An SNP downstream of the OsBEIIb gene is significantly associated with amylose content and viscosity properties in rice (Oryza sativa L.) |
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| Affiliation: | 1. Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 340-802, Republic of Korea;2. Legume Bio-Resource Center of Green Manure (LBRCGM), Kongju National University, Yesan 340-802, Republic of Korea;1. School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China;2. Joint Center for Single Cell Biology/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China;3. National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China;1. Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany;2. Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany;3. CIRAD, UMR AGAP, Avenue Agropolis, 34398 Montpellier, Cedex 5, France;1. Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China;2. School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China;3. Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China;4. Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China;5. Institute of Crop Research, Ningxia Academy of Agricultural and Forestry Sciences, Yongning 750105, China;6. Rice Research Institute, Linyi Academy of Agricultural Sciences, Shandong Linyi 276012, China;7. Rice Research Institute of Liaoning Province, Shenyang 110161, China |
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| Abstract: | Allele mining in starch synthesis-related genes (SSRGs) has facilitated the discovery of desired natural sequence variations for eating quality in rice. This study investigated the sequence variations from 10 SSRGs, and further evaluated their relationship with the amylose content (AC) and rapid viscosity analysis profiles in a global collection of rice accessions by association mapping (AM). In total, 83 sequence variations were found in 10 sequenced amplicons, including 73 single nucleotide polymorphisms (SNPs), eight insertion-deletions (InDels) and two polymorphic simple sequence repeats (SSRs). Four subpopulations were identified by population structure analysis based on 170 genome-wide SSR genotypes. AM revealed 11 significant associations between three phenotypic indices and three sequence variations. One SNP with a g/c transversion at the 63rd nucleotide downstream of the OsBEIIb gene termination codon on rice chromosome 2 was significantly associated with multiple trait indices in both the general linear and mixed linear models (GLM and MLM), including the final viscosity (p < 0.001, R2 = 23.87%) in both 2009 and 2010, and AC (p < 0.01, R2 = 11.25%) and trough viscosity (p < 0.01, R2 = 20.43) in 2010. This study provides a new perspective of allele mining for breeding strategies based on marker-assisted selection. |
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