Haplotype Block Structure in Portuguese Holstein Cattle

Haplotype blocks are DNA segments that are inherited from generation to generation as a single unit. Therefore, the favourable genes will inherit together with undesirable genes if found in the same haplotype block.  The objective of this work was to describe haplotype block structure in Portuguese dairy cattle, and scanning these haplotype blocks for genes affecting milk production traits and mastitis.  The average marker interval and MAF were 67.80 kb and 0.264, respectively. The total numbers of blocks identified were 969 blocks consisted of 4259 SNPs and covered 159.06 Mb on 29 autosomes. The maximum number of haplotypes was 91 Haplotype on BTA 1, and the minimum number of haplotypes was 7 on BTA 27. The average size of haplotypes ranged from 55.73 kb on BTA 27 to 218.04 kb on BTA 5. The maximum blocks coverage length on chromosome was 14800 kb on BTA 1 and the minimum was 390.15 kb on BTA 27. The average number of SNPs forming haplotype was 4.21. We observed several genes inside haplotype blocks. CSN1S2 gene was observed in haplotype block 51 on BTA 6. IL6 and B4GALT1 genes on BTA 8 were observed in haplotype block 6 and 33 respectively. IL1B and ID2 genes on BTA 11 were found in haplotype block 19 and 29. DGAT1 gene on BTA 14 was observed in haplotype block 1. Scanning the blocks that contain favourable genes for deleterious genes is important before using favourable genes in selection programs to avoid unfavourable genetic correlation between favourable genes and deleterious genes.