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Gautam RK, Singh PK, Venkatesan K, Rakesh B, Sakthivel K, Swain S, Srikumar M, Zamir Ahmed SK, Devakumar K, Rao SS, Vijayan J, Ali S, Langyan S. Harnessing intra-varietal variation for agro-morphological and nutritional traits in a popular rice landrace for sustainable food security in tropical islands. Front Nutr 2023; 10:1088208. [PMID: 36908925 PMCID: PMC9995847 DOI: 10.3389/fnut.2023.1088208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/19/2023] [Indexed: 02/25/2023] Open
Abstract
Introduction Rice crop meets the calorie and nutritional requirements of a larger segment of the global population. Here, we report the occurrence of intra-varietal variation in a popular rice landrace C14-8 traditionally grown under the geographical isolation of the Andaman Islands. Methods Based on grain husk color, four groups were formed, wherein the extent of intra-varietal variation was studied by employing 22 agro-morphological and biochemical traits. Results Among the traits studied, flavonoid and anthocyanin contents and grain yield exhibited a wider spectrum of variability due to more coefficients of variation (>25%). The first five principal components (PCs) of principal components analysis explained a significant proportion of the variation (91%) and the first two PCs explained 63.3% of the total variation, with PC1 and PC2 explaining 35.44 and 27.91%, respectively. A total of 50 highly variable SSR (HvSSR) markers spanning over 12 chromosomes produced 314 alleles, which ranged from 1 to 15 alleles per marker, with an average of 6.28. Of the 314 alleles, 64 alleles were found to be rare among the C14-8 selections. While 62% of HvSSR markers exhibited polymorphism among the C14-8 population, chromosomes 2, 7, 9, and 11 harbored the most polymorphic loci. The group clustering of the selections through HvSSR markers conformed to the grouping based on grain husk coloration. Discussion Our studies on the existence and pertinence of intra-varietal variations are expected to be of significance in the realms of evolutionary biology and sustainable food and nutritional security under the changing climate.
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Affiliation(s)
- Raj Kumar Gautam
- ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India.,ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, India
| | - Pankaj Kumar Singh
- ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Kannan Venkatesan
- ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Bandol Rakesh
- ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Krishnan Sakthivel
- ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India.,ICAR-Indian Institute of Oilseed Research, Hyderabad, Telangana, India
| | - Sachidananda Swain
- ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Muthulingam Srikumar
- ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - S K Zamir Ahmed
- ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Kishnamoorthy Devakumar
- ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India.,ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India
| | - Shyam Sunder Rao
- ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Joshitha Vijayan
- ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India.,ICAR-National Institute of Plant Biotechnology, Pusa, New Delhi, India
| | - Sharik Ali
- ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, India
| | - Sapna Langyan
- ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, India
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Population Dynamics of Wide Compatibility System and Evaluation of Intersubspecific Hybrids by indica-japonica Hybridization in Rice. PLANTS 2022; 11:plants11151930. [PMID: 35893634 PMCID: PMC9332614 DOI: 10.3390/plants11151930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/07/2022] [Accepted: 05/08/2022] [Indexed: 11/17/2022]
Abstract
The exploitation of heterosis through intersubspecific hybridisation between indica and japonica has been a major breeding target in rice, but is marred by the cross incompatibility between the genomes. Wide compatibility (WC) is a triallelic system at the S5 locus on chromosome 6 that ensures the specificity of hybridisation within and between indica and japonica. The S5n allele that favours intercrossing is sparsely distributed in the rice gene pool and therefore warrants identification of diverse WC sources to develop superior intersubspecific hybrids. In this study, we have identified several novel WC sources through the marker-assisted screening of a large set of 950 rice genotypes. Seventeen percent of the genotypes carried S5n, which fell into two subpopulations. The WC genotypes showed wide phenotypic and genotypic variability, including both indica and japonica lines. Based on phenotypic performance, the WC varieties were grouped into three clusters. A subset of 41 WC varieties was used to develop 164 hybrids, of which WC/japonica hybrids showed relative superiority over WC/indica hybrids. The multilocation evaluation of hybrids indicated that hybrids derived from WC varieties, such as IRG137, IRG143, OYR128, and IRGC10658, were higher yielding across all the three different locations. Most of the hybrids showed the stability of performance across locations. The identified diverse set of wide compatible varieties (WCVs) can be used in the development of intersubspecific hybrids and also for parental line development in hybrid rice breeding.
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Zargar SM, Mir RA, Ebinezer LB, Masi A, Hami A, Manzoor M, Salgotra RK, Sofi NR, Mushtaq R, Rohila JS, Rakwal R. Physiological and Multi-Omics Approaches for Explaining Drought Stress Tolerance and Supporting Sustainable Production of Rice. FRONTIERS IN PLANT SCIENCE 2022; 12:803603. [PMID: 35154193 PMCID: PMC8829427 DOI: 10.3389/fpls.2021.803603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/14/2021] [Indexed: 05/12/2023]
Abstract
Drought differs from other natural disasters in several respects, largely because of the complexity of a crop's response to it and also because we have the least understanding of a crop's inductive mechanism for addressing drought tolerance among all abiotic stressors. Overall, the growth and productivity of crops at a global level is now thought to be an issue that is more severe and arises more frequently due to climatic change-induced drought stress. Among the major crops, rice is a frontline staple cereal crop of the developing world and is critical to sustaining populations on a daily basis. Worldwide, studies have reported a reduction in rice productivity over the years as a consequence of drought. Plants are evolutionarily primed to withstand a substantial number of environmental cues by undergoing a wide range of changes at the molecular level, involving gene, protein and metabolite interactions to protect the growing plant. Currently, an in-depth, precise and systemic understanding of fundamental biological and cellular mechanisms activated by crop plants during stress is accomplished by an umbrella of -omics technologies, such as transcriptomics, metabolomics and proteomics. This combination of multi-omics approaches provides a comprehensive understanding of cellular dynamics during drought or other stress conditions in comparison to a single -omics approach. Thus a greater need to utilize information (big-omics data) from various molecular pathways to develop drought-resilient crop varieties for cultivation in ever-changing climatic conditions. This review article is focused on assembling current peer-reviewed published knowledge on the use of multi-omics approaches toward expediting the development of drought-tolerant rice plants for sustainable rice production and realizing global food security.
