Open Access Research article

Gene diversity, agroecological structure and introgression patterns among village chicken populations across North, West and Central Africa

Grégoire Leroy12, Boniface B Kayang3, Issaka AK Youssao4, Chia V Yapi-Gnaoré5, Richard Osei-Amponsah3, N’Goran E Loukou56, Jean-Claude Fotsa7, Khalid Benabdeljelil8, Bertrand Bed’hom2, Michèle Tixier-Boichard2 and Xavier Rognon12*

Author Affiliations

1 AgroParisTech, UMR1313 Génétique Animale et Biologie Intégrative, Paris 05, F-75231, France

2 INRA, UMR1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, 78352, France

3 University of Ghana, Legon, Ghana

4 Université d’Abomey-Calavi, Ecole Polytechnique d’Abomey-Calavi, Cotonou, 01 BP 2009, Bénin

5 Centre National de la Recherche Agronomique, Abidjan, 01 BP 1740, Côte d’Ivoire

6 Université de Cocody, Abidjan, 22 BP 1244, Côte d’Ivoire

7 Station Spécialisée de Recherche Agricole de Mankon (SRRAD), Bamenda, BP 4099, Cameroun

8 Institut Agronomique et Vétérinaire Hassan II, DPBA, Rabat Instituts, 10101, Rabat, BP 6202, Maroc

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BMC Genetics 2012, 13:34  doi:10.1186/1471-2156-13-34

Published: 7 May 2012

Additional files

Additional file 1:

Summary of polymorphic measures for microsatellite markers. For each and over all populations or within each African country’s population or commercial line, the following information are given: allele range, number of alleles (A), number of private alleles (Ap) and allelic richness (Ar).

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Additional file 2:

Pairwise genetic distances (DR) and levels of significance of genic differentiation among the 28 chicken populations. DR values are above the diagonal and levels of significance are below the diagonal. For population codes, see Table 1.

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Additional file 3:

STRUCTURE analysis involving all 28 populations (23 African local chicken populations and 5 commercial lines), for K = 2-16, using Q-matrix averaged overall 100 runs.

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Additional file 4:

STRUCTURE analysis involving all 28 populations (23 African local chicken populations and 5 commercial lines). Evolution of (a) likelihood Ln(P(D)) and (b) similarity function G’ according to the number of cluster K (K = 1 to 16).

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Additional file 5:

STRUCTURE analysis restricted to the 18 African local chicken populations from Ghana, Benin and Côte d’Ivoire. Evolution of likelihood Ln(P(D)) according to the number of cluster K (K = 1 to 6).

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Additional file 6:

Neighbor-Net for the complete dataset (23 African local chicken populations and 5 commercial lines), based on Reynolds DR distance.

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Additional file 7:

Individual neighbor-joining dendrogram based on DAS distance among 242 samples representing local chickens from Benin (n = 113) and 5 commercial lines (n = 129). red: Benin; orange: BS-D; dark green: BS-C; dark blue: Bel-C; light green: Wel-A; light blue: BD-B; black star indicates individuals with qi > 0.2, for clusters specific to commercial lines (STRUCTURE analysis for K = 6).

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Additional file 8:

Individual neighbor-joining dendrogram based on DAS distance among 250 samples representing local chickens from Côte d’Ivoire (n = 121) and 5 commercial lines (n = 129). red: Côte d’Ivoire; orange: BS-D; dark green: BS-C; dark blue: Bel-C; light green: Wel-A; light blue: BD-B; black star indicates individuals with qi > 0.2, for clusters specific to commercial lines (STRUCTURE analysis for K = 6).

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Additional file 9:

Individual neighbor-joining dendrogram based on DAS distance among 241 samples representing local chickens from Ghana (n = 112) and 5 commercial lines (n = 129). red: Ghana; orange: BS-D; dark green: BS-C; dark blue: Bel-C; light green: Wel-A; light blue: BD-B; black star indicates individuals with qi > 0.2, for clusters specific to commercial lines (STRUCTURE analysis for K = 6).

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Additional file 10:

Individual neighbor-joining dendrogram based on DAS distance among 214 samples representing local chickens from Cameroon (n = 85) and 5 commercial lines (n = 129). red: Cameroon; orange: BS-D; dark green: BS-C; dark blue: Bel-C; light green: Wel-A; light blue: BD-B; black star indicates individuals with qi > 0.2, for clusters specific to commercial lines (STRUCTURE analysis for K = 6).

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Additional file 11:

Individual neighbor-joining dendrogram based on DAS distance among 175 samples representing local chickens from Morocco (n = 46) and 5 commercial lines (n = 129). red: Morocco; orange: BS-D; dark green: BS-C; dark blue: Bel-C; light green: Wel-A; light blue: BD-B; black star indicates individuals with qi > 0.2, for clusters specific to commercial lines (STRUCTURE analysis for K = 6).

Format: PDF Size: 247KB Download file

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