以317份贵州香禾糯种质资源为试验材料,10份籼稻材料为对照,采用1 K mGPS SNP芯片对供试材料的遗传多样性和遗传结构进行分析,在此基础上构建贵州香禾糯核心种质并进行评价。结果表明,1 K mGPS SNP芯片在317份香禾糯材料中共获得731个...以317份贵州香禾糯种质资源为试验材料,10份籼稻材料为对照,采用1 K mGPS SNP芯片对供试材料的遗传多样性和遗传结构进行分析,在此基础上构建贵州香禾糯核心种质并进行评价。结果表明,1 K mGPS SNP芯片在317份香禾糯材料中共获得731个良好多态性SNP位点,多态性标记比例为17.89%,最小等位基因频率为0.0505~0.5000,观测杂合度为0~0.6940,期望杂合度为0.0959~0.5000,多态性信息含量为0.0913~0.5736。基于IBS遗传距离的NJ聚类分析将327份水稻材料分为籼、粳两个亚群,其中317份贵州香禾糯划分为粳稻亚群。利用Core Hunter 3对香禾糯原种质设置5%、10%、15%、20%、25%、30%等6种抽样比例,遗传多样性参数的t检验表明,15%的抽样比例即可保持遗传多样性参数的最大化,同时剔除了许多冗余材料,最终确定47份香禾糯资源为构建的核心种质。展开更多
Considering the advantages of single nucleotide polymorphisms（SNP） in genotyping and variety identification, the first set public SNP markers at Cotton Marker Database（http：//www.cottonmarker.org/） were validated...Considering the advantages of single nucleotide polymorphisms（SNP） in genotyping and variety identification, the first set public SNP markers at Cotton Marker Database（http：//www.cottonmarker.org/） were validated and screened across standard varieties of cotton distinctness, uniformity and stability（DUS） test, aiming to obtain an appropriate set of core SNP markers suitable for upland cotton cultivars in China. A total of 399 out of 1 005 SNPs from 270 loci including 170 insertions-deletions（In Dels） were evaluated for their polymorphisms among 30 standard varieties using Sanger sequencing. As a result, 147 loci were sequenced successfully, 377 SNPs and 49 In Dels markers were obtained. Among the 377 SNP markers, 333 markers（88.3%） were polymorphic between Gossypium hirsutum and G. barbadense, while 164 markers（43.5%） were polymorphic within upland cotton. As for In Del markers, the polymorphic rate is relatively lower than that of SNP both between species and within species. The homozygous DNA locus ratio of 121 SNPs was higher than 86.2% while that of other 43 SNPs was less than 70%. Only 64 SNPs displayed completely homozygous genotypes among all of the detected upland cotton varieties with 100% homozygous DNA locus ratio. At last, a set of 23 pairs of core SNPs were achieved in view of avoidance of linkage, with polymorphism information content（PIC） values varying from 0.21 to 0.38 with an average of 0.28. Genotype characteristics and genetic diversity were analyzed based on the set of core markers, while 40 pairs of core simple-sequence repeats（SSR） primers comprised of 10 sets of four multiplex PCR combinations were also used for analysis based on fluorescence detection system. Comparison results indicated that the genetic diversity level was almost equal, while various varieties were significantly different from each other. Genetic relationship revealed by SSR markers is related to geographic source to a certain extent. Meanwhile clustering results analyzed by SNP markers are more consistent with kinship, which demonstrated that the screen strategy for core SNP marker is effective.展开更多
纯度是玉米种子质量的重要指标之一,尤其杂交种自交株是影响田间产量的关键因素。KASP(kompetitive allele specific PCR)技术具有高通量、低成本的优点,适用于种子纯度检测。本研究基于12套杂交种及其父母本的三联体样本及335份玉米杂...纯度是玉米种子质量的重要指标之一,尤其杂交种自交株是影响田间产量的关键因素。KASP(kompetitive allele specific PCR)技术具有高通量、低成本的优点,适用于种子纯度检测。本研究基于12套杂交种及其父母本的三联体样本及335份玉米杂交种国家审定标准样品SNP指纹,从384个SNP基础位点筛选获得60个候选位点,位点转化为KASP引物的成功率为95%。综合考虑引物双亲互补率、多态性、稳定性和分型效果等多项指标,最终确定20个引物作为玉米杂交种纯度鉴定的核心引物,能够有效鉴定99.7%供试样品纯度。对于待测样品京科968通过SNP-DNA指纹数据库查询,并选择双亲互补型引物进行纯度鉴定。在检测的110个个体中,共检出1个自交苗和2个异型株,纯度为97.3%。同时,基于纯度核心引物对批量样品检测建立高通量纯度检测方案,具有快捷、准确、高通量和低成本的特点,为政府监管和企业提供了更多纯度鉴定方案的选择。展开更多
