Improving the quality of African robustas: QTLs for yield- and quality-related traits in Coffea canephora

Tree Genetics and Genomes

Volumn 7, Issue 4, 2011, Pages 781-798

  Leroy, Thierry ^a   De Bellis, Fabien ^a   Legnate, Hyacinthe ^c   Kananura, Edmund ^d   Gonzales, Gustavo ^e   Pereira, Luiz Felipe ^f   Andrade, Alan Carvalho ^g   Charmetant, Pierre ^a   Montagnon, Christophe ^b   Cubry, Philippe ^a   Marraccini, Pierre ^a   Pot, David ^a   de Kochko, Alexandre ^h  

^a UMR AGAP   (France)

^b Campus International de Baillarguet   (France)

^c Centre National de Recherche Agronomique (CNRA)   (France)

^d National Agricultural Research Organisation (NARO)   (Uganda)

^e UNIVERSITY OF SEVILLE   (Spain)

^f INSTITUTO AGRONÔMICO DO PARANÁ   (Brazil)

^g EMBRAPA RECURSOS GENÉTICOS E BIOTECNOLOGIA   (Brazil)

^h INSTITUT DE RECHERCHE POUR LE DÉVELOPPEMENT   (France)

Author keywords

Beverage quality; Biochemical traits; Coffee; Cup tasting; QTL; Yield

Indexed keywords

COFFEA CANEPHORA;

EID: 79960602159     PISSN: 16142942     EISSN: 16142950     Source Type: Journal    
DOI: 10.1007/s11295-011-0374-6     Document Type: Article

References (68)

