Genetic characterization and population structure of Indian rice cultivars and wild genotypes using core set markers

Genetic diversity among 23 rice genotypes including wild species and cultivars of indica , japonica , aus and aromatic type was investigated using 165 genomewide core set microsatellite (SSR) markers. This genotypic characterization was undertaken to know the genetic similarity among the parental li...

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Bibliographic Details
Published in:3 Biotech 2016-06, Vol.6 (1), p.95-11, Article 95
Main Authors: Surapaneni, Malathi, Balakrishnan, Divya, Mesapogu, Sukumar, Krishnam Raju, Addanki, Rao, Yadavalli Venkateswara, Neelamraju, Sarla
Format: Article
Language:English
Subjects:
Agriculture
Bioinformatics
Biomaterials
Biotechnology
Cancer Research
Chemistry
Chemistry and Materials Science
Chromosomes
Cluster analysis
Cultivars
Domestication
Genes
Genetic diversity
Genomes
Germplasm
Original
Original Article
Rice
Stem Cells
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Summary:Genetic diversity among 23 rice genotypes including wild species and cultivars of indica , japonica , aus and aromatic type was investigated using 165 genomewide core set microsatellite (SSR) markers. This genotypic characterization was undertaken to know the genetic similarity among the parental lines to be used in developing a set of chromosome segment substitution lines. In all, 253 alleles were identified using 77 polymorphic SSRs, and polymorphism information content ranged from 0.31 to 0.97 with a mean of 0.79. Cluster analysis grouped the genotypes into three clusters at a genetic similarity of 0.26–0.75. Wild accessions grouped together in cluster-I, indica cultivars formed cluster-II, and aromatic, japonica and aus types came under cluster-III. Principal component analysis also showed similar results. The genotypic data was analyzed using STRUCTURE, and genotypes were grouped into four populations. RM1018 on chromosome 4, RM8009 on chromosome 7, and RM273 on chromosome 12 amplified alleles specific to wild accessions. The information obtained from core set markers would help in selecting diverse parents including wild accessions and for tracking alleles in mapping or breeding populations.
ISSN:2190-572X
2190-5738
DOI:10.1007/s13205-016-0409-7