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Maize lethal necrosis (MLN) has emerged as the most challenging disease of maize in east and central Africa with yield losses of up to 100% in severe cases. Although MLN was first reported  in sub-Saharan Africa in 2011 in Kenya, the disease quickly spread within eastern and central Africa including South Sudan. Commercial lines used in South Sudan are highly susceptible to MLN. Given the urgency of need for MLN resistant varieties by farmers in South Sudan, incorporating modern breeding techniques could effectively reduce the time required  to  developed new maize lines with enhanced levels of resistance to MLN. Therefore, this study was carried out to: (1) introgress alleles for resistance to maize lethal necrosis into  genetic backgrounds of adapted but susceptible lines; (2) validate QTL conferring resistance to  MLN using different genetic backgrounds; (3) compare relative efficiencies of transmission of MLN resistance genes between Backcross (BC) and Doubled Haploid (DH) techniques; and (4) determine combining ability of selected BC3F2 and DH lines for yield and resistance to MLN. The present study generated 13 superior BC3F2 lines fixed for favourable alleles of two major  QTL for resistance to MLN and 57 DH lines homozygous for 6 loci associated with major QTL  for resistance to MLN. The lines were crossed to two elite but susceptible single cross testers and the three-way hybrids were evaluated across artificial MLN inoculations, low soil nitrogen and optimum conditions across Kenya and South Sudan. The genotype and  GxE  interactions  for grain yield and MLN severity were highly significant (p :S 0.01) and heritability estimates were high among hybrids for the same traits across managements and across locations. Hybrids DH70, DHL43, DH18, DH40, BH28 and BH01 showed good performances under artificial MLN inoculations and yielded consistently higher across management options. Lines including BCL5, BCL9, BCL13, D2, D55 and D60 demonstrated more significant negative GCA effects for MLN and positive GCA effects for yield than the testers. The study observed over performance of DH lines per se and in hybrid combinations across environments compared to the BC3F2 lines. Using different genetic backgrounds, the study detected seven major QTL populations on chromosomes 1, 3, 5 and 6 were on similar confidence interval (CI) as those reported in previous studies. These QTL could be adopted for marker assisted breeding for improvement of maize against MLN infections. Other three major QTL were not reported before hence further  research  is  warranted to confirm their reproducibility and use in breeding for resistance to MLN.  Both  linkage  mapping and joint linkage and association mapping (JLAM) can be incorporated to  confirm earlier reported QTLs and discover new sources of resistance. Incorporation of  genomic  prediction (GP) can help to capture both large effect and small effect  QTL hence  improves genetic gain. Comparatively, marker assisted DH lines had relatively higher genetic gain and superior performances over marker assisted BC3F2 for yield traits and resistance to MLN.