Association analysis for resistance to Striga hermonthica in diverse tropical maize inbred lines.

Striga hermonthica is a widespread, destructive parasitic plant that causes substantial yield loss to maize productivity in sub-Saharan Africa. Under severe Striga infestation, yield losses can range from 60 to 100% resulting in abandonment of farmers' lands. Diverse methods have been proposed for Striga management; however, host plant resistance is considered the most effective and affordable to small-scale famers. Thus, conducting a genome-wide association study to identify quantitative trait nucleotides controlling S. hermonthica resistance and mining of relevant candidate genes will expedite the improvement of Striga resistance breeding through marker-assisted breeding. For this study, 150 diverse maize inbred lines were evaluated under Striga infested and non-infested conditions for two years and genotyped using the genotyping-by-sequencing platform. Heritability estimates of Striga damage ratings, emerged Striga plants and grain yield, hereafter referred to as Striga resistance-related traits, were high under Striga infested condition. The mixed linear model (MLM) identified thirty SNPs associated with the three Striga resistance-related traits based on the multi-locus approaches (mrMLM, FASTmrMLM, FASTmrEMMA and pLARmEB). These SNPs explained up to 14% of the total phenotypic variation. Under non-infested condition, four SNPs were associated with grain yield, and these SNPs explained up to 17% of the total phenotypic variation. Gene annotation of significant SNPs identified candidate genes (Leucine-rich repeats, putative disease resistance protein and VQ proteins) with functions related to plant growth, development, and defense mechanisms. The marker-effect prediction was able to identify alleles responsible for predicting high yield and low Striga damage rating in the breeding panel. This study provides valuable insight for marker validation and deployment for Striga resistance breeding in maize.

Genetics of extra-early-maturing yellow and orange quality protein maize inbreds and derived hybrids under low soil nitrogen and Striga infestation.

The development and commercialization of extra-early quality protein maize (QPM)-provitamin A (PVA) hybrids that are tolerant of low soil N (LN) and Striga resistant are essential for addressing the food insecurity and undernourishment challenges currently faced by sub-Saharan Africa (SSA). This study was designed (a) to determine the genetic effects regulating grain yield (GY) and important secondary traits of extra-early yellow and orange QPM-PVA inbred lines under LN, Striga-infested, and high-N (HN) conditions, (b) to investigate whether maternal genes influenced the inheritance of GY and other secondary traits, (c) to assess the GY and stability of the hybrids across the three management conditions, and (d) to examine the relationship between single nucleotide polymorphism (SNP) marker-based genetic distances and GY. Twenty-four inbred lines were used to produce ninety-six single cross hybrids using the North Carolina Design II. The performance of the hybrids plus four checks was assessed across LN, Striga-infested, and HN management conditions in Ghana and Nigeria in 2018. Additive genetic variances were preponderant over nonadditive genetic variances for GY and most secondary traits in each and across environments. TZEEQI 358 exhibited significant and positive male and female GCA effects for GY under LN, Striga infestation, HN, and across management conditions indicating that favorable alleles for GY could be donated by TZEEQI 358. Maternal effects regulated the inheritance of plant height under the Striga-infested conditions. Genetic distances were associated with GY under LN, Striga infestation, and HN conditions. TZEEIORQ 58 × TZEEQI 397 demonstrated high GY and stability of performance; therefore, it should be further tested under multiple environments for commercialization.

Maize lethal necrosis and the molecular basis of variability in concentrations of the causal viruses in co-infected maize plant.

Maize lethal necrosis (MLN) disease is new to Africa. First report was in Kenya in 2012, since then the disease has rapidly spread to most parts of eastern and central Africa region including Tanzania, Burundi, DRC Congo, Rwanda, Uganda, Ethiopia and similar symptoms were observed in South Sudan. Elsewhere, the disease was caused by infection of Maize Chlorotic Mottle Virus (MCMV) in combination with any of the potyviruses namely; maize dwarf mosaic virus (MDMV), sugarcane mosaic virus (SCMV) and tritimovirus wheat streak mosaic virus (WSMV). In Africa, the disease occurs due to combined infections of maize by MCMV and SCMV, leading to severe yield losses. Efforts to address the disease spread have been ongoing. Serological techniques including enzyme-linked immuno-sorbent assay (ELISA), polymerase chain reaction (PCR), genome-wide association (GWAS) mapping and next generation sequencing have been effectively used to detect and characterize MLN causative pathogens. Various management strategies have been adapted to control MLN including use of resistant varieties, phytosanitary measures and better cultural practices. This review looks at the current knowledge on MLN causative viruses, genetic architecture and molecular basis underlying their synergistic interactions. Lastly, some research gaps towards MLN management will be identified. The information gathered may be useful for developing strategies towards future MLN management and maize improvement in Africa.

Genomics-assisted breeding for boosting crop improvement in pigeonpea (Cajanus cajan).

Pigeonpea is an important pulse crop grown predominantly in the tropical and sub-tropical regions of the world. Although pigeonpea growing area has considerably increased, yield has remained stagnant for the last six decades mainly due to the exposure of the crop to various biotic and abiotic constraints. In addition, low level of genetic variability and limited genomic resources have been serious impediments to pigeonpea crop improvement through modern breeding approaches. In recent years, however, due to the availability of next generation sequencing and high-throughput genotyping technologies, the scenario has changed tremendously. The reduced sequencing costs resulting in the decoding of the pigeonpea genome has led to the development of various genomic resources including molecular markers, transcript sequences and comprehensive genetic maps. Mapping of some important traits including resistance to Fusarium wilt and sterility mosaic disease, fertility restoration, determinacy with other agronomically important traits have paved the way for applying genomics-assisted breeding (GAB) through marker assisted selection as well as genomic selection (GS). This would accelerate the development and improvement of both varieties and hybrids in pigeonpea. Particularly for hybrid breeding programme, mitochondrial genomes of cytoplasmic male sterile (CMS) lines, maintainers and hybrids have been sequenced to identify genes responsible for cytoplasmic male sterility. Furthermore, several diagnostic molecular markers have been developed to assess the purity of commercial hybrids. In summary, pigeonpea has become a genomic resources-rich crop and efforts have already been initiated to integrate these resources in pigeonpea breeding.