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Article: Microsatellites, single nucleotide polymorphisms and a sequence tagged site in starch-synthesizing genes in relation to starch physicochemical properties in nonwaxy rice (Oryza sativa L.)

TitleMicrosatellites, single nucleotide polymorphisms and a sequence tagged site in starch-synthesizing genes in relation to starch physicochemical properties in nonwaxy 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. 1185-1196 How to Cite?
AbstractStarch characteristics determine the quality of various products of rice, e.g., eating, cooking and processing qualities. Our previous study indicated that molecular markers inside or close to starch synthesizing genes can differentiate the starch properties of 56 waxy rices. Here we report microsatellite (or simple sequence repeat, SSR) polymorphism in the Waxy (Wx) gene, soluble starch synthase I gene (SS1) and starch branching enzyme 1 gene (SBE1), single nucleotide polymorphism (SNP) in Wx and starch branching enzyme 3 gene (SBE3), and a sequence tagged site (STS) in starch branching enzyme 1 gene (SBE1) among 499 nonwaxy rice samples and their relationships with starch physicochemical properties. The nonwaxy rice samples consist of landraces (n = 172) obtained from germplasm centers and cultivars and breeding lines (n = 327) obtained from various breeding programs. Ten (CT) n microsatellite alleles, (CT) 8, (CT) 10, (CT) 11, (CT) 12, (CT) 17, (CT) 18, (CT) 19, (CT) 20, (CT) 21, and (CT) 22, were found at the Wx locus, of which (CT) 11 was the most frequent, and (CT) 12, (CT) 21 and (CT) 22 were identified for the first time. Four (CT) n microsatellite alleles were found at the SBE1 locus, (CT) 8, (CT) 9, and (CT) 10 together with an insertion sequence of CTCTCGGGCGA, and (CT) 8 alone without the insertion, of which (CT) 9 and the insertion was a new allele identified in only one rice, IR1552. Multiple microsatellites clustered at the SS1 locus, and in addition to the three alleles previously detected (SSS-A = (AC) 2...TCC(TC) 11...(TC) 5C(ACC) 11, SSS-B = (AC) 3...TCT(TC) 6...(TC) 4C(ACC) 9, and SSS-C = (AC) 3...TCT(TC) 6...(TC) 4C(ACC) 8), one new allele (SSS-D = (AC) 2...TCC(TC) 10...(TC) 4C(ACC) 9) was found. Analysis of the starch physicochemical properties of the samples with different microsatellites, SNPs and STS groups indicated that these molecular markers can differentiate almost all the physicochemical properties examined, e.g., apparent amylose content (AAC), pasting viscosity characteristics, and gel textural properties. Wx SSR and Wx SNP alone explained more variations for all physicochemical properties than the other molecular markers. The total six markers could explain 92.2, 81 and 86% of total variation of AAC, gel hardness (HD), and gel cohesiveness (COH), respectively, and they could explain more than 40% of the total variation of hot paste viscosity (HPV), cool paste viscosity (CPV), breakdown viscosity (BD), setback viscosity (SB) and gel adhesiveness (ADH). However, only 29% of the total variation of peak viscosity (PV) and 37% of pasting temperature (PT) could be explained by all the molecular markers. Some of these markers can differentiate the starch physicochemical properties among the rice samples with the same Wx allele, indicating that the variation within Wx allele classes can be explained by other starch synthesizing genes. These SSRs, SNPs and STS are useful in marker-assisted breeding for the improvement of starch quality of rice. © 2006 Springer-Verlag.
