Allelic variation for a candidate gene for GS7, responsible for grain shape in rice

State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
Theoretical and Applied Genetics (Impact Factor: 3.79). 07/2012; 125(6):1303-12. DOI: 10.1007/s00122-012-1914-7
Source: PubMed


Grain shape is an important component of end-use quality in rice. The genomic location of the grain shape QTL GS7 was narrowed to lie within a 4.8-kb segment on chromosome 7. The homologous region in cv. Nipponbare contains no annotated genes, while two open reading frames were predicted, one of which (ORF2) represented a likely candidate for GS7 gene on the basis of correlation between sequence variation and phenotype. Semi-quantitative and quantitative RT-PCR analysis of ORF2 transcription showed that the gene was active in both the leaf and panicle when the cv. D50 allele was present, but not in the presence of the cv. HB277 allele. A microsatellite-based phylogeny and a re-sequencing analysis of ORF2 among a set of 52 diverse rice accessions suggested that the cv. D50 GS7 allele may have originated from the tropical japonica genepool. The effect on grain length of the alternative alleles at GS7and GS3 showed that combination type 3/A was associated with longer grains than type 1/A. An Indel marker developed within the ORF2 sequence was informative for predicting grain length.

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    • "Multiple QTLs and genes controlling rice grain size have been mapped on the 12 chromosomes using molecular markers and different mapping populations (Huang et al., 2013). Several genes controlling grain size have been analyzed (Zuo and Li, 2014), for example, GS5 (Li et al., 2011), GS3 (Fan et al., 2006; Mao et al., 2010), GW2 (Song et al., 2007), GW5 (Weng et al., 2008), qSW5 (Shomura et al., 2008), qGL3 (Hu et al., 2012; Qi et al., 2012; Zhang et al., 2012), GW8 (Wang et al., 2012) and TGW6 (Ishimaru et al., 2013), and qGL7 and GS7 (Bai et al., 2010; Shao et al., 2012). Although a number of genes for grain size have been cloned, the underlying molecular mechanisms and the potential interaction of these genes in grain size regulation remain to be elucidated. "
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    ABSTRACT: Grain size is an important trait that directly influences the yield of rice. Validation and evaluation of grain genes is important in rice genetic studies and for breeding. In a population of 240 recombinant inbred lines (RILs) derived from a cross between an extra-large grain japonica variety TD70 and a small grain indica variety Kasalath, we mapped 19 QTLs controlling grain traits. These QTLs included six cloned grain genes, namely, GW2, GS3, qSW5, qGL3, GS5, and GW8. All of the alleles with the optimal effects on grain size came from TD70, the variety with extra-large grains. To verify these gene loci, we cloned and sequenced GW2, GS3, GW5 (qSW5), qGL3, GS5, GW8, and TGW6 in TD70 and Kasalath, and found several functional polymorphisms in the sequences of the genes. New functional markers for the cloned genes were designed to identify parents and RILs. The contributions of these polymorphisms to the improvement in rice grain size traits were evaluated. Our results indicate that at least six functional polymorphisms have additive effects on grain shape and that one non-functional polymorphism in TGW6 affects grain shape in TD70. The newly designed markers will be useful in further studies to identify functional grain genes. Our findings provide insight into the control of grain size in rice, and they will be of value for improving rice grain yield.
    Preview · Article · Nov 2015 · Genetics and molecular research: GMR
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    • "Grain shape in Asian cultivated rice is diverse, and extensive research has been conducted to identify QTLs controlling it. More than 100 papers have reported nearly 200 QTLs for grain length and grain width (reviewed by Huang et al. 2013), of which 15 have been mapped on a fine scale (Bai et al. 2010, Guo et al. 2009, Li et al. 2004, Qiu et al. 2012, Shao et al. 2012, Wan et al. 2006) and 16 have been cloned including GS3 (Fan et al. 2006, Mao et al. 2010), GW2 (Song et al. 2007), GW5/ qSW5 (Shomura et al. 2008, Weng et al. 2008), GS5 (Li et al. 2011), TGW6 (Ishimaru et al. 2013), and GW6a (Song et al. 2015). Although this progress has encouraged markerassisted breeding to target these QTLs and genes in rice, those studies focused mainly on QTLs with large effects, and the information available on QTL alleles is not currently sufficient for fine-tuning grain shape in practical breeding programs. "
