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Hameed K, Habib M, Awan FS, Sadia B, Hussain S, Qamar ZU, Alzahrani HAS. Detection of genetic divergence among putative ethyl methane sulfonate mutants of super basmati using microsatellite markers. Mol Biol Rep 2023; 50:8799-8808. [PMID: 37658932 DOI: 10.1007/s11033-023-08425-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 04/04/2023] [Indexed: 09/05/2023]
Abstract
BACKGROUND Seeds of super basmati were mutagenized with different ethyl methane sulphonate (EMS) doses for creating genetic variability. METHODS AND RESULTS A total of 48 randomly selected putative EMS mutants of super basmati were analyzed to dissect the genetic diversity by using 25 SSR primers located on twelve chromosomes of rice. SSRs analysis revealed that wide-range of genetic diversity is present among mutants of super basmati. A sum of 91 alleles were identified, out of these, 82 alleles were polymorphic and the rest of nine alleles were monomorphic in nature. The range of allele number was 2-10 with mean of 3.64 alleles/locus. The value of polymorphic information content was range between 0.039 (RM5) and 0.878 (RM44) with mean of 0.439 for each locus. A number of polymorphic markers showed unique bands of various sizes ranges from 75 to 1000 bp, during genetic dissection of mutant population. Dendrogram divided whole mutant population into four major groups. Phylogenic analyses revealed that 40-96%genetic similarity is present among individuals of mutant population. CONCLUSION It is concluded that EMS induced genetic variability and SSRs markers (RM44, RM154, RM1, RM252, RM334, RM487, RM110 and RM257) could be handy for the selection of rice mutants as parents for functional genomic and molecular breeding program.
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Affiliation(s)
- Kiran Hameed
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Jail Road, Faisalabad, 38040, Pakistan
| | - Madiha Habib
- National Institute for Genomics and Advanced Biotechnology, National Agriculture Research Centre, Park Road, Islamabad, 45500, Pakistan
| | - Faisal Saeed Awan
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Jail Road, Faisalabad, 38040, Pakistan.
| | - Bushra Sadia
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Jail Road, Faisalabad, 38040, Pakistan
| | - Shabbir Hussain
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Jail Road, Faisalabad, 38040, Pakistan
| | - Zia-Ul- Qamar
- Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, Pakistan
| | - Hind A S Alzahrani
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University, Dammam, 34212, Saudi Arabia
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Zhang P, Zhong K, Tong H, Shahid MQ, Li J. Association Mapping for Aluminum Tolerance in a Core Collection of Rice Landraces. FRONTIERS IN PLANT SCIENCE 2016; 7:1415. [PMID: 27757115 PMCID: PMC5047912 DOI: 10.3389/fpls.2016.01415] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 09/05/2016] [Indexed: 05/27/2023]
Abstract
Trivalent aluminum (Al3+) has drastic effect on the rice production in acidic soils. Elite genes for aluminum (Al) tolerance might exist in rice landraces. Therefore, the purpose of this research is to mine the elite genes within rice landraces. Association mapping for Al tolerance traits [i.e., relative root elongation (RRE)] was performed by using a core collection of 150 accessions of rice landraces (i.e., Ting's rice core collection). Our results showed that the Ting's rice core collection possessed a wide-range of phenotypic variation for Al tolerance, and the index of Al tolerance (RRE) was ranged from 0.22 to 0.89. Moreover, the groups with different origins and compositions of indica and japonica rice showed different degrees of tolerance to varying levels of Al. These rice landraces were further screened with 274 simple sequence repeat markers, and association mapping was performed using a mixed linear model approach. The mapping results showed that a total of 23 significant (P < 0.05) trait-marker associations were detected for Al tolerance. Of these, three associations (13%) were identical to the quantitative trait loci reported previously, and other 20 associations were reported for the first time in this study. The proportion of phenotypic variance (R2) explained by 23 significant associations ranged from 5.03 to 20.03% for Al tolerance. We detected several elite alleles for Al tolerance based on multiple comparisons of allelic effects, which could be used to develop Al tolerant rice cultivars through marker-assisted breeding.
