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11 pages, 2724 KiB

Open AccessArticle

Methylation Levels in the Promoter Region of FHIT and PIAS1 Genes Associated with Mastitis Resistance in Xinjiang Brown Cattle

by Liwei Zhong, Shengchao Ma, Dan Wang, Menghua Zhang, Yuezhen Tian, Junmin He, Xiaoxue Zhang, Lei Xu, Cuiling Wu, Mingming Dong, Murong Gou, Xixia Huang and Kechuan Tian

Genes 2023, 14(6), 1189; https://doi.org/10.3390/genes14061189 - 29 May 2023

Cited by 5 | Viewed by 1522

Abstract

Mastitis causes serious economic losses in the dairy industry, but there are no effective treatments or preventive measures. In this study, the ZRANB3, PIAS1, ACTR3, LPCAT2, MGAT5, and SLC37A2 genes in Xinjiang brown cattle, which are associated with [...] Read more.

Mastitis causes serious economic losses in the dairy industry, but there are no effective treatments or preventive measures. In this study, the ZRANB3, PIAS1, ACTR3, LPCAT2, MGAT5, and SLC37A2 genes in Xinjiang brown cattle, which are associated with mastitis resistance, were identified using a GWAS. Pyrosequencing analysis showed that the promoter methylation levels of the FHIT and PIAS1 genes in the mastitis group were higher and lower, respectively, than those in the healthy group (65.97 ± 19.82% and 58.00 ± 23.52%). However, the methylation level of the PIAS1 gene promoter region in the mastitis group was lower than that in the healthy group (11.48 ± 4.12% and 12.17 ± 4.25%). Meanwhile, the methylation levels of CpG3, CpG5, CpG8, and CpG15 in the promoter region of the FHIT and PIAS1 genes in the mastitis group were significantly higher than those in the healthy group (p < 0.01), respectively. RT-qPCR showed that the expression levels of the FHIT and PIAS1 genes were significantly higher in the healthy group than those in the mastitis group (p < 0.01). Correlation analysis showed that the promoter methylation level of the FHIT gene was negatively correlated with its expression. Hence, increased methylation in the promoter of the FHIT gene reduces the mastitis resistance in Xinjiang brown cattle. Finally, this study provides a reference for the molecular-marker-assisted selection of mastitis resistance in dairy cattle. Full article

(This article belongs to the Special Issue Genetics and Breeding of Cattle)

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16 pages, 3354 KiB

Open AccessArticle

Genetic and Genomic Analysis of Cow Mortality in the Israeli Holstein Population

by Joel Ira Weller, Ephraim Ezra, Eyal Seroussi and Moran Gershoni

Genes 2023, 14(3), 588; https://doi.org/10.3390/genes14030588 - 25 Feb 2023

Cited by 3 | Viewed by 3089

Abstract

“Livability” was defined as the inverse of the probability of death. The objectives of this study were to estimate the heritability, genetic and phenotypic trends for the livability of Israeli Holstein cows; estimate the genetic and environmental correlations between livability and the nine [...] Read more.

“Livability” was defined as the inverse of the probability of death. The objectives of this study were to estimate the heritability, genetic and phenotypic trends for the livability of Israeli Holstein cows; estimate the genetic and environmental correlations between livability and the nine traits included in the Israeli breeding index; estimate the effect of the inclusion of livability in the Israeli breeding index on expected genetic gains; and compute a genome-wide association study (GWAS) for livability. Seven data sets were analyzed. All data were derived from the database of the Israeli dairy cattle herd-book. The mean livability for the complete data set of 523,954 cows born from 2000 through 2016 was 89.6%. Pregnancy reduced livability by 15%. Livability generally increased with parity and days in milk within parity. Heritability of livability was 0.0082. Phenotypic and genetic trends over the 14-year period from 2000 through 2013 were −0.42% and −0.22% per year. If livability is included in the Israeli breeding index, accounting for 9% of the index, livability would increase by 1.3% and protein production would decrease by 11 kg over the next decade, as compared to the current index. A marker in proximity to the oxytocin–vasopressin locus had the greatest effect in the GWAS. Oxytocin activity in cattle affects calving-associated pathologies and maternal death. Inclusion of livability in the Israeli breeding index is not recommended. Full article

