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

Authors: KIM, H - PUSAN NATIONAL UNIVERSITY; HAN, D - PUSAN NATIONAL UNIVERSITY; KANG, J - PUSAN NATIONAL UNIVERSITY; CHOI, Y - PUSAN NATIONAL UNIVERSITY; Levi, Amnon; PARK, Y - PUSAN NATIONAL UNIVERSITY

Submitted to: Journal of Horticulture, Environment and Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/25/2015
Publication Date: 9/1/2015
Citation: Kim, H., Han, D., Kang, J., Choi, Y., Levi, A., Park, Y. 2015. Sequence-characterized amplified polymorphism markers for selecting rind stripe pattern in watermelon (Citrullus lanatus var. lanatus). Journal of Horticulture, Environment and Biotechnology. 56:341-349.

Interpretive Summary: Watermelon is an important crop in the U.S. and throughout the world. Recently, USDA, ARS scientists have collaborated with researchers at University of Illinois and Boyce Thompson Institute, and Cornell University on sequencing and assembly of the principle heirloom watermelon Charleston Gray genome. The watermelon genome data have proved useful for the identification of genes affecting fruit quality, disease, and pest resistance. There is a great interest by consumers and growers in watermelons with the dark green stripe rind pattern, known as Jubilee-type (JT) pattern. In this study, ARS scientists collaborated with scientists at Pusan National University, South Korea, on a genetic study that utilized the watermelon genome to identify DNA markers associated with watermelon fruit quality, particularly the stripe pattern on watermelon rind. This collaboration resulted in the identification and development of DNA markers linked to the rind pattern. The results of this study should be useful for watermelon breeders and scientists interested in accelerating the breeding process, particularly when selecting for rind pattern. Also, the results of this study should be useful for further studies aimed at identifying genes controlling watermelon fruit quality characters.

Technical Abstract: The inheritance of foreground stripe pattern in rind of watermelon fruits [Citrullus lanatus (Thunb.) Matsum. & Nakai] was evaluated and the molecular markers for selecting the 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) indicating the stripe pattern is a quantitative trait controlled by more than one gene. 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 ‘wsbin11’ are closely linked to AT14-900 on a genetic linkage map (developed using the F2 population derived from ‘AM’ x ‘TS’) are positioned 221 kb and 71 kb from AT14-900, respectively on the reference watermelon genome sequence. Marker genotyping of the F2 population showed wsbin6-11 is tightly linked to the JT stripe pattern of ‘TS’ and should be a useful co-dominant 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-type pattern) were homozygous for the wsbin6-11 marker (420 bp) derived ‘AM’. These results indicate that wsbin6-11 should be a useful marker in watermelon breeding programs aiming to select for the JT stripe pattern from other various foreground and background rind patterns.