cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23773597
title: Uncovering genes underlying coat color variation in indigenous cattle breeds through genome-wide positive selection

description: The identification of candidate genes related to pigmentation and under selective sweep provides insights into the genetic basis of pigmentation and the evolutionary forces that have shaped this variation. The selective sweep events in the genes responsible for normal coat color in Indian cattle groups are still unknown. To find coat color genes displaying signs of selective sweeps in the indigenous cattle, we compiled a list of candidate genes previously investigated for their association with coat color and pigmentation. After that, we performed a genome-wide scan of positive selection signatures using the BovineSNP50K Bead Chip in 187 individuals of seven indigenous breeds. We applied a wide range of methods to find evidence of selection, such as Tajima’s D, CLR, iHS, varLD, ROH, and F<sub>ST.</sub> We found a total of sixteen genes under selective sweep, that were involved in coat color and pigmentation physiology. These genes are <i>CRIM1</i> in Gir, <i>MC1R</i> in Sahiwal, <i>MYO5A, PMEL</i> and <i>POMC</i> in Tharparkar, <i>TYRP1, ERBB2,</i> and <i>ASIP</i> in Red Sindhi, <i>MITF, LOC789175, PAX3</i> and <i>TYR</i> in Ongole, and <i>IRF2, SDR165</i> and, <i>KIT</i> in Nelore, <i>ADAMTS19</i> in Hariana. These genes are related to melanin synthesis, the biology of melanocytes and melanosomes, and the migration and survival of melanocytes during development.
DOI: 10.6084/m9.figshare.23773597.v1
title: Uncovering genes underlying coat color variation in indigenous cattle breeds through genome-wide positive selection

description: The identification of candidate genes related to pigmentation and under selective sweep provides insights into the genetic basis of pigmentation and the evolutionary forces that have shaped this variation. The selective sweep events in the genes responsible for normal coat color in Indian cattle groups are still unknown. To find coat color genes displaying signs of selective sweeps in the indigenous cattle, we compiled a list of candidate genes previously investigated for their association with coat color and pigmentation. After that, we performed a genome-wide scan of positive selection signatures using the BovineSNP50K Bead Chip in 187 individuals of seven indigenous breeds. We applied a wide range of methods to find evidence of selection, such as Tajima’s D, CLR, iHS, varLD, ROH, and F<sub>ST.</sub> We found a total of sixteen genes under selective sweep, that were involved in coat color and pigmentation physiology. These genes are <i>CRIM1</i> in Gir, <i>MC1R</i> in Sahiwal, <i>MYO5A, PMEL</i> and <i>POMC</i> in Tharparkar, <i>TYRP1, ERBB2,</i> and <i>ASIP</i> in Red Sindhi, <i>MITF, LOC789175, PAX3</i> and <i>TYR</i> in Ongole, and <i>IRF2, SDR165</i> and, <i>KIT</i> in Nelore, <i>ADAMTS19</i> in Hariana. These genes are related to melanin synthesis, the biology of melanocytes and melanosomes, and the migration and survival of melanocytes during development.
DOI: 10.6084/m9.figshare.23599007
title: Detection of genome-wide copy number variation in Murrah buffaloes

description: Riverine Buffaloes, especially the Murrah breed because of their adaptability to harsh climatic conditions, is farmed in many countries to convert low-quality feed into valuable dairy products and meat. Here, we investigated the copy number variations (CNVs) in 296 Murrah buffalo using the Axiom<sup>®</sup> Buffalo Genotyping Array 90K (Affymetrix, Santa Clara, CA, USA). The CNVs were detected on the autosomes, using the Copy Number Analysis Module (CNAM) using the univariate analysis. 7937 CNVs were detected in 279 Buffaloes, the average length of the CNVs was 119,048.87 bp that ranged between 7800 and 4,561,030 bp. These CNVs were accounting for 10.33% of the buffalo genome, which was comparable to cattle, sheep, and goat CNV analyses. Further, CNVs were merged and 1541 CNVRs were detected using the Bedtools-mergeBed command. 485 genes were annotated within 196 CNVRs that were identified in at least 10 animals of Murrah population. Out of these, 40 CNVRs contained 59 different genes that were associated with 69 different traits. Overall, the study identified a significant number of CNVs and CNVRs in the Murrah breed of buffalo, with a wide range of lengths and frequencies across the autosomes. The identified CNVRs contained genes associated with important traits related to production and reproduction, making them potentially important targets for future breeding and genetic improvement efforts.
DOI: 10.6084/m9.figshare.23599007.v1
title: Detection of genome-wide copy number variation in Murrah buffaloes