(This article belongs to the Special Issue Genetics and Breeding of Cattle)

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14 pages, 8347 KiB

Open AccessArticle

Candidate Genes and Gene Networks Change with Age in Japanese Black Cattle by Blood Transcriptome Analysis

by Chencheng Chang, Yanda Yang, Le Zhou, Batu Baiyin, Zaixia Liu, Lili Guo, Fengying Ma, Jie Wang, Yuan Chai, Caixia Shi and Wenguang Zhang

Genes 2023, 14(2), 504; https://doi.org/10.3390/genes14020504 - 16 Feb 2023

Cited by 3 | Viewed by 2015

Abstract

Age is an important physiological factor that affects the metabolism and immune function of beef cattle. While there have been many studies using the blood transcriptome to study the effects of age on gene expression, few have been reported on beef cattle. To [...] Read more.

Age is an important physiological factor that affects the metabolism and immune function of beef cattle. While there have been many studies using the blood transcriptome to study the effects of age on gene expression, few have been reported on beef cattle. To this end, we used the blood transcriptomes of Japanese black cattle at different ages as the study subjects and screened 1055, 345, and 1058 differential expressed genes (DEGs) in the calf vs. adult, adult vs. old, and calf vs. old comparison groups, respectively. The weighted co-expression network consisted of 1731 genes. Finally, blue, brown, and yellow age-specific modules were obtained, in which genes were enriched in signaling pathways related to growth and development and immune metabolic dysfunction, respectively. Protein-protein interaction (PPI) analysis showed gene interactions in each specific module, and 20 of the highest connectivity genes were chosen as potential hub genes. Finally, we identified 495, 244, and 1007 genes by exon-wide selection signature (EWSS) analysis of different comparison groups. Combining the results of hub genes, we found that VWF, PARVB, PRKCA, and TGFB1I1 could be used as candidate genes for growth and development stages of beef cattle. CORO2B and SDK1 could be used as candidate marker genes associated with aging. In conclusion, by comparing the blood transcriptome of calves, adult cattle, and old cattle, the candidate genes related to immunity and metabolism affected by age were identified, and the gene co-expression network of different age stages was constructed. It provides a data basis for exploring the growth, development, and aging of beef cattle. Full article

(This article belongs to the Special Issue Genetics and Breeding of Cattle)

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17 pages, 1591 KiB

Open AccessArticle

Fitting Genomic Prediction Models with Different Marker Effects among Prefectures to Carcass Traits in Japanese Black Cattle

by Shinichiro Ogawa, Yukio Taniguchi, Toshio Watanabe and Hiroaki Iwaisaki

Genes 2023, 14(1), 24; https://doi.org/10.3390/genes14010024 - 22 Dec 2022

Cited by 3 | Viewed by 1910

Abstract

We fitted statistical models, which assumed single-nucleotide polymorphism (SNP) marker effects differing across the fattened steers marketed into different prefectures, to the records for cold carcass weight (CW) and marbling score (MS) of 1036, 733, and 279 Japanese Black fattened steers marketed into [...] Read more.

We fitted statistical models, which assumed single-nucleotide polymorphism (SNP) marker effects differing across the fattened steers marketed into different prefectures, to the records for cold carcass weight (CW) and marbling score (MS) of 1036, 733, and 279 Japanese Black fattened steers marketed into Tottori, Hiroshima, and Hyogo prefectures in Japan, respectively. Genotype data on 33,059 SNPs was used. Five models that assume only common SNP effects to all the steers (model 1), common effects plus SNP effects differing between the steers marketed into Hyogo prefecture and others (model 2), only the SNP effects differing between Hyogo steers and others (model 3), common effects plus SNP effects specific to each prefecture (model 4), and only the effects specific to each prefecture (model 5) were exploited. For both traits, slightly lower values of residual variance than that of model 1 were estimated when fitting all other models. Estimated genetic correlation among the prefectures in models 2 and 4 ranged to 0.53 to 0.71, all <0.8. These results might support that the SNP effects differ among the prefectures to some degree, although we discussed the necessity of careful consideration to interpret the current results. Full article

