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The USDA cucumber (Cucumis sativus L.) collection: genetic diversity, population structure, genome-wide association studies, and core collection development

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Horticulture Research 2018年第1期5卷 236-248页

作者： Xin Wang Kan Bao Umesh K.Reddy Yang Bai Sue A.Hammar Chen Jiao Todd C.Wehner Axel O.Ramírez-Madera Yiqun Weng Rebecca Grumet Zhangjun Fei Boyce Thompson Institute Cornell UniversityIthacaNY14853USA Gus R.Douglass Institute and Department of Biology West Virginia State UniversityInstituteVirginiaWV25112USA Department of Horticulture Michigan State UniversityEast LansingMI48824USA Horticultural Science Department North Carolina State UniversityRaleighNC27695USA Horticulture Department University of WisconsinMadisonWI53706USA USDA-ARS Vegetable Crops Research Unit MadisonWI53706USA USDA-ARS Robert W.Holley center for Agriculture and Health IthacaNY14853USA

Germplasm collections are a crucial resource to conserve natural genetic diversity and provide a source of novel traits essential for sustained crop *** collection,preservation and utilization of these materials depends upon knowledge of the genetic variation present within the *** we use the high-throughput genotyping-by-sequencing(GBS)technology to characterize the United States national plant Germplasm System(NPGS)collection of cucumber(Cucumis sativus L.).The GBS data,derived from 1234 cucumber accessions,provided more than 23 K high-quality single-nucleotide polymorphisms(SNPs)that are well distributed at high density in the genome(~1 SNP/10.6 kb).The SNP markers were used to characterize genetic diversity,population structure,phylogenetic relationships,linkage disequilibrium,and population differentiation of the NPGS cucumber *** results,providing detailed genetic analysis of the *** collection,complement NPGS descriptive information regarding geographic origin and phenotypic *** also identified genome regions significantly associated with 13 horticulturally important traits through genome-wide association studies(GWAS).Finally,we developed a molecularly informed,publicly accessible core collection of 395 accessions that represents at least 96%of the genetic variation present in the ***,the information obtained from the GBS data enabled deep insight into the diversity present and genetic relationships among accessions within the collection,and will provide a valuable resource for genetic analyses,gene discovery,crop improvement,and germplasm preservation.

关键词： sustained collection structure

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Preliminary Screening and Characterization of Microsatellite Markers in RAD-seq Data of Datnioides pulcher

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Animal Husbandry and Feed Science 2020年第2期12卷 23-28页

作者： Qu Zhengwei Song Hongmei Wang Xuejie Liu Yi Mu Xidong Liu Chao Hu Yinchang Key Laboratory of Leisure Fishery Ministry of Agriculture and Rural Affairs/Guangdong Modern Leisure Fishery Engineering Research Center/Pearl River Fishery Research InstituteChinese Academy of Fisheries SciencesGuangzhou 510380China College of Fisheries and Life Science Shanghai Ocean UniversityShanghai 201306China

[Objective]The paper was to develop the microsatellite markers of Datnioides pulcher,and to screen polymorphic SSR primers.[Method]*** was performed reduced-representation genome sequencing using RAD-seq(Restriction-site associated DNA sequencing).[Result]A total of 13308806 high-quality clean reads(HQ clean reads)lengths were obtained and 26359 simple sequence repeats(SSR)loci were detected in the obtained sequence by SSR search software,which consisted of 496 repeat *** most common types of repeat were A/T in single base repeat sequence,and AC/GT and A G/GT repeat units in di-base repeat ***/CCT,AGC/CTG and AGG/CCT were the dominant types in tri-base repeat *** quantity,the di-base repeat type SSR loci were the largest(19492),accounting for 73.95%of the total SSR *** for mono-nucleotide type,the repetition frequency of SSR loci was mainly ranged from 4 to 9,and the number of polymorphic SSR loci was *** 20066 pairs of SSR primers were successfully designed with Primer *** success rate of primer design was 76.13%.According to the repetition type and repetition number in the sequencing data,100 di-to penta-base repetition type SSRs were randomly selected and validated by PCR and polyacrylamide gel in six *** samples.A total of 73 pairs of primers were amplified by electrophoresis,and 20 of them were polymorphic.[Conclusion]The developed SSR sequences can be used for genetic analysis,genetic map construction and molecular marker assisted breeding of *** and its related species.

关键词： Datnioides pulcher RAD-seq Simple sequence repeats

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