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Zhang Y, He Q, Zhou X, Zheng S, Wang Y, Li P, Wang Y. Genetic diversity and population structure of 93 rice cultivars (lines) (Oryza sativa Xian group) in Qinba in China by 3 types of genetic markers. BMC Genomics 2022; 23:550. [PMID: 35918653 PMCID: PMC9347111 DOI: 10.1186/s12864-022-08707-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 06/20/2022] [Indexed: 12/02/2022] Open
Abstract
Background The Qinba region is the transition region between Indica and Japonica varieties in China. It has a long history of Indica rice planting of more than 7000 years and is also a planting area for fine-quality Indica rice. The aims of this study are to explore different genetic markers applied to the analysis population structure, genetic diversity, selection and optimization of molecular markers of Indica rice, thus providing more information for the protection and utilization on germplasm resources of Indica rice. Methods Fifteen phenotypic traits, a core set of 48 SSR markers which originated protocol for identification of rice varieties-SSR marker method in agricultural industry standard of the People's Republic of China (Ministry of Agriculture of the PRC, NY/T1433-2014, Protocol for identification of rice varieties-SSR marker method, 2014), and SNPs data obtained by genotyping-by-sequencing (GBS, NlaIII and MseI digestion, referred to as SNPs-NlaIII and SNPs-MseI, respectively) for this panel of 93 samples using the Illumina HiSeq2000 sequencing platform, were employed to explore the genetic diversity and population structure of 93 samples. Results The average of coefficient of variation (CV) and diversity index (He) were 29.72% and 1.83 ranging from 3.07% to 137.43%, and from 1.45 to 2.03, respectively. The correlation coefficient between 15 phenotypic traits ranged from 0.984 to -0.604. The first four PCs accounted for 70.693% phenotypic variation based on phenotypic analysis. A total of 379 alleles were obtained using SSR markers, encompassing an average of 8.0 alleles per primer. Polymorphic bands (PPB) and polymorphism information content (PIC) was 88.65% and 0.77, respectively. The Mantel test showed that the correlation between the genetic distance matrix based on SNPs-NlaIII and SNPs-MseI was the largest (R2=0.88), and that based on 15 phenotypic traits and SSR was the smallest (R2=0.09). The 93 samples could be clustered into two subgroups by 3 types of genetic markers. Molecular variance analysis revealed that the genetic variation was 2% among populations and 98% within populations (the Nm was 0.16), Tajima’s D value was 1.66, the FST between the two populations was 0.61 based on 72,824 SNPs. Conclusions The population genetic variation explained by SNPs was larger than that explained by SSRs. The gene flow of 93 samples used in this study was larger than that of naturally self-pollinated crops, which may be caused by long-term breeding selection of Indica rice in the Qinba region. The genetic structure of the 93 samples was simple and lacked rare alleles.
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Affiliation(s)
- Yu Zhang
- Shaanxi University of Technology, Hanzhong, 72300, Shaanxi, China. .,Shaanxi Province Key Laboratory of Bio-resources, Hanzhong, 72300, Shaanxi, China. .,QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Hanzhong, 72300, Shaanxi, China. .,Qinba State Key Laboratory of biological resources and ecological environment, Hanzhong, 72300, Shaanxi, China.
| | - Qiaoqiao He
- Shaanxi University of Technology, Hanzhong, 72300, Shaanxi, China.,Shaanxi Province Key Laboratory of Bio-resources, Hanzhong, 72300, Shaanxi, China.,QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Hanzhong, 72300, Shaanxi, China.,Qinba State Key Laboratory of biological resources and ecological environment, Hanzhong, 72300, Shaanxi, China
| | - Xixi Zhou
- Shaanxi University of Technology, Hanzhong, 72300, Shaanxi, China.,Shaanxi Province Key Laboratory of Bio-resources, Hanzhong, 72300, Shaanxi, China.,QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Hanzhong, 72300, Shaanxi, China.,Qinba State Key Laboratory of biological resources and ecological environment, Hanzhong, 72300, Shaanxi, China
| | - Shimao Zheng
- Shaanxi University of Technology, Hanzhong, 72300, Shaanxi, China.,Shaanxi Province Key Laboratory of Bio-resources, Hanzhong, 72300, Shaanxi, China.,QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Hanzhong, 72300, Shaanxi, China.,Qinba State Key Laboratory of biological resources and ecological environment, Hanzhong, 72300, Shaanxi, China
| | - Yewen Wang
- Shaanxi Rice Research Institute, Hanzhong, 723000, Shaanxi, China
| | - Peijiang Li
- Shaanxi Rice Research Institute, Hanzhong, 723000, Shaanxi, China
| | - Yuexing Wang
- College of Agronomy, Xinjiang Agricultural University, Urumqi, 830052, China
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Kaliswamy P, Vellingiri S, Nathan B, Selvaraj S. Microsatellite analysis in the genome of Acanthaceae: An in silico approach. Pharmacogn Mag 2015; 11:152-6. [PMID: 25709226 PMCID: PMC4329617 DOI: 10.4103/0973-1296.149731] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 05/19/2014] [Accepted: 01/21/2015] [Indexed: 11/07/2022] Open
Abstract
Background: Acanthaceae is one of the advanced and specialized families with conventionally used medicinal plants. Simple sequence repeats (SSRs) play a major role as molecular markers for genome analysis and plant breeding. The microsatellites existing in the complete genome sequences would help to attain a direct role in the genome organization, recombination, gene regulation, quantitative genetic variation, and evolution of genes. Objective: The current study reports the frequency of microsatellites and appropriate markers for the Acanthaceae family genome sequences. Materials and Methods: The whole nucleotide sequences of Acanthaceae species were obtained from National Center for Biotechnology Information database and screened for the presence of SSRs. SSR Locator tool was used to predict the microsatellites and inbuilt Primer3 module was used for primer designing. Results: Totally 110 repeats from 108 sequences of Acanthaceae family plant genomes were identified, and the occurrence of dinucleotide repeats was found to be abundant in the genome sequences. The essential amino acid isoleucine was found rich in all the sequences. We also designed the SSR-based primers/markers for 59 sequences of this family that contains microsatellite repeats in their genome. Conclusion: The identified microsatellites and primers might be useful for breeding and genetic studies of plants that belong to Acanthaceae family in the future.
