GW5

A major QTL on chromosome 5, qGW5, which is associated with reduced grain width not only in the isogenic Asominori background but also in the recombinant background of Asominori and IR24 under multiple environmental conditions

Brief Introduction

Rice grain width and shape play a crucial role in determining grain quality and yield. The genetic basis of rice grain width was dissected into six additive quantitative trait loci (QTL) and 11 pairs of epistatic QTL using an F7 recombinant inbred line (RIL) population derived from a single cross between Asominori (japonica) and IR24 (indica). QTL by environment interactions were evaluated in four environments. Chromosome segment substitution lines (CSSLs) harboring the six additive effect QTL were used to evaluate gene action across eight environments. A major, stable QTL, qGW-5, consistently decreased rice grain width in both the Asominori/IR24 RIL and CSSL populations with the genetic background Asominori. By investigating the distorted segregation of phenotypic values of rice grain width and genotypes of molecular markers in BC4F2 and BC4F3 populations, qGW-5 was dissected into a single recessive gene, GW5, which controlled both grain width and length–width ratio. GW5 was narrowed down to a 49.7-kb genomic region with high recombination frequencies on chromosome 5 using 6781 BC4F2 individuals and 10 newly developed simple sequence repeat markers. Our results provide a basis for map based cloning of the g GW5 gene and for marker-aided gene/QTL pyramiding in rice quality breeding. To gain a better understanding of how GW5 controls rice grain width, we conducted fine mapping of this locus and uncovered a 1212-bp deletion associated with the increased grain width in the rice cultivar Asominori, in comparison with the slender grain rice IR24. In addition, genotyping analyses of 46 rice cultivars revealed that this deletion is highly correlated with the grain-width phenotype, suggesting that the GW5 deletion might have been selected during rice domestication. GW5 encodes a novel nuclear protein of 144 amino acids that is localized to the nucleus. Furthermore, we show that GW5 physically interacts with polyubiquitin in a yeast two-hybrid assay. Together, our results suggest that GW5 represents a major QTL underlying rice width and weight, and that it likely acts in the ubiquitin-proteasome pathway to regulate cell division during seed development. This study provides novel insights into the molecular mechanisms controlling rice grain development and suggests that GW5 could serve as a potential tool for high-yield breeding of crops.

Annotated Information

Mutation

GW5 is associated with a 1 212-bp deletion in the Asominori cultivar For genetic analysis and isolation of the dominant narrow-grain QTL, named GW5, the F2 population was constructed from a cross between Asominori and CSSL28, and the QTL was dissected into a single gene . By means of linkage analysis using the genotype data of both the GW5 gene and simple sequence repeat (SSR) markers, the GW5 gene was mapped to an interval between markers RM3328 and RMw513 in 805 homozygotes . Thus, the GW5 gene was mapped to a genomic region 2.7 cM in length, located 2.3 cM from RM3328 and 0.37 cM from RMw513. In this region, three bacterial artificial chromosome (BAC) contigs were found – OJ1725_E07, OJ1097_A12 and B1007D10

Function

1.Stability of QTL for rice grain width and gene actionof identified QTL. The observed stability and gene action of these QTL indicates that qGW-5 is the most important genetic factor that controls rice grain width difference between the Asominori and IR24 parental lines. 2.GW5 physically interacts with polyubiquitin Sequence analysis indicated that GW5 encodes a novel protein without significant homology to any proteins of known biochemical function. The protein is predicted to contain an NLS and an arginine-rich domain. Transient expression in onion epidermal cells showed that the GW5-GFP fusion protein is exclusively localized to the Nucleus. In an effort to identify the functional partners of GW5, polyubiquitin protein interacts with GW5. This result was found 14 times in about 200 candidate positive clones on synthetic growth medium without leucine, tryptophan, histidine and adenine. X-gal filter lift assays also detected a clear interaction between GW5 and polyubiquitin . This suggests that the GW5 protein may play an important role in regulating the grain shape through involvement with the ubiquitin-proteasome pathway.

Expression

GW5 is expressed in slender-grain rice. The sequence of 9 311 (a narrow-grain indica rice cultivar) in the cognate region is similar to that in the GW5 region in CSSL28. Analysis of the indica rice genome sequence showed that GW5 represents a single copy gene without any expressed sequence tags (ESTs) or cDNA support. However, the expression of the candidate ORF was detected in the tiling microarray database of 9 311 (GenBank Acc: CL971152) To further confirm the expression of GW5, RT-PCR analysis were confirmed by sequencing analyses. Therefore, GW5 is expressed in CSSL28.

Labs working on this gene

National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University,

References

1.Jianfeng Weng etc. Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight. Cell Research, 2008, 18(12): 1199-1209

2.Xiangyuan Wan etc. Quantitative Trait Loci (QTL) Analysis For Rice Grain Width and Fine Mapping of an Identified QTL Allele gw-5 in a Recombination Hotspot Region on Chromosome 5 .Genetics, 2008, 179(4): 2239-2252

3.X. Y. Wan etc. Stability of QTLs for rice grain dimension and endosperm chalkiness characteristics across eight environments. Theoretical and Applied Genetics, 2005, 110(7): 1334-1346