Abstract
The short arm of Triticeae homeologous group 1 chromosomes is known to contain many agronomically important genes. The objectives of this study were to physically localize gene-containing regions of the group 1 short arm, enrich these regions with markers, and study the distribution of genes and recombination. We focused on the major gene-rich region ("1S0.8 region") and identified 75 useful genes along with 93 RFLP markers by comparing 35 different maps of Poaceae species. The RFLP markers were tested by gel blot DNA analysis of wheat group 1 nullisomic-tetrasomic lines, ditelosomic lines, and four single-break deletion lines for chromosome arm 1BS. Seventy-three of the 93 markers mapped to group 1 and detected 91 loci on chromosome 1B. Fifty-one of these markers mapped to two major gene-rich regions physically encompassing 14% of the short arm. Forty-one marker loci mapped to the 1S0.8 region and 10 to 1S0.5 region. Two cDNA markers mapped in the centromeric region and the remaining 24 loci were on the long arm. About 82% of short arm recombination was observed in the 1S0.8 region and 17% in the 1S0.5 region. Less than 1% recombination was observed for the remaining 85% of the physical arm length.
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- Ahn S., Anderson J. A., Sorrells M. E., Tanksley S. D. Homoeologous relationships of rice, wheat and maize chromosomes. Mol Gen Genet. 1993 Dec;241(5-6):483–490. doi: 10.1007/BF00279889. [DOI] [PubMed] [Google Scholar]
- Ahn S., Tanksley S. D. Comparative linkage maps of the rice and maize genomes. Proc Natl Acad Sci U S A. 1993 Sep 1;90(17):7980–7984. doi: 10.1073/pnas.90.17.7980. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Barakat A., Carels N., Bernardi G. The distribution of genes in the genomes of Gramineae. Proc Natl Acad Sci U S A. 1997 Jun 24;94(13):6857–6861. doi: 10.1073/pnas.94.13.6857. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Barakat A., Han D. T., Benslimane A., Rode A., Bernardi G. The gene distribution in the genomes of pea, tomato and date palm. FEBS Lett. 1999 Dec 10;463(1-2):139–142. doi: 10.1016/s0014-5793(99)01587-2. [DOI] [PubMed] [Google Scholar]
- Bennett M. D., Smith J. B. Nuclear dna amounts in angiosperms. Philos Trans R Soc Lond B Biol Sci. 1976 May 27;274(933):227–274. doi: 10.1098/rstb.1976.0044. [DOI] [PubMed] [Google Scholar]
- Bennetzen J. L., Freeling M. Grasses as a single genetic system: genome composition, collinearity and compatibility. Trends Genet. 1993 Aug;9(8):259–261. doi: 10.1016/0168-9525(93)90001-x. [DOI] [PubMed] [Google Scholar]
- Bennetzen J. L., SanMiguel P., Chen M., Tikhonov A., Francki M., Avramova Z. Grass genomes. Proc Natl Acad Sci U S A. 1998 Mar 3;95(5):1975–1978. doi: 10.1073/pnas.95.5.1975. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bernardi G. The isochore organization of the human genome and its evolutionary history--a review. Gene. 1993 Dec 15;135(1-2):57–66. doi: 10.1016/0378-1119(93)90049-9. [DOI] [PubMed] [Google Scholar]
- Burr B., Burr F. A., Thompson K. H., Albertson M. C., Stuber C. W. Gene mapping with recombinant inbreds in maize. Genetics. 1988 Mar;118(3):519–526. doi: 10.1093/genetics/118.3.519. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Büschges R., Hollricher K., Panstruga R., Simons G., Wolter M., Frijters A., van Daelen R., van der Lee T., Diergaarde P., Groenendijk J. The barley Mlo gene: a novel control element of plant pathogen resistance. Cell. 1997 Mar 7;88(5):695–705. doi: 10.1016/s0092-8674(00)81912-1. [DOI] [PubMed] [Google Scholar]
