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Article: Nucleotide diversity in starch synthase IIa and validation of single nucleotide polymorphisms in relation to starch gelatinization temperature and other physicochemical properties in rice (Oryza sativa L.)

TitleNucleotide diversity in starch synthase IIa and validation of single nucleotide polymorphisms in relation to starch gelatinization temperature and other physicochemical properties in rice (Oryza sativa L.)
Authors
Issue Date2006
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, 2006, v. 113 n. 7, p. 1171-1183 How to Cite?
AbstractThe characteristics of starch, such as gelatinization temperature (GT), apparent amylose content (AAC), pasting temperature (PT) and other physicochemical properties, determine the quality of various products of rice, e.g., eating, cooking and processing qualities. The GT of rice flour is controlled by the alk locus, which has been co-mapped to the starch synthase IIa (SSIIa) locus. In this study, we sequenced a 2,051 bp DNA fragment spanning part of intron 6, exon 7, intron 7, exon 8 and part of 3′ untranslated region of SSIIa for 30 rice varieties with diverse geographical distribution and variation in starch physicochemical properties. A total of 24 single nucleotide polymorphisms (SNPs) and one insertion/deletion (InDel) were identified, which could be classified into nine haplotypes. The mean pairwise nucleotide diversity π was 0.00292, and Watterson's estimator θ was 0.00296 in this collection of rice germplasm. Tajima's D test for selection showed no significant deviation from the neutral expectation (D = - 0.04612, P > 0.10). However, significant associations were found between seven of the SNPs and peak GT (T p) at P < 0.05, of which two contiguous SNPs (GC/TT) showed a very strong association with T p (P < 0.0001). With some rare exception, this GC/TT polymorphism alone can differentiate rice varieties with high or intermediate GT (possessing the GC allele) from those with low GT (possessing the TT allele). In contrast, none of these SNPs or InDel was significantly associated with amylose content. A further 509 rice varieties with known physicochemical properties (e.g., AAC and PT) and known alleles of other starch synthesizing genes were genotyped for the SSIIa GC/TT alleles. Association analysis indicated that 82% of the total variation of AAC in these samples could be explained by a (CT)n simple sequence repeat (SSR) and a G/T SNP of Waxy gene (Wx), and 62.4% of the total variation of PT could be explained by the GC/TT polymorphism. An additional association analysis was performed between these molecular markers and the thermal and retrogradation properties for a subset of 245 samples from the 509 rice varieties. The SSIIa GC/TT polymorphism explained more than 60% of the total variation in thermal properties, whereas the SSR and SNP of Wx gene explained as much as the SSIIa GC/TT of the total variation in retrogradation properties. Our study provides further support for the utilization of the GC/TT polymorphism in SSIIa. As shown in our study of 509 rice varieties, the GC/TT SNP could differentiate rice with high or intermediate GT from those with low GT in about 90% of cases. Using four primers in a single PCR reaction, the GC/TT polymorphism can be surveyed on a large scale. Thus, this SNP polymorphism can be very useful in marker-assisted selection for the improvement of GT and other physicochemical properties of rice. © 2006 Springer-Verlag.
