cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17935725
title: Anexo II

description: Anexo II. Base de datos y cartografías de los sistemas históricos de regadío estudiados

Tesis doctoral: "Poblamiento y paisaje medieval en los cursos altos de los ríos Guadalbullón y Jandulilla (Sierra Mágina, Jaén)"
DOI: 10.5281/zenodo.17898146
title: Anexo II

description: Anexo II. Base de datos y cartografías de los sistemas históricos de regadío estudiados

Tesis doctoral: "Poblamiento y paisaje medieval en los cursos altos de los ríos Guadalbullón y Jandulilla (Sierra Mágina, Jaén)"
DOI: 10.6084/m9.figshare.27002757
title: Sequencing and characterization of complete mitogenome DNA of worldwide turkey (<i>Meleagris gallopavo</i>) populations

description: The history of turkey (<i>Meleagris gallopavo</i>) domestication can be traced back to the period between 700 and 200 BC in Mexico. This process involved multiple contributors and resulted in the development of modern local turkey breeds. This research investigates the complete mitochondrial diversity across a diverse range of local turkeys. Seventy-three turkeys were sampled from various populations, including autochthonous Italian breeds, an American breed (Narragansett), as well as wild turkeys from the USA and Mexico. The mitochondrial DNA (mtDNA) was employed as a powerful tool for biodiversity and breed phylogeny investigation. An analysis of the entire mtDNA was conducted to identify breed-specific unique traits, mitochondrial-specific characteristics, and the phylogenetic relationship among turkey populations. A total of 44 polymorphic sites were identified. Brianzolo and Narragansett birds were characterized as genetically homogeneous populations. Thirty-two different haplotypes were identified when our samples were compared with mtDNA D-loop of 96 online available turkeys from various geographical countries. H1 and H2, differing for one mutation, were the most abundant, comprising 132 of the 185 sequences. H1 included samples coming from every region, while H2 was predominantly characterized by Italian samples. USA and Mexican samples appear to be more variable in their mtDNA than the other populations.
DOI: 10.6084/m9.figshare.27002757.v1
title: Sequencing and characterization of complete mitogenome DNA of worldwide turkey (<i>Meleagris gallopavo</i>) populations

description: The history of turkey (<i>Meleagris gallopavo</i>) domestication can be traced back to the period between 700 and 200 BC in Mexico. This process involved multiple contributors and resulted in the development of modern local turkey breeds. This research investigates the complete mitochondrial diversity across a diverse range of local turkeys. Seventy-three turkeys were sampled from various populations, including autochthonous Italian breeds, an American breed (Narragansett), as well as wild turkeys from the USA and Mexico. The mitochondrial DNA (mtDNA) was employed as a powerful tool for biodiversity and breed phylogeny investigation. An analysis of the entire mtDNA was conducted to identify breed-specific unique traits, mitochondrial-specific characteristics, and the phylogenetic relationship among turkey populations. A total of 44 polymorphic sites were identified. Brianzolo and Narragansett birds were characterized as genetically homogeneous populations. Thirty-two different haplotypes were identified when our samples were compared with mtDNA D-loop of 96 online available turkeys from various geographical countries. H1 and H2, differing for one mutation, were the most abundant, comprising 132 of the 185 sequences. H1 included samples coming from every region, while H2 was predominantly characterized by Italian samples. USA and Mexican samples appear to be more variable in their mtDNA than the other populations.
DOI: 10.6084/m9.figshare.26300243
title: A meta-analysis approach for annotation and identification of lncRNAs controlling perirenal fat deposition in suckling lambs

