1
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Pandita D, Mahajan R, Zargar SM, Nehvi FA, Dhekale B, Shafi F, Shah MUD, Sofi NR, Husaini AM. Trait specific marker-based characterization and population structure analysis in rice (Oryza sativa L.) germplasm of Kashmir Himalayas. Mol Biol Rep 2023; 50:4155-4163. [PMID: 36881341 DOI: 10.1007/s11033-023-08324-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 02/02/2023] [Indexed: 03/08/2023]
Abstract
BACKGROUND Rice is a key food grain contributor to the global food grain basket and is considered the main food crop in India with a large number of varieties released every year. SSR markers have proven to be an excellent tool for studying genetic diversity. As a result, the present study was done to characterize and assess genetic diversity as well as population structural aspects. METHODS AND RESULTS Fifty genotypes of rice were characterized using 40 SSR markers to assess the genetic diversity and genetic relationship. A total of 114 alleles were amplified with an average of 2.85 alleles per locus. The Polymorphism Information Content (PIC) values varied from 0.30 (RM162) to 0.58 (RM413) with an average of 0.44. Gene diversity was in the range of 0.35 (RM162) to 0.66 (RM413), with an average value of 0.52, while heterozygosity ranged from 0.18 (RM27) to 0.74 (RM55), with an average of 0.39. The population structure revealed a narrow genetic base with only three major subpopulations. Analysis of molecular variance revealed that 74% of the variation was attributed within individuals, 23% was among individuals, and 3% was among populations. Pairwise Fst value of population A & B is 0.024, population B & C is 0.120 and population A & C is 0.115. Dendrogram grouped the genotypes into three clusters with wide variation among the accessions. CONCLUSION Genotyping combined with phylogeny and population structure analysis proved to be a powerful method for characterizing germplasm in this study. There is significant gene flow within populations, as well as the presence of different combinations of alleles, and that allelic exchange rates within the populations are higher than among the populations. Assessing the genetic diversity among individual genotypes within populations is quite useful in selecting candidate parents for future breeding programs to improve the target traits in rice for the Himalayan region.
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Affiliation(s)
- Deepika Pandita
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, J&K, 190025, India
| | | | | | - Firdous A Nehvi
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, J&K, 190025, India
| | | | - Fouzia Shafi
- Division of Basic Sciences, SKUAST-K, Srinagar, India
| | | | | | - Amjad M Husaini
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, J&K, 190025, India.
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2
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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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3
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Sah RP, Behera S, Dash SK, Azharudheen TPM, Meher J, Kumar A, Marndi BC, Kar MK, Subudhi HN, Anilkumar C. Unravelling genetic architecture and development of core set from elite rice lines using yield-related candidate gene markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1217-1232. [PMID: 35910441 PMCID: PMC9334483 DOI: 10.1007/s12298-022-01190-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 05/08/2022] [Accepted: 05/17/2022] [Indexed: 06/03/2023]
Abstract
Assessing genetic diversity and development of a core set of elite breeding lines is a prerequisite for selective hybridization programes intended to improve the yield potential in rice. In the present study, the genetic diversity of newly developed elite lines derived from indicax tropical japonica and indicax indica crosses were estimated by 38 reported molecular markers. The markers used in the study consist of 24 gene-based and 14 random markers related to grain yield-related QTLs distributed across the rice genome. Genotypic characterization was carried out to determine the genetic similarities between the elite lines. In total, 75 alleles were found using 38 polymorphic markers, with polymorphism information content ranging from 0.10 to 0.51 with an average of 0.35. The genotypes were divided into three groups based on cluster analysis, structure analysis and also dispersed throughout the quadrangle of PCA, but nitrogen responsive lines clustered in one quadrangle. Seven markers (GS3_RGS1, GS3_RGS2, GS5_Indel1, Ghd 7_05SNP, RM 12289, RM 23065 and RM 25457) exhibited PIC values ≥ 0.50 indicating that they were effective in detecting genetic relationships among elite rice. Additionally, a core set of 11 elite lines was made from 96 lines in order to downsize the diversity of the original population into a small set for parental selection. In general, the genetic information collected in this work will aid in the study of grain yield traits at molecular level for other sets of rice genotypes and for selecting diverse elite lines to develop a strong crossing programme in rice. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-022-01190-8.
