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Genetics of the Colombian Paso Horse, Phylogenetics, Biotype, and Gaits)

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Genetics of the Colombian Paso Horse, Phylogenetics, Biotype, and Gaits) Genética del Caballo Colombiano de paso, filogenia, biotipo y andares (Genetics of the Colombian paso horse, phylogenetics, biotype, and gaits) Miguel Adriano Novoa Bravo Universidad Nacional de Colombia Facultad de Ciencias Área Curricular de Biología Bogotá, Colombia 2018 Genética del Caballo Colombiano de paso, filogenia, biotipo y andares (Genetics of the Colombian paso horse, phylogenetics, biotype, and gaits) Miguel Adriano Novoa Bravo Dissertation submitted in partial fulfillment of the requirements for the degree of: Doctor in Sciences (Biology) Supervisor and reviewer: Ph.D. Luis Fernando García Research area: Animal genetics Research groups: Genética Animal Aplicada Biodiversidad y Ecología Molecular Universidad Nacional de Colombia Facultad de Ciencias Área Curricular de Biología Bogotá, Colombia 2018 To my family, Eleonora, Sergio Adrian, Antonio, parents Mabel and Miguel and siblings Nidya Isabel, Delfin, Andrés y Juan. Acknowledgements I want to thank all the persons involved to achieve this study, specially to: To my supervisor Luis Fernando García and also to Gabriella Lindgren, for all the knowledge that you share with me, for your time and endeavor, for accepting me as a doctoral student and a foreign student respectively, and for being agreed with my research initiatives. It has been a huge enriching experience for me, work with you both. Also, I thank to Ernie Bailey and Samantha Brooks for your valuable comments during the first part of this project, and thanks to the juries Dr. Cristina Luis, Dr. Luz Alvarez, and Dr. Oscar Cortés for your suggestions at the end of this work. Also, I thank the Federación Nacional de Asociaciones Equinas - Fedequinas for providing the pedigree, kinematic and microsatellite data, and their support during the last years, especially to Enrique Neira, Eliseo Cárdenas, Beatriz Salgado, Yovanny Avendaño, Eliana Serrano, Alirio Galvis and Fabio Jaramillo. Also, I want to thank to Mr. Carlos Uribe for their comments. In addition, I want to thank the Colfuturo-Colciencias, National PhD program 6172 https://www.colfuturo.org/scolciencias for my scholarship. Thanks to my close friends William Usaquén and his family, and David Yaya for sharing and for inspiring me to be a better professional and person. Also, to Kim Jäderkvist, Laura Bas, Maria Rosengren, Juan Cordero, and Cano Merkan for your friendship and support during my internship in Sweden. To my wife Eleonora and sons Sergio Adrian y Antonio for your unconditional love, perseverance, and huge effort during these years of a fantastic and an unlikely journey. Also, to my parents Nidya Mabel, Miguel Angel, my siblings Nidya Isabel, Delfín, Andrés Felipe, Juan Miguel and to the Eleonora’s family Análida, Augusto, Jimena, Fernando, Camilo and Paula, thanks for all your love and support. VIII Genetics of Colombian paso horse, phylogenetics, biotype, and gaits Abstract and resumen IX Abstract The Colombian paso horse, also known as Colombian creole paso horse, the most important horse breed in Colombia, has been selected for conformation and gaits for at least the last 50 years. We hypothesize that this selection has led to the formation of two differentiated breeds. Hence, the aim of the study was to establish whether or not the Colombian paso horse corresponds to one or more breeds based on pedigree, genetic, and phenotypic data. To test our hypotheses, data from Colombian paso horses (220,000 pedigree records, 132,637 autosomal microsatellite genotypes, 900 X chromosome microsatellite genotypes, 198 mitochondrial d-loop sequences, conformation and kinematic measurements for 172 horses, and a DMRT3 nonsense mutation genotypes for 153 horses) were analyzed. The results indicated that there are significant genetic and phenotypic differences between the Colombian paso horses, where a continuum genetic differentiation has been occurring during the last 3 generations traced, in particular between the Colombian paso fino and the other groups. Also, there are significant kinematic and DMRT3 differences between the Colombian paso horse’s gaits, and those parameters can be used partially to select and control the horses’ gait performance. Finally, phylogenetic analyzes showed that the Colombian paso horses had a complex breed origin and that these horses share an evolutionary history with specific haplotypes, even, some of those haplotypes represent an ancestral Iberian haplogroup which had been described in just few modern horses until the present study. Hence, all the results strongly suggested that the Colombian paso horse breed became two breeds: the Colombian paso fino horse breed and the Colombian trocha and trot horse