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

2020 ◽  
Vol 03 (12) ◽  
Author(s):  
S. Somaratne ◽  
Keyword(s):  
Oryza Sativa ◽  
Sri Lanka ◽  
Oryza Sativa L ◽  
Morphological Characters ◽  
Morphological Features ◽  
Ex Situ ◽  
Rice Varieties ◽  
Diversity Panel ◽  
Breeding Programmes ◽  
Traditional Rice

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.

Development of a core collection from Sri Lankan traditional rice (Oryza sativa) varieties for phenotypic and genetic diversity

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Shyama Weerakoon ◽  
Seneviratne Somaratne
Keyword(s):  
Genetic Diversity ◽  
Oryza Sativa ◽  
Sri Lanka ◽  
Core Collection ◽  
Morphological Characters ◽  
Morphological Features ◽  
Sri Lankan ◽  
Rice Varieties ◽  
Traditional Rice ◽  
Phenotypic And Genetic Diversity

Abstract. Weerakoon SR, Somaratne S. 2021. Development of a core collection from Sri Lankan traditional rice (Oryza sativa) varieties for phenotypic and genetic diversity. Nusantara Bioscience 13: 61-67. A collection of over 2000 traditional rice varieties are conserved at Gene Bank, Plant Genetics Resource Center, Sri Lanka. Oryza sativa varieties grown in Sri Lanka from ancient times to the middle of the last century are known as traditional rice. These varieties show adaptability to biotic and abiotic stresses and, an important component of biodiversity of Sri Lanka. A detailed understanding of the diversity of traditional rice varieties is essential for effective utilization of rice genetic resources and identification of potential parents possessing valuable genetic traits for future crop improvement. Study objectives were phenotypic and molecular characterization of one-hundred traditional rice varieties and to identify a core collection for phenotypic and genetic diversity. Rice varieties were grown in a plant house following RCBD with 4 replicates and 5 plants per replicate. Thirty-two agro-morphological characters were observed/collected. Genomic DNA was extracted from 20-days-old seedlings. Thirty?three microsatellite (Simple Sequence Repeat-SSR) primer pairs were used to assay genetic variation and PCR products were subjected to fragment analysis by capillary electrophoresis. Descriptive statistics and basic inferential statistical analyses were performed to access variation of agro-morphological characters among rice varieties. Cluster analysis and Multidimensional scaling produced 07 groups which were further analyzed using Classification and Regression Analysis to extract the diagnostic agro-morphological features. Groups of rice varieties were characterized by lemma palea color, awn color at maturity, seedling height, and flag-leaf angle. Traditional varieties represent distant clusters on agro-morphological features. Molecular analyses revealed all 33 loci displayed polymorphism (66.7-96.9%) among 100 traditional rice varieties with a total of 387 alleles identified with an average of 11.72 alleles per variety. All varieties were genetically structured into fifteen well-separated groups. UPGMA analysis based on Jaccard's similarity separated varieties into 05 major clusters. Genetic diversity information is useful in the efficient use of Sri Lankan rice germplasm and managing in situ and ex situ germplasm collections in conserving traditional rice varieties.

Diversity among different populations of a locally common rice (Oryza sativa L.) landrace from north-western Indian Himalayas

2010 ◽  
Vol 8 (2) ◽  
pp. 151-158 ◽  
Author(s):  
S. Kumar ◽  
A. Pandey ◽  
I. S. Bisht ◽  
K. V. Bhat ◽  
P. S. Mehta
Keyword(s):  
Oryza Sativa ◽  
Oryza Sativa L ◽  
Morphological Characters ◽  
Ex Situ ◽  
Evolutionary Forces ◽  
Minimum Number ◽  
Environmental Adaptations ◽  
Farmer Management ◽  
Different Populations ◽  
On Farm

Genetic structure of five populations of a locally common rice (Oryza sativa L.) landrace Jaulia from parts of Uttarakhand state of India was studied using sequence tagged microsatellite site (STMS) markers. Of these, four populations were on-farm managed, assembled from different niche environments, and one population was conserved ex situ and represented static conservation. The 16 STMS primer pairs fully differentiated the inter- and intrapopulation diversity. A total of 72 alleles were recorded with a mean of 4.5 alleles per locus. Population wise, the total number of alleles ranged from 21 to 41, with maximum number of alleles for population IC 548358 and minimum number of alleles for population IC 100051 representing static conservation. A greater number of alleles specific to populations under farmer management could be recorded. Changes in yield parameters also seemed to be affected under farmer management besides other environmental adaptations for qualitative morphological characters. The marker diversity using STMS primer pairs indicates the genetic differentiation among populations resulting from joint effects of several evolutionary forces operating within the historical and biological context of the crop landrace. The variations in adaptations, on the other hand, indicate the degree to which populations are adapted to their environments and their potential for continued performance or as donors of characters in plant breeding. Both biotic and abiotic aspects of the environment are involved.

scholarly journals Diversity of grain quality characteristics of traditional rice (Oryza sativa L.) varieties in Sri Lanka

