S01 - Session P8 - QTL analysis with SNP-based HRM markers and identification of candidate genes controlling α-glucosidase inhibitory activity in pepper (Capsicum annuum L.)

Authors: Doie Park *, Jongbin Park, Jundae Lee

Diabetes mellitus is one of the most common diseases in modern society due to lifestyle changes in which physical activity is decreasing and the obesity rate is increasing. Diabetes is a type of metabolic disease characterized by postprandial hyperglycemia that causes defects in insulin secretion, insulin action, or both, and changes in the blood sugar balance leading to metabolic disorders such as hypoglycemia or hyperglycemia. α-Glucosidase inhibitors (AGIs) are one of the widely used anti-diabetic agents and are effective in reducing postprandial hyperglycemia and insulin levels by delaying carbohydrate absorption in the small intestine. Many plants having natural AGI substances are studied that can replace medicines with fewer if not without side effects. The ability to inhibit α-glucosidase activity has been reported for leaf and fruit of pepper ( Capsicum annuum L.). In a previous study, we identified a total of 8 candidate QTLs ( qAGI1.1 , qAGI11.1, qAGI5.1, qAGI9.1, qAGI12.1 , qAGI5.2 and qAGI12.2 ) in three different stages (April, July and October) of leaves and fruits in October by QTL analysis with genotyping-by-sequencing (GBS). In the present study, we aimed to develop SNP-based high-resolution melting (HRM) markers closely linked to the detected QTLs. Using flanking sequences of SNP sites around detected QTLs, 435 primer sets were designed for the development of HRM markers, 98 primer sets were separated into three genotypes and these polymorphic primers were selected for HRM analysis. Among the polymorphic HRM markers identified, 40 were mapped on an earlier genetic linkage map of pepper. Using a newly constructed linkage map with HRM markers, re-analysis revealed a different set of 8 QTLs ( qAGI11.1, qAGI5.1 , qAGI9.1, qAGI9.2, qAGI5.2 , qAGI7.1, 1qAGI12.1 and qAGI8.1 ), with qAGI5.1 , qAGI7.1 , qAGI12.1 being the most significant QTLs with high LOD values. To identify candidate genes, BLAST was performed using flanking sequences of closely linked SNP markers and a total of 8 candidate genes were selected as candidate genes. On chromosome 7 in the region between 215 and 220 Mbp, 4 genes ( CA07g12950 , CA07g12980 , CA07g13030 , CA07g13040 ) encoding MYB-related proteins were identified as candidate genes. Between 240 and 243 Mbp on chromosome 12, CA12g18010 encoding a 4-coumarate CoA ligase protein was identified and considered a gene controlling AGI activity in pepper fruits. Additionally, in the region between 227 and 229 Mbp on chromosome 5, 3 genes ( CA05g17030 , CA05g17040 , CA05g17060 ) encoding chalcone synthase 2 were considered as genes related to AGI activity in pepper leaves. This QTL and candidate gene information will contribute to the development of pepper varieties with high AGI activity.