Identification of Genetic Factors Controlling Multiple-flower per node in Pepper (Capsicum spp.)

Abstract

Flowering is enormously important in all crops, serving as the foundation for yield and increased profits. Capsicum annuum has a sympodial shoot structure with a solitary flower. In contrast, C. chinense produce multiple-flower per node. C. annuum is the most widely cultivated species which account for 80% of world pepper production. Therefore, identifying genes controlling multiple flowers and transferring the multiple flowering trait from C. chinense to C. annuum may be potentially useful to increase fruit yield. In this study, we performed two experiments to identify the genetic factors controlling the multiple-flower per node character in Capsicum. To find the quantitative trait loci (QTL) controlling multiple flowering, 85 recombinant inbred lines (RILs) between C. annuum TF68 and C. chinense Habanero were used. Average flower numbers of the first to sixth nodes with three replicates of each line was collected. A high density molecular genetic map was constructed by using genotyping by sequencing (GBS) technique. A total of 10,851 SNP markers on 12 chromosomes were converted to bin markers to construct a high-density linkage map. The map covered a total length of 1,713 cM with a mean bin marker distance of 0.96 cM. QTL analysis identified four novel QTLs on chromosome 1, 2, 7 and 11 for multiple-flower per node trait, accounting for 65% total phenotypic variation. To validate and clarify the detected QTLs, genome-wide association study was performed. A total of 276 C. annuum-clade accessions, including 98 C. annuum, 66 C. chinense, 67 C. frutescens and 45 Capsicum spp. were used. Genotyping was performed with GBS method and after filtering the SNPs, a total of 156,589 highly reliable SNPs were selected for association study. Genome-wide association analysis revealed that a total of 28 QTL regions were significantly associated with multiple-flower per node. Among the QTLs, three were collocated with the QTL region detected in the biparental population. In the QTL regions, we identified five candidate genes involved in the development of shoot and flower meristem for controlling multiple-flower per node in pepper. These results will contribute to understand multiple-flower per node character in Capsicum and will be useful for developing high yield cultivars.