Elite varieties that have gone through long term breeding have probably fixed some elite alleles that occur with low frequencies in ancestral gene pool. Those elite alleles contribute to the elite performance of the elite varieties. Traditionally, geneticists use quantitative trait loci (QTL) linkage mapping and association mapping to identify those elite agronomic genes. However, QTL mapping requires constructing segregating population which is time-consuming, and association mapping has a low power to identify alleles with low frequencies.

Wen Wang’s group in State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, in cooperation with Yunnan Academy of Agricultural sciences and BGI-Shenzhen, proposes a new approach named elite variety tag SNP analysis (abbreviation: ETAS analysis) . This approach is predicated on using a large amount of genomics data to identify elite variety tag SNP alleles (ETASs). Using ETAS analysis, this group identifies a series of tag SNPs for the famous elite rice varieties, including high-yield Guichao, good-quality Koshihikari and drought resistant IRAT104. Further studies focusing on one ETAS in IRAT104 reveal a SNP allele with huge allele frequency difference between upland and irrigated rice population (61% vs 3%), and a striking selective sweep was observed around that ETAS in upland rice. This ETAS is located within an NCED gene encoding a rate-limiting enzyme for abscisic acid (ABA) synthesis. ABA, as a well-known plant hormone for drought response and resistance, can regulate osmotic pressure and stoma, and influence root development. In-silico prediction shows that the ETAS in upland rice IRAT104, which causes a non-synonymous mutation, has probably altered the secondary structure around the NCED enzyme binding domain. Functional studies reveal that this ETAS is associated with significant higher ABA level and more lateral roots in upland rice, suggesting it has risen to high frequency probably because it contributes to the adaptive phenotypes in upland rice and has been selected.

This study proposed that the comparison of individual genome and population genomes can provide important clues for identifying elite alleles. To validate the candidate alleles, the authors emphasize that further functional studies are indispensable. The above work has been published recently in the international Journal Nature Communications. The full text can be downloaded from the following link (link).

This work was supported by the Department of Sciences and Technology of Yunnan Province (2011BB015), the Chinese 973 Program (2013CB835200, 2013CB835201) and the Key Project of Transgenic New Varieties Culture of China (2009ZX08009-021B).