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ARS Home » Midwest Area » Madison, Wisconsin » Vegetable Crops Research » Research » Publications at this Location » Publication #318585
Title: Genetic diversity, population structure, and formulation of a core collection of 1,197 Citrullus accessions

Author
item ZHANG, H - Beijing Academy Of Agricultural Sciences
item FAN, J - Beijing Academy Of Agricultural Sciences
item GUO, S - Beijing Academy Of Agricultural Sciences
item REN, Y - Beijing Academy Of Agricultural Sciences
item GONG, G - Beijing Academy Of Agricultural Sciences
item ZHANG, J - Beijing Academy Of Agricultural Sciences
item Weng, Yiqun
item Davis, Angela
item XU, Y - Beijing Academy Of Agricultural Sciences

Submitted to: HortScience
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/15/2015
Publication Date: 1/5/2016
Publication URL: http://handle.nal.usda.gov/10113/61963
Citation: Zhang, H., Fan, J., Guo, S., Ren, Y., Gong, G., Zhang, J., Weng, Y., Davis, A., Xu, Y. 2016. Genetic diversity, population structure, and formulation of a core collection of 1,197 Citrullus accessions. HortScience. 51(1):23-29.

Interpretive Summary: Watermelon belongs to the genus Citrullus. There has been continuing interests in breeding of watermelon for economic benefits, but information on the scope and utilization of genetic variations in Citrullus is still limited. The present study aimed to evaluating the genetic diversity and population structure of 1,197 watermelon collections maintained by the Beijing Vegetable Research Center, which belong to seven Citrullus species including C. naudinianus, C. colocynthis, C. rehmii, C. ecirrhosus, C. amarus, C. mucosospermus, and C. lanatus subsp. vulgaris. Twenty-three highly informative microsatellite markers evenly distributed in the watermelon genome were used to assess genetic diversity in this collection, which detected on average 6.1 alleles per locus with the average value of polymorphism information content (PIC) of 0.49. A high level of gene diversity (Nei’s gene diversity index H = 0.56) and a low observed heterozygosity (Ho = 0.10) were revealed within the 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. The groupings were consistent with the estimation of Fst and Nei’s genetic distances in collection. 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.

Technical Abstract: 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.