Advanced backcross QTL analysis reveals complicated genetic control of rice grain shape in a japonica × indica cross

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.

[1]  Takamasa Suzuki,et al.  Rare allele of a previously unidentified histone H4 acetyltransferase enhances grain weight, yield, and plant biomass in rice , 2014, Proceedings of the National Academy of Sciences.

[2]  Takuya Yamaguchi,et al.  Identification of a novel gene (Apq1) from the indica rice cultivar ‘Habataki’ that improves the quality of grains produced under high temperature stress , 2014, Breeding science.

[3]  M. Yano,et al.  Genetic mechanisms underlying yield potential in the rice high-yielding cultivar Takanari, based on reciprocal chromosome segment substitution lines , 2014, BMC Plant Biology.

[4]  M. Yano,et al.  Detection of QTLs to reduce cadmium content in rice grains using LAC23/Koshihikari chromosome segment substitution lines , 2013, Breeding science.

[5]  F. Taguchi-Shiobara,et al.  A natural variant of NAL1, selected in high-yield rice breeding programs, pleiotropically increases photosynthesis rate , 2013, Scientific Reports.

[6]  Atsuko Onishi,et al.  Loss of function of the IAA-glucose hydrolase gene TGW6 enhances rice grain weight and increases yield , 2013, Nature Genetics.

[7]  Z. Hong,et al.  Genetic bases of rice grain shape: so many genes, so little known. , 2013, Trends in plant science.

[8]  M. Yano,et al.  SmartGrain: High-Throughput Phenotyping Software for Measuring Seed Shape through Image Analysis1[C][W][OA] , 2012, Plant Physiology.

[9]  Sibin Yu,et al.  Mapping and characterization of the major quantitative trait locus qSS7 associated with increased length and decreased width of rice seeds , 2012, Theoretical and Applied Genetics.

[10]  Li-hong Xie,et al.  Allelic variation for a candidate gene for GS7, responsible for grain shape in rice , 2012, Theoretical and Applied Genetics.

[11]  Ashutosh Kumar Singh,et al.  Fine mapping of grain length QTLs on chromosomes 1 and 7 in Basmati rice (Oryza sativa L.) , 2012, Journal of Plant Biochemistry and Biotechnology.

[12]  M. Yano,et al.  A multiple gene complex on rice chromosome 4 is involved in durable resistance to rice blast , 2012, Theoretical and Applied Genetics.

[13]  Lijun Luo,et al.  Natural variation in GS5 plays an important role in regulating grain size and yield in rice , 2011, Nature Genetics.

[14]  M. Yano,et al.  Genetic structure revealed by a whole-genome single-nucleotide polymorphism survey of diverse accessions of cultivated Asian rice (Oryza sativa L.) , 2010 .

[15]  Chenwu Xu,et al.  Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.) , 2010, BMC Genomics.

[16]  Edward S. Buckler,et al.  Gramene database in 2010: updates and extensions , 2010, Nucleic Acids Res..

[17]  Jialing Yao,et al.  Linking differential domain functions of the GS3 protein to natural variation of grain size in rice , 2010, Proceedings of the National Academy of Sciences.

[18]  M. Yano,et al.  Q-TARO: QTL Annotation Rice Online Database , 2010, Rice.

[19]  Mallikarjuna Rao Kovi,et al.  Genetic dissection of rice grain shape using a recombinant inbred line population derived from two contrasting parents and fine mapping a pleiotropic quantitative trait locus qGL7 , 2010, BMC Genetics.

[20]  M. Yano,et al.  Detection of quantitative trait loci controlling pre-harvest sprouting resistance by using backcrossed populations of japonica rice cultivars , 2010, Theoretical and Applied Genetics.

[21]  M. Yano,et al.  Towards the Understanding of Complex Traits in Rice: Substantially or Superficially? , 2009, DNA research : an international journal for rapid publication of reports on genes and genomes.

