Genome scan of selective sweeps
To determine genetic modifications that occurred under different
temperatures, we analyzed selective sweeps between the two cattle
groups: northern (MG and YB) and southern (YN and HN). Selective sweep
analyses were preformed over the whole genomes based on the distribution
of F ST values, with the top 5% calculated in
50-kb windows with 25-kb steps using a Fisher’s
exact test to determine the
frequency spectrum in southern versus northern cattle. A total of 269
candidate genes were found to be with strong selective sweep signals in
Chinese cattle (Fig. 2a , Additional file 1: Fig. S3and Table S3 ). The top enriched KEGG pathway of the candidate
genes was RNA degradation (P =
5.5×10-3)(Additional file 1: Table S4 ), which
mainly acts on gene expression and
regulation and plays an important role in cellular mechanisms [31].
Several candidate genes (e.g., AOC3 and FASN ) were
involved in pathways related to the activation of thermogenic
metabolism, such as tyrosine metabolism (P =
5.3×10-2) and fatty acid biosynthesis (P =
5.8×10-2)(Additional file 1: Table S5 ).
This is expected as cold exposure
could increase tyrosine hydroxylase, leading to the increased secretion
of norepinephrine and enhanced non-shivering thermogenesis in BAT
[32]. In addition, AOC3 is related to diabetes and
membrane-bound WAT [33-34]. FASN plays a role in the de novobiosynthesis of fatty acids, and the down-regulation of FASN can
induce browning in WAT [35]. Many fatty acids exert a positive
effect on thermogenesis by activating BAT [36-38]. We also found
many candidate genes (e.g., APOA5, ACOX3 and ALDOB )
involved in fatty acid, fructose and mannose metabolism and associated
with signalling pathways, such as the PPAR signalling pathway
(Additional file 1: Table S5 ). APOA5 treatments can increase
gene expression levels of UCP1 in adipocytes, and fat
accumulation can cause ACOX3 to increase in blood [39]. ALDOB is
involved in insulin biosynthesis and secretion, as well as insulin
receptor signalling [40]. It is well-known that insulin pathways and
fat metabolism are inseparable and could affect the development of BAT,
leading to obesity and insulin resistance, for example [41-42].
Consistently,
enrichment
analysis of GO terms revealed that several candidate genes
(LOC100337001, PRDM16, SH3PXD2B and ZFPM1 ) are related to
fat cell differentiation (GO:0045598), brown fat differentiation
(GO:0050873) and white fat cell differentiation (GO:0050872)
(Additional file 1: Fig. S4 , Table S6 andS7 ).
Among those genes with signals of selective sweep, PRDM16 is of
most interest because it was reported to increase thermogenesis by
promoting the expression of the key gene UCP1 (Additional
file 1: Fig.
S5 ).
In addition, though the F ST (0.26) andθ π (0.2×10-3) values ofPRDM16 were similar to that of three other significant genes
(LOC100337001, SH3PXD2B and ZFPM1 ), the lowestP -value was observed for PRDM16 (P =
3.8×10-8 (Additional file 1: Table S3 andS8 ). In addition, Tajima’s D analysis also supported the
idea that PRDM16 was under selection (D= -0.34)
(Fig. 2b, Additional file 1: Table S8 ). The PRDM16genotypes found in northern and southern cattle were well-distinguished
from each other and consistent with the phylogenetic tree created using
the SNPs of this gene (Fig. 2c ). We discovered five
non-synonymous SNVs of which one (c.2336 T > C, p.L779P)
was found at a higher level (93%) in southern cattle than northern
cattle (Additional file 1: Fig. S6 and Table S8 ).
We then compared the PRDM16 protein sequences to other species
whose BAT had been found and reported (Fig. 2d ,Additional file 1: Fig.
S7 )
and it is interesting to find that the substitution that occurred at
position Leu779 of the PRDM16 gene in northern
cattle is the same as that in species that have complete BAT function
(e.g., mouse, rat and hamster)(Fig. 2d ). In rodents, BAT is
intact and persists throughout their lifetimes, and its thermogenesis
activity is complete [43-44]. However, in many large mammals, BAT is
incomplete or even non-existent. For example, the BAT is incomplete in
human adults and sheep in which it exists only during infancy and
degenerates as they grow [45-46]. Conversely, the substitution in
southern cattle, which is proline, is the same as that in species that
have an incomplete or null BAT function (sheep, pig, whale, horse,
platypus, elephant, sirenian, marsupial, human and rabbit (Fig.
2d ). Thus, we hypothesized that this substitution of residue 779 in thePRDM16 gene is probably related to the BAT function, and this
locus is likely to play a role in cold tolerance.