Polymorphisms in Oxytocin and α<sub>1a</sub>Adrenergic Receptor Genes and Their Effects on Production Traits in Dairy Buffaloes

Araújo, Daniele Neves; Camargo, Gregório Miguel Ferreira de; Fonseca, Patrícia Dias da Silva; Cardoso, Diércles Francisco; Hurtado-Lugo, Naudín; Aspilcueta-Borquis, Rusbel Raúl; Tonhati, Humberto

doi:10.1080/10495398.2013.877918

Cited by 10 publications

(7 citation statements)

References 16 publications

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“…Single-organism cellular process (GO:0044763) with 64 genes was significantly enriched (P = 0.05) in ROH islands, including MARS (methionyl-tRNA synthetase, on BTA5), and ADRA1D (adrenoceptor alpha 1D, on BTA13). MARS has been reported to influence milk and protein production in Chinese [52] and Portuguese [53] Holstein cattle, and ADRA1D largely affects milk protein in Murrah dairy buffalo [54]. INHBC and INHBE (inhibin beta C and E subunits, on BTA5) have been reported as candidate genes associated with reproductive performance in tropical young bulls [55], and composite reproductive traits in Lori-Bakhtiari sheep [56].…”

Section: Discussionmentioning

confidence: 99%

Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis

et al. 2020

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Background: Consecutive homozygous fragments of a genome inherited by offspring from a common ancestor are known as runs of homozygosity (ROH). ROH can be used to calculate genomic inbreeding and to identify genomic regions that are potentially under historical selection pressure. The dataset of our study consisted of 254 Azeri (AZ) and 115 Khuzestani (KHZ) river buffalo genotyped for~65,000 SNPs for the following two purposes: 1) to estimate and compare inbreeding calculated using ROH (F ROH ), excess of homozygosity (F HOM ), correlation between uniting gametes (F UNI ), and diagonal elements of the genomic relationship matrix (F GRM ); 2) to identify frequently occurring ROH (i.e. ROH islands) for our selection signature and gene enrichment studies. Results: In this study, 9102 ROH were identified, with an average number of 21.2 ± 13.1 and 33.2 ± 15.9 segments per animal in AZ and KHZ breeds, respectively. On average in AZ, 4.35% (108.8 ± 120.3 Mb), and in KHZ, 5.96% (149.1 ± 107.7 Mb) of the genome was autozygous. The estimated inbreeding values based on F HOM , F UNI and F GRM were higher in AZ than they were in KHZ, which was in contrast to the F ROH estimates. We identified 11 ROH islands (four in AZ and seven in KHZ). In the KHZ breed, the genes located in ROH islands were enriched for multiple Gene Ontology (GO) terms (P ≤ 0.05). The genes located in ROH islands were associated with diverse biological functions and traits such as body size and muscle development (BMP2), immune response (CYP27B1), milk production and components (MARS, ADRA1A, and KCTD16), coat colour and pigmentation (PMEL and MYO1A), reproductive traits (INHBC, INHBE, STAT6 and PCNA), and bone development (SUOX). Conclusion: The calculated F ROH was in line with expected higher inbreeding in KHZ than in AZ because of the smaller effective population size of KHZ. Thus, we find that F ROH can be used as a robust estimate of genomic inbreeding. Further, the majority of ROH peaks were overlapped with or in close proximity to the previously reported genomic regions with signatures of selection. This tells us that it is likely that the genes in the ROH islands have been subject to artificial or natural selection.

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Section: Discussionmentioning

confidence: 99%

Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis

et al. 2020

View full text Add to dashboard Cite

show abstract

“…Single-organism cellular process (GO:0044763) with 64 genes was significantly enriched (P=0.05) in ROH islands, including MARS (methionyl-tRNA synthetase, on BTA5), and ADRA1D (adrenoceptor alpha 1D, on BTA13). MARS has been reported to influence milk and protein production in Chinese [63] and Portuguese [64] Holstein cattle, and ADRA1D largely affects milk protein in Murrah dairy buffalo [65]. INHBC and INHBE (inhibin beta C and E subunits, on BTA5) have been reported as candidate genes associated with reproductive performance in tropical young bulls [66], and composite reproductive traits in Lori-Bakhtiari sheep [67].…”

