Genetic differentiation among Sri Lankan traditional rice (<i>Oryza sativa</i>) varieties and wild rice species by AFLP markers

Rajkumar, G.; Weerasena, Jagathpriya; Fernando, Kumudu; Liyanage, Athula; Silva, Rangika

doi:10.1111/j.1756-1051.2011.00998.x

Cited by 7 publications

(7 citation statements)

References 20 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Extensive studies on the population genetics of these two species have been carried out either in global scale (Banaticla-Hilario, Berg, Hamilton, & McNally, 2013;Huang et al, 2012;Liu et al, 2015;Zhu & Ge, 2005;Zheng & Ge, 2010;) or local scale (Kuroda, Sato, Bounphanousay, Kono, & Tanaka, 2007;Pusadee, Schaal, Rerkasem, & Jamjod, 2013;Samal et al, 2018;Zhou, Xie, & Ge, 2003;Zhou et al, 2008). However, the genetic variability and population genetic structure of these two species in Sri Lanka are not well understood (Rajkumar, Weerasena, Fernando, Liyanage, & Silva, 2011). Moreover, increasing threats on the wild plant populations have been observed in Sri Lanka in the past decades due to changes in farming systems, economic development, urbanization, and other human disturbances (Rajkumar et al, 2011;Seo, Mendelsohn, & Munasinghe, 2005).…”

mentioning

confidence: 99%

“…However, the genetic variability and population genetic structure of these two species in Sri Lanka are not well understood (Rajkumar, Weerasena, Fernando, Liyanage, & Silva, 2011). Moreover, increasing threats on the wild plant populations have been observed in Sri Lanka in the past decades due to changes in farming systems, economic development, urbanization, and other human disturbances (Rajkumar et al, 2011;Seo, Mendelsohn, & Munasinghe, 2005).…”

mentioning

confidence: 99%

See 1 more Smart Citation

Population genetics and evolutionary history of the wild rice species Oryza rufipogon and O. nivara in Sri Lanka

Sandamal

Tennakoon

Meng

et al. 2018

Ecology and Evolution

View full text Add to dashboard Cite

Genetic diversity and population genetic structure of the wild rice species Oryza rufipogon and O. nivara in Sri Lanka were studied using 33 microsatellite markers. A total of 315 individuals of 11 natural populations collected from the wet, intermediate, and dry zones of the country were used in the study. We found a moderate to high level of genetic diversity at the population level, with the polymorphic loci (P) ranging from 60.6% to 100% (average 81.8%) and the expected heterozygosity (H E) varying from 0.294 to 0.481 (average 0.369). A significant genetic differentiation between species and strong genetic structure within species were also observed. Based on species distribution modeling, we detected the dynamics of the preferred habitats for the two species in Sri Lanka and demonstrated that both O. rufipogon and O. nivara populations have expanded substantially since the last internal glacial. In addition, we showed that the geographical distribution of the two species corresponded to the climate zones and identified a few of key environmental variables that contribute to the distribution of the two species, implying the potential mechanism for ecological adaptation of these two species in Sri Lanka. These studies provided important insights into the population genetics and evolution of these wild species in Sri Lanka and are of great significance to the in situ conservation and utilization of these wild resources in genetic improvement of rice.

show abstract

mentioning

confidence: 99%

mentioning

confidence: 99%

Population genetics and evolutionary history of the wild rice species Oryza rufipogon and O. nivara in Sri Lanka

Sandamal

Tennakoon

Meng

et al. 2018

Ecology and Evolution

View full text Add to dashboard Cite

show abstract

“…Previous research was conducted on genetic diversity of Sri Lankan traditional and wild rice species (Rajkumar et al, 2011). The high level of polymorphism observed (92.84%) using different primer combinations indicates a remarkable amount of intraspecific genetic variation among Sri Lankan rice varieties.…”

Section: Discussionmentioning

confidence: 99%

“…The varieties cultivated from ancient time to middle of last century were all traditional types. In ancient times, farmers cultivated traditional rice varieties, because of their adaptability to Sri Lankan soil types, climate, geography and harsh environmental conditions even though the grain yield potential of those varieties were very low (Rajkumar et al, 2011). Therefore high yielding new improved varieties have been bred from crosses between traditional as well as exotic genotypes to gain better yield.…”

Section: Introductionmentioning

confidence: 99%

Genomic diversity of Sri Lankan New Improved Rice Varieties revealed by AFLP markers

Rajkumar

Weerasena

Silva

et al. 2016

Int J Appl Sci Biotechnol

Self Cite

View full text Add to dashboard Cite

Genetic relationships among 28 new improved rice varieties were established using Amplified Fragment Length Polymorphism (AFLP) markers. Cultivars were analyzed with 10 EcoR1 and MseI primer combinations. A total of 517 fluorescent AFLP markers were generated and analyzed. Of these 480 fragments were polymorphic (92.84%) and 37 (7.16%) fragments were monomorphic. The Jaccard's similarity indices (J) based on the AFLP profiles of the 28 varieties were computed and Unweighted Pair Group Method with Arithmetic mean (UPGMA) based dendrogram was constructed. The dendrogram separated varieties into three major clusters. Outliers used in the study were uniquely separated from the rest confirming the reliability of data and analysis. The Cophenetic correlation with 0.862 strongly supported the clustering pattern of UPGMA dendrogram. Principal Coordinate analysis and the unrooted tree also confirmed the clustering pattern of the UPGMA dendrogram. Rice varieties in the same cluster showed similar characteristic features (Eg. Grain colour, life span etc). Therefore this genetic diversity data at molecular level will provide detailed estimates of the genetic variation among Sri Lankan new improved rice varieties and also useful in ex situ and in situ genetic conservation, utilization and exchange of genetic material.