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Affiliation(s)
- Sajad Majeed Zargar
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Rakeeb Ahmad Mir
- Department of Biotechnology, School of Biosciences and Biotechnology, BGSB University, Rajouri, India
| | - Leonard Barnabas Ebinezer
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, Padua, Italy
| | - Antonio Masi
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, Padua, Italy
| | - Ammarah Hami
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Madhiya Manzoor
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Romesh K. Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | - Najeebul Rehman Sofi
- Division of Plant Breeding and Genetics, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Roohi Mushtaq
- Department of Biotechnology and Bioinformatics, SP College, Cluster University Srinagar, Srinagar, India
| | - Jai Singh Rohila
- Dale Bumpers National Rice Research Center, United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), Stuttgart, AR, United States
| | - Randeep Rakwal
- Faculty of Health and Sport Sciences, University of Tsukuba, Ibaraki, Japan
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Gaballah MM, Fiaz S, Wang X, Younas A, Khan SA, Wattoo FM, Shafiq MR. Identification of genetic diversity among some promising lines of rice under drought stress using SSR markers. JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2021. [DOI: 10.1080/16583655.2021.1989738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Mahmoud M. Gaballah
- Rice Research and Training Center (RRTC), Rice Research Department, Field Crops Research Institute, Agricultural Research Center, Kafr Elsheikh, Egypt
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Xiukang Wang
- College of Life Sciences, Yan’an University, Yan’an, People’s Republic of China
| | - Afifa Younas
- Department of Botany, Lahore College for Women University, Lahore Pakistan
| | - Sher Aslam Khan
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Fahad Masoud Wattoo
- Department of Plant Breeding and Genetics, PMAS- Arid Agriculture University Rawalpindi, Pakistan
| | - Muhammad Rizwan Shafiq
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Okara, Pakistan
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Gaballah MM, Metwally AM, Skalicky M, Hassan MM, Brestic M, EL Sabagh A, Fayed AM. Genetic Diversity of Selected Rice Genotypes under Water Stress Conditions. PLANTS 2020; 10:plants10010027. [PMID: 33374424 PMCID: PMC7824656 DOI: 10.3390/plants10010027] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 01/21/2023]
Abstract
Drought is the most challenging abiotic stress for rice production in the world. Thus, developing new rice genotype tolerance to water scarcity is one of the best strategies to achieve and maximize high yield potential with water savings. The study aims to characterize 16 rice genotypes for grain and agronomic parameters under normal and drought stress conditions, and genetic differentiation, by determining specific DNA markers related to drought tolerance using Simple Sequence Repeats (SSR) markers and grouping cultivars, establishing their genetic relationship for different traits. The experiment was conducted under irrigated (normal) and water stress conditions. Mean squares due to genotype × environment interactions were highly significant for major traits. For the number of panicles/plants, the genotypes Giza179, IET1444, Hybrid1, and Hybrid2 showed the maximum mean values. The required sterility percentage values were produced by genotypes IET1444, Giza178, Hybrid2, and Giza179, while, Sakha101, Giza179, Hybrid1, and Hybrid2 achieved the highest values of grain yield/plant. The genotypes Giza178, Giza179, Hybrid1, and Hybrid2, produced maximum values for water use efficiency. The effective number of alleles per locus ranged from 1.20 alleles to 3.0 alleles with an average of 1.28 alleles, and the He values for all SSR markers used varied from 0.94 to 1.00 with an average of 0.98. The polymorphic information content (PIC) values for the SSR were varied from 0.83 to 0.99, with an average of 0.95 along with a highly significant correlation between PIC values and the number of amplified alleles detected per locus. The highest similarity coefficient between Giza181 and Giza182 (Indica type) was observed and are susceptible to drought stress. High similarity percentage between the genotypes (japonica type; Sakha104 with Sakha102 and Sakha106 (0.45), Sakha101 with Sakha102 and Sakha106 (0.40), Sakha105 with Hybrid1 (0.40), Hybrid1 with Giza178 (0.40) and GZ1368-S-5-4 with Giza181 (0.40)) was also observed, which are also susceptible to drought stress. All genotypes are grouped into two major clusters in the dendrogram at 66% similarity based on Jaccard’s similarity index. The first cluster (A) was divided into two minor groups A1 and A2, in which A1 had two groups A1-1 and A1-2, containing drought-tolerant genotypes like IET1444, GZ1386-S-5-4 and Hybrid1. On the other hand, the A1-2 cluster divided into A1-2-1 containing Hybrid2 genotype and A1-2-2 containing Giza179 and Giza178 at coefficient 0.91, showing moderate tolerance to drought stress. The genotypes GZ1368-S-5-4, IET1444, Giza 178, and Giza179, could be included as appropriate materials for developing a drought-tolerant variety breeding program. Genetic diversity to grow new rice cultivars that combine drought tolerance with high grain yields is essential to maintaining food security.
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Affiliation(s)
- Mahmoud M. Gaballah
- Rice Research and Training Center (RRTC), Field Crops Research Institute, Agricultural Research Center, Kafr El-Sheikh 33717, Egypt;
| | - Azza M. Metwally
- Molecular Biology Department, Genetic Engineering and Biotechnology Institute, University of Sadat City, Sadat City 32897, Egypt; (A.M.M.); (A.M.F.)
| | - Milan Skalicky
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (M.S.); (M.B.)
| | - Mohamed M. Hassan
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Marian Brestic
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (M.S.); (M.B.)
- Department of Plant Physiology, Slovak University of Agriculture, Nitra, Tr. A. Hlinku 2, 949 01 Nitra, Slovakia
| | - Ayman EL Sabagh
- Department of Agronomy, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Sheikh 33516, Egypt
- Correspondence:
| | - Aysam M. Fayed
- Molecular Biology Department, Genetic Engineering and Biotechnology Institute, University of Sadat City, Sadat City 32897, Egypt; (A.M.M.); (A.M.F.)