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Affiliation(s)
- Peng Zhang
- State Key Laboratory of Rice Biology, China National Rice Research InstituteHangzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural UniversityGuangzhou, China
| | - Kaizhen Zhong
- State Key Laboratory of Rice Biology, China National Rice Research InstituteHangzhou, China
| | - Hanhua Tong
- State Key Laboratory of Rice Biology, China National Rice Research InstituteHangzhou, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural UniversityGuangzhou, China
| | - Jinquan Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural UniversityGuangzhou, China
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
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Zhang P, Li J, Li X, Liu X, Zhao X, Lu Y. Population structure and genetic diversity in a rice core collection (Oryza sativa L.) investigated with SSR markers. PLoS One 2011; 6:e27565. [PMID: 22164211 PMCID: PMC3229487 DOI: 10.1371/journal.pone.0027565] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Accepted: 10/19/2011] [Indexed: 11/19/2022] Open
Abstract
The assessment of genetic diversity and population structure of a core collection would benefit to make use of these germplasm as well as applying them in association mapping. The objective of this study were to (1) examine the population structure of a rice core collection; (2) investigate the genetic diversity within and among subgroups of the rice core collection; (3) identify the extent of linkage disequilibrium (LD) of the rice core collection. A rice core collection consisting of 150 varieties which was established from 2260 varieties of Ting's collection of rice germplasm were genotyped with 274 SSR markers and used in this study. Two distinct subgroups (i.e. SG 1 and SG 2) were detected within the entire population by different statistical methods, which is in accordance with the differentiation of indica and japonica rice. MCLUST analysis might be an alternative method to STRUCTURE for population structure analysis. A percentage of 26% of the total markers could detect the population structure as the whole SSR marker set did with similar precision. Gene diversity and MRD between the two subspecies varied considerably across the genome, which might be used to identify candidate genes for the traits under domestication and artificial selection of indica and japonica rice. The percentage of SSR loci pairs in significant (P<0.05) LD is 46.8% in the entire population and the ratio of linked to unlinked loci pairs in LD is 1.06. Across the entire population as well as the subgroups and sub-subgroups, LD decays with genetic distance, indicating that linkage is one main cause of LD. The results of this study would provide valuable information for association mapping using the rice core collection in future.
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Affiliation(s)
- Peng Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Jinquan Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- * E-mail: (JL); (YL)
| | - Xiaoling Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Xiangdong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Xingjuan Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Yonggen Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- * E-mail: (JL); (YL)
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Tan Y, Li S, Xie H, Duan S, Wang T, Zhu Y. Genetical and molecular analysis reveals a cooperating relationship between cytoplasmic male sterility- and fertility restoration-related genes in Oryza species. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:9-19. [PMID: 20714705 DOI: 10.1007/s00122-010-1418-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Accepted: 07/17/2010] [Indexed: 05/08/2023]
Abstract
Although the characterization of genes associated with cytoplasmic male sterility (CMS) and fertility restoration (Rf) has been well documented, the evolutionary relationship between nuclear Rf and CMS factors in mitochondria in Oryza species is still less understood. Here, 41 accessions from 7 Oryza species with AA genome were employed for analyzing the evolutionary relationships between the CMS factors and Rf candidates on chromosome 10. The phylogenetic tree based on restriction fragment length polymorphism patterns of CMS-associated mitochondrial genes showed that these 41 Oryza accessions fell into 3 distinct groups. Another phylogenetic tree based on PCR profiles of the nuclear Rf candidates on chromosome 10 was also established, and three groups were distinctively grouped. The accessions in each subgroup/group of the two phylogenetic trees are well parallel to each other. Furthermore, the 41 investigated accessions were test-crossed with Honglian (gametophytic type) and Wild-abortive (sporophytic type) CMS, and 5 groups were classified according to their restoring ability. The accessions in the same subgroup of the two phylogenetic trees shared similar fertility restoring pattern. Therefore, we conclude that the CMS-associated mitotypes are compatible to the Rf candidate-related nucleotypes, CMS and Rf have a parallel evolutionary relation in the Oryza species.
