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When the genome was partitioned into 1Mbp windows and the combined effects of SNPs within each interval estimated, the chromosome 5 93 94Mbp window accounted for 2.1% of the genetic variance in milk fat percentage, representing the third largest QTL genome wide (Supplementary Table S2). Of the top five genome wide window QTL, all except the chromosome 5 93 94Mbp locus contained genes with previously demonstrated causal roles in milk composition regulation. These were: chromosome 14 1 2Mbp (DGAT14), chromosome 27 36 37Mbp (AGPAT67), chromosome 11 103 104Mbp (PAEP20), and chromosome 20 31 32Mbp (GHR6).
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