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

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)


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.

Original languageEnglish
Title of host publicationBreeding Strategies for Sustainable Forage and Turf Grass Improvement
PublisherSpringer Netherlands
Number of pages8
ISBN (Electronic)9789400745551
ISBN (Print)9789400745544
Publication statusPublished - 2013 Jan 1
Externally publishedYes

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)


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