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Genetic diversity, population structure, and formulation of a core collection of 1,197 Citrullus accessions

Haiying Zhang, Jianguang Fan, Shaogui Guo, Yi Ren, Guoyi Gong, Jie Zhang, Yiqun Weng, Angela Davis, Yong Xu
HortScience 2016 v.51 no.1 pp. 23-29
Citrullus, alleles, ecotypes, genetic markers, genetic variation, genome-wide association study, germplasm, heterozygosity, microsatellite repeats, plant breeding, plant genetic resources, population structure, watermelons
There has been continuing interests in breeding of watermelon for economic benefits, but information on the scope and utilization of genetic variations in this genus (Citrullus) is still limited. We evaluated the genetic diversity and population structure of 1,197 watermelon collections, which belong to seven Citrullus species using 23 highly informative microsatellite (SSR) markers. On average, 6.1 alleles were detected per marker with the average value of PIC (polymorphism information content) of 0.49. A high level of gene diversity and low observed heterozygosity were revealed within this collection. Structure analysis grouped the 1,197 accessions into two main populations (Pop I and Pop II) and an admixture group. Pop I contained 450 accessions from C. lanatus subsp. vulgaris (446) and C. mucosospermus (4). Pop II comprised 465 accessions, 379 of which belonged to C. lanatus subsp. vulgaris, and 86 to C. naudinianus (3), C. ecirrhosus (2), C. rehmii (2), C. colocynthis (11), C. amarus (58) and C. mucosospermus (10).The remaining 282 accessions were classified as an admixture group. The two main populations were further subdivided into four subgroups. We confirmed the distinct genetic backgrounds between American and East Asian ecotypes. Subsequently, we defined a core set consisting of 130 accessions including 47 from Pop I, 68 from Pop II and 15 from the Admixture group. This core set was able to capture all 133 alleles detected by 23 SSRs in 1,197 accessions. These results may facilitate efficient use of genetic variations in Citrullus in watermelon breeding and help optimization of accessions in genome wide association studies.