Amplification profiling of grain zinc accumulation related candidate genes in rice using TRAP markers
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Date
2020
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DRPCAU, Pusa
Abstract
The present study was undertaken to examine the molecular level genetic
polymorphism in relation to grain zinc concentration among 18 genotypes of rice using
12 candidate gene specific TRAP markers. The purpose of the present investigation was
to evaluate the extent of genetic variability and diversity in respect of grain zinc
concentration among these rice genotypes.
Differential amplification profile was ascertained amongst the genotypes
subjected to molecular characterization by employing 12 TRAP markers. Altogether 141
polymorphic bands representing easily recognizable different types of amplified products
were categorized into 29 unique products and 112 shared products. Polymorphism
information content of 12 TRAP markers diverged from 0.437 to 0.776 around an average
measure of 0.611 across the markers.
The combination of fixed forward primers OsNRAMP7K, OsZIP3K, OsZIP4a and
OsZIP5K with an arbitrary reverse primer ME02 generated the lowest number of
polymorphic products. Furthermore, the forward primer OsZIP7K in combination with
the same arbitrary reverse primer yielded the highest number of polymorphic products.
The forward primers OsZIP1-1, OsZIP7K, OsZIP4a, OsZIP5K, OsZIP4K, OsYSL14K
and OsZIP5-3 along with ME02 yielded remarkably larger allelic size difference in
descending order of magnitude.
Numerical variation in polymorphism information content of the markers reflected
their allelic diversity and distribution frequency among the genotypes, which diverged
from 0.437 for the combination of primer OsZIP5-3+ME02 to 0.776 for the combination
of primer OsZIP7-2+ME02 with an average of 0.611 across all the primer pair
combinations. The fixed forward primers OsZIP7-2, OsZIP1-1 and OsZIP4K in
combination with ME02 seemed to be extremely polymorphic and informative, whereas
the remaining nine primer pair combinations were found less polymorphic.
Similarity coefficients measuring the genetic similarities on the basis of the total
count of shared polymorphic amplified products among pair-wise combinations of the
genotypes revealed sizeable molecular level genetic variation among the genotypes.
Experimental results clearly reflected the existence of plentiful diverseness at the
molecular level among the 18 genotypes under evaluation in the present study.
Hierarchical classification pattern based on target region amplification
polymorphism related genetic similarity among rice genotypes was almost in complete
agreement with principal coordinate analysis based two-dimensional dispersion pattern of
molecular genetic profiles of rice genotypes. Using both the modules, the genotypes were
conveniently grouped into four considerably discriminated multi-genotypic groups highly
consistent with their grain zinc concentration.
Candidate gene markers based analysis appeared remarkably effective in
differentiation of rice genotypes in relation to their grain zinc concentration. Hence, these
markers can be efficaciously and expeditiously employed for grain zinc concentration
associated distinction of rice genotypes and extraction of rice genotypes for their
utilization as parental lines during genetic enhancement in respect of grain zinc
biofortification. Significance of zinc transporters based target region amplification
polymorphism markers for differentiation and divergence analysis was established in
relation to grain zinc concentration in rice genotypes.