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Ganguly S, Saha S, Vangaru S, Purkayastha S, Das D, Saha AK, Roy A, Das S, Bhattacharyya PK, Mukherjee S, Bhattacharyya S. Identification and analysis of low light tolerant rice genotypes in field conditions and their SSR-based diversity in various abiotic stress tolerant lines. J Genet 2020. [DOI: 10.1007/s12041-020-01249-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Ali N, Li D, Eltahawy MS, Abdulmajid D, Bux L, Liu E, Dang X, Hong D. Mining of favorable alleles for seed reserve utilization efficiency in Oryza sativa by means of association mapping. BMC Genet 2020; 21:4. [PMID: 31948408 PMCID: PMC6966888 DOI: 10.1186/s12863-020-0811-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 01/07/2020] [Indexed: 11/12/2022] Open
Abstract
Background Wet direct-seeded rice is a possible alternative to conventional puddled transplanted rice; the former uses less water and reduces labor requirements. Improving seed reserve utilization efficiency (SRUE) is a key factor in facilitating the application of this technology. However, the QTLs controlling this trait are poorly investigated. In this study, a genome-wide association study (GWAS) was conducted using a natural population composed of 542 accessions of rice (Oryza sativa L.) which were genotyped using 266 SSR markers. Large phenotypic variations in SRUE were found in the studied population. Results The average SRUE over 542 accessions across two years (2016 and 2017) was 0.52 mg.mg− 1, ranging from 0.22 mg.mg-1 to 0.93 mg.mg− 1, with a coefficient of variation of 22.66%. Overall, 2879 marker alleles were detected in the population by 266 pairs of SSR markers, indicating a large genetic variation existing in the population. Using general linear model method, 13 SSR marker loci associated with SRUE were detected and two (RM7309 and RM434) of the 13 loci, were also detected using mixed linear model analyses, with percentage of phenotypic variation explained (PVE) greater than 5% across two years. The 13 association loci (P < 0.01) were located on all chromosomes except chromosome 11, with PVE ranging from 5.05% (RM5158 on chromosome 5) to 12% (RM297 on chromosome 1). Association loci RM7309 on chromosome 6 and RM434 on chromosome 9 revealed by both models were detected in both years. Twenty-three favorable alleles were identified with phenotypic effect values (PEV) ranging from 0.10 mg.mg− 1 (RM7309–135 bp on chromosome 9) to 0.45 mg.mg− 1 (RM297–180 bp on chromosome 2). RM297–180 bp showed the largest phenotypic effect value (0.44 mg.mg− 1 in 2016 and 0.45 mg.mg− 1 in 2017) with 6.72% of the accessions carrying this allele and the typical carrier accession was Manyedao, followed by RM297–175 bp (0.43 mg.mg− 1 in 2016 and 0.44 mg.mg− 1 in 2017). Conclusion Nine novel association loci for SRUE were identified, compared with previous studies. The optimal parental combinations for pyramiding more favorable alleles for SRUE were selected and could be used for breeding rice accessions suitable for wet direct seeding in the future.
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Affiliation(s)
- Nour Ali
- Nanjing Agricultural University, Nanjing, 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.,Laboratory of Crop Production and Multiplication, Field Crops Research Department, Agricultural Faculty, Damascus University, Damascus, Syria.,Laboratory of Crop Genetics and Germplasm Enhancement, Field Crops Research Department, Agricultural Faculty, Damascus University, Damascus, Syria
| | - Dalu Li
- Nanjing Agricultural University, Nanjing, 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Moaz S Eltahawy
- Nanjing Agricultural University, Nanjing, 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.,Agronomy Department, Faculty of Agriculture, Zagazig University, Zagazig, Sharqia, 44519, Egypt
| | - Dina Abdulmajid
- Nanjing Agricultural University, Nanjing, 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.,Rice Research and Training Center, Field Crops Research Institute, Agricultural Research Center, Kafr El-Sheikh, 33717, Egypt
| | - Lal Bux
- Nanjing Agricultural University, Nanjing, 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Erbao Liu
- Nanjing Agricultural University, Nanjing, 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaojing Dang
- Nanjing Agricultural University, Nanjing, 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Delin Hong
- Nanjing Agricultural University, Nanjing, 210095, China. .,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
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Genetic diversity and population structure analysis of Asian and African aromatic rice (Oryza sativa L.) genotypes. J Genet 2019. [DOI: 10.1007/s12041-019-1131-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Hoang GT, Van Dinh L, Nguyen TT, Ta NK, Gathignol F, Mai CD, Jouannic S, Tran KD, Khuat TH, Do VN, Lebrun M, Courtois B, Gantet P. Genome-wide Association Study of a Panel of Vietnamese Rice Landraces Reveals New QTLs for Tolerance to Water Deficit During the Vegetative Phase. RICE (NEW YORK, N.Y.) 2019; 12:4. [PMID: 30701393 PMCID: PMC6357217 DOI: 10.1186/s12284-018-0258-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 12/11/2018] [Indexed: 05/06/2023]
Abstract
BACKGROUND Drought tolerance is a major challenge in breeding rice for unfavorable environments. In this study, we used a panel of 180 Vietnamese rice landraces genotyped with 21,623 single-nucleotide polymorphism markers to perform a genome-wide association study (GWAS) for different drought response and recovery traits during the vegetative stage. These landraces originate from different geographical locations and are adapted to different agrosystems characterized by contrasted water regimes. Vietnamese landraces are often underrepresented in international panels used for GWAS, but they can contain original genetic determinants related to drought resistance. RESULTS The panel of 180 rice varieties was phenotyped under greenhouse conditions for several drought-related traits in an experimental design with 3 replicates. Plants were grown in pots for 4 weeks and drought-stressed by stopping irrigation for an additional 4 weeks. Drought sensitivity scores and leaf relative water content were measured throughout the drought stress. The recovery capacity was measured 2 weeks after plant rewatering. Several QTLs associated with these drought tolerance traits were identified by GWAS using a mixed model with control of structure and kinship. The number of detected QTLs consisted of 14 for leaf relative water content, 9 for slope of relative water content, 12 for drought sensitivity score, 3 for recovery ability and 1 for relative crop growth rate. This set of 39 QTLs actually corresponded to a total of 17 different QTLs because 9 were simultaneously associated with two or more traits, which indicates that these common loci may have pleiotropic effects on drought-related traits. No QTL was found in association with the same traits in both the indica and japonica subpanels. The possible candidate genes underlying the quantitative trait loci are reviewed. CONCLUSIONS Some of the identified QTLs contain promising candidate genes with a function related to drought tolerance by osmotic stress adjustment.
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Affiliation(s)
- Giang Thi Hoang
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, LMI RICE-2, Hanoi, 00000, Vietnam.
