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

Jun Lyu, Shilai Zhang, Yang Dong, Weiming He, Jing Zhang, Xianneng Deng, Yesheng Zhang, Xin Li, Baoye Li, Wangqi Huang, Wenting Wan, Yang Yu, Qiong Li, Jun Li, Xin Liu, Bo Wang, Dayun Tao, Gengyun Zhang, Jun Wang, Xun Xu, Fengyi Hu () and Wen Wang ()
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Jun Lyu: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences
Shilai Zhang: Food Crops Research Institute, Yunnan Academy of Agricultural Sciences
Yang Dong: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences
Weiming He: BGI-Shenzhen, Beishan Industrial Zone
Jing Zhang: Food Crops Research Institute, Yunnan Academy of Agricultural Sciences
Xianneng Deng: Food Crops Research Institute, Yunnan Academy of Agricultural Sciences
Yesheng Zhang: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences
Xin Li: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences
Baoye Li: Food Crops Research Institute, Yunnan Academy of Agricultural Sciences
Wangqi Huang: Food Crops Research Institute, Yunnan Academy of Agricultural Sciences
Wenting Wan: Food Crops Research Institute, Yunnan Academy of Agricultural Sciences
Yang Yu: Food Crops Research Institute, Yunnan Academy of Agricultural Sciences
Qiong Li: Food Crops Research Institute, Yunnan Academy of Agricultural Sciences
Jun Li: BGI-Shenzhen, Beishan Industrial Zone
Xin Liu: BGI-Shenzhen, Beishan Industrial Zone
Bo Wang: BGI-Shenzhen, Beishan Industrial Zone
Dayun Tao: Food Crops Research Institute, Yunnan Academy of Agricultural Sciences
Gengyun Zhang: BGI-Shenzhen, Beishan Industrial Zone
Jun Wang: BGI-Shenzhen, Beishan Industrial Zone
Xun Xu: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences
Fengyi Hu: Food Crops Research Institute, Yunnan Academy of Agricultural Sciences
Wen Wang: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences

Nature Communications, 2013, vol. 4, issue 1, 1-9

Abstract: Abstract 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.

Date: 2013
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DOI: 10.1038/ncomms3138

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