Genome-wide association study of a thermo-tolerance indicator in pregnant ewes exposed to an artificial heat-stressed environment

Pendleton, Alexander L.; Luna-Ramirez, Rosa I.; Limesand, Sean W.; Reyna-Granados, Javier R.; Luna‐Nevárez, Pablo

doi:10.1016/j.jtherbio.2021.103095

Cited by 16 publications

(5 citation statements)

References 55 publications

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“…The DNAJB5 gene chaperone complex controls polarized growth by repressing Hsf1-driven heat stress-associated transcription (Vjestica et al, 2013;Wang et al, 2019). The TSHR gene regulates HSPs, which are believed to function as cellular thermometers for environmental adaptation in heat-stressed small ruminants (Luna-Nevárez et al, 2021). The phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 beta (PIK3C2B) gene is categorized in a cluster of genes compatible with the PI3K isoform.…”

Section: Genes Related To Desert Adaptationmentioning

confidence: 99%

Genetic diversity, population structure, and selective signature of sheep in the northeastern Tarim Basin

Wang,

Suo,

Yang

et al. 2023

Front. Genet.

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Local sheep in the northeastern Tarim Basin can adapt to dry and low-rainfall regional environments. In this study, three local sheep breeds in the northeastern Tarim Basin, LOP (LOP) sheep, Bayinbuluke (BYK) sheep, and Kunlun (KUN, also known as the Qiemo sheep) sheep, and three introduced sheep breeds, Suffolk (SUF) sheep, Dorset (APD) sheep, and Texel (TEX) sheep, were analyzed for genetic diversity, population structure, and selective signature using the Illumina OvineSNP50K BeadChip. We found that LOP, BYK, and KUN had lower observed heterozygosity and expected heterozygosity than TEX, SUF, and ADP, which were differentiated based on geographic distribution. We performed fixation index (FST) analysis on three local sheep breeds in the northeastern Tarim Basin (LOP, BYK, and KUN) and introduced sheep breeds (TEX, SUF, and ADP) to measure genetic differentiation. Nucleotide diversity (PI) analysis was performed on single-nucleotide polymorphism (SNP) data of LOP, BYK, and KUN. A total of 493 candidate genes were obtained by taking the intersection at a threshold of 5%. Among them, SMAD2, ESR2, and HAS2 were related to reproductive traits. PCDH15, TLE4, and TFAP2B were related to growth traits. SOD1, TSHR, and DNAJB5 were related to desert environmental adaptation. Analyzing the genetic patterns of local sheep in the northeastern Tarim Basin can protect the germplasm resources of local sheep and promote the development and utilization of sheep genetic resources.

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Section: Genes Related To Desert Adaptationmentioning

confidence: 99%

Genetic diversity, population structure, and selective signature of sheep in the northeastern Tarim Basin

Wang,

Suo,

Yang

et al. 2023

Front. Genet.

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“…In addition to the genes related to early domestication, a panel of interesting genes associated with other economic traits was also revealed. These genes were previously reported in goats, sheep and other species, showing correlations with spermatogenesis and sperm motility ( KIF3B , KIF17 , KIAA0825 and TNFRSF21 ) [ 53 , 54 , 55 , 56 ], growth and development ( TNPO2 , IFT80 , UCP2 , UCP3 , GHRHR , SIM1 , CCM2L , CTNNA3 and CTNNA1 ) [ 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 ], fat deposition ( ACSF3 and FGGY ) [ 65 , 66 ], chicken heat tolerance ( TSHR and SUGCT ) [ 67 ], high-altitude hypoxia adaptation ( CHL1 ) [ 68 ], milk composition ( GHRHR ) [ 69 ], milk flavour ( ACSF3 ) [ 70 ], carcass traits ( GHRHR ) [ 71 ] and hair follicle morphogenesis ( GLI2 ) [ 72 ]. The iHS and ROH methods both detected some genes, but each method found additional genes not detected by the other.…”

Section: Discussionmentioning

confidence: 99%

Identifying Candidate Genes for Litter Size and Three Morphological Traits in Youzhou Dark Goats Based on Genome-Wide SNP Markers