1. Akaffou DS, Ky CL, Barre P, Hamon S, Louarn J, Noirot M (2003) Identification and mapping of a major gene (Ft1) involved in fructification time in the interspecific cross Coffea pseudozanguebariae x C. liberica var. Dewevrei: impact on caffeine content and seed weight. Theor Appl Genet 106: 1486-1490.
2. Alcazar A, Jurad JM, Martin MJ, Pablos F, Gonzales AG (2004) Enzymatic-spectrophotometric determination of sucrose in coffee beans. Talanta 67: 760-766.
3. Anthony F, Clifford MN, Noirot M (1993) Biochemical diversity in the genus Coffea L.: chlorogenic acids, caffeine and mozambioside contents. Genet Res Crop Evol 40: 61-70.
4. Anthony F, Bertrand B, Quiros O, Wilches A, Lashermes P, Berthaud J, Charrier A (2001) Genetic diversity of wild coffee (Coffea arabica L.) using molecular markers. Euphytica 118: 53-65.
5. Barre P, Akaffou S, Louarn J, Charrier A, Hamon S, Noirot M (1998) Inheritance of caffeine and heteroside contents in an interspecific cross between a cultivated coffee species Coffea liberica var dewevrei and a wild species caffeine-free C. pseudozanguebariae. Theor Appl Genet 96: 306-311.
6. Baruah A, Naik V, Hendre PS, Rajkumar R, Rajendrakumar P, Aggarwal K (2003) Isolation and characterization of nine microsatellite markers from Coffea arabica L. showing wide cross-species amplifications. Mol Ecol Notes 3: 647-650.
7. Berthaud J (1986) Les ressources génétiques pour l'amélioration des caféiers africains diploïdes. Evaluation de la richesse génétique des populations sylvestres et de ses mécanismes organisateurs. Conséquences pour l'application. ORSTOM, Paris.
8. Bertrand B, Guyot B, Anthony F, Lashermes P (2003a) Impact of the Coffea canephora gene introgression on beverage quality of C. Arabica. Theor Appl Genet 107: 387-394.
9. Bertrand C, Noirot M, Doulbeau S, de Kochko A, Hamon S, Campa C (2003b) Chlorogenic acid content swap during fruit maturation in Coffea pseudozanguebariae. Quantitative comparison with leaves. Plant Sci 165: 1355-1361.
10. Billote N, Marseillac N, Risterucci AM et al (2005) Microsatellite-based high density linkage map in oil palm (Elaeis guineensis Jacq.). Theor Appl Genet 110: 754-765.
11. Bouchet S, Marraccini P, Jourdan I, Leroy T, Vieira LGE, Ferreira LP, Musoli P, Pot D (2005) Nucleotide diversity and molecular evolution of five genes involved in the sucrose biosynthesis pathway of Coffea canephora. In: Proceedings of the 4th Plant Genomics European Meeting, Amsterdam, 20-23 Sept 2005.
12. Campa C, Noirot M, Bourgeois M, Pervent M, Ky CL, Chrestin H, Hamon S, de Kochko A (2003) Genetic mapping of a caffeoyl-coenzyme A 3-0-methltransferase gene in coffee trees. Impact on chlorogenic acid content. Theor Appl Genet 107: 751-756.
13. Causse M, Saliba V, Lesschaeve I, Buret M (2000) Genetic analysis of organoleptic quality in fresh-market tomato. 2. Mapping QTLs for sensory attributes. Theor Appl Genet 102: 257-272.
14. 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 genes and QTLs involved in tomato fruit size and composition. J Exp Bot 55: 1671-1685.
15. Charrier A, Berthaud J (1988) Principles and methods in coffee plant breeding Coffea canephora Pierre. In: Clarke RJ, Macrae R (eds) Coffee, vol 4, Agronomy. Elsevier Applied Science, London, pp 167-197.
16. Combes MC, Andrzejewski S, Anthony F, Bertrand B, Rovelli P, Grasiozi G, Lashermes P (2000) Characterization of microsatellite loci in Coffea arabica and related coffee species. Mol Ecol Notes 9: 1171-1193.
17. Coulibaly I, Revol B, Noirot M, Poncet V, Lorieux M, Carasco-Lacombe C, Minier J, Hamon P (2003) AFLP and SSR polymorphism in a Coffea interspecific backcross progeny ((C. heterocalyx x C. canephora) x C. canephora). Theor Appl Genet 107: 1148-1155.
18. D'Aoust MA, Yelle S, Nguyen-Quoc B (1999) Antisense inhibition of tomato fruit sucrose synthase decreases fruit setting and the sucrose unloading capacity of young fruit. Plant Cell 11: 2407-2418.
19. Dussert D, Lashermes P, Anthony F, Montagnon C, Trouslot P, Combes MC, Berthaud J, Noirot M, Hamon S (1999) Le caféier, Coffea canephora. In: Hamon P, Seguin M, Perrier X, Glaszmann JC (eds) Diversité génétique des plantes tropicales cultivées. CIRAD, Montpellier, pp 175-194.
20. Freire LP, Vieira NG, Vinecky F, Alvas GSC, Leroy T, Pot D, Elbelt S, Marques T, Rodrigues GC, Marraccini P, Andrade AC (2010). Expression analysis and nucleic polymorphism of candidate genes for drought tolerance in coffee (in press).
21. 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.