breed. In addition, the DMRT3 gene does not play a major role in controlling the trocha and the Colombian trot gaits. Therefore, additional genes or other DMRT3 mutations likely influence these gaits. This study has settled down the genetic and phenotypic foundations of these Colombian paso horse breeds; and also, has evidenced for the first time a breed formation process where the role of the microevolutionary process was registered by means of genetic data and phenotypic differentiation. X Genetics of Colombian paso horse, phylogenetics, biotype, and gaits Key words: breed, evolution, gait, genetics, horse, phenotype, phylogenetics. Resumen El Caballo Colombiano de paso, conocido también como Caballo criollo Colombiano de paso, la raza de caballos más importante de Colombia, ha sido seleccionada por su conformación y andar durante al menos los últimos 50 años. Nuestra hipótesis es que esta selección ha llevado a la formación de dos razas diferenciadas. Por lo tanto, el objetivo del estudio fue establecer si el Caballo Colombiano de paso corresponde a una o más razas basadas en datos de pedigrí, genéticos y fenotípicos. Para probar nuestras hipótesis, datos de Caballos Colombianos de paso (220,000 registros de pedigrí, 132,637 genotipos autosómicos de microsatélites, 900 genotipos de microsatélites de cromosoma X, 198 secuencias mitocondriales d-loop, mediciones de conformación y cinemáticas para 172 caballos y genotipos de la mutación sin sentido del gen DMRT3 para 153 caballos) fueron analizados. Los resultados indicaron que hay diferencias genéticas y fenotípicas significativas entre los caballos colombianos de paso, donde se ha producido una diferenciación genética continua durante las últimas 3 generaciones, en particular entre el Caballo Colombiano de paso fino y los otros grupos. Además, hay diferencias cinemáticas y del gen DMRT3 significativas entre los andares del Caballo Colombiano de paso y esos parámetros se pueden usar parcialmente para seleccionar y controlar el rendimiento de los andares de los caballos. Finalmente, los análisis filogenéticos mostraron que los Caballos Colombianos de paso tuvieron un origen racial complejo y que estos caballos comparten una historia evolutiva con haplotipos específicos, incluso, algunos de estos haplotipos representan un haplogrupo ibérico ancestral que se había descrito en unos pocos caballos modernos hasta el presente estudio. Por lo tanto, todos los resultados sugieren contundentemente que la raza Caballo Colombiano de paso se convirtió en dos razas: el Caballo Colombiano de paso fino y el Caballo Colombiano de trocha y trote. Además, el gen DMRT3 no juega un papel importante en el control de los andares de la trocha y el trote colombiano. Por lo tanto, es posible que genes adicionales u otras Abstract and resumen XI mutaciones en el gen DMRT3 probablemente influyan en estos andares. Este estudio ha establecido los fundamentos genéticos y fenotípicos de estas razas Colombianas de caballos de paso; y también ha evidenciado por primera vez un proceso de formación de razas donde el papel del proceso microevolutivo se registró por medio de datos genéticos y diferenciación fenotípica. Palabras claves: andar, caballos, evolución, fenotipo, filogenética, genética, raza. Content XIII Content Page Abstract ............................................................................................................................ IX Resumen ........................................................................................................................... X 1. Introduction ................................................................................................................ 1 1.1 Genetics of populations ........................................................................................ 1 1.1.1 Mendel´s principles. ........................................................................................... 1 1.1.2 Hardy-Weinberg principle .................................................................................. 2 1.1.3 Evolutionary process ......................................................................................... 2 1.1.4 Genetic Structure ............................................................................................... 4 1.1.5 Breed ................................................................................................................. 5 1.1.6 Phylogenetics .................................................................................................... 5 1.1.7 Genetic distances .............................................................................................. 6 1.1.8 Maximum Parsimony ......................................................................................... 7 1.1.9 Maximum Likelihood .........................................................................................
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