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Genetic diversity of different indigenous chicken ecotypes using highly polymorphic MHC-linked and non-MHC microsatellite markers

  • K. Ngeno (a1) (a2), E.H. van der Waaij (a2), H.J. Megens (a2), A.K. Kahi (a1), J.A.M. van Arendonk (a2) and R.P.M.A. Crooijmans (a2)...


The study investigated the genetic make-up of different ecotypes of indigenous chickens (ICs) in Kenya based on major histocompatibility complex (MHC)-linked and non-MHC microsatellite markers. Blood samples were collected from eight regions (48 birds per region) of Kenya: Kakamega (KK), Siaya (BN), West Pokot (WP), Turkana (TK), Bomet (BM), Narok (NR), Lamu (LM) and Taita-Taveta (TT) and genotyped using two MHC-linked and ten non-MHC markers. All MHC-linked and non-MHC markers were polymorphic with a total of 140 alleles, of which 56 were identified in MHC-linked markers. Mean number of alleles (Na and Ne), private alleles, heterozygosity and genetic distances were higher for MHC-linked markers compared with non-MHC markers. The ad hoc statistic ΔK detected the true numbers of clusters to be three for MHC-linked markers and two in non-MHC markers. In conclusion, Kenyan ICs belong into two to three genetically distinct groups. Different markers systems have different clustering system. MHC-linked markers divided ICs into three mixed clusters, composing of individuals from the different ecotypes whereas non-MHC markers grouped ICs into two groups. These IC ecotypes host many and highly diverse MHC-linked alleles. Higher allelic diversity indicated a huge amount of genetic variation in the MHC region of ICs and supported their reputation of being hardy and resistant to diseases.

Cette étude a cherché à connaître la configuration génétique de différents écotypes de poules autochtones du Kenya, sur la base de marqueurs microsatellites associés ou non au Complexe Majeur d'Histocompatibilité (CMH). Des échantillons sanguins ont été prélevés dans huit régions du Kenya (48 volailles par région): Kakamega (KK), Siaya (BN), Pokot Occidental (PO), Turkana (TK), Bomet (BM), Narok (NR), Lamu (LM) et Taita-Taveta (TT). Les échantillons ont été génotypés en utilisant deux marqueurs associés au CMH et 10 marqueurs non associés. Tous les marqueurs, aussi bien ceux associés au CMH que ceux non associés à celui-ci, ont été polymorphes avec un total de 140 allèles, dont 56 ont été identifiés avec des marqueurs associés au CMH. Le nombre moyen d'allèles (Na et Ne) et celui d'allèles privés, l'hétérozygotie et les distances génétiques ont été plus élevés pour les marqueurs associés au CMH que pour ceux non associés. La mesure statistique ad hoc ΔK a révélé que le vrai nombre de groupes est de trois pour les marqueurs associés au CMH et de deux pour les marqueurs non associés. En conclusion, les poules autochtones kényanes appartiennent à 2–3 groupes génétiques différents. Des systèmes différents de marqueurs présentent des méthodes différentes de groupement. Les marqueurs associés au CMH ont divisé les populations de poules autochtones en trois groupes mixtes, constitués d'individus provenant des différents écotypes, alors que les marqueurs non associés au CMH ont rassemblé les poules autochtones en deux groupes. Ces écotypes de poules autochtones abritent de nombreux et très divers allèles associés au CMH. Une plus grande diversité allélique est le reflet d'une grande quantité de variation génétique dans la région du CMH des poules autochtones, ce qui confirme leur renommée de volailles rustiques et résistantes aux maladies.

Este estudio investigó la configuración genética de diferentes ecotipos de gallinas autóctonas de Kenia, basándose en marcadores microsatélites asociados y no asociados al Complejo Mayor de Histocompatibilidad (CMH). Se tomaron muestras de sangre en ocho regiones de Kenia (48 aves por región): Kakamega (KK), Siaya (BN), Pokot Occidental (PO), Turkana (TK), Bomet (BM), Narok (NR), Lamu (LM) y Taita-Taveta (TT). Las muestras sanguíneas fueron genotipadas usando dos marcadores asociados al CMH y 10 marcadores no asociados. Todos los marcadores, tanto asociados como no asociados al CMH, fueron polimórficos con un total de 140 alelos, de los cuales 56 fueron identificados en marcadores asociados al CMH. El número medio de alelos (Na y Ne) y de alelos privados, la heterocigosis y las distancias genéticas fueron mayores para los marcadores asociados al CMH que para los marcadores no asociados. El estadístico ad hoc ΔK detectó que el número real de conglomerados era de tres para los marcadores asociados al CMH y de dos para los marcadores no asociados. En conclusión, las gallinas autóctonas keniatas pertenecen a 2–3 grupos genéticos distintos. Sistemas de marcadores distintos presentan diferentes modos de agrupación. Los marcadores asociados al CMH dividieron las poblaciones de gallinas autóctonas en tres conglomerados mixtos, formados por individuos de los diferentes ecotipos, mientras que los marcadores no asociados al CMH agruparon las gallinas autóctonas en dos grupos. Estos ecotipos de gallinas autóctonas albergan muchos y muy diversos alelos asociados al CMH. Una mayor diversidad alélica fue reflejo de una gran cantidad de variación genética en la región del CMH de las gallinas autóctonas, lo cual confirma la fama de estas aves de ser rústicas y resistentes a enfermedades.


Corresponding author

Correspondence to: K. Ngeno, Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands. email:


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Genetic diversity of different indigenous chicken ecotypes using highly polymorphic MHC-linked and non-MHC microsatellite markers

  • K. Ngeno (a1) (a2), E.H. van der Waaij (a2), H.J. Megens (a2), A.K. Kahi (a1), J.A.M. van Arendonk (a2) and R.P.M.A. Crooijmans (a2)...


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