description: Riverine Buffaloes, especially the Murrah breed because of their adaptability to harsh climatic conditions, is farmed in many countries to convert low-quality feed into valuable dairy products and meat. Here, we investigated the copy number variations (CNVs) in 296 Murrah buffalo using the Axiom<sup>®</sup> Buffalo Genotyping Array 90K (Affymetrix, Santa Clara, CA, USA). The CNVs were detected on the autosomes, using the Copy Number Analysis Module (CNAM) using the univariate analysis. 7937 CNVs were detected in 279 Buffaloes, the average length of the CNVs was 119,048.87 bp that ranged between 7800 and 4,561,030 bp. These CNVs were accounting for 10.33% of the buffalo genome, which was comparable to cattle, sheep, and goat CNV analyses. Further, CNVs were merged and 1541 CNVRs were detected using the Bedtools-mergeBed command. 485 genes were annotated within 196 CNVRs that were identified in at least 10 animals of Murrah population. Out of these, 40 CNVRs contained 59 different genes that were associated with 69 different traits. Overall, the study identified a significant number of CNVs and CNVRs in the Murrah breed of buffalo, with a wide range of lengths and frequencies across the autosomes. The identified CNVRs contained genes associated with important traits related to production and reproduction, making them potentially important targets for future breeding and genetic improvement efforts.
DOI: 10.6084/m9.figshare.21571885
title: Signatures of selection in riverine buffalo populations revealed by genome-wide SNP data

description: The detection of selection signatures assists in understanding domestication, evolution, and the identification of genomic regions related to adaptation and production traits in buffaloes. The emergence of high-throughput technologies like Next Generation Sequencing and SNP genotyping had expanded our ability to detect these signatures of selection. In this study, we sought to identify signatures of selection in five buffalo populations (Brazilian Murrah, Bulgarian Murrah, Indian Murrah, Nili-Ravi, and Kundi) using Axiom Buffalo 90 K Genotyping Array data. Using seven different methodologies (Tajima’s D, CLR, ROH, iHS, F<sub>ST</sub>, FLK and hapFLK), we identified selection signatures in 374 genomic regions, spanning a total of 381 genes and 350 quantitative trait loci (QTLs). Among these, several candidate genes were associated with QTLs for milk production, reproduction, growth and carcass traits. The genes and QTLs reported in this study provide insight into selection signals shaping the genome of buffalo breeds. Our findings can aid in further genomic association studies, genomic prediction, and the implementation of breeding programmes in Indian buffaloes.
DOI: 10.6084/m9.figshare.21571885.v1
title: Signatures of selection in riverine buffalo populations revealed by genome-wide SNP data

description: The detection of selection signatures assists in understanding domestication, evolution, and the identification of genomic regions related to adaptation and production traits in buffaloes. The emergence of high-throughput technologies like Next Generation Sequencing and SNP genotyping had expanded our ability to detect these signatures of selection. In this study, we sought to identify signatures of selection in five buffalo populations (Brazilian Murrah, Bulgarian Murrah, Indian Murrah, Nili-Ravi, and Kundi) using Axiom Buffalo 90 K Genotyping Array data. Using seven different methodologies (Tajima’s D, CLR, ROH, iHS, F<sub>ST</sub>, FLK and hapFLK), we identified selection signatures in 374 genomic regions, spanning a total of 381 genes and 350 quantitative trait loci (QTLs). Among these, several candidate genes were associated with QTLs for milk production, reproduction, growth and carcass traits. The genes and QTLs reported in this study provide insight into selection signals shaping the genome of buffalo breeds. Our findings can aid in further genomic association studies, genomic prediction, and the implementation of breeding programmes in Indian buffaloes.
DOI: 10.6084/m9.figshare.23987688
title: Transcriptomic analysis of yak <i>longissimus dorsi</i> muscle identifies genes associated with tenderness

