Influence of endogamy and mitochondrial DNA on immunological parameters in cattle

Macêdo, Auricélio A.; Bittar, Joely Ferreira Figueiredo; Bassi, Paula Boeira; Ronda, Juliano Bergamo; Bittar, Eustáquio Resende; Panetto, J. C. do C.; Araújo, Márcio Sobreira Silva; Santos, Renato L.; Martins‐Filho, Olindo Assis

doi:10.1186/1746-6148-10-79

Cited by 12 publications

(9 citation statements)

References 37 publications

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“…In cattle, inbreeding has been also associated with changes in the immune system [ 74 ] and an increased occurrence of respiratory diseases [ 75 ]. Our results also identified a metabolic pathway related to B-defensin genes.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2018

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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 FPED = 0.164; 0.103 to 0.306) and outbred Retinta bulls (LI; average FPED = 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 (FPED3 = 0.125). The correlation between the fraction of the genome covered by ROH (FROH) and FPED was high (0.79), suggesting that ROH-based estimations are indicative of inbreeding levels. On the other hand, the correlation between FPED and the microsatellite-based inbreeding coefficient (FMIC) 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.

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Section: Discussionmentioning

confidence: 99%

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

et al. 2018

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“…TLR5 is located extracellularly and recognizes flagellin, which is a structural component of the flagellum in flagellated bacteria (Hayashi et al, 2001;Smith et al, 2003), whereas TLR9 is located intracellularly and recognizes unmethylated CpG dinucleotides that are found in Gram-positive and Gramnegative bacteria (Griebel et al, 2005;Dalpke et al, 2006). Previous reports indicated that genotypic and phenotypic factors modulate the uterine defense mechanisms in cows (Horne et al, 2008;Sordillo et al, 2009), and a study verified that endogamy also interfere with immune parameters of Zebu cattle (Macêdo et al, 2014). Hypothetically, decreased transcription of TLR5 could increase susceptibility to flagellated bacteria in Gyr cows at 7 days post partum, whereas increased transcription of TLR9 could be associated with resistance against bacteria located intracellularly in the endosomal compartment (Janeway and Medzhitov, 2002).…”

Section: Resultsmentioning

confidence: 96%

Endometrial transcription of microbial molecular patterns receptors in Gyr and F1 Holstein x Gyr postpartum cows

Martins

Muniz

Paixão

et al. 2017

Arq. Bras. Med. Vet. Zootec.

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Zebu and Holstein x Zebu crossbred have low incidence of uterine infection when compared to Holstein cows. Resistance to uterine infections may be associated with the ability to recognize invading microorganisms. Endometrial transcription of microbial molecular patterns receptors has been investigated in the postpartum period of Holstein cows, but it is completely unknown in Zebu or Holstein x Zebu cows. In this study, 9 Gyr and 12 F1 Holstein x Gyr cows were submitted to endometrial biopsies at the first and seventh days postpartum, with the objective to measure transcription levels of toll-like receptors (TLRs) 1/6, 2, 4, 5, and 9; nucleotide-binding oligomerization domain (NOD)-like receptors 1 and 2; and coreceptors cluster of differentiation 14 (CD14) and myeloid differentiation protein-2 (MD-2). There was a significant (P<0.05) decrease in transcription of TLR5 in Gyr, and an increase in transcription of TLR9 in F1 cows, between the first and seventh day postpartum. Both groups had low incidences of uterine infections up to 42 days postpartum. Uterine involution completed at 27.7 ± 10.1 and 25.1 ± 4.7 days postpartum for Gyr and F1 cows, respectively. In Gyr cows, higher transcription levels of TLR1/6 and NOD1 correlated to a longer period required for uterine involution. In F1 cows, lower levels of TLR1/6, TLR2 and NOD2 correlated to a longer period required for uterine involution. In conclusion, some pathogen recognition receptors associated significantly with the time required for uterine involution in Gyr and F1 cows.

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“…In cattle, artificial reproduction technologies allow the reduction in the number of animals needed to produce the next generation and the reduction in generation intervals. Consequently, the increase in the relatedness levels in the population is usually a result of the selection process (Macedo et al., ; Panetto, Gutiérrez, Ferraz, Cunha, & Golden, ). Samples may capture such phenomena and association studies, and may be affected by the population genetic structure.…”

Section: Discussionmentioning

confidence: 99%

Reducing cryptic relatedness in genomic data sets via a central node exclusion algorithm

Fonseca

Leal

Santos

et al. 2018

Molecular Ecology Resources

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Cryptic relatedness is a confounding factor in genetic diversity and genetic association studies. Development of strategies to reduce cryptic relatedness in a sample is a crucial step for downstream genetic analyses. This study uses a node selection algorithm, based on network degrees of centrality, to evaluate its applicability and impact on evaluation of genetic diversity and population stratification. 1,036 Guzerá (Bos indicus) females were genotyped using Illumina Bovine SNP50 v2 BeadChip. Four strategies were compared. The first and second strategies consist on a iterative exclusion of most related individuals based on PLINK kinship coefficient (φij) and VanRaden's φij, respectively. The third and fourth strategies were based on a node selection algorithm. The fourth strategy, Network G matrix, preserved the larger number of individuals with a better diversity and representation from the initial sample. Determining the most probable number of populations was directly affected by the kinship metric. Network G matrix was the better strategy for reducing relatedness due to producing a larger sample, with more distant individuals, a more similar distribution when compared with the full data set in the MDS plots and keeping a better representation of the population structure. Resampling strategies using VanRaden's φij as a relationship metric was better to infer the relationships among individuals. Moreover, the resampling strategies directly impact the genomic inflation values in genomewide association studies. The use of the node selection algorithm also implies better selection of the most central individuals to be removed, providing a more representative sample.

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Influence of endogamy and mitochondrial DNA on immunological parameters in cattle

Cited by 12 publications

References 37 publications

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

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

Endometrial transcription of microbial molecular patterns receptors in Gyr and F1 Holstein x Gyr postpartum cows

Reducing cryptic relatedness in genomic data sets via a central node exclusion algorithm

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