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Affiliation(s)
- Priyadharsini Kaliswamy
- Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Srividhya Vellingiri
- Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Bharathi Nathan
- Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Saravanakumar Selvaraj
- Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
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Kaur S, Panesar PS, Bera MB, Kaur V. Simple Sequence Repeat Markers in Genetic Divergence and Marker-Assisted Selection of Rice Cultivars: A Review. Crit Rev Food Sci Nutr 2014; 55:41-9. [DOI: 10.1080/10408398.2011.646363] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Chin JH, Chu SH, Jiang W, Cho YI, Basyirin R, Brar DS, Koh HJ. Identification of QTLs for hybrid fertility in inter-subspecific crosses of rice (Oryza sativa L.). Genes Genomics 2011. [DOI: 10.1007/s13258-010-0100-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Han B, Xue Y, Li J, Deng XW, Zhang Q. Rice functional genomics research in China. Philos Trans R Soc Lond B Biol Sci 2007; 362:1009-21. [PMID: 17347106 PMCID: PMC2435567 DOI: 10.1098/rstb.2007.2030] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Rice functional genomics is a scientific approach that seeks to identify and define the function of rice genes, and uncover when and how genes work together to produce phenotypic traits. Rapid progress in rice genome sequencing has facilitated research in rice functional genomics in China. The Ministry of Science and Technology of China has funded two major rice functional genomics research programmes for building up the infrastructures of the functional genomics study such as developing rice functional genomics tools and resources. The programmes were also aimed at cloning and functional analyses of a number of genes controlling important agronomic traits from rice. National and international collaborations on rice functional genomics study are accelerating rice gene discovery and application.
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Affiliation(s)
- Bin Han
- National Center for Gene Research & Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, People's Republic of China.
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Mei H, Feng F, Lu B, Wen W, Paterson AH, Cai X, Chen L, Feltus FA, Xu X, Wu J, Yu X, Chen H, Li Y, Luo L. Experimental validation of inter-subspecific genetic diversity in rice represented by the differences between the DNA sequences of ‘Nipponbare’ and ‘93-11’. ACTA ACUST UNITED AC 2007. [DOI: 10.1007/s11434-007-0198-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Zhang Z, Deng Y, Tan J, Hu S, Yu J, Xue Q. A genome-wide microsatellite polymorphism database for the indica and japonica rice. DNA Res 2007; 14:37-45. [PMID: 17452422 PMCID: PMC2779893 DOI: 10.1093/dnares/dsm005] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Microsatellite (MS) polymorphism is an important source of genetic diversity, providing support for map-based cloning and molecular breeding. We have developed a new database that contains 52 845 polymorphic MS loci between indica and japonica, composed of ample Class II MS markers, and integrated 18 828 MS loci from IRGSP and genetic markers from RGP. Based on genetic marker positions on the rice genome (http://rise.genomics.org.cn/rice2/index.jsp ), we determined the approximate genetic distances of these MS loci and validated 100 randomly selected markers experimentally with 90% success rate. In addition, we recorded polymorphic MS positions in indica cv. 9311 that is the most important paternal parent of the two-line hybrid rice in China. Our database will undoubtedly facilitate the application of MS markers in genetic researches and marker-assisted breeding. The data set is freely available from www.wigs.zju.edu.cn/achievment/polySSR.
