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. 2024 Jul 12:15:1370891.
doi: 10.3389/fgene.2024.1370891. eCollection 2024.

Identifying selection signatures for immune response and resilience to Aleutian disease in mink using genotype data

Guoyu Hu  1 , Duy Ngoc Do  1 , Ghader Manafiazar  1 , Alyson A Kelvin  2 , Mehdi Sargolzaei  3   4 , Graham Plastow  5 , Zhiquan Wang  5 , Pourya Davoudi  1 , Younes Miar  1
Affiliations

Identifying selection signatures for immune response and resilience to Aleutian disease in mink using genotype data

Guoyu Hu et al. Front Genet. .

Abstract

Aleutian disease (AD) brings tremendous financial losses to the mink industry. Selecting AD-resilient mink has been conducted to control AD. Such selections could have altered the patterns of genetic variation responding to selection pressures. This study aimed to identify selection signatures for immune response (IRE) and resilience to AD. A total of 1,411 mink from an AD-positive facility were used. For IRE, 264 animals were categorized according to the combined results of enzyme-linked immunosorbent assay (ELISA) and counterimmunoelectrophoresis (CIEP). For resilience, two grouping methods were used: 1) general resilience performance (GRP, n = 30) was evaluated based on the feed conversion ratio, Kleiber ratio, and pelt quality; and 2) female reproductive performance (FRP, n = 36) was measured based on the number of kits alive 24 h after birth. Detection methods were the pairwise fixation index, nucleotide diversity, and cross-population extended haplotype homozygosity. A total of 619, 569, and 526 SNPs were identified as candidates for IRE, GRP, and FRP, respectively. The annotated genes were involved in immune system process, growth, reproduction, and pigmentation. Two olfactory-related Gene Ontology (GO) terms were significant (q < 0.05) for all traits, suggesting the impact of AD on the sense of smell of infected mink. Differences in detected genes and GO terms among different color types for IRE indicated variations in immune response to AD among color types. The mitogen-activated protein kinase (MAPK) signaling pathway was significant (q < 0.05) for FRP, suggesting that AD may disrupt MAPK signaling and affect FRP. The findings of this research contribute to our knowledge of the genomic architecture and biological mechanisms underlying AD resilience in mink.

Keywords: Aleutian disease resilience; American mink; genotypes; immune response; selection signatures.

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Conflict of interest statement

MS is employed by Select Sires Inc. This organization did not play any role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Genome-wide distribution of detected selection signatures for immune response trait across all autosomes in the whole population and different color types of individuals. The red lines of Z-transformed Fst and log2 (θπ ratio) plots display the threshold levels of 5%. The red lines of XP-EHH plots display the threshold levels of -log (p-value)>2.
FIGURE 2
FIGURE 2
Overlapped selection signatures detected in the whole population and different color types of individuals among three detection methods for the immune response trait.
FIGURE 3
FIGURE 3
Venn diagram shows the genes overlapping among the whole population and different color types for the immune response trait.
FIGURE 4
FIGURE 4
Pie charts of functional classifications of candidate genes under selection pressure in the whole population and different color types of individuals for immune response traits.
FIGURE 5
FIGURE 5
Genome-wide distribution of detected selection signatures for general resilience and female reproductive performance traits across all autosomes from the whole population. The red lines of Z-transformed Fst and log2 (θπ ratio) plots display the threshold levels of 5%. The red lines of XP-EHH plots display the threshold levels of -log (p-value)>2.
FIGURE 6
FIGURE 6
Overlapped selection signatures detected from the whole population individuals for general resilience and female reproductive performance traits.
FIGURE 7
FIGURE 7
Pie charts of functional classifications of candidate genes under selection pressure in the whole population individuals for general resilience and female reproductive performance traits.
FIGURE 8
FIGURE 8
Overlapped genes among immune response, general resilience, and female reproductive performance traits. The common 16 genes among all traits were ARHGAP19, COL14A1, DEPTOR, EXOSC1, FAM135B, FRAT1, FRAT2, LOC122905718, MMS19, MRPL13, PGAM1, PTCHD4, RRP12, TBX18, UBTD1, and ZDHHC16.
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