Genetic mapping reveals a marker for yellow skin in watermelon (Citrullus lanatus L.)

Abstract

As a diverse species, watermelon [Citrullus lanatus (Thunb.) Matsum. &Nakai var. lanatus] has different kinds of fruit sizes, shapes, flesh colors and skin colors. Skin color is among the major objectives for breeding. Yellow skin is an important trait in watermelon, but the underlying genetic mechanism is unknown. In this study, we identified a locus for yellow skin through BSA-seq and GWAS. A segregation analysis in F2 and BC1 populations derived from a cross of two inbred lines ‘94E1’(yellow skin) and ‘Qingfeng’(green skin) suggested that skin color is a qualitative trait. BSA-seq mapping confirmed the locus in the F2 population, which was detected on chromosome 4 by GWAS among 330 varieties. Several major markers, namely, 15 CAPS markers, 6 SSR markers and 2 SNP markers, were designed to delimit the region to 59.8 kb region on chromosome 4. Utilizing the two populations consisting of 10 yellow and 10 green skin watermelons, we found a tightly linked functional SNP marker for the yellow skin phenotype. The application of this marker as a selection tool in breeding programs will help to improve the breeder’s ability to make selections at early stages of growth, thus accelerating the breeding program.

Comparative Transcriptome Analysis Provides Insights Into Yellow Rind Formation and Preliminary Mapping of the Clyr (Yellow Rind) Gene in Watermelon

“…Most of the typical color appearance in cucurbitaceous plants is controlled by a single dominant/recessive gene. In a previous research, the gene for watermelon yellow rind was mapped to a 59.8 Kb interval, but no target gene was found (Dou et al, 2018). But according to the newly released watermelon genome and primer information, the interval in the previous research should be 711.96 kb, not 59.8 kb.…”

“…Color is a focused trait of consumers for fruits and vegetables. Watermelon with yellow rind has become increasingly desirable for its delightful appearance and high carotenoid contents (Dou et al, 2018). Variation in rind color, including black, dark green, light green, and yellow are exhibited in watermelon (Guo et al, 2013).…”

“…As the fruit matures, color of the fruit rind will change from dark green to golden yellow, and stem and older leaves will become golden yellow (Barham, 1956). Different with gene go, another watermelon yellow rind gene following the dominant pattern was mapped to a region on chromosome 4 (Dou et al, 2018). But according to information of the primers sequence and the new released watermelon genome (Watermelon 97103 genome v2) assembled with the PacBio long reads, the dominant gene for yellow rind should be within a region of 729.05 kb but not 59.8 kb (http://cucurbitgenomics.org/organism/21) on the top end of chromosome 4 (Dou et al, 2018).…”

“…Recently, watermelon with yellow rind has gained increasing popularity among consumers (Dou et al, 2018), whereas the genes regulating yellow rind and their molecular mechanisms are still unknown in watermelon. In the present study, comprehensive transcriptome analysis for DEG (differentially expressed genes) screening and function prediction between the yellow rind inbred line WT4 and the green rind inbred line WM102 was completed.…”

PyBSASeq: a novel, simple, and effective algorithm for BSA-Seq data analysis

“…one bulk has more allele A while the other bulk has more allele a. BSA was primarily used to develop genetic markers for detecting gene-trait association at its early stage (1,2). Application of the next generation sequencing (NGS) technology to BSA eliminated the time-consuming and labor-intensive marker development and genetic mapping steps, and dramatically sped up the detection of gene-trait associations (3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18). This technique was termed either QTL-seq or BSA-Seq in different publications (5,6,19), we adapted the latter here because it can be applied to study both qualitative and quantitative traits.…”