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Affiliation(s)
- YanPing Tan
- Key Laboratory of MOE for Plant Developmental Biology, College of Life Science, Wuhan University, Wuhan, 430072, China
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Wei C, Wang L, Yang Y, Chen Z, Shahid MQ, Li J, Liu X, Lu Y. Identification of an S 5 n allele in Oryza rufipogon Griff. and its effect on embryo sac fertility. ACTA ACUST UNITED AC 2010. [DOI: 10.1007/s11434-010-0154-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Fukuoka S, Namai H, Okuno K. Geographical variation of the genes controlling hybrid breakdown and genetic differentiation of the chromosomal regions harboring these genes in Asian cultivated rice, Oryza sativa L. Genes Genet Syst 1998. [DOI: 10.1266/ggs.73.211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Shuichi Fukuoka
- Department of Genetic Resources I, National Institute of Agrobiological Resources
- Institute of Agriculture and Forestry, University of Tsukuba
| | - Hyoji Namai
- Institute of Agriculture and Forestry, University of Tsukuba
| | - Kazutoshi Okuno
- Department of Genetic Resources I, National Institute of Agrobiological Resources
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Xie JH, Gao MW, Lu J, Zhuang JY, Lin HX, Qian HR, Zheng KL. Identifying different types of de-differentiated microspores from indica-japonica F(1) hybrids with subspecies-differentiating RFLP probes in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1997; 94:34-8. [PMID: 19352742 DOI: 10.1007/s001220050378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/1996] [Accepted: 06/14/1996] [Indexed: 05/27/2023]
Abstract
The indica, japonica and intermediary types of de-differentiated microspores from indica-japonica F(1) hybrids were identified with 11 subspecies-differentiating RELP probes in rice (Oryza sativa L.). The results showed that the distribution of indica, japonica and intermediary types of de-differentiated microspores could be easily detected in a simple and quick way using the RFLP method. Moreover, the microspores from the same F(1) hybrid but inoculated onto different media, or microspores from different F(1) hybrids when inoculated onto the same medium, often displayed distinctive distribution curves of de-differentiated microspores types, indicating that the media employed in this experiment had high selectivity for the de-differentiation of certain types of microspores. The application of the RELP method to de-differentiated microspore identification is of great theoretical and practical significance in rice doubled-haploid breeding.
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Affiliation(s)
- J H Xie
- Institute of Nuclear Agriculture Sciences, Zhejiang Agricultural University, 310029, Hangzhou, China
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Qian HR, Zhuang JY, Lin HX, Lu J, Zheng KL. Identification of a set of RFLP probes for subspecies differentiation in Oryza sativa L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1995; 90:878-884. [PMID: 24172933 DOI: 10.1007/bf00222026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/1994] [Accepted: 09/08/1994] [Indexed: 06/02/2023]
Abstract
Sixty-eight indica-japonica tester-differentiating RFLP probes were tested in seven indica and seven japonica varieties of rice (Oryza sativa L.) with four enzyme digestions (EcoRI, EcoRV, HindIII and DraI). Twenty-one DNA clones were isolated as indica-japonica subspecies-differentiating probes. A set of 13 probes was established as core probes for subspecies differentiation and a pooled blotting analysis was carried out to facilitate the application of RFLP in rice genetics and breeding practice. A dendrogram of 12 wide-compatibility varieties was constructed based on RFLPs detected by 13 core probes with single enzyme digestions. It was speculated that most RFLPs of indica-japonica differentiating probes were generated by insertions/deletions, which may be of great significance for the origin and differentiation of subspecies in Oryza sativa L.
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Affiliation(s)
- H R Qian
- Biotechnology Department, China National Rice Research Institute, 310006, Hangzhou, P. R. China
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