Section: Evaluation Of Different Methods Of Genomic Inbreedingmentioning

confidence: 99%

Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis

Ghoreishifar

Moradi-Shahrbabak

Fallahi

et al. 2019

Preprint

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Background: Consecutive homozygous fragments of the genome inherited from a common ancestor to offspring are known as runs of homozygosity (ROH). ROH can be used to calculate genomic inbreeding and to identifying genomic regions that are potentially under historical selection pressure. The dataset of our study consisted of 254 Azeri (AZ) and 115 Khuzestani (KHZ) river buffalo genotyped for ~65000 SNPs for the following two purposes: 1) to estimate and compare inbreeding calculated using ROH (FROH), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI), and diagonal elements of the genomic relationship matrix (FGRM); 2) to identify frequently occurring ROH (i.e. ROH islands) for our selection signature and gene enrichment studies. Results: In this study, 9102 ROH were identified, with an average number of 21.2±13.1 and 33.2±15.9 segments per animal in AZ and KHZ breeds, respectively. On average in AZ, 4.35% (108.8±120.3 Mb), and in KHZ, 5.96% (149.1±107.7 Mb) of the genome was autozygous. The estimated inbreeding values based on FHOM, FUNI and FGRM were higher in AZ than they were in KHZ, which was in contrast to the FROH estimates. We identified 11 ROH islands (four in AZ and seven in KHZ). In the KHZ breed, the genes located in ROH islands were enriched for multiple Gene Ontology (GO) terms (P<0.05). The genes located in ROH islands were associated with diverse biological functions and traits such as body size and muscle development (BMP2), immune response (CYP27B1), milk production and components (MARS, ADRA1A, and KCTD16), coat colour and pigmentation (PMEL and MYO1A), reproductive traits (INHBC, INHBE, STAT6 and PCNA), and bone development (SUOX). Conclusion: The calculated FROH was in line with expected higher inbreeding in KHZ than in AZ because of the smaller effective population size of KHZ. Thus, we find that FROH can be used as a robust estimate of genomic inbreeding. Further, the majority of ROH peaks were overlapped with or in close proximity to the previously reported genomic regions with signatures of selection. This tells us that it is likely that the genes in the ROH islands have been subject to artificial and/or natural selection.

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“…Single-organism cellular process (GO:0009987) with 64 genes was significantly enriched (p = 0.05), which contains the MARS (methionyl-tRNA synthetase) and ADRA1D (adrenoceptor alpha 1D also known as ADRA1A) genes on BTA5 and 13, respectively. Surprisingly, MARS has previously been reported to be in association with milk and protein production in Chines [47] and Portuguese [48] Holstein cattle, and ADRA1D with milk protein in Murrah dairy buffaloes [49]. Other interesting genes within this category were INHBC and INHBE (inhibin beta C and E subunits) on BTA 5 reported as candidate genes associate with reproductive ability of tropical young bulls [50], and with composite reproductive traits of Lori-Bakhtiari sheep [51].…”

Section: Candidate Genes Inside Frequently Occurred Roh Regionsmentioning

confidence: 99%

Inbreeding estimations based on runs of homozygosity revealed genes associated with local adaptation and dairy traits in Iranian water buffaloes, Bubalus bubalis

Ghoreishifar

Moradi-Shahrbabak

Fallahi

et al. 2019

Preprint

View full text Add to dashboard Cite

Background Consecutive homozygous fragments of the genome that inherited from a common ancestor to offspring are known as runs of homozygosity (ROH). The ROH stretches can be used to estimate the genomic inbreeding and also for identifying genomic regions under extensive selection pressure. The aims of this study were (i) to estimate inbreeding based on ROH (FROH); (ii) to compare FROH with FHOM (excess of homozygosity), FUNI (correlation between uniting gametes), and FGRM (genomic relationship matrix); and (iii) to identify frequently occurred ROH islands (i.e., shared by >20% of the population) for gene enrichment analyses. A dataset consisted of 396 buffalo including Azeri (N = 281) and Khuzestani (N = 115) breeds genotyped for ~65000 SNP were used. Results In total, 10,245 ROH were identified with an average number of 23.3±14.1 and 33.2±15.9 segments per animal for Azeri (AZ) and Khuzestani (KHZ) breeds, respectively. Our results showed that on average 4.71% (117.9±120.7 Mb) and 5.96% (149.15±107.7 Mb) of the genome of AZ and KHZ is autozygous, respectively. The amount of FHOM, FUNI and FGRM were 0.03, 0.03 and 0.03 in Azeri breed and 0.02, 0.02 and 0.02 in Khuzestani breed, respectively. Strong correlations between FROH-FHOM (0.93) and between FROH-FUNI (0.98 and 0.94) and moderate to strong correlations between FROH-FGRM (0.86 and 0.78) were obtained. Overall, we identified 13 frequently occurred ROH regions. The GO analyses revealed numerous enriched terms for the ROH gene list in KHZ breed. Genes associated with adaptation to hot and arid climate (BMP2), immune response (CYP27B1), milk production, protein, and fat percentage (MARS and ADRA1A, KCTD16), coat color and pigmentation (PMEL and MYO1A), reproductive traits (INHBE and INHBC, STAT6, PCNA), and bone development (SUOX) were identified. Conclusion Genes within common ROH spots present a modest phenotypic selection for milk production traits in Khuzestani buffalo. Further, our results suggest that natural selection may have a role in forming the genome of Iranian buffaloes in order to adapt them to the harsh environment of the country.

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Polymorphisms in Oxytocin and α_1aAdrenergic Receptor Genes and Their Effects on Production Traits in Dairy Buffaloes

Cited by 10 publications

References 16 publications

Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis

Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis

Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis

Inbreeding estimations based on runs of homozygosity revealed genes associated with local adaptation and dairy traits in Iranian water buffaloes, Bubalus bubalis

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Polymorphisms in Oxytocin and α1aAdrenergic Receptor Genes and Their Effects on Production Traits in Dairy Buffaloes

Cited by 10 publications

References 16 publications

Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis

Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis

Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis

Inbreeding estimations based on runs of homozygosity revealed genes associated with local adaptation and dairy traits in Iranian water buffaloes, Bubalus bubalis

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Product

Resources

About

Polymorphisms in Oxytocin and α_1aAdrenergic Receptor Genes and Their Effects on Production Traits in Dairy Buffaloes