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Genome-Wide SNP Marker Development and QTL Identification for Genomic Selection in Red Clover

  • S. Isobe
  • B. Boller
  • I. Klimenko
  • S. Kölliker
  • J. C. Rana
  • T. R. Sharma
  • K. Shirasawa
  • H. Hirakawa
  • S. Sato
  • S. Tabata
Conference paper

Abstract

Genomic selection (GS) has experienced remarkable advances in genome technologies over the past few years. However, employing GS for forage breeding has been considered difficult because forage species generally show short linkage disequilibrium (LD) across the genome. To elongate the LD, an Advanced Intercross Line (AIL) population was generated from crosses between six individuals originating from Switzerland, Russia and Japan. The suitability of this population was demonstrated for GS or association analysis. For high throughput genotyping, single nucleotide polymorphism (SNP) markers were developed by comparing transcriptome sequences obtained from two red clover individuals. An Illumina Golden Gate platform for 1,536 candidate SNPs was used for polymorphic analysis in the AIL population. A total of 784 SNP markers were identified as polymorphic. In addition, 75 polymorphic SSR markers were used for genotyping the AIL population. Approximately 200 plants each were established in 2010 in the fields of Palampur, Moscow region, Zurich and Chiba. Seed yields, flowering characteristics and morphological traits were evaluated in each region. Significant QTLs and QTL interactions were identified for the traits investigated by GMM analysis. The results suggest that the AIL population can be used for GS and association analysis.

Keywords

Genomic Selection Single Nucleotide Polymorphism Marker Candidate SNPs Significant QTLs Single Nucleotide Polymorphism Discovery 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • S. Isobe
    • 1
  • B. Boller
    • 2
  • I. Klimenko
    • 3
  • S. Kölliker
    • 2
  • J. C. Rana
    • 4
  • T. R. Sharma
    • 5
  • K. Shirasawa
    • 1
  • H. Hirakawa
    • 1
  • S. Sato
    • 1
  • S. Tabata
    • 1
  1. 1.Kazusa DNA Research InstituteKisarazuJapan
  2. 2.Agroscope FAL ReckenholzSwiss Federal Research Station for Agroecology and AgricultureZurichSwitzerland
  3. 3.All-Russian Williams Fodder Crop Research InstituteLugovayaRussia
  4. 4.National Bureau of Plant Genetic ResourcesShimlaIndia
  5. 5.CSK Himachal Pradesh Agricultural UniversityPalampurIndia

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