cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21215314.v1
title: <i>Neospora caninum</i> seroprevalence in water buffaloes in Guangxi, China

description: <i>Neospora caninum</i> is an important obligate intracellular apicomplexan parasite that causes spontaneous abortions in cattle and leads to huge economic losses to the farming industry. Although a high prevalence of <i>N. caninum</i> infection has been reported in Asia, data on the prevalence of water buffaloes in China remain unclear. To understand the seroprevalence of <i>N. caninum</i> infection in water buffaloes and its definitive host dogs in China, a total of 987 water buffalo sera from Guangxi Province were tested using an indirect enzyme-linked immunosorbent assay. We obtained an overall seroprevalence of 50.9% (502/987) for water buffalo samples. And the positive rate was higher in border cities (56.8%, 425/748) than in central cities (32.3%, 77/239). We further tested 240 serum samples from dogs in Guangxi and found an overall prevalence of 57.9% (139/240). The high prevalence of <i>N. caninum</i> infection in both dogs and water buffaloes was first reported in southern China, and these data will surely contribute to the prevention and control of the disease.
DOI: 10.6084/m9.figshare.21383586
title: Comparative transcriptome and proteome analyses of the longissimus dorsi muscle for explaining the difference between donkey meat and other meats

description: Domestic donkeys (<i>Equus asinus</i>) have been maintained mainly for service purposes in the past. Nowadays, there is an increasing interest in donkey milk and meat production in several countries, including China. Donkey meat is highly consumed because of its nutritional value and unique flavor. However, genomic studies on donkey meat are limited. Therefore, in this study, we aimed to examine the molecular difference of longissimus dorsi muscles of donkey, cow, and goat. RNA sequencing and Proteome sequencing technology were used to analyze the transcriptome and proteome of the longissimus dorsi muscle of donkey, cow, and goat. A total of 1338 and 1780 differentially expressed genes (DEGs) were identified in donkey meat compared with that in cow and goat meat, respectively. Most of the DEGs were involved in biological processes, including small GTPase-mediated signal transduction, protein ubiquitination, protein glycosylation, and MAP kinase tyrosine/serine/threonine phosphatase activity. Additionally, 764 and 1024 differentially expressed proteins (DEPs) were identified in cow vs. donkey, and goat vs. donkey, respectively; these DEPs were mainly involved in metabolism. Genetic variation and regulatory factors can combine as a database to provide more valuable molecular information for further analysis.
DOI: 10.6084/m9.figshare.21383586.v1
title: Comparative transcriptome and proteome analyses of the longissimus dorsi muscle for explaining the difference between donkey meat and other meats

description: Domestic donkeys (<i>Equus asinus</i>) have been maintained mainly for service purposes in the past. Nowadays, there is an increasing interest in donkey milk and meat production in several countries, including China. Donkey meat is highly consumed because of its nutritional value and unique flavor. However, genomic studies on donkey meat are limited. Therefore, in this study, we aimed to examine the molecular difference of longissimus dorsi muscles of donkey, cow, and goat. RNA sequencing and Proteome sequencing technology were used to analyze the transcriptome and proteome of the longissimus dorsi muscle of donkey, cow, and goat. A total of 1338 and 1780 differentially expressed genes (DEGs) were identified in donkey meat compared with that in cow and goat meat, respectively. Most of the DEGs were involved in biological processes, including small GTPase-mediated signal transduction, protein ubiquitination, protein glycosylation, and MAP kinase tyrosine/serine/threonine phosphatase activity. Additionally, 764 and 1024 differentially expressed proteins (DEPs) were identified in cow vs. donkey, and goat vs. donkey, respectively; these DEPs were mainly involved in metabolism. Genetic variation and regulatory factors can combine as a database to provide more valuable molecular information for further analysis.
DOI: 10.6084/m9.figshare.21395371
title: Mitogenome-wide association study on body measurement traits of Wenshang Barred chickens

