AI Article Synopsis
- High-density genetic markers are essential for analyzing linkage disequilibrium (LD) and conducting genome-wide association studies (GWAS) in crops, specifically in oilseed rape.
- The study sequenced 189 inbred lines of B. napus using ddRAD, mapping over 15,921 RAD tags to a reference genome, revealing an LD decay distance of 1,214 kb across the genome.
- The research identified distinct haplotype blocks and categorized the panel into two groups based on geographic origins, highlighting differences in selection processes, while also pinpointing two genetic loci significantly linked to seed oil content.
Article Abstract
High-density genetic markers are the prerequisite for understanding linkage disequilibrium (LD) and genome-wide association studies (GWASs) of complex traits in crops. To evaluate the LD pattern in oilseed rape, we sequenced a previous association panel containing 189 B. napus inbred lines using double-digested restriction-site associated DNA (ddRAD) and genotyped 19,327 RAD tags. A total of 15,921 RAD tags were assigned to a published genetic linkage map and the majority (71.1%) of these tags was uniquely mapped to the draft reference genome "Darmor-bzh." The distance of LD decay was 1,214 kb across the genome at the background level (r2 = 0.26), with the distances of LD decay being 405 kb and 2,111 kb in the A and C subgenomes, respectively. A total of 361 haplotype blocks with length > 100 kb were identified in the entire genome. The association panel could be classified into two groups, P1 and P2, which are essentially consistent with the geographical origins of varieties. A large number of group-specific haplotypes were identified, reflecting that varieties in the P1 and P2 groups experienced distinct selection in breeding programs to adapt their different growth habitats. GWAS repeatedly detected two loci significantly associated with oil content of seeds based on the developed SNPs, suggesting that the high-density SNPs were useful for understanding the genetic determinants of complex traits in GWAS.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4701484 | PMC |
| http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0146383 | PLOS |
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