Genetics of disease resistance: Molecular characterisation of the major histocompatibility Complex Class II genes in Bos species of different origin : A thesis submitted in partial fulfilment of the requirements for the Degree of Master of Science at Lincoln University

Breeding for genetic resilience in farm animals is becoming more important as a consequence of the increasing awareness of pathogen resistance to antibiotics and the need to build more resilient and sustainable agricultural production systems. In this context, the important role the Major Histocompatibility Complex (MHC) proteins play in immune responses would suggest that improved understanding of the MHC genes is vital to understanding and manipulating genetic resilience to infectious diseases. The genes of MHC are highly polymorphic, and studies have suggested that the large variation existing within the MHC region may be attributed to response to selective pressure from pathogens. It has therefore been suggested that the alleles of MHC genes carried by an individual animal may be influenced by the type of pathogens in its environment. An understanding of the allelic variation in MHC genes across multiple geographic regions and breeds could therefore assist us to better understand the influence of selective forces and to better characterise distinct populations of cattle. In this study, four breeds of cattle including White Fulani (n =24), Red Bororo (n =5) and Holstein-White x Fulani-cross (n = 11) from Nigeria, and New Zealand Holstein-Friesian x Jersey-cross (n = 40) were genotyped for variation in exon 2 of BoLA-DQA1. In addition: Yak (n= 47); 13 breeds of cattle including White Fulani (n = 30), Red Bororo (n= 20), and White Fulani × Holstein-cross (n = 16) from Nigeria; Holstein-Friesian × Jersey Cross (n = 22), Hereford (n = 20), Murray Grey (n = 20), Red poll (n = 20), Shorthorn (n =22), Angus (n = 20), Simmental (n = 20), Charolais (n = 20), South Devon (n =20) from New Zealand; and Marchigiana (n = 16) from Italy, were genotyped for variation in exon 2 of BoLA-DRA. A Single Strand Conformation Polymorphism approach was used to genotype the animals and selected cattle were subsequently subjected to direct sequencing of the regions of the genes investigated to reveal nucleotide sequence differences. A total of 10 alleles were identified from all samples investigated for BoLA-DQA1 variation. Allele BoLA-DQA*001:02 had the highest frequency of occurrence (17.5%) and BoLA-DQA*010:03 was the least common with a frequency of 6.9%. A total of 12.60% of all nucleotide positions analysed were revealed to be variable. Two novel BoLA-DQA1 alleles are reported in this study for the first time, but no new sequences were revealed for BoLA-DRA. In total, three BoLA-DRA allelic variants were observed in the cattle studied, namely 01011, 01013 and 01014. The New Zealand Holstein Friesian x Jersey (HF X J)-cross cattle and the Yak had only two BoLA-DRA alleles (BoLA-DRA*01011 and BoLA-DRA*01013), while the other breeds studied had the BoLA-DRA*01011, BoLA-DRA*01013 and BoLA-DRA*01014 alleles. This study is helpful in shaping our understanding of the bovine MHC genes. It may also be relevant to understanding how different breeds respond to pathogen challenges, thus determining their adaptability to their regions. Identifying genomic variation is however, only a first step in developing breeding programmes that enhance livestock genetic resilience to disease.