Microsatellite-based genotyping of MHC class II DRB1 gene in Iberian and Alpine ibex

Alasaad, Samer; Biebach, Iris; Grossen, Christine; Soriguer, Ramón C.; Pérez, Jesús M.; Keller, Lukas F.

doi:10.1007/s10344-011-0592-0

Cited by 14 publications

(10 citation statements)

References 46 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We extended the sequencing by Schaschl et al [27] and Alasaad et al [28] from 125 to 203 Alpine ibex from different populations and did not find additional alleles at the exon 2 of the MHC DRB locus. We found that the second allele ( Caib-DRB *2) was identical to the Cahi-DRB *16 allele of the domestic goat first reported from the Japanese breed Shiba ( [29] , Genbank accession AB008361).…”

Section: Resultsmentioning

confidence: 67%

“…The depletion of genetic variability is particularly striking at the DRB locus of the MHC class II. Only two alleles ( Caib-DRB *1 and Caib-DRB *2) were reported at the exon 2 of DRB in at total of 125 individuals [27] , [28] . In comparison, both the domestic goat ( C. aegagrus hircus ) and its wild ancestor the bezoar ( C. aegagrus ) are highly polymorphic at this exon.…”

Section: Introductionmentioning

confidence: 96%

See 1 more Smart Citation

Introgression from Domestic Goat Generated Variation at the Major Histocompatibility Complex of Alpine Ibex

Grossen¹,

Keller²,

Biebach³

et al. 2014

PLoS Genet

Self Cite

101

View full text Add to dashboard Cite

The major histocompatibility complex (MHC) is a crucial component of the vertebrate immune system and shows extremely high levels of genetic polymorphism. The extraordinary genetic variation is thought to be ancient polymorphisms maintained by balancing selection. However, introgression from related species was recently proposed as an additional mechanism. Here we provide evidence for introgression at the MHC in Alpine ibex (Capra ibex ibex). At a usually very polymorphic MHC exon involved in pathogen recognition (DRB exon 2), Alpine ibex carried only two alleles. We found that one of these DRB alleles is identical to a DRB allele of domestic goats (Capra aegagrus hircus). We sequenced 2489 bp of the coding and non-coding regions of the DRB gene and found that Alpine ibex homozygous for the goat-type DRB exon 2 allele showed nearly identical sequences (99.8%) to a breed of domestic goats. Using Sanger and RAD sequencing, microsatellite and SNP chip data, we show that the chromosomal region containing the goat-type DRB allele has a signature of recent introgression in Alpine ibex. A region of approximately 750 kb including the DRB locus showed high rates of heterozygosity in individuals carrying one copy of the goat-type DRB allele. These individuals shared SNP alleles both with domestic goats and other Alpine ibex. In a survey of four Alpine ibex populations, we found that the region surrounding the DRB allele shows strong linkage disequilibria, strong sequence clustering and low diversity among haplotypes carrying the goat-type allele. Introgression at the MHC is likely adaptive and introgression critically increased MHC DRB diversity in the genetically impoverished Alpine ibex. Our finding contradicts the long-standing view that genetic variability at the MHC is solely a consequence of ancient trans-species polymorphism. Introgression is likely an underappreciated source of genetic diversity at the MHC and other loci under balancing selection.

show abstract

Section: Resultsmentioning

confidence: 67%

Section: Introductionmentioning

confidence: 96%

Introgression from Domestic Goat Generated Variation at the Major Histocompatibility Complex of Alpine Ibex

Grossen¹,

Keller²,

Biebach³

et al. 2014

PLoS Genet

Self Cite

101

View full text Add to dashboard Cite

show abstract

“…Despite severe demographic changes over the past century, Iberian ibex were not affected by similar range and census reductions as Alpine ibex. The less severe bottlenecks experienced by Iberian ibex are reflected in higher genetic diversity at the major histocompatibility complex (MHC) (Alasaad et al, 2012;Amills et al, 2004).…”

mentioning

confidence: 99%

Population genomics analyses of European ibex species show lower diversity and higher inbreeding in reintroduced populations

