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

Nguyen, Tuan V.; Vander Jagt, Christy J.; Wang, Jianghui; Daetwyler, Hans D.; Xiang, Ruidong; Goddard, Michael E.; Nguyen, Loan T.; Ross, Elizabeth M.; Hayes, Ben J.; Chamberlain, Amanda J.; MacLeod, Iona M.

doi:10.1186/s12711-023-00783-5

Genetics Selection Evolution

Table 2 Structural variants detected in livestock based on two discovery approaches (RS: resequencing or PG: pangenome approach) with either short-read (SR) or long-read (LR) sequencing technology

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

Application	Species	Breed	Technique \| sequencing technology	Brief summary of key findings	Ref.
Genome-wide study of SV in dairy breeds	Cattle	Holstein, Montbéliarde, Normande	RS \| SR	This study discovered 6426 putative structural variants that segregated in whole-genome sequence data in a total of 62 bulls representing three major French dairy breeds	[6]
Detection of SV by large-scale sequencing revealed evolutionary evidence of breed divergence between Chinese and European pigs	Pig	Multiple breeds	RS \| SR	56,930 putative SV were discovered using genomes of 13 pigs from diverse breeds that originated from China and Europe	[100]
CNV in the sheep genome	Sheep	Multiple breeds	RS \| SR	A study of CNV in sheep, using multiple methods to identify and characterise copy number changes, resulted in 3488 autosomal CNV regions with an average length of 19 kb	[18]
Detection of a reciprocal translocation in a pig line	Pig	Large-White line	RS \| SR	A resequencing approach identified a translocation variant occurring within the coding region of the gene and results in a loss of expression of a disintegrin and metalloproteinase with thrombospondin motifs (ADAMTSL4), but no observable phenotype was detected with this translocation	[101]
Genome-wide mapping of large deletions and their population-genetic properties in dairy cattle	Cattle	Holstein, Jersey, Nordic Red cattle	RS \| SR	This study reported 8480 large deletions (199 bp–773 kb) from 175 cattle	[102]
Detection and assessment of CNV using PacBio long read and Illumina sequencing in New Zealand dairy cattle	Cattle	Holstein–Friesian	RS \| SR and LR	One LR sequenced and 556 SR sequenced New Zealand cattle revealed little overlap between the two platforms; PacBio sequencing resulted in 38,709 putative SV, of which 19,797 were CNV, while Illumina sequencing resulted in 43,708 putative CNV	[103]
Identification of CNV in domestic chicken with short read sequencing	Chicken	Multiple breeds	RS \| SR	Mining whole-genome sequences of 65 chickens from multiple breeds detected 663 domestication-specific CNVR across the autosomes	[104]
CNV in Holstein–Friesian cow genomes based on whole-genome sequence data	Cattle	Holstein–Friesian	RS \| SR	Thirty-two sequenced Holstein–Friesian cows were analyzed to evaluate the landscape of CNV; length of deletions ranged from 5234 to 9145 bp and the average length of duplications ranged from 7254 to 8843 bp, but most of the CNV were unique to a single cow although several were validated in previous studies	[105]
Database of CNV discovered in taurine cattle	Cattle	Multiple breeds	RS \| RS	More than 500 bulls from 17 breeds were used to reveal 26,223 CNVR covering 107.75 unique Mb of the bovine genome; this study also confirmed the genotypes of a CNVR at the KIT locus associated with the piebald coat colour phenotype in Hereford and Simmental cattle	[106]
Comparative analyses of CNV between Bos taurus and Bos indicus	Cattle	Multiple breeds	RS \| SR	This study identified 13,234 non-redundant CNV regions in 73 animals from 10 cattle breeds (4 Bos taurus and 6 Bos indicus)	[107]
CNV in Chinese indigenous cattle	Cattle	Multiple breeds	RS \| SR	Resequencing approach using genomes from 75 cattle individuals (including six Chinese indigenous cattle breeds and two non-native specialized beef cattle breeds) discovered 11,486 CNVR; many of these are related to traits of interest including meat production or quality, coat color, adaptation	[108]
Identification of CNV in Holstein dairy cattle from whole-genome sequence and genotype array data	Cattle	Holstein	RS \| SR and genotype	SR sequence and genotype arrays of 96 Holstein animals revealed high confidence CNV regions that overlapped using both methods	[109]
Haplotype-resolved genomes in Angus and Brahman cattle	Cattle	Angus × Brahman cross	PG \| LR	Chromosome-level genome assemblies of Angus and Brahman cattle revealed structural and copy number variants that may be subspecies specific; the study estimated that the total lengths in bp affected by SV in Angus and Brahman were 10.9 and 21.8 Mb, respectively	[66]
