Whole genome resequencing of watermelons to identify single nucleotide polymorphisms related to flesh color and lycopene content

Autoři: Saminathan Subburaj aff001;  Kayoun Lee aff001;  Yongsam Jeon aff001;  Luhua Tu aff001;  Gilwoo Son aff002;  SuBok Choi aff003;  Yong-Pyo Lim aff001;  Cecilia McGregor aff004;  Geung-Joo Lee aff001
Působiště autorů: Department of Horticulture, Chungnam National University, Daejeon, Republic of Korea aff001;  Breeding Institute, Hyundai Seed Co Ltd., Yeoju, Gyeonggi, Republic of Korea aff002;  Asia Seed, Co., Ltd., Seoul, Republic of Korea aff003;  Department of Horticulture, University of Georgia, Athens, GA, United States of America aff004
Vyšlo v časopise: PLoS ONE 14(10)
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pone.0223441


Cultivated watermelon (Citrullus lanatus) is one of the most important food crops in the Cucurbitaceae family. Diversification after domestication has led cultivated watermelons to exhibit diverse fruit flesh colors, including red, yellow, and orange. Recently, there has been increased interest in red-fleshed watermelons because they contain the antioxidant cis-isomeric lycopene. We performed whole genome resequencing (WGRS) of 24 watermelons with different flesh colors to identify single-nucleotide polymorphisms (SNPs) related to high lycopene content. The resequencing data revealed 203,894–279,412 SNPs from read mapping between inbred lines and the 97103 reference genome. In total, 295,065 filtered SNPs were identified, which had an average polymorphism information content of 0.297. Most of these SNPs were intergenic (90.1%) and possessed a transversion (Tv) rate of 31.64%. Overall, 2,369 SNPs were chosen at 0.5 Mb physical intervals to analyze genetic diversity across the 24 inbred lines. A neighbor-joining dendrogram and principal coordinate analysis (PCA) based on the 2,369 SNPs revealed that the 24 inbred lines could be grouped into high and low lycopene-type watermelons. In addition, we analyzed SNPs that could discriminate high lycopene content, red-fleshed watermelon from low lycopene, yellow or orange watermelon inbred lines. For validation, 19 SNPs (designated as WMHL1–19) were chosen randomly, and cleavage amplified polymorphic sequence (CAPS) markers were designed. Genotyping of the above 24 lines and 12 additional commercial cultivars using WMHL1–19 CAPS markers resulted in match rates of over 0.92 for most validated markers in correlation with the flesh color phenotypes. Our results provide valuable genomic information regarding the high lycopene content phenotype of red-fleshed cultivated watermelons, and the identified SNPs will be useful for the development of molecular markers in the marker-assisted breeding of watermelons with high lycopene content.

Klíčová slova:

Fruits – Chromosome mapping – Inbred strains – Introns – Invertebrate genomics – Molecular genetics – Seeds – Carotenoids


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