Biodiversity, evolution and adaptation of cultivated crops

[1] Vavilov, N.I. Origin and geography of cultivated plants, Cambridge University Press, New York, 1992

[2] Smith, B.D. The emergence of agriculture, Scientific American Library, New York, 1998

[3] Doebley, J.F.; Gaut, B.S.; Smith, B.D. The molecular genetics of crop domestication, Cell, Volume 127 (2006), pp. 1309-1321

[4] Matsuoka, Y.; Vigouroux, Y.; Goodman, M.M.; Sanchez, G.J.; Buckler, E.; Doebley, J. A single domestication for maize shown by multilocus microsatellite genotyping, Proc. Natl. Acad. Sci. U S A, Volume 99 (2002), pp. 6080-6084

[5] Salamini, F.; Ozkan, H.; Brandolini, A.; Schäfer-Pregl, R.; Martin, W. Genetics and geography of wild cereal domestication in the near east, Nat. Rev. Genet., Volume 3 (2002), pp. 429-441

[6] Oumar, I.; Mariac, C.; Pham, J.L.; Vigouroux, Y. Phylogeny and origin of Pearl Millet (Pennisetum glaucum [L.] R. Br) as revealed by microsatellite loci, Theor. Appl. Genet., Volume 117 (2008), pp. 489-497

[7] Londo, J.P.; Chiang, Y.C.; Hung, K.H.; Chiang, T.Y.; Schaal, B.A. Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa, Proc. Natl. Acad. Sci. U S A, Volume 103 (2006), pp. 9578-9583

[8] Purugganan, M.D.; Fuller, D.Q. The nature of selection during plant domestication, Nature, Volume 457 (2009), pp. 843-848

[9] Harlan, J.R. Crop and man, American Society of Agronomy and Crop Science Society of America, Madison, 1975

[10] Piperno, D.R.; Flannery, K.V. The earliest archaeological maize (Zea mays L.) from highland Mexico: new accelerator mass spectrometry dates and their implications, Proc. Natl. Acad. Sci. U S A, Volume 96 (2001), pp. 2101-2103

[11] Piperno, D.R.; Ranere, A.J.; Holst, I.; Iriarte, J.; Dickau, R. Starch grain and phytolith evidence for early ninth millennium B.P. maize from the Central Balsas River Valley, Mexico, Proc. Natl. Acad. Sci. U S A, Volume 106 (2009), pp. 5019-5024

[12] Fukunaga, K.; Hill, J.; Vigouroux, Y.; Matsuoka, Y.; Sanchez, J.; Liu, K.J.; Buckler, E.S.; Doebley, J. Genetic diversity and population structure of teosinte, Genetics, Volume 169 (2005), pp. 2241-2254

[13] Vigouroux, Y.; Glaubitz, J.C.; Matsuoka, Y.; Goodman, M.M.; Sanchez, G.J.; Doebley, J. Population structure and gene diversity of New World maize races assessed by DNA Microsatellites, Am. J. Bot., Volume 95 (2008), pp. 1240-1253

[14] Zarrillo, S.; Pearsall, D.M.; Raymond, J.S.; Tisdale, M.A.; Quon, D.J. Directly dated starch residues document early formative maize (Zea mays L.) in tropical Ecuador, Proc. Natl. Acad. Sci. U S A, Volume 105 (2008), pp. 5006-5011

[15] Fritz, G.J. New dates and data on early agriculture: the legacy of complex hunter-gatherers, Ann. Missouri Botan. Garden, Volume 82 (1995), pp. 3-15

[16] Janick, J.; Caneva, G. The first images of maize in Europe, Maydica, Volume 50 (2005), pp. 71-80

[17] Vigouroux, Y.; McMullen, M.; Hittinger, C.T.; Houchins, K.; Schulz, L.; Kresovich, S.; Matsuoka, Y.; Doebley, J. Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication, Proc. Natl. Acad. Sci. U S A, Volume 99 (2002), pp. 9650-9655

[18] Vigouroux, Y.; Mitchell, S.; Matsuoka, Y.; Hamblin, M.; Kresovich, S.; Smith, S.; Jaqueth, J.; Smith, O.; Doebley, J. An analysis of genetic diversity across the maize genome using microsatellites, Genetics, Volume 169 (2005), pp. 1617-1630

