Population Structure and Molecular Characterization of Nigerian Field Genebank Collections of Cacao, Theobroma cacao L.

AbstractInadequate knowledge of the population structure and diversity present often hamper the efficient use of germplasm collections. Using a high through-put system, twelve microsatellite loci were used to analyze genetic diversity and population structure in a national field genebank repository of 243 cacao accessions grouped into 11 populations based on their known sources. Based on multi-locus profiles, the Bayesian method was used for individual assignment to verify membership in each population, determine mislabeling and ancestry of some important accessions used in breeding program. A total of 218 alleles was revealed with a mean number of 18.2 alleles per locus. Gene diversity (He= 0.70) and allelic richness (4.34 alleles per locus) were highest in the F1 hybrid population. Differential mating system was suggested as responsible for the observed deficit and excess of heterozygotes observed among the populations. Analysis of molecular variance showed that within-population variance accounted for 63.0% of the total variance while the rest 37% was accounted for by the among-population variance. Cluster dendrogram based on UPGMA revealed two main subsets. The first group was made up of the Amelonado/Trinitario ancestry and the other of Nanay/Parinari ancestry. We found that Nanay and Parinari populations were the major source of Upper Amazon genes utilized while a large proportion of genetic diversity in the field genebank remained under-utilized in development of improved cultivars released to farmers in Nigeria. This study showed that the presence of alleles of the Upper Amazon Forasteros (Nanay, Parinari and Iquitos Mixed Calabacillo) genetic materials in the locally available accessions predated the formal large scale introduction of Upper Amazon materials in 1944. This is the first report of population structure of field genebank collections of cacao in Nigeria since more than seven decades of formal cacao breeding research

Performance of tropical maize hybrids under conditions of low and optimum levels of nitrogen fertilizer application – grain yield, biomass production and nitrogen accumulation

Nitrogen (N) is the most limiting mineral nutrient in the soils of the major maize producing areas of West and Central Africa. Low soil N and sub-optimal application of N fertilizers lead to N deficiency and poor grain yield (GY) in maize. Maize varieties with improved grain yield under low soil N and increased performance under optimal N availability could be beneficial to low input agriculture. This study evaluated the performance of a selection of experimental and commercial hybrids under suboptimal and optimal N fertilizer applications. Significant differences were observed among the hybrids, as well as significant interactions between hybrid and N level for GY and other measured attributes, with the severity of variation increasing as the level of N decreases. Mean GY reductions across the years was 76.5% at no-N and 35.4% at low-N. Depending on N treatment, GY varied from 0.48 to 4.42 Mg ha-1, grain N content from 0.17 to 1.26 g plant-1, total N content at harvest from 0.33 to 2.00 g plant-1, above ground biomass at silking from 30.6 to 91.2 g plant-1 and at maturity from 39.9 to 191.1 g plant-1. Number of kernels was the GY component most severely reduced by N stress and had significant (p = 0.001) positive correlation with GY at all N levels. Six hybrids (4001/4008, KU1409/4008, KU1409/9613, 4008/1808, 4058/Fun 47-4, and 1824/9432) which showed consistent above average grain yields under no-N, low-N, high-N and across N levels were found and their use could further be investigated

Genomic analysis of resistance to fall armyworm (Spodoptera frugiperda) in CIMMYT maize lines

The recent invasion, rapid spread, and widescale destruction of the maize crop by the fall armyworm (FAW; Spodoptera frugiperda (J.E. Smith)) is likely to worsen the food insecurity situation in Africa. In the present study, a set of 424 maize lines were screened for their responses to FAW under artificial infestation to dissect the genetic basis of resistance. All lines were evaluated for two seasons under screen houses and genotyped with the DArTseq platform. Foliar damage was rated on a scale of 1 (highly resistant) to 9 (highly susceptible) and scored at 7, 14, and 21 days after artificial infestation. Analyses of variance revealed significant genotypic and genotype by environment interaction variances for all traits. Heritability estimates for leaf damage scores were moderately high and ranged from 0.38 to 0.58. Grain yield was negatively correlated with a high magnitude to foliar damage scores, ear rot, and ear damage traits. The genome-wide association study (GWAS) revealed 56 significant marker–trait associations and the predicted functions of the putative candidate genes varied from a defense response to several genes of unknown function. Overall, the study revealed that native genetic resistance to FAW is quantitative in nature and is controlled by many loci with minor effects