description: Mitochondria are best known for synthesizing ATP through the tricarboxylic acid cycle and oxidative phosphorylation. The cytoplasmic mitochondrial DNA (mtDNA) is important for maintaining the function. This study was designed to reveal the effect of mtDNA on chicken body measurement traits (BMTs). A population of 605 Wenshang Barred chickens were recorded BMTs, including body slope length, keel length, chest width, etc. The single-nucleotide polymorphisms (SNPs) of their mitogenomes were detected by PCR amplification and DNA sequencing. Totally 69 mutations in mitogenome were discovered, including 18 in noncoding region and 51 in coding region. By multi-sequence alignment and haplotype construction, the chickens were clustered into eight haplotypes and further three haplogroups. The association between BMTs and mtDNA SNPs, haplotypes and haplogroups were analyzed in the linear model by ASReml, respectively. Among them, the SNP mt11086 T/C in ND3 was found to significantly affect chest dept (<i>p</i> &lt; .05) and was highly conservative by phylogenetic conservation analyses, which reflected the genetic effect on body size and growth of chickens. No significant association between the mitochondrial haplotypes or haplogroups and BMTs was found. The polymorphic site reflecting body size could be put into chicken breeding programs as the genetic marker.
DOI: 10.6084/m9.figshare.21395371.v1
title: Mitogenome-wide association study on body measurement traits of Wenshang Barred chickens

description: Mitochondria are best known for synthesizing ATP through the tricarboxylic acid cycle and oxidative phosphorylation. The cytoplasmic mitochondrial DNA (mtDNA) is important for maintaining the function. This study was designed to reveal the effect of mtDNA on chicken body measurement traits (BMTs). A population of 605 Wenshang Barred chickens were recorded BMTs, including body slope length, keel length, chest width, etc. The single-nucleotide polymorphisms (SNPs) of their mitogenomes were detected by PCR amplification and DNA sequencing. Totally 69 mutations in mitogenome were discovered, including 18 in noncoding region and 51 in coding region. By multi-sequence alignment and haplotype construction, the chickens were clustered into eight haplotypes and further three haplogroups. The association between BMTs and mtDNA SNPs, haplotypes and haplogroups were analyzed in the linear model by ASReml, respectively. Among them, the SNP mt11086 T/C in ND3 was found to significantly affect chest dept (<i>p</i> &lt; .05) and was highly conservative by phylogenetic conservation analyses, which reflected the genetic effect on body size and growth of chickens. No significant association between the mitochondrial haplotypes or haplogroups and BMTs was found. The polymorphic site reflecting body size could be put into chicken breeding programs as the genetic marker.
DOI: 10.6084/m9.figshare.20483626
title: Identification and analysis of circRNAs in the prefrontal cortices of wild boar and domestic pig

description: Domestication caused significant differences in morphology and behavior between wild and domestic pigs. However, the regulatory role of circRNA in this event is unclear. Here, we analyzed circRNA expression patterns in the prefrontal cortices of wild boar and domestic pigs to determine the potential role of circRNAs in domestication. We identified a total of 11,375 circRNAs and found that 349 and 354 circRNAs were up-regulated in wild boar and Rongchang pig, respectively. Functional enrichment analysis showed that host genes of significantly highly-expressed circRNAs in wild boar were significantly enriched in neural synapse-related categories and the categories of ‘regulation of defense response (<i>p</i> = 0.028)’ and ‘neural retina development (<i>p</i> = 4.32 × 10<sup>−3</sup>)’. Host genes of significantly highly-expressed circRNAs in Rongchang pig were specifically involved in ‘chordate embryonic development (<i>p</i> = 2.38 × 10<sup>−4</sup>)’. Additionally, we constructed circRNA-miRNA-mRNA regulatory axes in wild boar and Rongchang pig and found more regulatory axes in wild boar that potentially regulate synaptic activities. We identified multiple circRNAs that may be related to domesticated characteristics, such as ssc_circ_6179 (ssc_circ_6179—ssc-miR-9847—<i>HRH3</i>, related to aggression) and ssc_circ_3027 (ssc_circ_3027—ssc-miR-4334-5p—<i>HCRTR1</i>, related to attention). This study provides a resource for further investigation of the molecular basis of pig domestication.
DOI: 10.6084/m9.figshare.20483626.v1
title: Identification and analysis of circRNAs in the prefrontal cortices of wild boar and domestic pig

