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

David P Horvath,Jason Fiedler,Zahirul I Talukder,James V Anderson,Gregor A Horvath,Wun S Chao,Aidan P Horvath,Michael Stamm

doi:10.3390/agronomy10122006

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.

Highlights

Winter rapeseed is an economically valuable, cool season oilseed crop grown in the United States, ranging from Idaho to the central Mid-Atlantic states
We were left with 429 lines with 251,575 single nucleotide polymorphisms (SNPs) mapped to the reference canola genome
We report on a genotyped canola diversity panel, consisting primarily of winter biotypes, Here, wesufficient report ongenetic a genotyped canola diversity panel, consisting primarily of winter biotypes, that contains diversity to serve as a valuable resource for identifying loci associated that contains sufficient genetic diversity to serve as a valuable resource for identifying loci associated with a multitude of traits

Summary

Introduction

Winter rapeseed is an economically valuable, cool season oilseed crop grown in the United States, ranging from Idaho to the central Mid-Atlantic states. It has gained attention as a potential winter cover crop, with traits suitable for developing dual-cropping systems, since it generally outperforms spring biotypes in yield and matures early enough to allow for harvest before planting of some varieties of corn, soybean, and sunflower [1]. There are a number of traits that breeders would need to optimize in order to exploit the full potential of this crop. GWAS requires a diverse population of a given species to utilize the genetic diversity that has built up through evolutionary time [4]

Methods

Results

Discussion

Conclusion