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Mondal S, Pradhan P, Das B, Kumar D, Paramanik B, Yonzone R, Barman R, Saha D, Karforma J, Basak A, Dey P, Seleiman MF. Genetic characterization and diversity analysis of indigenous aromatic rice. Heliyon 2024; 10:e31232. [PMID: 38813207 PMCID: PMC11133840 DOI: 10.1016/j.heliyon.2024.e31232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 05/31/2024] Open
Abstract
Gangetic old alluvial zone in India has conserved many locally adapted aromatic rice landraces. In order to determine the extent of genetic divergence of ten morphological characters, the study was conducted to examine forty-eight aromatic rice genotypes for six Kharif seasons (2016-2021) at the Instructional Farm of Regional Research Station (Old Alluvial Zone), Uttar Banga Krishi Viswavidyalaya, Majhian, West Bengal, India. The experiment was laid out in Randomized Complete Block Design (RCBD) with three replications. A considerable degree of variation was noted for all the traits being investigated. It was found that the total number of tillers per plant, panicle numbers per plant, number of grains per panicle, fertility percentage, test weight, and grain length/breadth ratio had significantly positive correlated with seed yield per plant. Based on D2 analysis values, all the genotypes were grouped into six clusters. Cluster III (Tulaipanji, Patnai, Basmati 1121, Jugal, and Bahurupi) and Cluster VI (Kanakchur), containing genotypes were found most divergent with maximum inter-cluster distance (6941.51). According to the cluster means, Cluster II had the largest intra-cluster distance (1937.52), and important attributes including test weight, number of grains per panicle, seed yield per plant, and fertility percentage made remarkably significant contributions to this cluster. In terms of principal component analysis, maximum variability was found in PC1 (23.88 %), with high positive loading values for tillers per plant (0.459), panicle number per plant (0.441), seed yield per plant (0.408), fertility percentage (0.364), test weight (0.264), and grain length/breadth (L/B) ratio (0.263). On the basis of biplot analysis, four genotypes, namely Shakbhati, Sugandhi, Bahurupi and Kanakchur, were identified as the most divergent types for the yield-attributing traits of aromatic rice. The diverse genotypes could be used as potential donors in future breeding programmes.
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Affiliation(s)
- Sourav Mondal
- Department of Genetics and Plant Breeding, Uttar Banga Krishi Viswavidyalaya, Pundibari, 736165, Coochbehar, West Bengal, India
| | - Prajjwal Pradhan
- Department of Genetics and Plant Breeding, Uttar Banga Krishi Viswavidyalaya, Pundibari, 736165, Coochbehar, West Bengal, India
| | - Bimal Das
- College of Agriculture (Extended Campus), Uttar Banga Krishi Viswavidyalaya, Majhian, 733133, Dakshin Dinajpur, West Bengal, India
| | - Deepak Kumar
- College of Agriculture (Extended Campus), Uttar Banga Krishi Viswavidyalaya, Majhian, 733133, Dakshin Dinajpur, West Bengal, India
| | - Bappa Paramanik
- Dakshin Dinajpur Krishi Vigyan Kendra, Uttar Banga Krishi Viswavidyalaya, Majhian, 733133, Dakshin Dinajpur, West Bengal, India
| | - Rakesh Yonzone
- College of Agriculture (Extended Campus), Uttar Banga Krishi Viswavidyalaya, Majhian, 733133, Dakshin Dinajpur, West Bengal, India
| | - Ratul Barman
- Regional Research Station (OAZ), Uttar Banga Krishi Viswavidyalaya Majhian, 733133, Dakshin Dinajpur, West Bengal, India
| | - Debraj Saha
- Dakshin Dinajpur Krishi Vigyan Kendra, Uttar Banga Krishi Viswavidyalaya, Majhian, 733133, Dakshin Dinajpur, West Bengal, India
| | - Jyotirmay Karforma
- College of Agriculture (Extended Campus), Uttar Banga Krishi Viswavidyalaya, Majhian, 733133, Dakshin Dinajpur, West Bengal, India
- Regional Research Station (OAZ), Uttar Banga Krishi Viswavidyalaya Majhian, 733133, Dakshin Dinajpur, West Bengal, India
| | - Achyuta Basak
- Department of Genetics and Plant Breeding, Uttar Banga Krishi Viswavidyalaya, Pundibari, 736165, Coochbehar, West Bengal, India
| | - Prithwiraj Dey
