Genome Wide Association Mapping of Sclerotinia sclerotiorum Resistance in Soybean with a Genotyping‐by‐Sequencing Approach

Abstract

Sclerotinia stem rot (SSR) is one of the most important pests in cool soybean growing regions of the Northeastern United States and Canada. However, the intensity of infestations varies considerably from year to year according to weather conditions, thus making it difficult for breeders to select under uniform disease pressure. Selection for resistance to SSR would be greatly facilitated by the use of molecular markers. In this work, a collection of 130 lines was inoculated using the cotton pad method and was genetically characterized using a genotyping-by-sequencing (GBS) protocol optimized for soybean. Genome-wide association mapping (AM) and linkage disequilibrium (LD) analyses were performed with 7864 single nucleotide polymorphisms (SNPs). Linkage disequilibrium varied considerably over physical distance, reaching a r 2 value of 0.2 after 8.5 Mb in the pericentromeric region and 0.5 Mb in the telomeric region. The mixed linear model (MLM) performed very well in accounting for population structure and relatedness, as only 5.5% of the observed p-values were < 0.05. The strongest association was found on chromosome Gm15 (p-value = 1.38 × 10 -6

A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

“…The minimum number of markers that are required to conduct a successful association analysis depends on the extent of LD over physical distance in a given population. Many factors affect LD such as recombination and mutation rate, relatedness (kinship), gene conversion, selection (natural, artificial, and balancing), mating systems (self or cross pollination), genetic diversity, and population structure [29, 45]. In this study, the average LD decay was approximately 520 and 480 Kb in A t and D t sub-genome, respectively, and genome wide ~500 Kb (Fig.…”

“…Although scientists have successfully identified marker-trait associations using GBS-based SNPs in many plant species [14, 21, 28, 29], so far no GWAS study has been reported in Upland cotton using SNPs. There are a few GWAS studies that were reported using SSR markers in Upland cotton [2, 4, 23, 24, 26, 30] as mentioned earlier.…”

Diversity and genetic analysis through DArTseq in common bean(Phaseolus vulgaris L.) germplasm from Turkey

“…DArTseq combines genome complexity reduction methods and next-generation sequencing platforms (Courtois et al, 2013;Cruz et al, 2013;Raman et al, 2014;Kilian et al, 2016). Therefore, DArTseq represents a new implementation of sequencing of complexity-reduced representations (Huang et al, 2014) and more recent applications of this concept on the nextgeneration sequencing platforms (Sonah et al, 2013;Bastien et al, 2014).…”

Genome-wide association study for soybean cyst nematode resistance in Chinese elite soybean cultivars

“…However, due to the limited coverage of resistance sources, inadequate statistical procedures, and small mapping populations, many QTLs underlying SCN resistance, therefore, have remained un-detected. With the availability of a soybean reference genome sequence and the development of high-throughput single nucleotide polymorphism (SNP) assay platforms, association mapping (AM) has been demonstrated to be a powerful approach to dissect various traits, such as disease resistance, yield, and quality-related traits in soybean (Wen et al 2014(Wen et al , 2015Hao et al 2012a, b;Bastien et al 2014;Hwang et al 2014). Recent genomewide association study (GWAS) on 282 accessions of soybean breeding lines have detected significant signals at two loci corresponding to rhg1 and FGAM1, plus a third locus located at the end (55.9 Mb) of Chr.…”