Genetic and physical mapping of the SH3 region that confers resistance to leaf rust in coffee tree (Coffea arabica L.)
Tóm tắt
Resistance to coffee leaf rust is conferred by SH3, a major dominant gene that has been introgressed from a wild coffee species Coffea liberica (genome L) into the allotetraploid cultivated species, Coffea arabica (genome CaEa). As the first step toward the map-based cloning of the SH3 gene, using a bacterial artificial chromosome (BAC) library, we describe the construction of a physical map in C. arabica spanning the resistance locus. This physical map consists in two homeologous BAC-contigs of 1,170 and 1,208 kb corresponding to the subgenomes Ca and Ea, respectively. Genetic analysis was performed using a single nucleotide polymorphism detection assay based on Sanger sequencing of amplicons. The C. liberica-derived chromosome segment that carries the SH3 resistance gene appeared to be introgressed on the sub-genome Ca. The position of the SH3 locus was delimited within an interval of 550 kb on the physical map. In addition, our results indicated a sixfold reduction in recombination frequency in the introgressed SH3 region compared to the orthologous region in Coffea canephora.
Tài liệu tham khảo
Barker CL, Donald T, Pauquet J, Ratnaparkhe MB, Bouquet A, Adam-Blondon AF, Thomas MR, Dry I (2005) Genetic and physical mapping of the grapevine powdery mildew resistance gene, Run1, using a bacterial artificial chromosome library. Theor Appl Genet 111:370–377
Diniz LEC, Sakiyama NS, Lashermes P, Caixeta ET, Oliviera ACB, Zambolin EM, Loureiro ME, Pereira AA, Zambolin L (2005) Analysis of AFLP markers associated to the Mex-1 locus in Icatu progenies. Crop Breed App Biotech 5:387–393
Drouaud J, Camilleri C, Bourguignon PY, Canaguier A, Bérard A, Vezon D, Giancola S, Brunel D, Colot V, Prum B, Quesneville H, Mézard C (2006) Variation in crossing-over rates across chromosome 4 of Arabidopsis thaliana reveals the presence of meiotic recombination “hot spots”. Genome Res 16:106–114
Eskes AB (1989) Resistance. In: Kushalappa AC, Eskes AB (eds) Coffee rust: epidemiology, resistance, and management. CRC Press, Florida, pp 171–291
Etienne H, Lashermes P, Menéndez-Yuffá A, De Guglielmo-Cróquer Z, Alpizar E, Sreenath HL (2008) Coffee. In: Kole C, Hall TC (eds) A compendium of transgenic crop plants, volume 8, plantation crops, ornamentals and turf grasses. Blackwell Publishing, Oxford, UK, pp 57–84
Ganal MW, Tanksley SD (1996) Recombination around the Tm2a and Mi resistance genes in different crosses of Lycopersicon peruvianum. Theor Appl Genet 92:101–108
Herrera JC, D’Hont A, Lashermes P (2007) Use of fluorescent in situ hybridization as a tool for introgression analysis and chromosome identification in coffee (Coffea arabica L.). Genome 50:619–626
Hert DG, Fredlake CP, Barron AE (2008) Advantages and limitations of next-generation sequencing technologies: a comparison of electrophoresis and non-electrophoresis methods. Electrophoresis 29:4618–4626
Kushalappa AC, Eskes AB (1989) Advances in coffee rust research. Annu Rev Phytopathol 27:503–531
Lander ES, Green P, Abrahamson J, Bralow A, Daly MJ, Loincoln SE, Newburg L (1987) MAP MAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181
Lashermes P, Combes MC, Robert J, Trouslot P, D’hont A, Anthony F, Charrier A (1999) Molecular characterisation and origin of the Coffea arabica L. genome. Mol Gen Genet 261:259–266
Lashermes P, Combes MC, Prakash NS, Trouslot P, Lorieux M, Charrier A (2001) Genetic linkage map of Coffea canephora: effect of segregation distortion and analysis of recombination rate in male and female meiosis. Genome 44:589–596