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Affiliation(s)
- Rameswar Prasad Sah
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - Sasmita Behera
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - Sushant Kumar Dash
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha India
| | | | - Jitendriya Meher
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - Awadhesh Kumar
- Crop Physiology and Biochemistry, ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - Bishnu Charan Marndi
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - Meera Kumari Kar
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - H. N. Subudhi
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - C. Anilkumar
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha India
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4
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Khoury CK, Brush S, Costich DE, Curry HA, de Haan S, Engels JMM, Guarino L, Hoban S, Mercer KL, Miller AJ, Nabhan GP, Perales HR, Richards C, Riggins C, Thormann I. Crop genetic erosion: understanding and responding to loss of crop diversity. THE NEW PHYTOLOGIST 2022; 233:84-118. [PMID: 34515358 DOI: 10.1111/nph.17733] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
Crop diversity underpins the productivity, resilience and adaptive capacity of agriculture. Loss of this diversity, termed crop genetic erosion, is therefore concerning. While alarms regarding evident declines in crop diversity have been raised for over a century, the magnitude, trajectory, drivers and significance of these losses remain insufficiently understood. We outline the various definitions, measurements, scales and sources of information on crop genetic erosion. We then provide a synthesis of evidence regarding changes in the diversity of traditional crop landraces on farms, modern crop cultivars in agriculture, crop wild relatives in their natural habitats and crop genetic resources held in conservation repositories. This evidence indicates that marked losses, but also maintenance and increases in diversity, have occurred in all these contexts, the extent depending on species, taxonomic and geographic scale, and region, as well as analytical approach. We discuss steps needed to further advance knowledge around the agricultural and societal significance, as well as conservation implications, of crop genetic erosion. Finally, we propose actions to mitigate, stem and reverse further losses of crop diversity.
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Affiliation(s)
- Colin K Khoury
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, Apartado Aéreo 6713, 763537, Cali, Colombia
- Department of Biology, Saint Louis University, 1 N. Grand Blvd, St Louis, MO, 63103, USA
- San Diego Botanic Garden, 230 Quail Gardens Dr., Encinitas, CA, 92024, USA
| | - Stephen Brush
- University of California Davis, 1 Shields Ave., Davis, CA, 95616, USA
| | - Denise E Costich
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz, Km. 45, El Batán, 56237, Texcoco, México
| | - Helen Anne Curry
- Department of History and Philosophy of Science, University of Cambridge, Free School Lane, Cambridge, CB2 3RH, UK
| | - Stef de Haan
- International Potato Center (CIP), Avenida La Molina 1895, La Molina, Apartado Postal 1558, Lima, Peru
| | | | - Luigi Guarino
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113, Bonn, Germany
| | - Sean Hoban
- The Morton Arboretum, The Center for Tree Science, 4100 IL-53, Lisle, IL, 60532, USA
| | - Kristin L Mercer
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, 43210, USA
| | - Allison J Miller
- Department of Biology, Saint Louis University, 1 N. Grand Blvd, St Louis, MO, 63103, USA
- Donald Danforth Plant Science Center, 975 N Warson Rd, St Louis, MO, 63132, USA
| | - Gary P Nabhan
- Southwest Center and Institute of the Environment, University of Arizona, 1401 E. First St., PO Box 210185, Tucson, AZ, 85721-0185, USA
| | - Hugo R Perales
- Departamento de Agroecología, El Colegio de la Frontera Sur, San Cristóbal, Chiapas, 29290, México
| | - Chris Richards
- National Laboratory for Genetic Resources Preservation, United States Department of Agriculture, Agricultural Research Service, 1111 South Mason Street, Fort Collins, CO, 80521, USA
| | - Chance Riggins
- Department of Crop Sciences, University of Illinois, 331 Edward R. Madigan Lab, 1201 W. Gregory Dr., Urbana, IL, 61801, USA
| | - Imke Thormann
- Federal Office for Agriculture and Food (BLE), Information and Coordination Centre for Biological Diversity (IBV), Deichmanns Aue 29, 53179, Bonn, Germany
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5
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Jha TB. Karyotype diversity in cultivated and wild Indian rice through EMA-based chromosome analysis. J Genet 2021. [DOI: 10.1007/s12041-021-01332-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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6