description: Meat tenderness is an important sensory index when consumers choose meat products, which determines the value of meat products and consumers’ buying intentions. Yak meat is rich in nutrition and unique in flavor, which is favored by consumers. However, its meat has the deficiencies of low tenderness and poor taste, which has a negative impact on the value of its meat products and customer satisfaction. To identify the genes affecting the yak meat tenderness, we used RNA-seq to analyze the <i>longissimus dorsi</i> muscle of yaks with different tenderness, screened a total of 1120 differentially expressed genes (DEGs). Meanwhile, 23 pathways were significantly enriched. By further analysis, we identified eight genes related to yak meat tenderness (<i>WNT5A</i>, <i>ARID5B</i>, <i>SERPINE1 KLHL40</i>, <i>RUNX1</i>, <i>MAFF</i>, <i>RFX7</i> and <i>ARID5A</i>). Notably, <i>SERPINE1</i> was involved in the significant enrichment pathways of ‘complement and coagulation cascade pathway’, ‘HIF-1 signaling pathway’ and ‘AGE-RAGE signaling pathway in diabetic complications’ which can regulate meat tenderness. This implies that <i>SERPINE1</i> may play an important regulatory role among them. The DEGs associated with yak meat quality screened in this work will be helpful to identify potential biomarkers related to meat tenderness.
DOI: 10.6084/m9.figshare.23987688.v1
title: Transcriptomic analysis of yak <i>longissimus dorsi</i> muscle identifies genes associated with tenderness

description: Meat tenderness is an important sensory index when consumers choose meat products, which determines the value of meat products and consumers’ buying intentions. Yak meat is rich in nutrition and unique in flavor, which is favored by consumers. However, its meat has the deficiencies of low tenderness and poor taste, which has a negative impact on the value of its meat products and customer satisfaction. To identify the genes affecting the yak meat tenderness, we used RNA-seq to analyze the <i>longissimus dorsi</i> muscle of yaks with different tenderness, screened a total of 1120 differentially expressed genes (DEGs). Meanwhile, 23 pathways were significantly enriched. By further analysis, we identified eight genes related to yak meat tenderness (<i>WNT5A</i>, <i>ARID5B</i>, <i>SERPINE1 KLHL40</i>, <i>RUNX1</i>, <i>MAFF</i>, <i>RFX7</i> and <i>ARID5A</i>). Notably, <i>SERPINE1</i> was involved in the significant enrichment pathways of ‘complement and coagulation cascade pathway’, ‘HIF-1 signaling pathway’ and ‘AGE-RAGE signaling pathway in diabetic complications’ which can regulate meat tenderness. This implies that <i>SERPINE1</i> may play an important regulatory role among them. The DEGs associated with yak meat quality screened in this work will be helpful to identify potential biomarkers related to meat tenderness.
DOI: 10.6084/m9.figshare.24305293
title: The variation in the beta-casein genotypes and its effect on milk yield and genomic values in Holstein-Friesian cows

description: The A2 milk marker is gaining popularity worldwide; thus, many farms plan to convert their dairy cattle herds to the A2A2 genotype. Variation in beta-casein genotypes needs to be monitored in large dairy cattle populations. Therefore we aimed to evaluate the genotypic distributions, population genetics, and diversity parameters in Holstein-Friesian cows. A total of 1200 cattle were genotyped using the Affymetrix<sup>®</sup> Axiom<sup>®</sup> array system. We performed an association analysis regarding the <i>CSN2</i> genotypes and phenotypic traits, including lactation and test-day milk yield. We next evaluated the effects of the genotypes considering the genetic merit of the animals. Animals were grouped based on their PTAs for milk production, fat, protein, and daughter pregnancy rate. Thus, we tested the genotype × genetic merit interaction for significance. The A2 allele frequency is remarkably high (0.68), and the heterozygous genotype is predominant (46.25%). The marker showed intermediate variability and diversity levels, indicating a considerable frequency of the A1A1 genotype (9.33%) remains in the population. ANOVA results showed no significant association between the <i>CSN2</i> genotypes and milk yield traits. A similar finding is valid for the genotype × genetic merit regarding the genomic test results. The data presented here may be helpful for further investigations and applications on A2 milk production.
DOI: 10.6084/m9.figshare.24305293.v1
title: The variation in the beta-casein genotypes and its effect on milk yield and genomic values in Holstein-Friesian cows

description: The A2 milk marker is gaining popularity worldwide; thus, many farms plan to convert their dairy cattle herds to the A2A2 genotype. Variation in beta-casein genotypes needs to be monitored in large dairy cattle populations. Therefore we aimed to evaluate the genotypic distributions, population genetics, and diversity parameters in Holstein-Friesian cows. A total of 1200 cattle were genotyped using the Affymetrix<sup>®</sup> Axiom<sup>®</sup> array system. We performed an association analysis regarding the <i>CSN2</i> genotypes and phenotypic traits, including lactation and test-day milk yield. We next evaluated the effects of the genotypes considering the genetic merit of the animals. Animals were grouped based on their PTAs for milk production, fat, protein, and daughter pregnancy rate. Thus, we tested the genotype × genetic merit interaction for significance. The A2 allele frequency is remarkably high (0.68), and the heterozygous genotype is predominant (46.25%). The marker showed intermediate variability and diversity levels, indicating a considerable frequency of the A1A1 genotype (9.33%) remains in the population. ANOVA results showed no significant association between the <i>CSN2</i> genotypes and milk yield traits. A similar finding is valid for the genotype × genetic merit regarding the genomic test results. The data presented here may be helpful for further investigations and applications on A2 milk production.
DOI: 10.6084/m9.figshare.21648596
title: A novel deleterious oxytocin variant is associated with the lower twinning ratio in Awassi ewes