description: Long non-coding RNAs (lncRNAs) are being studied in farm animals due to their association with traits of economic interest, such as fat deposition. Based on the analysis of perirenal fat transcriptomes, this research explored the relevance of these regulatory elements to fat deposition in suckling lambs. To that end, meta-analysis techniques have been implemented to efficiently characterize and detect differentially expressed transcripts from two different RNA-seq datasets, one including samples of two sheep breeds that differ in fat deposition features, Churra and Assaf (<i>n</i> = 14), and one generated from Assaf suckling lambs with different fat deposition levels (<i>n</i> = 8). The joint analysis of the 22 perirenal fat RNA-seq samples with the <i>FEELnc</i> software allowed the detection of 3953 novel lncRNAs. After the meta-analysis, 251 differentially expressed genes were identified, 21 of which were novel lncRNAs. Additionally, a co-expression analysis revealed that, in suckling lambs, lncRNAs may play a role in controlling angiogenesis and thermogenesis, processes highlighted in relation to high and low fat deposition levels, respectively. Overall, while providing information that could be applied for the improvement of suckling lamb carcass traits, this study offers insights into the biology of perirenal fat deposition regulation in mammals.
DOI: 10.6084/m9.figshare.26300243.v1
title: A meta-analysis approach for annotation and identification of lncRNAs controlling perirenal fat deposition in suckling lambs

description: Long non-coding RNAs (lncRNAs) are being studied in farm animals due to their association with traits of economic interest, such as fat deposition. Based on the analysis of perirenal fat transcriptomes, this research explored the relevance of these regulatory elements to fat deposition in suckling lambs. To that end, meta-analysis techniques have been implemented to efficiently characterize and detect differentially expressed transcripts from two different RNA-seq datasets, one including samples of two sheep breeds that differ in fat deposition features, Churra and Assaf (<i>n</i> = 14), and one generated from Assaf suckling lambs with different fat deposition levels (<i>n</i> = 8). The joint analysis of the 22 perirenal fat RNA-seq samples with the <i>FEELnc</i> software allowed the detection of 3953 novel lncRNAs. After the meta-analysis, 251 differentially expressed genes were identified, 21 of which were novel lncRNAs. Additionally, a co-expression analysis revealed that, in suckling lambs, lncRNAs may play a role in controlling angiogenesis and thermogenesis, processes highlighted in relation to high and low fat deposition levels, respectively. Overall, while providing information that could be applied for the improvement of suckling lamb carcass traits, this study offers insights into the biology of perirenal fat deposition regulation in mammals.
DOI: 10.6084/m9.figshare.28000843
title: Identification of genomic regions affecting nitrogen excretion intensity in Brown Swiss dairy cows

description: Dairy cows with a lower nitrogen excretion intensity (N<sub>exi</sub>) excrete less nitrogen, ammonia (NH<sub>3</sub>) and nitrous oxide (N<sub>2</sub>O), a highly potent greenhouse gas (GHG), per kg of milk produced and therefore represent a lower environmental impact while maintaining food security. To date, the genomics background of N<sub>exi</sub> is unknown. Here we performed a genetic association study, overlap analysis and functional enrichment analysis for N<sub>exi</sub> in 875 genotyped dairy cows with 2,147 lactations from 200 herds. We identified 1456 single nucleotide polymorphisms (SNPs) that significantly affect N<sub>exi</sub>. We found 140 SNPs overlapping with 148 protein-coding genes. The <i>MAN1A1</i> gene is a strong candidate gene for N<sub>exi</sub>. Genotype CC of rs42786248, the most significantly associated SNP located in the <i>MAN1A1</i> gene, had higher N<sub>exi</sub> than genotypes AA (<i>p</i> &lt; 0.001) and AC (<i>p</i> &lt; 0.001). We identified 33 genes involved in biological processes related to nitrogen metabolism. Our results form the basis for further research on the genomics background of N<sub>exi</sub>. The identified SNPs serve as potential targets for selective breeding programs, aimed at reducing N<sub>exi</sub> and associated NH<sub>3</sub> and N<sub>2</sub>O emissions in cattle production, thus contributing to more environmentally sustainable milk production.
DOI: 10.6084/m9.figshare.28000843.v1
title: Identification of genomic regions affecting nitrogen excretion intensity in Brown Swiss dairy cows

