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Table 5 Association between measures of selection and genome-wide quantitative trait loci (i.e. type 3 loci) in Holstein and Jersey cattle

From: Selection for complex traits leaves little or no classic signatures of selection

   FAT MILK PROT STAT FERT FPC PPC
(a) QTL Holstein HAPH Holstein 31.4 32.8 35.6 34.0 31.0 30.6 30.8
(b) QTL Jersey HAPH Jersey 21.4 25.2 29.2 22.6 20.4 16.6 19.8
(c) QTL Holstein |iHS| Holstein 40.0 39.0 47.0* 40.2 39.6 36.0 34.6
(d) QTL Jersey |iHS| Jersey 31.8 36.4 35.0 43.0* 34.2 28.6 27.6
(e) QTL Holstein or Jersey F ST Dairy vs. Beef 55.2 47.0 48.0 42.6 44.0 44.0 45.8
(f) QTL Holstein QTL Jersey 46.0* 47.6* 47.6* 51.6* 34.2 50.4* 55.2*
  1. *Chi-squared test P < 0.05, Bonforroni corrected P-value.
  2. Values are the average number of windows showing both selection and type 3 loci for production traits in either Holstein or Jersey cattle (a-e) across 5 sets of 250 kb windows. Also shown is the number of overlapping windows with type 3 loci in both Holstein and Jersey (f). There are approximately 32 (a-d, f) and 46 (e) windows expected by chance. Additional file 3: Tables S1-S3 contain the full chi-squared tests.
  3. Evidence of selection was indicated by extreme (top 5%) values for haplotype homozygosity (HAPH), the integrated haplotype score (|iHS|) and Wright’s measure of population differentiation (F ST ).
  4. Traits analysed for type 3 loci are: fat yield (FAT, kg per lactation), milk yield (MILK, litres per lactation), protein yield (PROT, kg per lactation), stature (STAT), fertility (FERT, calving interval), FPC (fat percentage in milk) and PPC (protein percentage in milk).