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2016 | 85 | 3 |
Tytuł artykułu

Identification, evaluation, and application of the genomic-SSR loci in ramie

Treść / Zawartość
Warianty tytułu
Języki publikacji
EN
Abstrakty
EN
To provide a theoretical and practical foundation for ramie genetic analysis, simple sequence repeats (SSRs) were identified in the ramie genome and employed in this study. From the 115 369 sequences of a specific-locus amplified fragment library, a type of reduced representation library obtained by high-throughput sequencing, we identified 4774 sequences containing 5064 SSR motifs. SSRs of ramie included repeat motifs with lengths of 1 to 6 nucleotides, and the abundance of each motif type varied greatly. We found that mononucleotide, dinucleotide, and trinucleotide repeat motifs were the most prevalent (95.91%). A total of 98 distinct motif types were detected in the genomic-SSRs of ramie. Of them, The A/T mononucleotide motif was the most abundant, accounting for 41.45% of motifs, followed by AT/TA, accounting for 20.30%. The number of alleles per locus in 31 polymorphic microsatellite loci ranged from 2 to 7, and observed and expected heterozygosities ranged from 0.04 to 1.00 and 0.04 to 0.83, respectively. Furthermore, molecular identity cards (IDs) of the germplasms were constructed employing the ID Analysis 3.0 software. In the current study, the 26 germplasms of ramie can be distinguished by a combination of five SSR primers including Ibg5-5, Ibg3-210, Ibg1-11, Ibg6-468, and Ibg6-481. The allele polymorphisms produced by all SSR primers were used to analyze genetic relationships among the germplasms. The similarity coefficients ranged from 0.41 to 0.88. We found that these 26 germplasms were clustered into five categories using UPGMA, with poor correlation between germplasm and geographical distribution. Our study is the first large-scale SSR identification from ramie genomic sequences. We have further studied the SSR distribution pattern in the ramie genome, and proposed that it is possible to develop SSR loci from genomic data for population genetics studies, linkage mapping, quantitative trait locus mapping, cultivar fingerprinting, and as genetic diversity studies.
Słowa kluczowe
EN
Wydawca
-
Rocznik
Tom
85
Numer
3
Opis fizyczny
Article 3510 [12p.], fig.,ref.
Twórcy
autor
  • Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key laboratory of Stemfiber Biomass and Engineering Microbiology, Ministry of Agriculture, 348 West Xianjiahu Road, Changsha, Hunan, China
autor
  • Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key laboratory of Stemfiber Biomass and Engineering Microbiology, Ministry of Agriculture, 348 West Xianjiahu Road, Changsha, Hunan, China
autor
  • Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key laboratory of Stemfiber Biomass and Engineering Microbiology, Ministry of Agriculture, 348 West Xianjiahu Road, Changsha, Hunan, China
autor
  • Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key laboratory of Stemfiber Biomass and Engineering Microbiology, Ministry of Agriculture, 348 West Xianjiahu Road, Changsha, Hunan, China
autor
  • Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key laboratory of Stemfiber Biomass and Engineering Microbiology, Ministry of Agriculture, 348 West Xianjiahu Road, Changsha, Hunan, China
autor
  • Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key laboratory of Stemfiber Biomass and Engineering Microbiology, Ministry of Agriculture, 348 West Xianjiahu Road, Changsha, Hunan, China
autor
  • Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key laboratory of Stemfiber Biomass and Engineering Microbiology, Ministry of Agriculture, 348 West Xianjiahu Road, Changsha, Hunan, China
autor
  • Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key laboratory of Stemfiber Biomass and Engineering Microbiology, Ministry of Agriculture, 348 West Xianjiahu Road, Changsha, Hunan, China
autor
  • Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key laboratory of Stemfiber Biomass and Engineering Microbiology, Ministry of Agriculture, 348 West Xianjiahu Road, Changsha, Hunan, China
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Typ dokumentu
Bibliografia
Identyfikatory
Identyfikator YADDA
bwmeta1.element.agro-9de669d1-6944-4ed6-b33c-3d1cb73a5f18
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