Identification of a new variant allele of <i>CaGLK</i> that is responsible for white color fruit and development of a functional marker based on this variation in pepper

Pepper (<i>Capsicum annuum</i> L<i>.</i>) fruits at immature stage (IS) display colors that range from dark green to light green and white. Due to the influence of genetic factors and consumption habits, white-fruited pepper germplasms are rare in nature and depend on artificial creation. However, the unclear complex genetic basis, coupled with the absence of developed functional markers cosegregation with white fruit trait, has impeded the efficiency of breeding white-fruited peppers. Herein, an F₂ segregation population consisting of 3,000 individuals is derived from a cross between B1-2 with white fruit and D50 with dark green fruit at IS. Using bulked segregant analysis, a previously reported gene <i>CaGLK</i> (<i>Capana10g000333</i>) is identified as a candidate that is responsible for white/green fruit color. A single nucleotide polymorphism (SNP) (G/A) at the position of the last base of the second intron of <i>CaGLK</i>, resulting in alternative splicing at the junction of the second intron and the third exon, causing the exclusion of 31 bp in cDNA sequence of B1-2, is associated with white fruit trait. A KASP marker is developed and shown to distinguish white-fruited pepper from the F₂ population. The distinguishing efficiency of this marker reached up to 78.3% when tested in a natural population. This first report of a new allele <i>CaGLK</i>^<i>A</i> that controlled white color provided a new handle to develop pepper cultivars with white color fruit.