A high-throughput SNP array in the amphidiploid species Brassica napus shows diversity in resistance genes

Abstract

Single-nucleotide polymorphisms (SNPs)are molecular markers based on nucleotide variation and can be used for genotyping assays across populations and to track genomic inheritance. SNPs offer a comprehensive genotyping alternative to whole-genome sequencing for both agricultural and research purposes including molecular breeding and diagnostics, genome evolution and genetic diversity analyses, genetic mapping, and trait association studies. Here genomic SNPs were discovered between four cultivars of the important amphidiploid oilseed species Brassica napus and used to develop a B. napus Infinium™ array containing 5,306 SNPs randomly dispersed across the genome. Assay success was high, with >94 % of these producing a reproducible, polymorphic genotype in the 1,070 samples screened. Although the assay was designed to B. napus, successful SNP amplification was achieved in the B. napus progenitor species, Brassica rapa and Brassica oleracea, and to a lesser extent in the related species Brassica nigra. Phylogenetic analysis was consistent with the expected relationships between B. napus individuals. This study presents an efficient custom SNP assay development pipeline in the complex polyploid Brassica genome and demonstrates the utility of the array for high-throughput genotyping in a number of related Brassica species. It also demonstrates the utility of this assay in genotyping resistance genes on chromosome A7, which segregate amongst the 1,070 samples.

The development and application of bioinformatics methods and software tools for computational single nucleotide polymorphism discovery

“…In this study the Ts/Tv ratios range from 1.2 to 1.26 across all 10 chromosomes (Table 3.11) which is very similar to other B. napus studies such 1.29 (Dalton-Morgan et al, 2014) and 1.39 (Bus et al, 2012). These values are lower than Ts/Tv ratios observed in other plants such as 1.6 in eggplant (Barchi et al, 2011), 3.9 in maize, 1.9 in alfalfa, 1.6 in eikorn wheat (Triticum monococcum L.), 2.5 in barley and Lotus (Vitte and Bennetzen, 2006) A study of eight tomato cultivars identified more than 4 million SNPs (Causse et al, 2013).…”

“…In this study 6 cultivars were used and 638,593 SNPs were discovered, this is more than 50% more SNPs than idenfiried with four cultivars reflecting the additional data and diversity (Dalton-Morgan et al, 2014).…”

“…SGSautoSNP has been applied to call SNPs in canola, wheat (4 culitvars), wheat (6 cultivars) and in the fungal genome of L. maculans with a prediction accuracy of 95%, 93%, 95% and 90%, respectively (Dalton-Morgan et al, 2014, Lai et al, 2015, Zander et al, 2013. This compares to an accuracy of 35.8% in tetraploid durum wheat (Triticum durum Desf.)…”

Genetic mapping in polyploids

“…Examples of the former include alfalfa (Li et al, 2014b), chrysanthemum (van Geest et al, 2017c, potato (Hamilton et al, 2011;Felcher et al, 2012;Vos et al, 2015), rose and sour cherry (Peace et al, 2012). Examples of allopolyploid SNP arrays include cotton (Hulse-Kemp et al, 2015), oat (Tinker et al, 2014), oilseed rape (Dalton- Morgan et al, 2014;Clarke et al, 2016), peanut (Pandey et al, 2017), strawberry (Bassil et al, 2015) and wheat (Akhunov et al, 2009;Cavanagh et al, 2013;Wang et al, 2014b;Winfield et al, 2016). Untargeted approaches such as genotyping-by-sequencing have also been applied, for example in autopolyploids such as alfalfa Yu et al, 2017), blueberry (McCallum et al, 2016), bluestem prairie grass (Andropogon gerardii) (McAllister and Miller, 2016), cocksfoot (Dactylis glomerata) (Bushman et al, 2016), potato (Uitdewilligen et al, 2013;Sverrisdóttir et al, 2017), sugarcane (Balsalobre et al, 2017;Yang et al, 2017b) and sweet potato (Shirasawa et al, 2017), and in allopolyploids such as coffee (Moncada et al, 2016), cotton (Islam et al, 2015;Reddy et al, 2017), intermediate wheatgrass (Thinopyrum intermedium) (Kantarski et al, 2017), oat (Chaffin et al, 2016), prairie cordgrass (Spartina pectinata) (Crawford et al, 2016), shepherd's purse (Capsella bursa-pastoris) (Cornille et al, 2016), wheat (Poland et al, 2012;Edae et al, 2...…”

Oilseed rape: learning about ancient and recent polyploid evolution from a recent crop species

“…Large-scale SNP datasets are an important enabling resource for development of high-throughput molecular marker genotyping arrays (e.g. Dalton-Morgan et al 2014). These arrays comprise an extremely valuable resource for the genetics and breeding communities in Brassica, and have already been used for applications such as linkage mapping of agricultural traits for flowering time, plant height, seed yield, germination, seedling emergence and disease resistance Schiessl et al 2015), tracking allele inheritance in interspecific hybrid populations (Mason et al 2014a(Mason et al ,b, 2015a and species identification in germplasm collections (Mason et al 2015b).…”