show abstract

“…SSR markers have been extensively used to identify genetic variation among rice species to analyze genetic structure within cultivated rice (Ren et al 2005), and to evaluate genetic diversity among strains of wild rice (Shishido et al 2006) and among cultivars of cultivated rice (Yu et al 2003). Further, microsatellites have been used for studies of parentage (Roa et al 2000), genetic mapping and breeding, gene flow, genetic diversity and population differentiation (Cho et al 2000).Genetic differentiation among selected 46 Sri Lankan traditional rice (Oryza sativa ) varieties and wild rice species were conducted using AFLP markers by Rajkumar et al, (2011). Therefore, despite of limited studies conducted, there is still a strong need for more detailed characterization of the responses and acclimatization mechanisms of rice under stresses that is occurring in farmers' fields.…”

Section: Introductionmentioning

confidence: 99%

Development of a Diversity Panel for Traditional Rice (Oryza Sativa L.)Accessions/Varieties in Sri Lanka

Somaratne¹

2020

ijmra

View full text Add to dashboard Cite

Oryza sativa L. varieties grown in Sri Lanka from ancient times to the middle of the last century are known as traditional rice varieties and a collection of over 2000 traditional rice accessions conserved at Gene Bank, Plant Genetics Resource Center (PGRC), Peradeniya, Sri Lanka. Farmers preferred traditional rice varieties for their adaptability to biotic and abiotic stresses and are an important component of the biodiversity of Sri Lanka. A detailed understanding of the genetic structure and diversity of traditional rice varieties is essential for the effective utilization of rice genetic resources and identification of potential parents possessing valuable genetic traits for future crop improvement in rice breeding programmes. The objective of the present study was phenotypic and molecular characterization of one hundred (100) traditional rice accession/varieties collected from PGRC, Sri Lanka and identification of a broad diversity panel for these traditional rice accessions/varieties. Rice varieties were grown in a plant house following Randomized Complete Block design with 4 replicates and 5 plants per each replicate. Thirty-two (32) agro-morphological characters were observed. Green leaves of rice varieties were individually collected from 20 day-old seedlings for gDNA extraction using Plant genomic DNA kit followed by the CTAB protocol. Thirty‐three microsatellite (Simple Sequence Repeat – SSR) primer pairs were used to assay genetic variation. DNA amplification was carried out using a thermal cycler and PCR products were subjected to fragment analysis by capillary electrophoresis. Descriptive statistics and basic inferential statistical analyses were performed to access the variation of agro-morphological characters among rice varieties. Data were subjected to cluster analysis (CA) to examine the grouping tendencies and supplemented with Multidimensional scaling (MDS) to explore the procedural differences in the outcome. CA and MDS produced seven (07) groups which were further analyzed using Classification and Regression Analysis (CART) to extract the diagnostic agro-morphological features. Based on CART result, groups of rice varieties were characterized by lemma–palea color, presence or absence of awn, seedling height, and flag-leaf angle. Traditional rice accessions/varieties represent distant clusters on agro-morphological features. Molecular analyses revealed, all 33 loci displayed polymorphism (66.7-96.9 %) among 100 traditional rice accessions/varieties with a total of 387 alleles identified with an average of 11.72 alleles per accession. AMOVA results showed that 34% of the variation distributed among accessions/varieties, 59% of among individuals and 7% within individual indicating a comparatively high level of genetic differentiation among individuals of selected rice accessions/varieties. Structure analysis results illustrated that all 100 accessions/varieties were genetically structured into fifteen well-separated groups, high ΔK peak was recorded at K=15, K= 5, K= 19 and K= 2 respectively. UPGMA analysis based on Jaccard's similarity separated the accessions into five (5) major clusters. A cophenetic correlation with r=0.786 strongly supported the clustering pattern of UPGMA dendrogram. A principal coordinate analysis (PCoA) also confirmed the UPGMA clusters. The genetic diversity information obtained will be useful in efficient use of Sri Lankan rice germplasm collection in breeding programmes. This information will also be useful in management of in situ and ex situ germplasm collections in conservation programs for traditional rice varieties.

show abstract

Genetic differentiation among Sri Lankan traditional rice (Oryza sativa) varieties and wild rice species by AFLP markers

Cited by 7 publications

References 20 publications

Population genetics and evolutionary history of the wild rice species Oryza rufipogon and O. nivara in Sri Lanka

Population genetics and evolutionary history of the wild rice species Oryza rufipogon and O. nivara in Sri Lanka

Genomic diversity of Sri Lankan New Improved Rice Varieties revealed by AFLP markers

Development of a Diversity Panel for Traditional Rice (Oryza Sativa L.)Accessions/Varieties in Sri Lanka

Contact Info

Product

Resources

About