Analysis of elite variety tag SNPs reveals an important allele in upland rice

文献类型： 外文期刊

第一作者： Lyu, Jun

作者： Lyu, Jun;Dong, Yang;Zhang, Yesheng;Li, Xin;Xu, Xun;Wang, Wen;Lyu, Jun;Dong, Yang;Zhang, Yesheng;Li, Xin;Xu, Xun;Wang, Wen;Zhang, Shilai;Zhang, Jing;Deng, Xianneng;Li, Baoye;Huang, Wangqi;Wan, Wenting;Yu, Yang;Li, Qiong;Tao, Dayun;Hu, Fengyi;He, Weiming;Li, Jun;Liu, Xin;Wang, Bo;Zhang, Gengyun;Wang, Jun;Xu, Xun;Zhang, Gengyun;Xu, Xun

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期刊名称：NATURE COMMUNICATIONS （ 影响因子：14.919； 五年影响因子：15.805 ）

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收录情况： SCI

摘要： Elite crop varieties usually fix alleles that occur at low frequencies within non-elite gene pools. Dissecting these alleles for desirable agronomic traits can be accomplished by comparing the genomes of elite varieties with those from non-elite populations. Here we deep-sequence six elite rice varieties and use two large control panels to identify elite variety tag single-nucleotide polymorphism alleles (ETASs). Guided by this preliminary analysis, we comprehensively characterize one protein-altering ETAS in the 9-cis-epoxycarotenoid dioxygenase gene of the IRAT104 upland rice variety. This allele displays a drastic frequency difference between upland and irrigated rice, and a selective sweep is observed around this allele. Functional analysis indicates that in upland rice, this allele is associated with significantly higher abscisic acid levels and denser lateral roots, suggesting its association with upland rice suitability. This report provides a potential strategy to mine rare, agronomically important alleles.RI Li, Xin/A-4137-2011OI Li, Xin/0000-0001-8328-4894

分类号： N

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