Functional mapping in pea, as an aid to the candidate gene selection and for investigating synteny with the model legume Medicago truncatula
Tóm tắt
The identification of the molecular polymorphisms giving rise to phenotypic trait variability—both quantitative and qualitative—is a major goal of the present agronomic research. Various approaches such as positional cloning or transposon tagging, as well as the candidate gene strategy have been used to discover the genes underlying this variation in plants. The construction of functional maps, i.e. composed of genes of known function, is an important component of the candidate gene approach. In the present paper we report the development of 63 single nucleotide polymorphism markers and 15 single-stranded conformation polymorphism markers for genes encoding enzymes mainly involved in primary metabolism, and their genetic mapping on a composite map using two pea recombinant inbred line populations. The complete genetic map covers 1,458 cM and comprises 363 loci, including a total of 111 gene-anchored markers: 77 gene-anchored markers described in this study, 7 microsatellites located in gene sequences, 16 flowering time genes, the Tri gene, 5 morphological markers, and 5 other genes. The mean spacing between adjacent markers is 4 cM and 90% of the markers are closer than 10 cM to their neighbours. We also report the genetic mapping of 21 of these genes in Medicago truncatula and add 41 new links between the pea and M. truncatula maps. We discuss the use of this new composite functional map for future candidate gene approaches in pea.
Tài liệu tham khảo
Andersen PS, Jespersgaard C, Vuust J, Christiansen M, Larsen LA (2003) High-throughput single strand conformation polymorphism mutation detection by automated capillary array electrophoresis: validation of the method. Hum Mutat 21(2):116–122
Bhattacharyya MK, Smith AM, Ellis THN, Hedley C, Martin C (1990) The wrinkled seed character of pea described by Mendel is caused by a transposon-like insertion in a gene encoding starch branching enzyme. Cell 60:115–121
Burstin J, Deniot G, Potier J, Weinachter C, Aubert G, Baranger A (2001) Microsatellite polymorphism in Pisum sativum. Plant Breeding 120:311–317
Byrne PF, McMullen MD, Snook ME, Musket TA, Theuri JM, Widstrom NW, Wiseman BR, Coe EH (1996) Quantitative trait loci and metabolic pathways: genetic control of the concentration of maysin, a corn earworm resistance factor, in maize silks. Proc Natl Acad Sci USA 93(17):8820–8825
Causse M, Rocher JP, Henry AM, Charcosset A, Prioul JL and De Vienne D (1995) Genetic dissection of the relationship between carbon metabolism and early growth in maize, with emphasis on key-enzyme loci. Mol Breed 1:259–272
Causse M, Santoni S, Damerval C, Maurice A, Charcosset A, Deatrick J and De Vienne D (1996) A composite map of expressed sequences in maize. Genome 39:418–432
Causse M, Duffe P, Gomez MC, Buret M, Damidaux R, Zamir D, Gur A, Chevalier C, Lemaire-Chamley M, Rothan C (2004) A genetic map of candidate gene and QTLs involved in tomato fruit size and composition. J Exp Bot 55:1671–1685
Chen X, Salamini F and Gebhardt C (2001) A potato molecular function map for carbohydrate metabolims and transport. Theor Appl Genet 102:284–295
Choi HK, Mun JH, Dong-Jin K, Zhu H, Baek JM, Mudge J, Roe B, Ellis N, Doyle J, Kiss GB, Young ND, Cook DR (2004) Estimating genome conservation between crop and model legume species. Proc Natl Acad Sci USA 101(43):15289–15294
