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Article: Genetic diversity and population structure of a diverse set of rice germplasm for association mapping

TitleGenetic diversity and population structure of a diverse set of rice germplasm for association mapping
Authors
Issue Date2010
PublisherSpringer Verlag. The Journal's web site is located at http://link.springer.de/link/service/journals/00122/index.htm
Citation
Theoretical And Applied Genetics, 2010, v. 121 n. 3, p. 475-487 How to Cite?
Abstract
Germplasm 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.
Persistent Identifierhttp://hdl.handle.net/10722/143100
ISSN
2013 Impact Factor: 3.507
ISI Accession Number ID
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).

References

 

Author Affiliations
  1. The University of Hong Kong
  2. Zhejiang University
DC FieldValueLanguage
dc.contributor.authorJin, Len_HK
dc.contributor.authorLu, Yen_HK
dc.contributor.authorXiao, Pen_HK
dc.contributor.authorSun, Men_HK
dc.contributor.authorCorke, Hen_HK
dc.contributor.authorBao, Jen_HK
dc.date.accessioned2011-10-28T08:54:56Z-
dc.date.available2011-10-28T08:54:56Z-
dc.date.issued2010en_HK
dc.identifier.citationTheoretical And Applied Genetics, 2010, v. 121 n. 3, p. 475-487en_HK
dc.identifier.issn0040-5752en_HK
dc.identifier.urihttp://hdl.handle.net/10722/143100-
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.en_HK
dc.languageeng-
dc.publisherSpringer Verlag. The Journal's web site is located at http://link.springer.de/link/service/journals/00122/index.htmen_HK
dc.relation.ispartofTheoretical and Applied Geneticsen_HK
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 mappingen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=0040-5752&volume=121&issue=3&spage=475&epage=487&date=2010&atitle=Genetic+diversity+and+population+structure+of+a+diverse+set+of+rice+germplasm+for+association+mapping-
dc.identifier.emailSun, M: meisun@hkucc.hku.hken_HK
dc.identifier.emailCorke, H: harold@hku.hken_HK
dc.identifier.authoritySun, M=rp00779en_HK
dc.identifier.authorityCorke, H=rp00688en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1007/s00122-010-1324-7en_HK
dc.identifier.pmid20364375-
dc.identifier.scopuseid_2-s2.0-77957744643en_HK
dc.identifier.hkuros185538-
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-77957744643&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume121en_HK
dc.identifier.issue3en_HK
dc.identifier.spage475en_HK
dc.identifier.epage487en_HK
dc.identifier.isiWOS:000280090700006-
dc.publisher.placeGermanyen_HK
dc.identifier.scopusauthoridJin, L=35766833000en_HK
dc.identifier.scopusauthoridLu, Y=26321148700en_HK
dc.identifier.scopusauthoridXiao, P=34573749200en_HK
dc.identifier.scopusauthoridSun, M=7403181447en_HK
dc.identifier.scopusauthoridCorke, H=7007102942en_HK
dc.identifier.scopusauthoridBao, J=7201398486en_HK
dc.identifier.citeulike7016169-

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