Development and Application of InDel Markers Linked to Fruit-Shape and Peel-Colour Genes in Wax Gourd

Abstract

The wax gourd is commonly grown in many countries because of its high nutritional and economic value. While the genes for the fruit shape and peel colour of wax gourd have been reported, the InDel markers linked to these genes remain undeveloped. In this study, the InDel markers linked to fruit-shape (Bch02G016830) and peel-colour (Bch05G003950) genes were developed from resequenced data. We used 120 inbred lines, 536 isolated populations, and 4 commercial hybrids to evaluate the validity and application value of the InDel markers. The accuracy rates of nine pairs of fruit-shape InDel markers (GX1-GX9) were 84.16–91.66% in 120 inbred lines. The accuracy rates of 27 pairs of peel-colour InDel markers (PS1-PS27) within approximately 3.0 Mb upstream and 3.0 Mb downstream of the peel-colour gene were 100% and those of 6 pairs of peel-colour InDel markers (PS28-PS33) within 3.0–20 Mb upstream and downstream of the peel-colour gene were 55.83–90% in 120 inbred lines. The purity of four commercial hybrids determined using GX1, GX2, PS13, and PS14 was highly consistent with the field results for purity determination. Our results provide important information for genetic linkage map construction, molecular-marker-assisted selective breeding, and purity determination of wax gourd hybrids.

Whole-Genome Sequencing and Variant Discovery ofCitrus reticulata‘Kinnow’ from Pakistan

“…The finest alternative to SNP and SSR markers is InDel markers due to its simplicity, polymorphic nature, high transferability, efficient experimental procedure, low cost of development and richness across genome (Mills et al 2006; Gao et al 2012; Oliveira et al 2022; Huang et al 2022). These markers are also well studied to understand the phylogenetic relationship between closely related organisms (animals, plants, insects, bacteria) due to its ability of sequence divergence specifically from coding regions (Britten et al 2003).…”

Fine mapping of the major gene BhHLS1 controlling seed size in wax gourd (Benincasa hispida)

“…Progress has been made in developing and applying molecular markers of fruit-related traits in wax gourd (Cheng et al, 2021;Ma et al, 2021;Huang et al, 2022;Wu et al, 2022b). In this study, a CAPS marker based on an exon G/T mutation in BhHLS1 was developed for the testing of genotypic and phenotypic concordance using 60 extreme materials with an accuracy of 96.7% (Figure 5B) and can thus be used for future marker-assisted breeding.…”