Identification and development of a KASP functional marker of TaTAP46-5A associated with kernel weight in wheat (Triticum aestivum)

TAP46 (Type 2A-phosphatase-Associated Protein 46 kDa) is homologous to yeast TAP42 or the animal alpha 4 gene and is a crucial gene in the target of rapamycin regulation of protein phosphatase 2A. It has been proven to influence the thousand-kernel weight (TKW) and kernel size in transgenic wheat. To rapidly identify high-yield wheat germplasms of TaTAP46, four interlinked single nucleotide polymorphisms were identified by resequencing the TaTAP46-5A gene in 32 varieties, forming two haplotypes: Hap1 and Hap2. A KASP marker, -1462A/C, was developed to identify Hap1/Hap2. A 157 Chinese wheat mini core collection and 348 Chinese modern collection were constructed for association analysis of the two haplotypes and their phenotypes. The results showed that the Hap1/Hap2 of TaTAP46-5A was significantly associated with the TKW and kernel size. Hap1 was a favourable haplotype with higher TKW and larger kernel size compared to those of Hap2. Hap1 is a stable high yield type of the TaTAP46 gene that has been continuously selected in high-yield wheat breeding worldwide. The germplasm of Hap1 can be selected quickly using the KASP primer -1462A/C, to improve breeding efficiency.

Automated summary

By studying the two haplotypes Hap1 and Hap2 of the TaTAP46 gene, it was found that Hap1 is associated with high-yield wheat varieties, with higher TKW and larger kernel size, making it a widely selected type in high-yield wheat breeding worldwide.