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An H, Lee HY, Shin H, Bang JH, Han S, Oh YL, Jang KY, Cho H, Hyun TK, Sung J, So YS, Jo IH, Chung JW. Evaluation of Genetic Diversity and Population Structure Analysis among Germplasm of Agaricus bisporus by SSR Markers. MYCOBIOLOGY 2021; 49:376-384. [PMID: 34512081 PMCID: PMC8409946 DOI: 10.1080/12298093.2021.1940746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 06/13/2023]
Abstract
Agaricus bisporus is a popular edible mushroom that is cultivated worldwide. Due to its secondary homothallic nature, cultivated A. bisporus strains have low genetic diversity, and breeding novel strains is challenging. The aim of this study was to investigate the genetic diversity and population structure of globally collected A. bisporus strains using simple sequence repeat (SSR) markers. Agaricus bisporus strains were divided based on genetic distance-based groups and model-based subpopulations. The major allele frequency (MAF), number of genotypes (NG), number of alleles (NA), observed heterozygosity (HO), expected heterozygosity (HE), and polymorphic information content (PIC) were calculated, and genetic distance, population structure, genetic differentiation, and Hardy-Weinberg equilibrium (HWE) were assessed. Strains were divided into two groups by distance-based analysis and into three subpopulations by model-based analysis. Strains in subpopulations POP A and POP B were included in Group I, and strains in subpopulation POP C were included in Group II. Genetic differentiation between strains was 99%. Marker AB-gSSR-1057 in Group II and subpopulation POP C was confirmed to be in HWE. These results will enhance A. bisporus breeding programs and support the protection of genetic resources.
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Affiliation(s)
- Hyejin An
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Hwa-Yong Lee
- Department of Forest Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Hyeran Shin
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Jun Hyoung Bang
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Seahee Han
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Youn-Lee Oh
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Eumseong, Republic of Korea
| | - Kab-Yeul Jang
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Eumseong, Republic of Korea
| | - Hyunwoo Cho
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Tae Kyung Hyun
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
| | - Jwakyung Sung
- Department of Crop Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Yoon-Sup So
- Department of Crop Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Ick-Hyun Jo
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Eumseong, Republic of Korea
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
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7
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Utilization of genetic diversity and population structure to reveal prospective drought-tolerant donors in rice. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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8
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A novel barcode system for rapid identification of rice (Oryza sativa L.) varieties using agro-morphological descriptors and molecular markers. Mol Biol Rep 2021; 48:2209-2221. [PMID: 33675464 DOI: 10.1007/s11033-021-06230-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/10/2021] [Indexed: 10/22/2022]
Abstract
Rice varietal identification is a crucial aspect in breeding, seed production and trade in order to protect the interests of the farmers and consumers. As the number of varieties released is rising every year, the need to identify them unambiguously also increases. Here, we developed a novel barcode system to identify 62 rice genotypes using agro-morphological descriptors and molecular markers. In all, 62 rice genotypes, for 22 agro-morphological traits were recorded. In addition, 19 molecular markers were used for developing genotype-specific DNA fingerprints. The descriptor notes of 10 essential agro-morphological traits and allele codes of the polymorphic markers were used to generate two-dimensional (2-D) barcodes for the rice genotypes. Using agro-morphological traits, 31 rice genotypes were unambiguously distinguished while, with the polymorphic markers we were able to distinguish all rice genotypes except BPT2295 and Jaya. However, using both agro-morphological descriptors and molecular markers in combination, it was possible to distinguish all the rice genotypes used in the present study. These agro-morphological notes and allele codes from the molecular marker data together were used to develop QR (Quick Response) codes for rapid identification of rice genotypes as they facilitate storage of more data. In the present investigation, we have demonstrated the potentiality of agro-morphological traits and molecular markers in distinguishing rice genotypes. The novel QR code system proposed in the present study can also be extended to other crops not only for varietal identification but also for germplasm management and trade.