Genetic analyses of tropical maize lines under artificial infestation of fall armyworm and foliar diseases under optimum conditions

Development and deployment of high-yielding maize varieties with native resistance to Fall armyworm (FAW), turcicum leaf blight (TLB), and gray leaf spot (GLS) infestation is critical for addressing the food insecurity in sub-Saharan Africa. The objectives of this study were to determine the inheritance of resistance for FAW, identity hybrids which in addition to FAW resistance, also show resistance to TLB and GLS, and investigate the usefulness of models based on general combining ability (GCA) and SNP markers in predicting the performance of new untested hybrids. Half-diallel mating scheme was used to generate 105 F1 hybrids from 15 parents and another 55 F1 hybrids from 11 parents. These were evaluated in two experiments, each with commercial checks in multiple locations under FAW artificial infestation and optimum management in Kenya. Under artificial FAW infestation, significant mean squares among hybrids and hybrids x environment were observed for most traits in both experiments, including at least one of the three assessments carried out for foliar damage caused by FAW. Interaction of GCA x environment and specific combining ability (SCA) x environment interactions were significant for all traits under FAW infestation and optimal conditions. Moderate to high heritability estimates were observed for GY under both management conditions. Correlation between GY and two of the three scorings (one and three weeks after infestation) for foliar damage caused by FAW were negative (-0.27 and -0.38) and significant. Positive and significant correlation (0.84) was observed between FAW-inflicted ear damage and the percentage of rotten ears. We identified many superior-performing hybrids compared to the best commercial checks for both GY and FAW resistance associated traits. Inbred lines CML312, CML567, CML488, DTPYC9-F46-1-2-1-2, CKDHL164288, CKDHL166062, and CLRCY039 had significant and positive GCA for GY (positive) and FAW resistance-associated traits (negative). CML567 was a parent in four of the top ten hybrids under optimum and FAW conditions. Both additive and non-additive gene action were important in the inheritance of FAW resistance. Both GCA and marker-based models showed high correlation with field performance, but marker-based models exhibited considerably higher correlation. The best performing hybrids identified in this study could be used as potential single cross testers in the development of three-way FAW resistance hybrids. Overall, our results provide insights that help breeders to design effective breeding strategies to develop FAW resistant hybrids that are high yielding under FAW and optimum conditions

Genetic analyses of tropical maize lines under artificial infestation of fall armyworm and foliar diseases under optimum conditions

Development and deployment of high-yielding maize varieties with native resistance to Fall armyworm (FAW), turcicum leaf blight (TLB), and gray leaf spot (GLS) infestation is critical for addressing the food insecurity in sub-Saharan Africa. The objectives of this study were to determine the inheritance of resistance for FAW, identity hybrids which in addition to FAW resistance, also show resistance to TLB and GLS, and investigate the usefulness of models based on general combining ability (GCA) and SNP markers in predicting the performance of new untested hybrids. Half-diallel mating scheme was used to generate 105 F1 hybrids from 15 parents and another 55 F1 hybrids from 11 parents. These were evaluated in two experiments, each with commercial checks in multiple locations under FAW artificial infestation and optimum management in Kenya. Under artificial FAW infestation, significant mean squares among hybrids and hybrids x environment were observed for most traits in both experiments, including at least one of the three assessments carried out for foliar damage caused by FAW. Interaction of GCA x environment and specific combining ability (SCA) x environment interactions were significant for all traits under FAW infestation and optimal conditions. Moderate to high heritability estimates were observed for GY under both management conditions. Correlation between GY and two of the three scorings (one and three weeks after infestation) for foliar damage caused by FAW were negative (-0.27 and -0.38) and significant. Positive and significant correlation (0.84) was observed between FAW-inflicted ear damage and the percentage of rotten ears. We identified many superior-performing hybrids compared to the best commercial checks for both GY and FAW resistance associated traits. Inbred lines CML312, CML567, CML488, DTPYC9-F46-1-2-1-2, CKDHL164288, CKDHL166062, and CLRCY039 had significant and positive GCA for GY (positive) and FAW resistance-associated traits (negative). CML567 was a parent in four of the top ten hybrids under optimum and FAW conditions. Both additive and non-additive gene action were important in the inheritance of FAW resistance. Both GCA and marker-based models showed high correlation with field performance, but marker-based models exhibited considerably higher correlation. The best performing hybrids identified in this study could be used as potential single cross testers in the development of three-way FAW resistance hybrids. Overall, our results provide insights that help breeders to design effective breeding strategies to develop FAW resistant hybrids that are high yielding under FAW and optimum conditions