文摘以317份贵州香禾糯种质资源为试验材料,10份籼稻材料为对照,采用1 K mGPS SNP芯片对供试材料的遗传多样性和遗传结构进行分析,在此基础上构建贵州香禾糯核心种质并进行评价。结果表明,1 K mGPS SNP芯片在317份香禾糯材料中共获得731个良好多态性SNP位点,多态性标记比例为17.89%,最小等位基因频率为0.0505~0.5000,观测杂合度为0~0.6940,期望杂合度为0.0959~0.5000,多态性信息含量为0.0913~0.5736。基于IBS遗传距离的NJ聚类分析将327份水稻材料分为籼、粳两个亚群,其中317份贵州香禾糯划分为粳稻亚群。利用Core Hunter 3对香禾糯原种质设置5%、10%、15%、20%、25%、30%等6种抽样比例,遗传多样性参数的t检验表明,15%的抽样比例即可保持遗传多样性参数的最大化,同时剔除了许多冗余材料,最终确定47份香禾糯资源为构建的核心种质。
基金supported by the the Basic R&D Operation Special Fund for the Central Level, Non-Profit, Scientific Research Institutes, Ministry of Agriculture, China (1610162015A08)the National Key Technologies R&D Program of China during the 12th Five-Year Plan period (2011BAD35B09)
文摘Considering the advantages of single nucleotide polymorphisms（SNP） in genotyping and variety identification, the first set public SNP markers at Cotton Marker Database（http：//www.cottonmarker.org/） were validated and screened across standard varieties of cotton distinctness, uniformity and stability（DUS） test, aiming to obtain an appropriate set of core SNP markers suitable for upland cotton cultivars in China. A total of 399 out of 1 005 SNPs from 270 loci including 170 insertions-deletions（In Dels） were evaluated for their polymorphisms among 30 standard varieties using Sanger sequencing. As a result, 147 loci were sequenced successfully, 377 SNPs and 49 In Dels markers were obtained. Among the 377 SNP markers, 333 markers（88.3%） were polymorphic between Gossypium hirsutum and G. barbadense, while 164 markers（43.5%） were polymorphic within upland cotton. As for In Del markers, the polymorphic rate is relatively lower than that of SNP both between species and within species. The homozygous DNA locus ratio of 121 SNPs was higher than 86.2% while that of other 43 SNPs was less than 70%. Only 64 SNPs displayed completely homozygous genotypes among all of the detected upland cotton varieties with 100% homozygous DNA locus ratio. At last, a set of 23 pairs of core SNPs were achieved in view of avoidance of linkage, with polymorphism information content（PIC） values varying from 0.21 to 0.38 with an average of 0.28. Genotype characteristics and genetic diversity were analyzed based on the set of core markers, while 40 pairs of core simple-sequence repeats（SSR） primers comprised of 10 sets of four multiplex PCR combinations were also used for analysis based on fluorescence detection system. Comparison results indicated that the genetic diversity level was almost equal, while various varieties were significantly different from each other. Genetic relationship revealed by SSR markers is related to geographic source to a certain extent. Meanwhile clustering results analyzed by SNP markers are more consistent with kinship, which demonstrated that the screen strategy for core SNP marker is effective.
文摘纯度是玉米种子质量的重要指标之一,尤其杂交种自交株是影响田间产量的关键因素。KASP(kompetitive allele specific PCR)技术具有高通量、低成本的优点,适用于种子纯度检测。本研究基于12套杂交种及其父母本的三联体样本及335份玉米杂交种国家审定标准样品SNP指纹,从384个SNP基础位点筛选获得60个候选位点,位点转化为KASP引物的成功率为95%。综合考虑引物双亲互补率、多态性、稳定性和分型效果等多项指标,最终确定20个引物作为玉米杂交种纯度鉴定的核心引物,能够有效鉴定99.7%供试样品纯度。对于待测样品京科968通过SNP-DNA指纹数据库查询,并选择双亲互补型引物进行纯度鉴定。在检测的110个个体中,共检出1个自交苗和2个异型株,纯度为97.3%。同时,基于纯度核心引物对批量样品检测建立高通量纯度检测方案,具有快捷、准确、高通量和低成本的特点,为政府监管和企业提供了更多纯度鉴定方案的选择。
