Genome-wide characterization of microsatellites and genetic diversity assessment of spinach in the Chinese germplasm collection

Spinach is a nutritional leafy green vegetable, and it also serves as a model species for studying sex chromosome evolution. Genetic marker development and genome structure analysis are important in breeding practice and theoretical evolution studies of spinach. In this study, the frequency and dist...

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Bibliographic Details
Published in:Breeding Science 2018, Vol.68(4), pp.455-464
Main Authors: Li, Shu-Fen, Wang, Bing-Xiao, Guo, Yu-Jiao, Deng, Chuan-Liang, Gao, Wu-Jun
Format: Article
Language:English
Subjects:
Biological evolution
Breeding
Breeding methods
Cultivars
Evolution
Gene polymorphism
Genetic analysis
Genetic diversity
Genetic markers
Genomes
Germplasm
Microsatellites
motif
Polymorphism
Research Paper
simple sequence repeat (SSR)
Spinach
Spinacia
Structural analysis
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Summary:Spinach is a nutritional leafy green vegetable, and it also serves as a model species for studying sex chromosome evolution. Genetic marker development and genome structure analysis are important in breeding practice and theoretical evolution studies of spinach. In this study, the frequency and distribution of different microsatellites in the recently released draft spinach genome were characterized. A total of 261,002 perfect microsatellites were identified (estimated frequency: ~262.1 loci/Mbp). The most abundant microsatellites were tetranucleotide and trinucleotide, accounting for 33.2% and 27.7% of the total number of microsatellites, respectively. A total of 105 primer pairs were designed and screened, and 34 were polymorphic among the detected spinach cultivars. Combined with seven primer sets developed previously, 41 primer pairs were used to investigate genetic diversity among 43 spinach cultivars in China. The average polymorphism information content value of the 41 markers was 0.43, representing an intermediate level. The spinach cultivars had a low genetic diversity, and no detectable common factors were shared by each group in the UPGMA dendrogram. This study’s findings facilitate further investigations on the organization of the microsatellites in spinach genome and provide clues for future breeding applications of spinach in China.
ISSN:1344-7610
1347-3735
DOI:10.1270/jsbbs.18032