Runs of homozygosity in a selected cattle population with extremely inbred bulls: Descriptive and functional analyses revealed highly variable patterns

The analysis of runs of homozygosity (ROH), using high throughput genomic data, has become a valuable and frequently used methodology to characterize the genomic and inbreeding variation of livestock and wildlife animal populations. However, this methodology has been scarcely used in highly inbred d...

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Autores principales: Goszczynski, Daniel Estanislao, Molina, Antonio, Terán, Ester Mercedes, Morales Durand, Hernán F., Ross, Pablo, Cheng, Hao, Giovambattista, Guillermo, Demyda Peyrás, Sebastián
Formato: Articulo
Lenguaje:Inglés
Publicado: 2018
Materias:
Veterinaria
ROH
Cattle
Inbreeding
Acceso en línea:http://sedici.unlp.edu.ar/handle/10915/97110
https://ri.conicet.gov.ar/11336/82758
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0200069
Aporte de:
SEDICI (UNLP) de Universidad Nacional de La Plata
id I19-R120-10915-97110
record_format dspace
institution Universidad Nacional de La Plata
institution_str I-19
repository_str R-120
collection SEDICI (UNLP)
language Inglés
topic Veterinaria
ROH
Cattle
Inbreeding
spellingShingle Veterinaria
ROH
Cattle
Inbreeding
Goszczynski, Daniel Estanislao
Molina, Antonio
Terán, Ester Mercedes
Morales Durand, Hernán F.
Ross, Pablo
Cheng, Hao
Giovambattista, Guillermo
Demyda Peyrás, Sebastián
Runs of homozygosity in a selected cattle population with extremely inbred bulls: Descriptive and functional analyses revealed highly variable patterns
topic_facet Veterinaria
ROH
Cattle
Inbreeding
description The analysis of runs of homozygosity (ROH), using high throughput genomic data, has become a valuable and frequently used methodology to characterize the genomic and inbreeding variation of livestock and wildlife animal populations. However, this methodology has been scarcely used in highly inbred domestic animals. Here, we analyzed and characterized the occurrence of ROH fragments in highly inbred (HI; average pedigree-based inbreeding coefficient F<sub>PED</sub> = 0.164; 0.103 to 0.306) and outbred Retinta bulls (LI; average F<sub>PED</sub> = 0.008; 0 to 0.025). We studied the length of the fragments, their abundance, and genome distribution using high-density microarray data. The number of ROH was significantly higher in the HI group, especially for long fragments (>8Mb). In the LI group, the number of ROH continuously decreased with fragment length. Genome-wide distribution of ROH was highly variable between samples. Some chromosomes presented a larger number of fragments (BTA1, BTA19, BTA29), others had longer fragments (BTA4, BTA12, BTA17), while other ones showed an increased ROH accumulation over specific loci (BTA2, BTA7, BTA23, BTA29). Similar differences were observed in the analysis of 12 individuals produced by a similar inbred event (F<sub>PED3</sub> = 0.125). The correlation between the fraction of the genome covered by ROH (F<sub>ROH</sub>) and F<sub>PED</sub> was high (0.79), suggesting that ROH-based estimations are indicative of inbreeding levels. On the other hand, the correlation between F<sub>PED</sub> and the microsatellite-based inbreeding coefficient (F<sub>MIC</sub>) was only moderate (r = 0.44), suggesting that STR-based inbreeding estimations should be avoided. Similarly, we found a very low correlation (r = -0.0132) between recombination rate and ROH abundance across the genome. Finally, we performed functional annotation analyses of genome regions with significantly enriched ROH abundance. Results revealed gene clusters related to pregnancy-associated proteins and immune reaction. The same analysis performed for regions enriched with recently formed ROH (> 8 Mb) showed gene clusters related to flagellum assembly. In both cases, the processes were related to male and female reproductive functions, which may partially explain the reduced fertility associated with inbred populations.
format Articulo
Articulo
author Goszczynski, Daniel Estanislao
Molina, Antonio
Terán, Ester Mercedes
Morales Durand, Hernán F.
Ross, Pablo
Cheng, Hao
Giovambattista, Guillermo
Demyda Peyrás, Sebastián
author_facet Goszczynski, Daniel Estanislao
Molina, Antonio
Terán, Ester Mercedes
Morales Durand, Hernán F.
Ross, Pablo
Cheng, Hao
Giovambattista, Guillermo
Demyda Peyrás, Sebastián
author_sort Goszczynski, Daniel Estanislao
title Runs of homozygosity in a selected cattle population with extremely inbred bulls: Descriptive and functional analyses revealed highly variable patterns
title_short Runs of homozygosity in a selected cattle population with extremely inbred bulls: Descriptive and functional analyses revealed highly variable patterns
title_full Runs of homozygosity in a selected cattle population with extremely inbred bulls: Descriptive and functional analyses revealed highly variable patterns
title_fullStr Runs of homozygosity in a selected cattle population with extremely inbred bulls: Descriptive and functional analyses revealed highly variable patterns
title_full_unstemmed Runs of homozygosity in a selected cattle population with extremely inbred bulls: Descriptive and functional analyses revealed highly variable patterns
title_sort runs of homozygosity in a selected cattle population with extremely inbred bulls: descriptive and functional analyses revealed highly variable patterns
publishDate 2018
url http://sedici.unlp.edu.ar/handle/10915/97110
https://ri.conicet.gov.ar/11336/82758
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0200069
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