Molecular profiling of little millet genotypes using iron and zinc transporter based SSR markers of foxtail millet
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Date
2021
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Publisher
DRPCAU, PUSA
Abstract
The present study entitled "Molecular profiling of little millet genotypes using iron
and zinc transporter based SSR markers of foxtail millet" was carried out to identify useful
microsatellite-based markers of foxtail millet, which can be used for characterization of
little millet genotypes based on their iron and zinc content. Altogether, 2 genotypes of
foxtail millet and 26 genotypes of little millet were used for molecular profiling using iron
and zinc based designed genic SSR markers. The grain iron and zinc content were
determined in 26 genotypes of little millet and they were categorized in 3 groups having
high, medium and low iron and zinc content.
For molecular profiling of little millet genotypes, genic SSR markers were designed
using BatchPrimer3 against the 21 iron and zinc transporter genes of foxtail millet. The
SSRs were detected in all the genes except five genes. A total of 39 SSRs were detected
and 36 primers were designed. The trinucleotides repeats were found to be most common.
The most common repeat motif was found to be GCG/CGC. Using the 36 designed genic
SSR molecular markers, reproducible amplification was successfully achieved in foxtail
millet. Out of 36 designed genic SSR molecular markers, 14 genic SSR markers showed
successful amplification in 26 little millet genotypes. The 14 primers showed the
polymorphic bands in the little millet genotypes (38.88 % transferability).
Using a panel of 14 designed and transferable primers, 126 alleles were detected in
foxtail and little millet. In little millet, 108 alleles were obtained, in which 34 were unique
alleles. The molecular size of amplified product varied from 93 bp to 1083 bp. The
polymorphism per cent was 50 in the primer SI-ZT-1A and SI-ZT-1B whereas the lowest
value found in the primer SI-ZT-P29-E and SI-ZT-9A i.e. 0 with an average of 30.07. The
PIC value varied from 0.245 to 0.827 with an average of 0.578. The DC of the primer
ranged from 0.1826 in the primer SI-ITP-2 to 0.9947 in primer SI-ZT-1A with an average
of 0.6888. The primers having dinucleotides repeats were the most effective in determining
the allele in little millet and the maximum number of alleles was detected by the primer
targeting gene zinc transporter 7.
The Dice’s similarity coefficient was 0.8000 for the foxtail millet genotype pair
whereas for little millet pair wise combination, the maximum similarity coefficient (0.7222)
was found between the genotype WV-155 and WV-156 while 6 pair-wise combinations had
shown minimum possible similarity (0.000). According to the cluster analysis and the
principle coordinate analysis, the genotypes were differentiated into three groups which
clearly differentiate high and low iron and zinc containing genotypes. Cluster I has the 5
genotypes, cluster II has 11 genotypes, cluster III has 12 genotypes. The experimental
results amply emphasized that the panel of primers employed during experimentation was
useful and adequate to discriminate the little millet genotypes in relation to iron and zinc
content. These markers can therefore be used effectively and efficiently for further studies
in relation with grain iron and zinc content.