Genome Wide Association Mapping of Resistance in Soybean with a Genotyping-by-Sequencing Approach (original) (raw)
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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 ; q-value [adjusted p-value] = 0.011). Two additional SNP markers in the vicinity had a q-value < 0.1. This marker was validated in the progeny of a biparental cross, where F 4:6 lines carrying the susceptibility allele developed lesions 17.6 mm longer than lines carrying the resistance allele. Interestingly, other genes contributing to resistance to pathogens have been reported in this region of Gm15. Three other association peaks having a q-value < 0.1 were detected on chromosomes Gm01, Gm19, and Gm20.
BMC Plant Biology, 2015
Background: Sclerotinia stem rot (SSR) is the most important soybean disease in Eastern Canada. The development of resistant cultivars represents the most cost-effective means of limiting the impact of this disease. In view of ensuring durable resistance, it is imperative to identify germplasm harbouring different resistance loci and to provide breeders with closely linked molecular markers to facilitate breeding. With this end in view, we assessed resistance using a highly reproducible artificial inoculation method on a diverse collection of 101 soybean lines, mostly composed of plant introductions (PIs) and some of which had previously been reported to be resistant to sclerotinia stem rot. Results: Overall, 50% of the lines exhibited a level of resistance equal to or better than the resistant checks among elite material. Of the 50 lines previously reported to be resistant, only 20 were in this category and a few were highly susceptible under these inoculation conditions. The collection of lines was genetically characterized using a genotyping by sequencing (GBS) protocol that we have optimized for soybean. A total of 8,397 single nucleotide polymorphisms (SNPs) were obtained and used to perform an association analysis for SSR by using a mixed linear model as implemented in the TASSEL software. Three genomic regions were found to exhibit a significant association at a stringent threshold (q = 0.10) and all of the most highly resistant PIs shared the same alleles at these three QTLs. The strongest association was found on chromosome Gm03 (P-value = 2.03 × 10 −6). The other significantly associated markers were found on chromosomes Gm08 and Gm20 with P-values <10 −5. Conclusion: This work will facilitate breeding efforts for increased resistance to Sclerotinia stem rot through the use of these PIs.
Molecular markers for resistance to Heterodera glycines in advanced soybean germplasm
Germplasm line J87-233 is resistant to soybean cyst nematode (SCN) races 1, 2, 3, 5 and moderately resistant to race 14 with resistance derived from 3 primitive sources, 'Peking', PI 88788 and PI 90763. F 2:3 progeny of J87-233 and SCN-susceptible 'Hutcheson' cross were evaluated for response to SCN races 1, 2, 3, 5 and 14. Linkage groups (LG) A, B, F, G, J, M, N, S were tested with 215 genomic clones and 45 decamers for parental genotypes. QTL for race 1 and QTL for race 3 were detected on LG A2, the region of BLT65V and SCAR 548/563 1100/1025,975. The cluster analysis of 12 soybean cultivars and 38 plant introductions confirmed association of SCAR 1100/1025,975 with resistance to races 1 and 3, and suggested possible DNA rearrangements that might give rise to new resistance specificities in the region. The highly significant association of K69T marker with SCN race 1 resistance in conjunction with its location, 18.5 cM from the reported QTL, exemplifies the importance of the QTL locus on LG G and suggests expansion of the linkage map in the LG G-terminal region. Detected interaction between loci on LG A2 and LG G, and also with loci on LG F and LG M, may play a significant role in the genotype-specific response to SCN. Identification of two major regions on LG A2 and LG G for SCN resistance shows their applicability to advanced germplasm, however, transmission of molecular marker alleles indicates that applied markers are not yet reliable in revealing all possible recombination events in breeding for SCN resistance.
