Runs of Homozygosity and Gene Identification in Pelibuey Sheep Using Genomic Data

The runs of homozygosity (ROHs), the inbreeding coefficient, and the effective population size (<i>Ne</i>) in Pelibuey sheep were analyzed in 24 Pelibuey ewes from two lambs at parturition and 24 ewes that gave birth to a single lamb using the Ilumina OvineSNP50 BeadChip. The <i>Ne...

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Main Authors: Wilber Hernández-Montiel, Nubia Noemi Cob-Calan, Lilia E. Cahuich-Tzuc, José A. Rueda, Jorge Quiroz-Valiente, Víctor Meza-Villalvazo, Roberto Zamora-Bustillos
Format: Article
Language:English
Published: MDPI AG 2022-06-01
Series:Diversity
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Online Access:https://www.mdpi.com/1424-2818/14/7/522
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author Wilber Hernández-Montiel
Nubia Noemi Cob-Calan
Lilia E. Cahuich-Tzuc
José A. Rueda
Jorge Quiroz-Valiente
Víctor Meza-Villalvazo
Roberto Zamora-Bustillos
author_facet Wilber Hernández-Montiel
Nubia Noemi Cob-Calan
Lilia E. Cahuich-Tzuc
José A. Rueda
Jorge Quiroz-Valiente
Víctor Meza-Villalvazo
Roberto Zamora-Bustillos
author_sort Wilber Hernández-Montiel
collection DOAJ
description The runs of homozygosity (ROHs), the inbreeding coefficient, and the effective population size (<i>Ne</i>) in Pelibuey sheep were analyzed in 24 Pelibuey ewes from two lambs at parturition and 24 ewes that gave birth to a single lamb using the Ilumina OvineSNP50 BeadChip. The <i>Ne</i> decreased from 535 to 192 in the first ten generations. A total of 2194 ROHs were identified on the basis of single nucleotide polymorphisms (SNPs), were identified in the prolific group and 2185 SNPs in ROH in the non-prolific group. The distribution of the lengths of the ROH, considering both groups, were found to be: 4065 less than 6 Mb, 213 between 6 and 12 Mb, 72 between 12 and 24 Mb, twenty between 24 and 48 Mb and 8 greater than 48 Mb. In prolific sheep, the ROH associated with prolificacy were identified near the <i>LINGO2</i>, <i>FLRT2</i>, <i>ADGRB3</i> genes, related to “positive regulation of synapse assembly”; and the <i>DGKG</i>, <i>DGKE</i>, <i>DGKB</i> and <i>DGKI</i> genes, related to “protein kinase C-activating G-protein coupled receptor signaling pathway”. The present work present genes that can function as signal mediators or have activity in embryonic development, which is relevant to the economic activity of this species.
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spelling doaj.art-efe4fe41882b4fd6a7f8a62b76463cdb2023-12-03T14:54:23ZengMDPI AGDiversity1424-28182022-06-0114752210.3390/d14070522Runs of Homozygosity and Gene Identification in Pelibuey Sheep Using Genomic DataWilber Hernández-Montiel0Nubia Noemi Cob-Calan1Lilia E. Cahuich-Tzuc2José A. Rueda3Jorge Quiroz-Valiente4Víctor Meza-Villalvazo5Roberto Zamora-Bustillos6Instituto de Agroingeniería, Universidad del Papaloapan, Av. Ferrocarril s/n, Ciudad Universitaria, Campus Loma Bonita, Oaxaca 68400, Oaxaca, MexicoInstituto Tecnológico Superior de Calkiní en el Estado de Campeche Av. Ah-Canul S/N por Carretera Federal Campeche-Mérida, Calkiní 24900, Campeche, MexicoTecNM/Instituto Tecnológico de Conkal, Av. Tecnológico S/N, Conkal 97345, Yucatán, MexicoInstituto de Agroingeniería, Universidad del Papaloapan, Av. Ferrocarril s/n, Ciudad Universitaria, Campus Loma Bonita, Oaxaca 68400, Oaxaca, MexicoInstituto Nacional de Investigaciones Forestales, Agrícolas y Pecuaria (INIFAP), Campo Experimental Huimanguillo, Huimanguillo 86400, Tabasco, MexicoLaboratorio de Biotecnología Animal, Universidad del Papaloapan, Circuito Central No. 200, Parque Industrial, Tuxtepec 68301, Oaxaca, MexicoTecNM/Instituto Tecnológico de Conkal, Av. Tecnológico S/N, Conkal 97345, Yucatán, MexicoThe runs of homozygosity (ROHs), the inbreeding coefficient, and the effective population size (<i>Ne</i>) in Pelibuey sheep were analyzed in 24 Pelibuey ewes from two lambs at parturition and 24 ewes that gave birth to a single lamb using the Ilumina OvineSNP50 BeadChip. The <i>Ne</i> decreased from 535 to 192 in the first ten generations. A total of 2194 ROHs were identified on the basis of single nucleotide polymorphisms (SNPs), were identified in the prolific group and 2185 SNPs in ROH in the non-prolific group. The distribution of the lengths of the ROH, considering both groups, were found to be: 4065 less than 6 Mb, 213 between 6 and 12 Mb, 72 between 12 and 24 Mb, twenty between 24 and 48 Mb and 8 greater than 48 Mb. In prolific sheep, the ROH associated with prolificacy were identified near the <i>LINGO2</i>, <i>FLRT2</i>, <i>ADGRB3</i> genes, related to “positive regulation of synapse assembly”; and the <i>DGKG</i>, <i>DGKE</i>, <i>DGKB</i> and <i>DGKI</i> genes, related to “protein kinase C-activating G-protein coupled receptor signaling pathway”. The present work present genes that can function as signal mediators or have activity in embryonic development, which is relevant to the economic activity of this species.https://www.mdpi.com/1424-2818/14/7/522Pelibueyinbreeding coefficientsheephomozygosity
spellingShingle Wilber Hernández-Montiel
Nubia Noemi Cob-Calan
Lilia E. Cahuich-Tzuc
José A. Rueda
Jorge Quiroz-Valiente
Víctor Meza-Villalvazo
Roberto Zamora-Bustillos
Runs of Homozygosity and Gene Identification in Pelibuey Sheep Using Genomic Data
Diversity
Pelibuey
inbreeding coefficient
sheep
homozygosity
title Runs of Homozygosity and Gene Identification in Pelibuey Sheep Using Genomic Data
title_full Runs of Homozygosity and Gene Identification in Pelibuey Sheep Using Genomic Data
title_fullStr Runs of Homozygosity and Gene Identification in Pelibuey Sheep Using Genomic Data
title_full_unstemmed Runs of Homozygosity and Gene Identification in Pelibuey Sheep Using Genomic Data
title_short Runs of Homozygosity and Gene Identification in Pelibuey Sheep Using Genomic Data
title_sort runs of homozygosity and gene identification in pelibuey sheep using genomic data
topic Pelibuey
inbreeding coefficient
sheep
homozygosity
url https://www.mdpi.com/1424-2818/14/7/522
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