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9
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Beşer N, Mutafçılar ZÇ, Hasançebi S. Diversity analysis of the rice cultivars (
Oryza sativa
L.) by utilizing SSRs rice diversity by SSRs. J FOOD PROCESS PRES 2021. [DOI: 10.1111/jfpp.15232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Necmi Beşer
- Department of Genetics and Bioengineering Engineering Faculty Trakya University Edirne Turkey
| | - Zeynep Çisem Mutafçılar
- Department of Biotechnology and Genetics Institute of Science Trakya University Edirne Turkey
| | - Semra Hasançebi
- Department of Genetics and Bioengineering Engineering Faculty Trakya University Edirne Turkey
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10
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Shuaib M, Bahadur S, Hussain F. Enumeration of genetic diversity of wild rice through phenotypic trait analysis. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100797] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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11
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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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12
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Donde R, Kumar J, Gouda G, Gupta MK, Mukherjee M, Baksh SY, Mahadani P, Sahoo KK, Behera L, Dash SK. Assessment of Genetic Diversity of Drought Tolerant and Susceptible Rice Genotypes Using Microsatellite Markers. RICE SCIENCE 2019; 26:239-247. [DOI: 10.1016/j.rsci.2019.01.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
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13
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Jha UC, Jha R, Bohra A, Parida SK, Kole PC, Thakro V, Singh D, Singh NP. Population structure and association analysis of heat stress relevant traits in chickpea ( Cicer arietinum L.). 3 Biotech 2018; 8:43. [PMID: 29354354 PMCID: PMC5750240 DOI: 10.1007/s13205-017-1057-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 12/19/2017] [Indexed: 12/27/2022] Open
Abstract
Understanding genetic diversity and population structure is prerequisite to broaden the cultivated base of any crop. In the current investigation, we report discovery of a total of 319 alleles by assaying 81 SSRs on 71 chickpea genotypes. The cluster analysis based on Jaccard coefficient and unweighted neighbor joining algorithm categorized all genotypes into two major clusters. Cultivars grown within the same agro-climatic zones were clustered together, whereas the remaining genotypes particularly advanced breeding lines and accessions assigned to another cluster. Population structure analysis separated the entire collection into two subpopulations (K = 2) and the clustering pattern remained in close agreement with those of distance-based methods. Importantly, we also discovered marker trait association for membrane stability index (MSI) and leaf chlorophyll content measured as SPAD chlorophyll meter reading (SCMR), the two important physiological parameters indicative of heat stress (HS) tolerance in chickpea. Association analysis using both general linear and mixed linear models of the mean phenotypic data of traits recorded in 2016 and 2017 uncovered significant association of NCPGR206 and H2L102 with the MSI trait. Likewise, SSR markers GA9, TR31 and TA113 exhibited significant association with SCMR trait. The genomic regions putatively linked with two traits may be investigated in greater detail to further improve knowledge about the genetic architecture of HS tolerance in chickpea.
