Predicting the Size of the Progeny Mapping Population Required to Positionally Clone a Gene

A key frustration during positional gene cloning (map-based cloning) is that the size of the progeny mapping population is difficult to predict, because the meiotic recombination frequency varies along chromosomes. We describe a detailed methodology to improve this prediction using rice (Oryza sativa L.) as a model system. We derived and/or validated, then fine-tuned, equations that estimate the mapping population size by comparing these theoretical estimates to 41 successful positional cloning attempts. We then used each validated equation to test whether neighborhood meiotic recombination frequencies extracted from a reference RFLP map can help researchers predict the mapping population size. We developed a meiotic recombination frequency map (MRFM) for ∼1400 marker intervals in rice and anchored each published allele onto an interval on this map. We show that neighborhood recombination frequencies (R-map, >280-kb segments) extracted from the MRFM, in conjunction with the validated formulas, better predicted the mapping population size than the genome-wide average recombination frequency (R-avg), with improved results whether the recombination frequency was calculated as genes/cM or kb/cM. Our results offer a detailed road map for better predicting mapping population size in diverse eukaryotes, but useful predictions will require robust recombination frequency maps based on sampling more progeny.

[1]  S. Benzer,et al.  Targeted gene mutations in Drosophila. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[2]  S. Mccouch,et al.  The rice bacterial blight resistance gene xa5 encodes a novel form of disease resistance. , 2004, Molecular plant-microbe interactions : MPMI.

[3]  M. Raizada.  RescueMu protocols for maize functional genomics. , 2003, Methods in molecular biology.

[4]  Qian Qian,et al.  Control of tillering in rice , 2003, Nature.

[5]  J. Postlethwait,et al.  Sex-specific recombination rates in zebrafish (Danio rerio). , 2002, Genetics.

[6]  M. Matsuoka,et al.  The rice mutant dwarf bamboo shoot 1: a leaky mutant of the NACK-type kinesin-like gene can initiate organ primordia but not organ development. , 2005, Plant & cell physiology.

[7]  T. Lukácsovich,et al.  Suppression of intrachromosomal gene conversion in mammalian cells by small degrees of sequence divergence. , 1999, Genetics.

[8]  S. Lin,et al.  A high-density rice genetic linkage map with 2275 markers using a single F2 population. , 1998, Genetics.

[9]  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.

[10]  M. Takano,et al.  The Rice COLEOPTILE PHOTOTROPISM1 Gene Encoding an Ortholog of Arabidopsis NPH3 Is Required for Phototropism of Coleoptiles and Lateral Translocation of Auxinw⃞ , 2005, The Plant Cell Online.

[11]  L H. Rieseberg,et al.  Chromosomal rearrangements and speciation. , 2001, Trends in ecology & evolution.

[12]  H. Dooner,et al.  Remarkable variation in maize genome structure inferred from haplotype diversity at the bz locus , 2006, Proceedings of the National Academy of Sciences.

[13]  Hong Ma,et al.  The FLORAL ORGAN NUMBER4 Gene Encoding a Putative Ortholog of Arabidopsis CLAVATA3 Regulates Apical Meristem Size in Rice1[W] , 2006, Plant Physiology.

[14]  M. Yano,et al.  Hd1, a Major Photoperiod Sensitivity Quantitative Trait Locus in Rice, Is Closely Related to the Arabidopsis Flowering Time Gene CONSTANS , 2000, Plant Cell.

[15]  J. Bennetzen,et al.  Targeting xa13, a recessive gene for bacterial blight resistance in rice , 2006, Theoretical and Applied Genetics.

[16]  T. R. Sharma,et al.  High-resolution mapping, cloning and molecular characterization of the Pi-kh gene of rice, which confers resistance to Magnaporthe grisea , 2005, Molecular Genetics and Genomics.

[17]  H. Fu,et al.  The highly recombinogenic bz locus lies in an unusually gene-rich region of the maize genome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[18]  G. Martin,et al.  Chromosome landing: a paradigm for map-based gene cloning in plants with large genomes. , 1995, Trends in genetics : TIG.

[19]  H. Leung,et al.  Spotted leaf11, a Negative Regulator of Plant Cell Death and Defense, Encodes a U-Box/Armadillo Repeat Protein Endowed with E3 Ubiquitin Ligase Activityw⃞ , 2004, The Plant Cell Online.

[20]  M. Yano,et al.  A Novel Cytochrome P450 Is Implicated in Brassinosteroid Biosynthesis via the Characterization of a Rice Dwarf Mutant, dwarf11, with Reduced Seed Length , 2005, The Plant Cell Online.