description: Dairy cows with a lower nitrogen excretion intensity (N<sub>exi</sub>) excrete less nitrogen, ammonia (NH<sub>3</sub>) and nitrous oxide (N<sub>2</sub>O), a highly potent greenhouse gas (GHG), per kg of milk produced and therefore represent a lower environmental impact while maintaining food security. To date, the genomics background of N<sub>exi</sub> is unknown. Here we performed a genetic association study, overlap analysis and functional enrichment analysis for N<sub>exi</sub> in 875 genotyped dairy cows with 2,147 lactations from 200 herds. We identified 1456 single nucleotide polymorphisms (SNPs) that significantly affect N<sub>exi</sub>. We found 140 SNPs overlapping with 148 protein-coding genes. The <i>MAN1A1</i> gene is a strong candidate gene for N<sub>exi</sub>. Genotype CC of rs42786248, the most significantly associated SNP located in the <i>MAN1A1</i> gene, had higher N<sub>exi</sub> than genotypes AA (<i>p</i> &lt; 0.001) and AC (<i>p</i> &lt; 0.001). We identified 33 genes involved in biological processes related to nitrogen metabolism. Our results form the basis for further research on the genomics background of N<sub>exi</sub>. The identified SNPs serve as potential targets for selective breeding programs, aimed at reducing N<sub>exi</sub> and associated NH<sub>3</sub> and N<sub>2</sub>O emissions in cattle production, thus contributing to more environmentally sustainable milk production.
DOI: 10.6084/m9.figshare.24171169
title: Whole-genome resequencing reveals new mutations in candidate genes for Beichuan-white goat prolificacya

description: In this study, we evaluated the copy number variation in the genomes of two groups of Beichuan-white goat populations with large differences in litter size by <i>F</i><sub>ST</sub> method, and identified 1739 genes and 485 missense mutations in the genes subject to positive selection. Through functional enrichment, <i>ITGAV, LRP4, CDH23, TPRN, RYR2</i> and <i>CELSR1</i> genes, involved in <i>embryonic morphogenesis</i>, were essential for litter size trait, which received intensive attention. In addition, some mutation sites of these genes have been proposed (<i>ITGAV</i>: c.38C &gt; T; <i>TPRN</i>: c.133A &gt; T, c.1192A &gt; G, c.1250A &gt; C; <i>CELSR1</i>: c.7640T &gt; C), whose allele frequencies were significantly changed in the high fecundity goat group. Besides, we found that new mutations at these sites altered the hydrophilicity and 3D structure of the protein. Candidate genes related to litter size in this study and their missense mutation sites were identified. These candidate genes are helpful to understand the genetic mechanism of fecundity in Beichuan white goat, and have important significance for future goat breeding.
DOI: 10.6084/m9.figshare.24171169.v1
title: Whole-genome resequencing reveals new mutations in candidate genes for Beichuan-white goat prolificacya

description: In this study, we evaluated the copy number variation in the genomes of two groups of Beichuan-white goat populations with large differences in litter size by <i>F</i><sub>ST</sub> method, and identified 1739 genes and 485 missense mutations in the genes subject to positive selection. Through functional enrichment, <i>ITGAV, LRP4, CDH23, TPRN, RYR2</i> and <i>CELSR1</i> genes, involved in <i>embryonic morphogenesis</i>, were essential for litter size trait, which received intensive attention. In addition, some mutation sites of these genes have been proposed (<i>ITGAV</i>: c.38C &gt; T; <i>TPRN</i>: c.133A &gt; T, c.1192A &gt; G, c.1250A &gt; C; <i>CELSR1</i>: c.7640T &gt; C), whose allele frequencies were significantly changed in the high fecundity goat group. Besides, we found that new mutations at these sites altered the hydrophilicity and 3D structure of the protein. Candidate genes related to litter size in this study and their missense mutation sites were identified. These candidate genes are helpful to understand the genetic mechanism of fecundity in Beichuan white goat, and have important significance for future goat breeding.
DOI: 10.6084/m9.figshare.24633813
title: Whole genome resequencing revealed genomic variants and functional pathways related to adaptation in Indian yak populations

description: The present study aims to identify genomic variants through a whole genome sequencing (WGS) approach and uncover biological pathways associated with adaptation and fitness in Indian yak populations. A total of 30 samples (10 from each population) were included from Arunachali, Himachali and Ladakhi yak populations. WGS analysis revealed a total of 32171644, 27260825, and 32632460 SNPs and 4865254, 4429941, and 4847513 Indels in the Arunachali, Himachali, and Ladakhi yaks, respectively. Genes such as <i>RYR2</i>, <i>SYNE2</i>, <i>BOLA</i>, <i>HF1</i>, and the novel transcript <i>ENSBGRG00000011079</i> were found to have the maximum number of high impact variants in all three yak populations, and might play a major role in local adaptation. Functional enrichment analysis of genes harboring high impact SNPs revealed overrepresented pathways related to response to stress, immune system regulation, and high-altitude adaptation. This study provides comprehensive information about genomic variants and their annotation in Indian yak populations, thus would serve as a data resource for researchers working on the yaks. Furthermore, it could be well exploited for better yak conservation strategies by estimating population genetics parameters <i>viz</i>., effective population size, inbreeding, and observed and expected heterozygosity.
DOI: 10.6084/m9.figshare.24633813.v1
title: Whole genome resequencing revealed genomic variants and functional pathways related to adaptation in Indian yak populations

