Objective To analyze the inheritance patterns of key traits in peas, including pod parchment layer presence/absence, thick/thin pod wall, and resistance to powdery mildew, and to map the chromosomal locations of genes controlling these traits, followed by the development of linked molecular markers for marker-assisted breeding.

Method Genetic analysis was conducted by constructing segregating populations for the presence/absence of parchment layer, thick/thin pod walls, and resistance/susceptibility to powdery mildew in peas. Gene mapping was performed using BSA-seq (Bulked-segregant analysis by sequencing). Suitable SNPs or InDels were selected based on factors such as GC content of sequences, presence of repetitive sequences, and SNP base types, and KASP or InDel markers were developed within the candidate intervals.

Result The genetic analysis results showed that the three pairs of traits in the constructed populations all conformed to the inheritance pattern controlled by a single gene. BSA-seq results indicated that the candidate intervals regulating the parchment layer, thick/thin pod walls, and powdery mildew resistance were located in the 340.0~390.0 Mb region on Chr1, 35.0~65.0 Mb on Chr4, and 150.0~270.0 Mb on Chr1, respectively. A total of 5 molecular markers linked to different traits were developed within the mapping intervals. These markers showed 100.0% consistency between genotypes and phenotypes in parents with known phenotypes and F₂ individuals, indicating high accuracy in phenotype prediction. Based on this, marker-assisted selection was carried out, screening 11 germplasm resources carrying favorable genes from the collected pea germplasm, and identifying 21 individual plants in the segregating populations that carried resistance to powdery mildew, thick or thin pod walls, absence of parchment layer, and exhibited good field performance.

Conclusion Genetic analysis confirmed that the presence/absence of the parchment layer, the thick and thin skin trait of pods, and resistance/susceptibility to powdery mildew in pea are each controlled by a single gene. These traits were successfully mapped to specific chromosomal regions using BSA-seq. Based on the mapping information, five linked molecular markers were developed and preliminarily applied in breeding. This facilitated the screening of 32 germplasm resources and intermediate materials, including parental lines and progeny, carrying the favorable alleles.