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Genetic analysis of phenotypic variations of traits under drought stress to identify associated loci will facilitate crop improvement and performance in marginalized drought-prone areas. To this end, we identified genomic regions/loci underlying variations among recombinant inbred lines (RILs) of WAB638-1/BRS-PRIMAVERA rice under drought stress and control environments using diversity array technology (DArT)-based markers in linkage analysis. The linkage map of 94 RILs and 581 DArT-Based markers (295 SNP and 286 SilicoDArT) covers all the 12 rice chromosomes. The total length of the linkage map was 3057.85 cM, with an average of 254.82 cM per chromosome. The average interval between two adjacent markers was 5.82 cM and ranged from 0.56 cM to 39.8 cM, with 429 (73.8%) markers less than 5.0 cM from their nearest neighbours. A total of 28 additive effect QTLs associated with seven agronomic traits across the two environments were localized on chromosomes 1, 2, 3, 8, 10, and 11. The QTLs individually explained 0.96% to 41.6% of the phenotypic variance (PVE), with 11 (40%) major-effect QTLs, each explaining more than 10% PVE. Four major-effect QTLs were mapped to regions consistent with other studies, while seven are newly reported. The consistent QTLs can be deployed for marker-assisted breeding, and the new QTLs should be further characterized and validated. While the QTLs detected for various agronomic traits advances our understanding of phenotypic variability, those associated with drought treatments are significant for improving rice performance in drought-prone areas of the upland ecology.

The success of a hybrid breeding program is dependent on available heterotic patterns for exploitation of grain-yield heterosis. The efficiency of the assignment of germplasm lines into heterotic groups is a prerequisite for obtaining useful heterotic patterns among germplasm lines. A total of 256 maize hybrids, comprising 244 top crosses, six diallel cross hybrids, and six checks, were grown under Striga infestation, drought, and optimal conditions, from 2015 to 2017. The study determined the combining abilities of the parental inbreds, classified the inbreds into heterotic groups, and compared the efficiencies of the following four grouping methods for classifying the inbreds: specific combining ability (SCA) effect of grain yield, general combining ability (GCA) effects of multiple traits (HGCAMT), SCA and GCA (HSGCA) for yield, and single nucleotide polymorphism-based genetic distance (SNP-based genetic distance (GD)). Significant GCA and/or SCA mean squares were revealed for most measured traits in all test environments. Sums of squares (SS) due to GCA were higher than SCA SS for measured traits in all test environments. The HSGCA, SCA, and SNP-based GD methods identified four heterotic groups, whereas the HGCAMT identified three groups, in all environments. The additive gene effect was preponderant in the inheritance of most measured traits. The efficiencies of the grouping methods varied with the test environments. The HSGCA and SCA methods were the most efficient for grouping in all test conditions. For practical breeding purposes, the HGCAMT and HSGCA methods were recommended under Striga infestation and drought, respectively. The heterotic patterns, which were revealed in this study, were effective for planning hybridization schemes for developing high-yielding, Striga-tolerant/resistant, and drought-tolerant maize hybrids for stressful environments.