ABSTRACT

Human cytomegalovirus (HCMV) is carried lifelong by ∼80 % of adults worldwide, generating distinct disease syndromes in transplant recipients, people with HIV (PWH) and neonates. Amino acids 15–23 encoded by the HCMV gene UL40 match positions 3–11 of HLA-A and HLA-C, and constitute a “signal peptide” able to stabilise cell surface HLA-E as a restriction element and a ligand of NKG2A and NKG2C. We present next generation sequencing of UL40 amplified from 15 Australian renal transplant recipients (RTR), six healthy adults and four neonates, and 21 Indonesian PWH. We found no groupwise associations between the presence of multiple sequences and HCMV burden (highest in PWH) or HCMV-associated symptoms in neonates. Homology between UL40 and corresponding HLA-C and HLA-A peptides in 11 RTR revealed perfect matches with HLA-C in three individuals, all carrying HCMV encoding only VMAPRTLIL – a peptide previously associated with viremia. However indices of the burden of HCMV did not segregate in our cohort.

Waters, S., R. J. N. Allcock, S. Lee, J. Downing, I. Ariyanto, S. Leary, K. Munyard, A. Irish, and P. Price. 2023.Do variations in the HLA-E ligand encoded by UL40 distinguish individuals susceptible to HCMV disease?.Human Immunology 84 (2): 75-79.

ABSTRACT

Currently, there is a growing consumer demand for more ecologically sustainable practices in the textile industry. Fabric dyeing is highly pollutive, and one way to avoid dyeing is to use naturally coloured fibres. Alpacas exhibit a wide range of fleece colours, thereby making them a good source of fibre for sustainable textile production. Our understanding of the colour genetics of alpacas is improving, but there is still no explanation for all the variation seen in alpaca coat colours.

Aims
To identify a region or regions in the alpaca genome that contribute to differences in pigment intensity.

Methods
Colorimetric analysis using L*a*b* colourspace of fibre from white and black alpacas, that had been genotyped using the Neogen Australasia alpaca coat colour test, was used to classify the samples into intense and dilute groups for each colour. Illumina short-read genotyping by sequencing of the DNA from these alpacas was used to identify single nucleotide polymorphisms that were subsequently used in a case–control genome-wide association study (GWAS) comparing the extreme dilute and intensely pigmented animals.

Key results
Intense eumelanic fibre is darker (P = 0.0003), less red (P = 0.004), and more blue (P = 0.001) than is dilute eumelanic fibre. Intense pheomelanic fibre is darker (P = 1 × 10-7), more red (P = 3 × 10-20), and more yellow (P = 2 × 10-6) than is dilute pheomelanic fibre. The GWAS showed six regions of genome-wide significance. After manual inspection of these six regions, the best candidate region was upstream of KITLG, a gene previously associated with pigment intensity in dogs.

Conclusions
In combination with ASIP genotype, a regulatory mutation in a region upstream of KITLG in alpacas potentially has a major effect on pigment intensity in the species.

Implications
Successful identification of a marker for pigment intensity will allow breeders to select more precisely for breeding and production animals that will assist them in supplying the desired fibre colours to the textile industry.

Gray, N., I. Shah, D. Groth, and K. A. Munyard. 2023.Identification of six genomic regions associated with pigment intensity in alpacas.Animal Production Science 63 (11): 1052-1062.