22. Geromel C, Ferreira LP, Guerreiro SMC, Cavalari AA, Pot D, Pereira LFP, Leroy T, Vieira LGE, Mazzafera P, Marraccini P (2006) Biochemical and genomic analysis of sucrose metabolism during coffee (Coffea arabica) fruit development. J Exp Bot 57: 3243-3258.
23. Geromel C, Ferreira LP, Davrieux F, Guyot B, Ribeyre F, dos Santos Scholz MB, Pereira LFP, Vaast P, Pot D, Leroy T, Androcioli Filho A, Vieira LGE, Mazzafera P, Marraccini P (2008) Effects of shade on the development and sugar metabolism of coffee (Coffea arabica L.) fruits. Plant Physiol Biochem 46: 569-579.
24. Gomez C, Dussert S, Hamon P, Hamon S, de Kochko A, Poncet V (2009) Current genetic differentiation of Coffea canephora Pierre ex A. Froehn in the Guineo-Congolian African zone: cumulative impact of ancient climatic changes and recent human activities. BMC Evol Biol 9: 167.
25. Grattapaglia D, Sederoff R (1994) Genetic maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-test cross mapping strategy and RAPD markers. Genetics 137: 1121-1137.
26. Henery ML, Moran GF, Wallis IR, Foley WJ (2007) Identification of quantitative trait loci influencing foliar concentrations of terpenes and formylated phloroglucinol compounds in Eucalyptus nitens. New Phytol 176: 82-95.
27. Jansen RC, Stam P (1994) High resolution of quantitative traits into multiple loci via interval mapping. Genetics 136: 1447-1455.
28. Joët T, Laffargue A, Salmona J, Doulbeau S, Descroix F, Bertrand B, de Kochko A, Dussert S (2009) Metabolic pathways in tropical dicotyledonous albuminous seeds: Coffea arabica as a case study. New Phytol 182: 146-162.
29. Joët T, Salmona J, Laffargue A, Descroix F, Dussert S (2010) Use of the growing environment as a source of variation to identify the quantitative trait transcripts and modules of co-expressed genes that determine chlorogenic acid accumulation. Plant Cell Environ 33: 1220-1233.
30. Kenis K, Keulemans J, Davey MW (2008) Identification and stability of QTLs for fruit quality traits in apple. Tree Genet Gen 4: 647-661.
31. Klann EM, Hall B, Bennett AB (1996) Antisense acid invertase (TIV1) gene alters soluble sugar composition and size in transgenic tomato fruit. Plant Physiol 112: 1321-1330.
32. Ky CL, Louarn J, Guyot B, Charrier A, Hamon S, Noirot M (1999) Relations between and inheritance of chlorogenic acid contents in an interspecific cross between Coffea pseudozanguebariae and Coffea liberica var 'dewevrei'. Theor Appl Genet 98: 628-637.
33. Ky CL, Doulbeau S, Guyot B, Akaffou S, Charrier A, Hamon S, Louarn J, Noirot M (2000a) Inheritance of coffee bean sucrose content in the interspecific cross Coffea pseudozanguebariae x Coffea liberica 'dewevrei'. Plant Breed 119: 165-168.
34. Ky CL, Barre P, Lorieux M, Trouslot P, Akaffou S, Louarn J, Charrier A, Hamon S, Noirot M (2000b) Interspecific genetic linkage map, segregation distortion and genetic conversion in coffee (Coffea sp.). Theor Appl Genet 101: 669-676.
35. Ky CL, Louarn J, Dussert S, Guyot B, Hamon S, Noirot M (2001a) Caffeine, trigonelline, chlorogenic acids and sucrose diversity in wild Coffea arabica L. and C. canephora P. accessions. Food Chem 75: 223-230.
36. Ky CL, Guyot B, Louarn J, Hamon S, Noirot M (2001b) Trigonelline inheritance in the interspecific Coffea pseudozanguebariae x C. liberica var. dewevrei cross. Theor Appl Genet 102: 630-634.
37. Lashermes P, Couturon E, Moreau N, Paillard M, Louarn J (1996) Inheritance and genetic mapping of self -incompatibility in Coffea canephora Pierre. Theor Appl Genet 93: 458-462.
38. 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 meioses. Genome 44: 589-596.
39. Lefebvre-Pautigny F, Wu F, Philippot M, Rigoreau M, Priyono ZM, Frasse P, Bouzayen M, Broun P, Pétiard V, Tanksley SD, Crouzillat D (2010) High resolution syntheny maps allowing direct comparisons between the coffee and tomato genome. Tree Genet Gen 6: 565-577.
40. Lepelley M, Cheminade G, Tremillon N, Simkin A, Caillet V, McCarthy J (2007) Chlorogenic acid syntheses in coffee: An analysis of CGA content and real-time RT-PCR expression of HCT, HQT, C3H1, and CCoAOMT1 genes during grain development in C. canephora. Plant Sci 172: 978-996.
41. Leroy T, Montagnon C, Charrier A, Eskes AB (1993) Reciprocal recurrent selection applied to Coffea canephora Pierre I. Characterization and evaluation of breeding populations and value of intergroup hybrids. Euphytica 67: 113-125.
42. Leroy T, Montagnon C, Cilas C, Charrier A, Eskes AB (1994) Reciprocal recurrent selection applied to Coffea canephora Pierre II. Evaluation of genetic parameters. Euphytica 74: 121-128.