Persistent Identifierhttp://hdl.handle.net/10722/177187
ISSN
2015 Impact Factor: 3.9
2015 SCImago Journal Rankings: 1.930
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorBao, JSen_US
dc.contributor.authorCorke, Hen_US
dc.contributor.authorSun, Men_US
dc.date.accessioned2012-12-04T02:30:18Z-
dc.date.available2012-12-04T02:30:18Z-
dc.date.issued2006en_US
dc.identifier.citationTheoretical And Applied Genetics, 2006, v. 113 n. 7, p. 1185-1196en_US
dc.identifier.issn0040-5752en_US
dc.identifier.urihttp://hdl.handle.net/10722/177187-
dc.description.abstractStarch characteristics determine the quality of various products of rice, e.g., eating, cooking and processing qualities. Our previous study indicated that molecular markers inside or close to starch synthesizing genes can differentiate the starch properties of 56 waxy rices. Here we report microsatellite (or simple sequence repeat, SSR) polymorphism in the Waxy (Wx) gene, soluble starch synthase I gene (SS1) and starch branching enzyme 1 gene (SBE1), single nucleotide polymorphism (SNP) in Wx and starch branching enzyme 3 gene (SBE3), and a sequence tagged site (STS) in starch branching enzyme 1 gene (SBE1) among 499 nonwaxy rice samples and their relationships with starch physicochemical properties. The nonwaxy rice samples consist of landraces (n = 172) obtained from germplasm centers and cultivars and breeding lines (n = 327) obtained from various breeding programs. Ten (CT) n microsatellite alleles, (CT) 8, (CT) 10, (CT) 11, (CT) 12, (CT) 17, (CT) 18, (CT) 19, (CT) 20, (CT) 21, and (CT) 22, were found at the Wx locus, of which (CT) 11 was the most frequent, and (CT) 12, (CT) 21 and (CT) 22 were identified for the first time. Four (CT) n microsatellite alleles were found at the SBE1 locus, (CT) 8, (CT) 9, and (CT) 10 together with an insertion sequence of CTCTCGGGCGA, and (CT) 8 alone without the insertion, of which (CT) 9 and the insertion was a new allele identified in only one rice, IR1552. Multiple microsatellites clustered at the SS1 locus, and in addition to the three alleles previously detected (SSS-A = (AC) 2...TCC(TC) 11...(TC) 5C(ACC) 11, SSS-B = (AC) 3...TCT(TC) 6...(TC) 4C(ACC) 9, and SSS-C = (AC) 3...TCT(TC) 6...(TC) 4C(ACC) 8), one new allele (SSS-D = (AC) 2...TCC(TC) 10...(TC) 4C(ACC) 9) was found. Analysis of the starch physicochemical properties of the samples with different microsatellites, SNPs and STS groups indicated that these molecular markers can differentiate almost all the physicochemical properties examined, e.g., apparent amylose content (AAC), pasting viscosity characteristics, and gel textural properties. Wx SSR and Wx SNP alone explained more variations for all physicochemical properties than the other molecular markers. The total six markers could explain 92.2, 81 and 86% of total variation of AAC, gel hardness (HD), and gel cohesiveness (COH), respectively, and they could explain more than 40% of the total variation of hot paste viscosity (HPV), cool paste viscosity (CPV), breakdown viscosity (BD), setback viscosity (SB) and gel adhesiveness (ADH). However, only 29% of the total variation of peak viscosity (PV) and 37% of pasting temperature (PT) could be explained by all the molecular markers. Some of these markers can differentiate the starch physicochemical properties among the rice samples with the same Wx allele, indicating that the variation within Wx allele classes can be explained by other starch synthesizing genes. These SSRs, SNPs and STS are useful in marker-assisted breeding for the improvement of starch quality of rice. © 2006 Springer-Verlag.en_US
dc.languageengen_US
dc.publisherSpringer Verlag. The Journal's web site is located at http://link.springer.de/link/service/journals/00122/index.htmen_US
dc.relation.ispartofTheoretical and Applied Geneticsen_US
dc.subject.mesh1,4-Alpha-Glucan Branching Enzyme - Geneticsen_US
dc.subject.meshAgricultureen_US
dc.subject.meshDna Primersen_US
dc.subject.meshGene Frequencyen_US
dc.subject.meshMicrosatellite Repeats - Geneticsen_US
dc.subject.meshOryza Sativa - Geneticsen_US
dc.subject.meshPlant Proteins - Geneticsen_US
dc.subject.meshPolymorphism, Single Nucleotideen_US
dc.subject.meshSequence Analysis, Dnaen_US
dc.subject.meshSequence Tagged Sitesen_US
dc.subject.meshStarch - Chemistryen_US
dc.subject.meshStarch Synthase - Geneticsen_US
dc.titleMicrosatellites, single nucleotide polymorphisms and a sequence tagged site in starch-synthesizing genes in relation to starch physicochemical properties in nonwaxy rice (Oryza sativa L.)en_US
dc.typeArticleen_US
dc.identifier.emailCorke, H: harold@hku.hken_US
dc.identifier.emailSun, M: meisun@hkucc.hku.hken_US
dc.identifier.authorityCorke, H=rp00688en_US
dc.identifier.authoritySun, M=rp00779en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.doi10.1007/s00122-006-0394-zen_US
dc.identifier.pmid16964521-
dc.identifier.scopuseid_2-s2.0-33750053538en_US
dc.identifier.hkuros125967-
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-33750053538&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume113en_US
dc.identifier.issue7en_US
dc.identifier.spage1185en_US
dc.identifier.epage1196en_US
dc.identifier.isiWOS:000241261000002-
dc.publisher.placeGermanyen_US
dc.identifier.scopusauthoridBao, JS=7201398486en_US
dc.identifier.scopusauthoridCorke, H=7007102942en_US
dc.identifier.scopusauthoridSun, M=7403181447en_US
dc.identifier.citeulike954116-

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