Bouchet Sophie, Olatoye Marcus O, Marla Sandeep R, Perumal Ramasamy, Tesso Tesfaye, Yu Jianming, Tuinstra Mitch, Morris Geoffrey P
Department of Agronomy, Kansas State University, Manhattan, Kansas 66506.
Agricultural Research Center, Kansas State University, Hays, Kansas 67601.
Genetics. 2017 Jun;206(2):573-585. doi: 10.1534/genetics.116.198499.
Adaptation of domesticated species to diverse agroclimatic regions has led to abundant trait diversity. However, the resulting population structure and genetic heterogeneity confounds association mapping of adaptive traits. To address this challenge in sorghum [ (L.) Moench]-a widely adapted cereal crop-we developed a nested association mapping (NAM) population using 10 diverse global lines crossed with an elite reference line RTx430. We characterized the population of 2214 recombinant inbred lines at 90,000 SNPs using genotyping-by-sequencing. The population captures ∼70% of known global SNP variation in sorghum, and 57,411 recombination events. Notably, recombination events were four- to fivefold enriched in coding sequences and 5' untranslated regions of genes. To test the power of the NAM population for trait dissection, we conducted joint linkage mapping for two major adaptive traits, flowering time and plant height. We precisely mapped several known genes for these two traits, and identified several additional QTL. Considering all SNPs simultaneously, genetic variation accounted for 65% of flowering time variance and 75% of plant height variance. Further, we directly compared NAM to genome-wide association mapping (using panels of the same size) and found that flowering time and plant height QTL were more consistently identified with the NAM population. Finally, for simulated QTL under strong selection in diversity panels, the power of QTL detection was up to three times greater for NAM association mapping with a diverse panel. These findings validate the NAM resource for trait mapping in sorghum, and demonstrate the value of NAM for dissection of adaptive traits.
驯化物种对不同农业气候区域的适应导致了丰富的性状多样性。然而，由此产生的群体结构和遗传异质性混淆了适应性性状的关联作图。为了解决高粱[（L.）Moench]——一种广泛适应的谷类作物——中的这一挑战，我们利用10个不同的全球品系与一个优良参考品系RTx430杂交，构建了一个巢式关联作图（NAM）群体。我们使用简化基因组测序对2214个重组自交系群体的90000个单核苷酸多态性（SNP）进行了特征分析。该群体捕获了高粱中约70%已知的全球SNP变异以及57411个重组事件。值得注意的是，重组事件在基因的编码序列和5'非翻译区中富集了四到五倍。为了测试NAM群体用于性状剖析的能力，我们对两个主要适应性性状，即开花时间和株高进行了联合连锁作图。我们精确地定位了这两个性状的几个已知基因，并鉴定了几个额外的数量性状位点（QTL）。同时考虑所有SNP，遗传变异分别解释了开花时间变异的65%和株高变异的75%。此外，我们直接将NAM与全基因组关联作图（使用相同大小的群体）进行比较，发现NAM群体更一致地鉴定出开花时间和株高QTL。最后，对于多样性群体中强选择下的模拟QTL，NAM关联作图检测QTL的能力比多样性群体高出两倍。这些发现验证了NAM资源在高粱性状作图中的作用，并证明了NAM在剖析适应性性状方面的价值。