[19] Wright, S.I.; Bi, I.V.; Schroeder, S.G.; Yamasaki, M.; Doebley, J.F.; McMullen, M.D.; Gaut, B.S. The effects of artificial selection on the maize genome, Science, Volume 308 (2005), pp. 1310-1314

[20] Yamasaki, M.; Tenaillon, M.I.; Bi, I.V.; Schroeder, S.G.; Sanchez-Villeda, H.; Doebley, J.F.; Gaut, B.S.; McMullen, M.D. A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement, Plant Cell, Volume 17 (2005), pp. 2859-2872

[21] Doebley, J.; Stec, A.; Wendel, J.; Edwards, M. Genetic and morphological analysis of a maize-teosinte F2 population: implications for the origin of maize, Proc. Natl. Acad. Sci. U S A, Volume 87 (1990), pp. 9888-9892

[22] Wang, R.L.; Stec, A.; Hey, J.; Lukens, L.; Doebley, J. The limits of selection during maize domestication, Nature, Volume 398 (1999), pp. 236-239

[23] Wang, H.; Nussbaum-Wagler, T.; Li, B.; Zhao, Q.; Vigouroux, Y.; Faller, M.; Bomblies, K.; Lukens, L.; Doebley, J.F. The origin of the naked grains of maize, Nature, Volume 436 (2005), pp. 714-719

[24] Fu, H.; Zheng, Z.; Dooner, H.K. Recombination rates between adjacent genic and retrotransposon regions in maize vary by 2 orders of magnitude, Proc. Natl. Acad. Sci. U S A, Volume 99 (2002), pp. 1082-1087

[25] Clark, R.M.; Wagler, T.N.; Quijada, P.; Doebley, J. A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture, Nat. Genet., Volume 38 (2006), pp. 594-597

[26] Jaenicke-Després, V.; Buckler, E.S.; Smith, B.D.; Gilbert, M.T.; Cooper, A.; Doebley, J.; Pääbo, S. Early allelic selection in maize as revealed by ancient DNA, Science, Volume 302 (2003), pp. 1206-1208

[27] Camus-Kulandaivelu, L.; Veyrieras, J.B.; Madur, D.; Combes, V.; Fourmann, M.; Barraud, S.; Dubreuil, P.; Gouesnard, B.; Manicacci, D.; Charcosset, A. Maize adaptation to temperate climate: relationship between population structure and polymorphism in the Dwarf8 gene, Genetics, Volume 172 (2006), pp. 2459-2463

[28] Ducrocq, S.; Madur, D.; Veyrieras, J.B.; Camus-Kulandaivelu, L.; Kloiber-Maitz, M.; Presterl, T.; Ouzunova, M.; Manicacci, D.; Charcosset, A. Key impact of Vgt1 on flowering time adaptation in maize: evidence from association mapping and ecogeographical information, Genetics, Volume 178 (2008), pp. 2433-2437

[29] Whitt, S.R.; Wilson, L.M.; Tenaillon, M.I.; Gaut, B.S.; Buckler, E.S. Genetic diversity and selection in the maize starch pathway, Proc. Natl. Acad. Sci. U S A, Volume 99 (2002), pp. 12959-12962

[30] Manicacci, D.; Falque, M.; Le Guillou, S.; Piégu, B.; Henry, A.M.; Le Guilloux, M.; Damerval, C.; De Vienne, D. Maize Sh2 gene is constrained by natural selection but escaped domestication, J. Evol. Biol., Volume 20 (2007), pp. 503-516

[31] Harjes, C.E.; Rocheford, T.R.; Bai, L.; Brutnell, T.P.; Kandianis, C.B.; Sowinski, S.G.; Stapleton, A.E.; Vallabhaneni, R.; Williams, M.; Wurtzel, E.T.; Yan, J.; Buckler, E.S. Natural genetic variation in lycopene epsilon cyclase tapped for maize biofortification, Science, Volume 319 (2008), pp. 330-333

[32] Manicacci, D.; Camus-Kulandaivelu, L.; Fourmann, M.; Arar, C.; Barrault, S.; Rousselet, A.; Feminias, N.; Consoli, L.; Francès, L.; Méchin, V.; Murigneux, A.; Prioul, J.L.; Charcosset, A.; Damerval, C. Epistatic interactions between Opaque2 transcriptional activator and its target gene CyPPDK1 control kernel trait variation in maize, Plant Physiol., Volume 150 (2009), pp. 506-520