Craig J, Lloyd JR, Tomlinson K, Barber L, Edwards A, Wang TL, Martin C, Hedley CL, Smith AM (1998) Mutations in the gene encoding starch synthase II profoundly alter amylopectin structure in pea embryos. Plant Cell 10:413–426
Craig J, Barratt P, Tatge H, Déjardin A, Handley L, Gardner CD, Barber L, Wang TL, Hedley C, Martin C, Smith AM (1999) Mutations at the rug4 locus alter carbon and nitrogen metabolism of pea plants through an effect on sucrose synthase. Plant J 17:353–362
Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA minipreparation: version II. Plant Mol Biol Rep 1:19–21
Délye C, Calmes E, Matejicek A (2002) SNP markers for black-grass (Alopecurus myosuroides Huds.) genotypes resistant to acetyl CoA-carboxylase inhibiting herbicides. Theor Appl Genet 104(6–7):1114–1120
Ellis THN, Poyser SJ (2002) An integrated and comparative view of pea genetic and cytogenetic maps. New Phytol 153:17–25
Foucher F, Morin J, Courtiade J, Cadioux S, Ellis N, Banfield MJ, Rameau C (2003) Determinate and late flowering are two terminal flower1/centroradialis homologs that control two distinct phases of flowering initiation and development in pea. Plant Cell 15(11):2742–2754
Frewen BE, Chen TH, Howe GT, Davis J, Rohde A, Boerjan W, Bradshaw HD Jr (2000) Quantitative trait loci and candidate gene mapping of bud set and bud flush in populus. Genetics 154(2):837–845
Fridman E, Pleban T, Zamir D (2000) A recombination hotspot delimits a wild species quantitative trait locus for tomato sugar content to 484 bp within an invertase gene. Proc Natl Acad Sci USA 97:4718–4723
Gilpin BJ, McCallum JA, Frew TJ, Timmerman-Vaughan GM (1997) A linkage map of the pea Pisum sativum L. genome containing cloned sequences of known function and expressed tags ESTs. Theor Appl Genet 95:1289–1299
Gualtieri G, Kulikova O, Kim D-J, Cook DR, Bisseling T, Geurts R (2002) Microsynteny between pea and Medicago truncatula in the SYM2 region. Plant Mol Biol 50:225–235
Hall KJ, Parker JS, Ellis THN, Turner L, Know MR, Hofer JMI, Lu J, Ferrandiz C, Hunter PJ, Taylor JD, Baird K (1997) The relationship between genetic and cytogenetic maps of pea. II. Physical maps of linkage mapping populations. Genome 40:755–769
Harrison CJ, Hedley CL, Wang TL (1998) Evidence that the rug3 locus of pea (Pisum sativum L.) encodes a plastidial phospho glucomutase confirms that the imported substrate for starch synthesis in pea amyloplasts is glucose-6-phosphate. Plant J 13:753–762
Hecht V, Foucher F, Ferrandiz C, Macknight R, Navarro C, Morin J, Vardy ME, Ellis N, Beltran JP, Rameau C, Weller JL (2005) Conservation of Arabidopsis flowering genes in model legumes. Plant Physiol 137:1420–1434
Irzykowska L, Wolko B, Swiecicki WK (2001) The genetic linkage map of pea (Pisum sativum L.) based on molecular, biochemical, and morphological markers. Pisum genetics 33:13–18
Ishimaru K, Yano M, Aoki N, Ono K, Hirose T, Lin SY, Monna L, Sasaki T, Ohsugi R (2001) Toward the mapping of physiological and agronomic characters on a rice function map: QTL analysis and comparison between QTLs and expressed sequence tags. Theor Appl Genet 102:793–800
Kalo P, Seres A, Taylor SA, Jakab J, Kevei Z, Kereszt A, Endre G, Ellis TH, Kiss GB (2004) Comparative mapping between Medicago sativa and Pisum sativum. Mol Genet Genomics 272:235–246
Konovalov F, Toshchakova E, Gostimsky S (2005) A CAPS marker set for mapping in linkage group III of pea (Pisum sativum L.). Cell Mol Biol Lett 10:163–171