[21]  B. Burr,et al.  Recombinant inbreds for molecular mapping in maize: theoretical and practical considerations. , 1991, Trends in genetics : TIG.

[22]  R. Durrett,et al.  A simple formula useful for positional cloning. , 2002, Genetics.

[23]  Qifa Zhang,et al.  Fine mapping of f5-Du, a gene conferring wide-compatibility for pollen fertility in inter-subspecific hybrids of rice (Oryza sativa L.) , 2005, Theoretical and Applied Genetics.

[24]  M. Purugganan,et al.  Genomic Variation in Rice: Genesis of Highly Polymorphic Linkage Blocks during Domestication , 2006, PLoS genetics.

[25]  Adésio Ferreira,et al.  Estimating the effects of population size and type on the accuracy of genetic maps , 2006 .

[26]  Amanda J. Garris,et al.  Genetic Structure and Diversity in Oryza sativa L. , 2005, Genetics.

[27]  Qifa Zhang,et al.  Delimitation of the rice wide compatibility gene S5n to a 40-kb DNA fragment , 2005, Theoretical and Applied Genetics.

[28]  Dawei Li,et al.  The Genomes of Oryza sativa: A History of Duplications , 2005, PLoS biology.

[29]  Kede Liu,et al.  Map-based cloning of a novel rice cytochrome P450 gene CYP81A6 that confers resistance to two different classes of herbicides , 2006, Plant Molecular Biology.

[30]  P. Donnelly,et al.  The Fine-Scale Structure of Recombination Rate Variation in the Human Genome , 2004, Science.

[31]  Eric S. Lander,et al.  Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms , 1988, Nature.

[32]  J. Bennetzen,et al.  Exceptional haplotype variation in maize , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[33]  Z. Hong,et al.  A Rice Brassinosteroid-Deficient Mutant, ebisu dwarf (d2), Is Caused by a Loss of Function of a New Member of Cytochrome P450 Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.014712. , 2003, The Plant Cell Online.

[34]  W. Zhai,et al.  A B-lectin receptor kinase gene conferring rice blast resistance. , 2006, The Plant journal : for cell and molecular biology.

[35]  Takuji Sasaki,et al.  The map-based sequence of the rice genome , 2005, Nature.

[36]  M. Yano,et al.  qUVR-10, a Major Quantitative Trait Locus for Ultraviolet-B Resistance in Rice, Encodes Cyclobutane Pyrimidine Dimer Photolyase , 2005, Genetics.

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

[38]  Thomas D. Wu,et al.  GMAP: a genomic mapping and alignment program for mRNA and EST sequence , 2005, Bioinform..

[39]  Qi Xie,et al.  The rice HIGH-TILLERING DWARF1 encoding an ortholog of Arabidopsis MAX3 is required for negative regulation of the outgrowth of axillary buds. , 2006, The Plant journal : for cell and molecular biology.

[40]  M. Matsuoka,et al.  Analysis of the Rice Mutant dwarf and gladius leaf 1. Aberrant Katanin-Mediated Microtubule Organization Causes Up-Regulation of Gibberellin Biosynthetic Genes Independently of Gibberellin Signaling , 2005, Plant Physiology.

[41]  R. He,et al.  High-resolution genetic mapping at the Bph15 locus for brown planthopper resistance in rice (Oryza sativa L.) , 2004, Theoretical and Applied Genetics.

[42]  S. Luan,et al.  A rice quantitative trait locus for salt tolerance encodes a sodium transporter , 2005, Nature Genetics.

[43]  M. Yano,et al.  Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the α subunit of protein kinase CK2 , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[44]  M. Nachman,et al.  Variation in recombination rate across the genome: evidence and implications. , 2002, Current opinion in genetics & development.

[45]  M. Matsuoka,et al.  Isolation of a rice regeneration quantitative trait loci gene and its application to transformation systems. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[46]  Richard Robinson.  Jump-Starting a Cellular World: Investigating the Origin of Life, from Soup to Networks , 2005, PLoS biology.

[47]  The gene FLORAL ORGAN NUMBER1 regulates floral meristem size in rice and encodes a leucine-rich repeat receptor kinase orthologous to Arabidopsis CLAVATA1 , 2004, Development.

[48]  Dana C Crawford,et al.  Evidence for substantial fine-scale variation in recombination rates across the human genome , 2004, Nature Genetics.

[49]  M. Yano,et al.  A rice spotted leaf gene, Spl7, encodes a heat stress transcription factor protein , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[50]  M. Jean,et al.  The impact of sequence divergence and DNA mismatch repair on homeologous recombination in Arabidopsis. , 2006, The Plant journal : for cell and molecular biology.

