Runs of homozygosity and signatures of selection for number of oocytes and embryos in the Gir Indicine cattle

被引：4

作者：

Bretanha Rocha, Renata de Fatima ^{[1
]}

Garcia, Arielly Oliveira ^{[1
]}

Otto, Pamela Itajara ^{[2
]}

da Silva, Marcos Vinicius Barbosa ^{[3
]}

Martins, Marta Fonseca ^{[3
]}

Machado, Marco Antonio ^{[3
]}

Panetto, Joao Claudio do Carmo ^{[3
]}

Guimaraes, Simone Eliza Facioni ^{[1
]}

机构：

[1] Univ Fed Vicosa, Dept Anim Sci, Vicosa, MG, Brazil

[2] Univ Fed Santa Maria, Dept Anim Sci, Santa Maria, Rio Grande do S, Brazil

[3] EMBRAPA, Dairy Cattle Natl Res Ctr, Juiz De Fora, MG, Brazil

来源：

MAMMALIAN GENOME | 2023年 / 34卷 / 03期

关键词：

GENE ONTOLOGY CATEGORIES; CYTOSCAPE; TRANSCRIPTOME; AUTOZYGOSITY; STATISTICS; EXPRESSION; FERTILITY; REGIONS;

D O I：

10.1007/s00335-023-09989-w

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Runs of homozygosity (ROH) and signatures of selection are the results of selection processes in livestock species that have been shown to affect several traits in cattle. The aim of the current work was to verify the profile of ROH and inbreeding depression in the number of total (TO) and viable oocytes (VO) and the number of embryos (EMBR) in Gir Indicine cattle. In addition, we aim to identify signatures of selection, genes, and enriched regions between Gir subpopulations sorted by breeding value for these traits. The genotype file contained 2093 animals and 420,718 SNP markers. Breeding values used to sort Gir animals were previously obtained. ROH and signature of selection analyses were performed using PLINK software, followed by ROH-based (F-ROH) and pedigree-based inbreeding (F-ped) and a search for genes and their functions. An average of 50 +/- 8.59 ROHs were found per animal. ROHs were separated into classes according to size, ranging from 1 to 2 Mb (ROH(1-2)Mb: 58.17%), representing ancient inbreeding, ROH(2-4)Mb (22.74%), ROH(4-8)Mb (11.34%), ROH(8-16)Mb (5.51%), and ROH(>16)Mb (2.24%). Combining our results, we conclude that the increase in general F-ROH and F-ped significantly decreases TO and VO; however, in different chromosomes traits can increase or decrease with F-ROH. In the analysis for signatures of selection, we identified 15 genes from 47 significant genomic regions, indicating differences in populations with high and low breeding value for the three traits.

引用

页码：482 / 496

页数：15