Reference "A causal C-A mutation in the second exon of GS3 highly associated with rice grain length and validated as a functional marker"

Reference ID

51253

Title

A causal C-A mutation in the second exon of GS3 highly associated with rice grain length and validated as a functional marker

Source

Theor Appl Genet, 2009, vol. 118, pp. 465-472

Authors (4)

Fan-C	Yu-S
Wang-C	Xing-Y

Abstract

Comparative sequencing of GS3, the most important grain length (GL) QTL, has
shown that differentiation of rice GL might be principally due to a single
nucleotide polymorphism (SNP) between C and A in the second exon. A total of 180
varieties representing a wide range of rice germplasm were used for association
analysis between C-A mutation and GL in order to confirm the potential causal
mutation. A cleaved amplified polymorphic sequence (CAPS) marker, SF28, was
developed based on the C-A polymorphism in the GS3 gene. A total of 142
varieties carried allele C with GL from 6.4 to 8.8 mm, while the remaining 38
varieties carried allele A with GL from 8.8 to 10.7 mm. Twenty-four unlinked SSR
markers were selected to genotype 180 varieties for population structure
analysis. Population structure was observed when the population was classified
to three subpopulations. Average GL of either genotype A or genotype C within
japonica among the three subpopulations had no significant difference from that
in indica, respectively, although indica rice had longer grains on average than
japonica in the 180 varieties. However, genotype C always had longer grain
length on average than genotype A among three subpopulations. The mutation could
explain 79.1, 66.4 and 34.7% of GL variation in the three subpopulations,
respectively. These results clearly confirmed the mutation between C and A was
highly associated with GL. The SF28 could be a functional marker for improvement
of rice grain length.