In it for the long run: perspectives on exploiting long-read sequencing in livestock for population scale studies of structural variants

The Farm Animal Genotype-Tissue Expression (FarmGTEx) Project

Genetic mutation and drift, coupled with natural and human-mediated selection and migration, have produced a wide variety of genotypes and phenotypes in farmed animals. We here introduce the Farm Animal Genotype-Tissue Expression (FarmGTEx) Project, which aims to elucidate the genetic determinants of gene expression across 16 terrestrial and aquatic domestic species under diverse biological and environmental contexts. For each species, we aim to collect multiomics data, particularly genomics and transcriptomics, from 50 tissues of 1,000 healthy adults and 200 additional animals representing a specific context. This Perspective provides an overview of the priorities of FarmGTEx and advocates for coordinated strategies of data analysis and resource-sharing initiatives. FarmGTEx aims to serve as a platform for investigating context-specific regulatory effects, which will deepen our understanding of molecular mechanisms underlying complex phenotypes. The knowledge and insights provided by FarmGTEx will contribute to improving sustainable agriculture-based food systems, comparative biology and eventual human biomedicine.

Using bioinformatics to investigate functional diversity: a case study of MHC diversity in koalas

Conservation genomics can greatly improve conservation outcomes of threatened populations, including those impacted by disease. Understanding diversity within immune gene families, including the major histocompatibility complex (MHC) and toll-like receptors (TLR), is important due to the role they play in disease resilience and susceptibility. With recent advancements in sequencing technologies and bioinformatic tools, the cost of generating high-quality sequence data has significantly decreased and made it possible to investigate diversity across entire gene families in large numbers of individuals compared to investigating only a few genes or a few populations previously. Here, we use the koala as a case study for investigating functional diversity across populations. We utilised previous target enrichment data and 438 whole genomes to firstly, determine the level of sequencing depth required to investigate MHC diversity and, secondly, determine the current level of diversity in MHC genes in koala populations. We determined for low complexity, conserved genes such as TLR genes 10 × sequencing depth is sufficient to reliably genotype more than 90% of variants, whereas for complex genes such as the MHC greater than 20 × and preferably 30 × sequencing depth is required. We used whole genome data to identify 270 biallelic SNPs across 24 MHC genes as well as copy number variation (CNV) within class I and class II genes and conduct supertype analysis. Overall, we have provided a bioinformatic workflow for investigating variation in a complex immune gene family from whole genome sequencing data and determined current levels of diversity within koala MHC genes.

Structural variations in livestock genomes and their associations with phenotypic traits: a review

Genomic structural variation (SV) refers to differences in gene sequences between individuals on a genomic scale. It is widely distributed in the genome, primarily in the form of insertions, deletions, duplications, inversions, and translocations. Due to its characterization by long segments and large coverage, SVs significantly impact the genetic characteristics and production performance of livestock, playing a crucial role in studying breed diversity, biological evolution, and disease correlation. Research on SVs contributes to an enhanced understanding of chromosome function and genetic characteristics and is important for understanding hereditary diseases mechanisms. In this article, we review the concept, classification, main formation mechanisms, detection methods, and advancement of research on SVs in the genomes of cattle, buffalo, equine, sheep, and goats, aiming to reveal the genetic basis of differences in phenotypic traits and adaptive genetic mechanisms through genomic research, which will provide a theoretical basis for better understanding and utilizing the genetic resources of herbivorous livestock.

A large structural variant collection in Holstein cattle and associated database for variant discovery, characterization, and application

BACKGROUND

Structural variants (SVs) such as deletions, duplications, and insertions are known to contribute to phenotypic variation but remain challenging to identify and genotype. A more complete, accessible, and assessable collection of SVs will assist efforts to study SV function in cattle and to incorporate SV genotyping into animal evaluation.

RESULTS

In this work we produced a large and deeply characterized collection of SVs in Holstein cattle using two popular SV callers (Manta and Smoove) and publicly available Illumina whole-genome sequence (WGS) read sets from 310 samples (290 male, 20 female, mean 20X coverage). Manta and Smoove identified 31 K and 68 K SVs, respectively. In total the SVs cover 5% (Manta) and 6% (Smoove) of the reference genome, in contrast to the 1% impacted by SNPs and indels. SV genotypes from each caller were confirmed to accurately recapitulate animal relationships estimated using WGS SNP genotypes from the same dataset, with Manta genotypes outperforming Smoove, and deletions outperforming duplications. To support efforts to link the SVs to phenotypic variation, overlapping and tag SNPs were identified for each SV, using genotype sets extracted from the WGS results corresponding to two bovine SNP chips (BovineSNP50 and BovineHD). 9% (Manta) and 11% (Smoove) of the SVs were found to have overlapping BovineHD panel SNPs, while 21% (Manta) and 9% (Smoove) have BovineHD panel tag SNPs. A custom interactive database ( https://svdb-dc.pslab.ca ) containing the identified sequence variants with extensive annotations, gene feature information, and BAM file content for all SVs was created to enable the evaluation and prioritization of SVs for further study. Illustrative examples involving the genes POPDC3, ORM1, G2E3, FANCI, TFB1M, FOXC2, N4BP2, GSTA3, and COPA show how this resource can be used to find well-supported genic SVs, determine SV breakpoints, design genotyping approaches, and identify processed pseudogenes masquerading as deletions.