description: This study aimed to assess the possible association of oxytocin (<i>OXT</i>) gene with reproductive traits in two groups of Awassi ewes that differ in their reproductive potentials. Sheep were genotyped using PCR—single-stranded conformation polymorphism approach. Three genotypes were detected in exon 2, CC, CA, and AA, and a novel SNP was identified with a missense effect on oxytocin (c.188C &gt; A → p.Arg55Leu). A significant (<i>p</i> &lt; 0.01) association of p.Arg55Leu with the twinning rate was found as ewes with AA and CA genotypes exhibited, respectively a lower twinning ratio than those with the wild-type CC genotype. The deleterious impact of p.Arg55Leu was demonstrated by all <i>in silico</i> tools that were utilized to assess the effect of this variant on the structure, function, and stability of oxytocin. Molecular docking showed that p.Arg55Leu caused a dramatic alteration in the binding of oxytocin with its receptor and reduced the number of interacted amino acids between them. Our study suggests that ewes with AA and CA genotypes showed a lower reproductive performance due to the presence of p.Arg55Leu, which caused damaging impacts on oxytocin and is binding with the OXT receptor. The utilization of the p.Arg55Leu could be useful for improving Awassi reproductive potential.
DOI: 10.6084/m9.figshare.21648596.v1
title: A novel deleterious oxytocin variant is associated with the lower twinning ratio in Awassi ewes

description: This study aimed to assess the possible association of oxytocin (<i>OXT</i>) gene with reproductive traits in two groups of Awassi ewes that differ in their reproductive potentials. Sheep were genotyped using PCR—single-stranded conformation polymorphism approach. Three genotypes were detected in exon 2, CC, CA, and AA, and a novel SNP was identified with a missense effect on oxytocin (c.188C &gt; A → p.Arg55Leu). A significant (<i>p</i> &lt; 0.01) association of p.Arg55Leu with the twinning rate was found as ewes with AA and CA genotypes exhibited, respectively a lower twinning ratio than those with the wild-type CC genotype. The deleterious impact of p.Arg55Leu was demonstrated by all <i>in silico</i> tools that were utilized to assess the effect of this variant on the structure, function, and stability of oxytocin. Molecular docking showed that p.Arg55Leu caused a dramatic alteration in the binding of oxytocin with its receptor and reduced the number of interacted amino acids between them. Our study suggests that ewes with AA and CA genotypes showed a lower reproductive performance due to the presence of p.Arg55Leu, which caused damaging impacts on oxytocin and is binding with the OXT receptor. The utilization of the p.Arg55Leu could be useful for improving Awassi reproductive potential.
DOI: 10.6084/m9.figshare.21804163
title: Comparative genomic diversity analysis of copy number variations (CNV) in indicine and taurine cattle thriving in Europe and Indian subcontinent

description: Copy number variations (CNVs) include deletions, duplications, and insertions that are larger than 50 bp in size causing structural variation responsible for diversity, adaptation, and breed development. Indian cattle breeds are highly diverse from the taurine breeds. The pattern of CNVRs in 191 animals belonging to 39 cattle breeds (four Indicine and 35 Taurine) was studied based on Illumina 777K BovineHD chip data. The Indicine breeds revealed 2590 CNVs and 335 copy number variation regions (CNVRs) in autosomes. Out of the identified CNVs, 50 were found to be novel. Structure analysis revealed admixed nature of Siri. Neighbor joining tree from CNVR data showed that hot (Kankrej and Hallikar) and cold (Ladakhi and Siri) adapted cattle breeds clustered separately. CNVR of Indian and European breeds revealed that Balkan and Italian breeds of Podolian group are admixed with Indian cattle breeds corroborating indicine introgression (6.1–13.5%). CNVRs spanning the regions of olfactory receptors and immune system genes were identified. AMOVA revealed 9% variation among populations which is 2% greater than SNP based studies showing higher inclusion of variation by CNVR. Detailed analysis of CNVs/CNVRs in Indian cattle adapted to hot and cold climate, and their diversity among worldwide cattle is presented in this study.
DOI: 10.6084/m9.figshare.21804163.v2
title: Comparative genomic diversity analysis of copy number variations (CNV) in indicine and taurine cattle thriving in Europe and Indian subcontinent

