Breeding investigations and validation of molecular markers linked with spot blotch disease resistance in wheat (Triticum aestivum L.) germplasm for the rain-fed conditions of Zambia.

Doctor of Philosophy in Agriculture (Plant Breeding)Wheat (Triticum aestivum L.) is an important cereal crop, second after maize in Zambia. Its production during summer rainy season is hampered by several abiotic and biotic constraints. Among the biotic constraints, spot blotch disease caused by Bipolaris sorokiniana (Sacc.) Shoem is the most devastating causing large wheat yield losses and grain quality deterioration. Under severe cases complete crop losses result. This is because resistance to spot blotch disease in most of the genotypes in Zambia is inadequate. Breeding for high yielding disease resistant genotypes is the most cost effective and sustainable way of increasing summer rain-fed wheat yields and achieving sustainable wheat production. The study was, therefore, undertaken to: a) determine farmers` preferences for rain-fed wheat cultivars and identify production constraints, b) assess genetic diversity using agro-morphological traits, c) screen germplasm for resistance to spot blotch, d) determine gene action controlling the inheritance of resistance to spot blotch disease, and e) validate simple sequence repeat (SSR) molecular markers previously reported to be linked with resistance to spot blotch disease. A participatory rural appraisal established that wheat was an important crop among the small-scale farmers as it was a dual purpose crop used for home consumption and income generation. Coucal was the only wheat variety grown by the farmers under rain-fed conditions. The major constraints affecting summer wheat production in order of importance were; lack of good wheat seed, bird damage, weeds, termite damage, diseases (spot blotch being the most important), lack of markets and drought. High yielding cultivars with white coloured grain, combined with resistance to spot blotch disease, resistance to bird damage, termite damage and drought were the traits most preferred by the farmers. The genetic diversity study revealed the existence of genetic variability amongst the genotypes. Principal component analysis identified plant height, tillers/m2, peduncle length, days to heading, days to maturity and grain yield as the main traits that described the variability among the genotypes. The 150 genotypes tested were clustered into five groups based on Ward’s method, indicating that they were from different genetic backgrounds. This suggests that superior genotype combinations could be obtained by crossing genotypes in the opposing groups. The study also established that hectolitre weight, tillers/plant, thousand grain weight (TGW), grains/spike, peduncle length, and tillers/m2 could be effective selection criteria for high yield as they exhibited positive direct effects on yield and also significant and positive association with yield. One hundred and fifty wheat genotypes from Zambia and CIMMYT-Mexico were screened for resistance to spot blotch disease. The study revealed significant variability among the genotypes in their reaction to spot blotch disease. Genotypes were classified as resistant, moderately resistant, moderately susceptible, and susceptible. Genotypes 19HRWSN6 (Kenya Heroe), 19HRWSN7 (Prontia federal) were amongst the genotypes that were resistant across seasons. Most of the genotypes obtained from Zambia were moderately susceptible to susceptible across seasons. Nonetheless, eight genotypes with varying resistant reactions were selected for genetic analysis studies. A genetic analysis using Hayman diallel approach of 8 × 8 mating design and generation mean (GMA) analysis of six generations (P1, P2, F1, F2, BCP1 and BCP2) of two cross combinations was conducted. The two biometrical methods revealed the importance of additive gene effects in controlling resistance to spot blotch disease. The absence of maternal and non-maternal reciprocal effects indicated that choice of female parent was not important in breeding for resistance to this disease. Epistatic gene effects were absent in the inheritance of resistance suggesting that selection would be effective in early generation. Resistance exhibited partial dominance. Both diallel and GMA revealed moderately narrow sense heritability of 56.0% and 55.5%, respectively, an indication that the trait could be improved through selection. The Wr/Vr graph showed that parents 30SAWSN10 (P1), 30SAWSN5 (P3) and Coucal (P4) displayed the maximum number of dominant genes hence can be used in breeding for resistance to spot blotch. The molecular markers Xgwm570, Xgwm544 and Xgwm437 previously reported to be linked with resistance to Bipolaris sorokiniana were validated and their association with resistance confirmed. The markers amplified fragments in resistant parental genotypes that were similar to the F2 resistant and moderately resistant lines but not in susceptible ones. The significant relationship between the marker and resistance to Bipolaris sorokiniana was also established considering the significance of regression analysis (Xgwm570, P=0.003; Xgwm544, P=0.03 and Xgwm437, P=0.03). The adjusted R2 values observed (Xgwm570 =11.0%; Xgwm544=10.0% and Xgwm437=7.0%) further revealed the association between the marker and resistance. The study, therefore, shows that the markers can be useful in Zambia as they would increase the efficiency for the identification of resistant genotypes. This implies that screening of the genotypes could be done even in the absence of the disease epidemic. Overall, the results from this study indicate that the opportunity of improving resistance to spot blotch disease exists by utilizing the information generated. This information could be important during planning and implementation of breeding for resistance

Genetic variability among wheat (Triticum aestivum L.) germplasm for resistance to spot blotch disease