(This article belongs to the Special Issue Genetics and Breeding of Cattle)

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13 pages, 1081 KiB

Open AccessArticle

Identification of Genetic Effects of ACADVL and IRF6 Genes with Milk Production Traits of Holstein Cattle in China

by Peng Peng, Yanan Liu, Weijie Zheng, Bo Han, Kun Wang and Dongxiao Sun

Genes 2022, 13(12), 2393; https://doi.org/10.3390/genes13122393 - 16 Dec 2022

Cited by 1 | Viewed by 3348

Abstract

With the development of high-throughput sequencing, RNA sequencing has been widely used in the identification of candidate genes for complex traits in livestock, and the functional genes and mutations with large genetic effects on milk production traits can provide molecular information for marker-assisted [...] Read more.

With the development of high-throughput sequencing, RNA sequencing has been widely used in the identification of candidate genes for complex traits in livestock, and the functional genes and mutations with large genetic effects on milk production traits can provide molecular information for marker-assisted selection to increase the selection accuracy and accelerate genetic gain in dairy cattle. Our previous study on the liver transcriptome of Holstein cows found that acyl-CoA dehydrogenase (ACADVL) and interferon regulatory factor 6 (IRF6) are differentially expressed between dry and peak lactation periods, as well as that they are involved in lipid metabolism and the proliferation and differentiation of mammary epithelial cells. Thus, the two genes were considered candidates for milk traits. Hence, this study further collected 1186 Holstein cows from 110 sire families to investigate their genetic associations with milk yield and composition traits. By resequencing the entire exons and 2000 bp of the 5′ and 3′ flanking regions of the two genes, we identified eight SNPs in ACADVL and eight SNPs in IRF6. Subsequent single-locus association analyses showed that the eight SNPs in ACADVL were all significantly associated with milk fat yield, fat percentage, and protein yield (p values ≤ 0.0001–0.0414), and the eight SNPs in IRF6 were associated with milk, fat, and protein yields in the first or second lactation (p values ≤ 0.0001–0.0467). Using Haploview 4.2, one haplotype block with eight of the SNPs in ACADVL (D’ = 0.99–1.00) and two haplotype blocks in IRF6 with three of the SNPs in each were observed (D’ = 0.98–1.00). Similarly, the haplotype combinations of ACADVL were significantly associated with milk yield, fat percentage, fat yield, and protein yield in the two lactations (p values ≤ 0.0001–0.0125), and those of IRF6 were associated with five milk traits (p values ≤ 0.0001–0.0263). Furthermore, with the JASPAR software, it was predicted that the SNPs 19:g.26933503T>C in ACADVL and 16:g.73501985G>A in IRF6 changed the transcription factor binding sites of ZEB1, PLAGL2, and RHOXF1, implying their impacts on the expressions of the corresponding genes. Our findings demonstrated that the ACADVL and IRF6 genes have significant genetic effects on milk yield and composition traits, and the valuable SNPs might be used as genetic markers for genomic selection programs in dairy cattle. Full article

(This article belongs to the Special Issue Genetics and Breeding of Cattle)

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17 pages, 1354 KiB

Open AccessArticle

Differential Allele-Specific Expression Revealed Functional Variants and Candidate Genes Related to Meat Quality Traits in B. indicus Muscle

by Jennifer Jessica Bruscadin, Tainã Figueiredo Cardoso, Wellison Jarles da Silva Diniz, Marcela Maria de Souza, Juliana Afonso, Dielson Vieira, Jessica Malheiros, Bruno Gabriel Nascimento Andrade, Juliana Petrini, José Bento Sterman Ferraz, Adhemar Zerlotini, Gerson Barreto Mourão, Luiz Lehmann Coutinho and Luciana Correia de Almeida Regitano

Genes 2022, 13(12), 2336; https://doi.org/10.3390/genes13122336 - 11 Dec 2022

Cited by 1 | Viewed by 2036

Abstract

Traditional transcriptomics approaches have been used to identify candidate genes affecting economically important livestock traits. Regulatory variants affecting these traits, however, remain under covered. Genomic regions showing allele-specific expression (ASE) are under the effect of cis-regulatory variants, being useful for improving the [...] Read more.

