Development of new genomic microsatellite markers from robusta coffee (Coffea canephoraPierre ex A. Froehner) showing broad cross-species transferability and utility in genetic studies
Tóm tắt
Species-specific microsatellite markers are desirable for genetic studies and to harness the potential of MAS-based breeding for genetic improvement. Limited availability of such markers for coffee, one of the most important beverage tree crops, warrants newer efforts to develop additional microsatellite markers that can be effectively deployed in genetic analysis and coffee improvement programs. The present study aimed to develop new coffee-specific SSR markers and validate their utility in analysis of genetic diversity, individualization, linkage mapping, and transferability for use in other related taxa. A small-insert partial genomic library of Coffea canephora, was probed for various SSR motifs following conventional approach of Southern hybridisation. Characterization of repeat positive clones revealed a very high abundance of DNRs (1/15 Kb) over TNRs (1/406 kb). The relative frequencies of different DNRs were found as AT >> AG > AC, whereas among TNRs, AGC was the most abundant repeat. The SSR positive sequences were used to design 58 primer pairs of which 44 pairs could be validated as single locus markers using a panel of arabica and robusta genotypes. The analysis revealed an average of 3.3 and 3.78 alleles and 0.49 and 0.62 PIC per marker for the tested arabicas and robustas, respectively. It also revealed a high cumulative PI over all the markers using both sib-based (10-6 and 10-12 for arabicas and robustas respectively) and unbiased corrected estimates (10-20 and 10-43 for arabicas and robustas respectively). The markers were tested for Hardy-Weinberg equilibrium, linkage dis-equilibrium, and were successfully used to ascertain generic diversity/affinities in the tested germplasm (cultivated as well as species). Nine markers could be mapped on robusta linkage map. Importantly, the markers showed ~92% transferability across related species/genera of coffee. The conventional approach of genomic library was successfully employed although with low efficiency to develop a set of 44 new genomic microsatellite markers of coffee. The characterization/validation of new markers demonstrated them to be highly informative, and useful for genetic studies namely, genetic diversity in coffee germplasm, individualization/bar-coding for germplasm protection, linkage mapping, taxonomic studies, and use as conserved orthologous sets across secondary genepool of coffee. Further, the relative frequency and distribution of different SSR motifs in coffee genome indicated coffee genome to be relatively poor in microsatellites compared to other plant species.
Tài liệu tham khảo
Fitter R, Kaplinsky R: Who gains from product rents as the coffee market becomes more differentiated? A value chain analysis. IDS Bulletin (Special Issue). 2001, 32 (3): 69-82.
Powell W, Machray GC, Provan J: Polymorphism revealed by simple sequence repeats. Trends Plant Sci. 1996, 1: 215-222.
Gupta PK, Varshney RK: The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica. 2000, 113: 163-185.
Combes MC, Andrzejewski S, Anthony F, Bertrand B, Rovelli P, Graziosi G, Lashermes P: Characterization of microsatellite loci in Coffea arabica and related coffee species. Mol Ecol. 2000, 9: 1178-1180.
Rovelli P, Mettulio R, Anthony F, Anzueto F, Lashermes P, Graziosi G: Microsatellites in Coffea arabica L. Coffee Biotechnology and Quality. Edited by: Sera T, Soccol CR, Pandey A, Roussos S. Kluwer Academic Publishers; 2000:123-133.
Baruah A, Naik V, Hendre PS, Rajkumar R, Rajendrakumar P, Aggarwal RK: Isolation and characterization of nine microsatellite markers from Coffea arabica L., showing wide cross-species amplifications. Mol Ecol Notes. 2003, 3: 647-650.
Coulibaly I, Revol B, Noirot M, Poncet V, Lorieux M, Carasco-Lacombe C, Minier J, Dufour M, Hamon P: AFLP and SSR polymorphism in a Coffea interspecific backcross progeny [(C. heterocalyx X C. canephora) X C. canephora]. Theor Appl Genet. 2003, 107: 1148-1155.
Moncada P, McCouch S: Simple sequence repeat diversity in diploid and tetraploid Coffea species. Genome. 2004, 47: 501-509.
Poncet V, Hamon P, Minier J, Carasco C, Hamon S, Noirot M: SSR cross-amplification and variation within coffee trees (Coffea spp.). Genome. 2004, 47: 1071-1081.
Bhat PR, Krishnakumar V, Hendre PS, Rajendrakumar P, Varshney RK, Aggarwal RK: Identification and characterization of expressed sequence tags-derived simple sequence repeats markers from robusta coffee variety 'CXR' (an interspecific hybrid of Coffea canephora & Coffea congensis). Mol Ecol Notes. 2005, 80-83.
Aggarwal RK, Hendre PS, Varshney RK, Bhat PR, Krishnakumar V, Singh L: Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species. Theor Appl Genet. 2007, 114: 359-372.
Hendre PS, Aggarwal RK: DNA markers: development and application for genetic improvement of coffee. Genomic Assisted Crop Improvement: Genomics Applications in Crops. Edited by: Varshney RK, Tuberosa R. Springer-Verlag, Germany. 2007, 2: 399-434.
