Association of Copy Number Variation at Intron 3 of HMGA2 With Navel Length in Bos indicus

Abstract

Navel injuries caused by friction against the pasture can promote infection, reproductive problems and costly treatments in beef cattle raised in extensive systems. A haplotype-based genome-wide association study (GWAS) was performed for visual scores of navel length at yearling in Nellore cattle (Bos indicus) using data from 2,016 animals and 503,088 single nucleotide polymorphism (SNP) markers. The strongest signal (p = 1.01 × 10-9) was found on chromosome 5 spanning positions 47.9–48.2 Mbp. This region contains introns 3 and 4 and exons 4 and 5 of the high mobility group AT-hook 2 gene (HMGA2). Further inspection of the region with whole genome sequence data of 21 Nellore bulls revealed correlations between counts of the significant haplotype and copy number gains of a ∼6.2 kbp segment of intron 3 of HMGA2. Analysis of genome sequences from five African B. indicus and four European Bos taurus breeds revealed that the copy number variant (CNV) is indicine-specific. This intronic CNV was then validated through quantitative polymerase chain reaction (qPCR) using Angus animals as copy neutral controls. Importantly, the CNV was not detectable by means of conventional SNP-based GWAS or SNP probe intensity analyses. Given that HMGA2 affects the expression of the insulin-like growth factor 2 gene (IGF2) together with the pleomorphic adenoma gene 1 (PLAG1), and that the latter has been repeatedly shown to be associated with quantitative traits of economic importance in cattle, these findings highlight the emerging role of variants impacting the insulin-like growth factor pathway to cattle breeding.

Genome-Wide Runs of Homozygosity Revealed Selection Signatures in Bos indicus

“…HMGA2 polymorphism had earlier been found to be associated with the difference in body stature in mice (pygmy size) (Zhou et al, 1995), humans (oversize) (Ligon et al, 2005) and cattle (Pryce et al, 2011). Recently, the intronic copy number variation (CNV) of this gene has also been associated with navel length in Nellore cattle (Aguiar et al, 2018).The analysis of the annotated genes in these ROH regions of dairy and draft breeds also indicated that Kangayam was more resistant to diseases/had higher immunity (selection sweeps in LYZL1, SVIL and GPX4) and stress tolerant (CCT4). Whereas, dairy breeds had selection sweeps in key genes governing milk production (PTGFR, CSN1S1, CSN2, CSN1S2, and CSN3).…”

Selection signatures in tropical cattle are enriched for promoter and coding regions and reveal missense mutations in the damage response gene HELB

“…Other mutations, including regulatory mutations in HELB that modify its expression pattern, or mutations in other genes such as HMGA2, could also affect tropical adaptation. Recently, a tandem repeat that includes the third and fourth introns of HMGA2 has been associated with navel score and with visual scores of precocity and muscling in Nellore cattle [53]. We show that the mutations in HELB and the HMGA2-CNVR can be inherited independently, which means that they can potentially affect different phenotypes.…”

“…(48,074,233-48,080,443 bp) was reported to affect the third and fourth introns of HMGA2 in Nellore cattle and to be associated with navel length (similar to sheath score) at yearling (Fig. 2c) [53]. Taken together, these results indicate this 430-kb selective sweep is relevant for selective breeding programs aimed at improving adaptation of cattle to tropical conditions.…”

“…Duplicates reads were marked using Picard tools (http://broad insti tute.githu b.io/picar d/). We assessed the existence of copy number variants (CNV) in the known HMGA2-CNV region on chromosome 5 between 48,074,233 and 48,080,443 bp (~ 6.2 kb) [53] by comparing the coverage in the CNVR versus the coverage along the whole chromosome 5. In addition, the alignments of all 71 animals were visualized with Integrative Genomics Viewer (IGV) [54] to confirm the existence of reads that harbor a duplication of the HMGA2-CNV.…”

“…2b, c) and (see Additional file 1: Figure S11) for ARS-UCD1.2 coordinates). The latter gene is of particular interest because a 6.2-kb CNV that spans a segment of HMGA2 intron 3 in Nellore (indicine) cattle is associated with navel score [53] (Fig. 2c).…”