Genetic architecture of body size in mammals

Heterozygous GHR gene mutation in a child with idiopathic short stature

Several monogenic defects have been reported to be associated with idiopathic short stature. Focusing on growth hormone receptor (GHR)-gene alterations, the heterozygosity of the same gene defect may be associated with a range of growth deficits. We found a heterozygous mutation (V144I) within exon 6 of the GHR gene in a patient with a low level of insulin-like growth factor I (IGF-I), normal level of GH, and severe short stature. Despite the lack of statistical difference, an overall tendency for reduced wt-GH-induction of GHR activation and Jak/Stat signalling in cells transiently expressing GHR-V144I alone or co-expressing wt-GHR compared to cells expressing only wt-GHR was found when GH doses were increased. Our results suggest that, although GHR sequence variants are responsible for some functional alterations commonly observed in children with idiopathic short stature, these changes may not explain all the height deficits observed in these subjects.

Molecular consequences of animal breeding

The phenotypic diversity in domestic animals provides a unique opportunity to study genotype-phenotype relationships. The identification of causal mutations provides an insight into what types of mutations have contributed to phenotypic evolution in domestic animals. Whole genome sequencing has revealed that fixation of null alleles that inactivate genes, which are essential under natural conditions but disadvantageous on the farm, has not been a common mechanism for genetic adaptation in domestic animals. Numerous examples have been revealed where structural changes cause specific phenotypic effects by altering transcriptional regulation. An emerging feature is also the evolution of alleles by the accumulation of several consecutive mutations which affect gene function.

Complex inheritance of melanoma and pigmentation of coat and skin in Grey horses

The dominant phenotype of greying with age in horses, caused by a 4.6-kb duplication in intron 6 of STX17, is associated with a high incidence of melanoma and vitiligo-like skin depigmentation. However, the progressive greying and the incidence of melanoma, vitiligo-like depigmentation, and amount of speckling in these horses do not follow a simple inheritance pattern. To understand their inheritance, we analysed the melanoma grade, grey level, vitiligo grade, and speckling grade of 1,119 Grey horses (7,146 measurements) measured in six countries over a 9-year period. We estimated narrow sense heritability (h²), and we decomposed this parameter into polygenic heritability (h²_POLY), heritability due to the Grey (STX17) mutation (h²_STX17), and heritability due to agouti (ASIP) locus (h²_ASIP). A high heritability was found for greying (h² = 0.79), vitiligo (h² = 0.63), and speckling (h² = 0.66), while a moderate heritability was estimated for melanoma (h² = 0.37). The additive component of ASIP was significantly different from zero only for melanoma (h²_ASIP = 0.02). STX17 controlled large proportions of phenotypic variance (h²_STX17 = 0.18–0.55) and overall heritability (h²_STX17/h² = 0.28–0.83) for all traits. Genetic correlations among traits were estimated as moderate to high, primarily due to the effects of the STX17 locus. Nevertheless, the correlation between progressive greying and vitiligo-like depigmentation remained large even after taking into account the effects of STX17. We presented a model where four traits with complex inheritance patterns are strongly influenced by a single mutation. This is in line with evidence of recent studies in domestic animals indicating that some complex traits are, in addition to the large number of genes with small additive effects, influenced by genes of moderate-to-large effect. Furthermore, we demonstrated that the STX17 mutation explains to a large extent the moderate to high genetic correlations among traits, providing an example of strong pleiotropic effects caused by a single gene.

Clarifying the genetic architecture of complex traits is a problem with profound implications for agriculture, biology, and medicine. Using data from Lipizzan horses with the grey coat phenotype, we present an example of a single mutation (intronic duplication in STX17) that explains 18%–55% of phenotypic variation in four complex traits, while polygenic background additive effects also explain 11%–57% of phenotypic variation. This study provides a prime example of complex traits being influenced by genes of moderate-to-large effect and supports further the evidence of recent studies in domestic animals that some complex traits are, in addition to the large number of genes with small additive effects, influenced by genes of moderate-to-large effect. We further show that the STX17 mutation accounts for a large proportion of the estimated genetic correlations between the traits. This case of strong pleiotropic effects of a single mutation on complex traits makes this work of significant general interest for biology and medicine.

The future of livestock breeding: genomic selection for efficiency, reduced emissions intensity, and adaptation

As the global population and global wealth both continue to increase, so will the demand for livestock products, especially those that are highly nutritious. However, competition with other uses for land and water resources will also intensify, necessitating more efficient livestock production. In addition, as climate change escalates, reduced methane emissions from cattle and sheep will be a critical goal. Application of new technologies, including genomic selection and advanced reproductive technologies, will play an important role in meeting these challenges. Genomic selection, which enables prediction of the genetic merit of animals from genome-wide SNP markers, has already been adopted by dairy industries worldwide and is expected to double genetic gains for milk production and other traits. Here, we review these gains. We also discuss how the use of whole-genome sequence data should both accelerate the rate of gain and enable rapid discovery and elimination of genetic defects from livestock populations.

Precision editing of large animal genomes

Transgenic animals are an important source of protein and nutrition for most humans and will play key roles in satisfying the increasing demand for food in an ever-increasing world population. The past decade has experienced a revolution in the development of methods that permit the introduction of specific alterations to complex genomes. This precision will enhance genome-based improvement of farm animals for food production. Precision genetics also will enhance the development of therapeutic biomaterials and models of human disease as resources for the development of advanced patient therapies.