- Cai D., Kleine M., Kifle S., Harloff H. J., Sandal N. N., Marcker K. A., Klein-Lankhorst R. M., Salentijn E. M., Lange W., Stiekema W. J. Positional cloning of a gene for nematode resistance in sugar beet. Science. 1997 Feb 7;275(5301):832–834. doi: 10.1126/science.275.5301.832. [DOI] [PubMed] [Google Scholar]
- Carels N., Barakat A., Bernardi G. The gene distribution of the maize genome. Proc Natl Acad Sci U S A. 1995 Nov 21;92(24):11057–11060. doi: 10.1073/pnas.92.24.11057. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Causse M. A., Fulton T. M., Cho Y. G., Ahn S. N., Chunwongse J., Wu K., Xiao J., Yu Z., Ronald P. C., Harrington S. E. Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics. 1994 Dec;138(4):1251–1274. doi: 10.1093/genetics/138.4.1251. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Chaudhuri S., Messing J. RFLP mapping of the maize dzr1 locus, which regulates methionine-rich 10 kDa zein accumulation. Mol Gen Genet. 1995 Mar 20;246(6):707–715. doi: 10.1007/BF00290716. [DOI] [PubMed] [Google Scholar]
- Civardi L., Xia Y., Edwards K. J., Schnable P. S., Nikolau B. J. The relationship between genetic and physical distances in the cloned a1-sh2 interval of the Zea mays L. genome. Proc Natl Acad Sci U S A. 1994 Aug 16;91(17):8268–8272. doi: 10.1073/pnas.91.17.8268. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Devey M. E., Hart G. E. Chromosomal localization of intergenomic RFLP loci in hexaploid wheat. Genome. 1993 Oct;36(5):913–918. doi: 10.1139/g93-120. [DOI] [PubMed] [Google Scholar]
- Deynze A. E., Nelson J. C., Sorrells M. E., McCouch S. R., Dubcovsky J., Dvorák J., Gill K. S., Gill B. S., Lagudah E. S., Appels R. Molecular-genetic maps for group 1 chromosomes of Triticeae species and their relation to chromosomes in rice and oat. Genome. 1995 Feb;38(1):45–59. doi: 10.1139/g95-006. [DOI] [PubMed] [Google Scholar]
- Dubcovsky J., Luo M., Dvorak J. Differentiation between homoeologous chromosomes 1A of wheat and 1Am of Triticum monococcum and its recognition by the wheat Ph1 locus. Proc Natl Acad Sci U S A. 1995 Jul 3;92(14):6645–6649. doi: 10.1073/pnas.92.14.6645. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Dunford R. P., Kurata N., Laurie D. A., Money T. A., Minobe Y., Moore G. Conservation of fine-scale DNA marker order in the genomes of rice and the Triticeae. Nucleic Acids Res. 1995 Jul 25;23(14):2724–2728. doi: 10.1093/nar/23.14.2724. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Dvorák J., Chen K. C. Distribution of Nonstructural Variation between Wheat Cultivars along Chromosome Arm 6Bp: Evidence from the Linkage Map and Physical Map of the Arm. Genetics. 1984 Feb;106(2):325–333. doi: 10.1093/genetics/106.2.325. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Elgin S. C. The formation and function of DNase I hypersensitive sites in the process of gene activation. J Biol Chem. 1988 Dec 25;263(36):19259–19262. [PubMed] [Google Scholar]
- Faris J. D., Haen K. M., Gill B. S. Saturation mapping of a gene-rich recombination hot spot region in wheat. Genetics. 2000 Feb;154(2):823–835. doi: 10.1093/genetics/154.2.823. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Feuillet C., Keller B. High gene density is conserved at syntenic loci of small and large grass genomes. Proc Natl Acad Sci U S A. 1999 Jul 6;96(14):8265–8270. doi: 10.1073/pnas.96.14.8265. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gallego F., Feuillet C., Messmer M., Penger A., Graner A., Yano M., Sasaki T., Keller B. Comparative mapping of the two wheat leaf rust resistance loci Lr1 and Lr10 in rice and barley. Genome. 1998 Jun;41(3):328–336. doi: 10.1139/g98-024. [DOI] [PubMed] [Google Scholar]
