Genetic architecture of polyphenol oxidase activity in wheat flour by genome-wide association study

The primary cause of time-dependent discoloration in wheat (Triticum aestivum L.)-based products is polyphenol oxidase (PPO) activity. A comprehensive genetic characterization of PPO activity in wheat could expedite the development of wheat varieties with low PPO activity. To dissect the genetic architecture of PPO activity in wheat flour, a panel of 166 diverse bread wheat cultivars was phenotyped in four different environments and genotyped by high-density wheat 90K and 660K arrays. A genome-wide association study (GWAS) was performed by a mixed linear model that incorporated population structure and relative kinship. Four hundred and sixty-five stable marker-trait associations representative of 43 quantitative trait loci (QTL) for PPO activity identified in at least two environments were located on all wheat chromosomes except 5A, with each explaining 6.6-32.4% of the phenotypic variance. Based on IWGSC RefSeq v1.0, we found that QPPO2A.3, QPPO2B.1, QPPO2B.2, and QPPO2D.2 were consistent with the previously reported QTL, and 12 QTL located on homoeologous group 1 chromosomes (6 QTL), chromosomes 4B, 4D, and 7A (2 QTL), and chromosome 7B (2 QTL) are likely to be new PPO loci. Based on physical positions of QTL and previous studies, Ppo-A1, Ppo-A2, Ppo-B2, Ppo-D2, Pinb-D1, and genes encoding a Cu ion-binding protein and a Cu-transporting ATPase RAN1-like protein were considered as candidates for QPPO2A.3, QPPO2B.1, QPPO2D.2, QPPO5D.1, QPPO4A.2, and QPPO7D.2, respectively. This study provided insights into the molecular basis of wheat PPO activity, and associated markers can be used for selection of low PPO breeding lines as a means of improving the marketing quality of wheat products.