Identification of Elite Variety Tag SNPs (ETASs) - a New Approach Unraveling Loci Underlying Crop Improvement

Elite crop varieties usually fix elite alleles that occur with low frequency within non-elite gene pool. Hence a powerful way of dissecting these alleles for desirable agronomical traits is to compare the genomes of elite varieties with the non-elite population, and then identify the elite variety-specific alleles. In this study, we sequenced deeply six elite rice varieties and used two large control panels to identify the elite variety tag SNPs (ETASs). We identified many ETASs resulting in either amino acid changes or even gene structure disruption, providing a valuable checklist for quick identification of targeted genes during these elite rice improvement. As an example, we comprehensively characterized one such ETAS of the elite upland rice variety, IRAT104. This site shows a drastic frequency difference between upland and irrigated rice, and the striking selective sweep around it strongly suggests its association with upland rice suitability. Functional analysis also shows that thisETAS probably plays an important role in enhancing upland rice yield during the rice improvement. Our work demonstrates a novel and effective strategy to mine rare agronomically important alleles.