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ARS Home » Midwest Area » Madison, Wisconsin » Vegetable Crops Research » Research » Publications at this Location » Publication #326624
Title: Genome wide characterization of simple sequence repeats in watermelon genome and their application in comparative mapping and genetic diversity analysis

Author
item ZHU, HUAYU - Henan Agricultural University
item SONG, PENGYAO - Henan Agricultural University
item KOO, DAL-HOE - University Of Wisconsin
item GUO, LUQIN - Henan Agricultural University
item LI, YANMAN - Henan Agricultural University
item SUN, SHOURU - Henan Agricultural University
item Weng, Yiqun
item YANG, LUMING - Henan Agricultural University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/5/2016
Publication Date: 8/5/2016
Publication URL: http://handle.nal.usda.gov/10113/63262
Citation: Zhu, H., Song, P., Koo, D., Guo, L., Li, Y., Sun, S., Weng, Y., Yang, L. 2016. Genome wide characterization of simple sequence repeats in watermelon genome and their application in comparative mapping and genetic diversity analysis. Biomed Central (BMC) Genomics. 17(1):557. doi: 10.1186/s12864-016-2870-4.

Interpretive Summary: Microsatellite or SSR markers are one of the most informative and versatile DNA-based markers for many marker-based studies. The whole genome sequences with next-generation sequencing (NGS) technology make it possible to develop large numbers of SSRs through bioinformatic analysis of genome data. In this tduy, we developed genome wide SSR markers from the watermelon draft genome which were used in comparative mapping with cucumber and melon. We also applied these SSRs in genetic diversity and population structure analysis in watermelon germplasm. A total of 39,523 microsatellite sequences were identified in the watermelon genome with ~111 SSRs/Mbp from which 32,870 SSR primer sets were designed. The SSRs with AT dinucleotide motif were the most abundant. In silico PCR analysis identified 832 and 925 SSRs with one amplicon in the cucumber and melon genome, respectively. Chromosome synteny based on these shared SSR markers showed complicated mosaic patterns between watermelon and the melon or cucumber genomes. Genetic diversity and population structure analysis of 134 watermelon accessions with 32 SSR highly informative SSRs grouped these accessins into two major clusters with Group 1 containing all C. colocynthis accessions. Group II was further divided into two subclusters including all C.lanatus var. citorides accessions in Group II which were originated from Africa and all C. lanatus var. lanatus accessions in group III. Population structure analysis indicated that most accessions used in this study had an admixed ancestry. The large number of SSR markers developed herein provides a valuable resource for genetic linkage map construction, map-based gene or QTL cloning and marker-assisted selection in watermelon breeding. The cross species transferable SSR markers could also be used in other cucurt species that do not have draft genomes.

Technical Abstract: Simple sequence repeats (SSR) or microsatellite markers are one of the most informative and versatile DNA-based markers. The use of next-generation sequencing technologies allow whole genome sequencing and make it possible to develop large numbers of SSRs through bioinformatic analysis of genome data. In this tduy, we developed genome wide SSR markers from the watermelon draft genome which were used in comparative mapping with cucumber and melon. We also applied these SSRs in genetic diversity and population structure analysis in watermelon germplasm. A total of 39,523 microsatellite sequences were identified in the watermelon genome with ~111 SSRs/Mbp from which 32,870 SSR primer sets were designed. The SSRs with AT dinucleotide motif were the most abundant. In silico PCR analysis identified 832 and 925 SSRs with one amplicon in the cucumber and melon genome, respectively. Chromosome synteny based on these shared SSR markers showed complicated mosaic patterns between watermelon and the melon or cucumber genomes. Genetic diversity and population structure analysis of 134 watermelon accessions with 32 SSR highly informative SSRs grouped these accessins into two major clusters with Group 1 containing all C. colocynthis accessions. Group II was further divided into two subclusters including all C.lanatus var. citorides accessions in Group II which were originated from Africa and all C. lanatus var. lanatus accessions in group III. Population structure analysis indicated that most accessions used in this study had an admixed ancestry. The large number of SSR markers developed herein provides a valuable resource for genetic linkage map construction, map-based gene or QTL cloning and marker-assisted selection in watermelon breeding. The cross species transferable SSR markers could also be used in other cucurt species that do not have draft genomes.