Lanaud C, Risterucci AM, Pieretti I, N’Goran JAK, Forgeas D (2004) Characterisation and genetic mapping of resistance and defence gene analogs in cocoa (Theobroma cacao L.). Mol Breed 13:211–227
Lander ES, Green P, Abrahamson J, Barlow A, Daly M, Lincoln S, Newberg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181
Laucou V, Haurogné K, Ellis N, Rameau C (1998) Genetic mapping in pea. 1. RAPD-based genetic linkage map of Pisum sativum. Theor Appl Genet 97:905–915
Lincoln S, Daly M, Lander ES (1992) Constructing genetic maps with MAPMAKER/EXP 3.0. Whitehead Institute Technical Report, 3rd edn. Whitehouse Technical Institute, Cambridge
Loridon K, McPhee K, Morin J, Dubreuil P, Pilet-Nayel ML, Aubert G, Rameau C, Baranger A, Coyne C, Lejeune-Hènaut I, Burstin J (2005) Microsatellite marker polymorphism and mapping in pea (Pisum sativum L.) Theor Appl Genet. DOI 10.1007/s00122-005-0014-3
Martin C, Smith AM (1995) Starch biosynthesis. Plant Cell 7:971–985
Mc Phee KE (2005) Pea. In: Kole C (ed) Genome mapping and molecular breeding, vol III: pulse and tuber crops. Science Publishers, Enfield (in press)
Morgante M, Salamini F (2003) From plant genomics to breeding practice. Curr Opin Biotech 14:214–219
Murray MG, Thompson WF (1980) Rapid isolation of high-molecular-weight plant DNA. Nucleic Acids Res 8:4321–4325
Neff MM, Neff JD, Chory J, Pepper AE (1998) dCAPS, a simple technique for the genetic analysis of single nucleotide polymorphisms: experimental applications in Arabidopsis thaliana genetics. Plant J 14(3):387–392
Osterberg MK, Shavorskaya O, Lascoux M, Lagercrantz U (2002) Naturally occurring indel variation in the Brassica nigra COL1 gene is associated with variation in flowering time. Genetics 161(1):299–306
Page D, Aubert G, Duc G, Welham T, Domoney C (2002) Combinatorial variation in coding and promoter sequences of genes at the Tri locus in Pisum sativum accounts for variation in trypsin inhibitor activity in seeds. Mol Genet Genomics 267(3):359–369
Pelleschi S, Guy S, Kim JY, Pointe C, Mahé A, Barthes L, Leonardi A, and Prioul JL (1999) Ivr2, a candidate gene for a QTL of vacuolar invertase activity in maize leaves. Gene-specific expression under water stress. Plant Mol Biol 39:373–380
Pfaff T, Kahl G (2003) Mapping of gene-specific markers on the genetic map of chickpea (Cicer arietinum L.). Mol Gen Genomics 269:243–251
Pflieger S, Lefebvre V, Caranta C, Blattes A, Goffinet B, and Palloix A (1999) Disease resistance gene analogs as candidates for QTLs involved in pepper/pathogen interactions. Genome 42:1100–1110
Potokina E, Caspers M, Prasad M, Kota R, Zhang H, Sreenivasulu N, Wang M, Graner A (2004) Functional association between malting quality trait components and cDNA array based expression patterns in barley (Hordeum vulgare L.). Mol Breed 14:153–170
Prioul JL, Pelleschi S, Sene M, Thevenot C, Causse M, de Vienne D, Leonardi A (1999) From QTLs for enzyme activity to candidate genes in maize. J Exp Bot 50:1281–1288
Prioul S, Frankewitz A, Deniot G, Morin G, Baranger A (2004) Mapping of quantitative trait loci for partial resistance to Mycosphaerella pinodes in pea (Pisum sativum L.), at the seedling and adult plant stages. Theor Appl Genet 108:1322–1334
Ren X, Wang X, Yuan H, Weng Q, Zhu L, He G (2004) Mapping quantitative trait loci and expressed sequence tags related to brown planthopper resistance in rice. Plant Breed 123:342–348
