Spatio-temporal dynamics of genetic diversity in Sorghum bicolor in Niger

Allinne C, Mariac C, Vigouroux Y, Bezançon G, Couturon E, Moussa D, Tidjani M, Pham JL, Robert T (2008) 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 133:167–178 Barnaud A, Deu M, Garine E, McKey D, Joly H (2007) Local genetic diversity of sorghum in a village in northern Cameroon: structure and dynamics of landraces. Theor Appl Genet 114:237–248 Barry MB, Pham JL, Béavogui S, Ghesquière A, Ahmadi N (2008) Diachronic (1979–2003) analysis of rice genetic diversity in Guinea did not reveal genetic erosion. Genet Resour Crop Evol 55:723–733 Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F (2002) Genetix 4.04, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5000, Université de Montpellier II, Montpellier, France. (Available from http://www.univ-montp2.fr/~genetix/genetix/genetix.htm) Bellon MR (1996) The dynamics of crop infraspecific diversity: a conceptual framework at the farmer level. Econ Bot 50:26–39 Bellon MR (2009) Do we need crop landraces for the future? Realizing the global option value of in situ conservation. In: Kontoleon A, Pascual U, Smale M (eds) Agrobiodiversity, conservation and economic development. Routledge, New York, pp 51–61 Ben Mohamed A, Van Duivenbooden N, Abdoussallam S (2002) Impact of climate change on agricultural production in the Sahel—methodological approach and case study for millet in Niger. Clim Change 54:327–348 Bezançon G, Pham JL, Deu M, Vigouroux Y, Sagnard F, Mariac C, Kapran I, Mamadou A, Gérard B, Ndjeunga J, Chantereau J (2009) Changes in the diversity, geographic distribution of cultivated millet (Pennisetum glaucum [L.] R. Br.), sorghum (Sorghum bicolor (L.) Moench) varieties in Niger between 1976 and 2003. Genet Resour Crop Evol 56:223–236 Brown AHD (2000) The genetic structure of crop landraces and the challenge to conserve them in situ on farms. In: Brush SB (ed) Genes in the field: on-farm conservation of crop diversity. IPGRI/IDRC/Lewis Publishers, Boca Raton, pp 29–48 Brush SB (1989) Rethinking crop genetic resource conservation. Conserv Biol 3:19–29 Brush SB, Meng E (1998) Farmers’ valuation and conservation of crop genetic resources. Genet Resour Crop Evol 45:139–150 Casa AM, Mitchell SE, Hamblin MT, Sun H, Bowers JE, Paterson AH, Aquadro CF, Kresovich S (2005) Diversity and selection in sorghum: simultaneous analyses using simple sequence repeats. Theor Appl Genet 111:23–30 Comps B, Gömöry D, Letouzey J, Thiebaut B, Petit RJ (2001) Diverging trends between heterozygosity and allelic richness during postglacial colonization in the European beech. Genetics 157:389–397 Costis C (2005) Diversité des mils et sorghos cultivés au Niger: facteurs agro-économiques, socio-économiques et les modes de gestion des variétés. Mémoire de DESS “Gestion des systémes agro-sylvo-pastoraux en zones tropicales”, Université Paris XII, p 51 Cromwel E, van Oosterhoust S (2000) On-farm conservation of crop diversity: policy and institutional lessons from Zimbabwe. In: Brush SB (ed) Genes in the field: on-farm conservation of crop diversity. IPGRI/IRDC/Lewis Publishers, Boca Raton, pp 217–238 Deu M, Sagnard F, Chantereau J, Calatayud C, Hérault D, Mariac C, Pham JL, Vigouroux Y, Kapran I, Traoré PS, Mamadou A, Gérard B, Ndjeunga J, Bezançon G (2008) Niger-wide assessment of in situ sorghum genetic diversity with microsatellite markers. Theor Appl Genet 116:903–916 Donini R, Law JR, Koebner RMD, Reeves JC, Cooke RJ (2000) Temporal trends in the diversity of UK wheat. Theor Appl Genet 100:912–917 El Mousadik A, Petit RJ (1996) High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L.) Skeels] endemic