[51]  H. Seo,et al.  Rice Chlorina-1 and Chlorina-9 encode ChlD and ChlI subunits of Mg-chelatase, a key enzyme for chlorophyll synthesis and chloroplast development , 2006, Plant Molecular Biology.

[52]  Nori Kurata,et al.  PLASTOCHRON1, a timekeeper of leaf initiation in rice, encodes cytochrome P450. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[53]  Masatomo Kobayashi,et al.  GIBBERELLIN INSENSITIVE DWARF1 encodes a soluble receptor for gibberellin , 2005, Nature.

[54]  M. Yano,et al.  Expression of Xa1, a bacterial blight-resistance gene in rice, is induced by bacterial inoculation. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[55]  X. Liu,et al.  Genetic and physical mapping of Pi36(t), a novel rice blast resistance gene located on rice chromosome 8 , 2005, Molecular Genetics and Genomics.

[56]  R. Visser,et al.  Construction of a 10,000-Marker Ultradense Genetic Recombination Map of Potato: Providing a Framework for Accelerated Gene Isolation and a Genomewide Physical Map , 2006, Genetics.

[57]  Q. Qian,et al.  GOLD HULL AND INTERNODE2 Encodes a Primarily Multifunctional Cinnamyl-Alcohol Dehydrogenase in Rice1 , 2006, Plant Physiology.

[58]  Michael Freeling,et al.  Grains of knowledge: genomics of model cereals. , 2005, Genome research.

[59]  M. Yano,et al.  Physical maps and recombination frequency of six rice chromosomes. , 2003, The Plant journal : for cell and molecular biology.

[60]  Wei Zhu,et al.  The Institute for Genomic Research Osa1 Rice Genome Annotation Database1 , 2005, Plant Physiology.

[61]  Qian Qian,et al.  EUI1, encoding a putative cytochrome P450 monooxygenase, regulates internode elongation by modulating gibberellin responses in rice. , 2006, Plant & cell physiology.

[62]  Toshio Yamamoto,et al.  Fine genetic mapping of the nuclear gene, Rf-1, that restores the BT-type cytoplasmic male sterility in rice (Oryza sativa L.) by PCR-based markers , 2004, Euphytica.

[63]  M. Yano,et al.  An SNP Caused Loss of Seed Shattering During Rice Domestication , 2006, Science.

[64]  J. Dutheil,et al.  Recombination Difference between Sexes: A Role for Haploid Selection , 2005, PLoS biology.

[65]  M. Yano,et al.  The Pib gene for rice blast resistance belongs to the nucleotide binding and leucine-rich repeat class of plant disease resistance genes. , 1999, The Plant journal : for cell and molecular biology.

[66]  N. Su,et al.  Fine mapping of S32(t), a new gene causing hybrid embryo sac sterility in a Chinese landrace rice (Oryza sativa L.) , 2007, Theoretical and Applied Genetics.

[67]  Xinli Sun,et al.  Xa26, a gene conferring resistance to Xanthomonas oryzae pv. oryzae in rice, encodes an LRR receptor kinase-like protein. , 2004, The Plant journal : for cell and molecular biology.

[68]  Shiping Wang,et al.  Genetic and physical mapping of a new gene for bacterial blight resistance in rice , 2003, Theoretical and Applied Genetics.

[69]  W. Zhai,et al.  Characterizations and fine mapping of a mutant gene for high tillering and dwarf in rice (Oryza sativa L.) , 2005, Planta.

[70]  Y. Hiei,et al.  Map-based cloning of a fertility restorer gene, Rf-1, in rice (Oryza sativa L.). , 2004, The Plant journal : for cell and molecular biology.

[71]  M. Raizada,et al.  Inexpensive fine mapping and positional cloning in plants using visible, mapped transgenes , 2006 .

[72]  Q. Qian,et al.  BRITTLE CULM1, Which Encodes a COBRA-Like Protein, Affects the Mechanical Properties of Rice Plants Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.011775. , 2003, The Plant Cell Online.

[73]  D. Botstein,et al.  Construction of a genetic linkage map in man using restriction fragment length polymorphisms. , 1980, American journal of human genetics.

[74]  Y. Kamiya,et al.  ELONGATED UPPERMOST INTERNODE Encodes a Cytochrome P450 Monooxygenase That Epoxidizes Gibberellins in a Novel Deactivation Reaction in Rice[W] , 2006, The Plant Cell Online.