Identifying Hub Genes for Heat Tolerance in Water Buffalo (Bubalus bubalis) Using Transcriptome Data

Liu, Shenhe; Ye, Tingzhu; Li, Zipeng; Li, Jun; Ahmad, Muhammad Jamil; Zhou, Yang; Hua, Guohua; Liang, Aixin; Deng, Tingxian; Yang, Liguo

doi:10.3389/fgene.2019.00209

Cited by 30 publications

(23 citation statements)

References 96 publications

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“…Verma et al [30] determined RR and RT as the most sensitive indices of heat tolerance among all the physiological reactions studied. This study showed that the RT and RR in HT individuals were significantly lower when compared to NHT, similar to observation in cattle [31] and buffalo [32]. Elevated temperature increased the plasma HSP90 and HSP70 levels more markedly in HT than in NHT individuals, coinciding to previous study in cattle [33] and rodents [34].…”

Section: Discussionsupporting

confidence: 90%

“…A limited number of animals may limit the power of design as well as validity of results. However, several studies published previously using even the fewer animals compared with our study [32,55]. The results of our study are giving foundation for heat tolerance mechanism in dairy cows.…”

Section: Discussionsupporting

confidence: 49%

“…Moreover, our outcomes revealed that TGFB2 and FGF2 are part of MAPK signaling pathway. Previous work has discussed the activation of MAPK signaling pathway mediated by several extra-cellular stimuli, including UV radiation, osmotic shock and heat shock [32,36,44,45]. Of note, TGFB2 as stress-related gene was significantly induced when human lung fibroblast cell lines were exposed to radiofrequency radiation [46].…”

Section: Discussionmentioning

confidence: 99%

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Transcriptome Analysis Reveals Potential Regulatory Genes Related to Heat Tolerance in Holstein Dairy Cattle

Liu

Yue

Ahmad

et al. 2020

Genes

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Heat stress affects the physiology and production performance of Chinese Holstein dairy cows. As such, the selection of heat tolerance in cows and elucidating its underlying mechanisms are vital to the dairy industry. This study aimed to investigate the heat tolerance associated genes and molecular mechanisms in Chinese Holstein dairy cows using a high-throughput sequencing approach and bioinformatics analysis. Heat-induced physiological indicators and milk yield changes were assessed to determine heat tolerance levels in Chinese Holstein dairy cows by Principal Component Analysis method following Membership Function Value Analysis. Results indicated that rectal temperature (RT), respiratory rate (RR), and decline in milk production were significantly lower (p < 0.05) in heat tolerant (HT) cows while plasma levels of heat shock protein (HSP: HSP70, HSP90), and cortisol were significantly higher (p < 0.05) when compared to non-heat tolerant (NHT) Chinese Holstein dairy cows. By applying RNA-Seq analysis, we identified 200 (81 down-regulated and 119 up-regulated) significantly (|log2fold change| ≥ 1.4 and p ≤ 0.05) differentially expressed genes (DEGs) in HT versus NHT Chinese Holstein dairy cows. In addition, 14 of which were involved in protein–protein interaction (PPI) network. Importantly, several hub genes (OAS2, MX2, IFIT5 and TGFB2) were significantly enriched in immune effector process. These findings might be helpful to expedite the understanding for the mechanism of heat tolerance in Chinese Holstein dairy cows.

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Section: Discussionsupporting

confidence: 90%

Section: Discussionsupporting

confidence: 49%

Section: Discussionmentioning

confidence: 99%

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Transcriptome Analysis Reveals Potential Regulatory Genes Related to Heat Tolerance in Holstein Dairy Cattle

Liu

Yue

Ahmad

et al. 2020

Genes

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“…MicroRNAs play a significant role during follicle development in bovine 21 , 22 . In buffalo, heat stress was observed to alter the blood miRNA and mRNA content 23 . The role of miRNAs is also demonstrated in the regulation of lactating physiology in the buffalo mammary gland 24 , and miRNA expression changes were observed in buffalo corpus luteum during pregnancy 25 .…”

Section: Introductionmentioning

confidence: 99%

Seasonal effects on miRNA and transcriptomic profile of oocytes and follicular cells in buffalo (Bubalus bubalis)

