Study of population structure and phylogeny in Indian wheat (Triticum spp.) landraces using DNA markers
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Date
2018
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DIVISION OF MOLECULAR BIOLOGY AND BIOTECHNOLOGY NATIONAL RESEARCH CENTRE ON PLANT BIOTECHNOLOGY INDIAN AGRICULTURAL RESEARCH INSTITUTE NEW DELHI
Abstract
Since genetic diversity among genotypes offers prospects for improving the plant
characteristics, Indian wheat genetic diversity study is a key to wheat improvement
programs in India. To assess extent and pattern of genetic diversity to further our
understanding of population structure and phylogeny in Indian wheat landraces, 42
fluorescence-labelled SSR markers loci, evenly distributed throughout the hexaploid wheat
genome, were amplified among 618 accessions, and an high-resolution genotyping was
performed using capillary gel electrophoresis. It was found that there was a total of 771
polymorphic alleles ranging from 12 to 26 alleles per locus and a mean gene richness of
18.36. Substantial variations in allelic richness were detected by 42 SSR markers in all the
21 homologous chromosomes, 7 homoeologous groups, and the three subgenomes (A, B,
and D) among the genotypes. The average genetic diversity index was 0.901 with three
genomes having values ranging from 0.84 to 0.93. Analysis of variance (ANOVA) revealed
that subgenomes A and D had the highest (0.912) and the lowest (0.890) genetic diversity,
respectively. There were four major groups based on STRUCTURE, UPGMA cluster and
principal coordinate (PCoA) analyses. STRUCTURE analysis showed that the modelbased population was not correlated with the ecological origin of accessions; yet, an high
amount of diversity was present as indicated by ANOVA. Phylogenetic analysis revealed
that the studied set of 618 accessions belonged to four clads that diverged from a common
unknown ancestor. Analysis of molecular variance (AMOVA) partitioned the total genetic
variance, estimated in this study, into 90% within groups and 10% among groups, both at
individual subgenome and whole genome levels, suggesting that there was selective
adaptation of the landraces towards the local growth conditions specific to the geopolitical
state of their origin. Agro-morphological and phenological trait-based UPGMA tree
revealed the existence of five clusters, confirmed by principal component analysis (PCA).
However, there was no correlation between molecular and morphological data-based
clustering, suggesting that the results of both the methods are important and will be useful
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for identification of core set, conservation and utilization of Indian wheat germplasm in
wheat breeding programs.
In conclusion, evidences from this study suggest that Indian wheat landrace
accessions have high genetic richness and diversity and, therefore, they can be useful
sources of genes for various traits of agronomic importance that can be used by breeders
in different wheat hybridization programs. In addition, genetically diverse accessions
identified in this study can be used as parents for increasing the usefulness of the collections
by broadening the genetic base. Findings of the present study also indicate that fluorescent
labelled microsatellite markers permit high-resolution genotyping by generating a large set
of genotypic data that can be used for assessing genetic diversity and population structure,
facilitating the discovery of all the alleles present in the studied set of genotypes.
Finally, results of this study would be useful in traditional and molecular breeding
programs involving Indian wheat landraces, analysed in this study, so that sustainable
wheat production can be achieved in the face of ever changing climate and never receding
human population.
Key words: Triticum, Indian wheat, Landrace accessions, Microsatellite (SSR) markers,
ANOVA, AMOVA, STRUCTURE, Cluster, PCoA, PCA, Diversity, Population structure,
Phylogeny, Molecular data, Agro-morphological, Wheat breeding
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t-10052
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