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Affiliation(s)
- Uday Chand Jha
- Indian Institute of Pulses Research (IIPR), Kanpur, UP 208 024 India
| | - Rintu Jha
- Indian Institute of Pulses Research (IIPR), Kanpur, UP 208 024 India
| | - Abhishek Bohra
- Indian Institute of Pulses Research (IIPR), Kanpur, UP 208 024 India
| | - Swarup Kumar Parida
- National Institute of Plant Genome Research (NIPGR), New Delhi, 110067 India
| | - Paresh Chandra Kole
- Department of Genetics & Plant Breeding and Crop Physiology, Institute of Agriculture, Visva Bharati University, Sriniketan, Bolpur, West Bengal 731236 India
| | - Virevol Thakro
- National Institute of Plant Genome Research (NIPGR), New Delhi, 110067 India
| | - Deepak Singh
- Indian Agricultural Statistical Research Institute (IASRI), New Delhi, India
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14
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Jha UC, Jha R, Bohra A, Parida SK, Kole PC, Thakro V, Singh D, Singh NP. Population structure and association analysis of heat stress relevant traits in chickpea ( Cicer arietinum L.). 3 Biotech 2018. [PMID: 29354354 DOI: 10.1007/s1320] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Understanding genetic diversity and population structure is prerequisite to broaden the cultivated base of any crop. In the current investigation, we report discovery of a total of 319 alleles by assaying 81 SSRs on 71 chickpea genotypes. The cluster analysis based on Jaccard coefficient and unweighted neighbor joining algorithm categorized all genotypes into two major clusters. Cultivars grown within the same agro-climatic zones were clustered together, whereas the remaining genotypes particularly advanced breeding lines and accessions assigned to another cluster. Population structure analysis separated the entire collection into two subpopulations (K = 2) and the clustering pattern remained in close agreement with those of distance-based methods. Importantly, we also discovered marker trait association for membrane stability index (MSI) and leaf chlorophyll content measured as SPAD chlorophyll meter reading (SCMR), the two important physiological parameters indicative of heat stress (HS) tolerance in chickpea. Association analysis using both general linear and mixed linear models of the mean phenotypic data of traits recorded in 2016 and 2017 uncovered significant association of NCPGR206 and H2L102 with the MSI trait. Likewise, SSR markers GA9, TR31 and TA113 exhibited significant association with SCMR trait. The genomic regions putatively linked with two traits may be investigated in greater detail to further improve knowledge about the genetic architecture of HS tolerance in chickpea.
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Affiliation(s)
- Uday Chand Jha
- 1Indian Institute of Pulses Research (IIPR), Kanpur, UP 208 024 India
| | - Rintu Jha
- 1Indian Institute of Pulses Research (IIPR), Kanpur, UP 208 024 India
| | - Abhishek Bohra
- 1Indian Institute of Pulses Research (IIPR), Kanpur, UP 208 024 India
| | - Swarup Kumar Parida
- 2National Institute of Plant Genome Research (NIPGR), New Delhi, 110067 India
| | - Paresh Chandra Kole
- 3Department of Genetics & Plant Breeding and Crop Physiology, Institute of Agriculture, Visva Bharati University, Sriniketan, Bolpur, West Bengal 731236 India
| | - Virevol Thakro
- 2National Institute of Plant Genome Research (NIPGR), New Delhi, 110067 India
| | - Deepak Singh
- Indian Agricultural Statistical Research Institute (IASRI), New Delhi, India
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15
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Bohra A, Jha R, Pandey G, Patil PG, Saxena RK, Singh IP, Singh D, Mishra RK, Mishra A, Singh F, Varshney RK, Singh NP. New Hypervariable SSR Markers for Diversity Analysis, Hybrid Purity Testing and Trait Mapping in Pigeonpea [ Cajanus cajan (L.) Millspaugh]. FRONTIERS IN PLANT SCIENCE 2017; 8:377. [PMID: 28408910 PMCID: PMC5374739 DOI: 10.3389/fpls.2017.00377] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 03/06/2017] [Indexed: 05/21/2023]
Abstract
