Skip to main content Accessibility help
×
Home

Genetic diversity and structure of indica rice varieties from two heterotic pools of southern China and IRRI

Published online by Cambridge University Press:  14 October 2012

Fangming Xie
Affiliation:
International Rice Research Institute, Metro Manila, DAPO Box 7777, Philippines
Longbiao Guo
Affiliation:
China National Rice Research Institute, Hangzhou310006, People' Republic of China
Guangjun Ren
Affiliation:
Sichuan Academy of Agricultural Sciences, Chengdu610066, People' Republic of China
Peisong Hu
Affiliation:
China National Rice Research Institute, Hangzhou310006, People' Republic of China
Feng Wang
Affiliation:
Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou510640, People' Republic of China
Jianlong Xu
Affiliation:
Crop Science Institute, Chinese Academy of Agricultural Sciences, Beijing100081, People' Republic of China
Xinqi Li
Affiliation:
China National Hybrid Rice Research and Development Center, Changsha410125, People' Republic of China
Fulin Qiu
Affiliation:
International Rice Research Institute, Metro Manila, DAPO Box 7777, Philippines
Madonna Angelita dela Paz
Affiliation:
International Rice Research Institute, Metro Manila, DAPO Box 7777, Philippines
Corresponding
E-mail address:

Abstract

Investigation of genetic diversity and the relationships among varieties and breeding lines is of great importance to facilitate parental selection in the development of inbred and hybrid rice varieties and in the construction of heterotic groups. The technology of single nucleotide polymorphism (SNP) is being advanced for the assessment of population diversity and genetic structures. We characterized 215 widely cultivated indica rice varieties developed in southern China and at the International Rice Research Institute (IRRI) using IRRI-developed SNP oligonucleotide pooled assay (OPA) to provide grouping information of rice mega-varieties for further heterotic pool study. The results revealed that the Chinese varieties were more divergent than the IRRI varieties. Two major subpopulations were clustered for the varieties using a model-based grouping method. The IRRI varieties were closely grouped and separated clearly from the majority of the Chinese varieties. The Chinese varieties were subclustered into three subgroups, but there was no clear evidence to separate the Chinese varieties into subgroups geographically, indicating a great degree of genetic integration of alleles and shared ancestries among those high-yielding modern varieties.

Type
Research Article
Copyright
Copyright © NIAB 2012

Access options

Get access to the full version of this content by using one of the access options below.

