Draft Reference Genome Anchored to a High Density SNP Linkage Map Provides Better Resolution for Genetic Diversity Analysis and Trait-Dissection

Draft reference genome anchored to a high density SNP linkage map provides better resolution for genetic diversity analysis and trait-dissection

 Parwinder Kaur¹, Hideki Hirakawa², Kenta Shirasawa², Soichiro Nagano², Phillip Nichols⁴, Rudi Appels³, William Erskine¹ and Sachiko N. Isobe²

1.  Centre for Plant Genetics and Breeding, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
2. Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, Chiba 292-0818, Japan
3. Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
4. Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, WA 6151, Australia

 Abstract

Subterranean clover (Trifolium subterraneum L.) is the key forage pasture legume species in Australia and is also an ideal reference species for comparative mapping within the Leguminosae. It is a diploid (2n =16), predominantly inbreeding annual species that can be readily hybridised. It also has a wide range of diversity for both qualitative and quantitative agronomic and morphological characters. We have assembled 471.8 Mb the first draft genome sequence of subterranean clover and this assembled sequence covers 85.4% of the subterranean clover genome containing 42,706 genes. Eight pseudomolecules were constructed based on Illumina and Roche 454 assembled genome sequences and a high density SNP linkage map. The SNP linkage map was constructed with the F₂ population 92S80, generated from a cross between the subterranean clover cultivars Woogenellup and Daliak. A total of 899,064 candidate SNPs were identified by mapping the 25.8 Gb Woogenellup and 337.9 Gb F2 HiSeq 1000 PE reads onto the draft reference sequences, and 52,635 SNPs were subsequently selected for Affymetrix Axiom® myDesign™ TG Array. Based on the genotypes of the 155 F2 progenies obtained from the array, a SNP linkage map was constructed with 35,341 SNPs. The mapped SNPs generated a total of 2,153 bins that were randomly located on eight linkage groups totaling 2,084 cM in length.

Availability of a fully sequenced genome anchored to a high density SNP linkage map will be exploited for the analysis of genetic diversity and trait-dissection, as well as gene tagging for marker-assisted selection. Additionally, functional genomics, transcriptomics, and proteomics can be used more precisely and effectively in forage legume improvement.

 

Corresponding Author: Parwinder Kaur, Parwinder.kaur@uwa.edu.au