Draft genome sequence in pigeonpea offers unprecedented opportunities for genomics assisted crop improvement via enabling access to genome-wide genetic markers. In the present study, 421 hypervariable simple sequence repeat (SSR) markers from the pigeonpea genome were screened on a panel of eight pigeonpea genotypes yielding marker validation and polymorphism percentages of 95.24 and 54.11%, respectively. The SSR marker assay uncovered a total of 570 alleles with three as an average number of alleles per marker. Similarly, the mean values for gene diversity and PIC were 0.44 and 0.37, respectively. The number of polymorphic markers ranged from 39 to 89 for different parental combinations. Further, 60 of these SSRs were assayed on 94 genotypes, and model based clustering using STRUCTURE resulted in the identification of the two subpopulations (K = 2). This remained in close agreement with the clustering patterns inferred from genetic distance (GD)-based approaches i.e., dendrogram, factorial and principal coordinate analysis (PCoA). The AMOVA accounted majority of the genetic variation within groups (89%) in comparison to the variation existing between the groups (11%). A subset of these markers was implicated for hybrid purity testing. We also demonstrated utility of these SSR markers in trait mapping through association and bi-parental linkage analyses. The general linear (GLM) and mixed linear (MLM) models both detected a single SSR marker (CcGM03681) with R2 = 16.4 as associated with the resistance to Fusarium wilt variant 2. Similarly, by using SSR data in a segregating backcross population, the corresponding restorer-of-fertility (Rf) locus was putatively mapped at 39 cM with the marker CcGM08896. However, The marker-trait associations (MTAs) detected here represent a very preliminary type and hence demand deeper investigations for conclusive evidence. Given their ability to reveal polymorphism in simple agarose gels, the hypervariable SSRs are valuable genomic resource for pigeonpea research community, particularly in South Asia and East Africa where pigeonpea is primarily grown.
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Affiliation(s)
- Abhishek Bohra
- ICAR-Indian Institute of Pulses Research (IIPR)Kanpur, India
- *Correspondence: Abhishek Bohra
| | - Rintu Jha
- ICAR-Indian Institute of Pulses Research (IIPR)Kanpur, India
| | - Gaurav Pandey
- ICAR-Indian Institute of Pulses Research (IIPR)Kanpur, India
| | | | - Rachit K. Saxena
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Indra P. Singh
- ICAR-Indian Institute of Pulses Research (IIPR)Kanpur, India
| | - D. Singh
- ICAR-Indian Agricultural Statistics Research InstituteNew Delhi, India
| | - R. K. Mishra
- ICAR-Indian Institute of Pulses Research (IIPR)Kanpur, India
| | - Ankita Mishra
- ICAR-Indian Institute of Pulses Research (IIPR)Kanpur, India
| | - F. Singh
- ICAR-Indian Institute of Pulses Research (IIPR)Kanpur, India
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
- Rajeev K. Varshney
| | - N. P. Singh
- ICAR-Indian Institute of Pulses Research (IIPR)Kanpur, India
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16
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Singh N, Choudhury DR, Tiwari G, Singh AK, Kumar S, Srinivasan K, Tyagi RK, Sharma AD, Singh NK, Singh R. Genetic diversity trend in Indian rice varieties: an analysis using SSR markers. BMC Genet 2016; 17:127. [PMID: 27597653 PMCID: PMC5011800 DOI: 10.1186/s12863-016-0437-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/30/2016] [Indexed: 01/17/2023] Open
Abstract
Background The knowledge of the extent and pattern of diversity in the crop species is a prerequisite for any crop improvement as it helps breeders in deciding suitable breeding strategies for their future improvement. Rice is the main staple crop in India with the large number of varieties released every year. Studies based on the small set of rice genotypes have reported a loss in genetic diversity especially after green revolution. However, a detailed study of the trend of diversity in Indian rice varieties is lacking. SSR markers have proven to be a marker of choice for studying the genetic diversity. Therefore, the present study was undertaken with the aim to characterize and assess trends of genetic diversity in a large set of Indian rice varieties (released between 1940–2013), conserved in the National Gene Bank of India using SSR markers. Result A set of 729 Indian rice varieties were genotyped using 36 HvSSR markers to assess the genetic diversity and genetic relationship. A total of 112 alleles was amplified with an average of 3.11 alleles per locus with mean Polymorphic Information Content (PIC) value of 0.29. Cluster analysis grouped these varieties into two clusters whereas the model based population structure divided them into three populations. AMOVA