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    ABSTRACT: Grain shape is an important trait for improving rice yield. A number of quantitative trait loci (QTLs) for this trait have been identified by using primary F2 mapping populations and recombinant inbred lines, in which QTLs with a small effect are harder to detect than they would be in advanced generations. In this study, we developed two advanced mapping populations (chromosome segment substitution lines [CSSLs] and BC4F2 lines consisting of more than 2000 individuals) in the genetic backgrounds of two improved cultivars: a japonica cultivar (Koshihikari) with short, round grains, and an indica cultivar (IR64) with long, slender grains. We compared the ability of these materials to reveal QTLs for grain shape with that of an F2 population. Only 8 QTLs for grain length or grain width were detected in the F2 population, versus 47 in the CSSL population and 65 in the BC4F2 population. These results strongly suggest that advanced mapping populations can reveal QTLs for agronomic traits under complicated genetic control, and that DNA markers linked with the QTLs are useful for choosing superior allelic combinations to enhance grain shape in the Koshihikari and IR64 genetic backgrounds.
    Full-text · Article · Sep 2015 · Breeding Science
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    • "With the rapid development of DNA molecular marker technology and quantitative genetics, more than 10 genes regulating rice yield-related traits have been identified (Huang et al, 2013; Ikeda et al, 2013). For example, Gnla regulates grain formation and DEP1 enhances grain yield (Xie et al, 2006; Shomura et al, 2008; Asano et al, 2010; Mao et al, 2010; Shao et al, 2012; Singh et al, 2012; Zhang et al, 2012). In recent years, genome-wide association study (GWAS) achieved through whole genome re-sequencing and single nucleotide polymorphism (SNP) has become a powerful approach in rice for identifying favorable alleles and genetic variations associated with complex traits in large scale and high accuracy (Huang et al, 2010; Zhao et al, 2011; Han and Huang, 2013). "
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    ABSTRACT: Narrow genetic background is a key limiting factor in breeding stable high-yielding rice. The introduction and utilization of international rice core germplasm is an important way to increase the genetic diversity of domestic rice varieties. We conducted a genome-wide association study on 5 panicle traits of 315 rice accessions introduced from the international rice micro-core germplasm bank. Based on the tests from Yangzhou of China and Arkansas of American, environment exhibited a significant impacts on panicle length and primary branch number, while grain length, grain width and grain length/width ratio were insensitive to environment changes. We discovered a total of 7, 5, 10, 8 and 6 chromosomal regions or single nucleotide polymorphism marker loci that were significantly associated with primary branch number, panicle length, grain length, grain width and grain length/width ratio, respectively. Among them, eleven regions were associated with grain shape and one region associated with primary branch number, showing the good consistence in two different environments. Significant linear correlation was discovered between the average trait value and the number of favorable alleles carried by the varieties in all associated loci. Among the associated loci, varieties in aromatic and tropical japonica sub-groups possessed most favorable alleles, while those in temperate japonica sub-group contained the least. The domestic varieties mainly harbored unfavorable alleles in six of the associated loci being detected. On the contrary, 15 varieties from 11 different countries harbored more favorable alleles (as many as 30 or more) than the others. Remarkably, all these 15 varieties belonged to the tropical japonica sub-group. In conclusion, our study demonstrates that varieties in the tropical japonica sub-group had high potentials for breeding stable high-yielding rice. Based on this discovery, we proposed a new approach for improving the panicle traits of domestic rice by using tropical japonica varieties.
    Full-text · Article · Sep 2015 · Rice Science
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