Beef production is a source of wealth and food security to many countries. Beef production in tropical and sub-tropical regions depends on the environmental adaptation of cattle with varying degrees of Bos indicus content. While cattle with Bos indicus content are well adapted to heat, ectoparasites, and limited forage, they tend to have lower reproductive performance. Prominent among these reproductive issues is the late onset of puberty. Age at puberty has been shown to be moderately heritable and to vary significantly between and within beef cattle breeds, making this trait a promising target for improvement via animal selection. Genetic markers associated with puberty in Bos indicus-influenced cattle could aid selection, and lead to more efficient beef production.
The aim of this project was to identify genetic markers, genes and pathways associated with male and female puberty in tropically adapted beef cattle. We performed genome-wide association studies (GWAS) in four cattle populations with varying degrees of Bos indicus influence: 1) Tropical Composite females, 2) Brahman females, 3) Brangus females and 4) Brahman males. These cattle were measured for a range of growth, fatness, hormonal and reproductive traits, throughout puberty. Studying these traits serves the notion that puberty is complex biological process, influenced by growth, fat deposition and hormonal signals. Thus, we hypothesised that puberty is a complex trait influenced by multiple genes.
To test the hypothesis and perform GWAS targeting puberty, it was important to define age at puberty, as the principal phenotype under investigation. In the Brahman and Tropical Composite populations, the trait age at first corpus luteum (AGECL) was designed for studying puberty describing with precision the age when the ability to reproduce was first achieved. In the Brangus population the best indicator for puberty was first service conception (FSC). From the traits measured in the male population we studied a subset of bulls measured for scrotal circumference (SC) and a number of sperm traits including sperm chromatin integrity. We showed that sperm chromatin integrity could be measured in young bulls, but it was not a good indicator of puberty because it did not change during pubertal development. Sperm concentration, motility and the percentage of normal sperm did change during pubertal development and were related to SC, which was the trait most frequently measured in the male population. For these reasons age at puberty in bulls was estimated as the age when a bull achieved a SC of 26 cm (AGE26). Thus, AGE26 was investigated in our GWAS. ii
The GWAS resulted in more genetic markers associated with age at puberty than expected by chance alone. At P < 0.01, there were 679 markers associated with AGECL in Tropical Composites, 876 markers associated with AGECL in Brahmans, 284 markers associated with FSC in Brangus and 1,241 markers associated with AGE26 in Brahmans. These results support that cattle puberty is a complex trait, influenced by numerous genes. We detected breed differences and most genetic marker associations could not be validated across breeds, illustrating the challenge of organizing a genomic selection strategy across breeds. Some genetic markers explained over 5% of the genetic variance and some genomic regions were associated with more than one trait and breed. The region between 24.7 and 28.3 Mb of chromosome 14 was associated with insulin growth factor 1 (IGF1) serum concentrations, AGECL, post partum anoestrous interval, growth and fat traits, SC, AGE26 and sperm output. In chromosome X, two regions were relevant across traits: markers between 0.9 and 5.8 Mb were associated with percentage of normal sperm, SC, AGECL in Brahman and IGF1 in Tropical Composite; and markers between 80 and 92 Mb were associated with SC in Brahman, post partum anoestrous interval in Tropical Composite and heifer pregnancy in Brangus. A third region of chromosome X (53 Mb) was highly associated with percentage of normal sperm. Chromosomes 14 and X presented some of the most significant results, but many more chromosomes harboured genetic markers associated with pubertal traits. These results are evidence of the complexity underpinning puberty.
The complexity of genetics underpinning puberty identified with GWAS motivated the use of gene network analysis. Network analysis identified candidate genes, important transcription factors and biological pathways associated with puberty: axon guidance, cell adhesion, erbB (avian erythroblastic leukemia viral or v-erbB) signalling and glutamate signalling. These pathways are known to affect gonadotropin releasing hormone (GnRH) activity. The GWAS and network analysis revealed a list of genes associated with cattle puberty: NMDAR2B, ESRRG, PPARG, PROP1, ZNF462, HIVEP3, TOX, EYA1, NCOA2, ZFHX4, ZMAT3, STAT6, RFX4, PLAGL1, NR6A1, IGF1R, PENK, RPS20, SNORD54, PLAG1, MOS, XKR4, AR, TAF1, TAF9B, INHA, SERPINA7, EPHA4, WNT6, STK36, IHH, dynein, AR and POU3F4. Future studies targeting these genes, their pathways and interactions will continue to expand our knowledge of cattle puberty and it might lead to discovery of functional mutations, unfolding new strategies for selecting and breeding early-pubertal cattle to benefit beef production.