MAPPING AND CHARACTERIZATION OF PUTATIVE CANDIDATE GENES FOR GRAIN IRON AND ZINC CONTENT IN RICE BY MPSS SIGNATURE ANALYSIS
R. K. Zote*, R. N. Dhawale, G. Chandel, S. B. Verulkar3 and A. S. Kotasthane
ABSTRACT
Rice (Oryza sativa L.) grain iron and zinc content is a polygenic
complex trait having additive effect of multiple genes thus
identification of QTLs and sequence analysis of genomic region
encompassing them enable us to understand not only the inheritance of
grain micronutrient content but also to develop Fe/Zn rich rice using
marker assisted breeding techniques. Co-segregation analysis was
performed with the F6 mapping population derived from a cross
between rice cultivar Swarna x Moroberekan. The grain Fe content
ranged from 9.68 to 19.98 μg/g with an average of 16.87 μg/g and
grain Zn content ranged from 15.85 to 20.84 μg/g with an average of 25.76μg/g among the 73
homozygous rice mapping population. Similarly the grain protein content ranged from 5.34%
to 7.18% with an average of 9.23%. In order to identify novel SSR based molecular markers,
5 known QTLs (qFE-1, qFE-9, qZN-5, qZN-7 and qZN-11) identified [9] for grain Fe/Zn
content in rice were analyzed using in-silico tools. Out of 1063 novel SSRs loci present
within the 5 QTL regions, 161 Class I SSRs with 2-6 nt long repeat motifs and 12–80 nt
repeat lengths were identified. On the basis of position of metal related transporter or
membrane transporter genes primers were designed for 22 novel Class- I SSR and validated
in the parents for their polymorphism. Out of 34 previously designed primers, 4 randomly selected RM markers and 22 novel SSR designed markers, only 18 markers were found to be
polymorphic. The allelic segregation analysis indicated that indica parent Swarna contributed
about 60.6% whereas the japonica parent Moroberekan contributed about 34.32% of total
amplified alleles on an average which clearly showed departure from the theoretically
expected 1:1 ratio of equal contribution from the two parents. Out of 18 polymorphic SSRs,
the co-segregation analysis performed for the 5 randomly selected SSR‟s markers. The all
five markers; gRMm7-2, gRMm7-3, gRMm33-2, gRMm34-1 and gRMm33-3 were
significantly associated to grain iron and zinc contents.
Keywords: Japonica, Indica, Oryza Sativa L.
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