Marie D, Brown SC: A cytometric exercise in plant DNA histograms, with 2C values for 70 species. Biol Cell. 1993, 78: 41-51. [http://data.kew.org/cvalues/searchguide.html]
Zane L, Bargelloni L, Patarnello T: Strategies for microsatellite isolation: a review. Mol Ecol. 2002, 11: 1-16.
Butcher PA, Decroocq S, Gray Y, Moran GF: Development, inheritance and cross-species amplification of microsatellite markers from Acacia mangium. Theor Appl Genet. 2000, 101: 1282-1290.
Ferguson ME, Burow MD, Schulze SR, Bramel PJ, Paterson AH, Kresovich S, Mitchell S: Microsatellite identification and characterization in peanut (A. hypogaea L.). Theor Appl Genet. 2004, 108: 1064-1070.
Chen X, Temnykh S, Xu Y, Cho YG, McCouch SR: Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.). Theor Appl Genet. 1997, 95: 553-567.
Ashkenazi V, Chani E, Lavi U, Levy D, Hillel J, Veilleux RE: Development of microsatellite markers in potato and their use in phylogenetic and fingerprinting analyses. Genome. 2001, 44: 50-62.
Bryan GJ, Collins AJ, Stephenson P, Orry A, Smith JB, Gale MD: Isolation and characterisation of microsatellites from hexaploid bread wheat. Theor Appl Genet. 1997, 94: 557-563.
Rajora OP, Rahman MH, Dayanandan S, Mosseler A: Isolation, characterization, inheritance and linkage of microsatellite DNA markers in white spruce (Picea glauca) and their usefulness in other spruce species. Mol Gen Genet. 2001, 264 (6): 871-882.
Cardle L, Ramsay L, Milbourne D, Macaulay M, Marshall D, Waugh R: Computational and Experimental Characterization of Physically Clustered Simple Sequence Repeats in Plants. Genetics. 2000, 156: 847-854.
Guilford P, Prakash S, Zhu JM, Rikkerink E, Gardiner S, Bassett H, Forster R: Microsatellites in Malus X domestica (apple): abundance, polymorphism and cultivar identification. Theor Appl Genet. 1997, 94: 249-254.
Sharon D, Cregan PB, Mhameed S, Kusharska M, Hillel J, Lahav E, Lavi U: An integrated genetic linkage map of avocado. Theor Appl Genet. 1997, 95: 911-921.
Pekkinen M, Varvio S, Kulju KK, Karkkainen H, Smolander S, Vihera-Aarnio A, Koski V, Sillanpaa MJ: Linkage map of birch, Betula pendula Roth, based on microsatellites and amplified fragment length polymorphisms. Genome. 2005, 48: 619-625.
Sosinski B, Gannavarapu M, Hager LD, Beck LE, King GJ, Ryder CD, Rajapakse S, Baird WV, Ballard RE, Abbott AG: Characterization of microsatellite markers in peach [Prunus persica (L.) Batsch]. Theor Appl Genet. 2000, 101: 421-428.
Areshchenkova T, Ganal MW: Comparative analysis of polymorphism and chromosomal location of tomato microsatellite markers isolated from different sources. Theor Appl Genet. 2002, 104: 229-235.
Lagercrantz U, Ellegren H, Andersson L: The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. Nucleic Acids Res. 1993, 21: 1111-1115.
Wang Z, Weber JL, Zhong G, Tanksley SD: Survey of plant short tandem DNA repeats. Theor Appl Genet. 1994, 88: 1-6.
Miyao A, Zhong HS, Monna L, Yano M, Yamamoto K, Havukkala I, Minobe Y, Sasaki T: Characterization and genetic mapping of simple sequence repeats in the rice genome. DNA Res. 1996, 3: 233-238.
Akagi H, Yokozeki Y, Inagaki A, Fujimura T: Microsatellite DNA markers for rice chromosomes. Theor Appl Genet. 1996, 93: 1071-1077.
Song QJ, Fickus EW, Cregan PB: Characterization of trinucleotide SSR motifs in wheat. Theor Appl Genet. 2002, 104: 286-293.
Mba REC, Stephenson P, Edwards K, Melzer S, Nkumbira J, Gullberg U, Apel K, Gale M, Tohme J, Fregene M: Simple sequence repeat (SSR) markers survey of the cassava (Manihot esculenta Crantz) genome: towards an SSR-based molecular genetic map of cassava. Theor Appl Genet. 2001, 102: 21-31.
Sun GL, Salomon B, Bothmer RV: Characterization and analysis of microsatellite loci in Elymus caninus (Tritiaceae: Poaceae). Theor Appl Genet. 1998, 96: 676-682.
Pal N, Sandhu JS, Domier LL, Kolb FL: Development and characterization of microsatellite and RFLP-derived PCR markers in oat. Crop Sci. 2002, 42: 912-918.
