Genetic diversity provides the capacity for plants to meet changing environments and farmers' preferences, and to establish heterotic patterns, essential for an efficient and sustainable hybrid breeding program. Group interviews and formal surveys were conducted in North and South-Sudan agro-ecological zones of Burkina Faso to assess farmers’ preferences and evaluate their perception of constraints to maize production.

Fifty-nine INERA and forty one elite CIMMYT, IITA, U.S and European maize inbred lines were characterized using 1151 SNP markers to determine the level of genetic diversity in the INERA inbred lines and examine the genetic difference between local and exotic germplasms. A subset of 54 diverse maize inbred lines were selected to generate 100 hybrids using a line by tester mating design. Inbred parents and hybrids were evaluated under both well-watered and water-stressed conditions in two years (2011 and 2012) and under well-watered and high plant density condition in one year (2013), to examine genetic variation in grain yield and drought tolerance traits, and the heterotic patterns of the inbred lines.
The participatory rural appraisal (PRA) indicated that the farmers' maize ''ideotype'' includes traits such as yield potential, earliness, tolerance drought and Striga. Model-based population structure and principal component analyses of the 100 lines genotyped revealed the presence of 5 groups consistent, to some extent, with the origin of the germplasm. There was genetic diversity among INERA inbred lines which were less closely related and showed a low level of heterozygosity. These lines were divided into 3 majors groups and a mixed group consistent with the source population of the lines. Pairwise comparisons between local and exotic germplasms showed that the temperate lines and some IITA lines were differentiated from INERA lines. There appeared to be substantial levels of genetic variation between local and exotic germplasms as revealed by missing and unique alleles. Association mapping with phenotypic traits showed that 22 SNPs were consistently associated with at least one drought-related trait in individual and across environments. The contribution of GCA to total genetic variance was higher than SCA for grain yield and secondary traits under drought and non-drought conditions. However, the contribution of SCA for number of ears per plant (EPP) and leaf rolling (LR) was predominant under drought. The average relative contribution of SCA, indicative of non-additive gene effects, to total genetic variance for grain yield under drought accounted for 28% and 35% under non-drought conditions. The average high parent heterosis of CIMMYT (testers) x INERA (lines) and IITA (testers) x INERA (lines) were 299 % and 200 %, respectively. Based on SCA effects and testcross mean grain yield across environments, the two CIMMYT testers were able to separate 54 % of CIMMYT and INERA white lines into two opposite heterotic groups while the two IITA testers assigned all the IITA and INERA yellow lines. Based on this classification, 2 complementary heterotic groups were formed with VL0511298 and T02058 as testers for white lines and TZEI17 and ELN45111 as testers for yellow lines.
Four white hybrids, VL0511298xT020-58, VL0511298xVL057967, VL0511298xVL05616, VL0511298 x VL054794, and three yellow hybrids, TZEI17 x ELN45111, TZEI17 x TZEI146 and TZEI10 x ELN39427, with an average grain yield of 3 t/ha, high parent heterosis between 200 to 500 % and with favorable drought tolerance and stability indices, were identified as high yielding, and drought tolerant stable hybrids with a consistent heterotic response .
The results from this study will be useful to breeders in designing inbred-hybrid breeding program, association mapping studies and marker assisted breeding.