Identification of informative simple sequence repeat (SSR) markers for drought tolerance in maize

Maize is moderately sensitive to drought. Drought affects virtually all aspects of maize growth in varying degrees at all stages, from germination to maturity. Tolerance to drought is genetically and physiologically complicated and inherited quantitatively. Application of molecular-marker aided selection technique for improvement of drought tolerance would accelerate breeding progress by increasing selection efficiency. One of the most important aims in plant breeding is to determine the chromosomal regions related to drought tolerance. Therefore, 38 maize hybrids were planted in two separate experiments with well-watered (WW) and water-stressed (WS) conditions at grain filling period using a randomized complete block design (RCBD) with three replications. Drought tolerance indices such as stress susceptibility index (SSI), mean productivity (MP), tolerance (TOL) and stress tolerance index (STI) were used to evaluate the susceptibility and tolerance of the hybrids. Also, to assess the genetic relationships among the 38 maize hybrids used in the evaluation and breeding for drought tolerance, and to determine informative markers for drought tolerance, 12 microsatellite primers were used. Genomic DNA was extracted with the CTAB method and PCR was performed based on the common method for microsatellite markers. PCR products were separated using 6% polyacrylamide denaturing gel. Stepwise multiple regression analysis was used to determine the chromosomal regions related to drought tolerance. A total of 40 simple sequence repeat (SSR) alleles (bands) with a mean of 3.33 alleles per locus were identified. Polymorphism information content (PIC) of the 12 SSR loci ranged from 0.23 (Phi080) to 0.79 (UMC2359), with a mean PIC of 0.53. The analysis also led to identification of informative SSR markers, namely UMC1862 (bin 1.11), UMC1719 (bin 4.10-4.11), UMC1447 (bin 5.03), UMC2359 (bin 9.07) and UMC1432 (bin 10.02), which significantly contributed to the differentiation of the drought tolerant and susceptible genotypes analyzed in the study. These SSR markers could be further validated and potentially deployed in molecular marker-assisted breeding for drought tolerance in maize.