SV in cattle	Cattle	Multiple breeds	RS \| SR	This study applied sequencing approaches with 72 whole-genome sequences representing taurine and indicine cattle; 16,738 SV were identified, of which 1575 were novel	[110]
Novel functional sequences uncovered through a bovine multi-assembly graph	Cattle	Multiple breeds	PG \| LR	A pangenome approach to study SV using six genome assemblies from taurine and indicine cattle as well as yak identified 68,328 SV present in the multi-assembly graph	[7]
Analysis of SV in Meishan pigs	Pig	Multiple breeds	RS \| SR	Structural variants in Meishan pigs together with genomic data from 55 pig breeds from Africa, Europe, Asia, South-east Asia, and Central America, and included wild boars, this study curated 33,698 SV in 305 individuals	[111]
Detection and validation of SV in bovine whole-genome sequence data	Cattle	Holstein and Jersey	RS \| SR	Detection and validation of SV in bovine whole-genome sequence data from 252 Holstein and 64 Jersey bulls with 17,518 SV in Holstein and 4285 SV in Jersey	[23]
CNV in Chinese indigenous fine-wool sheep populations using whole-genome resequencing	Sheep	Multiple breeds	RS \| SR	Genomic CNV map for Chinese indigenous fine-wool sheep from 32 fine-wool sheep from three breeds were analyzed using resequencing approach; the analysis curated 1,747,604 CNV and 7228 CNV regions, which were estimated to represent 2.17% of the sheep reference genome	[112]
SV relate to domestication in small ruminants (goats and sheep)	Goat and sheep	Multiple breeds	RS \| SR	Study aimed at investigating the role of SV during the domestication and subsequent genetic improvement of goats and sheep that revealed 45,796 SV in the sheep and 15,047 SV in goat genomes, respectively	[113]
Chicken pangenome revealed a SV catalogue and a causal variant for body size	Chicken	Multiple breeds	RS \| SR	A pangenome approach using short read sequencing of 664 individuals discovered 66.5 Mb of sequences that are absent from the genome assembly; this study identified deletions on Chr 27 in the promoter region of IGF2BP1 that affects body size in chickens	[114]
Bovine pangenome reveals trait-associated structural variation from diverse assembly inputs	Cattle	Multiple breeds	PG \| LR	A pangenome approach revealed 900 SV overlapping with coding sequences; these included variants affecting the QRICH2, PRDM9, HSPA1A, TAS2R46 and GC genes that can affect phenotypes	[115]
Initial study of analysing SV detections in cattle	Cattle	Unknown breed	RS \| LR and SR	One individual sequenced using 10× Genomics linked read, PacBio as well as ONT; the study identified 21,164 SV, which amount to 186 Mb covering 7.07% of the whole genome	[116]
Sheep graph-based pangenome reveals the spectrum of SV and their effects on tail phenotypes	Sheep	Multiple breeds	PG \| LR	This study characterized 26 haplotype-resolved genome assemblies from 1342 genetically diverse sheep and performed a graph-based approach to genotype biallelic SV in 684 individuals from 45 domestic sheep breeds and two wild species; it resulted in 142,422 biallelic insertions and deletions, 7028 divergent alleles and 13,419 multiallelic variations	[117]
Novel SV and missing sequences providing new insights into bovine diversity and evolutionary history	Cattle	Multiple breeds	PG \| LR	A pangenome approach using 898 cattle from 57 bovine breeds identified 83 Mb of sequence not found in the cattle reference genome (~ 3% different from the reference genome). A catalogue of the SV revealed 3.3 × 10⁶ deletions, 0.12 × 10⁶ inversions, and 0.18 × 10⁶ duplications	[118]
Short read sequencing to characterise balanced reciprocal translocations in pigs	Pig	Unknown breed	RS \| SR	Deployment of a structural variant calling software and paired end short-read sequencing with a depth of at least 20-fold coverage that detected and characterized balanced reciprocal translocations in 7 carriers but did not detect any such translocation in 15 non-carriers; the results suggest that paired end short read sequence data can be used to detect and characterize balanced reciprocal translocations, but may be limited in the detection of translocations in repetitive regions	[119]
Detection of SV	Chicken	Multiple breeds	RS \| LR and SR	Sequencing of ten chickens from various breeds using the PacBio technology detected 49,501 high-confidence SV	[120]

SV structural variants, CNV copy number variants, SR short-read, LR long- read, PG pangenome, RS resequencing

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ISSN: 1297-9686

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