Traditional transcriptomics approaches have been used to identify candidate genes affecting economically important livestock traits. Regulatory variants affecting these traits, however, remain under covered. Genomic regions showing allele-specific expression (ASE) are under the effect of cis-regulatory variants, being useful for improving the accuracy of genomic selection models. Taking advantage of the better of these two methods, we investigated single nucleotide polymorphisms (SNPs) in regions showing differential ASE (DASE SNPs) between contrasting groups for beef quality traits. For these analyses, we used RNA sequencing data, imputed genotypes and genomic estimated breeding values of muscle-related traits from 190 Nelore (Bos indicus) steers. We selected 40 contrasting unrelated samples for the analysis (N = 20 animals per contrasting group) and used a beta-binomial model to identify ASE SNPs in only one group (i.e., DASE SNPs). We found 1479 DASE SNPs (FDR ≤ 0.05) associated with 55 beef-quality traits. Most DASE genes were involved with tenderness and muscle homeostasis, presenting a co-expression module enriched for the protein ubiquitination process. The results overlapped with epigenetics and phenotype-associated data, suggesting that DASE SNPs are potentially linked to cis-regulatory variants affecting simultaneously the transcription and phenotype through chromatin state modulation. Full article

(This article belongs to the Special Issue Genetics and Breeding of Cattle)

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14 pages, 3410 KiB

Open AccessArticle

Bta-miR-106b Regulates Bovine Mammary Epithelial Cell Proliferation, Cell Cycle, and Milk Protein Synthesis by Targeting the CDKN1A Gene

by Xin Wu, Jinfeng Huang, Yanan Liu, Houcheng Li, Bo Han and Dongxiao Sun

Genes 2022, 13(12), 2308; https://doi.org/10.3390/genes13122308 - 7 Dec 2022

Cited by 6 | Viewed by 2056

Abstract

Our previous studies found that bta-miR-106b and its corresponding target gene, CDKN1A, were differentially expressed between the mammary epithelium of lactating Holstein cows with extremely high and low milk protein and fat percentage, implying the potential role of bta-miR-106b in milk composition [...] Read more.

Our previous studies found that bta-miR-106b and its corresponding target gene, CDKN1A, were differentially expressed between the mammary epithelium of lactating Holstein cows with extremely high and low milk protein and fat percentage, implying the potential role of bta-miR-106b in milk composition synthesis. In this study, with luciferase assay experiment, bta-miR-106b was validated to target the 3′-untranslated region (UTR) of bovine CDKN1A, thereby regulating its expression. Moreover, in bovine mammary epithelial cells (BMECs), over-expression of bta-miR-106b significantly down-regulated the CDKN1A expression at both mRNA and protein levels, and inhibitors of bta-miR-106b increased CDKN1A expression. Of note, we observed that bta-miR-106b accelerated cell proliferation and cell cycle, and changed the expressions of protein synthesis related pathways such as JAK-STAT and PI3K/AKT/mTOR through regulating CDKN1A expression. Our findings highlight the important regulatory role of bta-miR-106b in milk protein synthesis by targeting CDKN1A in dairy cattle. Full article

(This article belongs to the Special Issue Genetics and Breeding of Cattle)

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18 pages, 4127 KiB

Open AccessArticle

A Comprehensive Sequencing Analysis of Testis-Born miRNAs in Immature and Mature Indigenous Wandong Cattle (Bos taurus)

by Hongyu Liu, Ibrar Muhammad Khan, Yong Liu, Nazir Muhammad Khan, Kaiyuan Ji, Huiqun Yin, Wenliang Wang, Xinqi Zhou and Yunhai Zhang

Genes 2022, 13(12), 2185; https://doi.org/10.3390/genes13122185 - 23 Nov 2022

Cited by 4 | Viewed by 2106

Abstract

Micro RNAs (miRNAs) have been recognized as important regulators that are indispensable for testicular development and spermatogenesis. miRNAs are endogenous transcriptomic elements and mainly regulate the gene expression at post-transcriptional levels; however, the key role of miRNA in bovine testicular growth is not [...] Read more.

