Identification of Candidate Chromosome Region Related to Melon (Cucumis melo L.) Fruit Surface Groove Trait Through Biparental Genetic Mapping and Genome-Wide Association Study

Abstract

The melon fruit surface groove (fsg) not only affects peel structure and causes stress-induced fruit cracking but also fits consumers’ requirements in different regions. In this study, genetic inheritance analysis of three F2 populations derived from six parental lines revealed that the fsg trait is controlled by a simple recessive inherited gene. Through bulked segregant analysis sequencing (BSA-seq), the Cmfsg locus was detected in an 8.96 Mb interval on chromosome 11 and then initially mapped to a region of approximately 1.15 Mb. Further fine mapping with a large F2 population including 1,200 plants narrowed this region to 207 kb containing 11 genes. A genome-wide association study (GWAS) with 187 melon accessions also produced the same chromosome region for the Cmfsg locus. Due to the rare molecular markers and lack of mutations in the coding and promoter regions of the 11 candidate genes in the fine-mapped interval, we conducted in silico BSA to explore the natural melon panel to predict candidate genes for the Cmfsg locus. A 1.07 kb segment upstream of MELO3C019694.2 (annotated as the AGAMOUS MADS-box transcription factor) exhibited a correlation with the grooved and non-grooved accessions among the F2 individuals, and a natural panel consisted of 17 melon accessions. The expression level of MELO3C019694.2 in the pericarp was higher in grooved lines than in non-grooved lines and was specifically expressed in fruit compared with other tissues (female flower, male flower, root, and leaf). This work provides fundamental information for further research on melon fsg trait formation and molecular markers for melon breeding.

Identification of inheritance and genetic loci responsible for wrinkled fruit surface phenotype in chili pepper (Capsicum annum) by quantitative trait locus analysis

“…In related research, a genetic study focusing on the fruit surface grooves in melon (Cucumis melo) identi ed the locus responsible on chromosome 11 (Zhao et al 2019). Subsequently, the gene MELO3C019694 encoding an AGAMOUS MADS-box transcription factor, was identi ed as being responsible for this trait (Du et al 2022). Previous studies highlighted the diverse regulatory roles of MADS-box family in fruit maturation, fruit skin development, and embryonic development in tomatoes (Busi et al 2003;Hileman et al 2006).…”

Three-dimensional fruit growth analysis clarifies developmental mechanisms underlying complex shape diversity in persimmon fruit

“…Yao et al (2018) found that overexpression of Malus domestica PISTILLATA causes vertical groove development on fruit from 12 days after pollination. Du et al (2022) identified a 1.07-kb deletion of a chromosome segment in groove lines of Cucumis melo and proposed that CmMADS-Box may be a candidate gene regulating the groove formation. It was also reported that certain Arabidopsis mutants with defects in the YABBY and SVP genes produced flowers with abnormal carpel fusions, which can possibly lead to groove-like structures (Nole-Wilson and Krizek, 2006; Gregis et al, 2009).…”

Epidermal Patterning Factor 2-like (McEPFL2): A Putative Candidate for the Continuous Ridge (cr) Fruit Skin Locus in Bitter Gourd (Momordica charantia L.)

“…We searched the cucumber genome assemblies (9930v3.0 and Gy14v2.1; https://cucurbitgenomcs.org/, accessed on 1 April 2022) and there were 13 genes annotated as "Epidermal patterning factor-like protein", but none of them were located on cucumber Chr5. Similarly, the single gene (Cmfsg) for the fruit surface groove of melon was proposed to encode an AGAMOUS MADS-box transcription factor [16]. These observations suggest that the cucumber ribbing/nonribbing or melon fruit groove may have different genetic bases from fruit ridge continuity (CR/DCR) in bitter gourd.…”

“…In luffa, Luffa acutangula (L.) Roxb, the fruit ridge is also controlled by one major gene with partial dominance [ 15 ]. The ‘fruit surface groove’ described in melon ( Cucumis melo L.) is probably similar to fruit ridge, too; a simply inherited gene encoding an AGAMOUS MADS-box transcription factor was proposed to control this fruit skin feature [ 16 ]. Molecular mapping of fruit epidermal feature-related traits in bitter gourd is limited.…”