description: The present study aims to identify genomic variants through a whole genome sequencing (WGS) approach and uncover biological pathways associated with adaptation and fitness in Indian yak populations. A total of 30 samples (10 from each population) were included from Arunachali, Himachali and Ladakhi yak populations. WGS analysis revealed a total of 32171644, 27260825, and 32632460 SNPs and 4865254, 4429941, and 4847513 Indels in the Arunachali, Himachali, and Ladakhi yaks, respectively. Genes such as <i>RYR2</i>, <i>SYNE2</i>, <i>BOLA</i>, <i>HF1</i>, and the novel transcript <i>ENSBGRG00000011079</i> were found to have the maximum number of high impact variants in all three yak populations, and might play a major role in local adaptation. Functional enrichment analysis of genes harboring high impact SNPs revealed overrepresented pathways related to response to stress, immune system regulation, and high-altitude adaptation. This study provides comprehensive information about genomic variants and their annotation in Indian yak populations, thus would serve as a data resource for researchers working on the yaks. Furthermore, it could be well exploited for better yak conservation strategies by estimating population genetics parameters <i>viz</i>., effective population size, inbreeding, and observed and expected heterozygosity.
DOI: 10.6084/m9.figshare.25336066
title: Weighted single step GWAS reveals genomic regions associated with economic traits in Murrah buffaloes

description: The objective of the present study was to identify genomic regions influencing economic traits in Murrah buffaloes using weighted single step Genome Wide Association Analysis (WssGWAS). Data on 2000 animals, out of which 120 were genotyped using a double digest Restriction site Associated DNA (ddRAD) sequencing approach. The phenotypic data were collected from NDRI, India, on growth traits, viz., body weight at 6M (month), 12M, 18M and 24M, production traits like 305D (day) milk yield, lactation length (LL) and dry period (DP) and reproduction traits like age at first calving (AFC), calving interval (CI) and first service period (FSP). The biallelic genotypic data consisted of 49353 markers post-quality check. The heritability estimates were moderate to high, low to moderate, low for growth, production, reproduction traits, respectively. Important genomic regions explaining more than 0.5% of the total additive genetic variance explained by 30 adjacent SNPs were selected for further analysis of candidate genes. In this study, 105 genomic regions were associated with growth, 35 genomic regions with production and 42 window regions with reproduction traits. Different candidate genes were identified in these genomic regions, of which important are OSBPL8, NAP1L1 for growth, CNTNAP2 for production and ILDR2, TADA1 and POGK for reproduction traits.
DOI: 10.6084/m9.figshare.25336066.v1
title: Weighted single step GWAS reveals genomic regions associated with economic traits in Murrah buffaloes

description: The objective of the present study was to identify genomic regions influencing economic traits in Murrah buffaloes using weighted single step Genome Wide Association Analysis (WssGWAS). Data on 2000 animals, out of which 120 were genotyped using a double digest Restriction site Associated DNA (ddRAD) sequencing approach. The phenotypic data were collected from NDRI, India, on growth traits, viz., body weight at 6M (month), 12M, 18M and 24M, production traits like 305D (day) milk yield, lactation length (LL) and dry period (DP) and reproduction traits like age at first calving (AFC), calving interval (CI) and first service period (FSP). The biallelic genotypic data consisted of 49353 markers post-quality check. The heritability estimates were moderate to high, low to moderate, low for growth, production, reproduction traits, respectively. Important genomic regions explaining more than 0.5% of the total additive genetic variance explained by 30 adjacent SNPs were selected for further analysis of candidate genes. In this study, 105 genomic regions were associated with growth, 35 genomic regions with production and 42 window regions with reproduction traits. Different candidate genes were identified in these genomic regions, of which important are OSBPL8, NAP1L1 for growth, CNTNAP2 for production and ILDR2, TADA1 and POGK for reproduction traits.
DOI: 10.6084/m9.figshare.24198314
title: Deciphering the miRNA transcriptome of granulosa cells from dominant and subordinate follicles at first follicular wave in goat

