Theoretical and Applied Genetics

, Volume 122, Issue 5, pp 905–913

Functional markers developed from multiple loci in GS3 for fine marker-assisted selection of grain length in rice

Original Paper


The gene GS3 has major effect on grain size and plays an important role in rice breeding. The C to A mutation in the second exon of GS3 was reported to be functionally associated with enhanced grain length in rice. In the present study, besides the C-A mutation at locus SF28, three novel polymorphic loci, SR17, RGS1, and RGS2, were discovered in the second intron, the last intron and the final exon of GS3, respectively. A number of alleles at these four polymorphic loci were observed in a total of 287 accessions including Chinese rice varieties (Oryza sativa), African cultivated rice (O. glaberrima) and AA-genome wild relatives. The haplotype analysis revealed that the simple sequence repeats (AT)n at RGS1 and (TCC)n at RGS2 had differentiated in the wild rice whilst the C-A mutation occurred in the cultivated rice recently during domestication. It also indicated that A allele at SF28 was highly associated with long rice grain whilst various motifs of (AT)n at RGS1 and (TCC)n at RGS2 were mainly associated with medium to short grain in Chinese rice. The C-A mutation at SF28 explained 33.4% of the grain length variation in the whole rice population tested in this study, whereas (AT)n at RGS1 and (TCC)n at RGS2 explained 26.4 and 26.2% of the variation, respectively. These results would be helpful for better understanding domestication of GS3 and its manipulation for grain size in rice. The genic marker RGS1 based on the motifs (AT)n was further validated as a functional marker using two sets of backcross recombinant inbred lines. These results suggested that the functional markers developed from four different loci within GS3 could be used for fine marker-assisted selection of grain length in rice breeding.

Supplementary material

122_2010_1497_MOESM1_ESM.pdf (162 kb)
Figure S1. The PCR products amplified at the four polymorphic sites of GS3. A panel from left to right for RGS2: DNA marker, 9311 genotype (TCC)6, ZS97B genotype (TCC) 5, Y4 genotype (TCC)3. B panel from left to right for SF28: DNA marker, the PCR products digested by PstI of 9311 genotype with A mutation, ZS97B genotype with C mutation, WR8 genotype with C-2 bp deletion, Y4 genotype with C-6 bp deletion. C panel from left to right for RGS1: Y4 genotype (AT)85, ACC9 genotype (AT)13, 9311 genotype (AT)12, ZS97B genotype (AT)5. D panel from left to right for SR17: M, DNA marker; 1 and 2, 338 bp insertion (ZS97B); 3 and 4, genotype without insertion and deletion (9311); 5 and 6, 300 bp deletion (Y4). (PDF 161 kb)
122_2010_1497_MOESM2_ESM.pdf (13 kb)
Figure S2. The graphical genotype of the NIL pairs (-H3 and -H5) with or without the introduced segment containing GS3 of ‘ACC9’ in the similar background of ‘ZS97’. Those genic markers and tightly linked markers to grain length QTLs used for screening the background are also presented. (PDF 12 kb)
122_2010_1497_MOESM3_ESM.xls (86 kb)
Table S1. List of 287 accessions used in this study. (XLS 86 kb)

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  1. 1.National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
  2. 2.School of Plant Biology, and International Centre for Plant Breeding Education and ResearchThe University of Western AustraliaCrawleyAustralia

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