description: Domestication caused significant differences in morphology and behavior between wild and domestic pigs. However, the regulatory role of circRNA in this event is unclear. Here, we analyzed circRNA expression patterns in the prefrontal cortices of wild boar and domestic pigs to determine the potential role of circRNAs in domestication. We identified a total of 11,375 circRNAs and found that 349 and 354 circRNAs were up-regulated in wild boar and Rongchang pig, respectively. Functional enrichment analysis showed that host genes of significantly highly-expressed circRNAs in wild boar were significantly enriched in neural synapse-related categories and the categories of ‘regulation of defense response (<i>p</i> = 0.028)’ and ‘neural retina development (<i>p</i> = 4.32 × 10<sup>−3</sup>)’. Host genes of significantly highly-expressed circRNAs in Rongchang pig were specifically involved in ‘chordate embryonic development (<i>p</i> = 2.38 × 10<sup>−4</sup>)’. Additionally, we constructed circRNA-miRNA-mRNA regulatory axes in wild boar and Rongchang pig and found more regulatory axes in wild boar that potentially regulate synaptic activities. We identified multiple circRNAs that may be related to domesticated characteristics, such as ssc_circ_6179 (ssc_circ_6179—ssc-miR-9847—<i>HRH3</i>, related to aggression) and ssc_circ_3027 (ssc_circ_3027—ssc-miR-4334-5p—<i>HCRTR1</i>, related to attention). This study provides a resource for further investigation of the molecular basis of pig domestication.
DOI: 10.6084/m9.figshare.19658940
title: Morphometric characteristics and microsatellite markers based diversity and differentiation recognizes the first prospective cattle breed from the Jharkhand state of India

description: India is bestowed with immense cattle biodiversity with 50 registered breeds. However, the majority (59.3%) is yet not characterized. Identification and characterization are the gateways to the management of prized indigenous resources. Present research described a unique cattle population of Jharkhand state, managed under a traditional low-input, low-output system. It was characterized by morphological traits, performance parameters, and management practices. Animals have the characteristic pre-scapular location of the hump. Genetic variation within this population and its differentiation with the six closely distributed cattle breeds were evaluated using FAO recommended microsatellite markers. Jharkhandi cattle have substantial genetic variation based on gene diversity (&gt;0.6) and the average number of alleles per locus (&gt;8). The population did not suffer from a genetic bottleneck in the recent past. Pairwise Nei’s genetic distance, phylogenetic relationship, population differentiation, and the correct assignment of all the animals to self group substantiated its separate genetic identity. Since gene flow (Nm = 2.8–7.32) was identified and admixture was indicated by the Bayesian analysis there is a pressing need for scientific management of this population. Results endow authorities with critical information for registering a new Indian cattle breed (Medini) that contributes to the food security, livelihood, and economic sustainability of rural tribal households.
DOI: 10.6084/m9.figshare.19658940.v1
title: Morphometric characteristics and microsatellite markers based diversity and differentiation recognizes the first prospective cattle breed from the Jharkhand state of India

description: India is bestowed with immense cattle biodiversity with 50 registered breeds. However, the majority (59.3%) is yet not characterized. Identification and characterization are the gateways to the management of prized indigenous resources. Present research described a unique cattle population of Jharkhand state, managed under a traditional low-input, low-output system. It was characterized by morphological traits, performance parameters, and management practices. Animals have the characteristic pre-scapular location of the hump. Genetic variation within this population and its differentiation with the six closely distributed cattle breeds were evaluated using FAO recommended microsatellite markers. Jharkhandi cattle have substantial genetic variation based on gene diversity (&gt;0.6) and the average number of alleles per locus (&gt;8). The population did not suffer from a genetic bottleneck in the recent past. Pairwise Nei’s genetic distance, phylogenetic relationship, population differentiation, and the correct assignment of all the animals to self group substantiated its separate genetic identity. Since gene flow (Nm = 2.8–7.32) was identified and admixture was indicated by the Bayesian analysis there is a pressing need for scientific management of this population. Results endow authorities with critical information for registering a new Indian cattle breed (Medini) that contributes to the food security, livelihood, and economic sustainability of rural tribal households.
DOI: 10.6084/m9.figshare.20412309
title: Salivary cell-free <i>HSD17B1</i> and <i>HSPA1A</i> transcripts as potential biomarkers for estrus identification in buffaloes (<i>Bubalus bubalis</i>)

