All sheeps and sizes: a genetic investigation of mature body size across sheep breeds reveals a polygenic nature

Posbergh, Christian J.; Huson, Heather J.

doi:10.1111/age.13016

Cited by 34 publications

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“… 2009 ). Recent work (Posbergh and Huson 2021 ) used GWAS to explore genomic associations for body size that might serve as a starting point for optimizing this trait in mature sheep. Reproductive traits have remained at the forefront of selection, particularly in production settings where nutritional resources are adequate.…”

Section: Climate Landscape and Production Systemsmentioning

confidence: 99%

Evolution of the sheep industry and genetic research in the United States: opportunities for convergence in the twenty‐first century

et al. 2021

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Summary The continuous development and application of technology for genetic improvement is a key element for advancing sheep production in the United States. The US sheep industry has contracted over time but appears to be at a juncture where a greater utilization of technology can facilitate industry expansion to new markets and address inefficiencies in traditional production practices. Significant transformations include the increased value of lamb in relation to wool, and a downtrend in large‐scale operations but a simultaneous rise in small flocks. Additionally, popularity of hair breeds not requiring shearing has surged, particularly in semi‐arid and subtropical US environments. A variety of domestically developed composite breeds and newly established technological approaches are now widely available for the sheep industry to use as it navigates these ongoing transformations. These genetic resources can also address long‐targeted areas of improvement such as growth, reproduction and parasite resistance. Moderate progress in production efficiency has been achieved by producers who have employed estimated breeding values, but widespread adoption of this technology has been limited. Genomic marker panels have recently shown promise for reducing disease susceptibility, identifying parentage and providing a foundation for marker‐assisted selection. As the ovine genome is further explored and genomic assemblies are improved, the sheep research community in the USA can capitalize on new‐found information to develop and apply genetic technologies to improve the production efficiency and profitability of the sheep industry.

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Section: Climate Landscape and Production Systemsmentioning

confidence: 99%

Evolution of the sheep industry and genetic research in the United States: opportunities for convergence in the twenty‐first century

et al. 2021

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“…Mature body size has been extensively studied in humans, cattle, and other domestic animals but not in sheep (Posbergh and Huson, 2021). In sheep, the mature body size is more polygenic than in other domesticated animals, which suggests that the development of genomic trait selection might be the optimal option for evaluating body size in sheep (Posbergh and Huson, 2021). GWAS (Genome-wide association study) is a method that uses millions of single nucleotide polymorphism (SNP) in genomes as molecular genetic markers to conduct control analysis or correlation analysis at the whole genome level so as to investigate the genetic mutation of complex traits.…”

Section: Introductionmentioning

confidence: 99%

“…In sheep, body size has been widely recognized as an important indicator of growth and health ( Kemper et al, 2012 ), which impacts animal feeding and management as well as adaptation to the environment. Mature body size has been extensively studied in humans, cattle, and other domestic animals but not in sheep ( Posbergh and Huson, 2021 ). In sheep, the mature body size is more polygenic than in other domesticated animals, which suggests that the development of genomic trait selection might be the optimal option for evaluating body size in sheep ( Posbergh and Huson, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The GWAS Analysis of Body Size and Population Verification of Related SNPs in Hu Sheep

et al. 2021

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Body size is an important indicator of growth and health in sheep. In the present study, we performed Genome-Wide Association Studies (GWAS) to detect significant single-nucleotide polymorphisms (SNPs) associated with Hu sheep’s body size. After genotyping parental (G1) and offspring (G2) generation of the nucleus herd for meat production of Hu sheep and conducting GWAS on the body height, chest circumference, body length, tail length, and tail width of the two groups, 5 SNPs associated with body height and 4 SNPs correlated with chest circumference were identified at the chromosomal significance level. No SNPs were significantly correlated to body length, tail length, and width. Four out of the 9 SNPs were found to be located within the 4 genes. KITLG and CADM2 are considered as candidate functional genes related to body height; MCTP1 and COL4A6 are candidate functional genes related to chest circumference. The 9 SNPs found in GWAS were verified using the G3 generation of the nucleus herd for meat production. Nine products were amplified around the 9 sites, and 29 SNPs were found; 3 mutation sites, G > C mutation at 134 bp downstream of s554331, T > G mutation at 19 bp upstream of s26859.1, and A > G mutation at 81 bp downstream of s26859.1, were significantly correlated to the body height. Dual-luciferase reporter gene experiments showed that the 3 SNPs could significantly impact dual-luciferase and gene transcription activity.

