Whole-Genome Resequencing Points to Candidate DNA Loci Affecting Body Temperature under Cold Stress in Siberian Cattle Populations

Igoshin, Alexander V.; Yudin, N. A.; Aitnazarov, R. B.; Yurchenko, Andrey A.; Larkin, Denis M.

doi:10.3390/life11090959

Cited by 10 publications

(5 citation statements)

References 56 publications

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“…Cold water intake is a primary factor that leads to lower rumen temperature [11]. Peterson et al [12] observed a decrease in rumen temperature to 31.6 • C following the ingestion of water at 8.2 ± 0.4 • C, which subsequently returned to normal levels within approximately 2 h. In regions characterized by temperate and cold temperate climates, such as Korea and Siberia [13,14], the intake of ambient water can have adverse effects on rumen temperature, consequently impacting animal performance. Guo et al [15] reported that, in cold environments, a significant portion of propionate may enter the gluconeogenesis pathway in sheep, which can be attributed to the elevated energy requirements of ruminants under cold conditions, and the propionate serves as a key precursor in gluconeogenesis and plays a vital role in providing energy to ruminants [16].…”

Section: Introductionmentioning

confidence: 99%

Calcium Propionate Supplementation Mitigated Adverse Effects of Incubation Temperature Shift on In Vitro Fermentation by Modulating Microbial Composition

Wang

Long

et al. 2023

Fermentation

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The ingestion of cold water in winter results in fluctuating decreases in rumen temperature, impacting rumen fermentation function and methane production. This study aimed to investigate the impact of calcium propionate (CaP) on rumen fermentation characteristics, methane production, and microbial microbiome under different in vitro incubation temperatures. A 2 × 2 factorial experiment was conducted over 72 h, with or without 2.5% CaP (dry matter [DM] basis) in substrate under a constant incubation temperature (39 °C, CIT) or shifting incubation temperatures (12 cycles in total, with each cycle consisting of 4 h of incubation at 39 °C followed by immediate transfer to 30 °C for 2 h, ITS). The results showed that ITS inhibited the gas production, methane production, and methane concentration at 12 and 72 h (p < 0.05), and reduced the concentration of ammonium nitrogen (−14.25%), propionate (−16.14%), butyrate (−12.67%), and total volatile fatty acid (−8.50%) at 72 h more than the CIT groups (p < 0.05). The addition of 2.5% CaP significantly increased the gas production at 72 h (+4.84%), asymptotic gas production (+5.08%, per 0.2 g DM substrate), concentration of propionate (+18.05%), and valerate (+9.45%) (p < 0.05) compared to CaP-free groups, while it had no observable effect on the production or concentration of methane. Furthermore, the addition of 2.5% CaP yielded a significant increase in the relative abundance of Bacteroides (p < 0.05). Under the ITS condition, the relative abundance of Methanomicrobiales decreased and was positively correlated with methane production at 72 h (r = 0.47, p < 0.05). Additionally, CaP decreased the abundance of Prevotella_UCG_003 (p < 0.05), which was negatively correlated with the asymptotic gas production (r = 0.45, p < 0.05). Overall, our study suggests that the addition of 2.5% CaP can alleviate the adverse effects of ITS on in vitro fermentation parameters by regulating microbial composition and sustaining a reduction in methane production.

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Section: Introductionmentioning

confidence: 99%

Calcium Propionate Supplementation Mitigated Adverse Effects of Incubation Temperature Shift on In Vitro Fermentation by Modulating Microbial Composition

Wang

Long

et al. 2023

Fermentation

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“…As we know, the villi hair development is partly a result of adaptation to cold (or hot) climates, so, we searched all of the genes near or within the 15 CNVRs with cold or hot adaptation. Among these genes, activating transcription factor 1 ( ATF1 ) could modulate the heat shock response, and was related to thermal adaptations in cattle [ 36 , 37 ]. In the report of Saravanan et al, dnaJ heat shock protein family (Hsp40) member B4 ( DNAJB4 ) was also a candidate gene that may be related to heat stress in cattle [ 38 ].…”

Section: Discussionmentioning

confidence: 99%

Identification of Candidate Genes for Min Pig Villi Hair Traits by Genome-Wide Association of Copy Number Variation

Wang

Feng

et al. 2023

Veterinary Sciences

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The Min pig is a famous native pig breed in northeast China, which has the special genetic character of villi hair growth in cold seasons. At present, little research has focused on the genetic mechanism of villi hair growth in Min pigs. Copy number variations (CNVs) are a type of variant that may influence many traits. In this study, we first investigated the phenotype of Large White × Min pigs’ F2 pig villi hair in detail and then performed a CNV-based genome-wide association study (GWAS) between CNVs and pig villi hair appearance. Finally, a total number of 15 significant CNVRs were found to be associated with Min pig villi hair. The most significant CNVR was located on chromosome 1. Nearest gene annotation analysis indicated that the pig villi hair traits may be associated with the biological process of the G-protein-coupled receptor signaling pathway. QTL overlapping analysis found that among the CNVRs, 14 CNVRs could be co-located with known QTLs. Some genes such as MCHR2, LTBP2, and GFRA2 may be candidate genes for pig villi traits and are worth further study. Our study may provide a basic reference for the selection and breeding of cold-resistant pigs and outdoor breeding.

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“…The strongest selection signal was around TBC1D12, on OAR22, which plays a role in GTPase regulation. The F ST approach was also applied to Siberian cattle populations in order to understand the genetic basis of adaptation to cold environments [154]. Results identified several genes that have been implicated in thermal adaptation in cattle, such as GRIA4, COX17, MAATS1, UPK1B, IFNGR1, DDX23, PPT1, THBS1, CCL5, ATF1, PLA1A, PRKAG1, and NR1I2.…”

Section: Selection Signaturesmentioning

confidence: 99%

The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock

Passamonti

Somenzi

Barbato

et al. 2021

Animals

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Livestock radiated out from domestication centres to most regions of the world, gradually adapting to diverse environments, from very hot to sub-zero temperatures and from wet and humid conditions to deserts. The climate is changing; generally global temperature is increasing, although there are also more extreme cold periods, storms, and higher solar radiation. These changes impact livestock welfare and productivity. This review describes advances in the methodology for studying livestock genomes and the impact of the environment on animal production, giving examples of discoveries made. Sequencing livestock genomes has facilitated genome-wide association studies to localize genes controlling many traits, and population genetics has identified genomic regions under selection or introgressed from one breed into another to improve production or facilitate adaptation. Landscape genomics, which combines global positioning and genomics, has identified genomic features that enable animals to adapt to local environments. Combining the advances in genomics and methods for predicting changes in climate is generating an explosion of data which calls for innovations in the way big data sets are treated. Artificial intelligence and machine learning are now being used to study the interactions between the genome and the environment to identify historic effects on the genome and to model future scenarios.

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Whole-Genome Resequencing Points to Candidate DNA Loci Affecting Body Temperature under Cold Stress in Siberian Cattle Populations

Cited by 10 publications

References 56 publications

Calcium Propionate Supplementation Mitigated Adverse Effects of Incubation Temperature Shift on In Vitro Fermentation by Modulating Microbial Composition

Calcium Propionate Supplementation Mitigated Adverse Effects of Incubation Temperature Shift on In Vitro Fermentation by Modulating Microbial Composition

Identification of Candidate Genes for Min Pig Villi Hair Traits by Genome-Wide Association of Copy Number Variation

The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock

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