- Agricultural & Food Engineering Department, Indian Institute of Technology Kharagpur, West Bengal, India
| | - Mahmoud F. Seleiman
- Department of Plant Production, College of Food and Agriculture Sciences, King Saud University, Saudi Arabia
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Bordoloi D, Sarma D, Sarma Barua N, Das R, Das BK. Morpho-molecular and nutritional profiling for yield improvement and value addition of indigenous aromatic Joha rice of Assam. Sci Rep 2024; 14:3509. [PMID: 38346994 PMCID: PMC10861566 DOI: 10.1038/s41598-023-42874-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/15/2023] [Indexed: 02/15/2024] Open
Abstract
Short-grain aromatic Joha rice of Assam is a unique class of specialty rice having tremendous potential in domestic and international markets. The poor yielding ability of Assam's Joha rice demands its systematic characterization for an effective breeding program. This study investigates the morphological, molecular and biochemical profiles of twenty popular Joha (aromatic) rice cultivars indigenous to Assam. Distinctiveness, Uniformity and Stability (DUS) characterization of the cultivars revealed polymorphism in thirty-seven traits, establishing distinctiveness for their utilization in breeding programs. Unweighted Neighbor Joining (UNJ) clustering based on usual Euclidean distances for the polymorphic morphological markers grouped the cultivars into three clusters with eight, eleven, and one genotypes. The Joha rice cultivars showed significant differences for all the quantitative traits except for panicle length. The genotypic and phenotypic coefficients of variability (GCV & PCV) were high for grain yield ha-1 (24.62 & 24.85%) and filled grains panicle-1 (23.69 & 25.02%). Mahalanobis D2 analysis revealed three multi-genotypic and four mono-genotypic clusters of the cultivars. The first five principal components explain 85.87% of the variation among the cultivars for the traits under study; filled grain panicle-1 (0.91) and stem thickness (0.55) positively contributed to the first PC. The cultivars' average polyunsaturated fatty acids were 37.9% oleic acid, 39.22% linoleic acid, and 0.5% linolenic acid. Kon Joha 4 and Ronga Joha contained the highest iron (82.88 mg kg-1) and zinc (47.39 mg kg-1), respectively. Kalijeera, Kunkuni Joha, Kon Joha-5, Manimuni Joha and Kon Joha-2 accorded a strong aroma. PCR amplified 174 alleles with a mean value 2.64 across the 66 polymorphic SSR markers. PIC values ranged from 0.091 to 0.698, with an average of 0.326. The highly informative (PIC > 0.50) markers were RM316, RM283, RM585, RM1388, RM3562, RM171, R1M30, RM118, RM11and RM29 for identification of the twenty aromatic rice cultivars. PCR amplification of 27 SSR markers identified 28 unique alleles (97-362 bp) in 13 Joha rice cultivars, which can help their identification/DNA fingerprinting. The UNJ clustering based on Jaccard's coefficients classified the cultivars into three distinct clusters with eight, ten, and two genotypes. Our study revealed the nutritional richness of these specialty Joha rice cultivars and sufficient scope for yield enhancement through their interbreeding to keep quality intact.
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Grants
- 35/14/17/2016-BRNS/35056 Dated. 04/06/2016 Board of Research in Nuclear Sciences, Department of Atomic Energy, Government of India, Mumbai-400085
- 35/14/17/2016-BRNS/35056 Dated. 04/06/2016 Board of Research in Nuclear Sciences, Department of Atomic Energy, Government of India, Mumbai-400085
- 35/14/17/2016-BRNS/35056 Dated. 04/06/2016 Board of Research in Nuclear Sciences, Department of Atomic Energy, Government of India, Mumbai-400085
- 35/14/17/2016-BRNS/35056 Dated. 04/06/2016 Board of Research in Nuclear Sciences, Department of Atomic Energy, Government of India, Mumbai-400085
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Affiliation(s)
- Dibosh Bordoloi
- AAU-Zonal Research Station, Assam Agricultural University, Karimganj, 788712, India
| | - Debojit Sarma
- Department of Plant Breeding and Genetics, Assam Agricultural University, Jorhat, 785013, India.