A retrospective DNA marker assessment of the development of insect resistant soybean
2001
There has been limited success over the past 30 yr in the developthe quantitative nature of resistance and to the retention ment of superior soybean cultivars [Glycine max (L.) Merr] with of undesirable PI donor alleles affecting any number insect resistance. Success may be hampered by the quantitative nature of resistance and by linkage drag from resistant plant introduction of traits because of their tight linkage with the insect (PI) donor parents. Soybean insect resistance quantitative trait loci resistance alleles, or QTL. This condition is often associ-(SIR QTLs) have been identified from PI 229358 and PI 171451 ated with the use of nondomesticated germplasm for the by restriction fragment length polymorphism (RFLP) analysis. The introgression of novel alleles and is generally referred to objective of this study was to tag the SIR QTLs from PI 229358 with as linkage drag. simple sequence repeat (SSR) markers and to determine the extent The use of marker-assisted selection (MAS) could to which the SIR QTLs have been introgressed in registered cultivars, circumvent linkage drag by enabling concurrent selecgermplasm releases, or breeding lines that have resistance derived tion for SIR QTLs and against undesired genomic refrom this PI or from PI 171451. Marker analysis defined intervals by gions from a resistant PI during backcrossing. MAS 5 centimorgans (cM) or less for a SIR QTL on linkage group D1b could also reduce the need for phenotypic selection that (SIR-D1b), and for SIR-G, SIR-H, and SIR-M. SIR QTLs were tracked through pedigrees by evaluating the inheritance of PI alleles may be inefficient in identifying genotypic differences at marker loci tightly linked to the QTLs during the phenotypic selecfor SIR. Towards this end, Rector et al. (1998, 1999, tion for insect resistance. It was inferred that at least 13 of the 15 SIR 2000) used RFLP markers to map SIR QTLs from PI genotypes studied had introgressed SIR-M. PI genome introgression 229358 and from PI 171451. They detected a major SIR around SIR-M was measured to assess linkage drag. Some genotypes QTL conditioning antixenosis and antibiosis within a exhibited a dramatic reduction in the amount of linked PI genome, similar interval on linkage group (LG) M (SIR-M) from which likely occurred in response to phenotypic selection for agroboth PI 229358 and PI 171451. Another QTL associated nomic performance as a means of reducing linkage drag. Only a few with antixenosis in both PI 229358 and PI 171451 was genotypes were inferred to possess SIR-G or SIR-H, and no genotypes detected on LG H (Rector et al., 1998; 1999). From PI possessed SIR-D1b. The results of this study indicate that marker-229358, SIR-D1b was detected for resistance on the assisted selection for SIR QTLs is needed to introgress these loci into elite genetic backgrounds.
Phytopathology, 2016
Genetic resistance is a key strategy for disease management in soybean. Over the last 50 years, soybean germplasm has been phenotyped for resistance to many pathogens, resulting in the development of disease-resistant elite breeding lines and commercial cultivars. While biparental linkage mapping has been used to identify disease resistance loci, genome-wide association studies (GWAS) using high-density and high-quality markers such as single nucleotide polymorphisms (SNPs) has become a powerful tool to associate molecular markers and phenotypes. The objective of our study was to provide a comprehensive understanding of disease resistance in the United States Department of Agriculture Agricultural Research Service Soybean Germplasm Collection by using phenotypic data in the public Germplasm Resources Information Network and public SNP data (SoySNP50K). We identified SNPs significantly associated with disease ratings from one bacterial disease, five fungal diseases, two diseases caus...
