Development and mapping of functional expressed sequence tag-derived simple sequence repeat markers in a rubber tree RRIM600 × PB217 population

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• 作者：Kanlaya Nirapathpongporn ; Panida Kongsawadworakul ; Unchera Viboonjun…
• 关键词：EST ; SSR marker ; Functional markers ; Genetic linkage map ; Hevea brasiliensis ; Rubber tree
• 刊名：Molecular Breeding
• 出版年：2016
• 出版时间：April 2016
• 年：2016
• 卷：36
• 期：4
• 全文大小：1,496 KB
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• 作者单位：Kanlaya Nirapathpongporn (1) (2)
  Panida Kongsawadworakul (3)
  Unchera Viboonjun (3)
  Kanikar Teerawattanasuk (2)
  Hervé Chrestin (4)
  Marc Segiun (5)
  André Clément-Dement (5)
  Jarunya Narangajavana (1)
  
  1. Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
  2. Rubber Research Institute of Thailand (RRIT), Bangkok, Thailand
  3. Department of Plant Science, Faculty of Science, Mahidol University, Bangkok, Thailand
  4. Institut de Recherche pour le Développement (IRD), Montpellier, France
  5. Agricultural Research for Development (CIARD), Montpellier, France
  
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Life Sciences
  Plant Sciences
  
• 出版者：Springer Netherlands
• ISSN：1572-9788

文摘

Sets of polymorphic expressed sequence tag–simple sequence repeat (EST-SSR) markers from the rubber tree (Hevea brasiliensis) have been published by many researchers, but none has been specifically developed to study latex and wood yield traits. In this study, a total 10,321 rubber tree EST sequences, generated from suppression subtractive hybridization-cDNA libraries of bark and latex of high- and low-yielding clones, were used as sources for SSR searching. A total of 432 EST-SSR loci were identified and it was possible to design primer pairs for a subset of 298 EST-SSRs. The highest proportion of EST-SSRs was represented by dinucleotide repeats (46.6 %), followed by trinucleotide repeats (44.3 %). Based on BLASTX analysis, 234 ESTs (80 %) showed similarity to genes in NCBI databases and could be divided into 120 putative proteins with known function and 114 unknown proteins. To enhance the resolution of an existing linkage map from previous work on a rubber tree RRIM600 × PB217 population, 69 EST-SSR markers from the above set were tested to be integrated into the reference genetic map. The enriched map of 18 linkage groups spanned 2054.2 cM in length, showed an average genetic distance of 4.3 cM between adjacent markers, and included 63 new EST-SSR markers. The enhanced map from this study provides a basis for comparative mapping using PCR-based markers and identification of expressed genes possibly affecting important traits of interest.