Genome-wide association study of four composite reproductive traits in Iranian fat-tailed sheep

Abdoli, Ramin; Mirhoseini, Seyed Ziaeddin; Hossein-Zadeh, Navid Ghavi; Zamani, P.; Ferdosi, Mohammad; Gondro, Cedric

doi:10.1071/rd18282

Cited by 24 publications

(19 citation statements)

References 21 publications

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“…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]. KCTD16 (potassium channel tetramerization domain containing 16, on BTA7) was reported as a candidate gene for meat quality in Simmental beef cattle [57], for residual feed intake in Junmu White pigs [58], and for fat yield in Nordic Holstein cattle [59].…”

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

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“…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]. KCTD16 gene on BTA7 were reported as candidate gene for fat yield in Nordic Holstein cattle [52], with meat quality in Simmental beef cattle [53].…”

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

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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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“…Therefore, genetic improvement of ewe productivity is a key target in sheep breeding programs [3]. Common composite reproductive traits in sheep are total litter weight at birth (TLWB) and total litter weight at weaning (TLWW) and have the excellence of being better coordinate to the market, where producers are paid on a per kilogram and not on a per head [6].…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…Although estimates of genetic parameters have been reported for composite traits of different Iranian sheep breeds [6,7], reports on genes and pathways affecting these traits are limited. To our knowledge, there is only one published report of genes and genomic regions associated with composite traits in sheep [6]. A whole-genome scan carried out by the authors and five genes neighboring the top SNPs (on OAR2, OAR3, OAR15, and OAR16), including TEX12, BCO2, WDR70, INHBE, and INHBC reported as possible candidate genes affecting composite traits of the Lori-Bakhtiari sheep.…”

Section: Introductionmentioning

confidence: 99%

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Maternal genes and pathways affecting birth weight and weaning weight traits in sheep: A GWAS and pathway enrichment analysis

Esmaeili-Fard

Hafezian

Gholizadeh

et al. 2020

Preprint

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Background Ewe productivity is considered as the most important economic trait in sheep meat production. Due to very limited reports, the objective of this study was the application of alternative GWAS approaches followed by gene set enrichment analysis (GSEA) on the maternal genome to unravel the genomic architecture underlying ewe productivity in Iranian Baluchi sheep. Six maternal composite traits including progeny birth weight (PBW), litter mean weight at birth (LMWB), total litter weight at birth (TLWB), progeny weaning weight (PWW), litter mean weight at weaning (LMWW) and total litter weight at weaning (TLWW) were studied. Results Genes such as RDX , FDX1 , ARHGAP20 , ZC3H12C , THBS1 , and EPG5 on OAR6, OAR7, OAR15, and OAR23 were identified for composite traits at birth. The genes are involved in pregnancy, including autophagy in the placenta, progesterone production by the placenta, maternal immune response and placenta formation. Some maternal pathways, related to calcium ion transport, signal transduction, neurogenesis, and immune response were also identified for birth weight traits. Moreover, many genes including NR2C1 , VEZT , HSD17B4 , RSU1 , CUBN , VIM , PRLR , and FTH1 were located on OAR2, OAR3, OAR5, OAR7, OAR13, OAR16, and OAR25 identified as maternal genes affecting weaning weight traits. Most of the identified genes were involved in mammary glands development and milk components production. Also, many GO terms related to protein processing and transport, ion transport and homeostasis, proteins and lipid phosphorylation, and phospholipid translocation were identified in association with weaning weight traits. Conclusions The results of the present study revealed that calcium ion homeostasis and transport and the maternal immune system could have an important role in progeny’s birth weight. Also, the results showed that genes and pathways affecting mammary glands development during pregnancy and milk components production have the most impact on lambs weaning weight. These findings contribute to a better understanding of the genetic architecture of the studied traits and providing opportunities for improving ewe productivity via marker-assisted selection.

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Genome-wide association study of four composite reproductive traits in Iranian fat-tailed sheep

Cited by 24 publications

References 21 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

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

Maternal genes and pathways affecting birth weight and weaning weight traits in sheep: A GWAS and pathway enrichment analysis

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