Micro RNAs (miRNAs) have been recognized as important regulators that are indispensable for testicular development and spermatogenesis. miRNAs are endogenous transcriptomic elements and mainly regulate the gene expression at post-transcriptional levels; however, the key role of miRNA in bovine testicular growth is not clearly understood. Thus, supposing to unveil the transcriptomics expression changes in the developmental processes of bovine testes, we selected three immature calves and three sexually mature bulls of the local Wandong breed for testicular-tissue sample collection. The cDNA libraries of experimental animals were established for RNA-sequencing analysis. We detected the miRNA expression in testes by using high-throughput sequencing technology, and bioinformatics analysis followed. The differentially expressed (DE) data showed that 151 miRNAs linked genes were significantly DE between immature and mature bull testes. Further, in detail, 64 were significantly up-regulated and 87 were down-regulated in the immature vs. mature testes (p-value < 0.05). Pathway analyses for miRNA-linked genes were performed and identified JAG2, BCL6, CFAP157, PHC2, TYRO3, SEPTIN6, and BSP3; these genes were involved in biological pathways such as TNF signaling, T cell receptor, PI3KAkt signaling, and functions affecting testes development and spermatogenesis. The DE miRNAs including MIR425, MIR98, MIR34C, MIR184, MIR18A, MIR136, MIR15A, MIR1388 and MIR210 were associated with cattle-bull sexual maturation and sperm production. RT-qPCR validation analysis showed a consistent correlation to the sequencing data findings. The current study provides a good framework for understanding the mechanism of miRNAs in the development of testes and spermatogenesis. Full article

(This article belongs to the Special Issue Genetics and Breeding of Cattle)

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11 pages, 657 KiB

Open AccessEditor’s ChoiceArticle

Single Nucleotide Polymorphisms of ALDH18A1 and MAT2A Genes and Their Genetic Associations with Milk Production Traits of Chinese Holstein Cows

by Wen Ye, Lingna Xu, Yanhua Li, Lin Liu, Zhu Ma, Dongxiao Sun and Bo Han

Genes 2022, 13(8), 1437; https://doi.org/10.3390/genes13081437 - 12 Aug 2022

Cited by 4 | Viewed by 2260

Abstract

Our preliminary work had suggested two genes, aldehyde dehydrogenase 18 family member A1 (ALDH18A1) and methionine adenosyltransferase 2A (MAT2A), related to amino acid synthesis and metabolism as candidates affecting milk traits by analyzing the liver transcriptome and proteome of [...] Read more.

Our preliminary work had suggested two genes, aldehyde dehydrogenase 18 family member A1 (ALDH18A1) and methionine adenosyltransferase 2A (MAT2A), related to amino acid synthesis and metabolism as candidates affecting milk traits by analyzing the liver transcriptome and proteome of dairy cows at different lactation stages. In this study, the single nucleotide polymorphisms (SNPs) of ALDH18A1 and MAT2A genes were identified and their genetic effects and underlying causative mechanisms on milk production traits in dairy cattle were analyzed, with the aim of providing effective genetic information for the molecular breeding of dairy cows. By resequencing the entire coding and partial flanking regions of ALDH18A1 and MAT2A, we found eight SNPs located in ALDH18A1 and two in MAT2A. Single-SNP association analysis showed that most of the 10 SNPs of these two genes were significantly associated with the milk yield traits, 305-day milk yield, fat yield, and protein yield in the first and second lactations (corrected p ≤ 0.0488). Using Haploview 4.2, we found that the seven SNPs of ALDH18A1 formed two haplotype blocks; subsequently, the haplotype-based association analysis showed that both haplotypes were significantly associated with 305-day milk yield, fat yield, and protein yield (corrected p ≤ 0.014). Furthermore, by Jaspar and Genomatix software, we found that 26:g.17130318 C>A and 11:g.49472723G>C, respectively, in the 5′ flanking region of ALDH18A1 and MAT2A genes changed the transcription factor binding sites (TFBSs), which might regulate the expression of corresponding genes to affect the phenotypes of milk production traits. Therefore, these two SNPs were considered as potential functional mutations, but they also require further verification. In summary, ALDH18A1 and MAT2A were proved to probably have genetic effects on milk production traits, and their valuable SNPs might be used as candidate genetic markers for dairy cattle’s genomic selection (GS). Full article

