GWAS-Based Prediction of Genes Associated with Potato Compound Leaf Size and Apical Leaflet Size

Potato leaf size directly affects photosynthetic efficiency and yield; therefore, elucidating the genetic regulation of this trait is important for breeding improvement. In this study, a natural population of 476 tetraploid potato accessions was used to evaluate compound leaf size and apical leaflet size. Both traits were scored on a 1–9 ordinal scale in accordance with the national standard GB/T 19557.28-2018. The two-year (2019–2020) phenotypic means showed continuous variation consistent with polygenic quantitative trait architecture. Correlation analysis revealed a strong, highly significant positive association between compound leaf size and apical leaflet size (R = 0.71, p < 2.2 × 10−16). Genome-wide association analysis identified 211 SNPs significantly associated with compound leaf size, predominantly located on chromosomes Chr05 and Chr06, from which 75 candidate genes were identified. KEGG enrichment analysis showed that these candidate genes were significantly enriched in pathways related to RNA degradation, ribosomes, phenylalanine biosynthesis and genetic information processing. Putative candidate genes potentially regulating compound leaf size include DM8C10G01290.1 (Rcd1-like), DM8C11G02500.1 (ADH_zinc_N domain-containing), DM8C10G01180.1 (Ribosomal_S8e domain-containing), DM8C06G16880.1 (Methyltransf_2 domain-containing) and DM8C05G27660.1 (Inositol_P domain-containing). A total of 671 SNP loci were identified as significantly associated with apical leaflet size, primarily localised on chromosomes Chr04 and Chr06, which led to the identification of 175 candidate genes. KEGG enrichment analysis showed that candidate genes for apical leaflet size were mainly enriched in pathways related to energy metabolism, secondary metabolism and plant hormone signal transduction. Putative candidate genes potentially regulating apical leaflet size include DM8C10G13560.1 (Malic_M domain-containing), DM8C01G21400.1 (PPDK_N domain-containing), DM8C08G02250.1 (UDPGT domain-containing), DM8C03G19930.1 (Orn_Arg_deC_N domain-containing), DM8C04G29090.1 (peroxidase), DM8C02G10960.2 (Pro_CA domain-containing), DM8C01G45290.1 (NIR_SIR domain-containing), DM8C08G02280.1 (Glyco_tranf_2_3 domain-containing), DM8C06G27780.1 (UDPGT domain-containing), DM8C06G27490.1 (Transket_pyr domain-containing), DM8C04G23010.1 (LRRNT_2 domain-containing) and DM8C03G01180.1 (BES1_N domain-containing). This study elucidated the genetic basis of potato leaf size and provided promising candidate markers and genetic resources, which require further validation in independent populations and environments before deployment in molecular marker-assisted breeding.