| | - Nagendra Sarma Barua
- Department of Plant Breeding and Genetics, Assam Agricultural University, Jorhat, 785013, India
| | - Ranjan Das
- Department of Crop Physiology, Assam Agricultural University, Jorhat, 785013, India
| | - Bikram Kishore Das
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
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Assessment of allelic and genetic diversity, and population structure among farmers' rice varieties using microsatellite markers and morphological traits. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Sanghamitra P, Bose LK, Bagchi TB, Kumar A, Roy PS, Moharana N, Patra BC, Padmavati G, Chattopadhyay K. Characterization and exploring genetic potential of landraces from Odisha with special emphasis on grain micronutrient content for benefaction of biofortification in rice. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:203-221. [PMID: 35221580 PMCID: PMC8847517 DOI: 10.1007/s12298-021-01119-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
UNLABELLED Assessing genetic variability of micronutrient content in association with qualitative and quantitative traits in germplasm is prerequisite for effective biofortification programme. Odisha, a state of eastern India is considered as one of the most potential hot spot of diversity of cultivated rice for grain yield and nutritional traits. Significant variability for most of the qualitative and quantitative traits including Fe and Zn content was observed in a set of 293 germplasm with varying kernel colour encompassing 14 districts of Odisha. Mostly these landraces were low yielding with some exception (Haldigundi: AC 36454, 50.08 g/plant). These landraces were mostly represented by medium Fe (10-20 ppm)-medium Zn group (20-30 ppm). Fe and Zn content had positive association with each other and also with grain size. Landraces with red kernel colour were observed to have slightly higher average Zn content (26.30 ppm) as compared to white (25.87 ppm) grains. Diversity analysis of 14 districts revealed that Nayagarh, a south-eastern district was rich in Fe content while Deogarh, Keonjhar and Mayurbhanj, all north-western districts were rich in Zn content. This study identified 10 superior micronutrient dense genotypes with medium to high Fe and Zn content. This set of donors for micronutrient content was validated in another year. Champeisiali (AC 43368) and Gedemalati (AC 34306) with highest Fe (44.1 ppm) and Zn (40.48 ppm) content, respectively were detected over the environments. Identified donors and associated traits could be utilized in biofortificaion programme using appropriate breeding methodologies for enhancing micronutrients in high yielding background. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01119-7.
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Affiliation(s)
| | - Lotan Kumar Bose
- ICAR-National Rice Research Institute, Cuttack, Odisha 753006 India
| | | | - Awadhesh Kumar
- ICAR-National Rice Research Institute, Cuttack, Odisha 753006 India
| | | | - Nutan Moharana
- ICAR-National Rice Research Institute, Cuttack, Odisha 753006 India
| | | | - G. Padmavati
- ICAR-Indian Institute of Rice Research, Hyderabad, India
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Genetic Structure and Geographical Differentiation of Traditional Rice ( Oryza sativa L.) from Northern Vietnam. PLANTS 2021; 10:plants10102094. [PMID: 34685903 PMCID: PMC8540186 DOI: 10.3390/plants10102094] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/01/2021] [Accepted: 10/01/2021] [Indexed: 11/24/2022]
Abstract
Northern Vietnam is one of the most important centers of genetic diversity for cultivated rice. Over thousands of years of cultivation, natural and artificial selection has preserved many traditional rice landraces in northern Vietnam due to its geographic situation, climatic conditions, and many ethnic groups. These local landraces serve as a rich source of genetic variation—an important resource for future crop improvement. In this study, we determined the genetic diversity and population structure of 79 rice landraces collected from northern Vietnam and 19 rice accessions collected from different countries. In total, 98 rice accessions could be differentiated into japonica and indica with moderate genetic diversity and a polymorphism information content of 0.382. Moreover, we found that genetic differentiation was related to geographical regions with an overall PhiPT (analog of fixation index FST) value of 0.130. We also detected subspecies-specific markers to classify rice (Oryza sativa L.) into indica and japonica. Additionally, we detected five marker-trait associations and rare alleles that can be applied in future breeding programs. Our results suggest that rice landraces in northern Vietnam have a dynamic genetic system that can create different levels of genetic differentiation among regions, but also maintain a balanced genetic diversity between regions.
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Evaluation of indigenous aromatic rice cultivars from sub-Himalayan Terai region of India for nutritional attributes and blast resistance. Sci Rep 2021; 11:4786. [PMID: 33637778 PMCID: PMC7910543 DOI: 10.1038/s41598-021-83921-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/03/2021] [Indexed: 01/12/2023] Open
Abstract
Indigenous folk rice cultivars often possess remarkable but unrevealed potential in terms of nutritional attributes and biotic stress tolerance. The unique cooking qualities and blissful aroma of many of these landraces make it an attractive low-cost alternative to high priced Basmati rice. Sub-Himalayan Terai region is bestowed with great agrobiodiversity in traditional heirloom rice cultivars. In the present study, ninety-nine folk rice cultivars from these regions were collected, purified and characterized for morphological and yield traits. Based on traditional importance and presence of aroma, thirty-five genotypes were selected and analyzed for genetic diversity using micro-satellite marker system. The genotypes were found to be genetically distinct and of high nutritive value. The resistant starch content, amylose content, glycemic index and antioxidant potential of these genotypes represented wide variability and 'Kataribhog', 'Sadanunia', 'Chakhao' etc. were identified as promising genotypes in terms of different nutritional attributes. These cultivars were screened further for resistance against blast disease in field trials and cultivars like 'Sadanunia', 'T4M-3-5', 'Chakhao Sampark' were found to be highly resistant to the blast disease whereas 'Kalonunia', 'Gobindabhog', 'Konkanijoha' were found to be highly susceptible. Principal Component analysis divided the genotypes in distinct groups for nutritional potential and blast tolerance. The resistant and susceptible genotypes were screened for the presence of the blast resistant pi genes and association analysis was performed with disease tolerance. Finally, a logistic model based on phenotypic traits for prediction of the blast susceptibility of the genotypes is proposed with more than 80% accuracy.