[33] Palaisa, K.A.; Morgante, M.; Williams, M.; Rafalski, A. Contrasting effects of selection on sequence diversity and linkage disequilibrium at two phytoene synthase loci, Plant Cell, Volume 15 (2003), pp. 1795-1806

[34] Tian, F.; Stevens, N.M.; Buckler, E.S. Tracking footprints of maize domestication and evidence for a massive selective sweep on chromosome 10, Proc. Natl. Acad. Sci. U S A, Volume 106 (2009), pp. 9979-9986

[35] Troyer, A.F. Background of US hybrid corn II: breeding, climate, and food, Crop science, Volume 44 (2004), pp. 370-380

[36] Glémin, S.; Bataillon, T. A comparative view of the evolution of grasses under domestication, New Phytol., Volume 183 (2009), pp. 273-290

[37] Jarvis, D.I.; Brown, A.H.; Cuong, P.H.; Collado-Panduro, L.; Latournerie-Moreno, L.; Gyawali, S.; Tanto, T.; Sawadogo, M.; Mar, I.; Sadiki, M.; Hue, N.T.; Arias-Reyes, L.; Balma, D.; Bajracharya, J.; Castillo, F.; Rijal, D.; Belqadi, L.; Rana, R.; Saidi, S.; Ouedraogo, J.; Zangre, R.; Rhrib, K.; Chavez, J.L.; Schoen, D.; Sthapit, B.; De Santis, P.; Fadda, C.; Hodgkin, T. A global perspective of the richness and evenness of traditional crop-variety diversity maintained by farming communities, Proc. Natl. Acad. Sci. U S A, Volume 105 (2008), pp. 2101-2103

[38] Morton, J.F. The impact of climate change on smallholder and subsistence agriculture, Proc. Natl. Acad. Sci. U S A, Volume 104 (2007), pp. 19680-19685

[39] S.B. Brush, The issue of in situ conservation of crop genetic resources, in: S.B. Brush (Ed.), Genes in the field: on-farm conservation of crop diversity, IDRC/IPGRI/Lewis Publishers, Boca Raton, USA, 2000, pp. 3–26.

[40] Bellon, M.R. The dynamics of crop infraspecific diversity: a conceptual framework at the farmer level, Econ. Bot., Volume 50 (1996), pp. 26-39

[41] Altieri, M.A. The ecological role of biodiversity in agroecosystems, Agricul. Ecosys. Environ., Volume 74 (1999), pp. 19-31

[42] Sagnard, F.; Barnaud, A.; Deu, M.; Barro, C.; Luce, C.; Billot, C.; Rami, J.F.; Bouchet, S.; Dembele, D.; Pomies, V.; Calatayud, C.; Rivallan, R.; Joly, H.; Brocke, K.V.; Toure, A.; Chantereau, J.; Bezancon, G.; Vaksmann, M. Multi-scale analysis of sorghum genetic diversity: understanding the evolutionary processes for in situ conservation, Cah. Agricul., Volume 17 (2008), pp. 114-121

[43] Baco, M.N.; Biaou, G.; Pham, J.L.; Lescure, J.P. Facteurs géographiques et sociaux de la diversité des ignames cultivées au nord Bénin, Cah. Agricul., Volume 17 (2008), pp. 172-177

[44] Louette, D.; Smale, M. Farmers’ seed selection practices and traditional maize varieties in Cuzalapa, Mexico, Euphytica, Volume 113 (2000), pp. 25-41

[45] Perales, R.H.; Benz, B.F.; Brush, S.B. Maize diversity and ethnolinguistic diversity in Chiapas, Mexico, Proc. Natl. Acad. Sci. U S A, Volume 102 (2005), pp. 949-954

[46] Allinne, C.; Mariac, C.; Vigouroux, Y.; Bezançon, G.; Couturon, E.; Moussa, D.; Tidjani, M.; Pham, J.L.; Robert, T. Role of seed flow on the pattern and dynamics of pearl millet (Pennisetum glaucum [L.] R. Br.) genetic diversity assessed by AFLP markers: a study in south-western Niger, Genetica, Volume 133 (2008), pp. 167-178

[47] Barnaud, A.; Deu, M.; Garine, E.; McKey, D.; Joly, H.I. Local genetic diversity of sorghum in a village in northern Cameroon: structure and dynamics of landraces, Theor. Appl. Genet., Volume 114 (2007), pp. 237-248