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Affiliation(s)
- Zhonghua Zhang
- James D. Watson Institute of Genome Science, Zhejiang University, Hangzhou 310008, China
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yajun Deng
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China
| | - Jun Tan
- Institute of Bioinformation, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Songnian Hu
- James D. Watson Institute of Genome Science, Zhejiang University, Hangzhou 310008, China
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China
| | - Jun Yu
- James D. Watson Institute of Genome Science, Zhejiang University, Hangzhou 310008, China
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing 101300, China
| | - Qingzhong Xue
- James D. Watson Institute of Genome Science, Zhejiang University, Hangzhou 310008, China
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310029, China
- To whom correspondence should be addressed. Tel. +86-571-86971611. Fax. +86-571-86971117, E-mail:
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Yang S, Jiang K, Araki H, Ding J, Yang YH, Tian D. A molecular isolation mechanism associated with high intra-specific diversity in rice. Gene 2007; 394:87-95. [PMID: 17379459 DOI: 10.1016/j.gene.2007.02.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2006] [Revised: 02/10/2007] [Accepted: 02/12/2007] [Indexed: 11/21/2022]
Abstract
High levels of inter-specific diversity are expected due to genetic isolation, the reproductive or geographical barriers, which lead to the accumulation of nucleotide variation. However, high levels of genetic variation are repeatedly observed even within species, notably at loci of the human major histocompatability complex and of plant resistance genes. Are molecular isolations responsible for the high intra-specific variation? To address this issue, we performed a genome-wide survey of the relationship between the possible factors that could cause genetic isolation, and the level of polymorphism, based on two rice genome comparisons. Here, we show that the levels of polymorphism in rice genes are positively correlated with the proportions of non-alignable flanking sequences, and that the correlation is observed even in single-copy genes. The physical locations of the genes were also investigated, and a strong association between the asymmetric architecture of genomes and the levels of polymorphism was revealed. These results suggest that the flank heterogeneity and the asymmetric architecture between genomes serve as isolation mechanisms at the molecular level that result in accumulation of higher genetic variation. This mechanism is of fundamental importance to understand natural genetic variation within species.
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Affiliation(s)
- Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, Nanjing 210093, China
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Xie X, Song MH, Jin F, Ahn SN, Suh JP, Hwang HG, McCouch SR. Fine mapping of a grain weight quantitative trait locus on rice chromosome 8 using near-isogenic lines derived from a cross between Oryza sativa and Oryza rufipogon. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:885-94. [PMID: 16850315 DOI: 10.1007/s00122-006-0348-5] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2006] [Accepted: 06/09/2006] [Indexed: 05/05/2023]
Abstract
A quantitative trait locus (QTL) for grain weight (GW) was detected near SSR marker RM210 on chromosome 8 in backcross populations derived from a cross between the Korean japonica cultivar Hwaseongbyeo and Oryza rufipogon (IRGC 105491). The O. rufipogon allele increased GW in the Hwaseongbyeo background despite the fact that O. rufipogon was the small-seeded parent. Using sister BC(3)F(3) near-isogenic lines (NILs), gw8.1 was validated and mapped to a 6.1 cM region in the interval between RM42 and RM210 (P < or = 0.0001). Substitution mapping with eight BC(3)F(4) sub-NILs further narrowed the interval containing gw8.1 to about 306.4 kb between markers RM23201.CNR151 and RM30000.CNR99. A yield trial using homozygous BC(3)F(4) sister sub-NILs and the Hwaseongbyeo recurrent parent indicated that the NIL carrying an O. rufipogon chromosome segment across the entire gw8.1 target region out-yielded its sister NIL (containing Hwaseongbyeo chromosome in the RM42-RM210 interval) by 9% (P=0.029). The higher-yielding NIL produced 19.3% more grain than the Hwaseongbyeo recurrent parent (P=0.018). Analysis of a BC(3)F(4) NIL indicated that the variation for GW is associated with variation in grain shape, specifically grain length. The locus, gw8.1 is of particular interest because of its independence from undesirable height and grain quality traits. SSR markers tightly linked to the GW QTL will facilitate cloning of the gene underlying this QTL as well as marker-assisted selection for variation in GW in an applied breeding program.
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Affiliation(s)
- Xiaobo Xie
- Department of Agronomy, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 305-764, Korea
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Li L, Wang X, Stolc V, Li X, Zhang D, Su N, Tongprasit W, Li S, Cheng Z, Wang J, Deng XW. Genome-wide transcription analyses in rice using tiling microarrays. Nat Genet 2005; 38:124-9. [PMID: 16369532 DOI: 10.1038/ng1704] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2005] [Accepted: 10/14/2005] [Indexed: 11/09/2022]
Abstract
Sequencing and computational annotation revealed several features, including high gene numbers, unusual composition of the predicted genes and a large number of genes lacking homology to known genes, that distinguish the rice (Oryza sativa) genome from that of other fully sequenced model species. We report here a full-genome transcription analysis of the indica rice subspecies using high-density oligonucleotide tiling microarrays. Our results provided expression data support for the existence of 35,970 (81.9%) annotated gene models and identified 5,464 unique transcribed intergenic regions that share similar compositional properties with the annotated exons and have significant homology to other plant proteins. Elucidating and mapping of all transcribed regions revealed an association between global transcription and cytological chromosome features, and an overall similarity of transcriptional activity between duplicated segments of the genome. Collectively, our results provide the first whole-genome transcription map useful for further understanding the rice genome.
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Affiliation(s)
- Lei Li
- National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing 102206, China
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