Evaluation of soybean genotypes for resistance against the rust-causing fungus Phakopsora pachyrhizi in East Africa

Soybean rust, caused by the biotrophic fungus Phakopsora pachyrhizi, is the most important foliar disease of soybean (Glycine max) worldwide. Deployment of resistant soybean cultivars is the best option for managing this disease. Genes conferring resistance to P. pachyrhizi have been identified, but pathotypes of the rust fungus overcoming these resistance genes have also been found. To identify novel resistance genes, soybean genotypes from both local and international sources were screened at multiple locations in Tanzania and Uganda in 2016 and 2017. The results from this screening revealed that infection types, disease severities, and sporulation levels varied among the genotypes and locations. The majority of the genotypes had tan-coloured (TAN) lesions and developed moderate sporulation, implying susceptibility, while only seven of the 71 lines had reddish-brown (RB) lesions and showed low disease severities in all of the screening environments. We identified seven genotypes that were the most resistant to rust in the most locations over the two years. These genotypes will be useful for further studies and, ultimately, for rust management, as they show broad resistance to various pathotypes of the rust fungus.     

Yield stability of rust-resistant soybean lines at four mid-altitude tropical locations

Asian soybean rust is a major threat to worldwide soybean production at present. Host plant resistance offers the most sustainable control strategy to resource poor farmers in sub-Saharan Africa and worldwide. Using 13 soybean lines bred for resistance to soybean rust, and 2 checks, yield trials were conducted at four regions of Uganda for four consecutive seasons to determine yield stability and reaction to soybean rust disease. An additive main effects and multiplicative interaction (AMMI) model was used to assess the yield stability of the soybean lines. Stable lines identified included MNG 7.13, MNG 8.10, and MNG 1.63, which showed the lowest environmental interaction. These lines also out-yielded the local checks by over 300 kg ha⁻¹, indicating that they have potential to boost soybean yields in the tropics. Line MNG 8.10 showed adaptability to most of the locations and had the highest yield among the three most stable lines, making it the most promising line; it is therefore recommended for release to improve soybean production and productivity in the region.     

Combining ability and heritability of soybean resistance to groundnut leaf miner

Groundnut leaf miner (GLM) (Aproaerema modicella) (Deventer) is one of the most destructive pests of soybean and groundnuts. In this study, the mode of inheritance, general combining ability (GCA), specific combining ability (SCA) effects, maternal effects of resistance to GLM and grain yield ha^?1 were determined. Thirteen soybean parental genotypes and 81 F₂ populations were evaluated for resistance to GLM in a 5?×?19 alpha lattice diallel design with two replications under natural GLM infestation in northern (Arua) and eastern (Iki-iki) Uganda during September to December 2016 rainy season. Highly significant differences were observed among parental genotypes and F₂ populations for GLM incidence, severity, and grain yield. The estimates of GCA effects were significant for GLM incidence and severity scores but not for the number of larvae per plant and grain yield ha^?1. SCA effects were non-significant for all the studied traits, suggesting that GCA effects were the major component responsible for soybean resistance to GLM with additive gene effects being more important for these traits. Baker’s ratio ranged from 0.44-1.0 for most of resistant traits except number of larvae per plant and grain yield ha^?1. The results indicated also that cultivars Maksoy1 N, PI615437, PI578457A and NIIGC4.1-2 were good combiners against GLM incidence and severity. Parent PI615437 was a good combiner for grain yield and Maksoy1 N?×?PI615437 was a superior cross for grain yield and against GLM incidence. There were no maternal effects for the inheritance of resistance to GLM. The study provides a basis for understanding patterns of inheritance of soybean resistance to groundnut leaf miner for an efficient breeding program.     

Prediction of candidate genes associated with resistance to soybean rust (Phakopsora pachyrhizi) in line UG-5

Online databases containing genetic information are crucial to extract new candidate genes from existing data and web-based resources. The objective of this study was, therefore, to predict putative candidate genes associated with resistance to SBR in line UG-5 and understand their functions using different bioinformatics tools from the online available databases. The physical positions for the flanking markers of the identified putative QTLs were searched on the SoyBase database genome browser based on Glyma 1.01 assembly. The putative candidate genes and annotated functions of the surrounding genes were discovered in the vicinity using SoyBase and Phytozome databases. A total of 18 putative candidate genes were predicted on approximately 482.7 kb region of QTL-3 (chromosome 18), among which, six putative candidate genes were found to encode leucine-rich repeat (LRR), Ser/Thr protein phosphatase, leucine-rich repeat receptor-like protein kinase (LRR-RLK) and chitinase-related proteins, which are associated with plant defence signalling pathways. Moreover, F-box and leucine-rich repeat, glycosyltransferase family member and serine/threonine-protein phosphatase 2A catalytic subunit coding genes were predicted on the novel putative QTL detected on chromosome 9. This information could, therefore, be used for further prediction and annotation of candidate genes from sequenced regions of line UG-5 as these putative candidate genes were predicted from the Glyma 1.01 assembly.     