- University of Science and Technology of Hanoi, LMI RICE-2, Hanoi, 00000, Vietnam.
| | - Lam Van Dinh
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, LMI RICE-2, Hanoi, 00000, Vietnam
| | - Thom Thi Nguyen
- IRD, Université de Montpellier, LMI RICE-2, Hanoi, 00000, Vietnam
| | - Nhung Kim Ta
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, LMI RICE-2, Hanoi, 00000, Vietnam
- University of Science and Technology of Hanoi, LMI RICE-2, Hanoi, 00000, Vietnam
| | - Floran Gathignol
- IRD, Université de Montpellier, LMI RICE-2, Hanoi, 00000, Vietnam
| | - Chung Duc Mai
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, LMI RICE-2, Hanoi, 00000, Vietnam
- University of Science and Technology of Hanoi, LMI RICE-2, Hanoi, 00000, Vietnam
| | - Stefan Jouannic
- University of Science and Technology of Hanoi, LMI RICE-2, Hanoi, 00000, Vietnam
- IRD, Université de Montpellier, UMR DIADE, 34095, Montpellier, France
| | - Khanh Dang Tran
- Genetic Engineering Division, Agricultural Genetics Institute, Hanoi, 00000, Vietnam
| | - Trung Huu Khuat
- Genetic Engineering Division, Agricultural Genetics Institute, Hanoi, 00000, Vietnam
| | - Vinh Nang Do
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, LMI RICE-2, Hanoi, 00000, Vietnam
| | - Michel Lebrun
- University of Science and Technology of Hanoi, LMI RICE-2, Hanoi, 00000, Vietnam
- IRD, Université de Montpellier, LMI RICE-2, Hanoi, 00000, Vietnam
- IRD, Université de Montpellier, UMR LSTM, 34095, Montpellier, France
| | - Brigitte Courtois
- Cirad, UMR-AGAP, F-34398, Montpellier, France
- CIRAD, INRA, Univ Montpellier, Montpellier SupAgro, Montpellier, France
| | - Pascal Gantet
- University of Science and Technology of Hanoi, LMI RICE-2, Hanoi, 00000, Vietnam.
- IRD, Université de Montpellier, LMI RICE-2, Hanoi, 00000, Vietnam.
- IRD, Université de Montpellier, UMR DIADE, 34095, Montpellier, France.
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Dang X, Fang B, Chen X, Li D, Sowadan O, Dong Z, Liu E, She D, Wu G, Liang Y, Hong D. Favorable Marker Alleles for Panicle Exsertion Length in Rice ( Oryza sativa L.) Mined by Association Mapping and the RSTEP-LRT Method. FRONTIERS IN PLANT SCIENCE 2017; 8:2112. [PMID: 29312380 PMCID: PMC5732986 DOI: 10.3389/fpls.2017.02112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/27/2017] [Indexed: 05/14/2023]
Abstract
The panicle exsertion length (PEL) in rice (Oryza sativa L.) is an important trait for hybrid seed production. We investigated the PEL in a chromosome segment substitution line (CSSL) population consisting of 66 lines and a natural population composed of 540 varieties. In the CSSL population, a total of seven QTLs for PEL were detected across two environments. The percentage of phenotypic variance explained (PVE) ranged from 10.22 to 50.18%, and the additive effect ranged from -1.77 to 6.47 cm. Among the seven QTLs, qPEL10.2 had the largest PVE, 44.05 and 50.18%, with an additive effect of 5.91 and 6.47 cm in 2015 and in 2016, respectively. In the natural population, 13 SSR marker loci were detected that were associated with PEL in all four environments, with the PVE ranging from 1.20 to 6.26%. Among the 13 loci, 7 were novel. The RM5746-170 bp allele had the largest phenotypic effect (5.11 cm), and the typical carrier variety was Qiaobinghuang. An RM5620-RM6100 region harboring the EUI2 locus on chromosome 10 was detected in both populations. The sequencing results showed that the accessions with a shorter PEL contained the A base, while the accessions with a longer PEL contained the G base at the 1,475 bp location of the EUI2 gene.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Delin Hong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
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Swamy BPM, Shamsudin NAA, Rahman SNA, Mauleon R, Ratnam W, Sta. Cruz MT, Kumar A. Association Mapping of Yield and Yield-related Traits Under Reproductive Stage Drought Stress in Rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2017; 10:21. [PMID: 28523639 PMCID: PMC5436998 DOI: 10.1186/s12284-017-0161-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 05/09/2017] [Indexed: 05/05/2023]
Abstract
BACKGROUND The identification and introgression of major-effect QTLs for grain yield under drought are some of the best and well-proven approaches for improving the drought tolerance of rice varieties. In the present study, we characterized Malaysian rice germplasm for yield and yield-related traits and identified significant trait marker associations by structured association mapping. RESULTS The drought screening was successful in screening germplasm with a yield reduction of up to 60% and heritability for grain yield under drought was up to 78%. There was a wider phenotypic and molecular diversity within the panel, indicating the suitability of the population for quantitative trait loci (QTL) mapping. Structure analyses clearly grouped the accessions into three subgroups with admixtures. Linkage disequilibrium (LD) analysis revealed that LD decreased with an increase in distance between marker pairs and the LD decay varied from 5-20 cM. The Mixed Linear model-based structured association mapping identified 80 marker trait associations (MTA) for grain yield (GY), plant height (PH) and days to flowering (DTF). Seven MTA were identified for GY under drought stress, four of these MTA were consistently identified in at least two of the three analyses. Most of these MTA identified were on chromosomes 2, 5, 10, 11 and 12, and their phenotypic variance (PV) varied from 5% to 19%. The in silico analysis of drought QTL regions revealed the association of several drought-responsive genes conferring drought tolerance. The major-effect QTLs are useful in marker-assisted QTL pyramiding to improve drought tolerance. CONCLUSION The results have clearly shown that structured association mapping is one of the feasible options to identify major-effect QTLs for drought tolerance-related traits in rice.
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Affiliation(s)
- B. P. Mallikarjuna Swamy
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777 Metro Manila, Philippines
| | - Noraziyah Abd Aziz Shamsudin
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777 Metro Manila, Philippines
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
| | - Site Noorzuraini Abd Rahman
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777 Metro Manila, Philippines
- MARDI, Seberang Perai, P.O. Box No. 203, 13200 Kepala Batas, Pulau Pinang Malaysia
| | - Ramil Mauleon
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777 Metro Manila, Philippines
| | - Wickneswari Ratnam
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
| | - Ma. Teressa Sta. Cruz
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777 Metro Manila, Philippines
| | - Arvind Kumar
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777 Metro Manila, Philippines
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Swamy BPM, Shamsudin NAA, Rahman SNA, Mauleon R, Ratnam W, Sta Cruz MT, Kumar A. Association Mapping of Yield and Yield-related Traits Under Reproductive Stage Drought Stress in Rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2017. [PMID: 28523639 DOI: 10.1186/s12284-017-0161-6©] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
BACKGROUND The identification and introgression of major-effect QTLs for grain yield under drought are some of the best and well-proven approaches for improving the drought tolerance of rice varieties. In the present study, we characterized Malaysian rice germplasm for yield and yield-related traits and identified significant trait marker associations by structured association mapping. RESULTS The drought screening was successful in screening germplasm with a yield reduction of up to 60% and heritability for grain yield under drought was up to 78%. There was a wider phenotypic and molecular diversity within the panel, indicating the suitability of the population for quantitative trait loci (QTL) mapping. Structure analyses clearly grouped the accessions into three subgroups with admixtures. Linkage disequilibrium (LD) analysis revealed that LD decreased with an increase in distance between marker pairs and the LD decay varied from 5-20 cM. The Mixed Linear model-based structured association mapping identified 80 marker trait associations (MTA) for grain yield (GY), plant height (PH) and days to flowering (DTF). Seven MTA were identified for GY under drought stress, four of these MTA were consistently identified in at least two of the three analyses. Most of these MTA identified were on chromosomes 2, 5, 10, 11 and 12, and their phenotypic variance (PV) varied from 5% to 19%. The in silico analysis of drought QTL regions revealed the association of several drought-responsive genes conferring drought tolerance. The major-effect QTLs are useful in marker-assisted QTL pyramiding to improve drought tolerance. CONCLUSION The results have clearly shown that structured association mapping is one of the feasible options to identify major-effect QTLs for drought tolerance-related traits in rice.
