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

Abstract TAP46 (Type 2A‐phosphatase‐Associated Protein 46 kDa) is homologous to yeast TAP42 or the animal α4 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.