description: Copy number variations (CNVs) include deletions, duplications, and insertions that are larger than 50 bp in size causing structural variation responsible for diversity, adaptation, and breed development. Indian cattle breeds are highly diverse from the taurine breeds. The pattern of CNVRs in 191 animals belonging to 39 cattle breeds (four Indicine and 35 Taurine) was studied based on Illumina 777K BovineHD chip data. The Indicine breeds revealed 2590 CNVs and 335 copy number variation regions (CNVRs) in autosomes. Out of the identified CNVs, 50 were found to be novel. Structure analysis revealed admixed nature of Siri. Neighbor joining tree from CNVR data showed that hot (Kankrej and Hallikar) and cold (Ladakhi and Siri) adapted cattle breeds clustered separately. CNVR of Indian and European breeds revealed that Balkan and Italian breeds of Podolian group are admixed with Indian cattle breeds corroborating indicine introgression (6.1–13.5%). CNVRs spanning the regions of olfactory receptors and immune system genes were identified. AMOVA revealed 9% variation among populations which is 2% greater than SNP based studies showing higher inclusion of variation by CNVR. Detailed analysis of CNVs/CNVRs in Indian cattle adapted to hot and cold climate, and their diversity among worldwide cattle is presented in this study.
DOI: 10.6084/m9.figshare.21804163.v1
title: Comparative genomic diversity analysis of copy number variations (CNV) in indicine and taurine cattle thriving in Europe and Indian subcontinent

description: Copy number variations (CNVs) include deletions, duplications, and insertions that are larger than 50 bp in size causing structural variation responsible for diversity, adaptation, and breed development. Indian cattle breeds are highly diverse from the taurine breeds. The pattern of CNVRs in 191 animals belonging to 39 cattle breeds (four Indicine and 35 Taurine) was studied based on Illumina 777K BovineHD chip data. The Indicine breeds revealed 2590 CNVs and 335 copy number variation regions (CNVRs) in autosomes. Out of the identified CNVs, 50 were found to be novel. Structure analysis revealed admixed nature of Siri. Neighbor joining tree from CNVR data showed that hot (Kankrej and Hallikar) and cold (Ladakhi and Siri) adapted cattle breeds clustered separately. CNVR of Indian and European breeds revealed that Balkan and Italian breeds of Podolian group are admixed with Indian cattle breeds corroborating indicine introgression (6.1–13.5%). CNVRs spanning the regions of olfactory receptors and immune system genes were identified. AMOVA revealed 9% variation among populations which is 2% greater than SNP based studies showing higher inclusion of variation by CNVR. Detailed analysis of CNVs/CNVRs in Indian cattle adapted to hot and cold climate, and their diversity among worldwide cattle is presented in this study.
DOI: 10.6084/m9.figshare.23654402
title: Two novel SNPs identified in <i>STAT1</i> gene adjoining a QTL for milk production in Holstein Friesian crossbreds of Kerala

description: We analyzed the effect of a single nucleotide polymorphism, g. C3141T in the 3′ UTR of Signal transducer and activator of transcription-1 gene (<i>STAT1</i>) on milk production traits in the Holstein Friesian crossbred cattle of Kerala (n = 144) by association analysis and expression study. The population was genotyped by restriction fragment length polymorphism using <i>Pag</i>1. Association study using the General Linear Model-Analysis of Variance revealed that none of the yield or composition traits analyzed were significantly differed. The expression profile of <i>STAT1</i> gene in leucocytes of animals bearing homozygous genotypes was compared by quantitative real time PCR using SYBR green chemistry with and relative expression was not found to be significantly differed. The second stage of the study, the <i>STAT1</i> mRNA spanning 3213 bp was amplified from leucocytes and sequenced (GenBank: MT459802.1). Two novel SNPs were identified; one synonymous mutation in the coding region (g.A1212G) and the other in the 3'UTR (g.T3042C). The novel SNPs might contribute to <i>STAT1</i> gene regulation mediated by alternate spicing or binding sites for regulatory molecules. The results reiterate the importance of extensive studies of <i>STAT1</i> gene variants to substantiate the presence of a quantitative trait loci for dairy traits in the vicinity of <i>STAT1</i> gene.