Indian Society of Genetics & Plant Breeding


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

Published on Aug 16, 2018 02:29 PM

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.

Keywords: Maize, drought, SSRs, candidate genes, consensus QTL, anchor markers


Year: 2009
Volume: 69
Issue: 4
Article DOI: N/A
Print ISSN: 0019-5200
Online ISSN: 0975-6906


L. Dubey, B. M. Prasanna info_circle
B. Ramesh info_circle
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