Genetic analysis of agronomic traits among tropical and sub- tropical maize (Zea Mays L.) inbred lines for drought tolerance in South Africa.

Abstract

Maize (Zea mays L.) production plays a crucial role in the economies of most southern African countries. However, these countries have recently experienced significant decreases in maize yields due to the increased occurrence of drought events. In the future, the situation is anticipated to worsen. Several studies have predicted increased frequency and severity of droughts, highlighting South Africa as one of the global hotspots for climate change-induced drought events. Hence, it will be important to breed maize cultivars that can adapt to the prevalent climate challenges to meet the requirements of local and regional markets. Tropical and sub-tropical germplasm adapted to sub-Saharan African (SSA) environments can enhance the tolerance of South African maize to moisture stress. These genotypes are renowned for their native traits that ensure maize productivity in multiple-stress environments. Therefore, these genetic resources can provide a valuable source of genetic diversity needed to enhance the resilience of South African maize germplasm against climate change-related challenges, particularly drought stress. The knowledge of the mechanism regulating drought tolerance in maize will also facilitate the integration of the desired genes into local germplasm. Therefore, the specific objectives of the study were: (i) to assess genetic diversity and population structure of tropical and sub-tropical maize inbred lines using phenotypic traits and single nucleotide polymorphism (SNP) markers; (ii) to assess genetic variance parameters and heritability among tropical and subtropical maize inbred lines under well-watered and drought-stressed conditions; (iii) to identify candidate genes significantly associated with maize yield and yield component traits under well-watered and drought-stressed environments; and (iv) to evaluate the genotype by environment interaction of tropical and sub-tropical maize inbred lines under well-watered and drought-stressed environments and identify parental inbred lines for further breeding. The first study assessed the genetic diversity and population structure among one hundred and twenty-eight (128) maize inbred lines sourced from the International Institute of Tropical Agriculture (IITA), the International Maize and Wheat Improvement Centre (CIMMYT), and the University of KwaZulu-Natal (UKZN). This was done using 15 phenotypic traits assessed across two locations and 11,450 SNP markers. The inbred lines showed highly significant (p < 0.001) levels of variability for traits such as days to anthesis, days to silking, plant height, and grain yield. This indicates substantial genetic variation among the studied inbred lines. The highest grain-yielding genotypes included TZISTR1190, TZISTR1261, CML540, CML571, and TZISTR1119, achieving yields of 5.9, 5.8, 5.6, 5.6, and 5.5 t ha-1, respectively. The modelbased population structure analysis revealed the existence of three sub-populations (K = 3) among the inbred lines. This was supported by the phenotypic and molecular hierarchical cluster analyses which grouped the inbred lines into three clusters, respectively. The second study assessed the interrelationship between grain yield and its components among tropical and sub-tropical germplasm to confirm the utility of the traits in selecting highperforming inbred lines under well-watered and drought-stressed conditions. Analysis of variance revealed significant differences (p < 0.001) among genotypes for all traits. High heritability (H2) estimates were recorded for ear height (76.10%), plant height (62.74%), ear length (58.97%), and grain yield (64.02%) in a well-watered treatment. Under drought stress, ear height (61.98%) demonstrated the highest heritability, while all other traits exhibited heritability estimates below 50%. Correlation and principal component analyses identified traits such as field weight, kernels rows per ear, ear length, ear diameter, plant height, and ear height as significant factors with direct association with grain yield under well-watered and drought-stress environments. The third experiment was a genome-wide association study conducted using a panel of 182 maize inbred lines, to reveal the genetic basis of ear height, ear length, ear diameter, kernels per row, kernel rows per ear under drought and well-watered conditions. The panel was genotyped using a 50,941-SNP array, of which 7119 SNPs together with the best linear unbiased estimates (BLUPs) were used for the GWAS using a mixed linear model. In total, 25 and 21 significant SNPs were detected for the traits under well-watered and drought-stressed environments, respectively. These loci included SNP 4583772 located on Chromosome (Chr) 2 which was significant for EH with pleiotropic effects for ED. In addition, SNP 2382814 located on Chr 7, significant for ED was co-localized under well-watered and drought-stressed environments. From the candidate regions of the 46 significant loci, 15 genes expressed in maize ear traits, participated in biological pathways such as amino acid biosynthesis, enzyme regulation, growth, and stress hormone function. These candidate genes included putative functional genes such as Zm00001e032263, Zm00001eb206490, Zm00001eb099810, Zm00001eb332890 (smk501 - small kernel 501), and Zm00001eb418870, of which Zm00001eb099810 is located on QTL for height above the ear. These results have the potential to be useful in starting marker-assisted selection and targeted trait introgression in maize under well-watered and drought-stressed conditions. The fourth study examined the performance of the 182 tropical and sub-tropical inbred lines over five seasons at Ukulinga, Makhathini, and Cedara research stations in the KwaZulu-Natal province of South Africa. Genotype and genotype × environment (GGE) interaction effects were significant (p ≤ 0.001) for grain yield and related traits among the inbred lines. Notably, the GGE biplot clustered the environments into three distinct mega-environments. Inbred lines TZISTR1190, TZISTR1231, and TZ-14 exhibiting stable high yield in well-watered and drought-stressed conditions can be incorporated into local maize breeding pipelines to develop stable and high-yielding resilient hybrids.