Spot blotch caused by Bipolaris sorokiniana (Sacc.) Shoem. is the most devastating disease limiting wheat productivity in warm and humid environments. One hundred and fifty wheat genotypes were evaluated under field conditions in 2013 and 2014 in six different locations in Zambia. The genotypes showed different levels of resistance to spot blotch. Genotypes 19HRWSN6 (Kenya Heroe), 19HRWSN7 (Prontia Federal) and 19HRWSN15 (BRBT2/METSO) were resistant lines across environments. The genotype plus genotype by environment (GGE) biplot grouped the six environments (E) into three mega-environments (ME) with respect to spot blotch severity. ME I contained Golden Valley Agricultural Research Trust (GART) (E6) only. Mpongwe (E4), Mt. Makulu (E5 and E2) and GART (E3) formed ME II, while ME III contained only Mutanda (E1). Genotypes 16HRWYT5, SB50 and 20HRWSN33 were the most susceptible genotypes in ME I, II and III, respectively. Genotype 19HRWSN7 was the most resistant across test locations. The locations in ME III were highly correlated indicating that they provided similar information on genotypes. This suggests that one location could be chosen among the locations in ME III for screening spot blotch resistance each year if the pattern repeats across years. This could aid in reducing the cost of genotype evaluation and improve efficiency as genotypes would be handled in fewer environments

Pathways to wheat self-sufficiency in Africa

A growing urban population and dietary changes increased wheat import bills in Africa to 9% per year. Though wheat production in the continent has been increasing over the past decades, to varying degrees depending on regions, this has not been commensurate with the rapidly increasing demand for wheat. Analyses of wheat yield gaps show that there is ample opportunity to increase wheat production in Africa through improved genetics and agronomic practices. Doing so would reduce import dependency and increase wheat self-sufficiency at national level in many African countries. In view of the uncertainties revealed by the global COVID-19 pandemic, extreme weather events, and world security issues, national policies in Africa should re-consider the value of self-sufficiency in production of staple food crops, specifically wheat. This is particularly so for areas where water-limited wheat yield gaps can be narrowed through intensification on existing cropland and judicious expansion of rainfed and irrigated wheat areas. Increasing the production of other sources of calories (and proteins) should also be considered to reduce dependency on wheat imports

Genomic surveillance uncovers a pandemic clonal lineage of the wheat blast fungus

Wheat, one of the most important food crops, is threatened by a blast disease pandemic. Here, we show that a clonal lineage of the wheat blast fungus recently spread to Asia and Africa following two independent introductions from South America. Through a combination of genome analyses and laboratory experiments, we show that the decade-old blast pandemic lineage can be controlled by the Rmg8 disease resistance gene and is sensitive to strobilurin fungicides. However, we also highlight the potential of the pandemic clone to evolve fungicide-insensitive variants and sexually recombine with African lineages. This underscores the urgent need for genomic surveillance to track and mitigate the spread of wheat blast outside of South America and to guide preemptive wheat breeding for blast resistance

Detection and characterization of fungus (Magnaporthe oryzae pathotype Triticum) causing wheat blast disease on rain-fed grown wheat (Triticum aestivum L.) in Zambia.

Wheat blast caused by Magnaporthe oryzae pathotype Triticum (MoT) is a threat to wheat production especially in the warmer-humid environments. In Zambia, wheat blast symptoms were observed for the first time on wheat (Triticum aestivum L.) grown in experimental plots and five farmers' fields in Mpika district of Muchinga Province during the 2017-18 rainy season. Infected plants showed the typical wheat blast symptoms with the spike becoming partially or completely bleached with the blackening of the rachis in a short span of time. Incidence of blast symptoms on nearly all wheat heads was high and ranged from 50 to 100%. Examination of diseased plant leaves showed the presence of elliptical, grayish to tan necrotic lesions with dark borders on the leaf often mixed with other foliar diseases. A study was conducted to isolate and identify the causal pathogen(s) using classical and molecular methods and determine the pathogenicity of the detected disease causal agent. Morphobiometrical determination of causal pathogen revealed conidia with characteristic pear shaped 2-septate hyaline spores associated with M. oryzae species. Preliminary polymerase chain reaction screening of six isolates obtained from wheat blast infected samples with diagnostic primers (MoT3F/R) was conducted at ZARI, Zambia, and subsequent analysis of two isolates with MoT3F/R and C17F/R was performed at USDA-ARS, USA. Both experiments confirmed that MoT is the causal agent of wheat blast in Zambia. Further, pathogenicity tests performed with pure culture isolates from samples WS4 and WS5 produced typical blast symptoms on all the six inoculated wheat genotypes. Results of this study indicate that MoT is causing wheat blast in rain-fed wheat grown in Zambia, thus making it the first report of MoT in Zambia and Africa. This inter-continental movement of the pathogen (disease) has serious implication for wheat production and trade that needs to be urgently addressed

Genomic surveillance uncovers a pandemic clonal lineage of the wheat blast fungus.

Wheat, one of the most important food crops, is threatened by a blast disease pandemic. Here, we show that a clonal lineage of the wheat blast fungus recently spread to Asia and Africa following two independent introductions from South America. Through a combination of genome analyses and laboratory experiments, we show that the decade-old blast pandemic lineage can be controlled by the Rmg8 disease resistance gene and is sensitive to strobilurin fungicides. However, we also highlight the potential of the pandemic clone to evolve fungicide-insensitive variants and sexually recombine with African lineages. This underscores the urgent need for genomic surveillance to track and mitigate the spread of wheat blast outside of South America and to guide preemptive wheat breeding for blast resistance