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Bhuvaneswari S, Gopala Krishnan S, Bollinedi H, Saha S, Ellur RK, Vinod KK, Singh IM, Prakash N, Bhowmick PK, Nagarajan M, Singh NK, Singh AK. Genetic Architecture and Anthocyanin Profiling of Aromatic Rice From Manipur Reveals Divergence of Chakhao Landraces. Front Genet 2020; 11:570731. [PMID: 33193672 PMCID: PMC7593561 DOI: 10.3389/fgene.2020.570731] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/04/2020] [Indexed: 01/21/2023] Open
Abstract
Aromatic rice of Manipur popularly known as Chakhao is a speciality glutinous rice, for which protection under geographical indication in India has been granted recently. The agronomic and nutraceutical variability of the Chakhao rice germplasm is yet to be genetically characterized. To address this gap, characterization of ninety-three landraces for agro-morphological traits, grain pigmentation, antioxidant properties, and molecular genetic variation was carried out to unravel their population genetic structure. Two major groups were identified based on pericarp color, namely, purple and non-purple, which showed a significant variation for plant height, panicle length, and grain yield. Molecular marker analysis revealed three subpopulations that could be associated with pericarp pigmentation. Deep purple genotypes formed POP3, japonica genotypes adapted to hill environment formed POP1, while POP2 comprised of both indica and aus types. Liquid chromatography-mass spectrometry (LC-MS) analysis revealed two major anthocyanin compounds in pigmented rices, namely, cyanidin-3-O-glucoside (C3G) and peonidin-3-O-glucoside (P3G). The total anthocyanin content among pigmented genotypes ranged from 29.8 to 275.8 mg.100g-1 DW. Total phenolics ranged from 66.5 to 700.3 mg GAE.100g-1 DW with radical scavenging activity (RSA) varying between 17.7 and 65.7%. Anthocyanins and phenolics showed a direct relationship with RSA implying the nutraceutical benefits of deep pigmented rice such as Manipur black rice. Aromatic rices from Manipur were found to be genetically diverse. Therefore, efforts need to be made for maintaining the geographic identity of these rice and utilization in breeding for region-specific cultivar improvement.
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Affiliation(s)
- S. Bhuvaneswari
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
- ICAR-Research Complex for North Eastern Hill Region, Manipur Centre, Imphal, India
| | - S. Gopala Krishnan
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Haritha Bollinedi
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Supradip Saha
- Division of Agricultural Chemicals, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Ranjith Kumar Ellur
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - K. K. Vinod
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | | | - Narendra Prakash
- ICAR-Research Complex for North Eastern Hill Region, Manipur Centre, Imphal, India
| | - Prolay Kumar Bhowmick
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - M. Nagarajan
- Rice Breeding and Genetics Research Centre, ICAR-Indian Agricultural Research Institute, Aduthurai, India
| | | | - Ashok Kumar Singh
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
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Islam MZ, Arifuzzaman M, Banik S, Hossain MA, Ferdous J, Khalequzzaman M, Pittendrigh BR, Tomita M, Ali MP. Mapping QTLs underpin nutrition components in aromatic rice germplasm. PLoS One 2020; 15:e0234395. [PMID: 32525930 PMCID: PMC7289389 DOI: 10.1371/journal.pone.0234395] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/22/2020] [Indexed: 12/22/2022] Open
Abstract
As rice is an important staple food globally, research for development and enhancement of its nutritional value it is an imperative task. Identification of nutrient enriched rice germplasm and exploiting them for breeding programme is the easiest way to develop better quality rice. In this study, we analyzed 113 aromatic rice germplasm in order to identify quantitative trait loci (QTL) underpinning nutrition components and determined by measuring the normal frequency distribution for Fe, Zn, amylose, and protein content in those rice germplasm. Comparatively, the germplasm Radhuni pagal, Kalobakri, Thakurbhog (26.6 ppm) and Hatisail exhibited the highest mean values for Fe (16.9 ppm), Zn (34.1 ppm), amylose (26.6 ppm) and protein content (11.0 ppm), respectively. Moreover, a significant linear relationship (R2 = 0.693) was observed between Fe and Zn contents. Cluster analysis based on Mahalanobis D2 distances revealed four major clusters of 113 rice germplasm, with cluster III containing a