study based on hierarchical cluster and model based approach showed 3 % and 11 % variation between the populations, respectively. Decadal analysis for gene diversity and PIC showed increasing trend from 1940 to 2005, thereafter values for both the parameters showed decreasing trend between years 2006-2013. In contrast to this, allele number demonstrated increasing trend in these varieties released and notified between1940 to 1985, it remained nearly constant during 1986 to 2005 and again showed an increasing trend. Conclusion Our results demonstrated that the Indian rice varieties harbors huge amount of genetic diversity. However, the trait based improvement program in the last decades forced breeders to rely on few parents, which resulted in loss of gene diversity during 2006 to 2013. The present study indicates the need for broadening the genetic base of Indian rice varieties through the use of diverse parents in the current breeding program. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0437-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nivedita Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India
| | - Debjani Roy Choudhury
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India
| | - Gunjan Tiwari
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India
| | - Amit Kumar Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India
| | - Sundeep Kumar
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India
| | - Kalyani Srinivasan
- Division of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India
| | - R K Tyagi
- Division of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India
| | - A D Sharma
- Division of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India
| | - N K Singh
- ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, IARI, New Delhi, 110012, India
| | - Rakesh Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India.
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17
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Salem KFM, Sallam A. Analysis of population structure and genetic diversity of Egyptian and exotic rice (Oryza sativa L.) genotypes. C R Biol 2015; 339:1-9. [PMID: 26727453 DOI: 10.1016/j.crvi.2015.11.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 11/10/2015] [Accepted: 11/16/2015] [Indexed: 01/07/2023]
Abstract
Understanding the population structure and genetic diversity is a very important goal to improve the economic value of crops. In rice, a loss of genetic diversity in the last few centuries is observed. To address this challenge, a set of 22 lines from three different regions - India (two), and Philippines (six), and Egypt (14) - were used to assess the genetic diversity and the features of population structure. These genotypes were analyzed using 106 SSR alleles that showed a clear polymorphism among the lines. Genetic diversity was estimated based on the number of different alleles, polymorphism information content (PIC), and gene diversity. A total of 106 SSR alleles was identified from the 23 SSR loci and used to study the population structure and carry out a cluster analysis. All SSR loci showed a wide range of the number of different alleles extended from two (one loci) to seven alleles (three loci). Five and eight loci showed high PIC and gene diversity (≥0.70), respectively. The results of population structure are in agreement with cluster analysis results. Both analyses revealed two different subpopulations (G1 and G2) with different genetic properties in number of private alleles, number of different alleles (Na), number of effective alleles (Ne), expected heterozygosity (He), and Shannon's Information Index (SII). Our findings indicate that five SSR loci (RM 111, RM 307, RM 22, RM 19, and RM 271) could be used in breeding programs to enhance the marker-assisted selection through QTL mapping and association studies. A high genetic diversity found between genotypes which can be exploited to improve and produce rice cultivars for important traits (e.g. high agronomic features and tolerance to biotic or/and abiotic stresses).
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Affiliation(s)
- Khaled F M Salem
- Plant Biotechnology Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City, P. O. Box 79, Sadat City, Egypt
| | - Ahmed Sallam
- Department of Genetics, Faculty of Agriculture, Assiut Univeristy, Assiut 71526, Egypt; Department of Agronomy & Horticulture, University of Nebraska-Lincoln, NE 68683-0915, USA.
