Allele mining of wheat ABA receptor at TaPYL4 suggests neo-functionalization among the wheat homoeologs

ABA receptors (PYR/PYL/RCAR) play a central role in the water loss control of plants. A previous report indicated that TaPYL4 is a critical gene in wheat that improves grain production under drought conditions and increases water use efficiency. In this study, we analyzed the sequence polymorphisms and genetic effects of TaPYL4s. Based on isolated TaPYL4 genes from chromosomes 2A, 2B and 2D, three haplotypes were detected in the promoter region of TaPYL4-2A, and two haplotypes were present in TaPYL4-2B and TaPYL4-2D, respectively. Marker/trait association analysis indicated that TaPYL4-2A was significantly associated with plant height in 262 Chinese wheat core collection accessions, as well as the drought tolerance coefficient (DTC) for plant height in 239 wheat varieties from Shanxi Province in multiple environments. However, the frequencies of favored drought-tolerant haplotype TaPYL4-2A-Hap2 were considerably low, accounting for only 10%, and lines with this certain Hap could be reserved in the breeding program. TaPYL4-2B was significantly associated with grain number, and the favored haplotype TaPYL4-2B-Hap1 was the dominant allele of above 90% in the collection. For TaPYL4-2D, there were no significant differences in these traits between the two haplotypes in either of the two panels. These results indicate that variation might lead to functional differentiation among the homoeologs and the haplotypes had undergone artificial selection during breeding. Two molecular markers developed to distinguish these haplotypes could be used for breeding in water-limited regions.