Sun,

Niu,

Jiang

et al. 2023

Genes

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This study aimed to reveal the potential genetic basis for litter size, coat colour, black middorsal stripe and skin colour by combining genome-wide association analysis (GWAS) and selection signature analysis and ROH detection within the Youzhou dark (YZD) goat population (n = 206) using the Illumina GoatSNP54 BeadChip. In the GWAS, we identified one SNP (snp54094-scaffold824-899720) on chromosome 11 for litter size, two SNPs on chromosome 26 (snp11508-scaffold142-1990450, SORCS3) and chromosome 12 (snp55048-scaffold842-324525, LOC102187779) for coat colour and one SNP on chromosome 18 (snp56013-scaffold873-22716, TCF25) for the black middorsal stripe. In contrast, no SNPs were identified for skin colour. In selection signature analysis, 295 significant iHS genomic regions with a mean |iHS| score > 2.66, containing selection signatures encompassing 232 candidate genes were detected. In particular, 43 GO terms and one KEGG pathway were significantly enriched in the selected genes, which may contribute to the excellent environmental adaptability and characteristic trait formation during the domestication of YZD goats. In ROH detection, we identified 4446 ROH segments and 282 consensus ROH regions, among which nine common genes overlapped with those detected using the iHS method. Some known candidate genes for economic traits such as reproduction (TSHR, ANGPT4, CENPF, PIBF1, DACH1, DIS3, CHST1, COL4A1, PRKD1 and DNMT3B) and development and growth (TNPO2, IFT80, UCP2, UCP3, GHRHR, SIM1, CCM2L, CTNNA3 and CTNNA1) were revealed by iHS and ROH detection. Overall, this study is limited by the small population size, which affects the results of GWAS to a certain extent. Nevertheless, our findings could provide the first overview of the genetic mechanism underlying these important traits and provide novel insights into the future conservation and utilisation of Chinese goat germplasm resources.

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“…Interestingly, genes associated with thermotolerance in pregnant ewes have also been reported as markers for fertility, suggesting a close relationship between the genetic ability to tolerate heat stress and the reproductive performance. In this regard, the genes PAM , STAT1 and FBXO11 were reported as markers for heat stress tolerance in Columbia–Rambouillet pregnant ewes [ 9 , 76 ]. These three genes were later confirmed as markers associated with reproductive traits and physiological variables indicative of thermotolerance in Pelibuey pregnant ewes [ 10 ].…”

Section: Discussionmentioning

confidence: 99%

Blood Transcriptomic Analyses Reveal Functional Pathways Associated with Thermotolerance in Pregnant Ewes Exposed to Environmental Heat Stress

Luna-Ramirez

Limesand

Goyal

et al. 2023

Genes

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Environmental heat stress triggers a series of compensatory mechanisms in sheep that are dependent on their genetic regulation of thermotolerance. Our objective was to identify genes and regulatory pathways associated with thermotolerance in ewes exposed to heat stress. We performed next-generation RNA sequencing on blood collected from 16 pregnant ewes, which were grouped as tolerant and non-tolerant to heat stress according to a physiological indicator. Additional samples were collected to measure complete blood count. A total of 358 differentially expressed genes were identified after applying selection criteria. Gene expression analysis detected 46 GO terms and 52 KEGG functional pathways. The top-three signaling pathways were p53, RIG-I-like receptor and FoxO, which suggested gene participation in biological processes such as apoptosis, cell signaling and immune response to external stressors. Network analysis revealed ATM, ISG15, IRF7, MDM4, DHX58 and TGFβR1 as over-expressed genes with high regulatory potential. A co-expression network involving the immune-related genes ISG15, IRF7 and DXH58 was detected in lymphocytes and monocytes, which was consistent with hematological findings. In conclusion, transcriptomic analysis revealed a non-viral immune mechanism involving apoptosis, which is induced by external stressors and appears to play an important role in the molecular regulation of heat stress tolerance in ewes.

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Genome-wide association study of a thermo-tolerance indicator in pregnant ewes exposed to an artificial heat-stressed environment

Cited by 16 publications

References 55 publications

Genetic diversity, population structure, and selective signature of sheep in the northeastern Tarim Basin

Genetic diversity, population structure, and selective signature of sheep in the northeastern Tarim Basin

Identifying Candidate Genes for Litter Size and Three Morphological Traits in Youzhou Dark Goats Based on Genome-Wide SNP Markers

Blood Transcriptomic Analyses Reveal Functional Pathways Associated with Thermotolerance in Pregnant Ewes Exposed to Environmental Heat Stress

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