Sequence variations inOsAGPasesignificantly associated with amylose content and viscosity properties in rice (Oryza sativaL.)
- 1 February 2012
- journal article
- research article
- Published by Hindawi Limited in Genetics Research
- Vol. 94 (4), 179-189
- https://doi.org/10.1017/s0016672312000390
Abstract
Summary: Sequence-based variations in starch synthesis-related genes (SSRGs) exert a basic influence on the determination of eating quality in rice (Oryza sativaL.). This study aimed to investigate the relationship between the sequence variations from parts of 10 SSRGs and the amylose content (AC) plus rapid viscosity analysis (RVA) profiles in a heuristic rice core set by association mapping (AM). In total, 86 sequence variations were found in 10 sequenced amplicons, including 79 single-nucleotide polymorphisms (SNPs), six insertion-deletions (InDels) and one polymorphic simple sequence repeat (SSR). Among them, 61 variations were exon-based, of which 41 should lead to amino acid changes. Four subpopulations were revealed by population structure analysis based on 170 genome-wide SSR genotypes. The final AM showed a sum of four significant associations between three phenotypic indices and three sequence variations. AnADP-glucose pyrophosphorylase small unit 1(OsAGPS1) SNP (A–G) was significantly associated with increased AC (PR2=15·6%), while a 12-bp deletion ofAGPase large unit 4(OsAGPL4) was significantly related to the decreased breakdown viscosity (BDV) (PR2=16·6%) in both general linear model (GLM) and mixed linear model (MLM). This study provides a new perspective of allele mining for breeding strategies based on marker-assisted selection.Keywords
This publication has 40 references indexed in Scilit:
- Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativaNature Communications, 2011
- MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony MethodsMolecular Biology and Evolution, 2011
- Joint linkage–linkage disequilibrium mapping is a powerful approach to detecting quantitative trait loci underlying drought tolerance in maizeProceedings of the National Academy of Sciences of the United States of America, 2010
- Genome-wide association studies of 14 agronomic traits in rice landracesNature Genetics, 2010
- Genetic diversity and population structure of a diverse set of rice germplasm for association mappingTheoretical and Applied Genetics, 2010
- Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualitiesProceedings of the National Academy of Sciences of the United States of America, 2009
- PCR Marker-Based Evaluation of the Eating Quality of Japonica Rice (Oryza sativa L.)Journal of Agricultural and Food Chemistry, 2009
- Rice 2020: A Call For An International Coordinated Effort In Rice Functional GenomicsMolecular Plant, 2008
- A unified mixed-model method for association mapping that accounts for multiple levels of relatednessNature Genetics, 2005
- Statistical significance for genomewide studiesProceedings of the National Academy of Sciences of the United States of America, 2003