Persistent Identifierhttp://hdl.handle.net/10722/68575
ISSN
2015 Impact Factor: 3.9
2015 SCImago Journal Rankings: 1.930
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorBao, JSen_HK
dc.contributor.authorCorke, Hen_HK
dc.contributor.authorSun, Men_HK
dc.date.accessioned2010-09-06T06:05:49Z-
dc.date.available2010-09-06T06:05:49Z-
dc.date.issued2006en_HK
dc.identifier.citationTheoretical And Applied Genetics, 2006, v. 113 n. 7, p. 1171-1183en_HK
dc.identifier.issn0040-5752en_HK
dc.identifier.urihttp://hdl.handle.net/10722/68575-
dc.description.abstractThe characteristics of starch, such as gelatinization temperature (GT), apparent amylose content (AAC), pasting temperature (PT) and other physicochemical properties, determine the quality of various products of rice, e.g., eating, cooking and processing qualities. The GT of rice flour is controlled by the alk locus, which has been co-mapped to the starch synthase IIa (SSIIa) locus. In this study, we sequenced a 2,051 bp DNA fragment spanning part of intron 6, exon 7, intron 7, exon 8 and part of 3′ untranslated region of SSIIa for 30 rice varieties with diverse geographical distribution and variation in starch physicochemical properties. A total of 24 single nucleotide polymorphisms (SNPs) and one insertion/deletion (InDel) were identified, which could be classified into nine haplotypes. The mean pairwise nucleotide diversity π was 0.00292, and Watterson's estimator θ was 0.00296 in this collection of rice germplasm. Tajima's D test for selection showed no significant deviation from the neutral expectation (D = - 0.04612, P > 0.10). However, significant associations were found between seven of the SNPs and peak GT (T p) at P < 0.05, of which two contiguous SNPs (GC/TT) showed a very strong association with T p (P < 0.0001). With some rare exception, this GC/TT polymorphism alone can differentiate rice varieties with high or intermediate GT (possessing the GC allele) from those with low GT (possessing the TT allele). In contrast, none of these SNPs or InDel was significantly associated with amylose content. A further 509 rice varieties with known physicochemical properties (e.g., AAC and PT) and known alleles of other starch synthesizing genes were genotyped for the SSIIa GC/TT alleles. Association analysis indicated that 82% of the total variation of AAC in these samples could be explained by a (CT)n simple sequence repeat (SSR) and a G/T SNP of Waxy gene (Wx), and 62.4% of the total variation of PT could be explained by the GC/TT polymorphism. An additional association analysis was performed between these molecular markers and the thermal and retrogradation properties for a subset of 245 samples from the 509 rice varieties. The SSIIa GC/TT polymorphism explained more than 60% of the total variation in thermal properties, whereas the SSR and SNP of Wx gene explained as much as the SSIIa GC/TT of the total variation in retrogradation properties. Our study provides further support for the utilization of the GC/TT polymorphism in SSIIa. As shown in our study of 509 rice varieties, the GC/TT SNP could differentiate rice with high or intermediate GT from those with low GT in about 90% of cases. Using four primers in a single PCR reaction, the GC/TT polymorphism can be surveyed on a large scale. Thus, this SNP polymorphism can be very useful in marker-assisted selection for the improvement of GT and other physicochemical properties of rice. © 2006 Springer-Verlag.en_HK
dc.languageengen_HK
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.titleNucleotide diversity in starch synthase IIa and validation of single nucleotide polymorphisms in relation to starch gelatinization temperature and other physicochemical properties in rice (Oryza sativa L.)en_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=0040-5752&volume=113&spage=1171&epage=1183&date=2006&atitle=Nucleotide+diversity+in+starch+synthase+IIa+and+validation+of+single+nucleotide+polymorphisms+in+relation+to+starch+gelatinization+temperature+and+other+physicochemical+properties+in+rice+(Oryza+sativa+L.)en_HK
dc.identifier.emailCorke, H: harold@hku.hken_HK
dc.identifier.emailSun, M: meisun@hkucc.hku.hken_HK
dc.identifier.authorityCorke, H=rp00688en_HK
dc.identifier.authoritySun, M=rp00779en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1007/s00122-006-0355-6en_HK
dc.identifier.pmid16850313-
dc.identifier.scopuseid_2-s2.0-33750038248en_HK
dc.identifier.hkuros125969en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-33750038248&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume113en_HK
dc.identifier.issue7en_HK
dc.identifier.spage1171en_HK
dc.identifier.epage1183en_HK
dc.identifier.eissn1432-2242-
dc.identifier.isiWOS:000241261000001-
dc.publisher.placeGermanyen_HK
dc.identifier.scopusauthoridBao, JS=7201398486en_HK
dc.identifier.scopusauthoridCorke, H=7007102942en_HK
dc.identifier.scopusauthoridSun, M=7403181447en_HK
dc.identifier.citeulike954117-

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