Sequence-characterized amplified polymorphism markers for selecting rind stripe pattern in watermelon (Citrullus lanatus L.)

Abstract

The inheritance of foreground stripe pattern in rind of watermelon fruits [Citrullus lanatus (Thunb.) Matsum. & Nakai] was evaluated and molecular markers for selecting the Jubilee-type (JT) stripe pattern were developed based on bulked segregant analysis (BSA). Divergence in rind pattern among F2 progeny derived from crossing Crimson-type (CT) 'Arka Manik' (AM) with JT 'TS34' (TS) indicated that stripe pattern is a quantitative trait controlled by more than one gene. The BSA of F2 plants (derived from a cross between 'AM' and 'TS') using 60 random amplified polymorphic DNA (RAPD) primers revealed a distinct RAPD band (AT14-900) polymorphic between 'AM' (CT) and 'TS' (JT). The AT14-900 sequence (925 bp) was blasted to the reference watermelon (97103) genome and high sequence similarity (97.8%) was identified on physical location of 26246077 to 26246993 bp on chromosome 6. Two expressed sequence tags (ESTs) designated 'wsbin6-10' and 'wsbin6-11' that were closely linked to AT14-900 on a genetic linkage map (developed using the F2 population derived from 'AM' x 'TS') were positioned 2,216 kb and 71 kb from AT14-900, respectively on the reference watermelon genome sequence. Marker genotyping of the F2 population showed that wsbin6-11 was tightly linked to the JT stripe pattern of 'TS' and could be a useful codominant marker for selecting this trait. In a test using 100 breeding lines, 34 of the 36 lines carrying the JT stripe pattern were homozygous for the wsbin6-11 marker (450 bp) derived from 'TS', while other lines (e.g., with no stripe or CT stripe pattern) were homozygous for the wsbin6-11 marker (420 bp) derived 'AM'. These results indicated that wsbin6-11 would be a useful marker in watermelon breeding programs aiming to select for the JT stripe pattern from other various foreground and background rind patterns.

Genome-Wide Sequence Variation in Watermelon Inbred Lines and Its Implication for Marker-Assisted Breeding

“…2). Thus, PCA in this study using SNPs detected in 19 inbred lines further confirmed that a striped rind pattern is one representative fruit trait that distinguishes the Crimson-type from the non-Crimson-type as previously noted (Kim et al, 2015a).…”

“…4. In our previous study (Kim et al, 2015a), a major QTL for fruit shape was detected from Chr. 3; however, no SNP hot spot was found for the fruit shape trait in this study.…”

Evaluation of DNA Markers for Fruit-related Traits and Genetic Relationships Based on Simple Sequence Repeat in Watermelon Accessions

“…for 1 min; 35 cycles at 94°C for 15 s, 55°C for 30 s, and 72°C for 1 min; and ending at 72°C for 3 min. For fruit stripe pattern, a SCAR marker wsb6 -11 reported by Kim et al (2015b), was examined (Table 1). PCR amplification of the wsb6 -11 marker was performed using a touch -down PCR program, as described above.…”

“…This marker was developed by BSA of F2 progeny derived from AM [Crimson -type stripe pattern (CSP)] × TS [Jubilee -type stripe pattern (JSP)], and was reported to be effective in selecting the Jubilee -type stripe pattern (Kim et al, 2015b).…”

“…In watermelon, the number of publicly available markers for marker -assisted selection (MAS) is limited. Based on bulked segregant analysis (BSA), Kim et al (2015b) demonstrated that a sequence characterized amplified region (SCAR) marker (wsb6 -11) is tightly linked to the stripe pattern observed in the JT cultivar, which is useful for discriminating this cultivar from CT and non -striped rind types. By constructing an intraspecific genetic map and performing quantitative trait locus (QTL) analysis, Kim et al (2015c) identified two cleaved amplified polymorphic sequence (CAPS) markers, SUN -Cla011257 and wsb3 -24, for fruit shape.…”