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Vemireddy LR, Satyavathi VV, Siddiq EA, Nagaraju J. Review of methods for the detection and quantification of adulteration of rice: Basmati as a case study. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2015; 52:3187-202. [PMID: 26028701 PMCID: PMC4444904 DOI: 10.1007/s13197-014-1579-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 09/08/2014] [Accepted: 09/16/2014] [Indexed: 11/24/2022]
Abstract
Rice is a staple and widely grown crop endowed with rich genetic diversity. As it is difficult to differentiate seeds of various rice varieties based on visual observation accurately, the harvested seeds and subsequent processed products are highly prone to adulteration with look-alike and low quality seeds by the dishonest traders. To protect the interests of importing countries and consumers, several methods have been employed over the last few decades for unambiguous discrimination of cultivars, accurate quantification of the adulterants, and for determination of cultivated geographical area. With recent advances in biotechnology, DNA based techniques evolved rapidly and proved successful over conventional non-DNA based methods to purge the problem of adulteration at commercial level. In the current review, we made an attempt to summarize the existing methods of adulteration detection and quantification in a comprehensive manner by providing Basmati as a case study to enable the traders to arrive at a quick resolution in choosing the apt method to eliminate the adulteration practice in the global rice industry.
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Affiliation(s)
- Lakshminarayana R. Vemireddy
- />Institute of Biotechnology, Acharya NG Ranga Agricultural University, Rajendranagar, Hyderabad, 500030 AP India
| | - V. V. Satyavathi
- />Laboratory of Molecular Genetics, Centre for DNA Fingerprinting and Diagnostics, Nampally, Hyderabad, AP India
| | - E. A. Siddiq
- />Institute of Biotechnology, Acharya NG Ranga Agricultural University, Rajendranagar, Hyderabad, 500030 AP India
| | - J. Nagaraju
- />Laboratory of Molecular Genetics, Centre for DNA Fingerprinting and Diagnostics, Nampally, Hyderabad, AP India
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Molla KA, Debnath AB, Ganie SA, Mondal TK. Identification and analysis of novel salt responsive candidate gene based SSRs (cgSSRs) from rice (Oryza sativa L.). BMC PLANT BIOLOGY 2015; 15:122. [PMID: 25982586 PMCID: PMC4435636 DOI: 10.1186/s12870-015-0498-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/21/2015] [Indexed: 05/19/2023]
Abstract
BACKGROUND Majority of the Asian people depend on rice for nutritional energy. Rice cultivation and yield are severely affected by soil salinity stress worldwide. Marker assisted breeding is a rapid and efficient way to develop improved variety for salinity stress tolerance. Genomic microsatellite markers are an elite group of markers, but there is possible uncertainty of linkage with the important genes. In contrast, there are better possibilities of linkage detection with important genes if SSRs are developed from candidate genes. To the best of our knowledge, there is no such report on SSR markers development from candidate gene sequences in rice. So the present study was aimed to identify and analyse SSRs from salt responsive candidate genes of rice. RESULTS In the present study, based on the comprehensive literature survey, we selected 220 different salt responsive genes of rice. Out of them, 106 genes were found to contain 180 microsatellite loci with, tri-nucleotide motifs (56%) being most abundant, followed by di-(41%) and tetra nucleotide (2.8%) motifs. Maximum loci were found in the coding sequences (37.2%), followed by in 5'UTR (26%), intron (21.6%) and 3'UTR (15%). For validation, 19 primer sets were evaluated to detect polymorphism in diversity analysis among the two panels consisting of 17 salt tolerant and 17 susceptible rice genotypes. Except one, all primer sets exhibited polymorphic nature with an average of 21.8 alleles/primer and with a mean PIC value of 0.28. Calculated genetic similarity among genotypes was ranged from 19%-89%. The generated dendrogram showed 3 clusters of which one contained entire 17 susceptible genotypes and another two clusters contained all tolerant genotypes. CONCLUSION The present study represents the potential of salt responsive candidate gene based SSR (cgSSR) markers to be utilized as novel and remarkable candidate for diversity analysis among rice genotypes differing in salinity response.
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Affiliation(s)
- Kutubuddin Ali Molla
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, IARI Campus, Pusa, New Delhi, 110012, India.
| | - Ananda Bhusan Debnath
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, IARI Campus, Pusa, New Delhi, 110012, India.
| | - Showkat Ahmad Ganie
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, IARI Campus, Pusa, New Delhi, 110012, India.
| | - Tapan Kumar Mondal
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, IARI Campus, Pusa, New Delhi, 110012, India.
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