Genetic Diversity and Population Structure of Basmati Rice (Oryza sativa L.) Germplasm Collected from North Western Himalayas Using Trait Linked SSR Markers

Salgotra, Romesh Kumar; Gupta, B. B.; Bhat, Javaid Akhter; Sharma, Sandeep

doi:10.1371/journal.pone.0131858

Cited by 66 publications

(61 citation statements)

References 36 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Among molecular markers, SSRs have been used to indicate genetic diversity of crop germplasms and have been widely applied in the genetic diversity analysis (Salgotra et al 2015). The importance of plant genetic diversity is now being recognized as a specific area since exploding population with urbanization and decreasing cultivable lands are the critical factors contributing to food insecurity in developing world (Govindaraj et al, 2015).…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity of rice from Iran region assessed by simple sequence repeat (SSR) markers

Vazirzanjani¹,

Kawai²,

Korrani³

et al. 2017

Afr. J. Agric. Res.

View full text Add to dashboard Cite

Simple sequence repeat (SSR) markers (36 microsatellite pairs) were used to assess genetic diversity among sixteen rice (Oriza sativa L.) cultivars from Iran, four from Uzbekistan, and one from Afghanistan, and to compare this diversity with that of three control cultivars including Nipponbare, Jasmine 85 and Basmati 370. Among the 36 microsatellite pairs, 31 produced polymorphisms ranging from 1 to 7 alleles (average = 3.72 per microsatellite). There were 134 alleles detected using all the SSR primers, 103 of which (76.9%) showed polymorphisms, while 31 did not. The genetic similarity coefficient among the 24 rice cultivars was 0.601. The genetic diversity revealed by this survey will be useful to designate the most appropriate parental cv. to initiate a breeding program aimed at developing new rice varieties with traits adapted for Middle Eastern agriculture.

show abstract

Section: Discussionmentioning

confidence: 99%

Genetic diversity of rice from Iran region assessed by simple sequence repeat (SSR) markers

Vazirzanjani¹,

Kawai²,

Korrani³

et al. 2017

Afr. J. Agric. Res.

View full text Add to dashboard Cite

show abstract

“…The SSR markers are an ideal choice for the large scope of the markers availability and have been used for genetic variability assessment, molecular characterization, genotypic identification, and population structure estimations in rice [13,14]. Besides diversity studies [15], the SSR markers have also been used extensively for the construction of linkage maps [16][17][18] and QTL analysis [19] in rice. Genic SSRs are located in the coding region of the genome relatively easy and inexpensive, and highly transferable to related taxa [20,21].…”

Section: Introductionmentioning

confidence: 99%

Mining and Characterizing the SSR Markers for Black Rice Using the Illumina Sequencing Platform

Kumar¹,

Das²,

Singha³

et al. 2020

Preprint

View full text Add to dashboard Cite

Study in black rice has gain prominence in recent times due to its high nutritive value, curative effect, and anti-oxidant properties. However, its poor agronomic traits, including low yield necessitates the incorporation of the colour-grain trait into elite varieties through plant breeding techniques. SSR markers play an important role in plant identification and breeding. Here, the generation of reference-based transcriptome, annotation of transcriptome datasets, and a large set of simple sequence repeat (SSR) markers derived from Black rice have been described. In all 28664 SSRs were predicted in 34978 (48.59%) expressed transcripts. However, 7068 (20.20%) transcripts were found to have more than one SSR. The identified SSRs were dominated by tri-nucleotide and tetra-nucleotide repeats representing about 54.11% and 33.31% respectively, of total SSRs. Validation of selected markers associated with anthocyanin trait performed across different black rice accessions established the reliability of the process used for mining SSR markers. The SSR markers identified in this study could be used to select varieties with desired traits, and to investigate the genetic mechanism underlying anthocyanin accumulation in the pericarps of black rice. Furthermore, the findings from this study may prove beneficial in future genetic diversity studies, primer development, and selective breeding programs.

show abstract

“…In rice, the commonly used techniques for diversity evaluation include: restriction fragment length polymorphism (RFLP) (Sun et al, 2001), amplified fragment length polymorphism (AFLP) (Bao et al, 2006), random amplified polymorphic DNA (RAPD) (Rabbani et al, 1998), simple sequence repeat (SSR) (Salgotra et al, 2015), and single nucleotide polymorphism (SNP) (Chen et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity in Aus Rice Genotypes using ILP Markers

Siddique¹,

Khalequzzaman²,

Islam³

et al. 2017

Bangladesh Rice J.

View full text Add to dashboard Cite

Assessment of genetic diversity is essential for germplasm characterization, utilization and conservation. Genetic diversity of 31 Aus rice genotypes of Bangladesh was assessed using 11 ILP (intron length polymorphism) markers. A total of 28 alleles were detected and the number of alleles per locus varied from 2 (RI01779, RI05751, RI05304, RI03205, RI00299, RI05407) to 4 (RI05559). The PIC values ranged from 0.06 (RI05407) to 0.57 (RI05559) with an average of 0.33. PIC value revealed that RI05559 was the best ILP markers for the studied 31 Aus rice genotypes. The dendrogram from unweighted pair-group method with arithmetic average clustering classified the genotypes into five groups at a coefficient of 0.57. Two dimensional graphical views of Principal Coordinate Analysis (PCoA) revealed that the genotypes Kuchmuch, Kalo dhan, Aus dhan, Sadey aus, Chaina and Dighi bawalia were found far away from the centroid of the cluster and can be seslected as parents for further breeding programmes. Parangi and V3, Adubali and H1-2, Begunbichi and Hashikalmi had closest distance (0.000) in the distance matrix might have same genetic background. This information will be useful for the selection of genetically diversed parents and assist in trait development using genotypes in rice breeding programmes in future. The results provided some useful implications for establishment of sovereignty of Bangladeshi rice gene pool. It was also suggested that ILP markers could be very useful for the genetic study and breeding in rice.

show abstract

Genetic Diversity and Population Structure of Basmati Rice (Oryza sativa L.) Germplasm Collected from North Western Himalayas Using Trait Linked SSR Markers

Cited by 66 publications

References 36 publications

Genetic diversity of rice from Iran region assessed by simple sequence repeat (SSR) markers

Genetic diversity of rice from Iran region assessed by simple sequence repeat (SSR) markers

Mining and Characterizing the SSR Markers for Black Rice Using the Illumina Sequencing Platform

Genetic Diversity in Aus Rice Genotypes using ILP Markers

Contact Info

Product

Resources

About