Inheritance of Pod Length and Other Yield Components in Two Cowpea and Yard-Long Bean Crosses

This study determined the gene effects involved in the inheritance of pod length and other yield-related traits and relationships among traits in crosses between two cowpea lines (TVu 2280 and TVu 2027) and a yard-long bean (TVu 6642) line with long pods. Plants of six generations (P1, P2, F1, F2, BC1P1, and BC1P2) derived from TVu 2280 × TVu 6642 and TVu 2027 × TVu 6642 were evaluated under field conditions. Data collected on 14 yield components of each cross were used for generation mean analysis. Gene effects and their magnitudes varied with the crosses; digenic epistatic gene effects were detected for 10 traits in TVu 2280 × TVu 6642 and 11 traits in TVu 2280 × TVu 6642. Only additive gene effect was significant for pod length in TVu 2280 × TVu 6642 while additive, dominant, and two of the three digenic epistatic gene effects were significant in TVu 2027 × TVu 6642. Models that incorporated only significant additive, dominant, and digenic epistasis were adequate for all 14 traits in TVu 2280 × TVu 6642 and eight of the 12 traits in TVu 2027 × TVu 6642 for which model-fitting was possible. Across segregating generation of the two crosses, pod length (PodLNT) was significantly (p < 0.001) correlated with three major yield components viz. pod weight (0.84, 0.77), number of seeds per pod (0.41, 0.30) and seed weight per pod (0.61, 0.29). Significant correlation of PodLNT with seed yield per plant was moderate and significant (p < 0.01–0.001) in the BC1P1 of the two crosses (0.31 and 0.41). An improvement in cowpea seed yield is feasible through selection for long pods in segregating generations involving crosses with yard-long bean

Hybrid breeding for fall armyworm resistance Combining ability and hybrid prediction

Fall armyworm (FAW, Spodoptera frugiperda) emerged as a major lepidopteran pest destroying maize in sub-Saharan Africa. A diallel mating design was used to generate 210 experimental hybrids from 21 lines. Experimental hybrids and four checks were evaluated in two locations. Commercial checks suffered higher foliar and ear damage compared to the top 15 hybrids. Mean squares associated with the genotypic variation were higher than genotype-by-environment interactions for foliar and ear damage traits. Heritabilities were moderate to high. Significant correlations were observed between grain yield (GY) with ear rot (−0.54) and ear damage (−0.45). Positive and significant GCA effects were observed for GY in seven parental lines, which were developed from multiple insect resistance breeding programmes. CKSBL10153 has the highest GCA value for GY and shows significant GCA effects for foliar and ear damage traits. These lines were identified as the ideal combiners for GY and FAW resistance and are therefore recommended for utilization as testers in the development of FAW-resistant three-way cross-hybrid maize with correlated response for increased GY. GCA and marker-based prediction correlations of GY were 0.79 and 0.96, respectively. Both GCA effects and marker-based models were effective in predicting hybrid performance for FAW resistance