A New Diversity Panel for Winter Rapeseed (Brassica napus L.) Genome-Wide Association Studies

Abstract

A diverse population (429 member) of canola (Brassica napus L.) consisting primarily of winter biotypes was assembled and used in genome-wide association studies. Genotype by sequencing analysis of the population identified and mapped 290,972 high-quality markers ranging from 18.5 to 82.4% missing markers per line and an average of 36.8%. After interpolation, 251,575 high-quality markers remained. After filtering for markers with low minor allele counts (count > 5), we were left with 190,375 markers. The average distance between these markers is 4463 bases with a median of 69 and a range from 1 to 281,248 bases. The heterozygosity among the imputed population ranges from 0.9 to 11.0% with an average of 5.4%. The filtered and imputed dataset was used to determine population structure and kinship, which indicated that the population had minimal structure with the best K value of 2–3. These results also indicated that the majority of the population has substantial sequence from a single population with sub-clusters of, and admixtures with, a very small number of other populations. Analysis of chromosomal linkage disequilibrium decay ranged from ~7 Kb for chromosome A01 to ~68 Kb for chromosome C01. Local linkage decay rates determined for all 500 kb windows with a 10kb sliding step indicated a wide range of linkage disequilibrium decay rates, indicating numerous crossover hotspots within this population, and provide a resource for determining the likely limits of linkage disequilibrium from any given marker in which to identify candidate genes. This population and the resources provided here should serve as helpful tools for investigating genetics in winter canola.

Genetic loci associated with freezing tolerance in a European rapeseed (Brassica napus L.) diversity panel identified by genome‐wide association mapping

“…Thermo Fisher Scientific). The GBS library was constructed using the same protocol described in Horvath et al (2020). The GBS library was sequenced on an Illumina (San Diego, CA) HiSeq 4000 to generate single-end, 100-bp reads at the Genomic Sequencing and Analysis Facility at the University of Texas Southwestern Medical Center at Dallas, TX.…”

“…Local LD decay rates for 500 Kb with a 10 Kb sliding window was determined based on the method done previously (Horvath et al, 2020) to produce an LD decay In total, 69,554 SNP markers were identified for the 222 accessions with missing values less than 50%. Model-based cluster analysis suggested that there were eight subgroups (Figure 2 and Table S1, spreadsheet "Class and Country of origin"); there was no clear relationship between geographic distribution and the subgroups.…”

Genome-Wide Association Studies and Transcriptome Changes during Acclimation and Deacclimation in Divergent Brassica napus Varieties

“…The most significantly associated marker (S1_750314091) maps to position 37,666,286 on chromosome Ann_random from the B. napus reference assembly [15]. This region of the genome has a fast linkage decay rate with loss of linkage occurring within 100 bases in this population [16]. There are no known B. napus gene models within this narrow region, but the marker does fall in the middle of a characterized EST (DMBras.unigeneT00180796001).…”

“…A well-characterized diversity panel of primarily winter B. napus varieties [16] composed of 397 varieties was used in this studied. Briefly, this population is diverse with a minimal population structure with a K vs. Ln likelihood plot showing a drop between K-values of 2 and 4 and a neighbor-joining tree indicated as few as 6 major branches.…”

“…Candidate genes surrounding 4 of the top-most associated markers from the Tassel5 analyses and one marker that was indicated as significant by all three of the additional programs were chosen. The region of interest surrounding each marker was based on the physical distance where the local linkage decay (R2) crossed a threshold of 0.2 (see [16] for details).…”