Genetic diversity and population structure of rice landraces from Eastern and North Eastern States of India

Das, B. N.; Sengupta, Samik; Parida, Swarup K.; Roy, B.; Ghosh, Mrityunjay; Prasad, Manoj; Ghose, Tapas

doi:10.1186/1471-2156-14-71

Cited by 123 publications

(133 citation statements)

References 35 publications

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“…The average PIC value was almost identical using both marker systems, showing the discriminatory power of iPBS-retrotransposon markers. The average PIC value based on the SSR data used in this study was comparable with values from other rice genetic diversity studies, but lower than those reported in studies on rice varieties from Argentina (0.69) that were performed using 28 SSRs (Giarrocco et al, 2007), from India (0.61) using 30 SSRs , from Australia (0.74) using 10 SSRs (Garland et al, 1999), or from India using 23 SSRs among 91 landraces (Das et al, 2013).…”

Section: Discussionsupporting

confidence: 51%

Population structure of rice varieties used in Turkish rice breeding programs determined using simple-sequence repeat and inter-primer binding site-retrotransposon data

Cömertpay¹,

Baloch²,

Derya³

et al. 2016

Genet. Mol. Res.

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ABSTRACT. Effective breeding programs based on genetic diversity are needed to broaden the genetic basis of rice (Oryza sativa L.) in Turkey. In this study, 81 commercial varieties from seven countries were studied in order to estimate the genomic relationships among them using nine interprimer binding site (iPBS)-retrotransposon and 17 simple-sequence repeat (SSR) markers. A total of 59 alleles for the SSR markers and 96 bands for the iPBS-retrotransposon markers were detected, with an average of 3.47 and 10.6 per locus, respectively. Each of the varieties could be unequivocally identified by the SSR and iPBS-retrotransposon profiles. The iPBS-retrotransposon-and SSR-based clustering were identical and closely mirrored each other, with a significantly high correlation (r = 0.73). A neighbor-joining cluster based on the combined SSR and iPBSretrotransposon data divided the rice varieties into three clusters. The population structure was determined using the STRUCTURE software, and three populations (K = 3) were identified among the varieties studied, showing that the diversity harbored by Turkish rice varieties is low. The results indicate that iPBS-retrotransposon markers are a very powerful technique to determine the genetic diversity of rice varieties.

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Section: Discussionsupporting

confidence: 51%

Population structure of rice varieties used in Turkish rice breeding programs determined using simple-sequence repeat and inter-primer binding site-retrotransposon data

Cömertpay¹,

Baloch²,

Derya³

et al. 2016

Genet. Mol. Res.

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“…Several workers also reported that these markers are highly polymorphic (Mohammadi-nejad et al 2008;Karmakar et al 2012;Chattopadhyay et al 2014;Ganie et al 2014). The PCR profile obtained from the SSR markers generated a total of 99 alleles including 20 rare alleles and 16 null alleles, accounting an average of 12.37 alleles/ locus which is higher than the numbers reported by other groups using the SSR markers (Mohammadi-Nejad et al 2008;Islam et al 2012;Karmakar et al 2012;Das et al 2013). Based upon the PIC value, amplicon size range and the number of alleles, RM8094 is advocated to be the most useful and informative marker than others for studying the diversity of Saltol QTL.…”

Section: Discussionmentioning

confidence: 85%

Assessment of genetic diversity of Saltol QTL among the rice (Oryza sativa L.) genotypes

Ganie

Borgohain

Kritika

et al. 2016

Physiol Mol Biol Plants

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Eight Saltol quantitative trait locus (QTL) linked simple sequence repeat (SSR) markers of rice (Oryza sativa L.) were used to study the polymorphism of this QTL in 142 diverse rice genotypes that comprised salt tolerant as well as sensitive genotypes. The SSR profiles of the eight markers generated 99 alleles including 20rare alleles and 16 null alleles. RM8094 showed the highest number (13) of alleles followed by RM3412 (12), RM562 (11), RM493 (9) and RM1287 (8) while as, RM10764 and RM10745 showed the lowest number (6) of alleles. Based on the highest number of alleles and PIC value (0.991), we identified RM8094 as suitable marker for discerning salt tolerant genotypes from the sensitive ones. Based upon the haplotype analysis using FL478 as a reference (salt tolerant genotypes containing Saltol QTL), we short listed 68 rice genotypes that may have at least one allele of FL478 haplotype. Further study may confirm that some of these genotypes might have Saltol QTL and can be used as alternative donors in salt tolerant rice breeding programmes.

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“…The DNA was PCR amplified using a protocol standardized in our lab and used in our previous paper [28]. …”

Section: Methodsmentioning

confidence: 99%

Genetic diversity of the conserved motifs of six bacterial leaf blight resistance genes in a set of rice landraces

et al. 2014

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BackgroundBacterial leaf blight (BLB) caused by the vascular pathogen Xanthomonas oryzae pv. oryzae (Xoo) is one of the most serious diseases leading to crop failure in rice growing countries. A total of 37 resistance genes against Xoo has been identified in rice. Of these, ten BLB resistance genes have been mapped on rice chromosomes, while 6 have been cloned, sequenced and characterized. Diversity analysis at the resistance gene level of this disease is scanty, and the landraces from West Bengal and North Eastern states of India have received little attention so far. The objective of this study was to assess the genetic diversity at conserved domains of 6 BLB resistance genes in a set of 22 rice accessions including landraces and check genotypes collected from the states of Assam, Nagaland, Mizoram and West Bengal.ResultsIn this study 34 pairs of primers were designed from conserved domains of 6 BLB resistance genes; Xa1, xa5, Xa21, Xa21(A1), Xa26 and Xa27. The designed primer pairs were used to generate PCR based polymorphic DNA profiles to detect and elucidate the genetic diversity of the six genes in the 22 diverse rice accessions of known disease phenotype. A total of 140 alleles were identified including 41 rare and 26 null alleles. The average polymorphism information content (PIC) value was 0.56/primer pair. The DNA profiles identified each of the rice landraces unequivocally. The amplified polymorphic DNA bands were used to calculate genetic similarity of the rice landraces in all possible pair combinations. The similarity among the rice accessions ranged from 18% to 89% and the dendrogram produced from the similarity values was divided into 2 major clusters. The conserved domains identified within the sequenced rare alleles include Leucine-Rich Repeat, BED-type zinc finger domain, sugar transferase domain and the domain of the carbohydrate esterase 4 superfamily.ConclusionsThis study revealed high genetic diversity at conserved domains of six BLB resistance genes in a set of 22 rice accessions. The inclusion of more genotypes from remote ecological niches and hotspots holds promise for identification of further genetic diversity at the BLB resistance genes.

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Genetic diversity and population structure of rice landraces from Eastern and North Eastern States of India

Cited by 123 publications

References 35 publications

Population structure of rice varieties used in Turkish rice breeding programs determined using simple-sequence repeat and inter-primer binding site-retrotransposon data

Population structure of rice varieties used in Turkish rice breeding programs determined using simple-sequence repeat and inter-primer binding site-retrotransposon data

Assessment of genetic diversity of Saltol QTL among the rice (Oryza sativa L.) genotypes

Genetic diversity of the conserved motifs of six bacterial leaf blight resistance genes in a set of rice landraces

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