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Article: Genetic diversity and population structure of a diverse set of rice germplasm for association mapping
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TitleGenetic diversity and population structure of a diverse set of rice germplasm for association mapping
 
AuthorsJin, L2
Lu, Y2
Xiao, P2
Sun, M1
Corke, H1
Bao, J2
 
Issue Date2010
 
PublisherSpringer Verlag. The Journal's web site is located at http://link.springer.de/link/service/journals/00122/index.htm
 
CitationTheoretical And Applied Genetics, 2010, v. 121 n. 3, p. 475-487 [How to Cite?]
DOI: http://dx.doi.org/10.1007/s00122-010-1324-7
 
AbstractGermplasm diversity is the mainstay for crop improvement and genetic dissection of complex traits. Understanding genetic diversity, population structure, and the level and distribution of linkage disequilibrium (LD) in target populations is of great importance and a prerequisite for association mapping. In this study, 100 genome-wide simple sequence repeat (SSR) markers were used to assess genetic diversity, population structure, and LD of 416 rice accessions including landraces, cultivars and breeding lines collected mostly in China. A model-based population structure analysis divided the rice materials into seven subpopulations. 63% of the SSR pairs in these accessions were in LD, which was mostly due to an overall population structure, since the number of locus pairs in LD was reduced sharply within each subpopulation, with the SSR pairs in LD ranging from 5.9 to 22.9%. Among those SSR pairs showing significant LD, the intrachromosomal LD had an average of 25-50 cM in different subpopulations. Analysis of the phenotypic diversity of 25 traits showed that the population structure accounted for an average of 22.4% of phenotypic variation. An example association mapping for starch quality traits using both the candidate gene mapping and genome-wide mapping strategies based on the estimated population structure was conducted. Candidate gene mapping confirmed that the Wx and starch synthase IIa (SSIIa) genes could be identified as strongly associated with apparent amylose content (AAC) and pasting temperature (PT), respectively. More importantly, we revealed that the Wx gene was also strongly associated with PT. In addition to the major genes, we found five and seven SSRs were associated with AAC and PT, respectively, some of which have not been detected in previous linkage mapping studies. The results suggested that the population may be useful for the genome-wide marker-trait association mapping. This new association population has the potential to identify quantitative trait loci (QTL) with small effects, which will aid in dissecting complex traits and in exploiting the rich diversity present in rice germplasm. © 2010 Springer-Verlag.
 
ISSN0040-5752
2012 Impact Factor: 3.658
2012 SCImago Journal Rankings: 1.730
 
DOIhttp://dx.doi.org/10.1007/s00122-010-1324-7
 
ISI Accession Number IDWOS:000280090700006
Funding AgencyGrant Number
Program for New Century Excellent Talents in UniversityNCET-08-0484
National High Technology Development Project of China2006AA10Z193
Zhejiang Provincial Natural Science Foundation of ChinaR3080016
Natural Science Foundation of China30771327
Hong Kong Research Grants Council7507/06M
Funding Information:

The authors thank Yun Shen and Jian Chen for assistance in SSR marker genotyping. Financial support for this research was provided in part by the Program for New Century Excellent Talents in University (NCET-08-0484), National High Technology Development Project of China (2006AA10Z193), Zhejiang Provincial Natural Science Foundation of China (R3080016), Natural Science Foundation of China (30771327), and a Hong Kong Research Grants Council GRF award (7507/06M).

