IDENTIFICATION OF SOURCES AND LOCI FOR DEVELOPMENT OF SOYABEAN [GLYCINE MAX (L.) MERR] 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, some information on diseases of soyabean in Ghana has been published, it did not include incidence, severity and distribution. Secondly, SARI has accumulated considerable number of soyabean genotypes most of which were sourced from IITA and the USDA. Efficient use of germplasm depends on knowledge of variation that exist among genotypes for traits of interest coupled with an understanding of the genetic diversity. Therefore, it is 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 released varieties in Ghana are early and medium maturing lines 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 has been carried out. Also 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 study also evaluated genotypes for pod clearance. The objective of this study were to: (1) carry out a survey of soybean diseases across major production centres in Ghana and access their incidence and severity, (2) evaluate SARI’s soybean germplasm for resistance to bacterial leaf pustule, (3) evaluate SARI’s soybean germplasm for resistance to soybean seed decay, (4) assess diversity, population structure and identify lines with high pod clearance among genotypes in SARI’s germplasm, (5) identify PSD and BLP resistant loci through genome-wide association mapping, (6 ) Identify loci associated with pod clearance.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 virus, alfafa mosaic, and soyabean seed decay due to Diaporthe sp. were revealed by the survey. Bacterial pustule was the widest 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 successfully identified the causal agent as Diaporthe sp. and tentatively designated the isolate as MTB-1. Twenty-eight lines were identified with immune response to Xanthomonas campestris pv. glycine 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 resistant to bacterial pustule. Area under chlorophyll retention curve could replace disease severity score in bacterial pustule resistant screening. 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 parameters including plant height, pod clearance and number of branches, all of which were highly heritable except for number of branches. Likewise, high variation exists among genotypes for yield components, most of which were under genetic control. 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 as a result 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 is linked to a genomic region that harbours the candidate gene AT3G07040.1 (NB-ARC-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 resistant and resistant loci, and the discovery of informative markers that can alter the architecture of future varieties.
Programme:
PhD