Genome-Phenome Wide Association in Maize and Arabidopsis Identifies a Common Molecular and Evolutionary Signature
Genome-Phenome Wide Association in Maize and Arabidopsis Identifies a Common Molecular and Evolutionary Signature
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DOI：
10.1016/j.molp.2020.03.003
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发表时间：
2020-06-01
期刊：
影响因子：
27.5
通讯作者：
Schnable, James C.
中科院分区：
文献类型：
--
作者：
Liang, Zhikai;Qiu, Yumou;Schnable, James C.
将自然遗传变异与性状变异联系起来可以帮助确定不同基因的功能作用。一个或几个性状的变异通常单独评估。高通量表型分析和数据挖掘可以从同一个体中捕获数十或数百个性状。在这里，我们同时测试了一个基因内的标记与许多性状之间的关联。这种全基因组-表型关联研究（GPWAS）是一种多标记和多性状的测试。使用GPWAS鉴定的玉米260个表型性状的基因富集了与表型变异独立连锁的基因。与经典突变体相关的性状与报道的突变等位基因的表型一致。利用GPWAS与玉米表型变异相关的基因与玉米中的经典突变体共享分子、群体遗传和进化特征。利用GPWAS在拟南芥中与表型变异相关的基因在具有已知功能丧失表型的基因中显著富集。GPWAS可能是一种有效的策略，以确定基因的功能丧失等位基因产生突变表型。使用GPWAS鉴定的经典突变体和基因中存在的共享标签可以是在一般地指定植物表型或特异性地指定多效性中起作用的基因的标记。
Linking natural genetic variation to trait variation can help determine the functional roles of different genes. Variations of one or several traits are often assessed separately. High-throughput phenotyping and data mining can capture dozens or hundreds of traits from the same individuals. Here, we test the association between markers within a gene and many traits simultaneously. This genome-phenome wide association study (GPWAS) is both a multi-marker and multi-trait test. Genes identified using GPWAS with 260 phenotypic traits in maize were enriched for genes independently linked to phenotypic variation. Traits associated with classical mutants were consistent with reported phenotypes for mutant alleles. Genes linked to phenomic variation in maize using GPWAS shared molecular, population genetic, and evolutionary features with classical mutants in maize. Genes linked to phenomic variation in Arabidopsis using GPWAS are significantly enriched in genes with known loss-of-function phenotypes. GPWAS may be an effective strategy to identify genes in which loss-of-function alleles produce mutant phenotypes. The shared signatures present in classical mutants and genes identified using GPWAS may be markers for genes with a role in specifying plant phenotypes generally or pleiotropy specifically.