CONCLUSIONS

The resources developed through this study can be used to explore sequence variation in Holstein cattle and to develop strategies for studying SVs of interest. The lack of overlapping and tag SNPs from commonly used SNP chips for most of the SVs suggests that other genotyping approaches will be needed (for example direct genotyping) to understand their potential contributions to phenotype. The included SV genotype assessments point to challenges in characterizing SVs, especially duplications, using short-read data and support ongoing efforts to better characterize cattle genomes through long-read sequencing. Lastly, the identification of previously known functional SVs and additional CDS-overlapping SVs supports the phenotypic relevance of this dataset.

An overview of recent technological developments in bovine genomics

Cattle are regarded as highly valuable animals because of their milk, beef, dung, fur, and ability to draft. The scientific community has tried a number of strategies to improve the genetic makeup of bovine germplasm. To ensure higher returns for the dairy and beef industries, researchers face their greatest challenge in improving commercially important traits. One of the biggest developments in the last few decades in the creation of instruments for cattle genetic improvement is the discovery of the genome. Breeding livestock is being revolutionized by genomic selection made possible by the availability of medium- and high-density single nucleotide polymorphism (SNP) arrays coupled with sophisticated statistical techniques. It is becoming easier to access high-dimensional genomic data in cattle. Continuously declining genotyping costs and an increase in services that use genomic data to increase return on investment have both made a significant contribution to this. The field of genomics has come a long way thanks to groundbreaking discoveries such as radiation-hybrid mapping, in situ hybridization, synteny analysis, somatic cell genetics, cytogenetic maps, molecular markers, association studies for quantitative trait loci, high-throughput SNP genotyping, whole-genome shotgun sequencing to whole-genome mapping, and genome editing. These advancements have had a significant positive impact on the field of cattle genomics. This manuscript aimed to review recent advances in genomic technologies for cattle breeding and future prospects in this field.

Uncovering structural variants in Creole cattle from Guadeloupe and their impact on environmental adaptation through whole genome sequencing

Structural variants play an important role in evolutionary processes. Besides, they constitute a large source of inter individual genetic variation that might represent a major factor in the aetiology of complex, multifactorial traits. Their importance in adaptation is becoming increasingly evident in literature. Yet, the characterization of the genomic landscape of structural variants in local breeds remains scarce to date. Herein, we investigate patterns and gene annotation of structural variants in the Creole cattle from Guadeloupe breed using whole genome sequences from 23 bulls representative of the population. In total, we detected 32821 ascertained SV defining 15258 regions, representing ~ 17% of the Creole cattle genome. Among these, 6639 regions have not been previously reported in the Database of Genomic Variants archive. Average number of structural variants detected per individual in the studied population is in the same order of magnitude of that observed in indicine populations and higher than that reported in taurine breeds. We observe an important within-individual variability where approximately half of the detected structural variants have low frequency (MAF < 0.25). Most of the detected structural variants (55%) occurred in intergenic regions. Genic structural variants overlapped with 7793 genes and the predicted effect of most of them is ranked as "modifier". Among the structural variants that were predicted to have a high functional impact on the protein, a 5.5 Kb in length, highly frequent deletion on chromosome 2, affects ALPI, a gene associated with the interaction between gut microbiota and host immune system. The 6639 newly identified structural variants regions include three deletions and three duplications shared by more than 80% of individuals that are significantly enriched for genes related to tRNA threonylcarbamoyladenosine metabolic process, important for temperature adaptation in thermophilic organisms, therefore suggesting a potential role in the thermotolerance of Creole cattle from Guadeloupe cattle to tropical climate. Overall, highly frequent structural variants that are specific to the Creole cattle population encompass olfactory receptor and immunity genes as well as genes involved in muscle tone, muscle development and contraction. Beyond mapping and characterizing structural variants in the Creole cattle from Guadeloupe breed, this study provides valuable information for a better understanding of the potential role of chromosomal rearrangements in adaptive traits in cattle.

