Mapping genomic regions for reproductive traits in beef cattle: Inclusion of the X chromosome

X-linked genes influence various complex traits in dairy cattle

BACKGROUND

The search for quantitative trait loci (QTL) affecting traits of interest in mammals is frequently limited to autosomes, with the X chromosome excluded because of its hemizygosity in males. This study aimed to assess the importance of the X chromosome in the genetic determinism of 11 complex traits related to milk production, milk composition, mastitis resistance, fertility, and stature in 236,496 cows from three major French dairy breeds (Holstein, Montbéliarde, and Normande) and three breeds of regional importance (Abondance, Tarentaise, and Vosgienne).

RESULTS

Estimates of the proportions of heritability due to autosomes and X chromosome (h²_X) were consistent among breeds. On average over the 11 traits, h²_X=0.008 and the X chromosome explained ~ 3.5% of total genetic variance. GWAS was performed within-breed at the sequence level (~ 200,000 genetic variants) and then combined in a meta-analysis. QTL were identified for most breeds and traits analyzed, with the exception of Tarentaise and Vosgienne and two fertility traits. Overall, 3, 74, 59, and 71 QTL were identified in Abondance, Montbéliarde, Normande, and Holstein, respectively, and most were associated with the most-heritable traits (milk traits and stature). The meta-analyses, which assessed a total of 157 QTL for the different traits, highlighted new QTL and refined the positions of some QTL found in the within-breed analyses. Altogether, our analyses identified a number of functional candidate genes, with the most notable being GPC3, MBNL3, HS6ST2, and DMD for dairy traits; TMEM164, ACSL4, ENOX2, HTR2C, AMOT, and IRAK1 for udder health; MAMLD1 and COL4A6 for fertility; and NRK, ESX1, GPR50, GPC3, and GPC4 for stature.

CONCLUSIONS

This study demonstrates the importance of the X chromosome in the genetic determinism of complex traits in dairy cattle and highlights new functional candidate genes and variants for these traits. These results could potentially be extended to other species as many X-linked genes are shared among mammals.

The roles and expression of HOXA/Hoxa10 gene: A prospective marker of mammalian female fertility?

This review addresses the influence of homebox A10/a10 (HOXA/Hoxa10) gene on reproductive tract anatomy and functional fertility in mammalian species, and discusses major endocrine and environmental regulators of HOXA/Hoxa10 expression. Female reproductive efficiency or success is a function of several factors including the ovulation and fertilization rate, and uterine receptivity. A family of HOX/Hox genes establishes the segmental identity of the reproductive tract during embryogenesis and retains its physiological plasticity in sexually mature animals and humans. In particular, the HOXA/Hoxa10 gene is an intrinsic component of implantation, decidualization, and immunomodulation in the adult uterus. It was, therefore, suggested that knowledge of HOXA/Hoxa10 regulation might be essential in navigating molecular mechanisms with the aim of enhancing female reproductive potential. However, a recent study in pigs revealed a lack of associations between endometrial HOXA10 expression and reproductive tract morphology, and very poor correlations with sows' fertility metrics. Retinoic acid mainly regulates 3' HOX/Hox paralogs but may also modify the expression of downstream HOX/Hox genes, including HOXA/Hoxa10. Sex steroids directly regulate HOXA/Hoxa10 expression. The vitamin D receptor pathway modulates HOXA/Hoxa10 expression in the adult reproductive tract. Lastly, endocrine disruptors such as diethylstilbestrol, methoxychlor, bisphenol A, and isoflavones were shown to alter HOXA/Hoxa10 expression, thus affecting reproductive competence of the female.

The effect of mitochondrial DNA polymorphisms on cattle reproduction

The aim of this study was to identify SNPs located in mitochondrial DNA that are associated with reproductive traits in beef cows. A total of 1999 Nelore females genotyped with the high-density Illumina BovineHD BeadChip (Illumina Inc., San Diego, CA, USA) were used to study the association of mitochondrial DNA variants with reproductive traits using a single-step procedure. In a preliminary analysis, the present results indicate a small participation of the mitogenome in the expression of reproductive traits in beef cattle. However, possible difficulties related to the biological characteristics of mitochondrial DNA and its inheritance, genotyping, and annotation of the phenotypes studied may also explain the results.