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Identification and High-Density Mapping of Gene-Rich Regions in Chromosome Group 5 of Wheat

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Identification and High-Density Mapping of Gene-Rich Regions in Chromosome Group 5 of Wheat Copyright 8 1996 by the Genetics Society of America Identification and High-Density Mapping of Gene-Rich Regions in Chromosome Group 5 of Wheat Kulvinder S. Gill,* Bikram S. Gill,* Takashi R. Endot and Elena V. Boyko* *Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66506 and tLaboratory of Genetics, Faculty of Agnculture, Kyoto University, Kyoto, 606 Japan Manuscript received August 17, 1995 Accepted for publication March 13, 1996 ABSTRACT The distribution of genes and recombination in the wheat genome was studied by comparing physical maps with the genetic linkage maps. The physical maps were generated by mapping 80 DNA and two phenotypic markers on an array of 65 deletion lines for homoeologous group 5 chromosomes. The genetic maps were constructed for chromosome 5B in wheat and 50 in Triticum tauschii. No marker mapped in the proximal 20% chromosome region surrounding the centromere.More than 60% of the long arm markers were present in three major clusters that physically encompassed <18% of the arm. Because 48% of the markers were cDNA clones and the distributions of the cDNA and genomic clones were similar, the marker distribution may represent the distribution of genes. The gene clusters were identified and allocated to very small chromosome regions because of a higher number of deletions in their surrounding regions. The recombination was suppressed in the centromeric regions and mainly occurred in the gene-rich regions. The bp/cM estimates varied from 118 kb for gene-rich regions to 22 Mb for gene-poor regions. The wheat genes present in these clusters are, therefore, amenable tomolecu- lar manipulations parallel to the plants with smaller genomes like rice. HE bread wheat (Triticum aestivum L. em. Thell., resultant physical maps are then compared with the T 2n = 6X = 42) possesses a large genome (16 bil- corresponding genetic linkage maps to analyze the lion bp per haploid genome), which is about six times physical distribution of recombination and order of the size of maize and 35 times that of rice (BENNETT markers within each chromosome region. The genetic and SMITH1976). The three crop plants most probably mapping may be performed in wheat or in any of its originated from a common ancestor -60 million years relative species. A physical map is compared with a ge- ago (BENNETZENand FREELING1993). Besidespoly- netic linkage map by drawing lines to join the common ploidy in wheat, a key step in the evolution of these markers. The resultant composite map is called a cyto- three crops was differential amplification of DNA, to a genetic ladder map (CLM) (GILL andGILL 1994b). The greaterextent in wheat than in maize or rice. The previously constructed CLMs have established that the amount of actively transcribing DNA is probably not distributions of markers and recombination are uneven much different