description: Estrus detection is a major problem in buffaloes because of the poor expression of estrus signs leading to low reproductive efficiency. Salivary transcripts analysis is a promising tool to identify biomarkers; therefore, the present study was carried out to evaluate their potential as estrus biomarkers. The levels of <i>HSD17B1</i>, <i>INHBA</i>, <i>HSPA1A</i>, <i>TES</i> transcripts were compared in saliva during estrous cycle stages [early proestrus (day −2, EP), late proestrus (day-1, LP), estrus (E), metestrus (ME) and diestrus (DE)] of cyclic heifers (<i>n</i> = 8) and pluriparous (<i>n</i> = 8) buffaloes by employing quantitative real-time polymerase chain reaction (qRT-PCR). The levels of <i>HSD17B1</i> (EP/DE 1.46–2.43 fold, LP/DE 2.49–3.06 fold; E/DE 7.21–11.9-fold <i>p</i> &lt; 0.01; ME/D 1.0–1.16 fold) and <i>HSPA1A</i> (EP/DE 0.93–2.39 fold, LP/DE 2.68–3.23 fold; E/DE 8.52–15.18 fold <i>p</i> &lt; 0.01; ME/D 0.86–1.01 fold) were significantly altered during the estrus than other estrous cycle stages in both cyclic heifers and pluriparous buffaloes. Receiver operating characteristic curve analysis revealed the ability of salivary <i>HSD17B1</i> (AUC 0.96; <i>p</i> &lt; 0.001) and <i>HSPA1A</i> (AUC 0.99; <i>p</i> &lt; 0.01) to differentiate E from other stages of the estrous cycle. Significantly higher levels of <i>HSD17B1</i> and <i>HSPA1A</i> transcripts in saliva during the estrus phase suggest their biomarkers potential for estrus detection in buffaloes.
DOI: 10.6084/m9.figshare.20412309.v1
title: Salivary cell-free <i>HSD17B1</i> and <i>HSPA1A</i> transcripts as potential biomarkers for estrus identification in buffaloes (<i>Bubalus bubalis</i>)

description: Estrus detection is a major problem in buffaloes because of the poor expression of estrus signs leading to low reproductive efficiency. Salivary transcripts analysis is a promising tool to identify biomarkers; therefore, the present study was carried out to evaluate their potential as estrus biomarkers. The levels of <i>HSD17B1</i>, <i>INHBA</i>, <i>HSPA1A</i>, <i>TES</i> transcripts were compared in saliva during estrous cycle stages [early proestrus (day −2, EP), late proestrus (day-1, LP), estrus (E), metestrus (ME) and diestrus (DE)] of cyclic heifers (<i>n</i> = 8) and pluriparous (<i>n</i> = 8) buffaloes by employing quantitative real-time polymerase chain reaction (qRT-PCR). The levels of <i>HSD17B1</i> (EP/DE 1.46–2.43 fold, LP/DE 2.49–3.06 fold; E/DE 7.21–11.9-fold <i>p</i> &lt; 0.01; ME/D 1.0–1.16 fold) and <i>HSPA1A</i> (EP/DE 0.93–2.39 fold, LP/DE 2.68–3.23 fold; E/DE 8.52–15.18 fold <i>p</i> &lt; 0.01; ME/D 0.86–1.01 fold) were significantly altered during the estrus than other estrous cycle stages in both cyclic heifers and pluriparous buffaloes. Receiver operating characteristic curve analysis revealed the ability of salivary <i>HSD17B1</i> (AUC 0.96; <i>p</i> &lt; 0.001) and <i>HSPA1A</i> (AUC 0.99; <i>p</i> &lt; 0.01) to differentiate E from other stages of the estrous cycle. Significantly higher levels of <i>HSD17B1</i> and <i>HSPA1A</i> transcripts in saliva during the estrus phase suggest their biomarkers potential for estrus detection in buffaloes.
DOI: 10.6084/m9.figshare.20134174
title: Identification of Dezhou donkey muscle development-related genes and long non-coding RNA based on differential expression analysis

description: Long non-coding RNAs (lncRNAs) play a critical role in the development of muscles. However, the role of lncRNAs in regulating skeletal muscle development has not been studied systematically in the donkey. In this study, we performed the RNA sequencing for different stages of muscles in donkeys, and investigate their expression profile, which showed that 3215 mRNAs (<i>p</i>-adjust &lt;0.05) and 471 lncRNAs (<i>p</i>-value &lt;0.05) were significantly differently expressed (DE) verified by RT-qPCR. GO and KEGG enrichment analysis indicated that DE genes and target genes of DE lncRNAs were associated with muscle development in the donkey. We also found these four target genes (<i>DCN</i>, <i>ITM2A</i>, <i>MUSTN1</i>, <i>ARRDC2</i>) involved in skeletal muscle growth and development. Combined with transcriptome data, network, and RT-qPCR results showed that four co-expression networks of <i>DCN</i> and lnc-008278, <i>ITM2A</i> and lnc_017247, <i>MUSTN1</i> and lnc_030153, and <i>ARRDC2</i> and lnc_033914, which may play an important role in the formation and development of muscle in the donkey.
DOI: 10.6084/m9.figshare.20134174.v1
title: Identification of Dezhou donkey muscle development-related genes and long non-coding RNA based on differential expression analysis

