title: Analysis of elite variety tag SNPs reveals an important allele in upland rice.
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.
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, Yunnan 650223, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Lyu
authors.forename: Shilai
authors.initials: S
authors.lastname: Zhang
authors.forename: Yang
authors.initials: Y
authors.lastname: Dong
authors.forename: Weiming
authors.initials: W
authors.lastname: He
authors.forename: Jing
authors.initials: J
authors.lastname: Zhang
authors.forename: Xianneng
authors.initials: X
authors.lastname: Deng
authors.forename: Yesheng
authors.initials: Y
authors.lastname: Zhang
authors.forename: Xin
authors.initials: X
authors.lastname: Li
authors.forename: Baoye
authors.initials: B
authors.lastname: Li
authors.forename: Wangqi
authors.initials: W
authors.lastname: Huang
authors.forename: Wenting
authors.initials: W
authors.lastname: Wan
authors.forename: Yang
authors.initials: Y
authors.lastname: Yu
authors.forename: Qiong
authors.initials: Q
authors.lastname: Li
authors.forename: Jun
authors.initials: J
authors.lastname: Li
authors.forename: Xin
authors.initials: X
authors.lastname: Liu
authors.forename: Bo
authors.initials: B
authors.lastname: Wang
authors.forename: Dayun
authors.initials: D
authors.lastname: Tao
authors.forename: Gengyun
authors.initials: G
authors.lastname: Zhang
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Xun
authors.initials: X
authors.lastname: Xu
authors.forename: Fengyi
authors.initials: F
authors.lastname: Hu
authors.forename: Wen
authors.initials: W
authors.lastname: Wang
mesh_terms: D000040:Abscisic Acid / Q000378:metabolism; D000483:Alleles; D020029:Base Pairing / Q000235:genetics; D017753:Ecosystem; D017343:Genes, Plant / Q000235:genetics; D005828:Genetics, Population; D012275:Oryza / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*
chemical_list: D010940:Plant Proteins; D000040:Abscisic Acid