Development of functional markers and expression analysis for a Peroxidase gene TaPod-A3 on chromosome 7AL in wheat

Peroxidase (POD) is one of the key factors affecting the wheat flour quality. Characterization and development of functional markers, as well as expression analysis of POD genes, will help in breeding wheat cultivars and advanced lines with better flour quality. Here, we cloned a POD gene, TaPod-A3, on chromosome 7AL and developed its functional marker in common wheat (Triticum aestivum L). Based on single nucleotide polymorphisms (SNPs) and Indel between TaPod-A3 allele sequences, functional markers POD-7A1, POD-7A2, and POD-7A3 were developed, amplifying 216, 882, and 156 bp fragments in wheat cultivars and advanced lines with lower, middle, and higher POD activities, respectively. The analysis of variance of 228 wheat cultivars and advanced lines showed that the mean POD activity (668.6 U min^-1 g^-1) of 113 wheat cultivars and advanced lines supplemented with TaPod-A3a was lower than 17 wheat cultivars and advanced lines supplemented with TaPod-A3b (679.7 U min^-1 g^-1) and the 98 wheat cultivars and advanced lines supplemented with TaPod-A3c (731.2 U min^-1 g^-1). A total of 228 wheat cultivars and advanced lines were found using the functional markers of TaPod-A1, TaPod-D1, and TaPod-A3 genes located on chromosomes 3A, 7D, and 7AL of the functional markers developed in this study. The wheat cultivars and advanced lines with favorable allele combination of TaPod-A1b/TaPod-A3c/TaPod-D1b had higher POD activity (mean POD activity 780.6 U min^-1 g^-1) than those with alleles TaPod-A1a/TaPod-A3a/TaPod-D1a (625.7 U min^-1 g^-1). Six wheat cultivars and advanced lines with the same genotype and phenotype were selected for quantitative real-time polymerase chain reaction, and we found that the expression level of F49-70 in wheat cultivars and advanced lines with high POD activity was significantly higher than that in Wanmai 29 with low POD activity at each stage after flowering (p < 0.05). Based on correction analyses on the TaPod-A3 gene expression, the expression level was positively correlated with POD activity. This study provides useful information on the POD genes in bread wheat, insight into the TaPod-A3 gene structure and functional markers, as well as valuable resources for improving the quality of wheat flour.