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Affiliation(s)
- B P Mallikarjuna Swamy
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Noraziyah Abd Aziz Shamsudin
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Site Noorzuraini Abd Rahman
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
- MARDI, Seberang Perai, P.O. Box No. 203, 13200, Kepala Batas, Pulau Pinang, Malaysia
| | - Ramil Mauleon
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Wickneswari Ratnam
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Ma Teressa Sta Cruz
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Arvind Kumar
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines.
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Umakanth B, Vishalakshi B, Sathish Kumar P, Rama Devi SJS, Bhadana VP, Senguttuvel P, Kumar S, Sharma SK, Sharma PK, Prasad MS, Madhav MS. Diverse Rice Landraces of North-East India Enables the Identification of Novel Genetic Resources for Magnaporthe Resistance. FRONTIERS IN PLANT SCIENCE 2017; 8:1500. [PMID: 28912793 PMCID: PMC5583601 DOI: 10.3389/fpls.2017.01500] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Accepted: 08/14/2017] [Indexed: 05/30/2023]
Abstract
North-East (NE) India, the probable origin of rice has diverse genetic resources. Many rice landraces of NE India were not yet characterized for blast resistance. A set of 232 landraces of NE India, were screened for field resistance at two different hotspots of rice blast, viz., IIRR-UBN, Hyderabad and ICAR-NEH, Manipur in two consecutive seasons. The phenotypic evaluation as well as gene profiling for 12 major blast resistance genes (Pitp, Pi33, Pi54, Pib, Pi20, Pi38, Pita2, Pi1, Piz, Pi9, Pizt, and Pi40) with linked as well as gene-specific markers, identified 84 resistant landraces possessing different gene(s) either in singly or in combinations and also identified seven resistant landraces which do not have the tested genes, indicating the valuable genetic resources for blast resistance. To understand the molecular diversity existing in the population, distance and model based analysis were performed using 120 SSR markers. Results of both analyses are highly correlated by forming two distinct subgroups and the existence of high diversity (24.9% among the subgroups; 75.1% among individuals of each subgroup) was observed. To practically utilize the diversity in the breeding program, a robust core set having an efficiency index of 0.82 which consists of 33 landraces were identified through data of molecular, blast phenotyping, and important agro-morphological traits. The association of eight novel SSR markers for important agronomic traits which includes leaf and neck blast resistance was determined using genome-wide association analysis. The current study focuses on identifying novel resources having field resistance to blast as well as markers which can be explored in rice improvement programs. It also entails the development of a core set which can aid in representing the entire diversity for efficiently harnessing its properties to broaden the gene pool of rice.
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Affiliation(s)
- Bangale Umakanth
- Biotechnology Division, ICAR-Indian Institute of Rice ResearchHyderabad, India
| | - Balija Vishalakshi
- Biotechnology Division, ICAR-Indian Institute of Rice ResearchHyderabad, India
| | - P. Sathish Kumar
- Biotechnology Division, ICAR-Indian Institute of Rice ResearchHyderabad, India
| | - S. J. S. Rama Devi
- Biotechnology Division, ICAR-Indian Institute of Rice ResearchHyderabad, India
| | - Vijay Pal Bhadana
- Plant Breeding, ICAR-Indian Institute of Rice ResearchHyderabad, India
| | - P. Senguttuvel
- Hybrid Rice Division, ICAR-Indian Institute of Rice ResearchHyderabad, India
| | - Sudhir Kumar
- Plant Breeding Section, ICAR Research Complex for NEH Region, Manipur CentreImphal, India
| | - Susheel Kumar Sharma
- Plant Pathology Section, ICAR Research Complex for NEH Region, Manipur CentreImphal, India
| | - Pawan Kumar Sharma
- Plant Pathology Section, ICAR Research Complex for NEH Region, Manipur CentreImphal, India
| | - M. S. Prasad
- Plant Pathology Division, ICAR-Indian Institute of Rice ResearchHyderabad, India
| | - Maganti S. Madhav
- Biotechnology Division, ICAR-Indian Institute of Rice ResearchHyderabad, India
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Dang X, Liu E, Liang Y, Liu Q, Breria CM, Hong D. QTL Detection and Elite Alleles Mining for Stigma Traits in Oryza sativa by Association Mapping. FRONTIERS IN PLANT SCIENCE 2016; 7:1188. [PMID: 27555858 PMCID: PMC4977947 DOI: 10.3389/fpls.2016.01188] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 07/22/2016] [Indexed: 05/20/2023]
Abstract
Stigma traits are very important for hybrid seed production in Oryza sativa, which is a self-pollinated crop; however, the genetic mechanism controlling the traits is poorly understood. In this study, we investigated the phenotypic data of 227 accessions across 2 years and assessed their genotypic variation with 249 simple sequence repeat (SSR) markers. By combining phenotypic and genotypic data, a genome-wide association (GWA) map was generated. Large phenotypic variations in stigma length (STL), stigma brush-shaped part length (SBPL) and stigma non-brush-shaped part length (SNBPL) were found. Significant positive correlations were identified among stigma traits. In total, 2072 alleles were detected among 227 accessions, with an average of 8.3 alleles per SSR locus. GWA mapping detected 6 quantitative trait loci (QTLs) for the STL, 2 QTLs for the SBPL and 7 QTLs for the SNBPL. Eleven, 5, and 12 elite alleles were found for the STL, SBPL, and SNBPL, respectively. Optimal cross designs were predicted for improving the target traits. The detected genetic variation in stigma traits and QTLs provides helpful information for cloning candidate STL genes and breeding rice cultivars with longer STLs in the future.