Journal of Plant Genome Sciences, 2012
Soybeans [Glycine max (L.) Merr.] are susceptible to many diseases including fungal diseases such as soybean sudden death syndrome (SDS). Several studies reported SDS resistance quantitative trait loci (QTL) on the soybean genome using different recombinant inbred line (RIL) populations and low density genetic linkage maps. High density exclusively single nucleotide polymorphisms-based (SNP-based) maps were not yet reported in soybean. The objectives of this study were (1) to construct a high density SNP-based genetic linkage map of soybean using the 'PI438489B' by 'Hamilton' (PIxH, n=50) recombinant inbred line population, and (2) to map QTL for SDS resistance using this high-density reliable genetic SNP-based map. The PI438489B by Hamilton high-density SNP-based genetic map was a high density map composed of 31 LGs, 648 SNPs, and covered 1,524.7 cM with an average of 2.37 cM between two adjacent SNP markers. Fourteen significant QTL were identified for SDS resistance using interval mapping (IM) and composite interval mapping (CIM) with LOD scores that ranged between 2.6 and 5.0. Twelve QTL were identified for foliar disease severity (FDS) and three QTL for root rot severity (RRS) of which one QTL underlain both FDS and RRS. The fourteen QTL were mapped onto ten separate chromosomes of the soybean genome. Seven of the intervals encompassing the QTL had been identified previously (on LGs C1, C2, D1b, G, L, N and O) associated with resistance to SDS but seven were novel (LGs A2 (2), B1, C2, D1a, D1b and O). We constructed the first PI438489B by Hamilton exclusively SNP-Based map and identified fourteen QTL that underlie SDS resistance including both resistances to foliar and root rot symptoms caused by Fusarium virguliforme infection. The QTL discovered here for SDS resistance could be useful to include in breeding programs in developing soybean cultivars resistant to SDS.
genes for disease resistance and some 30 Quantitative Trait Loci for a broad range
2015
Common bean is grown and consumed principally in developing coun-tries in Latin America, Africa, and Asia. It is largely a subsistence crop eaten by its producers and, hence, is underestimated in production and commerce statis-tics. Common bean is a major source of dietary protein, which complements carbohydrate-rich sources such as rice, maize, and cassava. It is also a rich source of minerals, such as iron and zinc, and certain vitamins. Several large germplasm collections have been established, which contain large amounts of genetic diversity, including the five domesticated Phaseolus species and wild species, as well as an incipient stock collection. The genealogy and genetic diversity of P. vulgaris are among the best known in crop species through the systematic use of molecular markers, from seed proteins and isozymes to simple sequence repeats, and DNA sequences. Common bean exhibits a high level of genetic diversity, compared with other selfing species. A hierarchical organi...
Molecular Breeding, 2012
Septoria tritici blotch (STB), caused by S. tritici, Stagonospora glume blotch (SGB), caused by S. nodorum, and Fusarium head blight (FHB), caused by F. graminearum and F. culmorum, are the most important diseases of wheat (Triticum aestivum L.) in temperate growing areas. The main goals of this study were to detect (1) new quantitative trait loci (QTL) for STB resistance in two adapted European biparental populations (Arina/Forno, History/Rubens) and (2) QTL regions for broad-spectrum resistance (BSR) to the above-mentioned diseases during the adult-plant stage in the field. The three resistances Electronic supplementary material The online version of this article (were phenotyped across 4-7 field environments and phenotypic data revealed significant (P \ 0.01) genotypic differentiation in all cases. Entry-mean heritabilities (h 2 ) ranged from 0.73 to 0.93. For STB resistance, correlations between disease ratings and heading date were significant (P \ 0.01), but moderate (r = -0.23 to -0.30) in both populations. Correlations between STB and plant height were higher in Arina/Forno (r = -0.45) and History/ Rubens (r = -0.55), the latter population segregating at the Rht-D1 locus. During the initial QTL analysis, 5 QTL were detected for STB resistance in each of the populations, amounting to an explained genotypic variance of 45-63%, thus, showing the same ranges as FHB and SGB resistances in Arina/ Forno and FHB resistance in History/Rubens. In total, 7 BSR QTL were found in the meta-analysis with the raw data, including the QTL on chromosome 4D at the Rht-D1 locus. A BSR QTL for all three diseases was not found but several BSR QTL for combinations with two diseases were detected. Combining the BSR QTL detected in the present breeding material by applying marker-assisted selection seems a promising approach.