Comprehensive genotyping of the USA national maize inbred seed bank.
Comprehensive genotyping of the USA national maize inbred seed bank.
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DOI：
10.1186/gb-2013-14-6-r55
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发表时间：
2013-06-11
期刊：
影响因子：
12.3
通讯作者：
Gardner CA
中科院分区：
文献类型：
--
作者：
Romay MC;Millard MJ;Glaubitz JC;Peiffer JA;Swarts KL;Casstevens TM;Elshire RJ;Acharya CB;Mitchell SE;Flint-Garcia SA;McMullen MD;Holland JB;Buckler ES;Gardner CA
通过测序进行基因分型，这是一种新的低成本、高通量测序技术，用于对2，815份玉米自交系种质进行基因分型，这些种质大部分保存在美国国家植物种质系统中。该系列包括来自世界各地育种计划的近交系。该方法产生了分布在整个基因组中的681，257个单核苷酸多态性（SNP）标记，能够以高置信水平检测稀有等位基因。收集的SNP中有一半以上是罕见的。虽然大多数稀有等位基因已被纳入公共温带育种计划，只有少量的可用的多样性存在于商业种质。遗传距离的分析显示了群体分层，包括以关键品系为中心的少数大簇。然而，0.06的平均固定指数表明三个主要玉米亚群之间的中度分化。连锁不平衡（LD）衰减非常迅速，但LD的程度高度依赖于特定的种质组和基因组区域。这些数据的效用进行全基因组关联研究进行了测试，两个简单的遗传性状和一个复杂的性状。我们确定了与籽粒颜色、甜玉米和开花时间的已知候选基因非常接近的SNP的性状关联;然而，结果表明，需要更多的SNP来更好地探索复杂性状的遗传结构。这里描述的基因型信息允许这个公开可用的面板被开发的研究人员面临的挑战，通过更好地了解遗传多样性的性质，可持续农业。
Genotyping by sequencing, a new low-cost, high-throughput sequencing technology was used to genotype 2,815 maize inbred accessions, preserved mostly at the National Plant Germplasm System in the USA. The collection includes inbred lines from breeding programs all over the world. The method produced 681,257 single-nucleotide polymorphism (SNP) markers distributed across the entire genome, with the ability to detect rare alleles at high confidence levels. More than half of the SNPs in the collection are rare. Although most rare alleles have been incorporated into public temperate breeding programs, only a modest amount of the available diversity is present in the commercial germplasm. Analysis of genetic distances shows population stratification, including a small number of large clusters centered on key lines. Nevertheless, an average fixation index of 0.06 indicates moderate differentiation between the three major maize subpopulations. Linkage disequilibrium (LD) decays very rapidly, but the extent of LD is highly dependent on the particular group of germplasm and region of the genome. The utility of these data for performing genome-wide association studies was tested with two simply inherited traits and one complex trait. We identified trait associations at SNPs very close to known candidate genes for kernel color, sweet corn, and flowering time; however, results suggest that more SNPs are needed to better explore the genetic architecture of complex traits. The genotypic information described here allows this publicly available panel to be exploited by researchers facing the challenges of sustainable agriculture through better knowledge of the nature of genetic diversity.
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DOI：
10.1073/pnas.132259199
发表时间：
2002-07-09
影响因子：
11.1
作者：
Fu, HH;Dooner, HK
通讯作者：
Dooner, HK
影响因子：
11.6
作者：
BUCKNER, B;KELSON, TL;ROBERTSON, DS
通讯作者：
ROBERTSON, DS
影响因子：
5.8
作者：
Bradbury, Peter J.;Zhang, Zhiwu;Buckler, Edward S.
通讯作者：
Buckler, Edward S.
影响因子：
30.8
作者：
Chia, Jer-Ming;Song, Chi;Ware, Doreen
通讯作者：
Ware, Doreen
影响因子：
56.9
作者：
Buckler, Edward S.;Holland, James B.;McMullen, Michael D.
通讯作者：
McMullen, Michael D.