 
ReferencesReferences in Scopus
 
DC FieldValue
dc.contributor.authorJin, L
 
dc.contributor.authorLu, Y
 
dc.contributor.authorXiao, P
 
dc.contributor.authorSun, M
 
dc.contributor.authorCorke, H
 
dc.contributor.authorBao, J
 
dc.date.accessioned2011-10-28T08:54:56Z
 
dc.date.available2011-10-28T08:54:56Z
 
dc.date.issued2010
 
dc.description.abstractGermplasm diversity is the mainstay for crop improvement and genetic dissection of complex traits. Understanding genetic diversity, population structure, and the level and distribution of linkage disequilibrium (LD) in target populations is of great importance and a prerequisite for association mapping. In this study, 100 genome-wide simple sequence repeat (SSR) markers were used to assess genetic diversity, population structure, and LD of 416 rice accessions including landraces, cultivars and breeding lines collected mostly in China. A model-based population structure analysis divided the rice materials into seven subpopulations. 63% of the SSR pairs in these accessions were in LD, which was mostly due to an overall population structure, since the number of locus pairs in LD was reduced sharply within each subpopulation, with the SSR pairs in LD ranging from 5.9 to 22.9%. Among those SSR pairs showing significant LD, the intrachromosomal LD had an average of 25-50 cM in different subpopulations. Analysis of the phenotypic diversity of 25 traits showed that the population structure accounted for an average of 22.4% of phenotypic variation. An example association mapping for starch quality traits using both the candidate gene mapping and genome-wide mapping strategies based on the estimated population structure was conducted. Candidate gene mapping confirmed that the Wx and starch synthase IIa (SSIIa) genes could be identified as strongly associated with apparent amylose content (AAC) and pasting temperature (PT), respectively. More importantly, we revealed that the Wx gene was also strongly associated with PT. In addition to the major genes, we found five and seven SSRs were associated with AAC and PT, respectively, some of which have not been detected in previous linkage mapping studies. The results suggested that the population may be useful for the genome-wide marker-trait association mapping. This new association population has the potential to identify quantitative trait loci (QTL) with small effects, which will aid in dissecting complex traits and in exploiting the rich diversity present in rice germplasm. © 2010 Springer-Verlag.
 
dc.description.natureLink_to_subscribed_fulltext
 
dc.identifier.citationTheoretical And Applied Genetics, 2010, v. 121 n. 3, p. 475-487 [How to Cite?]
DOI: http://dx.doi.org/10.1007/s00122-010-1324-7
 
dc.identifier.citeulike7016169
 
dc.identifier.doihttp://dx.doi.org/10.1007/s00122-010-1324-7
 
dc.identifier.epage487
 
dc.identifier.hkuros185538
 
dc.identifier.isiWOS:000280090700006
Funding AgencyGrant Number
Program for New Century Excellent Talents in UniversityNCET-08-0484
National High Technology Development Project of China2006AA10Z193
Zhejiang Provincial Natural Science Foundation of ChinaR3080016
Natural Science Foundation of China30771327
Hong Kong Research Grants Council7507/06M
Funding Information:

The authors thank Yun Shen and Jian Chen for assistance in SSR marker genotyping. Financial support for this research was provided in part by the Program for New Century Excellent Talents in University (NCET-08-0484), National High Technology Development Project of China (2006AA10Z193), Zhejiang Provincial Natural Science Foundation of China (R3080016), Natural Science Foundation of China (30771327), and a Hong Kong Research Grants Council GRF award (7507/06M).

 
dc.identifier.issn0040-5752
2012 Impact Factor: 3.658
2012 SCImago Journal Rankings: 1.730
 
dc.identifier.issue3
 
dc.identifier.openurl
 
dc.identifier.pmid20364375
 
dc.identifier.scopuseid_2-s2.0-77957744643
 
dc.identifier.spage475
 
dc.identifier.urihttp://hdl.handle.net/10722/143100
 
dc.identifier.volume121
 
dc.languageeng
 
dc.publisherSpringer Verlag. The Journal's web site is located at http://link.springer.de/link/service/journals/00122/index.htm
 
dc.publisher.placeGermany
 
dc.relation.ispartofTheoretical and Applied Genetics
 
dc.relation.referencesReferences in Scopus
 
dc.rightsThe original publication is available at www.springerlink.com
 
dc.subject.meshChromosome Mapping
 
dc.subject.meshChromosomes, Plant - genetics
 
dc.subject.meshGenetic Variation
 
dc.subject.meshOryza sativa - genetics
 
dc.subject.meshStarch - chemistry
 
dc.titleGenetic diversity and population structure of a diverse set of rice germplasm for association mapping
 
dc.typeArticle
 
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Author Affiliations
  1. The University of Hong Kong
  2. Zhejiang University