Table 1 Structural variant discoveries using a “focused approach” in livestock, using either short-read (SR) and/or long-read (LR) sequencing
Phenotype/disease name | Species | Breed | Sequencing platform | Summarized of key findings | Ref. |
|---|---|---|---|---|---|
Recessive lethal and increased milk production | Cattle | Nordic Red | SR | A 660-kb deletion on chromosome 12 encompassing four genes is believed to be the putative recessive causative variant, and results in embryonic death; this outcome is thought to result from the loss of the ribonuclease H2, subunit B (RNASEH2B) gene | [51] |
Polled | Cattle | Friesian | SR | An 80-kb duplication on chromosome 1 was found to cause a dominant poll phenotype in Friesian cattle; it was confirmed in 6000 animals that were genetically tested for the polled phenotype | [87] |
Cholesterol deficiency | Cattle | Holstein | SR | A 1.3-kb insertion on chromosome 11 of a transposable long terminal repeat element (ERV2-1) in the APOB gene was reported to cause early death in Holstein cattle | [88] |
Muffs and beard (Mb) phenotype | Chicken | Multiple breeds | SR | A complex SV (three duplications, one in tandem and two that are translocated to that of the tandem repeat on chromosome 27) was found to have an incomplete dominant effect on the Mb phenotype in chicken; this SV leads to continuous high ectopic expression of the HOXB8 gene in the facial skin | [89] |
Holstein lethal haplotype 5 (HH5) | Cattle | Holstein | SR | A 138 k-bp deletion on chromosome 9, covering the dimethyl-adenosine transferase 1 (TFB1M) gene was reported to have a recessive effect causing embryonic death | [90] |
Finching or line-backed spotting | Cattle | Pinzgauer | SR and LR | A complex structural variant consisting of a 9.4-kb deletion and an inversely inserted 1.5-kb duplication fused to a 310-kb duplicated segment from chromosome 4 was confirmed to be causative and dominant for the phenotype | [91] |
Tetradysmelia | Cattle | Holstein Friesian | SR | A 50-kb deletion on chromosome 14 identified in several members of a Holstein–Friesian family, which most likely disrupts the bovine R-spondin 2 (RSPO2) gene, causing the autosomal recessive condition (tetradysmelia) | [92] |
Colour-sidedness | Cattle | Gloucester | SR | A complex structural variant, caused by two related translocations (chromosomes 6 and 29) downstream of the KIT gene; all three alleles potentially disrupt several putative regulatory elements downstream of KIT, that result in the dominant colour-sidedness phenotype | [93] |
Mastitis resistance | Cattle | Holstein Friesian | SR | A 12-kb multi-allelic CNV on chromosome 6 covering the GC gene enhancer is associated with mastitis resistance in dairy cattle and GC gene expression | [50] |
Bulldog calf syndrome (BDS) | Cattle | Holstein | SR | A 3513-bp deletion on chromosome 5, spanning 10 coding exons of the collagen type II alpha 1 chain (COL2A1) gene was reported as the causative variant for BDS, a dominant inheritance lethal syndrome | [94] |
Polled | Cattle | Brahman | LR | Long read sequencing study revealed a 212-bp insertion in place of a 10-bp deletion on chromosome 1 in Brahman poll animals; this structural variant was found to be absent in horned animals | [95] |
Polled intersex syndrome (PIS) | Goat | Multiple breed | SR and LR | A complex structural casual variant consisting of a 10,159-bp deletion and an inversely inserted 480-kb-sized duplication on chromosome 1; these regions appeared to span across two functional genes resulting in a dominant female intersex phenotype | [96] |
X-Linked hypohidrotic ectodermal dysplasia | Cattle | Red Angus-Simmental | SR | A 53-kb deletion of the X chromosome that includes a section of the ectodysplasin (EDA) gene as well as the entire acyl-CoA wax alcohol acyltransferase 2 (AWAT2) gene; it was reported in a family of cattle diagnosed with X-linked hypohidrotic ectodermal dysplasia | [97] |
Coat color darkening | Cattle | Nellore and Brahman | SR and LR | A complex structural rearrangement consisting of a 1155-bp deletion combined with an insertion of more than 150 bp including a SINE element seemed to be the most plausible causal candidate due to its size and location near the agouti signalling protein gene (ASIP) on chromosome 13 | [98] |
Plumage colour | Chicken | Rhode Island Red crossed to White Leghorn | SR | A 7.6-kb deletion in the non-coding region upstream of the SOX10 gene responsible for light yellow/dark brown plumage | [99] |