[48] Ellstrand, N.C.; Prentice, H.C.; Hancock, J.F. Gene flow and introgression from domesticated plants into their wild relatives, Annu. Rev. Ecol. Syst., Volume 30 (1999), pp. 539-563

[49] Jarvis, D.I.; Hodgkin, T. Wild relatives and crop cultivars: detecting natural introgression and farmer selection of new genetic combinations in agroecosystems, Mol. Ecol., Volume 8 (1999), p. S159-S173

[50] McKey, D.; Elias, M.; Pujol, B.; Duputie, A. The evolutionary ecology of clonally propagated domesticated plants, New Phytol., Volume 186 (2010), pp. 318-332

[51] Zizumbo-Villarreal, D.; Colunga-GaríaMarín, P.; de la Cruz, E.P.; Delgado-Valerio, P.; Gepts, P. Population structure and evolutionary dynamics of wild–weedy–domesticated complexes of common bean in a Mesoamerican region, Crop Sci., Volume 45 (2005), pp. 1073-1083

[52] Scarcelli, N.; Tostain, S.; Vigouroux, Y.; Agbangla, C.; Daïnou, O.; Pham, J.L. Farmers’ use of wild relatives and sexual reproduction in a vegetatively propagated crop. The case of yam in Benin, Mol. Ecol., Volume 15 (2006), pp. 2421-2431

[53] Barnaud, A.; Deu, M.; Garine, E.; Chantereau, J.; Bolteu, J.; Koida, E.O.; Mckey, D.; Joly, H.I. A weed-crop complex in sorghum: the dynamics of genetic diversity in a traditional farming system, Am. J. Bot., Volume 96 (2009), pp. 1869-1879

[54] Ndjuenga, J. Local village seed system and Pearl millet seed quality in Niger, Exp. Agricul., Volume 38 (2002), pp. 149-162

[55] Bezançon, G.; Pham, J.L.; Deu, M.; Vigouroux, Y.; Sagnard, F.; Mariac, C.; Kapran, I.I.; Manadou, A.; Gérard, B.; Ndjeunga, J.; Chantereau, J. Changes in the diversity and geographic distribution of cultivated millet (Pennisetum glaucum [L.] R. Br.) and sorghum (Sorghum bicolor (L.) Moench) varieties in Niger between 1976 and 2003, Genet. Res. Crop Evol., Volume 56 (2009), pp. 223-236

[56] Deu, M.; Sagnard, F.; Chantereau, J.; Calatayud, C.; Vigouroux, Y.; Pham, J.L.; Mariac, C.; Kapran, I.; Mamadou, A.; Gérard, B.; Ndjeunga, J.; Bezançon, G. Spatiotemporal dynamics of genetic diversity in Sorghum bicolor in Niger, Theor. Appl. Genet., Volume 120 (2010), pp. 1301-1313

[57] J. Chantereau, M. Deu, J.L. Pham, Y. Vigouroux, G. Bezançon, Évolution des diversités phénotypiques et génétique des sorghos et mils cultivés au Niger de 1976 à 2003. Le sélectionneur français (2010) (in press).

[58] Y. Vigouroux, C. Mariac, J.L. Pham, B. Gérard, I. Kapran, F. Sagnard, M. Deu, J. Chantereau, A. Ali, J. Ndjeunga, V. Luong, A.C. Thuillet, A.A. Saïdou, G. Bezançon, Selection for earlier flowering crop associated with climate variation in the Sahel (submitted).

[59] Saïdou, A.A.; Mariac, C.; Luong, V.; Pham, J.L.; Bezançon, G.; Vigouroux, Y. Association studies identify natural variation at PHYC linked to flowering time and morphological variation in Pennisetum glaucum [(L.) R. Br.], Genetics, Volume 182 (2009), pp. 899-910

[60] Mariac, C.; Jehin, L.; Saïdou, A.A.; Thuillet, A.C.; Couderc, M.; Sire, P.; Jugdé, H.; Adam, H.; Bezançon, G.; Pham, J.L.; Vigouroux, Y. Genetic basis of pearl millet adaptation along an environmental gradient investigated by a combination of genome scan and association mapping, Mol. Ecol., Volume 20 (2011), pp. 80-91