Skip to main content

Research Repository

Advanced Search

Genetic characterisation of the Connemara pony and the Warmblood horse using a within-breed clustering approach

Lindsay-McGee, V; Sanchez-Molano, E; Banos, G; Clark, EL; Piercy, RJ; Psifidi, A

Authors

V Lindsay-McGee

E Sanchez-Molano

G Banos

EL Clark

RJ Piercy

A Psifidi



Abstract

BackgroundThe Connemara pony (CP) is an Irish breed that has experienced varied selection by breeders over the last fifty years, with objectives ranging from the traditional hardy pony to an agile athlete. We compared these ponies with well-studied Warmblood (WB) horses, which are also selectively bred for athletic performance but with a much larger census population. Using genome-wide single nucleotide polymorphism (SNP) and whole-genome sequencing data from 116 WB (94 UK WB and 22 European WB) and 36 CP (33 UK CP and 3 US CP), we studied the genomic diversity, inbreeding and population structure of these breeds.ResultsThe k-means clustering approach divided both the CP and WB populations into four genetic groups, among which the CP genetic group 1 (C1) associated with non-registered CP, C4 with US CP, WB genetic group 1 (W1) with Holsteiners, and W3 with Anglo European and British WB. Maximum and mean linkage disequilibrium (LD) varied significantly between the two breeds (mean from 0.077 to 0.130 for CP and from 0.016 to 0.370 for WB), but the rate of LD decay was generally slower in CP than WB. The LD block size distribution peaked at 225 kb for all genetic groups, with most of the LD blocks not exceeding 1 Mb. The top 0.5% harmonic mean pairwise fixation index (F-ST) values identified ontology terms related to cancer risk when the four CP genetic groups were compared. The four CP genetic groups were less inbred than the WB genetic groups, but C2, C3 and C4 had a lower proportion of shorter runs of homozygosity (ROH) (74 to 76% < 4 Mb) than the four WB genetic groups (80 to 85% < 4 Mb), indicating more recent inbreeding. The CP and WB genetic groups had a similar ratio of effective number of breeders (N-eb) to effective population size (N-e).ConclusionsDistinct genetic groups of individuals were revealed within each breed, and in WB these genetic groups reflected population substructure better than studbook or country of origin. Ontology terms associated with immune and inflammatory responses were identified from the signatures of selection between CP genetic groups, and while CP were less inbred than WB, the evidence pointed to a greater degree of recent inbreeding. The ratio of N-eb to N-e was similar in CP and WB, indicating the influence of popular sires is similar in CP and WB.

Citation

Lindsay-McGee, V., Sanchez-Molano, E., Banos, G., Clark, E., Piercy, R., & Psifidi, A. (2023). Genetic characterisation of the Connemara pony and the Warmblood horse using a within-breed clustering approach. Genetics Selection Evolution, 55(1), https://doi.org/10.1186/s12711-023-00827-w

Journal Article Type Article
Acceptance Date Jul 7, 2023
Online Publication Date Aug 17, 2023
Publication Date 2023
Deposit Date Sep 6, 2023
Publicly Available Date Sep 6, 2023
Print ISSN 0999-193X
Electronic ISSN 1297-9686
Publisher BioMed Central
Peer Reviewed Peer Reviewed
Volume 55
Issue 1
DOI https://doi.org/10.1186/s12711-023-00827-w
Keywords EFFECTIVE POPULATION-SIZE; SKELETAL-MUSCLE; LINKAGE DISEQUILIBRIUM; DIVERSITY; EXERCISE; PERFORMANCE; TRAITS; TOOL; HOMOZYGOSITY; APOPTOSIS

Files




You might also like



Downloadable Citations