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Molecular biology reports
Aug, 2021;48 (8): 5943-5953.

SSR marker-based genetic diversity analysis and SNP haplotyping of genes associating abiotic and biotic stress tolerance, rice growth and development and yield across 93 rice landraces.

Smitha Kunhiraman Vasumathy, Manickavelu Alagu
Author Information
  1. Smitha Kunhiraman Vasumathy: Department of Genomic Science, Central University of Kerala, Periye, Kasaragod, Kerala, 671316, India.
  2. Manickavelu Alagu: Department of Genomic Science, Central University of Kerala, Periye, Kasaragod, Kerala, 671316, India. amanicks@cukerala.ac.in. ORCID
PMID: 34319545 DOI: 10.1007/s11033-021-06595-4

Abstract

BACKGROUND: As rice is the staple food for more than half of the world's population, enhancing grain yield irrespective of the variable climatic conditions is indispensable. Many traditionally cultivated rice landraces are well adapted to severe environmental conditions and have high genetic diversity that could play an important role in crop improvement.
METHODS AND RESULTS: The present study revealed a high level of genetic diversity among the unexploited rice landraces cultivated by the farmers of Kerala. Twelve polymorphic markers detected a total of seventy- seven alleles with an average of 6.416 alleles per locus. Polymorphic Information Content (PIC) value ranged from 0.459 to 0.809, and to differentiate the rice genotypes, RM 242 was found to be the most appropriate marker with a high value of 0.809. The current study indicated that the rice landraces are highly diverse with higher values of the adequate number of alleles, PIC, and Shannon information index. Utilizing these informative SSR markers for future molecular characterization and population genetic studies in rice landraces are advisable. Haplotypes are sets of genomic regions within a chromosome inherited together, and haplotype-based breeding is a promising strategy for designing next-generation rice varieties. Here, haplotype analysis explored 270 haplotype blocks and 775 haplotypes from all the chromosomes of landraces under study. The number of SNPs in each haplotype block ranged from two to 28. Haplotypes of genes related to biotic and abiotic stress tolerance, yield-enhancing, and growth and development in rice landraces were also elucidated in the current study.
CONCLUSIONS: The present investigation revealed the genetic diversity of rice landraces and the haplotype analysis will open the way for genome-wide association studies, QTL identification, and marker-assisted selection in the unexplored rice landraces collected from Kerala.

Keywords

Genetic diversity Haplotype Rice landraces SNP SSR

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Grants

  1. ECR/2016/001934/Science and Engineering Research Board

MeSH Term

Alleles
Gene Frequency
Genetic Variation
Genome-Wide Association Study
Genomics
Genotype
Haplotypes
India
Microsatellite Repeats
Oryza
Phylogeny
Plant Breeding
Polymorphism, Single Nucleotide
Stress, Physiological
Journal Article

Word Cloud

Created with Highcharts 10.0.0ricelandracesgeneticdiversitystudyhaplotypehighalleles0SSRanalysispopulationyieldconditionscultivatedpresentrevealedKeralamarkersPICvalueranged809currentnumberstudiesHaplotypesgenesbioticabioticstresstolerancegrowthdevelopmentSNPBACKGROUND:staplefoodhalfworld'senhancinggrainirrespectivevariableclimaticindispensableManytraditionallywelladaptedsevereenvironmentalplayimportantrolecropimprovementMETHODSANDRESULTS:levelamongunexploitedfarmersTwelvepolymorphicdetectedtotalseventy-sevenaverage6416perlocusPolymorphicInformationContent459differentiategenotypesRM242foundappropriatemarkerindicatedhighlydiversehighervaluesadequateShannoninformationindexUtilizinginformativefuturemolecularcharacterizationadvisablesetsgenomicregionswithinchromosomeinheritedtogetherhaplotype-basedbreedingpromisingstrategydesigningnext-generationvarietiesexplored270blocks775haplotypeschromosomesSNPsblocktwo28relatedyield-enhancingalsoelucidatedCONCLUSIONS:investigationwillopenwaygenome-wideassociationQTLidentificationmarker-assistedselectionunexploredcollectedmarker-basedhaplotypingassociatingacross93GeneticHaplotypeRice

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