Author TK performed most of the statistical analyses and the genotyping and contributed substantially to the first draft of the manuscript.
The genotypes of 777,962 single nucleotide polymorphisms (SNPs) were analysed and the genotypes were checked for extended regions of homozygosity.
Phylogenetic and epidemiological analyses suggest that the genotypes and subtypes with greater epidemic potential regularly displace those that have lower epidemic potential.
XST and ZDL prepared the materials; XST, ZDL LQ and CY performed the analyses of the genotype and phenotype; LZG and WWD participated to determine the phenotype; ST constructed the linkage maps; YJB, LJS and YXH designed the experiments and analyzed the chip raw data; XST, FA and YJB wrote the manuscript.
JR coordinated the data and samples collections from the different Belgian centres, analysed the clinical data and the genotypes, and drafted the manuscript.
These trees are based on the eight genes analysed by direct sequencing and the genotypes where most of the sequences were present, with the P. trichocarpa gene model and P. tremula sequences included or excluded to improve resolution around the Salix samples.
Replication samples: To validate the findings, a replication sample of n = 62 unrelated elite (Group and Listed race winners) Thoroughbreds was re-sampled from the original repository and supplemented with additional samples collected following the original analyses and genotyped for the g.66493737C>T SNP (Replication sample I).
GH prepared the sequencing samples, participated in the bioinformatic analyses, conducted the genotyping, and evaluated the genotyping data.
The placentas were subjected to various analyses, and the embryos were used for genotyping.
JMM, MvdS, AVSH, HCW, AJ and AMP conceived of and designed the research; JMM conducted the plasma iron and ACT analyses, BJH conducted the genotyping and MvdS was responsible for the TB diagnoses; JMM analyzed the data and drafted the manuscript; all authors read and approved the final manuscript.