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Affiliation(s)
- Xiaojing Dang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University Nanjing, China
| | - Erbao Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University Nanjing, China
| | - Yinfeng Liang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University Nanjing, China
| | - Qiangming Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural UniversityNanjing, China; Rice Research Institute, Chongqing Academy of Agricultural SciencesChongqing, China
| | - Caleb M Breria
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University Nanjing, China
| | - Delin Hong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University Nanjing, China
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Tracing QTLs for Leaf Blast Resistance and Agronomic Performance of Finger Millet (Eleusine coracana (L.) Gaertn.) Genotypes through Association Mapping and in silico Comparative Genomics Analyses. PLoS One 2016; 11:e0159264. [PMID: 27415007 PMCID: PMC4944987 DOI: 10.1371/journal.pone.0159264] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 06/29/2016] [Indexed: 02/04/2023] Open
Abstract
Finger millet is one of the small millets with high nutritive value. This crop is vulnerable to blast disease caused by Pyricularia grisea, which occurs annually during rainy and winter seasons. Leaf blast occurs at early crop stage and is highly damaging. Mapping of resistance genes and other quantitative trait loci (QTLs) for agronomic performance can be of great use for improving finger millet genotypes. Evaluation of one hundred and twenty-eight finger millet genotypes in natural field conditions revealed that leaf blast caused severe setback on agronomic performance for susceptible genotypes, most significant traits being plant height and root length. Plant height was reduced under disease severity while root length was increased. Among the genotypes, IE4795 showed superior response in terms of both disease resistance and better agronomic performance. A total of seven unambiguous QTLs were found to be associated with various agronomic traits including leaf blast resistance by association mapping analysis. The markers, UGEP101 and UGEP95, were strongly associated with blast resistance. UGEP98 was associated with tiller number and UGEP9 was associated with root length and seed yield. Cross species validation of markers revealed that 12 candidate genes were associated with 8 QTLs in the genomes of grass species such as rice, foxtail millet, maize, Brachypodium stacei, B. distachyon, Panicum hallii and switchgrass. Several candidate genes were found proximal to orthologous sequences of the identified QTLs such as 1,4-β-glucanase for leaf blast resistance, cytokinin dehydrogenase (CKX) for tiller production, calmodulin (CaM) binding protein for seed yield and pectin methylesterase inhibitor (PMEI) for root growth and development. Most of these QTLs and their putatively associated candidate genes are reported for first time in finger millet. On validation, these novel QTLs may be utilized in future for marker assisted breeding for the development of fungal resistant and high yielding varieties of finger millet.
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Genetic characterization and population structure of Indian rice cultivars and wild genotypes using core set markers. 3 Biotech 2016; 6:95. [PMID: 28330165 PMCID: PMC4808523 DOI: 10.1007/s13205-016-0409-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 03/01/2016] [Indexed: 11/12/2022] Open
Abstract
Genetic diversity among 23 rice genotypes including wild species and cultivars of indica, japonica, aus and aromatic type was investigated using 165 genomewide core set microsatellite (SSR) markers. This genotypic characterization was undertaken to know the genetic similarity among the parental lines to be used in developing a set of chromosome segment substitution lines. In all, 253 alleles were identified using 77 polymorphic SSRs, and polymorphism information content ranged from 0.31 to 0.97 with a mean of 0.79. Cluster analysis grouped the genotypes into three clusters at a genetic similarity of 0.26–0.75. Wild accessions grouped together in cluster-I, indica cultivars formed cluster-II, and aromatic, japonica and aus types came under cluster-III. Principal component analysis also showed similar results. The genotypic data was analyzed using STRUCTURE, and genotypes were grouped into four populations. RM1018 on chromosome 4, RM8009 on chromosome 7, and RM273 on chromosome 12 amplified alleles specific to wild accessions. The information obtained from core set markers would help in selecting diverse parents including wild accessions and for tracking alleles in mapping or breeding populations.
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Prasanth VV, Basava KR, Babu MS, V.G.N. VT, Devi SJSR, Mangrauthia SK, Voleti SR, Sarla N. Field level evaluation of rice introgression lines for heat tolerance and validation of markers linked to spikelet fertility. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2016; 22:179-92. [PMID: 27436910 PMCID: PMC4938818 DOI: 10.1007/s12298-016-0350-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 03/13/2016] [Accepted: 03/28/2016] [Indexed: 05/14/2023]
Abstract
Rice lines derived from wild species and mutants can serve as a good resource for favorable alleles for heat tolerance. In all, 48 stable lines including 17 KMR3/O. rufipogon introgression lines (KMR3 ILs), 15 Swarna/O. nivara ILs (Swarna ILs) along with their parents, Nagina 22 (N22) and its 4 EMS induced mutants and 7 varieties were evaluated for heat tolerance under irrigated conditions under field in two seasons, wet season 2012 using poly cover house method and dry season 2013 using late sown method. Spikelet fertility (SF), yield per plant (YP) and heat susceptibility index (HSI) for these two traits were considered as criteria to assess heat tolerance compared to control. Four KMR3 ILs and eight Swarna ILs were identified as heat tolerant based on SF and YP and their HSIs in both wet and dry seasons. S-65 and S-70 showed low SF and high YP consistently in response to heat in both seasons. We provide evidence that SF alone may not be the best criterion to assess heat tolerance and including YP is important as lines with low SF but high YP and vice versa were identified under heat stress. Out of 49 SSR markers linked to spikelet fertility, 18 were validated for five traits. RM229 in wet season and RM430 and RM210 in dry season were significantly associated with both SF and its HSI under heat stress. RM430 was also significantly associated with both YP and its HSI in dry season. Thirty two candidate genes were identified close to nine markers associated with traits under heat stress.
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Affiliation(s)
- V. Vishnu Prasanth
- ICAR - Indian Institute of Rice Research (Directorate of Rice Research), Rajendranagar, Hyderabad, Telangana 500030 India
| | - Kumari Ramana Basava
- ICAR - Indian Institute of Rice Research (Directorate of Rice Research), Rajendranagar, Hyderabad, Telangana 500030 India
| | - M. Suchandranath Babu
- ICAR - Indian Institute of Rice Research (Directorate of Rice Research), Rajendranagar, Hyderabad, Telangana 500030 India
| | - Venkata Tripura V.G.N.
