Abstract
Estimation of genetic diversity in rapeseed is important for sustainable breeding program to provide an option for the development of new breeding lines. The objective of this study was to elucidate the patterns of genetic diversity within and among different structural groups, and measure the extent of linkage disequilibrium (LD) of 383 globally distributed rapeseed germplasm using 8,502 single nucleotide polymorphism (SNP) markers. We divided the germplasm collection into five subpopulations (P1 to P5) according to geographic and growth habit-related patterns. All subpopulations showed moderate genetic diversity (average H = 0.22 and I = 0.34). The pairwise Fst comparison revealed a great degree of divergence (Fst > 0.24) between most of the combinations. The rutabaga type showed highest divergence with spring and winter types. Higher divergence was also found between winter and spring types. Admixture model based structure analysis, principal component and neighbor-joining tree analysis placed all subpopulations into three distinct clusters. Admixed genotype constituted 29.24% of total genotypes, while remaining 70.76% belongs to identified clusters. Overall, mean linkage disequilibrium was 0.03 and it decayed to its half maximum within < 45 kb distance for whole genome. The LD decay was slower in C genome (< 93 kb); relative to the A genome (< 21 kb) which was confirmed by availability of larger haplotype blocks in C genome than A genome. The findings regarding LD pattern and population structure will help to utilize the collection as an important resource for association mapping efforts to identify genes useful in crop improvement as well as for selection of parents for hybrid breeding.
Highlights
Rapeseed (Brassica napus L., AACC, 2n = 4x = 38), is a recent allopolyploid of polyphyletic origin that evolved from hybridization events between two parental ancestors of B. oleracea (Mediterranean cabbage, CC, 2n = 2x = 18) and B. rapa (Asian cabbage, AA, 2n = 2x = 20) [1]
The core is composed of 67 advanced breeding lines developed by North Dakota State University (NDSU) canola breeding program, 252 germplasm accessions collected from North Central Regional Plant Introduction Station (NCRPIS), Ames, Iowa, United States of America (USA) and 64 varieties collected from different countries
The inbreeding coefficient within individuals (Fit), inbreeding coefficient within subpopulations (Fis), observed heterozygosity (Ho) and fixation index (F) of all the markers ranged from -0.45 to 1.00, 0 to 0.73, 0 to 0.57 and 0.40 to 1.00, respectively
Summary
Rapeseed (Brassica napus L., AACC, 2n = 4x = 38), is a recent allopolyploid of polyphyletic origin that evolved from hybridization events between two parental ancestors of B. oleracea (Mediterranean cabbage, CC, 2n = 2x = 18) and B. rapa (Asian cabbage, AA, 2n = 2x = 20) [1]. Rapeseed genotypes having < 2% erucic acid in seed and < 30 μM glucosinolates in seed meal. LD and population structure Brassica napus www.ebi.ac.uk/eva/?eva-study=PRJEB42419), respectively
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