description: Long non-coding RNAs (lncRNAs) play a critical role in the development of muscles. However, the role of lncRNAs in regulating skeletal muscle development has not been studied systematically in the donkey. In this study, we performed the RNA sequencing for different stages of muscles in donkeys, and investigate their expression profile, which showed that 3215 mRNAs (<i>p</i>-adjust &lt;0.05) and 471 lncRNAs (<i>p</i>-value &lt;0.05) were significantly differently expressed (DE) verified by RT-qPCR. GO and KEGG enrichment analysis indicated that DE genes and target genes of DE lncRNAs were associated with muscle development in the donkey. We also found these four target genes (<i>DCN</i>, <i>ITM2A</i>, <i>MUSTN1</i>, <i>ARRDC2</i>) involved in skeletal muscle growth and development. Combined with transcriptome data, network, and RT-qPCR results showed that four co-expression networks of <i>DCN</i> and lnc-008278, <i>ITM2A</i> and lnc_017247, <i>MUSTN1</i> and lnc_030153, and <i>ARRDC2</i> and lnc_033914, which may play an important role in the formation and development of muscle in the donkey.
DOI: 10.6084/m9.figshare.20182409
title: Selection of a stable reference gene for relative copy number profiling of porcine chromosomal genes using SYBR green qPCR

description: Reference gene with stable copy number is essential for normalization in qPCR based copy number assay. Present study aims to identify a suitable reference gene in pigs for qPCR based relative copy number profiling of chromosomal genes. A total of 30 crossbred pigs of both sexes were cyto-screened and gDNA was extracted from the pigs having numerically normal karyotypes. The copy number stability was studied for 7 genes (FSHB, IL4, IGF1R, TCF24, BRMS1L, ARMC1 and SRSF4) selected on the basis of the chromosomal location, reports of single copy and lack of involvement in structural chromosomal abnormalities. The copy number was estimated from <i>Ct</i> values in 3 technical replicates using 6 animals from either sex for each gene. The stability was evaluated from the variations in Ct values using different (Delta Ct, geNorm, BestKeeper and normFinder) algorithms. While the moderate variation was observed among relative copy number stabilities among the genes, comprehensive ranking revealed the most stable gene for normalization (IGF1R &gt; FSHB &gt; TCF24 &gt; IL4 &gt; ARMC1&gt; SRSF4 &gt; BRMS1L) across the samples. The selected reference gene was validated using DNA of cyto-screened pigs to find out ratio of X and Y chromosome fragments using qPCR based copy number analysis.
DOI: 10.6084/m9.figshare.20182409.v1
title: Selection of a stable reference gene for relative copy number profiling of porcine chromosomal genes using SYBR green qPCR

description: Reference gene with stable copy number is essential for normalization in qPCR based copy number assay. Present study aims to identify a suitable reference gene in pigs for qPCR based relative copy number profiling of chromosomal genes. A total of 30 crossbred pigs of both sexes were cyto-screened and gDNA was extracted from the pigs having numerically normal karyotypes. The copy number stability was studied for 7 genes (FSHB, IL4, IGF1R, TCF24, BRMS1L, ARMC1 and SRSF4) selected on the basis of the chromosomal location, reports of single copy and lack of involvement in structural chromosomal abnormalities. The copy number was estimated from <i>Ct</i> values in 3 technical replicates using 6 animals from either sex for each gene. The stability was evaluated from the variations in Ct values using different (Delta Ct, geNorm, BestKeeper and normFinder) algorithms. While the moderate variation was observed among relative copy number stabilities among the genes, comprehensive ranking revealed the most stable gene for normalization (IGF1R &gt; FSHB &gt; TCF24 &gt; IL4 &gt; ARMC1&gt; SRSF4 &gt; BRMS1L) across the samples. The selected reference gene was validated using DNA of cyto-screened pigs to find out ratio of X and Y chromosome fragments using qPCR based copy number analysis.