to Morocco. Theor Appl Genet 92:832–839 Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620 FAO-Orstom (1977) Prospections des mils pénicillaires et sorghos en Afrique de l’Ouest – Niger- Campagne 1976. Report FAO (2008) FAOSTAT database. Available from http://www.fao.org/ Figliuolo G, Mazzeo M, Greco I (2007) Temporal variation of diversity in Italian durum wheat germplasm. Genet Resour Crop Evol 54:615–626 Gao H, Williamson S, Bustamante CD (2007) An MCMC approach for the joint inference of population structure and inbreeding rate from multi-locus genotype data. Genetics 176:1635–1651 Goudet J (2002) FSTAT, a program to estimate and test gene diversity and fixation indices (version 2.9.3.2). Available from http://www.unil.ch/izea/softwares/fstat.html Harlan JR, de Wet JMJ (1972) Simplified classification of cultivated sorghum. Crop Sci 12:172–176 Hulme M (2001) Climatic perspectives on Sahelian desiccation: 1973–1998. Global Environ Change 11:19–29 Jarvis DI, Brown AHD, Hung Cuong P, Collado-Panduro L, Latournerie-Moreno L, Gyawali S, Tanto T, Sawadogo M, Mar I, Sadiki M, Thi-Ngoc Hue G, Arias-Reyes L, Balma D, Bajracharya J, Castillo F, Rijal D, Belqadi L, Rana R, Saidi S, Ouedraogo J, Zangre R, Rhrib K, Rhrib K, Chavez JL, Schoen D, Sthapit B, De Santis P, Fadda C, Hogdkin T (2008) A global perspective of the richness and evenness of traditional crop-variety diversity maintained by farming communities. Proc Natl Acad Sci USA 105:5326–5331 Kim J-S, Klein PE, Klein RR, Price HJ, Mullet JE, Stelly DM (2005) Chromosome identification and nomenclature of Sorghum bicolor. Genetics 169:955–965 Kouressy M, Traoré S, Vaksmann M, Grum M, Maikano I, Soumaré M, Traoré PS, Bazile D, Dingkuhn M, Sidibé A (2008) Adaptation des sorghos du Mali à la variabilité climatique. Cah Agric 17(2):95–100 Lacy SM, Cleveland DA, Soleri D (2006) Farmer choice of sorghum varieties in southern Mali. Hum Ecol 34(3):331–353 Le Clerc V, Bazante F, Baril C, Guiard J, Zhang D (2005) Assessing temporal changes in genetic diversity of maize varieties using microsatellite markers. Theor Appl Genet 100:294–302 Le Clerc V, Cadot V, Canadas M, Lallemand J, Guèrin D, Boulineau F (2006) Indicators to assess temporal genetic diversity in the French catalogue: no losses for maize and peas. Theor Appl Genet 113:1197–1209 Lewis PO, Zaykin D (2001) Genetic data analysis: computer program for the analysis of allelic data. Available from http://hydrodictyon.eeb.uconn.edu/people/plewis/software.php Malysheva-Otto L, Ganal MW, Law JR, Reeves JC, Röder MS (2007) Temporal trends of genetic diversity in European barley cultivars (Hordeum vulgare L.). Mol Breed 20:309–322 Martos V, Royo C, Rharrabti Y, Garcia del Moral LF (2005) Using AFLPs to determine phylogenetic relationships and genetic erosion in durum wheat cultivars released in Italy and Spain throughout the 20th century. Fields Crop Res 91:107–111 Mekbib F (2007) Infra-specific folk taxonomy in sorghum (Sorghum bicolor (L.) Moench) in Ethiopia: folk nomenclature, classification and criteria. J Ethnobiol Ethnomed 3:38 Mekbib F (2008) Genetic erosion of sorghum (Sorghum bicolor (L.) Moench) in the centre of diversity, Ethiopia. Genet Resour Crop Evol 55:351–364 Morin SR, Calibo M, Garcia-Belen M, Pham JL, Palis F (2002) Natural hazards and genetic diversity in rice. Agric Hum Values 19:133–149 Nei M (1987) Molecular evolutionary genetics. Columbia University press, New York Nersting LG, Andersen SB, Von Bothmer R, Gullord M, Jørgensen RB (2006) Morphological and molecular diversity of Nordic oat through one hundred years of breeding. Euphytica 150:327–337 Nicholson S (2005) On the question of the ‘‘recovery’’ of the rains in the West African Sahel. J Arid Environ 63:615–641 Olsson L, Eklundh L, Ardö J (2005) A recent greening of the Sahel—trends, patterns and potential causes. J Arid Environ 63:556–566 Ostrowski MF, David J, Santoni S, McKhann H, Reboud X, Le Corre V, Camilleri C, Brunel D, Bouchez D, Faure B, Bataillon T (2006) Evidence for a large-scale population structure among accessions of Arabidopsis thaliana: possible causes and consequences for the distribution of linkage disequilibrium. Mol Ecol 15:1507–1517 Peroni N, Hanazaki N (2002) Current and lost diversity of cultivated varieties, especially cassava, under swidden cultivation systems in the Brazilian Atlantic Forest. Agric Ecosyst Environ 92:171–183 Petit RJ, El Mousadik A, Pons O (1998) Identifying populations for conservation on the basis of genetic markers. Conserv Biol 12:844–855 Pritchard JK, Wen W (2002) Documentation for Structure software: version 2 (http://pritch.bsd.uchicago.edu) Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959 Rana RB, Garforth C, Stapith B, Jarvis D (2007) Influence of socio-economic and cultural factors in rice varietal diversity management on-farm in Nepal. Agric Hum Values 24:461–472 Reif JC, Hamrit S, Heckenberger M, Schipprack W, Maurer HP, Bohn M, Melchinger AE (2005) Trends in genetic diversity among European maize cultivars and their parental components during the past 50 years. Theor Appl Genet 111:838–845 Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldmann MW (2002) Genetic structure of human populations. Science 298:2381–2385 Roussel V, Koenig J, Beckert M, Balfourier F (2004) Molecular diversity in French bread wheat accessions related to temporal trends and breeding programmes. Theor Appl Genet 108:920–930 Roussel V, Leisova L, Exbrayat F, Stehno Z, Balfourier F (2005) SSR allelic diversity changes in 480 European bread wheat varieties released from 1840 to 2000. Theor Appl Genet 111:162–170 Snowden JD (1936) The cultivated races of sorghum. Adlard, London, pp 1–274 Teklu Y, Hammer K (2006) Farmers’ perception and genetic erosion of tetraploid wheat landraces in Ethiopia. Genet Resour Crop Evol 53:1099–1113 Teshome A, Patterson D, Asfew Z, Torrance JK, Arnason JT (2007) Changes of Sorghum bicolor landrace diversity and farmers’ selection criteria over space and time, Ethiopia. Genet Resour Crop Evol 54:1219–1233 Thomas DSG, Twyman C, Osbahr H, Hewitson B (2007) Adaptation to climate changes and variability: farmer responses to intra-seasonal precipitation trends in South Africa. Clim Change 83:301–322 Traoré SB, Reyniers FN, Vaksmann M, Koné B, Sidibé A, Yoroté A, Yattara K, Kouressy M (2000) Adaptation à la sècheresse des écotypes locaux de sorghos au Mali. Sècheresse 11:227–237 Van Etten J (2006) Changes in farmers’ knowledge of maize diversity in highland Guatemala, 1927/37–2004. J Ethnobiol Ethnomed 2:12 Vigouroux Y, Jaqueth JS, Matsuoka Y, Smith OS, Beavis WD, Smith JS, Doebley J (2002) Rate and pattern of mutation at microsatellite loci in maize. Mol Biol Evol 19(8):1251–1260 Vigouroux Y, Mitchell S, Matsuoka Y, Hamblin M, Kresovich S, Smith JSC, Jaqueth J, Smith OS, Doebley J (2005) An analysis of genetic diversity across the maize genome using microsatellites. Genetics 169:1617–1630 Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370 Willemen L, Scheldeman X, Soto Cabellos V, Rafael Salazar S, Guarino L (2007) Spatial patterns of diversity and genetic erosion of traditional cassava (Manihot esculenta Crantz) in the Peruvian Amazon: an evaluation of socio-economic and environmental indicators. Genet Resour Crop Evol 54:1599–1612