC=0.313),Suwan群的多态性最低(GD=0.280,PIC=0.226)。分子方差分析结果表明,4个类群内的遗传变异差异显著,占总遗传变异的83.1%,类群间的遗传变异为16.9%,Suwan群与Non-Reid群的遗传距离最大,其次是Suwan群与Reid群,Suwan群与墨黄群的遗传距离最小。按照30.00%~10.00%的取样比例,采取模拟退火算法逐级构建核心种质,经遗传多样性分析及不同取样比例t检验,最终确定取样比例为17.20%,筛选出90份核心种质并构建形成核心种质库。【结论】利用SNP分子标记可将523份广西玉米种质材料划分为Suwan群、墨黄群、Reid群和Non-Reid群4个类群,且各类群间存在显著遗传差异,能代表广西玉米主要杂种优势类群;以17.20%的取样比例筛选形成的90份玉米核心种质库,其遗传多样性评价结果与523份玉米种质材料聚类的4个类群保持一致,具有较好的代表性。展开更多
基金supported by the Science and Technology Talent Support Project of Hunan Province,China (2022TJ-N15)the Hunan Agricultural Science and Technology Innovation Fund,China (2024CX90 and 2024CX65)the Science and Technology Innovation Program of Hunan Province,China (2021NK1006)。
文摘High-throughput single nucleotide polymorphism(SNP) arrays have emerged as essential genotyping tools,significantly accelerating breeding programs and advancing basic research.In this study,a high-throughput 10K SNP genotyping array for wax gourd was developed using genotyping by target sequencing(GBTS),featuring 10,722 SNPs evenly distributed across all 12 chromosomes,including 278 functional loci associated with key economic traits.To demonstrate its utility,genetic distances among 19 elite inbred lines were calculated from SNP data and correlated with heterosis for single fruit weight.The results revealed that greater genetic distance was associated with higher middle parent heterosis(MPH) for single fruit weight.Furthermore,56 commercial wax gourd cultivars collected from eight regions were selected and genotyped.Population structure analysis,phylogenetic analysis,and principal component analysis(PCA) collectively indicated that these cultivars fall into two major groups.Group I,comprising black or dark green skinned wax gourds,exhibited lower genetic diversity than Group II,which includes green or light green skinned varieties,reflecting shorter genetic distances within Group I.Finally,60 polymorphic SNPs were used to construct DNA fingerprints for distinguishing the 56 cultivars.As the first high-throughput genotyping platform for wax gourd,this SNP array provides an effective and powerful tool for genetic analysis.
文摘为更好地保护、开发和利用乌饭树资源,采用基因分型测序(GBS,genotyping by sequencing)技术对采集于5个地区的70份乌饭树野生种质进行了SNP分子标记开发,利用开发的标记研究了乌饭树种质的遗传多样性和群体遗传结构。结果显示,通过测序数据分析共筛选得到9752个高质量SNP标记用于后续研究;乌饭树5个群体均具有丰富的遗传多样性,平均有效等位基因数为1.523,平均期望杂合度为0.219,平均观测杂合度为0.231,其中江苏溧阳群体的遗传多样性最高。分子方差分析显示整个群体的遗传变异主要来自个体间(65.45%)。群体间遗传分化系数显示5个群体间遗传分化程度高,其中江苏溧阳与江西上犹群体间的遗传分化系数最高,为0.406。系统进化树(邻接法)显示乌饭树种质聚类为3个进化分支,种质的聚集与其地理来源无确定性关系;群体结构分析将乌饭树种质分为3个亚群,主成分分析结果与群体结构的结果类似,不同地区的乌饭树种质在3个亚群中均有分布,显示了乌饭树资源存在着广泛的基因交流。本研究可为今后乌饭树良种选育和资源保护提供参考。
文摘【目的】对广西玉米种质材料进行类群结构分析和核心种质构建,为广西玉米种质资源的高效利用、多样性保护及品种改良提供参考依据。【方法】利用SNP分子标记对523份具有重要育种价值的玉米种质材料进行遗传多样性分析,基于主成分判别分析(Discriminant analysis of principal components,DAPC)法、K-means聚类法和系谱关系分析材料的群体结构和遗传差异;采用模拟退火算法,在30.00%~10.00%取样范围内,以5.00%梯度取样比例逐级探索构建广西玉米核心种质。【结果】通过7888个SNP分子标记分析发现,523份玉米种质材料的基因多样性(Genetic diversity,GD)平均值为0.391,多态信息含量(Polymorphism information content,PIC)平均值为0.309,遗传多样性总体上处于中度多态。基于DAPC法和K-means聚类法,可将523份玉米种质材料划分为4个类群,分别为Suwan群、墨黄群、Reid群和Non-Reid群,其遗传多态性排序为Suwan群<墨黄群<Non-Reid群<Reid群,其中,Reid群的遗传多样性最高(GD=0.398,PIC=0.313),Suwan群的多态性最低(GD=0.280,PIC=0.226)。分子方差分析结果表明,4个类群内的遗传变异差异显著,占总遗传变异的83.1%,类群间的遗传变异为16.9%,Suwan群与Non-Reid群的遗传距离最大,其次是Suwan群与Reid群,Suwan群与墨黄群的遗传距离最小。按照30.00%~10.00%的取样比例,采取模拟退火算法逐级构建核心种质,经遗传多样性分析及不同取样比例t检验,最终确定取样比例为17.20%,筛选出90份核心种质并构建形成核心种质库。【结论】利用SNP分子标记可将523份广西玉米种质材料划分为Suwan群、墨黄群、Reid群和Non-Reid群4个类群,且各类群间存在显著遗传差异,能代表广西玉米主要杂种优势类群;以17.20%的取样比例筛选形成的90份玉米核心种质库,其遗传多样性评价结果与523份玉米种质材料聚类的4个类群保持一致,具有较好的代表性。
