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 populations which is time consuming, and association mapping is of low power in identifying alleles with low frequencies.
To assist in the allele mining of elite rice varieties, by collaborating with Yunnan Academy of Agricultural sciences and BGI-Shenzhen, Prof. WANG Wen’s group of the State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, CAS，has developed a new approach named elite variety tag SNP analysis (ETAS), which is predicated on using a large amount of genomics data to identify ETASs.
Attribute to ETAS analysis, Prof. WANG’s group has identified 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 revealed a SNP allele with huge allele frequency difference between upland and irrigated rice population (61% vs 3%), meanwhile, 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, a well-known plant hormone for drought response and resistance, could regulate osmotic pressure and stoma, and influence root development. Moreover, the in-silico prediction showed 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 also revealed that this ETAS is associated with significantly higher ABA level and more lateral roots in upland rice. These results suggested that the high frequency of the ETAS were probably due to its contributions in the adaptive phenotypes of upland rice.
This study proposed that the comparisons of individual genomes and population genomes could give important leads in identifying elite alleles. But, to validate the candidate alleles, the further functional studies are indispensable.
The main findings of this work have been published in 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).
(By Jun Lǚ)