43. Leroy T, Marraccini P, Dufour M, Montagnon C, Lashermes P, Sabau X, Ferreira LP, Jourdan I, Pot D, Andrade AC, Glaszmann JC, Vieira LGE, Piffanelli P (2005) Construction and characterization of a Coffea canephora BAC library to study the organization of sucrose biosynthesis genes. Theor Appl Genet 111: 1032-1041.
44. Leroy T, Ribeyre F, Bertrand B, Charmetant P, Dufour M, Montagnon C, Marraccini P, Pot D (2006) Genetics of coffee quality. Braz J Plant Physiol 18: 229-242.
45. Lin C, Mueller LA, McCarthy J, Crouzillat D, Pétiard V, Tanksley S (2005) Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts. Theor Appl Genet 112: 114-130.
46. Lu H, Romero-Severson J, Bernardo R (2002) Chromosomal regions associated with segregation distortion in maize. Theor Appl Genet 105: 622-628.
47. Misako K, Kouichi M (2004) Caffeine synthase and related methyltransferases in plants. Front Biosci 9: 1833-1842.
48. Moncada P, McCouch S (2004) Simple sequences repeat diversity in diploid and tetraploid Coffea species. Genome 47: 501-509.
49. Montagnon C, Leroy T, Yapo A (1992) Diversité génotypique et phénotypique de quelques groupes de caféiers (Coffea canephora Pierre) en collection. Conséquences sur leur utilisation en sélection. Café Cacao Thé 36: 187-198.
50. Montagnon C, Guyot B, Cilas C, Leroy T (1998) Genetic parameters of several biochemical compounds from green coffee, Coffea canephora. Plant Breed 117: 576-578.
51. Montagnon C, Leroy T, Cilas C, Charrier A (2003) Heritability of Coffea canephora yield estimated from several mating designs. Euphytica 133: 209-218.
52. Moschetto D, Montagnon C, Guyot B, Perriot JJ, Leroy T, Eskes AB (1996) Studies on the effect of genotype on cup quality of Coffea canephora. Trop Sci 36: 18-31.
53. N'Diaye A, Noirot M, Hamon S, Poncet V (2007) Genetic basis of species differentiation between Coffea liberica Hiern and C. canephora Pierre: analysis of an interspecific cross. Genet Resour Crop Evol 54: 1011-1021.
54. Paillard M, Lashermes P, Pétiard V (1996) Construction of a molecular linkage map in coffee. TheorAppl Genet 93: 41-47.
55. Poncet V, Hamon P, Minier J, Carasco C, Hamon S, Noirot M (2004) SSR cross-amplification and variation within coffee trees (Coffea spp.). Genome 47: 1071-1081.
56. Poncet V, Dufour M, Hamon P, Hamon S, de Kochko A, Leroy T (2007) Development of genomic microsatellite markers in Coffea canephora and their transferability to other coffee species. Genome 50: 1156-1161.
57. Priyono FB, Rigoreau M, Ducos JP, Sumirat U, Mawardi S, Lambot C, Broun P, Pétiard V, Wahyudi T, Crouzillat D (2010) Somatic embryogenesis and vegetative cutting capacity are under distinct control in Coffea canephora Pierre. Plant Cell Rep 29: 343-357.
58. Risterucci AM, Grivet L, N'Goran JAK et al (2000) A high-density linkage map of Theobroma cacao L. Theor Appl Genet 101: 948-955.
59. Saliba V, Causse M, Langlois D, Philouze J, Buret M (2001) Genetic analysis of organoleptic quality in fresh-market tomato. 1. Mapping QTLs for physical and chemical traits. Theor Appl Genet 102: 273-283.
60. Segura V, Durel CE, Costes E (2009) Dissecting apple architecture into genetic, ontogenetic and environmental effects: QTL mapping. Tree Genet Gen 5: 165-179.
61. van Ooijen JW (2004) MapQTL 5, software for the mapping of quantitative trait loci in experimental populations. Kyazma BV, Wageningen.
62. van Ooijen JW (2006) JoinMap 4 software for the calculation of genetic linkage maps. Kyazma BV, Wageningen.
63. Venkateswarlu M, Urs SR, Nath BS, Shashidar HE, Maheswaran M, Veeraiah TM, Sabitha MG (2006) A first genetic linkage map of mulberry (Morus spp.) using RAPD, ISSR and SRR markers and pseudo testcross mapping strategy. Tree Genet Gen 3: 15-24.
64. Voorrips RE (2002) Mapchart: software for the graphical presentation of linkage maps and QTLs. J Hered 93: 77-78.
65. Wintgens JN (2004) Coffee: growing, processing, sustainable production A guidebook for growers, processors, traders, and researchers. Wiley-VCG Verlag GmbH & Co., Weinheim.
66. Xu S (2008) QTL mapping can benefit from segregation distortion. Genetics 180: 2201-2208.
67. Zamir D, Tadmor Y (1986) Unequal segregation of nuclear genes in plants. Bot Gaz 147: 355-358.
68. Zhang L, Wang S, Li H, Deng Q, Zheng A, Li S, Li P, Li Z, Wang J (2010) Effects of missing markers and segregation distortion on QTL mapping in F2 populations. Theor Appl Genet. doi: 10. 1007/s00122-010-1372-z.