Validation of sorghum quality control (QC) markers across African breeding lines.

Sorghum [Sorghum bicolor (L.) Moench] is a cereal crop of critical importance in the semi-arid tropics, particularly in Africa where it is second only to maize (Zea mays L.) by area of cultivation. The International Crops Research Institute for the Semi-Arid Tropics sorghum breeding program for Eastern and Southern Africa is the largest in the region and develops improved varieties for target agro-ecologies. Varietal purity and correct confirmation of new crosses are essential for the integrity and efficiency of a breeding program. We used 49 quality control (QC) kompetitive allele-specific PCR single nucleotide polymorphism (SNP) markers to genotype 716 breeding lines. Note that 46 SNPs were polymorphic with the top 10 most informative revealing polymorphism information content (PIC), minor allele frequency (MAF), and observed heterozygosity (Ho) of 0.37, 0.43, and 0.02, respectively, and explaining 45% of genetic variance within the first two principal components (PC). Thirty-nine markers were highly informative across 16 Burkina Faso breeding lines, out of which the top 10 revealed average PIC, MAF, and Ho of 0.36, 0.39, and 0.05, respectively. Discriminant analysis of principal components done using top 30 markers separated the breeding lines into five major clusters, three of which were distinct. Six of the top 10 most informative markers successfully confirmed hybridization of crosses between genotypes IESV240, KARIMTAMA1, F6YQ212, and FRAMIDA. A set of 10, 20, and 30 most informative markers are recommended for routine QC applications. Future effort should focus on the deployment of these markers in breeding programs for enhanced genetic gain.

On-farm performance and farmers' participatory assessment of new stress-tolerant maize hybrids in Eastern Africa.

The development and deployment of high-yielding stress tolerant maize hybrids are important components of the efforts to increase maize productivity in eastern Africa. This study was conducted to: i) evaluate selected, stress-tolerant maize hybrids under farmers' conditions; ii) identify farmers' selection criteria in selecting maize hybrids; and iii) have farmers evaluate the new varieties according to those criteria. Two sets of trials, one with 12 early-to-intermediate maturing and the other with 13 intermediate-to-late maturing hybrids, improved for tolerance to multiple stresses common in farmers' fields in eastern Africa (drought, northern corn leaf blight, gray leaf spot, common rust, maize streak virus), were evaluated on-farm under smallholder farmers' conditions in a total of 42 and 40 environments (site-year-management combinations), respectively, across Kenya, Uganda, Tanzania and Rwanda in 2016 and 2017. Farmer-participatory variety evaluation was conducted at 27 sites in Kenya and Rwanda, with a total of 2025 participating farmers. Differential performance of the hybrids was observed under low-yielding (<3 t ha-1) and high-yielding (>3 t ha-1) environments. The new stress-tolerant maize hybrids had a much better grain-yield performance than the best commercial checks under smallholder farmer growing environments but had a comparable grain-yield performance under optimal conditions. These hybrids also showed better grain-yield stability across the testing environments, providing an evidence for the success of the maize-breeding approach. In addition, the new stress- tolerant varieties outperformed the internal genetic checks, indicating genetic gain under farmers' conditions. Farmers gave high importance to grain yield in both farmer-stated preferences (through scores) and farmer-revealed preferences of criteria (revealed by regressing the overall scores on the scores for the individual criteria). The top-yielding hybrids in both maturity groups also received the farmers' highest overall scores. Farmers ranked yield, early maturity, cob size and number of cobs as the most important traits for variety preference. The criteria for the different hybrids did not differ between men and women farmers. Farmers gave priority to many different traits in addition to grain yield, but this may not be applicable across all maize-growing regions. Farmer-stated importance of the different criteria, however, were quite different from farmer- revealed importance. Further, there were significant differences between men and women in the revealed-importance of the criteria. We conclude that incorporating farmers' selection criteria in the stage-gate advancement process of new hybrids by the breeders is useful under the changing maize-growing environments in sub-Saharan Africa, and recommended to increase the turnover of new maize hybrids.

Genetic Analysis of QTL for Resistance to Maize Lethal Necrosis in Multiple Mapping Populations.

Maize lethal necrosis (MLN) occurs when maize chlorotic mottle virus (MCMV) and sugarcane mosaic virus (SCMV) co-infect maize plant. Yield loss of up to 100% can be experienced under severe infections. Identification and validation of genomic regions and their flanking markers can facilitate marker assisted breeding for resistance to MLN. To understand the status of previously identified quantitative trait loci (QTL)in diverse genetic background, F3 progenies derived from seven bi-parental populations were genotyped using 500 selected kompetitive allele specific PCR (KASP) SNPs. The F3 progenies were evaluated under artificial MLN inoculation for three seasons. Phenotypic analyses revealed significant variability (P ≤ 0.01) among genotypes for responses to MLN infections, with high heritability estimates (0.62 to 0.82) for MLN disease severity and AUDPC values. Linkage mapping and joint linkage association mapping revealed at least seven major QTL (qMLN3_130 and qMLN3_142, qMLN5_190 and qMLN5_202, qMLN6_85 and qMLN6_157qMLN8_10 and qMLN9_142) spread across the 7-biparetal populations, for resistance to MLN infections and were consistent with those reported previously. The seven QTL appeared to be stable across genetic backgrounds and across environments. Therefore, these QTL could be useful for marker assisted breeding for resistance to MLN.