among the three genomes. The genes along the wheat chromosomes (WERNERet al. 1992; in wheat may be present in uninterrupted clusters, indi- GILLet al. 1993a; KOTA et al. 1993; HOHMANNet al. 1994; vidually interspersed by repetitive DNA blocks, or in a DELANEYet al. 1995a,b; MICKELSON-YOUNGet al. 1995). combination of the two arrangements. Thedistribution In the present study, we illustrate the effectiveness of pattern of genes will greatly influence the choice and the CLM strategy to identify and preferentially map success of techniques for molecular manipulation of gene-rich regions in homoeologous group 5 chromo- the genome. Map-based cloning of the genes individu- somes of wheat. ally interspersed by noncoding repetitive DNA would be difficult. Conversely, clustered genes will be amena- MATERIALS AND METHODS ble to such manipulations, parallel to the plants with smaller genomes like rice. Genetic stocks: Genetic markers were physically mapped We proposed a mapping strategy to target gene-rich using 65 deletion lines for wheat group 5 chromosomes (5A, 54 and 50).Twenty of these deletion lines were for the short regions of the wheat genome (GILL and GILL1994b). arms and 45 were for thelong arms. There were eight deletion Briefly, single-break deletion lines are used to divide lines each for the short arm of chromosomes 5A and 54 and each wheat chromosome into small regions marked by four for 5D. For the long arm, there were 22, 14 and nine chromosome bands, protein and DNA markers. The deletion lines for chromosomes 54 54 and 50, respectively. The deletion lines were generated using the gametocidal Corresponding author: Kulvinder S. Gill, Wheat Genetics Resource chromosome of Aegilops qlindn'ca (ENDO1988; ENDOand GILL Center, Department of Plant Pathology, 4307 Throckrnorton Hall, 1996). Nullisomic-tetrasomic (NT) lines (missing apair of Kansas State University, Manhattan, KS 66506. chromosomes, the deficiency of which is compensated by a E-mail: [email protected] pair of homoeologous chromosomes) and ditelosomic lines Genetics 143 1001-1012 (June, 1996) 1002 K. S. Gill et al. TABLE 1 The clones used for genetic and physical mappingof wheat homoeologous group 5 chromosomes No. of bands Chromosome locationChromosome bands cDNA/ Total no. Clone"genomic of bands Enzyme 5A5D 5B T. tauschii Wheat PgsP C 3 EcoRI 1115s pTa71 C 8 EcoRI 0015 lBS, 5DS dhn2 C 12 EcoRI 2115 5L pHvabc309 C 5 HindIII 0115 51, pHvabg705 G 3 HindIII 111 5s pHvcnlbcdl57 C 4 HindIII 1215 5L pHudcd204 C 6 EcoRI 2125 5L pHvmlbcd351 C 7 EcoRI 2225 5L pHbcnlbcd450 C 3 HindIII 1115 5L pHvmlbcd508 C 10 HindIII 1111, 5 5L, IL pHvmlbcdlO87 C 2 HindIII 0015 5L pAsmlcdo57 C 7 HindIII 0127s 5L, 2A,7AS, 7BL, 7DL pAsnlcdo213 C 3 HindIII 1115 5L pAsdcdo388 C 13 HindIII 103IS, 2L, 3L, 4S, 5, 6 5L, lBS, IDS, 2DL PAsdcdo400 C 5 EcoRI 1125 5L, 1L pAsmlcdo412 C 3 HindIII 1115 5L PAsdCdo484 C 4 EcoRI 011 5L, 4L, 2L pAscnlcdo677 C 3 EcoRI 1115 5s pAsmlcdo687 C 8 HindIII 0117s 5s, 7L pAsmlcdo786 C 4 HindIII 0017s 5L pAscnlcdol049 C 3 EcoRI 1115 5L pAsmlcdo1312 C 4 EcoRI 1004, 5 5AL, 4BL,4DL pAsmlcdo1333 C 6 EcoRI 1004, 5 5AL, 4BL, 4DL pAsmlcdol335 C 4 