2015 ◽  
Vol 25 (4) ◽  
pp. 570 ◽  
Author(s):  
S.P. Rebeira ◽  
H.A.M. Wickramasinghe ◽  
W.L.G. Samarasinghe ◽  
B.D.R. Prashantha
Keyword(s):  
Oryza Sativa ◽  
Sri Lanka ◽  
Grain Quality ◽  
Oryza Sativa L ◽  
Quality Characteristics ◽  
Traditional Rice

scholarly journals Assessing Seed Vigor Characters of Selected Rice (Oryza sativa L.) Genotypes Using Accelerated Ageing Method

2019 ◽  
pp. 1-5
Author(s):  
S. A. Henga ◽  
W. M. Thagana ◽  
Hunja Hurage ◽  
M. W. Githendu
Keyword(s):  
Oryza Sativa ◽  
Relative Humidity ◽  
Storage Temperature ◽  
Oryza Sativa L ◽  
Storage Period ◽  
Seed Vigor ◽  
Ex Situ ◽  
Accelerated Ageing ◽  
Rice Varieties ◽  
Duration Of Storage

Rice (Oryza sativa L.) is an annual grass with the third-highest world production after sugarcane and maize. However, due to losses in vigor caused by poor seed storage, global consumption has surpassed production. Preservation of germ plasma both in-situ and ex-situ is the key to the conservation of rich biodiversity. Seed vigor is a key element of seed quality and high vigor seeds give uniform plants stand and higher yields per area. Accelerated ageing tests enable testing the vigor of stored seeds by subjecting the seeds to a particular temperature and relative humidity over time and then performing standard germination tests. Viability of most seeds normally reduces with the storage period, storage temperature and relative humidity. There is limited information on the duration of storage for rice seeds. Accelerated ageing is considered an excellent option as a vigor test when compared to seedling emergence and index of emergence speed because of the shortest time of acquisition and efficient results. Accelerated ageing tests at 0, 24, 48 and 72 hours (45ºC and 98% RH) were carried out JKUAT post-harvest laboratory using eight rice varieties’ in four replications of 100 seeds each. Data were analyzed using GENSTAT statistical package. ANOVA and T-tests at 5% significant level. Results showed that there was significant variation in both coleorhiza and coleoptile formation among rice varieties (p<0.001), treatments (p<0.001) and interaction between rice varieties and treatment (p<0.001). The difference between all treatments was significant with 72 hours’ treatment having the highest number of days to coleorhiza and coleoptile formation. The present study has shown that prolonged duration of higher temperatures results in a reduction of seed viability. The earliest coleorhiza formation was observed on day 2 and the latest on day 6. Results from this study will guide farmers and seed processors on considerations regarding storage period and storage temperature to ensure high-quality seeds.

scholarly journals Karakter morfologi akar sebagai indikator kekurangan air pada padi lokal Superwin (Root-morphological characters as water-deficit indicators in local rice Superwin)

2014 ◽  
Vol 3 (2) ◽  
Author(s):  
Patricia Claudya Torey ◽  
Song Ai Nio ◽  
Parluhutan Siahaan ◽  
Susan M Mambu
Keyword(s):  
Oryza Sativa ◽  
Water Deficit ◽  
Upland Rice ◽  
Oryza Sativa L ◽  
Weight Ratio ◽  
Field Capacity ◽  
Dry Weight ◽  
Morphological Characters ◽  
Limited Area ◽  
Rice Varieties

Abstrak Evaluasi karakter morfologi akar telah dilakukan untuk menentukan karakter morfologi akar yang potensial sebagai indikator adanya kekurangan air pada padi (Oryza sativa L.) di antara panjang akar, volume akar, berat basah akar, berat kering akar, rasio akar:tajuk dan rasio panjang akar:tinggi tanaman. Eksperimen ini dilakukan di rumah kaca dan menggunakan 2 varietas padi (Superwin dan IR 64) pada fase vegetatif  yang ditumbuhkan pada media tanah di polybag dengan perlakuan kekeringan (tidak disirami selama 14 hari) dan disirami sampai kapasitas lapang (kontrol). Panjang akar dan rasio panjang akar:tinggi tanaman dapat dijadikan indikator kekurangan air pada padi Superwin dan IR 64. Superwin yang merupakan padi sawah dapat dipertimbangkan untuk ditanam di lahan kering. Kata kunci: indikator, kekeringan, morfologi akar Abstract Root-morphological characters in rice (Oryza sativa L.) were evaluated to determine the potential characters as water-deficit indicators among the length, volume, fresh weight, dry weight, ratio root:shoot and ratio root length:plant height. The experiment was conducted in the glasshouse using 2 rice varieties (cv. Superwin and IR 64) grown in the soil mixture at the vegetative phase. The treatments in this experiment were water deficit (without water for 14 days) and well-watered (watering until field capacity). The root length and ratio root length:plant height were potential as water- deficit indicators in Superwin dan IR 64. The upland rice, Superwin, should be considered to be cultivated in the water limited area. Keywords: drought, indicator, root morphology

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