Genome-wide association study on dairy cow mortality in three US regions
Cow mortality, from DHI reports, is farmer provided information. The termination code = “dead” is the primary reason given for a cow leaving a herd, particularly late in lactation. This trait can be difficult to interpret because its definition and recording method may differ across farms. Our objective was to do a genome-wide association study (GWAS) on cow mortality and 305-d milk yield for three lactations and determine if there were differences in the genetic architecture associated with these traits in three different regions of the US.
Genomic EBV of cow mortality and 305-d milk yield were estimated with a single-step GBLUP using a threshold-linear model. The SNP file contained 42,503 usable SNP markers for 34,506 bulls obtained from USDA-AIPL. Data consisted of the entire US DHI data for three lactations (10,748,430 animals; 6,233,306 records) for cows calving from 1999 to 2008. Three US regions SE: southeast (648,991 animals; 293,494 records), SW: southwest (541,777 animals; 272,934 records), and NE: northeast (1,690,481 animals; 883,887 records)) were selected for regional comparison.
Heritability estimate for 305-d milk first lactation yield was 29%. Heritability for mortality within the first lactation was 0.04, 0.06, 0.06, and 0.04 for SE, SW, NE, and US, respectively. Genetic correlations between first lactation mortality and 305-d milk yield were 0.14, -0.01, 0.02, and 0.25 for SE, SW, NE, and US, respectively.
The genome was divided into equal segments of 20 sequential SNPs. As expected, a segment on chromosome 14 was significantly associated with milk production in all regions. The proportion of the total genetic variance for 305-d milk yield, explained by this segment, was 1%, 1%, 3% and 4% for SE, SW, NE region, and total US, respectively. Chromosome 14 showed a strong association with first parity mortality for the entire US, with the NE showing a strong association for all three parities. Milk components (higher or lower %fat) could be a possible explanation. Within the SE and SW regions, chromosome 14 did not show a significant association for any of the three parities. These results suggest that this farmer-recorded trait on mortality is being interpreted differently and/or there are different traits (genomic segments) responsible for cow mortality in different regions of the country.