- ICAR - Indian Institute of Rice Research (Directorate of Rice Research), Rajendranagar, Hyderabad, Telangana 500030 India
| | - S. J. S. Rama Devi
- ICAR - Indian Institute of Rice Research (Directorate of Rice Research), Rajendranagar, Hyderabad, Telangana 500030 India
| | - S. K. Mangrauthia
- ICAR - Indian Institute of Rice Research (Directorate of Rice Research), Rajendranagar, Hyderabad, Telangana 500030 India
| | - S. R. Voleti
- ICAR - Indian Institute of Rice Research (Directorate of Rice Research), Rajendranagar, Hyderabad, Telangana 500030 India
| | - N. Sarla
- ICAR - Indian Institute of Rice Research (Directorate of Rice Research), Rajendranagar, Hyderabad, Telangana 500030 India
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Sehgal D, Singh R, Rajpal VR. Quantitative Trait Loci Mapping in Plants: Concepts and Approaches. MOLECULAR BREEDING FOR SUSTAINABLE CROP IMPROVEMENT 2016. [DOI: 10.1007/978-3-319-27090-6_2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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19
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Ganie SA, Borgohain MJ, Kritika K, Talukdar A, Pani DR, Mondal TK. Assessment of genetic diversity of Saltol QTL among the rice (Oryza sativa L.) genotypes. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2016; 22:107-14. [PMID: 27186024 PMCID: PMC4840144 DOI: 10.1007/s12298-016-0342-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 01/14/2016] [Accepted: 01/19/2016] [Indexed: 05/03/2023]
Abstract
Eight Saltol quantitative trait locus (QTL) linked simple sequence repeat (SSR) markers of rice (Oryza sativa L.) were used to study the polymorphism of this QTL in 142 diverse rice genotypes that comprised salt tolerant as well as sensitive genotypes. The SSR profiles of the eight markers generated 99 alleles including 20rare alleles and 16 null alleles. RM8094 showed the highest number (13) of alleles followed by RM3412 (12), RM562 (11), RM493 (9) and RM1287 (8) while as, RM10764 and RM10745 showed the lowest number (6) of alleles. Based on the highest number of alleles and PIC value (0.991), we identified RM8094 as suitable marker for discerning salt tolerant genotypes from the sensitive ones. Based upon the haplotype analysis using FL478 as a reference (salt tolerant genotypes containing Saltol QTL), we short listed 68 rice genotypes that may have at least one allele of FL478 haplotype. Further study may confirm that some of these genotypes might have Saltol QTL and can be used as alternative donors in salt tolerant rice breeding programmes.
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Affiliation(s)
- Showkat Ahmad Ganie
- />Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012 India
| | - Mrinmoi Jyoti Borgohain
- />Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012 India
| | - Kashyap Kritika
- />Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012 India
| | - Akshay Talukdar
- />Division of Genetics, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, 110012 India
| | | | - Tapan Kumar Mondal
- />Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012 India
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Dang X, Giang Tran Thi T, Mawuli Edzesi W, Liang L, Liu Q, Liu E, Wang Y, Qiang S, Liu L, Hong D. Population genetic structure of Oryza sativa in East and Southeast Asia and the discovery of elite alleles for grain traits. Sci Rep 2015; 5:11254. [PMID: 26059752 PMCID: PMC4462027 DOI: 10.1038/srep11254] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 05/05/2015] [Indexed: 01/16/2023] Open
Abstract
We investigated the nuclear simple sequence repeat (SSR) genotypes of 532 rice (Oryza sativa L.) accessions collected from East and Southeast Asia and detected abundant genetic diversity within the population. We identified 6 subpopulations and found a tendency towards directional evolution in O. sativa from low to high latitudes, with levels of linkage disequilibrium (LD) in the 6 subpopulations ranging from 10 to 30 cM. We then investigated the phenotypic data for grain length, grain width, grain thickness and 1,000-grain weight over 4 years. Using a genome-wide association analysis, we identified 17 marker-trait associations involving 14 SSR markers on 12 chromosome arms, and 8 of the 17 associations were novel. The elite alleles were mined based on the phenotypic effects of the detected quantitative trait loci (QTLs). These elite alleles could be used to improve target traits through optimal cross designs, with the expected results obtained by pyramiding or substituting the elite alleles per QTL (independent of possible epistatic effects). Together, these results provide an in-depth understanding of the genetic diversity pattern among rice-grain traits across a broad geographic scale, which has potential use in future research work, including studies related to germplasm conservation and molecular breeding by design.
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Affiliation(s)
- Xiaojing Dang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Thu Giang Tran Thi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- College of Agronomy, Hue University of Agriculture and Forestry, Hue University,102 Phung Hung Street, Hue City, Vietnam
| | - Wisdom Mawuli Edzesi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lijun Liang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qiangming Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Erbao Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yang Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Agricultural Resource and Environment, Heilongjiang University, Harbin, 150080, China
| | - Sheng Qiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Linglong Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Delin Hong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
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Garino C, Rinaldi M, de Paolis A, Travaglia F, Coïsson JD, Arlorio M. Improving the application of SSR polymorphism analysis coupled with Lab-on-a-chip® capillary electrophoresis to assess food authenticity: Italian pigmented rice as case study. Food Res Int 2014; 64:790-798. [DOI: 10.1016/j.foodres.2014.08.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 08/01/2014] [Accepted: 08/14/2014] [Indexed: 10/24/2022]
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22
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Dang X, Thi TGT, Dong G, Wang H, Edzesi WM, Hong D. Genetic diversity and association mapping of seed vigor in rice (Oryza sativa L.). PLANTA 2014; 239:1309-19. [PMID: 24668487 DOI: 10.1007/s00425-014-2060-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 03/06/2014] [Indexed: 05/20/2023]
Abstract
Seed vigor is closely related to direct seeding in rice (Oryza sativa L.). Previous quantitative trait locus (QTL) studies for seed vigor were mainly derived from bi-parental segregating populations and no report from natural populations. In this study, association mapping for seed vigor was performed on a selected sample of 540 rice cultivars (419 from China and 121 from Vietnam). Population structure was estimated on the basis of 262 simple sequence repeat (SSR) markers. Seed vigor was evaluated by root length (RL), shoot length (SL) and shoot dry weight in 2011 and 2012. Abundant phenotypic and genetic diversities were found in the studied population. The population was divided into seven subpopulations, and the levels of linkage disequilibrium (LD) ranged from 10 to 80 cM. We identified 27 marker-trait associations involving 18 SSR markers for three traits. According to phenotypic effects for alleles of the detected QTLs, elite alleles were mined. These elite alleles could be used to design parental combinations and the expected results would be obtained by pyramiding or substituting the elite alleles per QTL (apart from possible epistatic effects). Our results demonstrate that association mapping can complement and enhance previous QTL information for marker-assisted selection and breeding by design.
