Genome-wide association studies of grain yield and quality traits under optimum and low-nitrogen stress in tropical maize (Zea mays L.)

Soils in sub-Saharan Africa are nitrogen deficient due to low fertilizer use and inadequate soil fertility management practices. This has resulted in a significant yield gap for the major staple crop maize, which is undermining nutritional security and livelihood sustainability across the region. Dissecting the genetic basis of grain protein, starch and oil content under nitrogen-starved soils can increase our understanding of the governing genetic systems and improve the efficacy of future breeding schemes. An association mapping panel of 410 inbred lines and four bi-parental populations were evaluated in field trials in Kenya and South Africa under optimum and low nitrogen conditions and genotyped with 259,798 SNP markers. Genetic correlations demonstrated that these populations may be utilized to select higher performing lines under low nitrogen stress. Furthermore, genotypic, environmental and GxE variations in nitrogen-starved soils were found to be significant for oil content. Broad sense heritabilities ranged from moderate (0.18) to high (0.86). Under low nitrogen stress, GWAS identified 42 SNPs linked to grain quality traits. These significant SNPs were associated with 51 putative candidate genes. Linkage mapping identified multiple QTLs for the grain quality traits. Under low nitrogen conditions, average prediction accuracies across the studied genotypes were higher for oil content (0.78) and lower for grain yield (0.08). Our findings indicate that grain quality traits are polygenic and that using genomic selection in maize breeding can improve genetic gain. Furthermore, the identified genomic regions and SNP markers can be utilized for selection to improve maize grain quality traits

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

Relationship between grain yield and quality traits under optimum and low-nitrogen stress environments in tropical maize

Breeding for nitrogen use efficiency (NUE) is important to deal with food insecurity and its effect on grain quality, particularly protein. A total of 1679 hybrids were evaluated in 16 different trials for grain yield (GY), grain quality traits (protein, starch and oil content) and kernel weight (KW) under optimum and managed low soil nitrogen fields in Kiboko, Kenya, from 2011 to 2014. The objectives of our study were to understand (i) the effect of low soil N stress on GY and quality traits, (ii) the relationship between GY and quality traits under each soil management condition and (iii) the relationship of traits with low-N versus optimum conditions. From the results, we observed the negative effects of low N on GY, KW and the percentage of protein content, and a positive effect on the percentage of starch content. The correlation between GY and all quality traits was very weak under both soil N conditions. GY had a strong relationship with KW under both optimum and low soil N conditions. Protein and starch content was significantly negative under both optimum and low-N conditions. There was no clear relationship among quality traits under optimum and low N, except for oil content. Therefore, it seems feasible to simultaneously improve GY along with quality traits under both optimum and low-N conditions, except for oil content. However, the negative trend observed between GY (starch) and protein content suggests the need for the regular monitoring of protein and starch content to identify varieties that combine both high GY and acceptable quality. Finally, we recommend further research with a few tropical maize genotypes contrasting for NUE to understand the relationship between the change in grain quality and NUE under low-N conditions

Host plant resistance for fall armyworm management in maize: relevance, status and prospects in Africa and Asia

The fall armyworm [Spodoptera frugiperda (J.E. Smith); FAW] has emerged as a serious pest since 2016 in Africa, and since 2018 in Asia, affecting the food security and livelihoods of millions of smallholder farmers, especially those growing maize. Sustainable control of FAW requires implementation of integrated pest management strategies, in which host plant resistance is one of the key components. Significant strides have been made in breeding elite maize lines and hybrids with native genetic resistance to FAW in Africa, based on the strong foundation of insect-resistant tropical germplasm developed at the International Maize and Wheat Improvement Center, Mexico. These efforts are further intensified to develop and deploy elite maize cultivars with native FAW tolerance/resistance and farmer-preferred traits suitable for diverse agro-ecologies in Africa and Asia. Independently, genetically modified Bt maize with resistance to FAW is already commercialized in South Africa, and in a few countries in Asia (Philippines and Vietnam), while efforts are being made to commercialize Bt maize events in additional countries in both Africa and Asia. In countries where Bt maize is commercialized, it is important to implement a robust insect resistance management strategy. Combinations of native genetic resistance and Bt maize also need to be explored as a path to more effective and sustainable host plant resistance options. We also highlight the critical gaps and priorities for host plant resistance research and development in maize, particularly in the context of sustainable FAW management in Africa and Asia

A linear profit function for economic weights of linear phenotypic selection indices in plant breeding

The profit function (net returns minus costs) allows breeders to derive trait economic weights to predict the net genetic merit (H) using the linear phenotypic selection index (LPSI). Economic weight is the increase in profit achieved by improving a particular trait by one unit and should reflect the market situation and not only preferences or arbitrary values. In maize (Zea mays L.) and wheat (Triticum aestivum) breeding programs, only grain yield has a specific market price, which makes application of a profit function difficult. Assuming the traits’ phenotypic values have multivariate normal distribution, we used the market price of grain yield and its conditional expectation given all the traits of interest to construct a profit function and derive trait economic weights in maize and wheat breeding. Using simulated and real maize and wheat datasets, we validated the profit function by comparing its results with the results obtained from a set of economic weights from the literature. The criteria to validate the function were the estimated values of the LPSI selection response and the correlation between LPSI and H. For our approach, the maize and wheat selection responses were 1,567.13 and 1,291.5, whereas the correlations were .87 and .85, respectively. For the other economic weights, the selection responses were 0.79 and 2.67, whereas the correlations were .58 and .82, respectively. The simulated dataset results were similar. Thus, the profit function is a good option to assign economic weights in plant breeding

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