(This article belongs to the Special Issue Genetics and Breeding of Cattle)

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11 pages, 2972 KiB

Open AccessArticle

Effects of SNPs in AANAT and ASMT Genes on Milk and Peripheral Blood Melatonin Concentrations in Holstein Cows (Bos taurus)

by Songyang Yao, Yunjie Liu, Xuening Liu and Guoshi Liu

Genes 2022, 13(7), 1196; https://doi.org/10.3390/genes13071196 - 4 Jul 2022

Cited by 6 | Viewed by 2092

Abstract

Aralkylamine N-acetyltransferase (AANAT) and acetylserotonin O-methyltransferase (ASMT), the two rate-limiting enzymes for melatonin synthesis, regulate melatonin production in mammals. Through analysis of the milk melatonin level and dairy herd improvement (DHI) index, it was found that the melatonin concentration in milk was significantly [...] Read more.

Aralkylamine N-acetyltransferase (AANAT) and acetylserotonin O-methyltransferase (ASMT), the two rate-limiting enzymes for melatonin synthesis, regulate melatonin production in mammals. Through analysis of the milk melatonin level and dairy herd improvement (DHI) index, it was found that the melatonin concentration in milk was significantly negatively correlated with the 305 day milk yield (305M) and peak milk yield (PeakM) (p < 0.05), while it was significantly positively correlated with the serum melatonin concentration (p < 0.05). The full-length of AANAT and ASMT were sequenced and genotyped in 122 cows. Three SNPs in AANAT and four SNPs in ASMT were significantly related to MT levels in the milk and serum (p < 0.05). The SNPs in AANAT were temporarily denoted as N-SNP1 (g.55290169 T>C), N-SNP2 (g.55289357 T>C), and N-SNP3 (g.55289409 C>T). The SNPs in ASMT were temporarily denoted as M-SNP1 (g.158407305 G>A), M-SNP2 (g.158407477 A>G), M-SNP3 (g.158407874 G>A), and M-SNP4 (g.158415342 T>C). The M-SNP1, M-SNP2, and M-SNP3 conformed to the Hardy−Weinberg equilibrium (p > 0.05), while other SNPs deviated from the Hardy−Weinberg equilibrium (p < 0.05). The potential association of MT production and each SNP was statistically analyzed using the method of linkage disequilibrium (LD). The results showed that N-SNP2 and N-SNP3 had some degree of LD (D′ = 0.27), but M-SNP1 and M-SNP2 had a strong LD (D′ = 0.98). Thus, the DHI index could serve as a prediction of the milk MT level. The SNPs in AANAT and ASMT could be used as potential molecular markers for screening cows to produce high melatonin milk. Full article

(This article belongs to the Special Issue Genetics and Breeding of Cattle)

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8 pages, 1360 KiB

Open AccessEditor’s ChoiceArticle

Initial Analysis of Structural Variation Detections in Cattle Using Long-Read Sequencing Methods

by Yahui Gao, Li Ma and George E. Liu

Genes 2022, 13(5), 828; https://doi.org/10.3390/genes13050828 - 6 May 2022

Cited by 5 | Viewed by 2907

Abstract

Structural variations (SVs), as a great source of genetic variation, are widely distributed in the genome. SVs involve longer genomic sequences and potentially have stronger effects than SNPs, but they are not well captured by short-read sequencing owing to their size and relevance [...] Read more.