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Affiliation(s)
- Xiaojing Dang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
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Association studies of dormancy and cooking quality traits in direct-seeded indica rice. J Genet 2014; 93:3-12. [DOI: 10.1007/s12041-014-0319-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Dan Z, Liu P, Huang W, Zhou W, Yao G, Hu J, Zhu R, Lu B, Zhu Y. Balance between a higher degree of heterosis and increased reproductive isolation: a strategic design for breeding inter-subspecific hybrid rice. PLoS One 2014; 9:e93122. [PMID: 24667442 PMCID: PMC3965518 DOI: 10.1371/journal.pone.0093122] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 03/03/2014] [Indexed: 11/19/2022] Open
Abstract
The application of heterosis (hybrid vigor) has brought great success to plant breeding, particularly of hybrid rice, achieving significant yield increases. Attempts to explore the heterosis of inter-subspecific hybrids between indica and japonica rice, which result in even greater yield increases, have greatly increased in the past decades. However, because of the reduced seed setting rate in F1 hybrids as a result of increased reproductive isolation, the application of inter-subspecific hybrids in rice has slowed. Understanding the balance between heterosis and the reproductive isolation of inter-subspecific hybrids will facilitate the strategic design of inter-subspecific hybrid breeding. In this study, five indica and seven japonica rice varieties were chosen as the parental lines of a complete diallel mating design. Data from six group traits from all of the hybrids and inbred lines were collected. We found that the grain weight per plant, grain number per panicle, tiller per plant, thousand grain weight and plant height, which reflected increased heterosis, were associated with the genetic divergence index (GDI) of the parents. Meanwhile, owing to the reduced seed setting rate, which was also associated with the parents' GDI, the grain production of the hybrids was negatively affected. After analyzing the relationships between the GDI of indica-japonica parents and the grain weight per plant of the F1 hybrids, an ideal GDI value (0.37) for the two indica-japonica parents that could provide an optimal balance between the inter-subspecific heterosis and reproductive isolation was proposed. Our findings will help in the strategic design of an inter-subspecific hybrid rice breeding program by identifying the ideal indica and japonica parents for a hybrid combination to achieve hybrid rice with an optimal yield. This strategic design of an inter-subspecific hybrid rice breeding program will be time saving and cost effective.
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Affiliation(s)
- Zhiwu Dan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Engineering Research Center for Plant Biotechnology and Germplasm Utilization, Ministry of Education, Wuhan University, Wuhan, China
| | - Ping Liu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Wenchao Huang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Engineering Research Center for Plant Biotechnology and Germplasm Utilization, Ministry of Education, Wuhan University, Wuhan, China
| | - Wei Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Engineering Research Center for Plant Biotechnology and Germplasm Utilization, Ministry of Education, Wuhan University, Wuhan, China
| | - Guoxin Yao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Engineering Research Center for Plant Biotechnology and Germplasm Utilization, Ministry of Education, Wuhan University, Wuhan, China
| | - Jun Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Engineering Research Center for Plant Biotechnology and Germplasm Utilization, Ministry of Education, Wuhan University, Wuhan, China
| | - Renshan Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Engineering Research Center for Plant Biotechnology and Germplasm Utilization, Ministry of Education, Wuhan University, Wuhan, China
| | - Baorong Lu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Yingguo Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Engineering Research Center for Plant Biotechnology and Germplasm Utilization, Ministry of Education, Wuhan University, Wuhan, China
- * E-mail:
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Cai C, Ye W, Zhang T, Guo W. Association analysis of fiber quality traits and exploration of elite alleles in Upland cotton cultivars/accessions (Gossypium hirsutum L.). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:51-62. [PMID: 24428209 DOI: 10.1111/jipb.12124] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Accepted: 10/28/2013] [Indexed: 05/02/2023]
Abstract
Exploring the elite alleles and germplasm accessions related to fiber quality traits will accelerate the breeding of cotton for fiber quality improvement. In this study, 99 Gossypium hirsutum L. accessions with diverse origins were used to perform association analysis of fiber quality traits using 97 polymorphic microsatellite marker primer pairs. A total of 107 significant marker-trait associations were detected for three fiber quality traits under three different environments, with 70 detected in two or three environments and 37 detected in only one environment. Among the 70 significant marker-trait associations, 52.86% were reported previously, implying that these are stable loci for target traits. Furthermore, we detected a large number of elite alleles associated simultaneously with two or three traits. These elite alleles were mainly from accessions collected in China, introduced to China from the United States, or rare alleles with a frequency of less than 5%. No one cultivar contained more than half of the elite alleles, but 10 accessions were collected from China and the two introduced from the United States did contain more than half of these alleles. Therefore, there is great potential for mining elite alleles from germplasm accessions for use in fiber quality improvement in modern cotton breeding.
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Affiliation(s)
- Caiping Cai
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
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Assessment of genetic diversity in Indian rice germplasm (Oryza sativa L.): use of random versus trait-linked microsatellite markers. J Genet 2013; 92:545-57. [DOI: 10.1007/s12041-013-0312-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Swamy BPM, Kumar A. Genomics-based precision breeding approaches to improve drought tolerance in rice. Biotechnol Adv 2013; 31:1308-18. [PMID: 23702083 DOI: 10.1016/j.biotechadv.2013.05.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 04/23/2013] [Accepted: 05/08/2013] [Indexed: 12/15/2022]
Abstract
Rice (Oryza sativa L.), the major staple food crop of the world, faces a severe threat from widespread drought. The development of drought-tolerant rice varieties is considered a feasible option to counteract drought stress. The screening of rice germplasm under drought and its characterization at the morphological, genetic, and molecular levels revealed the existence of genetic variation for drought tolerance within the rice gene pool. The improvements made in managed drought screening and selection for grain yield under drought have significantly contributed to progress in drought breeding programs. The availability of rice genome sequence information, genome-wide molecular markers, and low-cost genotyping platforms now makes it possible to routinely apply marker-assisted breeding approaches to improve grain yield under drought. Grain yield QTLs with a large and consistent effect under drought have been indentified and successfully pyramided in popular rice mega-varieties. Various rice functional genomics resources, databases, tools, and recent advances in "-omics" are facilitating the characterization of genes and pathways involved in drought tolerance, providing the basis for candidate gene identification and allele mining. The transgenic approach is successful in generating drought tolerance in rice under controlled conditions, but field-level testing is necessary. Genomics-assisted drought breeding approaches hold great promise, but a well-planned integration with standardized phenotyping is highly essential to exploit their full potential.
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Roychowdhury R, Karmakar J, Karmakar J, Kumar Adak M, Dey N. Physio-Biochemical and Microsatellite Based Profiling of Lowland Rice (<i>Oryza sativa</i> L.) Landraces for Osmotic Stress Tolerance. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/ajps.2013.412a3007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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