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Plant Science Today (PST)

Research Articles

Early Access

Genetic association and diversity pattern among the prominent West Bengal rice (Oryza sativa L.) landraces based on simple sequence repeat (SSR) mapped from chromosome 1

DOI
https://doi.org/10.14719/pst.14154
Submitted
18 February 2026
Published
02-07-2026
Versions

Abstract

Genetic relationships and diversity patterns in cereal crops are prerequisites for any improvement efforts that help determine suitable breeding strategies. As the principal staple food, rice possesses a large number of genetic resources, including landraces, high-yielding cultivars, wild species (Oryza rufipogon) and wild relatives (Porteresia coarctata). However, the present post-Green Revolution scenario depicts the erosion of potential rice landraces and wild species due to the widespread adoption of high-yielding varieties (HYVs), although the former have the potential to withstand ongoing environmental fluctuations. However, a deep investigation into such diversity trends in West Bengal rice varieties is lacking. Simple sequence repeat (SSR) markers have demonstrated their efficacy as preferred tools for investigating genetic relationships and variation among genotypes. The current investigation was conducted with the objective of characterising and assessing the genetic diversity of rice accessions using SSR marker-based genotyping. Eight West Bengal rice accessions, including landraces, a wild species and a wild relative, were genotyped using six chromosome-1 specific SSR markers linked to osmotic stress tolerance (specifically from the SalTol QTL region). Genomic DNA was amplified with selected SSR markers, PCR amplified allelic profiles were scored to estimate polymorphism and the polymorphism information content (PIC) values of each SSR markers and genetic relationships among rice lines were inferred through similarity analysis and hierarchical clustering. The fingerprint profile indicates that all SSRs are polymorphic in the rice lines studied. A total of 22 alleles were amplified, with an average of 3.67 per locus. A microsatellite panel was constructed and the PIC values for all microsatellite markers were calculated. Cluster analysis categorised these genotypes into two distinct clusters. The results demonstrated that the rice genotypes harbour high genetic diversity. The present study is useful for varietal identification, characterisation and genetic analysis; thus, it signifies the necessity of expanding the genetic foundation of rice species by incorporating diverse progenitors into the existing breeding programme.

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