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- W2065989833 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. Quantitative trait loci mapping has traditionally been used to discover desirable alleles in plants. In this study, Lyu et al. use a comparative genome approach to identify an allele that is prevalent in upland rice varieties and alters the function of a protein involved in abscisic acid biosynthesis." @default.
- W2065989833 created "2016-06-24" @default.
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- W2065989833 date "2013-07-05" @default.
- W2065989833 modified "2023-10-18" @default.
- W2065989833 title "Analysis of elite variety tag SNPs reveals an important allele in upland rice" @default.
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- W2065989833 doi "https://doi.org/10.1038/ncomms3138" @default.
- W2065989833 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/3715847" @default.
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