Slavov GT, Howe GT, Yakovlev I, Edwards KJ, Krutovskii KV, Tuskan GA, Carlson JE, Strauss SH, Adams WT: Highly variable SSR markers in Douglas-fir: Mendelian inheritance and map locations. Theor Appl Genet. 2004, 108: 873-880.
Danin-Poleg Y, Reis N, Tzuri G, Katzir N: Development and characterization of microsatellite markers in Cucumis. Theor Appl Genet. 2001, 102: 61-72.
Pfeiffer A, Oliveri AM, Morgante M: Identification and characterisation of microsatellites in Norway spruce (Picea abies K.). Genome. 1997, 40: 419-
Hicks M, Adams D, O'Keefe S, MacDonald E, Hodgegetts R: The development of RAPD and microsatellite markers in lodgepole pine (Pinus contorta var. latifolia). Genome. 1998, 41: 797-805.
Soranzo N, Provan J, Powell W: Characterisation of microsatellite loci in Pinus sylvestris L. Mol Ecol. 1998, 7: 1260-1261.
Garner TW: Genome size and microsatellites: the effect of nuclear size on amplification potential. Genome. 2002, 45: 212-215.
Varshney RK, Graner A, Sorrells ME: Genic microsatellite markers in plants: features and applications. Trends Biotechnol. 2005, 23: 48-55.
Lashermes P, Combes MC, Trouslot P, Anthony F, Charrier A: Molecular analysis of the origin and genetic diversity of Coffea arabica L.: implications for coffee improvement. Proceedings of EUCARPIA meeting on tropical plants. Montpellier, France; 1996:23-29.
Aggarwal RK, Rajkumar R, Rajendrakumar P, Hendre PS, Baruah A, Phanindranath R, Annapurna V, Prakash NS, Santaram A, Sreenivasan CS, Singh L: Fingerprinting of Indian coffee selections and development of reference DNA polymorphism panels for creating molecular IDs for variety identification. Proceedings of 20th international conference on coffee science (ASIC). Bangalore, India; 2004:751-755.
Lashermes P, Combes MC, Prakash NS, Trouslot P, Lorieux M, Charrier A: Genetic linkage map of Coffea canephora : effect of segregation distortion and analysis of recombination rate in male and female meioses. Genome. 2001, 44: 589-596.
Peakall R, Gilmore S, Keys W, Morgante M, Rafalski A: Cross-species amplification of soybean (Glycine max) simple sequence repeats (SSRs) within the genus and other legume genera: implications for the transferability of SSRs in plants. Mol Biol Evol. 1998, 15: 1275-1287.
Chevalier A: Les cafeiers du globe. III. Systematique des caféiers at Faux cafeiers. Maladieset insect nuisible. Encyclopedie de biologique 28. Edited by: Lechevalier P. Paris, France; 1947:356-
Ruas PM, Ruas CF, Rampim L, Carvaljo VP, Ruas EA, Sera T: Genetic relationship in Coffea species and parentage determination of interspecific hybrids using ISSR (inter-simple sequence repeat) markers. Genet Mol Biol. 2003.
Orozco-Castillo C, Chalmers KJ, Powell W, Waugh R: RAPD and organelle specific PCR re-affirms taxonomic relationships within the genus Coffea. Plant Cell Reports. 1996, 15: 337-341.
Lashermes P, Combes MC, Trouslot P, Charrier A: Phylogenetic relationship of coffee-tree species (Coffea L.) as inferred from ITS sequences of nuclear ribosomal DNA. Theor Appl Genet. 1997, 94: 947-955.
Aggarwal RK, Shenoy VV, Ramadevi J, Rajkumar R, Singh L: Molecular characterization of some Indian Basmati and other elite rice genotypes using fluorescent-AFLP. Theor Appl Genet. 2002, 105: 680-690.
Sambrook J, Fritsch EF, Maniatis T: Molecular cloning: A laboratory manual. New York: Cold Spring Harbor Press; 1989.
Excoffier L, Laval G, Schneider S: Arlequin ver 3.0: an integrated software package for population genetics data analysis. Evol Bioinform Online. 2005, 1: 47-50.
Botstein D, White RL, Skolnick M, Davis RW: Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet. 1980, 32: 314-331.
Valiere N: Gimlet: a computer program for analysing genetic individual identification data. Mol Ecol Notes. 2002, 2: 377-379.
Glaubitz JC: Convert: a user-friendly program to reformat diploid genotypic data for commonly used population genetic software packages. Mol Ecol Notes. 2004, 4: 309-310.
Waits LP, Luikart G, Taberlet P: Estimating the probability of identity among genotypes in natural populations: cautions and guidelines. Mol Ecol. 2001, 10: 249-256.
Dieringer D, Schlotterer C: MicroSatellite Analyser (MSA): a platform independent analysis tool for large microsatellite data sets. Mol Ecol. 2003, 3: 167-169.
Nei M: Genetic distance between populations. Am Naturalist. 1972, 106: 238-292.
Felsenstein J: PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle; 2004.