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“…In vertebrates, somatic growth is a complex quantitative and highly polygenic trait (De-Santis & Jerry, 2007;Posbergh & Huson, 2021;Yuan et al, 2018). It is sensitive to a range of intrinsic (within individual), natural and extrinsic factors (Enberg et al, 2012;Morrongiello & Thresher, 2015).…”

Section: Growth Is a Complex Traitmentioning

confidence: 99%

Big fish, little fish: a multi-omics investigation of growth traits in silver trevally (Pseudocaranx georgianus – araara)

Valenza-Troubat

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Understanding the relationship between DNA sequence variation and the diversity of observable traits across the tree of life is a central research theme in biology. In all organisms, most traits vary continuously between individuals. Explaining the genetic basis of this quantitative variation requires disentangling genetic from non-genetic factors, as well as their interactions. The identification of causal genetic variants yields fundamental insights into how evolution creates diversity across the tree of life. Ultimately, this information can be used for medical, environmental and agricultural applications. Aquaculture is an industry that is experiencing significant global growth and is benefiting from the advances of genomic research. Genomic information helps to improve complex commercial phenotypes such as growth traits, which are easily quantified visually, but influenced by polygenes and multiple environmental factors, such as temperature. In the context of a global food crisis and environmental change, there is an urgent need not only to understand which genetic variants are potential candidates for selection gains, but also how the architecture of these traits are composed (e.g. monogenes, polygenes) and how they are influenced by and interact with the environment. The overall goal of this thesis research was to generate a genome-wide multi-omics dataset matched with exhaustive phenotypic information derived from a F0-F1 pedigree to investigate the quantitative genetic basis of growth in the New Zealand silver trevally (Pseudocaranx georgianus). These data were used to identify genomic regions that co-segregate with growth traits, and to describe the regulation of the genes involved in response to temperature fluctuations. The findings of this research helped gain fundamental insights into the genotype–phenotype map in an important teleost species and understand its ability to dynamically respond to temperature variations. This will ultimately support the establishment of a genomics-informed New Zealand aquaculture breeding programme. Chapter 1 of this thesis provides an overview of how genes interact with the environment to produce various growth phenotypes and how an understanding of this is important in aquaculture. This first chapter provides the deeper context for the research in subsequent data chapters. Chapter 2 describes the study population, the collection of phenotypic and genotypic data, and a first description of the genetic parameters of growth traits in trevally. A combination of Whole Genome Sequencing (WGS) and Genotyping-By-Sequencing (GBS) techniques were used to generate 60 thousand Single Nucleotide Polymorphism (SNP) markers for individuals in a two-generation pedigree. Together with phenotypic data, the genotyping data were used to reconstruct the pedigree, measure inbreeding levels, and estimate heritability for 10 growth traits. Parents were identified for 63% of the offspring and successful pedigree reconstruction indicated highly uneven contributions of each parent, and between the sexes, to the subsequent generation. The average inbreeding levels did not change between generations, but were significantly different between families. Growth patterns were found to be similar to that of other carangids and subject to seasonal variations. Heritability as well as genetic and phenotypic correlations were estimated using both a pedigree and a genomic relatedness matrix. All growth trait heritability estimates and correlations were found to be consistently high and positively correlated to each other. In Chapter 3, genotypic and phenotypic data were used to carry out linkage mapping and a genome-wide association study (GWAS) to map quantitative trait loci (QTLs) associated with growth differences in the F1 population. A linkage map was generated using the largest family, which allowed to scan for rare variants associated with the traits. The linkage map reported in this thesis is the first one for the Pseudocaranx genus and one of the densest for the carangid family. It included 19,861 SNPs contained in 24 linkage groups, which correspond to the 24 trevally chromosomes. Eight significant QTLs associated with height, length and weight were discovered on three linkage groups. Using GWAS, 113 SNPs associated with nine traits were identified and 29 genetic growth hot spots were uncovered. Two of the GWAS markers co-located with the QTLs discovered with the linkage mapping analysis. This demonstrates that combining QTL mapping and GWAS represents a powerful approach for the identification and validation of loci controlling complex phenotypes, such as growth, and provides important insights into the genetic architecture of these traits. Chapter 4, the last data chapter, investigates plasticity in gene expression patterns and growth of juvenile trevally, in response to different temperatures. Temperature conditions were experimentally manipulated for 1 month to mimic seasonal extremes. Phenotypic differences in growth were measured in 400 individuals, and the gene expression patterns of the pituitary gland and the liver were compared across treatments in a subset of 100 individuals, using RNA sequencing. Results showed that growth increased 50% more in the warmer compared with the colder condition, suggesting that temperature has a large impact on the metabolic activity associated with growth. We were able to annotate 27,887 gene models and found 39 differentially expressed genes (DEGs) in the pituitary, and 238 in the liver. Of these, 6 DEGs showed a common expression pattern between the tissues. Annotated blast matches of all DEGs revealed genes linked to major pathways affecting metabolism and reproduction. Our results indicate that native New Zealand trevally exhibit predictable plastic regulatory responses to temperature stress and the genes identified provide excellent for selective breeding objectives and studied how populations may adapt to increasing temperatures. Finally, Chapter 5 discusses the implications, future directions, and application of this research for trevally and other breeding programmes. It more broadly highlights the insights that were gained on the genetic architecture of growth, and the role of temperature in interacting and modulating genes involved in plastic growth responses.

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All sheeps and sizes: a genetic investigation of mature body size across sheep breeds reveals a polygenic nature

Cited by 34 publications

References 34 publications

Evolution of the sheep industry and genetic research in the United States: opportunities for convergence in the twenty‐first century

Evolution of the sheep industry and genetic research in the United States: opportunities for convergence in the twenty‐first century

The GWAS Analysis of Body Size and Population Verification of Related SNPs in Hu Sheep

Big fish, little fish: a multi-omics investigation of growth traits in silver trevally (Pseudocaranx georgianus – araara)

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