Potential for soybean rust tolerance among elite soybean lines in Uganda

Soybean rust, (Phakopsora pachyrhizi), currently the most devastating disease of soybeans worldwide, is known to challenge single resistance genes deployed against it and therefore, disease tolerance is indisputably the most viable measure in controlling the pathogen. Studies were conducted at Namulonge in Central Uganda to assess the level of tolerance to soybean rust among selected elite soybean lines. Seven elite lines together with three local checks were tested in a split-plot design where some plots were protected with fungicide to estimate the level of tolerance to soybean rust. The experiment was conducted for three cropping seasons beginning second rains of 2005. A rust tolerance index (RTI) was computed for each test line as the ratio of yield from unprotected plots to yield from protected plots. The study showed that high levels of tolerance to soybean rust were present in the test lines. The soybean lines that showed high levels of tolerance included MNG 10.3 and MNG 3.26 all showing RTIs higher than 0.93. These lines also out-yielded the local checks by about 400 kg ha⁻¹ and are recommended for multi-location testing.     

Genetic components of pod shattering in soybean

Half diallel crosses among ten pure breeding lines of soybean were made in 1997 and 1998 to study the inheritance of pod shattering in soybean. Evaluation for pod shattering among F₂ segregating populations was carried out in an oven set at 80 ^°C for 12 hours. Diallel analysis was carried out to estimate genetic parameters and detect presence of non allelic interaction of genes affecting pod shattering. Hayman's diallel analysis indicated significant variation of Wr + Vr and Wr – Vr over arrays, suggesting epistatic gene action. Similarly results from a joint regression coefficient over replications were significantly (p < 0.05) different from unity and zero, suggesting presence of non allelic interaction of genes. The intercept was positive, suggesting partial dominance for the shattering trait. Both general combining ability (GCA) and specific combining ability (SCA) effects were significant (p < 0.05). This revised version was published online in July 2006 with corrections to the Cover Date.     

Ureide essay to assess N<Subscript>2</Subscript>-fixation abilities of soybean (<Emphasis Type="Italic">Glycine max</Emphasis>) genotypes under different <Emphasis Type="Italic">Bradyrhizobium</Emphasis> strains

The high protein content of soybean (Glycine max) seeds results in high nitrogen demand, causing a huge nitrogen uptake during plant growth. As a legume crop, soybean can fix atmospheric N through symbiotic associations with Bradyrhizobia and perform well in African nitrogen poor soils. This study aimed at establishing the ability of promiscuous soybean genotypes to fix nitrogen and devise the relationship between nodule scores and amount of nitrogen fixed. Twelve soybean genotypes were inoculated with Bradyrhizobium japonicum Strain USDA 110 (specific) and Bradyrhizobium sp. Strain USDA 3456 (native) and raised in pots in a greenhouse. At the R3.5 growth stage, nodules were scored and xylem sap was extracted, which xylem sap was used to carry out ureide, amino-N, and nitrates assays. The relative abundance of ureide was used to devise the proportion of nitrogen fixed by each genotype. The proportion of nitrogen derived from atmospheric N2 (Ndfa) ranged from 47.9 to 78.8% under USDA 3456 and from 36.7 to 78.7% under USDA 110. A strong correlation was found between nodule scores, especially nodules’ effectiveness, and Ndfa. The genotypes Wondersoya (78.8%), Maksoy 2N (78.4%), Namsoy 3 (78.3%), and Maksoy 3N (75.7%) had high nitrogen-fixing ability in response to USDA 3456. Promiscuous soybean genotypes can fix nitrogen equally under both native and specific Bradyrhizobium types. Nodules’ effectiveness can be a good predictor of biological nitrogen fixation. This study highlighted that crop improvement to boost soybean production in Africa should target promiscuous varieties for better yield with less inputs.     

Soybean production in eastern and southern Africa and threat of yield loss due to soybean rust caused by Phakopsora pachyrhizi

Soybean is a major source of oil and proteins worldwide. The demand for soybean has increased in Africa, driven by the growing feed industry for poultry, aquaculture and home consumption in the form of processed milk, baked beans and for blending with maize and wheat flour. Soybean, in addition to being a major source of cooking oil, is also used in other industrial processes such as in the production of paints and candle wax. The demand for soybean in Africa so far outweighs the supply, hence the deficit is mainly covered through imports of soybean products such as soybean meal. The area under soybean production has increased in response to the growing demand, a trend that is expected to continue in the coming years. As the production area increases, diseases and insect pests, declining soil fertility and other abiotic factors pose a major challenge. Soybean rust disease, caused by the fungus Phakopsora pachyrhizi, presents one of the major threats to soybean production in Africa due to its rapid spread as a result of the ease by which its spores are dispersed by the wind. Disease control by introducing resistant soybean varieties has been difficult due to the presence of different populations of the fungus that vary in pathogenicity, virulence and genetic composition. Improved understanding of the dynamics of rust ecology, epidemiology and population genetics will enhance the effectiveness of targeted interventions that, in turn, will safeguard soybean productivity.