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2024 Vol.42, Issue 4 Preview Page

Research Article

Development of Single-Nucleotide Polymorphism Markers for Seed Coat Color in Watermelon
Yoon Jeong Jang1†
,
Ki Ryong Kim1†
,
Jisu Ryu1
,
Yongjae Kim2
,
Sang-Min Chung3
,
Gung Pyo Lee1*
1Department of Plant Science and Technology, Chung-Ang University, Anseong 17546, Korea
2Partner Seeds Co., Ltd., Gimje 54324, Korea
3Department of Life Sciences, Dongguk University, Seoul 04620, Korea
*Corresponding Author
†These authors contributed equally to this work.
31 August 2024. pp. 480-491
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Abstract

Seed coat color affects water absorption, gas diffusion, seed dormancy, seed quality, germination, and seedling appearance. These attributes of watermelon seeds thus necessitate the establishment of watermelon breeding programs that produce desired seed coat colors. However, the hereditary and molecular mechanisms underlying this feature remain unknown. Here, we aimed to identify the genomic region responsible for seed coat color in watermelon and to design single-nucleotide polymorphism (SNP) markers that are closely associated with this characteristic. We crossed two inbred lines, RG-21 (white seed coat, WSC) and Wr-609 (red seed coat, RSC), to generate F1 hybrids (tan seed coat) and F2 populations for locus mapping and a SNP marker analysis. Our findings indicated that the F2 seed coat color is controlled by negative epistasis-expressing WSC. A bulked segregant analysis combined with Illumina whole-genome resequencing revealed a putative causative genomic area for WSC at 5.1–9.7 Mb on chromosome (Chr.) 6 and RSC at 3.6–7.7 Mb on Chr. 5. Based on the four-gene hypothesis, the genotypes of the WSC, RSC, and F1 hybrids were Rtwd, rtWd, and RtWd, respectively. We then applied 19 high-resolution melting markers to 106 F2 progeny to identify the causative genomic regions. We created a strongly co-segregated SNP marker for WSC at 6.9–7.1 Mb on Chr. 6 and RSC at 4.2–4.8 Mb on Chr. 5. Our findings serve as a basis for utilizing seed coat color in watermelon breeding programs and for expediting F1 cultivar generation.

Keywords
bulked segregant analysis
delta single-nucleotide polymorphism index
high-resolution melting
linkage marker
next-generation sequencing
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Information
  • Publisher :KOREAN SOCIETY FOR HORTICULTURAL SCIENCE
  • Publisher(Ko) :한국원예학회
  • Journal Title :Horticultural Science and Technology
  • Journal Title(Ko) :원예과학기술지
  • Volume : 42
  • No :4
  • Pages :480-491
  • Received Date : 2024-06-14
  • Revised Date : 2024-07-03
  • Accepted Date : 2024-07-05
  • DOI :https://doi.org/10.7235/HORT.20240060
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