- Gill K. S., Gill B. S., Endo T. R., Boyko E. V. Identification and high-density mapping of gene-rich regions in chromosome group 5 of wheat. Genetics. 1996 Jun;143(2):1001–1012. doi: 10.1093/genetics/143.2.1001. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gill K. S., Gill B. S., Endo T. R., Taylor T. Identification and high-density mapping of gene-rich regions in chromosome group 1 of wheat. Genetics. 1996 Dec;144(4):1883–1891. doi: 10.1093/genetics/144.4.1883. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Group of Fifth-Year Medical Students. Richardson I. M. Career Choice in Medicine. Br Med J. 1962 Sep 1;2(5304):582–585. [PMC free article] [PubMed] [Google Scholar]
- Ikemura T., Wada K. Evident diversity of codon usage patterns of human genes with respect to chromosome banding patterns and chromosome numbers; relation between nucleotide sequence data and cytogenetic data. Nucleic Acids Res. 1991 Aug 25;19(16):4333–4339. doi: 10.1093/nar/19.16.4333. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kilian A., Chen J., Han F., Steffenson B., Kleinhofs A. Towards map-based cloning of the barley stem rust resistance genes Rpg1 and rpg4 using rice as an intergenomic cloning vehicle. Plant Mol Biol. 1997 Sep;35(1-2):187–195. [PubMed] [Google Scholar]
- Kota R. S., Gill K. S., Gill B. S., Endo T. R. A cytogenetically based physical map of chromosome 1B in common wheat. Genome. 1993 Jun;36(3):548–554. doi: 10.1139/g93-075. [DOI] [PubMed] [Google Scholar]
- Künzel G., Korzun L., Meister A. Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints. Genetics. 2000 Jan;154(1):397–412. doi: 10.1093/genetics/154.1.397. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lahaye T., Shirasu K., Schulze-Lefert P. Chromosome landing at the barley Rar1 locus. Mol Gen Genet. 1998 Oct;260(1):92–101. doi: 10.1007/s004380050874. [DOI] [PubMed] [Google Scholar]
- Laurent A. M., Puechberty J., Prades C., Roizès G. Informative genetic polymorphic markers within the centromeric regions of human chromosomes 17 (D17S2205) and 11 (D11S4975). Genomics. 1998 Sep 1;52(2):166–172. doi: 10.1006/geno.1998.5428. [DOI] [PubMed] [Google Scholar]
- Laurie D. A., Pratchett N., Snape J. W., Bezant J. H. RFLP mapping of five major genes and eight quantitative trait loci controlling flowering time in a winter x spring barley (Hordeum vulgare L.) cross. Genome. 1995 Jun;38(3):575–585. doi: 10.1139/g95-074. [DOI] [PubMed] [Google Scholar]
- Lindsley D. L., Sandler L. The genetic analysis of meiosis in female Drosophila melanogaster. Philos Trans R Soc Lond B Biol Sci. 1977 Mar 21;277(955):295–312. doi: 10.1098/rstb.1977.0019. [DOI] [PubMed] [Google Scholar]
- McKee B. D., Handel M. A. Sex chromosomes, recombination, and chromatin conformation. Chromosoma. 1993 Jan;102(2):71–80. doi: 10.1007/BF00356023. [DOI] [PubMed] [Google Scholar]
- Mouchiroud D., D'Onofrio G., Aïssani B., Macaya G., Gautier C., Bernardi G. The distribution of genes in the human genome. Gene. 1991 Apr;100:181–187. doi: 10.1016/0378-1119(91)90364-h. [DOI] [PubMed] [Google Scholar]
- Puechberty J., Laurent A. M., Gimenez S., Billault A., Brun-Laurent M. E., Calenda A., Marçais B., Prades C., Ioannou P., Yurov Y. Genetic and physical analyses of the centromeric and pericentromeric regions of human chromosome 5: recombination across 5cen. Genomics. 1999 Mar 15;56(3):274–287. doi: 10.1006/geno.1999.5742. [DOI] [PubMed] [Google Scholar]
