Genetic structure and linkage disequilibrium pattern of a rapeseed (Brassica napus L.) association mapping panel revealed by microsatellites

Abstract

Understanding the population structure and linkage disequilibrium (LD) is a prerequisite for association mapping of complex traits in a target population. In this study, we assessed the genetic diversity, population structure and the extent of LD in a panel of 192 inbred lines of Brassica napus from all over the world using 451 single-locus microsatellite markers. The inbred lines could be divided into P1 and P2 groups by a model-based population structure analysis. Out of the 142 inbred lines in the P1 group, 126 lines were from China and Japan, and the remaining 16 lines were from Europe, Canada and Australia. In the P2 group, 33 out of the 50 lines were from Europe, Canada, and Australia, and the remaining 17 lines were from China. Structure analysis further divided each group into two subgroups. AMOVA, pairwise F (ST) and neutrality analyses confirmed the differentiation between groups and subgroups. More than 80 % of the pairwise kinship estimates between inbred lines were <0.05, indicating that relative kinship is weak in our panel. Only 6 % linked marker pairs showed LD, suggesting the low level of LD in this association panel. The LD decayed within 0.5-1 cM at the genome level, and varied considerably across each group and subgroup, due to the population size, genetic background and genetic drift. The characterization of the population structure and LD patterns would be useful for performing association studies for complex agronomic traits in rapeseed.

Genome-Wide Association Study Dissects the Genetic Architecture of Seed Weight and Seed Quality in Rapeseed (Brassica napus L.)

“…60,61 The kinship analysis revealed that most lines in the panel have no or weak kinship, together with significant differences in phenotype performance, indicating that this panel is suitable for association analysis. The mean pairwise r 2 values is close to previous estimates of 0.0117 26 or 0.0247 34 and lower than 0.037 estimated for the population used by Delourme et al , 32 confirming the low overall level of LD in B. napus . At the genome level, mean LD decay was estimated to be 0.5–1.2 cM in rapeseed germplasm.…”

Natural Allelic Diversity, Genetic Structure and Linkage Disequilibrium Pattern in Wild Chickpea

“…The extensive LD estimates and extended chromosomal LD decay (∼500–600 kb) determined in the six population groups using the microsatellite and SNP markers were much higher than that reported previously in cross-pollinated [58], [79]–[83] and non-domesticated [84], [85] self-pollinated plant species, but comparable to domesticated selfing crop species like barley [86], [87]. The extensive LD estimates and extended LD decay in the domesticated self-pollinated crop species like chickpea in contrast to other domesticated self-pollinated crops like rice and soybean could be due to extensive contribution of four sequential bottlenecks during the domestication of chickpea [1], [3]–[5], which resulted in the reduction of genetic diversity in cultivated chickpea than that of other domesticated selfing crop plant species.…”

Association mapping of seed quality traits in Brassica napus L. using GWAS and candidate QTL approaches

“…In this respect, the current study increases our understanding of the genetic composition of wintertype oilseed rape and expands on previous work in this field. Approximately 80 % of the lines exhibit low relative kinship, a phenomenon that has also been observed in other B. napus association panels (Xiao et al 2012;Fritsche et al 2012). The evaluation of both, population structure and kinship, suggested a favorable scenario to conduct AM (Soto-Cerda and Cloutier 2012).…”

“…These have helped to identify and/or confirm QTL underlying seed quality traits (Hasan et al 2008;Honsdorf et al 2010;Fritsche et al 2012;Harper et al 2012;Li et al 2014), demonstrating the power of AM to discover marker-trait associations in genetically diverse panels or populations (reviewed in Gupta et al 2005;Soto-Cerda and Cloutier 2012). Taking into account the low extension of LD and rapid LD decay observed in different B. napus populations (Bus et al 2011;Xiao et al 2012;Delourme et al 2013), the use of 4025 evenly spaced SNP markers provided an adequate genome coverage to conduct GWAS.…”

“…There have been attempts to characterize the extent of LD and define the number of markers required for suitable mapping resolution in B. napus Bus et al 2011;Xiao et al 2012). Recently, a more extensive study (Delourme et al 2013) generated a high-density SNP-based genetic map (2.56 SNP per cM) using 5764 SNP markers and 1603 PCR markers in four segregating double haploid (DH) populations.…”