Capra

Lazzari

Russo

et al. 2020

Sci Rep

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Season clearly influences oocyte competence in buffalo (Bubalus bubalis); however, changes in the oocyte molecular status in relation to season are poorly understood. This study characterizes the microRNA (miRNA) and transcriptomic profiles of oocytes (OOs) and corresponding follicular cells (FCs) from buffalo ovaries collected in the breeding (BS) and non-breeding (NBS) seasons. In the BS, cleavage and blastocyst rates are significantly higher compared to NBS. Thirteen miRNAs and two mRNAs showed differential expression (DE) in FCs between BS and NBS. DE-miRNAs target gene analysis uncovered pathways associated with transforming growth factor β (TGFβ) and circadian clock photoperiod. Oocytes cluster in function of season for their miRNA content, showing 13 DE-miRNAs between BS and NBS. Between the two seasons, 22 differentially expressed genes were also observed. Gene Ontology (GO) analysis of miRNA target genes and differentially expressed genes (DEGs) in OOs highlights pathways related to triglyceride and sterol biosynthesis and storage. Co-expression analysis of miRNAs and mRNAs revealed a positive correlation between miR-296-3p and genes related to metabolism and hormone regulation. In conclusion, season significantly affects female fertility in buffalo and impacts on oocyte transcriptomic of genes related to folliculogenesis and acquisition of oocyte competence. Water buffalo (Bubalus bubalis) is an important livestock resource for both developing and developed countries. The major factor affecting buffalo farming profitability is reproductive seasonality, resulting in cycles of calving and milk production. Buffalo is a short-day breeder, with increased fertility in response to decreasing day length 1,2. This photoperiod-dependent seasonality pattern is more pronounced as distance from the equator, together with variations in the light/dark ratio, increases. In Italy, in order to satisfy market demand, out of breeding mating strategy (OBMS), consisting in interrupting sexual promiscuity or the use of artificial insemination (AI) during the breeding season (BS), is commonly utilized 2. The OBMS improves the distribution of calving throughout the year, but it reduces fertility 3. Longer post-partum anoestrus periods as well as higher incidence of embryonic mortality are observed in months with increasing daylight length and particularly in midwinter , which coincides with the transition to seasonal anoestrus at Italian latitudes 1,4. The embryonic mortality is due to inadequate luteal growth and function, resulting in reduced progesterone secretion 5. This has a negative impact on embryo growth, associated with alterations in transcriptomic and proteomic profiles of the embryos and chorioamnios/caruncles 6,7 , which ultimately impair embryo attachment to the uterine endometrium.

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“…Through a weighted gene co‐expression network analysis, they identified a set of 12 hub genes ( BNIPL , TUBA1C , C2CD4B , DCP1B , MAP3K5 , PDCD11 , SRGAP1 , GDPD5 , BARX2 , SCARA3 , CTU2 and RPL27A ) involved in several pathways related to milk production. With a similar approach, the mRNA and microRNA expression profiles of heat‐tolerant and non‐heat‐tolerant buffaloes have been analysed (Liu et al ). The analysis highlighted a total of 753 differentially expressed genes and 16 microRNAs differentially expressed between the two groups of animals.…”

Section: Introductionmentioning

confidence: 99%

Asian water buffalo: domestication, history and genetics

Colli

Barker

2020

Animal Genetics

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Summary The domestic Asian water buffalo (Bubalus bubalis) is found on all five continents, with a global population of some 202 million. The livelihoods of more people depend on this species than on any other domestic animal. The two distinct types (river and swamp) descended from different wild Asian water buffalo (Bubalus arnee) populations that diverged some 900 kyr BP and then evolved in separate geographical regions. After domestication in the western region of the Indian subcontinent (ca. 6300 years BP), the river buffalo spread west as far as Egypt, the Balkans and Italy. Conversely, after domestication in the China/Indochina border region ca. 3000–7000 years BP, swamp buffaloes dispersed through south‐east Asia and China as far as the Yangtze River valley. Molecular and morphological evidence indicates that swamp buffalo populations have strong geographic genetic differentiation and a lack of gene flow, but strong phenotypic uniformity. In contrast, river buffalo populations show a weaker phylogeographic structure, but higher phenotypic diversity (i.e. many breeds). The recent availability of a high‐quality reference genome and of a medium‐density marker panel for genotyping has triggered a number of genome‐wide investigations on diversity, evolutionary history, production traits and functional elements. The growing molecular knowledge combined with breeding programmes should pave the way to improvements in production, environmental adaptation and disease resistance in water buffalo populations worldwide.

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Identifying Hub Genes for Heat Tolerance in Water Buffalo (Bubalus bubalis) Using Transcriptome Data

Cited by 30 publications

References 96 publications

Transcriptome Analysis Reveals Potential Regulatory Genes Related to Heat Tolerance in Holstein Dairy Cattle

Transcriptome Analysis Reveals Potential Regulatory Genes Related to Heat Tolerance in Holstein Dairy Cattle

Seasonal effects on miRNA and transcriptomic profile of oocytes and follicular cells in buffalo (Bubalus bubalis)

Asian water buffalo: domestication, history and genetics

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