Association mapping of a locus that confers southern stem canker resistance in soybean and SNP marker development

BACKGROUND

Southern stem canker (SSC), caused by Diaporthe aspalathi (E. Jansen, Castl. & Crous), is an important soybean disease that has been responsible for severe losses in the past. The main strategy for controlling this fungus involves the introgression of resistance genes. Thus far, five main loci have been associated with resistance to SSC. However, there is a lack of information about useful allelic variation at these loci. In this work, a genome-wide association study (GWAS) was performed to identify allelic variation associated with resistance against Diaporthe aspalathi and to provide molecular markers that will be useful in breeding programs.

RESULTS

We characterized the response to SSC infection in a panel of 295 accessions from different regions of the world, including important Brazilian elite cultivars. Using a GBS approach, the panel was genotyped, and we identified marker loci associated with Diaporthe aspalathi resistance through GWAS. We identified 19 SNPs associated with southern stem canker resistance, all on chromosome 14. The peak SNP showed an extremely high degree of association (p-value = 6.35E-27) and explained a large amount of the observed phenotypic variance (R2 = 70%). This strongly suggests that a single major gene is responsible for resistance to D. aspalathi in most of the lines constituting this panel. In resequenced soybean materials, we identified other SNPs in the region identified through GWAS in the same LD block that clearly differentiate resistant and susceptible accessions. The peak SNP was selected and used to develop a cost-effective molecular marker assay, which was validated in a subset of the initial panel. In an accuracy test, this SNP assay demonstrated 98% selection efficiency.

CONCLUSIONS

Our results suggest relevance of this locus to SSC resistance in soybean cultivars and accessions from different countries, and the SNP marker assay developed in this study can be directly applied in MAS studies in breeding programs to select materials that are resistant against this pathogen and support its introgression.

Size of AT(n) insertions in promoter region modulates Gmhsp17.6-L mRNA transcript levels

During earlier experiments, an SSR molecular marker (176 Soy HSP) showing high correlation (70%) with resistance/susceptibility to javanese root-knot nematode Meloidogyne javanica was identified in soybean. After being sequenced, results indicated that the SSR 176 Soy HSP marker was inserted in the promoter region of Gmhsp17.6-L gene. It was also detected in this region that resistant genotypes presented insertions between AT(31) and AT(33) in size and susceptible genotypes, AT(9). Gmhsp17.6-L gene coding region presented a perfect match in amino acid sequence in all soybean genotypes. A ribonuclease protection assay showed that Gmhsp17.6-L gene mRNA transcripts were present in all genotypes. A real-time relative quantification (qPCR) indicated in the resistant individuals higher mRNA transcripts levels, which presented in the sequencing more AT(n) insertions. These results suggest that the number of AT(n) insertions inside this promoter region could modulate up or down gene levels. Those findings can lead to the possibility of manipulating, between some limits, the mRNA transcripts levels using different sizes of AT(n) insertions.

Genetic variance and covariance components related to intra- and interpopulation recurrent selection in maize (Zea mays L.)

New genetic variance and covariance components related to intra- and interpopulational recurrent selection methods have been theoretically developed by Souza Jr. (Rev. Bras. Genet. 16: 91-105, 1993) to explain the failure of these methods to concomitantly develop hybrid and per se populations. Intra- and interpopulation half-sib progenies of 100 genotypes were sampled from maize (Zea mays L.) populations BR-106 and BR-105 to estimate variance and covariance components and to compare the expected responses to reciprocal (RRS), intrapopulational (HSS), and modified (MRS) recurrent selection in interpopulation hybrid, populations per se, and to determine heterosis. Four sets of 100 progenies, two intra- and two interpopulational, were evaluated in partially balanced 10 x 10 lattices arranged in split-blocks with two replications in two years (1991/92 and 1992/93) and two locations in Piracicaba, SP. Data for ear weight, plant and ear height, and ear by plant height ratio were recorded. Populations and interpopulation crosses were high yielding and showed high breeding potential for production of hybrids from inbred lines. Mid parent and the highest parent heterosis were relatively high, but lower than values reported for these populations under other environmental conditions. Additive variance estimates of populations per se and interpopulation crosses confirmed the high potential of these materials. The magnitude of the variance estimates for the deviations from intra- and interpopulation additive effects (<img src="http:/img/fbpe/gmb/v21n4/1918f1.jpg" alt="1918f1.jpg (1262 bytes)" align="middle"> for BR-106 and <img src="http:/img/fbpe/gmb/v21n4/1918f3.jpg" alt="1918f3.jpg (1259 bytes)" align="middle">for BR-105) and covariance between additive effects with these deviations (<img src="http:/img/fbpe/gmb/v21n4/1918f2.jpg" alt="1918f2.jpg (2022 bytes)" align="middle"> for BR-106 and <img src="http:/img/fbpe/gmb/v21n4/1918f4.jpg" alt="1918f4.jpg (1995 bytes)" align="middle"> for BR-105) indicated that these new components can significantly influence the effectiveness of breeding methods. Genetic component estimates for BR-105 had relatively small errors, with <img src="http:/img/fbpe/gmb/v21n4/1918f4.jpg" alt="1918f4.jpg (1995 bytes)" align="middle"> negative for all traits. Estimates of <img src="http:/img/fbpe/gmb/v21n4/1918f1.jpg" alt="1918f1.jpg (1262 bytes)" align="middle">and <img src="http:/img/fbpe/gmb/v21n4/1918f2.jpg" alt="1918f2.jpg (2022 bytes)" align="middle"> had relatively larger errors for BR-106. The MRS method was more effective than the RRS and HSS methods in producing hybrids from inbred lines. The choice of a population tester for the MRS method based on population means per se may be incorrect. The additional use, when possible, of intra- and interpopulation additive genetic variances from each population would be more appropriate.