Analysis of drought tolerant and susceptible maize genotypes using SSR markers tagging candidate genes and consensus QTLs for drought tolerance

Abstract

Drought stress, particularly at flowering stage, has been identified as the most important factor limiting maize production and productivity in India. In this study, a set of 24 tropical maize lines with differential responses to drought stress, including 16 lines from CIMMYT (Mexico) and eight lines from India, were characterized using 37 polymorphic microsatellite/SSR markers, including 29 SSRs tagging specific candidate genes involved in drought stress tolerance in maize. These genes, distributed on nine of the ten maize chromosomes, also colocalized with 17 ‘consensus QTLs’ for various morpho-physiological traits associated with drought tolerance at flowering stage. The analysis using these 37 candidate gene-specific and drought ‘anchor’ markers tagging consensus QTLs led to unambiguous differentiation of the genotypes as well as assessment of genetic diversity in these important genetic resources. A total of 119 SSR alleles with a mean of 3.22 alleles per locus were identified. Polymorphism Information Content (PIC) of the 37 SSR loci ranged from 0.09 (umc1627) to 0.78 (umc1056 and bnlg1866), with a mean PIC of 0.56. The study resulted in identification of eleven highly informative markers with PIC values >0.65, as well as five unique SSR alleles in DTPW-C9-F55-2-3, DTPW-C9-F115-1-4, DTPY-C9-F142-1-2, K64R and CML537. Pair-wise genetic similarity (GS) values, estimated using Jaccard’s coefficient, ranged between 0.14 (HKI1025- K64R; HKI1025-CML247) and 0.74 (HKI-335-HKI-209), with a mean GS of 0.31, indicating high level of genetic divergence among the genotypes selected for the study. Cluster analysis revealed clear genetic differentiation of the DTP (drought tolerant population) lines developed at CIMMYT (Mexico) from those developed and identified in India (e.g. CM140). Principal Component Analysis (PCA) aided in further elucidation of the genetic relationships as well as differentiation of genotypes largely based on their phenotypic responses to drought stress. The analysis also led to identification of specific, highly informative SSR markers, namely dupssr12 (bin 1.08), umc1042 (bin 2.07), bnlg1866 (bin 1.03), umc1056 (bin 5.03), dup13 (bin 7.04), umc1069 (bin 8.08), umc1962 (bin 10.03), bnlg1028 (bin 10.06) and umc1344 (bin 10.07), which significantly contributed to the differentiation of the drought tolerant and susceptible genotypes analysed in the study. These SSR markers could be further validated and potentially deployed in molecular marker-assisted breeding for drought tolerance in maize.