Grossen

Biebach

Angelone

et al. 2017

Evolutionary Applications

Self Cite

View full text Add to dashboard Cite

Restoration of lost species ranges to their native distribution is key for the survival of endangered species. However, reintroductions often fail and long‐term genetic consequences are poorly understood. Alpine ibex (Capra ibex) are wild goats that recovered from <100 individuals to ~50,000 within a century by population reintroductions. We analyzed the population genomic consequences of the Alpine ibex reintroduction strategy. We genotyped 101,822 genomewide single nucleotide polymorphism loci in 173 Alpine ibex, the closely related Iberian ibex (Capra pyrenaica) and domestic goat (Capra hircus). The source population of all Alpine ibex maintained genetic diversity comparable to Iberian ibex, which experienced less severe bottlenecks. All reintroduced Alpine ibex populations had individually and combined lower levels of genetic diversity than the source population. The reintroduction strategy consisted of primary reintroductions from captive breeding and secondary reintroductions from established populations. This stepwise reintroduction strategy left a strong genomic footprint of population differentiation, which increased with subsequent rounds of reintroductions. Furthermore, analyses of genomewide runs of homozygosity showed recent inbreeding primarily in individuals of reintroduced populations. We showed that despite the rapid census recovery, Alpine ibex carry a persistent genomic signature of their reintroduction history. We discuss how genomic monitoring can serve as an early indicator of inbreeding.

show abstract

“…(e.g. Alasaad et al, 2012;Brambilla et al, 2018;Grossen et al, 2014). Underlining the relevance of performing large-scale targeted amplicon sequencing of immune loci are recent findings that high heterozygosity at the MHC was correlated with higher resistance to infectious keratoconjunctivitis, a major disease factor in some Alpine ibex populations (Brambilla et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

A robust sequencing assay of a thousand amplicons for the high-throughput population monitoring of Alpine ibex immunogenetics

Kessler

Brambilla

Waldvogel

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

Genetic variation is a major factor determining susceptibility to diseases. Polymorphism at the major histocompatibility complex (MHC) and other immune function loci can underlie health and reproductive success of individuals. Endangered species of low population size could be severely compromised to evolve disease resistance due to reduced adaptive variation. A major impediment to screen adaptive genetic variation in wild species is the difficulty to comprehensively genotype immune-related loci based on low input material. Here, we design and validate a targeted amplicon sequencing assay to parallelize the analysis of a thousand loci of the MHC, other immunity-related genes, and genome-wide markers for the assessment of population structure. We apply the approach to Alpine ibex, one of the most successful examples of restoration of a large mammal in Europe. We used 51 whole genome sequenced individuals to select representative target SNPs. We integrated SNP call data from four related species for amplification robustness and genotyped 158 Alpine ibex individuals for validation. We show that the genome-wide markers perform equally well at resolving population structure as RAD-seq or low-coverage genome sequencing datasets with orders of magnitude more markers. The targeted amplicon sequencing assay is robust to >100-fold variation in input DNA quantity and generates useful genotype information from fecal samples. The amplicon marker set also identified recent species hybridization events with domestic goats. The immune loci show unexpectedly high degrees of differentiation within the species. Our assay strategy can realistically be implemented into population genetic surveys of a large range of species.

show abstract

Microsatellite-based genotyping of MHC class II DRB1 gene in Iberian and Alpine ibex

Cited by 14 publications

References 46 publications

Introgression from Domestic Goat Generated Variation at the Major Histocompatibility Complex of Alpine Ibex

Introgression from Domestic Goat Generated Variation at the Major Histocompatibility Complex of Alpine Ibex

Population genomics analyses of European ibex species show lower diversity and higher inbreeding in reintroduced populations

A robust sequencing assay of a thousand amplicons for the high-throughput population monitoring of Alpine ibex immunogenetics

Contact Info

Product

Resources

About