Identification of single nucleotide polymorphism in StCWIN1 and development of Kompetitive Allele-Specific PCR (KASP) marker associated with tuber traits in potato

Crop yield and quality are significantly affected by carbon partitioning between the source and sink tissues and organs, a biological process that requires the functions of cell wall invertases (CWINs). However, the nucleotide diversity, key polymorphism site and tuber trait association of cell wall invertase in potato are still unknown. In this work, the genomic sequences of potato StCWIN1 gene from 155 accessions were amplified, and nucleotide diversities and natural variations associated with tuber traits were estimated. A total number of 456 variants in StCWIN1 , including 389 single nucleotide polymorphisms (SNPs) and 67 insertions and deletions (indels), were identified. After quality controlled and filtered, 66 variants were found to be significantly associated with different tuber traits, with 5 of them were closely associated with dry matter. Among the 5 variants, one SNP, which constituted a linkage disequilibrium block with other adjacent 6 SNPs, formed the allelic marker allele - T . Based on this SNP (G/T) designated as SNP00075, a KASP marker was developed to distinguish allelic variation among potato genotypes for tuber starch content (SC) and dry matter (DM). Association analysis between StCWIN1 allelic variation and agronomic traits demonstrated that accessions possessing allele - T had higher SC (17.1%) and DM (22.9%) than those possessing allele - G (13.6% SC and 19.5% DM), indicating that Allele - T was a favorable allelic variation in StCWIN1 . Our findings suggest that the KASP marker may be used for the molecular marker-assisted breeding of new potato varieties with improved tuber weight and yield, and the favorable allelic variation allele - T has a great potential in increasing tuber yield through improving the transport of sucrose from source to sink in crop plants.