description: In goats, most follicles in the ovaries will be atresia and only a few dominant follicles (DFs) may eventually mature and ovulate at a follicular wave. To investigate the potential microRNAs (miRNAs) that regulate the expression of genes associated with follicular dominance or atresia, small RNA sequencing was performed on granulosa cells of DF and subordinate follicle at the first follicular wave in goats. A total of 108 differentially expressed miRNAs were detected in the two types of follicle granulosa cells: 16 upregulated miRNAs and 92 downregulated miRNAs. Kyoto Encyclopedia of Genes and Genomes analysis of the target genes showed that <i>TKTL1</i>, <i>LOC102187810</i>, <i>LOC102184409</i> and <i>ALDOA</i> are closely associated with follicle dominance and are involved in the pentose phosphate pathway. Furthermore, a coexpression network of miRNAs and follicular dominance-related genes was constructed. The qPCR results well correlated with the small RNA sequencing data. Our findings provide new insight for exploring the molecular mechanism of miRNAs in regulating follicular development in goats.
DOI: 10.6084/m9.figshare.24198314.v1
title: Deciphering the miRNA transcriptome of granulosa cells from dominant and subordinate follicles at first follicular wave in goat

description: In goats, most follicles in the ovaries will be atresia and only a few dominant follicles (DFs) may eventually mature and ovulate at a follicular wave. To investigate the potential microRNAs (miRNAs) that regulate the expression of genes associated with follicular dominance or atresia, small RNA sequencing was performed on granulosa cells of DF and subordinate follicle at the first follicular wave in goats. A total of 108 differentially expressed miRNAs were detected in the two types of follicle granulosa cells: 16 upregulated miRNAs and 92 downregulated miRNAs. Kyoto Encyclopedia of Genes and Genomes analysis of the target genes showed that <i>TKTL1</i>, <i>LOC102187810</i>, <i>LOC102184409</i> and <i>ALDOA</i> are closely associated with follicle dominance and are involved in the pentose phosphate pathway. Furthermore, a coexpression network of miRNAs and follicular dominance-related genes was constructed. The qPCR results well correlated with the small RNA sequencing data. Our findings provide new insight for exploring the molecular mechanism of miRNAs in regulating follicular development in goats.
DOI: 10.6084/m9.figshare.24968733
title: Effects of selenium-enriched yeast dietary supplementation on egg quality, gut morphology and caecal microflora of laying hens

description: Selenium (Se) is an essential micronutrient for humans and animals and is a powerful antioxidant that can promote reproductive and immune functions. The purpose of this study was to evaluate the effects of supplemental dietary selenium-enriched yeast (SeY) on egg quality, gut morphology and microflora in laying hens. In total, 100 HY-Line Brown laying hens (45-week old) were randomly allocated to two groups with 10 replicates and fed either a basal diet (without Se supplementation) or a basal diet containing 0.2 mg/kg Se in the form of SeY for 8 weeks. The Se supplementation did not have a significant effect on egg quality and intestinal morphology of laying hens. Based on the 16S rRNA sequencing, SeY dietary supplementation effectively modulated the cecal microbiota structure. An alpha diversity analysis demonstrated that birds fed 100 mg/kg SeY had a higher cecal bacterial diversity. SeY dietary addition elevated <i>Erysipelotrichia</i> (class), <i>Lachnospiraceae</i> (family), <i>Erysipelotrichaceae</i> (family) and <i>Ruminococcus_torques_group</i> (genus; <i>p</i> &lt; .05). Analysis of microbial community-level phenotypes revealed that SeY supplementation decreased the microorganism abundance of facultatively anaerobic and potentially pathogenic phenotypes. Overall, SeY supplementation cannot significantly improve intestinal morphology; however, it modulated the composition of cecal microbiota toward a healthier gut.