[22]  M. Yano,et al.  Detection of a quantitative trait locus controlling carbon isotope discrimination and its contribution to stomatal conductance in japonica rice , 2009, Theoretical and Applied Genetics.

[23]  M. Yano,et al.  Major QTLs for eating quality of an elite Japanese rice cultivar, Koshihikari, on the short arm of chromosome 3 , 2008 .

[24]  Zhijun Cheng,et al.  Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight , 2008, Cell Research.

[25]  Lanzhi Li,et al.  Dominance, Overdominance and Epistasis Condition the Heterosis in Two Heterotic Rice Hybrids , 2008, Genetics.

[26]  J. Zhuang,et al.  Genetic dissection of a thousand-grain weight quantitative trait locus on rice chromosome 1 , 2008 .

[27]  Gurdev S. Khush,et al.  Progress in ideotype breeding to increase rice yield potential , 2008 .

[28]  Kaworu Ebana,et al.  Deletion in a gene associated with grain size increased yields during rice domestication , 2008, Nature Genetics.

[29]  M. Yano,et al.  Genetic dissection and pyramiding of quantitative traits for panicle architecture by using chromosomal segment substitution lines in rice , 2008, Theoretical and Applied Genetics.

[30]  Wei Huang,et al.  A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase , 2007, Nature Genetics.

[31]  F. Jin,et al.  Fine mapping of a grain weight quantitative trait locus on rice chromosome 8 using near-isogenic lines derived from a cross between Oryza sativa and Oryza rufipogon , 2006, Theoretical and Applied Genetics.

[32]  J. L. Wang,et al.  QTL analysis for rice grain length and fine mapping of an identified QTL with stable and major effects , 2006, Theoretical and Applied Genetics.

[33]  Bin Han,et al.  GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein , 2006, Theoretical and Applied Genetics.

[34]  M. Yano,et al.  Chromosomal regions with quantitative trait loci controlling cadmium concentration in brown rice (Oryza sativa). , 2005, The New phytologist.

[35]  Q. Qian,et al.  Cytokinin Oxidase Regulates Rice Grain Production , 2005, Science.

[36]  Yoshinobu Takeuchi,et al.  Construction and evaluation of chromosome segment substitution lines carrying overlapping chromosome segments of indica rice cultivar 'Kasalath' in a genetic background of japonica elite cultivar 'Koshihikari' , 2005 .

[37]  S. Mccouch,et al.  Fine Mapping of a Grain-Weight Quantitative Trait Locus in the Pericentromeric Region of Rice Chromosome 3 , 2004, Genetics.

[38]  Keiko Nakamura,et al.  Reciprocal chromosome segment substitution series derived from japonica and indica cross of rice (Oryza sativa L.) , 2002 .

[39]  M. Yano,et al.  Genetic and molecular dissection of quantitative traits in rice , 1997, Plant Molecular Biology.

[40]  A. Paterson,et al.  Epistasis for three grain yield components in rice (Oryza sativa L.). , 1997, Genetics.

[41]  S. Tanksley,et al.  Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines , 1996, Theoretical and Applied Genetics.

[42]  S. Tanksley,et al.  Fine mapping of quantitative trait loci using selected overlapping recombinant chromosomes, in an interspecies cross of tomato. , 1990, Genetics.

[43]  M. Daly,et al.  MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. , 1987, Genomics.

[44]  T. Takita.  Breeding of a Rice Line with Extraordinarily Large Grains as a Genetic Source for High Yielding Varieties , 1983 .

[45]  M. D. Ewell.  THE RELATION OF THE METER AND THE YARD. , 1909, Science.

[46]  Q. Qian,et al.  Genetic analysis and fine mapping of two genes for grain shape and weight in rice. , 2009, Journal of integrative plant biology.

[47]  Chen Li-yun.  QTLs Mapping and Epistasis Analysis for Grain Shape and Chalkiness Degree of Rice , 2008 .