Linkage disequilibrium and population structure in a core collection of Brassica napus (L.)

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.

“Late” effectors from Leptosphaeria maculans as tools for identifying novel sources of resistance in Brassica napus

“…rapifera , three genotypes) grouped with semi‐winter types, mainly of Asian origin (approximately 16 genotypes) (Figure 4 ). The grouping and representative diversity was consistent with other collection studies (Rahman et al, 2021 ; Wu et al, 2019 ). Additionally, a set of 31 “modern” winter‐type varieties grown in France, known for their behavior in the field with regard to stem canker resistance, was also genotyped (Figure 4 ; Table S2B ).…”

“…The identification of genotypes recognizing late effectors mainly in the semi‐winter group could be explained by the recent domestication of B. napus , occurring about 400 years ago. The first oilseed rape is hypothesized to be a semi‐winter type (Rahman et al, 2021 ). After this, a selection of genotypes adapted to more diverse environmental conditions was conducted, leading to the development of winter and spring genotypes, accompanied by a reduced diversity in both these groups and possible loss of interesting agronomic traits.…”

“…The semi winter‐type/rutabaga genepool, with a prevalence of Asian genotypes, is thus a peculiarly promising source of novel resistances. Different studies have recently obtained deep molecular data on large collections (Rahman et al, 2021 ; Wu et al, 2019 ), showing that the genebank collections hold 75–145 accessions that could be related to this semi‐winter‐type/rutabaga genepool and thus representing promising routes for more resistance gene discovery.…”

The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata genome

“…However, subgenomic bias resulting from selection pressure is not as clear in B. napus. The An subgenome exhibits more genetic diversity ( Huang et al, 2013 ; Qian et al, 2014 ; Sun et al, 2017 ) and has evolved at a faster rate ( Chen et al, 2021 ) than the Cn subgenome, but exhibits faster LD decay ( Qian et al, 2014 ; Rahman et al, 2022 ). The increased genetic diversity and recombination rates in the An genome could have been influenced by the prevalence of introgressions with B. rapa (Ar) during the breeding history of B. napus ( Qian et al, 2014 ; An et al, 2019 ).…”

Identification of candidate genes for LepR1 resistance against Leptosphaeria maculans in Brassica napus

“…The average number of heterozygous SNPs was 427,970 SNPs per B. napus genotype (7.77% of the 3,235,008 high quality SNPs) (Figure S1, Table S3). LD also showed a slower decay rate (Figure S2) over the previous B. napus LD findings obtained using less dense markers (845 RFLP, 89 and 451 SSR, 8,502 and 251,575 GBS SNP markers) (Bus et al, 2011;Xiao et al, 2012;Horvath et al, 2020;Rahman et al, 2022).…”