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This research conducted out to investigate genetic control of root traits and indices, water use efficiency and transpiration efficiency using genome wide association study. 3321 SNP markers with at least 5% minor frequency for alleles along with a mixed linear model on evaluated traits applied to association analysis in a structured population (112 genotypes in three subpopulations). Seminal roots were associated with two markers on 2A and 1B chromosomes. But the length of extended roots was under control of 1A and 6B chromosomes. Some markers on 2B and 5B chromosomes were significant with root dry weight. The volume of roots was associated to a marker on 7B chromosome. Root surface and diameter also were under genetic control. Twenty markers were associate to water use efficiency, eleven of them on genome A (1A, 2A, 3A, 5A and 6A) and nine on genome B (2B, 3B and 4B). Genetic control of transpiration efficiency was in association with 2A, 3A, 6A, 2B and 3B chromosomes. Genomic selection is an efficient strategy for early screening of segregated population in breeding programs when just few markers determine majority of variation for a phenotypic trait.

Keywords: Informative markers, Genomic selection, Germplasm, Association analysis.

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