Robertson DS (1985) A possible technique for isolating genic DNA for quantitative traits in plants. J Theor Biol 117:1–10
Rolletschek H, Borisjuk L, Radchuk R, Miranda M, Heim U et al (2004) Seed specific expression of a bacterial phosphoenolpyruvate carboxylase in Vicia narbonensis increases protein content and improves carbon economy. Plant Biotech J 2:211–220
Rosov SM, Kosterin O, Borisov AY, Tsyganov V (1999) The history of the pea gene map: last revolutions and the new symbiotic genes. Pisum genetics 31:555–570
Schiex T, Chabrier P, Bouchez M, Milan D (2001) Boosting EM for radiation hybrid and genetic mapping. In: Proceedings of the WABI’2001 (First workshop on algorithms in bioInformatics), LNCS 2149, pp 41–51
Tar’an B, Warkentin T, Somers DJ, Miranda D, Vandenberg A, Blade S, Bing D (2004) Identification of quantitative trait loci for grain yield, seed protein concentration and maturity in field pea (Pisum sativum L.). Euphityca 136:297–306
Thévenot C, Simond-Côte E, Reyss A, Manicacci D, Trouverie J, Le Guilloux M, Ginhoux V, Sidicina F, Prioul JL (2005) QTLs for enzyme activities and soluble carbohydrates involved in starch accumulation during grain filling in maize. J Exp Bot 56:945–958
Thoquet P, Ghérardi M, Journet EP, Kereszt A, Ané JM, Prosperi JM, Huguet T (2002) The molecular genetic linkage map of the model legume Medicago truncatula: an essential tool for comparative legume genomics and the isolation of agronomically important genes, BMC Plant Biol 2:1. http://www.biomedcentral.com/1471-2229/2/1
Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ES IV (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28(3):286–289
Timmerman-Vaughan GM, McCallum JA, Frew TJ, Weeden NF, Russell AC (1996) Linkage mapping of quantitative trait loci controlling seed weight in pea (Pisum sativum L.). Theor Appl Genet 93:431–439
Timmerman-Vaughan GM, Frew TJ, Weeden NF (2000) Characterization and linkage mapping of R-gene analogous DNA sequences in pea (Pisum sativum L.). Theor Appl Genet 101:241–247
Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93(1):77–78
Waddington CH (1943) Polygenes and oligogenes. Nature 151:394
Wang Z, Taramino G, Yang D, Liu G, Tingey SV, Miao GH, Wang GL (2001) Rice ESTs with disease resistance gene- or defence-response gene-like sequences mapped to regions containing major resistance genes or QTLs. Mol Genet Genomics 265:302–310
Weber H, Borisjuk L, Wobus U (2005) Molecular physiology of legume seed development. Annu Rev Plant Biol 56:253–279
Weeden NF, Marx GA (1987) Further genetic analysis and linkage relationships of isozyme loci in pea. J Hered 78:153–159
Weeden NF, Wolko B (1990) Linkage map of the garden pea (Pisum sativum). In: O’Brien SJ (ed) Genetic maps—locus maps of complex genomes, 5th edn. Book 6 Plants. Cold Spring Harbor, New York
Weeden NF, Ellis THN, Timmerman-Vaughan GM, Swiecicki WK, Rozov SM, Berdnikov VA (1998) A consensus linkage map for Pisum sativum. Pisum genetics 30:1–3
Weeden NF, Tonguc M, Boone WE (1999) Mapping coding sequences in pea by PCR. Pisum genet 31:30–32
Young ND, Cannon SB, Sato S, Kim D, Cook DR, Town CD, Roe BA, Tabata S (2005). Sequencing the genespaces of Medicago truncatula and Lotus japonicus. Plant Physiology 137:1174–1181
Zhu HY, Kim DJ, Baek JM, Choi HK, Ellis LC, Kuester H, McCombie WR, Peng HM, Cook DR (2003) Syntenic relationships between Medicago truncatula and Arabidopsis reveal extensive divergence of genome organization. Plant Physiol 131:1018–1026