Structural variations (SVs), as a great source of genetic variation, are widely distributed in the genome. SVs involve longer genomic sequences and potentially have stronger effects than SNPs, but they are not well captured by short-read sequencing owing to their size and relevance to repeats. Improved characterization of SVs can provide more advanced insight into complex traits. With the availability of long-read sequencing, it has become feasible to uncover the full range of SVs. Here, we sequenced one cattle individual using 10× Genomics (10 × G) linked read, Pacific Biosciences (PacBio) continuous long reads (CLR) and circular consensus sequencing (CCS), as well as Oxford Nanopore Technologies (ONT) PromethION. We evaluated the ability of various methods for SV detection. We identified 21,164 SVs, which amount to 186 Mb covering 7.07% of the whole genome. The number of SVs inferred from long-read-based inferences was greater than that from short reads. The PacBio CLR identified the most of large SVs and covered the most genomes. SVs called with PacBio CCS and ONT data showed high uniformity. The one with the most overlap with the results obtained by short-read data was PB CCS. Together, we found that long reads outperformed short reads in terms of SV detections. Full article

(This article belongs to the Special Issue Genetics and Breeding of Cattle)

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12 pages, 3507 KiB

Open AccessArticle

Identification of Alternative Splicing Events Associated with Paratuberculosis in Dairy Cattle Using Multi-Tissue RNA Sequencing Data

by Houcheng Li, Jinfeng Huang, Junnan Zhang, Yahui Gao, Bo Han and Dongxiao Sun

Genes 2022, 13(3), 497; https://doi.org/10.3390/genes13030497 - 11 Mar 2022

Cited by 7 | Viewed by 3162

Abstract

Paratuberculosis is a major endemic disease caused by Mycobacterium avium subspecies paratuberculosis (MAP) infection and leads to huge economic loss in the dairy sector worldwide. Alternative splicing (AS) events, playing indispensable regulatory roles in many protein functions and biological pathways, are shown to [...] Read more.

Paratuberculosis is a major endemic disease caused by Mycobacterium avium subspecies paratuberculosis (MAP) infection and leads to huge economic loss in the dairy sector worldwide. Alternative splicing (AS) events, playing indispensable regulatory roles in many protein functions and biological pathways, are shown to be associated with complex traits and diseases. In this study, by integrating the RNA sequencing (RNA-seq) data of 24 samples from three tissues (peripheral blood, jejunum and salivary gland) of Holstein cows, we obtained 2,706,541,696 uniquely mapped reads in total that represented 12,870 expressed genes, and detected 4285 differentially expressed genes (DEGs) between MAP-infected and healthy cows (p < 0.05). Of them, 92 differentially expressed splicing factors (DESFs) were included. Further, 119, 150 and 68 differential alternative splicing (DAS) events between MAP-infected and healthy cows were identified in peripheral blood, jejunum and salivary glands, respectively. Of note, six DAS events were highly and significantly correlated with the DESFs (R² > 0.9; p < 0.01), and their corresponding genes (COPI coat complex subunit gamma 2gene (COPG2), kinesin family member 2C gene (KIF2C), exocyst complex component 7 (EXOC7), Rab9 effector protein with kelch motifs gene (RABEPK), deoxyribonuclease 1 gene (DNASE1) and early endosome antigen 1gene (EEA1)) were significantly enriched in immune response such as vesicle-mediated transport, regulation of acute inflammatory response and tuberculosis through gene ontology (GO) and KEGG analysis. KS test showed that the DAS events in the EXOC7 and KIF2C genes indeed displayed differences between MAP-infected cows and healthy cows. The DAS in EXOC7 might produce a new protein sequence with lack of 23 amino acids, and the DAS in KIF2C induced a stop codon of premature occurrence and resulted in a lack of functional domain. In summary, this study identified the DAS events and corresponding genes related to MAP-infection base on the RNA-seq data from multiple tissues of Holstein cows, providing novel insights into the regulatory mechanisms underpinning paratuberculosis in dairy cattle. Full article

