title: Evaluation of Linkage Disequilibrium Pattern and Association Study on Seed Oil Content in Brassica napus Using ddRAD Sequencing.
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.
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China.
authors.forename: Zhikun
authors.initials: Z
authors.lastname: Wu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China.
authors.forename: Xun
authors.initials: X
authors.lastname: Chen
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China.
authors.forename: Jiangsheng
authors.initials: J
authors.lastname: Wu
authors.affiliation: Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia.
authors.forename: Graham J
authors.initials: GJ
authors.lastname: King
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China.
authors.forename: Yingjie
authors.initials: Y
authors.lastname: Xiao
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China.
authors.forename: Kede
authors.initials: K
authors.lastname: Liu
mesh_terms: D001315:Australia; D029688:Brassica napus / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D002681:China; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D005819:Genetic Markers / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics; D005838:Genotype; D005843:Geography; D006239:Haplotypes; D007178:Inbreeding; D015810:Linkage Disequilibrium; D010938:Plant Oils / Q000378:metabolism*; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci / Q000235:genetics; D012639:Seeds / Q000737:chemistry*; D017422:Sequence Analysis, DNA / Q000379:methods*; D013045:Species Specificity
chemical_list: D005819:Genetic Markers; D010938:Plant Oils