Identification of Sources and Loci for Development of Soyabean (Glycine Max (L.) Merrill] Cultivars That Combine Bacterial Pustule and Seed Decay Resistance with High Pod Clearance

Abstract

Globally, diseases constitute a major biotic constraint to soyabean production. Although, the list of diseases of soyabean in Ghana has been published, the incidence, severity, and distribution of listed diseases were not indicated. Secondly, the Savannah Agriculture Research Institute (SARI) has accumulated considerable number of soyabean genotypes most of which were sourced from the International Institute of Tropical Agriculture (IITA) and the United States Department of Agriculture (USDA). Efficient use of germplasm depends on knowledge of variation that exists among genotypes for traits of interest coupled with an understanding of genetic diversity. Therefore, it was imperative to morphologically and genetically characterise genotypes in SARI’s germplasm to guide breeding efforts. Lastly, it is important to consider the architecture of released varieties in relation to farming systems including commercial farming. Most of the released soyabean varieties in Ghana belong to the early and medium maturing groups with low pod clearance. Low pod clearance is not a problem with subsistence farming systems where harvesting is manually done, but in commercial farms that use combine harvesters, low pod clearance could be the source of considerable losses. Detailed assessment of soyabean disease situation at production centres and detailed characterisation of genotypes in SARI’s soyabean germplasm have been carried out to identify sources and loci of resistance to predominant diseases of soyabean in Ghana. The objective of this study were to: (1) carry out a survey of soyabean diseases across major production centres in Ghana and their incidence and severity, (2) evaluate SARI’s soyabean germplasm for resistance to bacterial leaf pustule, (3) evaluate SARI’s soyabean germplasm for resistance to soyabean seed decay, (4) assess diversity, population structure and identify lines with high pod clearance among genotypes in SARI’s germplasm, (5) identify Phomopsis seed decay (PSD) and bacterial leaf pustule (BLP) resistant loci through genome-wide association mapping, (6 ) identify loci associated with pod clearance. Results of the survey revealed that some of the important diseases of soyabean in Ghana included Cercospora leaf blight (Cercospora kikuuchi), frog eye leaf spot (Cercospora sojina); target spot Corynespora cassiicola), bacterial leaf pustule (Xanthomonas campestris pv. glycine), downy mildew (Peronospor manshurica), leaf blight (Rhizoctonia solani), brown spot (Septoria glycine), soyabean mosaic, alfafa mosaic, and soyabean seed decay due to Diaporthe sp. Bacterial pustule was the most wide spread with incidence ranging from 15.3% at Wenchi to 84.7% at Malzire in the Yendi municipality. Two viral diseases, soyabean mosaic virus and alfalfa mosaic virus were present at all 15 locations but mostly at very low incidence except for Ejura and Wenchi where incidence was very high. Cercospora leaf blight and Frog eye leaf spot both occurred at 13 of 15 locations surveyed. Generally, incidence and severity of identified diseases was higher at Malzire, Karaga and Gushegu than other locations with the exception of soyabean mosaic virus for which the highest incidence occurred at Ejura followed by Wenchi. Furthermore, this study identified soyabean seed decay disease, and molecularly identified the causal agent as Diaporthe phaeolorum var. sojae and tentatively designated the isolate as MTB-1. This is the first report of Diaporthe phaeolorum var. sojae occurrence on soyabean pods and seeds in Ghana. Twenty-eight lines were identified with immune response to Xanthomonas axonopodis pv. glycines which could be used to develop resistant varieties. Area under chlorophyll retention curve had a negative correlation with area under disease progress curve, which translates to a positive correlation with resistance to bacterial pustule. Area under chlorophyll retention curve could replace disease severity score in bacterial pustule screening trials. Though disease pressure was high, eleven lines, PI416806B, PI224271, PI417120 BRS 361, PI417013, TGX 1903-7F, PI594767B, PI423958, TGX 1485-1D, TGX 2006-3F and Liu Yuemang were highly resistant to PSD infection. Genotypes within SARI’s germplasm differed widely for growth and reproductive parameters including plant height, number of branches, pod clearance, flowering and maturity periods, all of which were highly heritable except for number of branches. Likewise, high variation among genotypes for yield components, most of which were under genetic control was recorded. Principal component analyses identified number of pods per plants, number of seeds per plant, days to flowering and days to maturity as the main drivers of variation in SARI’s germplasm. Genetic diversity analyses of a 96 representative panel showed high diversity among genotypes. Structure analyses revealed nine sub-populations within the panel. Genetic variation among sub-populations was high as indicated by high allele divergence frequency among sub-population. All genotypes in the 96 representative panel were distinct and most were almost fixed as reflected in high Fst values. Genome-wide association studies identified two SNP markers, S3_14585048 and S3_1991311 with large negative effect on pod clearance. SAUR like-auxin responsive protein known to positively regulate cell expansion to promote hypocotyl growth was identified at the physical position of the SNPs. Associations between genomic locations and resistance to bacterial leaf pustule were identified but the associations were not significant because of low statistical power due to small sample size. Nonetheless, three SNP markers, S16_34242886, S16_35202484 and S1_38672307 were found linked to three candidate genes, Glyma.01go93200, Glyma.g187500 and Glyma.g187400. All three candidate genes code for Leucine-rich repeat receptor like protein kinases known for eliciting immune response to pathogen infection. The SNP, S18_7792728 associated with PSD resistance occurred at a genomic region that harbours the candidate gene AT3G07040.1 (NBARC-domain-containing disease resistance protein) known to play critical roles in plants response to pathogens. This confirms the existence of resistant genes for PSD among the lines in the representative panel. The identified SNP could be validated to aid with marker-assisted selection. This study presents a series of useful information on SARI’s soyabean germplasm, prevailing diseases of soyabean and their distribution, sources of resistance and resistant loci, and the discovery of informative markers that can alter the architecture of future varieties.