Abstract
The orientation of fruits is a distinguishing morphological feature of pepper (Capsicum spp.) varieties. The pendent (downward curved) growth of the fruit stalks, known as pedicels, is highly correlated with fruit weight and pedicel length. A previous genetic analysis revealed that the pendent fruit orientation is governed by a dominant gene, and incomplete inheritance is also observed in some Capsicum accessions. To identify and localize this gene, a single quantitative trait locus (QTL) analysis was performed on one F2 and two recombinant inbred line (RIL) populations, and a genome-wide association study (GWAS) was performed using a core collection. Common QTL regions associated with fruit orientation were detected on chromosome 12. A total of 187,966 SNPs were identified in a genotyping-by-sequencing (GBS) for GWAS analysis of 196 Capsicum annuum, 25 Capsicum baccatum, 21 Capsicum chinense, and 14 Capsicum frutescens accessions, representing the germplasm collection of South Korea. The results of these analyses enabled us to narrow down the CapUp region of interest to 200–250 Mbp on chromosome 12. Seven candidate genes were found to be located between two markers that were completely cosegregated with the fruit orientation phenotype. The findings and markers developed in this study will be helpful for additional understanding of pepper fruit development and breeding for fruit orientation.
Highlights
Peppers (Capsicum spp.) originated in the New World of Central and South America, and are one of the most important cultivated crops in the Solanaceae family (Bai and Lindhout, 2007; Li et al, 2013)
A core collection composed of 196 C. annuum, 25 C. baccatum, 21 C. chinense, and 14 C. frutescens genotypes was used for the genome-wide association study (GWAS) (Table 1; Lee et al, 2016)
Fruit orientation, which is mainly governed by the curvature of the pedicels, may vary depending on the relative position at which the bending occurs on the pedicel: near the point of attachment with the branch or further away toward the fruit (Figure 1A)
Summary
Peppers (Capsicum spp.) originated in the New World of Central and South America, and are one of the most important cultivated crops in the Solanaceae family (Bai and Lindhout, 2007; Li et al, 2013). The change in fruit position from erect, in which the fruit is held in an upright position, to pendent, where the fruits are pendulous or hang freely, has been described as an important step in pepper selection and domestication (Paran and Van Der Knaap, 2007; Albrecht et al, 2012; Chunthawodtiporn et al, 2018). Since the erect phenotype is controlled by a recessive gene, development of molecular markers is necessary for breeding erect type cultivars
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