(This article belongs to the Special Issue Genetics and Breeding of Cattle)

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9 pages, 694 KiB

Open AccessArticle

Comparing BeadChip and WGS Genotyping: Non-Technical Failed Calling Is Attributable to Additional Variation within the Probe Target Sequence

by Moran Gershoni, Andrey Shirak, Rotem Raz and Eyal Seroussi

Genes 2022, 13(3), 485; https://doi.org/10.3390/genes13030485 - 9 Mar 2022

Cited by 7 | Viewed by 2744

Abstract

Microarray-based genomic selection is a central tool to increase the genetic gain of economically significant traits in dairy cattle. Yet, the effectivity of this tool is slightly limited, as estimates based on genotype data only partially explain the observed heritability. In the analysis [...] Read more.

Microarray-based genomic selection is a central tool to increase the genetic gain of economically significant traits in dairy cattle. Yet, the effectivity of this tool is slightly limited, as estimates based on genotype data only partially explain the observed heritability. In the analysis of the genomes of 17 Israeli Holstein bulls, we compared genotyping accuracy between whole-genome sequencing (WGS) and microarray-based techniques. Using the standard GATK pipeline, the short-variant discovery within sequence reads mapped to the reference genome (ARS-UCD1.2) was compared to the genotypes from Illumina BovineSNP50 BeadChip and to an alternative method, which computationally mimics the hybridization procedure by mapping reads to 50 bp spanning the BeadChip source sequences. The number of mismatches between the BeadChip and WGS genotypes was low (0.2%). However, 17,197 (40% of the informative SNPs) had extra variation within 50 bp of the targeted SNP site, which might interfere with hybridization-based genotyping. Consequently, with respect to genotyping errors, BeadChip varied significantly and systematically from WGS genotyping, introducing null allele-like effects and Mendelian errors (<0.5%), whereas the GATK algorithm of local de novo assembly of haplotypes successfully resolved the genotypes in the extra-variable regions. These findings suggest that the microarray design should avoid polymorphic genomic regions that are prone to extra variation and that WGS data may be used to resolve erroneous genotyping, which may partially explain missing heritability. Full article

(This article belongs to the Special Issue Genetics and Breeding of Cattle)

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13 pages, 316 KiB

Open AccessReview

Assessment of Genetic and Health Management of Tunisian Holstein Dairy Herds with a Focus on Longevity

by Chaima Sdiri, Ikram Ben Souf, Imen Ben Salem, Naceur M’Hamdi and Mohamed Ben Hamouda

Genes 2023, 14(3), 670; https://doi.org/10.3390/genes14030670 - 8 Mar 2023

Cited by 1 | Viewed by 1769

Abstract

In Tunisia, the recognition of the possibility of including longevity and disease resistance in dairy cattle selection objectives has been hypothesized as a useful strategy by both researchers and producers. However, in this paper, the state of the art, with a focus on [...] Read more.

In Tunisia, the recognition of the possibility of including longevity and disease resistance in dairy cattle selection objectives has been hypothesized as a useful strategy by both researchers and producers. However, in this paper, the state of the art, with a focus on health and longevity, is reviewed. Along the same lines, the heritability for the milk traits, fertility traits, and longevity of Tunisian Holstein dairy cows complies with the literature. Therefore, the influence of genetics on some diseases of the dairy cow was investigated. In addition, a decreasing efficiency in cow fertility has been observed over the last few years. The results showed that the risk of culling increased with common diseases. When analyzed with the Weibull model, functional lifespan was strongly influenced by milk yield; therefore, the risk increased with a reduced milk yield. In her first three lactations, the relative risk of selection increased gradually with lactation. Thus, the risk of thinning is highest at the beginning and end of the first feeding and the end of her second feeding. In conclusion, the risk of culling was reduced in parity. The factors that influence the life of the herd, such as health, husbandry, environmental conditions, and management, are often ignored when evaluating longevity. Full article

(This article belongs to the Special Issue Genetics and Breeding of Cattle)

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