Identifying loci with breeding potential across temperate and tropical adaptation via EigenGWAS and EnvGWAS
Identifying loci with breeding potential across temperate and tropical adaptation via EigenGWAS and EnvGWAS
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DOI：
10.1111/mec.15169
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发表时间：
2019-08-18
影响因子：
4.9
通讯作者：
Li, Huihui
中科院分区：
文献类型：
--
作者：
Li, Jing;Chen, Guo-Bo;Li, Huihui
了解玉米适应性的基因组基础对于基因发现和育种种质的改进具有重要意义，但尽管有大量的群体遗传学和考古学研究，许多事情仍然是一个谜。识别支持适应的信号是具有挑战性的，因为适应往往与遗传漂移重合，并且物种的基础基因组多样性巨大。本研究利用tGBS技术对来自20个国家的1143份不同玉米种质和热带低地、高原、亚热带/中海拔和温带生态区的优良种质进行了基因分型。基于355,442个高质量单核苷酸多态，采用自下而上搜索策略，检测到13个基因组区域处于选择之中。在13个选择区域中，有10个为首次报道，2个与环境参数有关，146个基因被浓缩。结合大规模的基因组和生态数据，我们的研究支持玉米的多基因适应模型，并提供了一个框架，以加强我们对玉米驯化和适应的机制基础和进化后果的理解。这里确定的区域是进一步的、有针对性的探索的有前景的候选者，以确定在玉米育种中部署的有益等位基因和单倍型。
Understanding the genomic basis of adaptation in maize is important for gene discovery and the improvement of breeding germplasm, but much remains a mystery in spite of significant population genetics and archaeological research. Identifying the signals underpinning adaptation are challenging as adaptation often coincided with genetic drift, and the base genomic diversity of the species in massive. In this study, tGBS technology was used to genotype 1,143 diverse maize accessions including landraces collected from 20 countries and elite breeding lines of tropical lowland, highland, subtropical/midaltitude and temperate ecological zones. Based on 355,442 high-quality single nucleotide polymorphisms, 13 genomic regions were detected as being under selection using the bottom-up searching strategy, EigenGWAS. Of the 13 selection regions, 10 were first reported, two were associated with environmental parameters via EnvGWAS, and 146 genes were enriched. Combining large-scale genomic and ecological data in this diverse maize panel, our study supports a polygenic adaptation model of maize and offers a framework to enhance our understanding of both the mechanistic basis and the evolutionary consequences of maize domestication and adaptation. The regions identified here are promising candidates for further, targeted exploration to identify beneficial alleles and haplotypes for deployment in maize breeding.