- Saccone S., De Sario A., Della Valle G., Bernardi G. The highest gene concentrations in the human genome are in telomeric bands of metaphase chromosomes. Proc Natl Acad Sci U S A. 1992 Jun 1;89(11):4913–4917. doi: 10.1073/pnas.89.11.4913. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schmidt R., West J., Love K., Lenehan Z., Lister C., Thompson H., Bouchez D., Dean C. Physical map and organization of Arabidopsis thaliana chromosome 4. Science. 1995 Oct 20;270(5235):480–483. doi: 10.1126/science.270.5235.480. [DOI] [PubMed] [Google Scholar]
- Segal G., Sarfatti M., Schaffer M. A., Ori N., Zamir D., Fluhr R. Correlation of genetic and physical structure in the region surrounding the I2 Fusarium oxysporum resistance locus in tomato. Mol Gen Genet. 1992 Jan;231(2):179–185. doi: 10.1007/BF00279789. [DOI] [PubMed] [Google Scholar]
- Spielmeyer W., Moullet O., Laroche A., Lagudah E. S. Highly recombinogenic regions at seed storage protein loci on chromosome 1DS of Aegilops tauschii, the D-genome donor of wheat. Genetics. 2000 May;155(1):361–367. doi: 10.1093/genetics/155.1.361. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sumner A. T., de la Torre J., Stuppia L. The distribution of genes on chromosomes: a cytological approach. J Mol Evol. 1993 Aug;37(2):117–122. doi: 10.1007/BF02407346. [DOI] [PubMed] [Google Scholar]
- Tanksley S. D., Ganal M. W., Prince J. P., de Vicente M. C., Bonierbale M. W., Broun P., Fulton T. M., Giovannoni J. J., Grandillo S., Martin G. B. High density molecular linkage maps of the tomato and potato genomes. Genetics. 1992 Dec;132(4):1141–1160. doi: 10.1093/genetics/132.4.1141. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Tranquilli G., Lijavetzky D., Muzzi G., Dubcovsky J. Genetic and physical characterization of grain texture-related loci in diploid wheat. Mol Gen Genet. 1999 Dec;262(4-5):846–850. doi: 10.1007/s004380051149. [DOI] [PubMed] [Google Scholar]
- Wei F., Gobelman-Werner K., Morroll S. M., Kurth J., Mao L., Wing R., Leister D., Schulze-Lefert P., Wise R. P. The Mla (powdery mildew) resistance cluster is associated with three NBS-LRR gene families and suppressed recombination within a 240-kb DNA interval on chromosome 5S (1HS) of barley. Genetics. 1999 Dec;153(4):1929–1948. doi: 10.1093/genetics/153.4.1929. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Weintraub H., Groudine M. Chromosomal subunits in active genes have an altered conformation. Science. 1976 Sep 3;193(4256):848–856. doi: 10.1126/science.948749. [DOI] [PubMed] [Google Scholar]
- Werner J. E., Endo T. R., Gill B. S. Toward a cytogenetically based physical map of the wheat genome. Proc Natl Acad Sci U S A. 1992 Dec 1;89(23):11307–11311. doi: 10.1073/pnas.89.23.11307. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Yunis J. J., Kuo M. T., Saunders G. F. Localization of sequences specifying messenger RNA to light-staining G-bands of human chromosomes. Chromosoma. 1977 Jun 23;61(4):335–344. doi: 10.1007/BF00288617. [DOI] [PubMed] [Google Scholar]
- Zhang H. B., Martin G. B., Tanksley S. D., Wing R. A. Map-based cloning in crop plants: tomato as a model system II. Isolation and characterization of a set of overlapping yeast artificial chromosomes encompassing the jointless locus. Mol Gen Genet. 1994 Sep 28;244(6):613–621. doi: 10.1007/BF00282751. [DOI] [PubMed] [Google Scholar]