HindIII 1115 5s pHvh8 C 12 EcoRI 1625 5L pHvksu24 C 8 EcoRI 3225 5L pHvksu26 C 3 HindIII 1115 5L pHvksu5S C 5 HindIII 2125 5L pTtkma3 G 7 EcoRI 2125 5L pTtksudl6 G 4 HindIII 1115 5L pTtksud30 G 7 EcoRI 2225 5L pTtksud42 G 3 HindIII 111- 5L PTtksufl G 5 EcoRI 1115 5L pTtksug7 G 13 HindIII 1025, 7 5AL, 5DL, 7L pTtksugl2 G 6 EcoRI 0015, 7L 5DL,7AL pThgl4 G 3 EcoRI 1115 5L pTtksug44 G 3 HindIII 1115 5L pTtksug5 7 G 3 HindIII 1115, 2 5L pTtksug60 G 5 HindIII 2105 5s pTtksuh8 G 15 HindIII 0102, 3, 5, 7 5BS,7L pTtksui26 G 7 EcoRI 1125 5s pTtksum2 G 4 BamHl 1125 5L pTtksus1 G 4 HindIII 1115 5L pTamwg522 G 4 EcoRI 1215 5L pTamwg602 G 3 HindIII 0115 5L pTapsr 79 C 5 EcoRI 1115 5L pTapsrll5 C 7 EcoRI 0215 4AL, 5BL, 5DL pTapsrll8 C 5 HindIII 1115 5s pTapsrl20 C 8 EcoRI 2235 5L pTapsrl28 C 3 EcoRI 1115 5L pTapsrl45 C 12 EcoRI 3445 5L p Tapsrl70 C 8 EcoRI 1003 54 3L pTapsr3 70 C 4 EcoRI 2115 51 pTapsr580 C 3 EcoRI 0115 4AL, 5BL, 5DL pTapsr628 C 4 EcoRI 1115 51 pTapsr63 7 C 3 EcoRI 1115 51 pTagl65 G -3 HindIII 0125 5 Mapping Gene-Rich Regions of Wheat 1003 TABLE 1 Continued ~~ ~~~ No. of bands Chromosome location cDNA/ Total no. Clone“genomic of bands Enzyme5B 5A 50 T. tauschii Wheat pTag222 G 1 HindIII 0 102 WL, 5BL pTag251 G 6 HindIII 1105 5L pTag317 G 10 HindIII1 1 0 3,4,5 5, 6A pTag319 G 7 HindIII 0 2 25 5s pTag354 G 4 HindIII 0 115 4A, 4B, 5BL, 5DL pTag614 G 6 HindIII 2 115 5L, 6B, 6D pTag621 G 1 HindIII 00 15 5L pTag644 G 3 HindIII 11 15 5L pTag651 G 3 HindIII 0 115 5, 7AS pTag695 G 7 EcoRI 2 125 5L pTag754 G 6 EcoRI 0 105 5, 7B pTacnlwgl14 G 4 HindIII 10 04 4BL, 4DL, 5AL pTantlwg363 G 3 HindIII 111 5s pTacnlwg341 G 4 EcoRI 11 15 5L, 6L, 7L pTantlwg419 G 3 EcoRI 11 15 5L pTanlwg530 G 3 EcoRI 0 115 5L pTacnlwg564 G 10 HindIII 14 35 5L pTanlwg583 G 3 EcoRI 11 15 5L pTacnlwg444 G 3 EcoRI 11 15 5L pTanlwg889 G 6 EcoRI 011 5L, 3L pTacnlwg908 G 5 EcoRI 12 15 5L pTacnlwg909 G 5 EcoRI 11 15 5L, 2BS, 7BS pTacnEwglO26 G 5 EcoRI 13 15 5L “Total no. of bands” and “No. of bands for5A, 5B, and 50” are from mappingon nulli-tetra lines of wheat cultivar Chinese Spring. The type of probe is indicated as C for the cDNA clones and G for the genomic. The restriction enzyme used for genomic DNA digestion of the aneuploid lines is mentioned under “Enzyme.” The probes shown boldface were mapped on the 5B population of RSLs. a bcd, cdo, and wg were barley cDNA, oats cDNA, and wheat genomic clones, respectively, from Dr. MARK SORRELLS;mwgwere barley genomic from Dr. A. GRANER;psrwere wheat cDNA from Dr. MIKEGALE; Tagwere wheat ”genomic from Dr. KOICHIROTSUNEWAKI: Huksu and Ttlzsu were barley cDNA and T. tauschii PstI genomic clones, respectively, from our laboratory. (SEARS1954) were used to assign DNA restriction fragment were only interchromosomally mapped to group 5 chromo- bands to theirrespective chromosome arms. The populations somes using NT lines. The “dhn2” probe is a barley dehydrin used for linkage analyses are described in the later sections. gene that mapped to chromosome5H (TIMCLOSE, personal All the deletion lines, genetic and aneuploidstocks are main- communication).
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