References

Boppenmaier, J, Melchinger, AE, Seitz, G, Geiger, HH and Herrmann, RG (1993) Genetic diversity for RFLPs in European maize inbreds III. Performance of crosses within versus between heterotic groups for grain traits. Plant Breeding 111: 217226.CrossRefGoogle Scholar
Cavalli-Sforza, LL and Edwards, AWF (1967) Phylogenetic analysis: models and estimation procedures. American Journal of Human Genetics 19: 233257.Google ScholarPubMed
Chen, HD, He, H, Zou, YJ, Chen, W, Yu, RB, Liu, X, Yang, Y, Gao, YM, Xu, JL, Fan, LM, Li, Y, Li, ZK and Deng, XW (2011) Development and application of a set of breeder-friendly SNP markers for genetic analyses and molecular breeding of rice (Oryza sativa L.). Theoretical and Applied Genetics 123: 869879.CrossRefGoogle Scholar
Collard, BCY, Vera Cruz, CM, McNally, KL, Virk, PS and Mackill, DJ (2008) Rice molecular breeding laboratories in the genomics era: current status and future considerations. International Journal of Plant Genomics, Article ID 524847: 25.Google ScholarPubMed
Dudley, JW, Saghai Maroof, MA and Rufener, GK (1991) Molecular markers and grouping of parents in maize breeding programs. Crop Science 31: 718723.CrossRefGoogle Scholar
Evanno, G, Regnaut, S and Goudet, J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14: 26112620.CrossRefGoogle ScholarPubMed
Falush, D, Stephens, M and Pritchard, JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 15671587.Google ScholarPubMed
Lee, M, Godshalk, EB, Lamkey, KR and Woodman, WW (1989) Association of restriction fragment length polymorphisms among maize inbreds with agronomic performance of their crosses. Crop Science 94: 10231030.Google Scholar
Liu, K and Muse, SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21: 21282129.CrossRefGoogle ScholarPubMed
Lu, ZM and Xu, BQ (2010) On significance of heterotic group theory in hybrid rice breeding. Rice Science 17: 9498.CrossRefGoogle Scholar
McCouch, SR, Zhao, K, Wright, M, Tung, CW, Ebana, K, Thomson, M, Reynolds, A, Wang, D, DeClerck, G, Ali, ML, McClung, A, Eizenga, G and Bustamante, C (2010) Development of genome-wide SNP assays for rice. Breeding Science 60: 524535.CrossRefGoogle Scholar
McNally, KL, Childs, KL, Bohnert, R, Davidson, RM, Zhao, K, Ulat, VJ, Zeller, G, Clark, RM, Hoen, DR, Bureau, TE, Stokowski, R, Ballinger, DG, Frazer, KA, Cox, DR, Padhukasahasram, B, Bustamante, CD, Weigel, D, Mackill, DJ, Bruskiewich, RM, Ratsch, G, Buell, CB, Leung, H and Leach, JE (2009) Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proceedings of the National Academy of Sciences of the United States of America 106: 1227312278.CrossRefGoogle ScholarPubMed
Moose, SP and Mumm, RH (2008) Molecular plant breeding as the foundation of the 21st century crop improvement. Plant Physiology 147: 969977.CrossRefGoogle ScholarPubMed
Murray, MG and Thompson, WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Research 8: 43214326.CrossRefGoogle ScholarPubMed
Peakall, R and Smouse, PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6: 288295.CrossRefGoogle Scholar
Pritchard, JK, Stephens, M and Donnelly, P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945959.Google ScholarPubMed
Reif, JC, Melchinger, AE, Xia, XC, Warburton, ML, Hoisington, DA, Vasal, SK, Srinivasan, G, Bohn, M and Frisch, M (2003) Genetic distance based on simple sequence repeats and heterosis in tropical maize populations. Crop Science 43: 12751282.CrossRefGoogle Scholar
Tamura, K, Peterson, D, Peterson, N, Stecher, G, Nei, M and Kumar, S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28: 27312739.CrossRefGoogle ScholarPubMed
Thomson, MJ, Zhao, K, Wright, M, McNally, KL, Rey, J, Tung, CW, Reynolds, A, Scheffler, B, Eizenga, G, McClung, A, Kim, H, Ismail, AM, Ocampo, M, Mojica, C, Reveche, MY, Dilla-Ermita, CJ, Mauleon, R, Leung, H, Bustamante, C and McCouch, SR (2012) High-throughput single nucleotide polymorphism genotyping for breeding applications in rice using the BeadXpress platform. Molecular Breeding 29: 875886.CrossRefGoogle Scholar
Wright, MH, Tung, CW, Zhao, K, Reynolds, A, McCouch, SR and Bustamante, CD (2010) ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations. Bioinformatics 26: 29522960.CrossRefGoogle ScholarPubMed
Xie, FM (1993) Hybrid performance and genetic diversity as revealed by RFLPs in Rice (Oryza sativa L.). PhD Thesis, Texas A&M University.Google Scholar
Yuan, LP (1977) Practice and theory of breeding hybrid rice. Scientia Agricultura Sinica 10: 2731.Google Scholar
Zhang, Q, Gao, YJ, Yang, S, Ragab, R, Saghai Maroof, MA and Li, ZB (1994) A diallel analysis of heterosis in elite hybrid rice based on RFLPs and microsatellites. Theoretical and Applied Genetics 89: 185192.Google ScholarPubMed
Zhang, Q, Gao, YJ, Saghai Maroof, MA, Yang, SH and Li, JX (1995) Molecular divergence and hybrid performance in rice. Molecular Breeding 1: 133142.CrossRefGoogle Scholar
Zhao, K, Wright, MH, Kimball, J, Eizenga, G, McClung, AM, Kovach, M, Tyagi, W, Ali, ML, Tung, CW, Reynolds, A, Bustamante, CD and McCouch, SR (2010) Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome. PLoS ONE 5: 111.CrossRefGoogle Scholar
Zhao, K, Tung, CW, Eizenga, GC, Wright, MH, Ali, ML, Price, AH, Norton, GJ, Islam, MR, Reynolds, A, Mezey, J, McClung, AM, Bustamante, CD and McCouch, SR (2011) Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nature Communication 2: 467.CrossRefGoogle ScholarPubMed

Xie Supplementary Material

Appendix

File 1 MB

Xie Supplementary Material

Figure S1

File 2 MB

Xie Supplementary Material

Table S1

File 67 KB

Full text views

Full text views reflects PDF downloads, PDFs sent to Google Drive, Dropbox and Kindle and HTML full text views.

Total number of HTML views: 10
Total number of PDF views: 53 *
View data table for this chart

* Views captured on Cambridge Core between September 2016 - 22nd January 2021. This data will be updated every 24 hours.

Hostname: page-component-76cb886bbf-fv2z2 Total loading time: 0.306 Render date: 2021-01-22T23:29:25.260Z Query parameters: { "hasAccess": "0", "openAccess": "0", "isLogged": "0", "lang": "en" } Feature Flags: { "shouldUseShareProductTool": true, "shouldUseHypothesis": true, "isUnsiloEnabled": true, "metricsAbstractViews": false, "figures": false, "newCiteModal": false }

Send article to Kindle

To send this article to your Kindle, first ensure no-reply@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about sending to your Kindle. Find out more about sending to your Kindle.

Note you can select to send to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be sent to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Genetic diversity and structure of indica rice varieties from two heterotic pools of southern China and IRRI
Available formats
×

Send article to Dropbox

To send this article to your Dropbox account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your <service> account. Find out more about sending content to Dropbox.

Genetic diversity and structure of indica rice varieties from two heterotic pools of southern China and IRRI
Available formats
×

Send article to Google Drive

To send this article to your Google Drive account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your <service> account. Find out more about sending content to Google Drive.

Genetic diversity and structure of indica rice varieties from two heterotic pools of southern China and IRRI
Available formats
×
×

Reply to: Submit a response


Your details


Conflicting interests

Do you have any conflicting interests? *