maximum 37 germplasm and a maximum inter-cluster distance between clusters III and IV. The 45 polymorphic SSRs and four trait associations exhibited eight significant quantitative trait loci (QTL) located on eight different chromosomes using composite interval mapping (CIM). The highly significant QTL (variance 7.89%, LOD 2.02) for protein content (QTL.pro.1) was observed on chromosome 1 at 94.9cM position. Also, four QTLs for amylose content were observed with the highly significant QTL.amy.8 located on chromosome 8 exhibiting 7.2% variance with LOD 1.83. Only one QTL (QTL.Fe.9) for Fe content was located on chromosome 9 (LOD 1.24), and two (QTL.Zn.4 and QTL.Zn.5) for Zn on chromosome 4 (LOD 1.71) and 5 (LOD 1.18), respectively. Overall, germplasm from clusters III and IV might offer higher heterotic response with the identified QTLs playing a significant role in any rice biofortification breeding program and released with development of new varieties.
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Affiliation(s)
- M. Z. Islam
- Genetic Resources and Seed Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
- * E-mail: (MZI); (MPA); (MT)
| | - M. Arifuzzaman
- Department of Genetics and Plant Breeding, Hajee Mohammad Danesh Science and Technology University, Dinajpur, Bangladesh
| | - S. Banik
- Grain Quality and Nutrition Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
| | - M. A. Hossain
- Regional Station, Barisal, Bangladesh Rice Research Institute, Gazipur, Bangladesh
| | - J. Ferdous
- Biotechnology Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
| | - M. Khalequzzaman
- Genetic Resources and Seed Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
| | - B. R. Pittendrigh
- Department of Entomology, Michigan State University, East Lansing, Michigan, United States of America
| | - M. Tomita
- Genetics and Genome Engineering Laboratory, Green Biology Research Division, Research Institute of Green Science and Technology, Shizuoka University, Shizuoka City, Shizuoka, Japan
- * E-mail: (MZI); (MPA); (MT)
| | - M. P. Ali
- Entomolgy Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
- * E-mail: (MZI); (MPA); (MT)
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Verma H, Borah JL, Sarma RN. Variability Assessment for Root and Drought Tolerance Traits and Genetic Diversity Analysis of Rice Germplasm using SSR Markers. Sci Rep 2019; 9:16513. [PMID: 31712622 PMCID: PMC6848176 DOI: 10.1038/s41598-019-52884-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 10/23/2019] [Indexed: 11/16/2022] Open
Abstract
The studies on genetic variation, diversity and population structure of rice germplasm of North East India could be an important step for improvements of abiotic and biotic stress tolerance in rice. Genetic diversity and genetic relatedness among 114 rice genotypes of North East India were assessed using genotypic data of 65 SSR markers and phenotypic data. The phenotypic diversity analysis showed the considerable variation across genotypes for root, shoot and drought tolerance traits. The principal component analysis (PCA) revealed the fresh shoot weight, root volume, dry shoot weight, fresh root weight and drought score as a major contributor to diversity. Genotyping of 114 rice genotypes using 65 SSR markers detected 147 alleles with the average polymorphic information content (PIC) value of 0.51. Population structure analysis using the Bayesian clustering model approach, distance-based neighbor-joining cluster and principal coordinate analysis using genotypic data grouped the accession into three sub-populations. Population structure analysis revealed that rice accession was moderately structured based on FST value estimates. Analysis of molecular variance (AMOVA) and pairwise FST values showed significant differentiation among all the pairs of sub-population ranging from 0.152 to 0.222 suggesting that all the three subpopulations were significantly different from each other. AMOVA revealed that most of the variation in rice accession mainly occurred among individuals. The present study suggests that diverse germplasm of NE India could be used for the improvement of root and drought tolerance in rice breeding programmes.
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Affiliation(s)
- H Verma
- Department of Plant Breeding & Genetics, Assam Agricultural University, Jorhat, 785013, Assam, India.
| | - J L Borah
- Department of Plant Breeding & Genetics, Assam Agricultural University, Jorhat, 785013, Assam, India
| | - R N Sarma
- Department of Plant Breeding & Genetics, Assam Agricultural University, Jorhat, 785013, Assam, India.
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