Figure 1.
Cattle genetic differences: (a) a Tropical Composite (left) and a Brahman bull (right).
(b) Distribution of indicine% across the two samples showing a mode at ∼30% for Tropical Composite (red) and ∼95% for Brahman (blue) cattle. (c) Multi-dimensional scaling plot showing a clustering of the Brahman (blue) and Tropical Composite (red) cattle relative to the reference samples of Angus (black) and Nelore (green). (d) Genetic relationship matrices based on genotype similarity among individuals for Tropical Composite (left) and Brahman (right) samples where the diagonal blocks show paternal half-sib families.
Table 1.
Adaptation phenotypes in Brahman and Tropical Composite cattle.
Table 2.
Heritabilities (diagonal), genetic (top) and phenotypic (bottom) correlations.
Table 3.
Estimated effect of indicine content (indicine%).
Figure 2.
Genetic architecture of climatic adaptive traits: (a) Heat map of the number of significant SNP (P<0.0001) from few (blue) to many (red) across the 30 chromosomes for the ten traits in Tropical Composite and Brahman.
(b) Manhattan plots of the significance (-logP on the y-axis) of each SNP in genome order (x-axis) for Sheath score (left panels) and Coat Colour (right panels) for Tropical Composite (upper panels) and Brahman (lower panel) cattle. Note the similarity on BTA5 for Sheath score in both samples but different genes for colour, (c) Average frequency of the forward allele for sliding windows of 100 consecutive SNP along BTA5 at 1 SNP pace for Brahman (blue) and Tropical Composite (red) cattle relative to the reference samples of Angus (black) and Nelore (green). The insert shows regions of divergent allele frequencies between taurine and indicine cattle on BTA5 from 20 to 60 Mb. (d) Heat map of LD (r2) on BTA5 in the Tropical Composite sample, with red dots corresponding to r2>0.1, showing LD blocks spanning several Mb. (e) The effect of BTA5 on Sheath score in Tropical Composite and Brahman cattle was not due to indicine% but to a major gene. 50 SNP were selected from 5 regions of BTA5 with divergent alleles in Angus and Nelore cattle. The average additive association (based on –log(P), y-axis) of these 50 SNP across the ten traits was calculated (green bars) and compared with the association of 50 SNP (orange bars) also with divergent alleles in Angus and Nelore cattle but randomly located to regions other than BTA5 or BTAX. A total of 10 random selections were chosen and the average plotted. (f) Genes close (< = 3 Kb) to SNP significantly associated (P<0.0001) with Sheath in both breeds.
Table 4.
Locations of the SNP explaining the largest genetic variance for each trait within each breed of cattle1.
Table 5.
Studentized effect (estimated effect divided by its standard error) of seven selected pleiotropic SNP and its colosest genes across five adaptation phenotypes in Brahman (BB) and Tropical Composite (TC) cattle.
Table 6.
Selected positional-candidate genes (P<0.01 both breeds) and its different-expression (P<0.05) in muscle before and after undernutrition period*.