The Ruminant Telomere-to-Telomere (RT2T) Consortium

Telomere-to-telomere (T2T) assemblies reveal new insights into the structure and function of the previously 'invisible' parts of the genome and allow comparative analyses of complete genomes across entire clades. We present here an open collaborative effort, termed the 'Ruminant T2T Consortium' (RT2T), that aims to generate complete diploid assemblies for numerous species of the Artiodactyla suborder Ruminantia to examine chromosomal evolution in the context of natural selection and domestication of species used as livestock.

Pangenome-genotyped structural variation improves molecular phenotype mapping in cattle

Expression and splicing quantitative trait loci (e/sQTL) are large contributors to phenotypic variability. Achieving sufficient statistical power for e/sQTL mapping requires large cohorts with both genotypes and molecular phenotypes, and so, the genomic variation is often called from short-read alignments, which are unable to comprehensively resolve structural variation. Here we build a pangenome from 16 HiFi haplotype-resolved cattle assemblies to identify small and structural variation and genotype them with PanGenie in 307 short-read samples. We find high (>90%) concordance of PanGenie-genotyped and DeepVariant-called small variation and confidently genotype close to 21 million small and 43,000 structural variants in the larger population. We validate 85% of these structural variants (with MAF > 0.1) directly with a subset of 25 short-read samples that also have medium coverage HiFi reads. We then conduct e/sQTL mapping with this comprehensive variant set in a subset of 117 cattle that have testis transcriptome data, and find 92 structural variants as causal candidates for eQTL and 73 for sQTL. We find that roughly half of the top associated structural variants affecting expression or splicing are transposable elements, such as SV-eQTL for STN1 and MYH7 and SV-sQTL for CEP89 and ASAH2 Extensive linkage disequilibrium between small and structural variation results in only 28 additional eQTL and 17 sQTL discovered when including SVs, although many top associated SVs are compelling candidates.

Unmapped short reads from whole-genome sequencing indicate potential infectious pathogens in german black Pied cattle

When resequencing animal genomes, some short reads cannot be mapped to the reference genome and are usually discarded. In this study, unmapped reads from 302 German Black Pied cattle were analyzed to identify potential pathogenic DNA. These unmapped reads were assembled and blasted against NCBI's database to identify bacterial and viral sequences. The results provided evidence for the presence of pathogens. We found sequences of Bovine parvovirus 3 and Mycoplasma species. These findings emphasize the information content of unmapped reads for gaining insight into bacterial and viral infections, which is important for veterinarians and epidemiologists.

Genomics in the long-read sequencing era

Long-read sequencing (LRS) technologies have provided extremely powerful tools to explore genomes. While in the early years these methods suffered technical limitations, they have recently made significant progress in terms of read length, throughput, and accuracy and bioinformatics tools have strongly improved. Here, we aim to review the current status of LRS technologies, the development of novel methods, and the impact on genomics research. We will explore the most impactful recent findings made possible by these technologies focusing on high-resolution sequencing of genomes and transcriptomes and the direct detection of DNA and RNA modifications. We will also discuss how LRS methods promise a more comprehensive understanding of human genetic variation, transcriptomics, and epigenetics for the coming years.

Evaluating the potential of (epi)genotype-by-low pass nanopore sequencing in dairy cattle: a study on direct genomic value and methylation analysis

BACKGROUND

Genotype-by-sequencing has been proposed as an alternative to SNP genotyping arrays in genomic selection to obtain a high density of markers along the genome. It requires a low sequencing depth to be cost effective, which may increase the error at the genotype assigment. Third generation nanopore sequencing technology offers low cost sequencing and the possibility to detect genome methylation, which provides added value to genotype-by-sequencing. The aim of this study was to evaluate the performance of genotype-by-low pass nanopore sequencing for estimating the direct genomic value in dairy cattle, and the possibility to obtain methylation marks simultaneously.

RESULTS

Latest nanopore chemistry (LSK14 and Q20) achieved a modal base calling accuracy of 99.55%, whereas previous kit (LSK109) achieved slightly lower accuracy (99.1%). The direct genomic value accuracy from genotype-by-low pass sequencing ranged between 0.79 and 0.99, depending on the trait (milk, fat or protein yield), with a sequencing depth as low as 2 × and using the latest chemistry (LSK114). Lower sequencing depth led to biased estimates, yet with high rank correlations. The LSK109 and Q20 achieved lower accuracies (0.57-0.93). More than one million high reliable methylated sites were obtained, even at low sequencing depth, located mainly in distal intergenic (87%) and promoter (5%) regions.

CONCLUSIONS

This study showed that the latest nanopore technology in useful in a LowPass sequencing framework to estimate direct genomic values with high reliability. It may provide advantages in populations with no available SNP chip, or when a large density of markers with a wide range of allele frequencies is needed. In addition, low pass sequencing provided nucleotide methylation status of > 1 million nucleotides at ≥ 10 × , which is an added value for epigenetic studies.