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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    • "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.
    Breeding Science 09/2015; 65(4):308-18. DOI:10.1270/jsbbs.65.308 · 2.13 Impact Factor
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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.
    Rice Science 09/2015; 22(5):217-226. DOI:10.1016/j.rsci.2015.07.001
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    • "In case of grain width MLM analysis (p < 0.0001) detected 130 sites with 73 SNP markers on chromosomes 7 and 4 markers on chromosome 8 (Figure 6c). The significant markers on chromosome 7 (22.7 – 26 Mb) co-localized with the grain breadth QTL identified in the study by Redoña and Mackill (1998) and was near a grain shape QTL GS7 (Shao et al. 2012). The significant markers on chromosome 8 (26.4 -27.2 Mb) co-localized with GW8 OSSPL16 QTL for grain width and yield potential (Wang et al. 2012). "
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    ABSTRACT: Background This article describes the development of Multi-parent Advanced Generation Inter-Cross populations (MAGIC) in rice and discusses potential applications for mapping quantitative trait loci (QTLs) and for rice varietal development. We have developed 4 multi-parent populations: indica MAGIC (8 indica parents); MAGIC plus (8 indica parents with two additional rounds of 8-way F1 inter-crossing); japonica MAGIC (8 japonica parents); and Global MAGIC (16 parents – 8 indica and 8 japonica). The parents used in creating these populations are improved varieties with desirable traits for biotic and abiotic stress tolerance, yield, and grain quality. The purpose is to fine map QTLs for multiple traits and to directly and indirectly use the highly recombined lines in breeding programs. These MAGIC populations provide a useful germplasm resource with diverse allelic combinations to be exploited by the rice community. Results The indica MAGIC population is the most advanced of the MAGIC populations developed thus far and comprises 1328 lines produced by single seed descent (SSD). At the S4 stage of SSD a subset (200 lines) of this population was genotyped using a genotyping-by-sequencing (GBS) approach and was phenotyped for multiple traits, including: blast and bacterial blight resistance, salinity and submergence tolerance, and grain quality. Genome-wide association mapping identified several known major genes and QTLs including Sub1 associated with submergence tolerance and Xa4 and xa5 associated with resistance to bacterial blight. Moreover, the genome-wide association study (GWAS) results also identified potentially novel loci associated with essential traits for rice improvement. Conclusion The MAGIC populations serve a dual purpose: permanent mapping populations for precise QTL mapping and for direct and indirect use in variety development. Unlike a set of naturally diverse germplasm, this population is tailor-made for breeders with a combination of useful traits derived from multiple elite breeding lines. The MAGIC populations also present opportunities for studying the interactions of genome introgressions and chromosomal recombination.
    Rice 11/2013; 6(1). DOI:10.1186/1939-8433-6-11 · 3.92 Impact Factor
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