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 analysis of seed morphological traits and its correlations with Grain yield in common bean

This work investigated the genetic control of seed morphological traits and its correlations with grain yield in common bean. Three crossings among bean cultivars with different growth habit and seed characteristics were analyzed. F1 progenies gave origin to F2, RC1P1F1 and RC1P2F1 generations. Random samples of seeds from F2 generations and parents, F1 and backcrossings were sown during the season 2003/2004. Plant grain yield and seed morphological traits were determined by a sample of 150 plants from F2 generations and 20 plants from parents, F1 and backcrosssings. Genetic effects involved in each crossing were obtained from estimates of genetic components means and genetic and environmental components of phenotypical variance. Results showed that the seed morphological traits were controlled by a complex of genes, with additive effects predominance although dominance effects were present. High and negative correlations among seed length and thickness with grain yield suggested greater grain yield in bean plants with smaller seeds.

Este trabalho estudou o controle genético de características morfológicas de sementes e suas correlações com a produtividade de grãos em feijoeiro comum. Para tanto, foram efetuados três cruzamentos entre cultivares de feijoeiro com diferentes características de sementes. As progênies F1 deram origem às gerações F2, RC1P1F1 e RC1P2F1. Uma amostra aleatória de sementes das gerações dos parentais, F1, F2 e retrocruzamentos foram semeadas na safra das águas de 2003/2004. Na maturação fisiológica foram amostradas 150 plantas das gerações F2 e 20 plantas dos parentais, F1 e retrocruzamentos, nas quais foram determinados a produtividade de grãos por planta e as seguintes características morfológicas de sementes: comprimento, largura e espessura. Os efeitos genéticos envolvidos em cada cruzamento foram obtidos por meio das estimativas dos componentes das médias e variâncias fenotípicas. As características morfológicas de sementes foram controladas por um complexo de genes, com predominância de efeitos aditivos, embora os efeitos de dominância foram presentes. Correlações altas e negativas entre a largura e espessura de semente com produtividade de grãos sugeriram maiores produtividades de grãos em feijoeiros que possuem sementes menores.

New soybean (Glycine max Fabales, Fabaceae) sources of qualitative genetic resistance to Asian soybean rust caused by Phakopsora pachyrhizi (Uredinales, Phakopsoraceae)

Asian soybean rust (ASR), caused by the phytopathogenic fungi Phakopsora pachyrhizi, has caused large reductions in soybean (Glycine max) yield in most locations in Brazil where it has occurred since it was first reported in May 2001. Primary efforts to combat the disease involve the development of resistant cultivars, and four dominant major genes (Rpp1, Rpp2, Rpp3 and Rpp4) controlling resistance to ASR have been reported in the literature. To develop new long-lasting soybean ASR resistance genes, we used field experiments to assess ASR leaf lesion type in 11 soybean genotypes (BR01-18437, BRS 184, BRS 231, BRS 232, BRSGO Chapadões, DM 339, Embrapa 48, PI 200487, PI 230970, PI 459025-A and PI 200526) and the 55 F2 generations derived from their biparental diallel crosses. The results indicated that PI 200487 and PI 200526 carry different dominant resistance major genes which are both different from Rpp2 through Rpp4. Furthermore, resistance to ASR in BR01-18437 is controlled by a single recessive major gene, also different from Rpp1 through Rpp4 and different from the genes in PI 200487 and PI 200526.

Genetic control of soybean (Glycine max) yield in the absence and presence of the Asian rust fungus (Phakopsora pachyrhizi)

Soybean is one of the most important crops in Brazil and continuously generates demands for production technologies, such as cultivars resistant to diseases. In recent years, the Asian rust fungus (Phakopsora pachyrhizi Syd. & P. Syd 1914) has caused severe yield losses and the development of resistant cultivars is the best means of control. Understanding the genetic control and estimating parameters associated with soybean (Glycine max) resistance to P. pachyrhizi will provide essential information for cultivar selection. We investigated quantitative genetic control of P. pachyrhizi and estimated parameters associated to soybean yield in the absence and presence of this phytopathogen. Six cultivars and their 15 diallel derived F2 and F3 generations were assessed in experiments carried out in the absence and presence of P. pachyrhizi. The results indicated that soybean yield in the presence and absence of P. pachyrhizi is controlled by polygenes expressing predominantly additive effects that can be selected to develop new cultivars resistant or tolerant to P. pachyrhizi. These cultivars may prove to be a useful and more durable alternative than cultivars carrying major resistance genes.

Genetic relationships between Chinese, Japanese, and Brazilian soybean gene pools revealed by simple sequence repeat (SSR) markers

An understanding of the relationship of geographically different soybean gene pools, based on selectively neutral DNA markers would be useful for the selection of divergent parental cultivars for use in breeding. We assessed the relationships of 194 Chinese, 59 Japanese, and 19 Brazilian soybean cultivars (n = 272) using 12 simple sequence repeat (SSR) markers. Quantification Theory III and clustering analyses showed that the Chinese and Japanese cultivars were genetically quite distant to each other but not independent, while Brazilian cultivars were distantly related to the cultivars from the other two countries and formed a cluster that was distant from the other two gene pool clusters. Our results indicated that the Brazilian soybean gene pool is different from the Chinese and Japanese pool. Exchanges of these gene pools might be useful to increase the genetic variability in soybean breeding.