Lashermes P, Combes MC, Ansaldi C, Gichuru E, Noir S (2010) Analysis of alien introgression in coffee tree (Coffea arabica L.). Mol Breed. doi:10.1007/s11032-010-9424-2, in press
Mahé L, Combes MC, Lashermes P (2007) Comparison between a coffee single copy chromosomal region and Arabidopsis duplicated counterparts evidenced high level synteny between the coffee genome and the ancestral Arabidopsis genome. Plant Mol Biol 64:699–711
Mahé L, Combes MC, Varzea VMP, Guilhaumon C, Lashermes P (2008) Development of sequence characterized DNA markers linked to leaf rust (Hemileia vastatrix) resistance in coffee (Coffea arabica L.). Mol Breed 21:105–113
Marra MA, Kucaba TA, Dietrich NL, Green ED, Brownstein B, Wilson RK, McDonald KM, Hillier L, McPherson J, Waterston R (1997) High throughput fingerprint analysis of large-insert clones. Genome Res 7:1072–1084
Martin GB, Bogdanove AJ, Sessa G (2003) Understanding the functions of plant disease resistance proteins. Annu Rev Plant Biol 54:23–61
Nachman MW (2002) Variation in recombination rate across the genome: evidence and implications. Curr Opin Genet Dev 12:657–663
Neu C, Stein N, Keller B (2002) Genetic mapping of the Lr20–Pm1 resistance locus reveals suppressed recombination on chromosome arm 7AL in hexaploid wheat. Genome 45:737–744
Noir S, Patheyron S, Combes MC, Lashermes P, Chalhoub B (2004) Construction and characterisation of a BAC library for genome analysis of the allotetraploid coffee species (Coffea arabica L.). Theor Appl Genet 109:225–230
Peters JL, Cnudde F, Gerats T (2003) Forward genetics and map-based cloning approaches. Trends Plant Sci 8(10):484–491
Prakash NS, Combes MC, Naveen KS, Lashermes P (2002) AFLP analysis of introgression in coffee cultivars (Coffea arabica L.) derived from a natural interspecific hybrid. Euphytica 124:265–271
Prakash NS, Marques DV, Varzea VMP, Silva MC, Combes MC, Lashermes P (2004) Introgression molecular analysis of a leaf rust resistance gene from Coffea liberica into Coffea arabica L. Theor Appl Genet 109:1311–1317
Prakash NS, Ganesh D, Bhat SS (2005) Population dynamics of coffee leaf rust (Hemileia vastatrix) and recent advances in India. In: Zambolim L, Zambolim E, Várzea VMP (eds) Durable resistance to coffee leaf rust. Universidade Federal de Viçosa, Brasil, pp 411–442
Rafalski JA (2002) Novel genetic mapping tools in plants: SNPs and LD-based approaches. Plant Sci 162:329–333
Ramachandran M, Srinivasan CS (1979) Four generations of selection for resistance to race I of leaf rust in arabica cv. S.288 × ‘Kents’. Indian Coffee 43(6):159–161
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463–5467
Srinivasan KH, Narasimhaswamy RL (1975) A review of coffee breeding work done at the Government coffee experiment station, Balehonnur. Indian coffee 34:311–321
Staden R, Judge DP, Bonfield JK (2000) The Staden package, 1998. Meth Mol Biol 132:115–130
Stirling B, Newcombe G, Vrebalov J, Bosdet I, Bradshaw HD (2001) Suppressed recombination around the MXC3 locus, a major gene for resistance to poplar leaf rust. Theor Appl Genet 103:1129–1137
Van der Vossen HAM (2001) Coffee breeding practices. In: Clarke RJ, Vitzthum OG (eds) Coffee. Recent developments – agronomy, vol 1. Blackwell Science Ltd, London, pp 184–201
Várzea VMP, Marques DV (2005) Population variability of Hemileia vastatrix vs coffee durable resistance. In: Zambolim L, Zambolim E, Várzea VMP (eds) Durable resistance to coffee leaf rust. Universidade Federal de Viçosa, Brasil, pp 53–74
Wei F, Gobel-Werner K, Morroll SM, Kurth J, Mao L, Wing RA, Leister D, Schulze-Lefert P, Wise RP (1999) 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 153:1929–1948