Pub Date : 2024-11-01Epub Date: 2024-03-18DOI: 10.1080/10495398.2024.2329106
Mervan Bayraktar
This study analysed the genetic diversity and population structure of eight sheep breeds in Turkey and nearby countries. Moderate genetic diversity was observed, with the Sakiz (SKZ) exhibiting the highest diversity based on heterozygosity and allelic richness (AR) values. Genetic distances revealed differentiation between the populations, with the most significant divergence between the Cyprus Fat Tail (CFT) and SKZ breeds. PCA demonstrated SKZ and Chios (CHI) clustering together, indicating genetic similarity. Karakas (KRS), Norduz (NDZ), Afshari (AFS), Moghani (MOG) and others showed overlap, reflecting genetic relationships. Ancestry analysis found that KRS was predominantly inherited from the second ancestral population, while SKZ and NDZ were primarily derived from the first and second ancestral lineages. This illustrated the populations' diverse origins. Most genetic variation (96.84%) was within, not between, populations. The phi-statistic (PhiPT) indicated moderate differentiation overall. Phylogenetic analysis further demonstrated the genetic distinctiveness of the SKZ breed. ROH and FROH analyses showed that SKZ exhibited the highest homozygosity and inbreeding, while KRS displayed the lowest. This study elucidates these breeds' genetic diversity, structure and relationships. Key findings include moderate diversity, evidence of differentiation between breeds, diverse ancestral origins and distinct ROH patterns. This provides insights into the population's genetic characteristics and conservation requirements.
{"title":"Analysing the genetic diversity of three sheep breeds in Turkey and nearby countries using 50 K SNPs data.","authors":"Mervan Bayraktar","doi":"10.1080/10495398.2024.2329106","DOIUrl":"10.1080/10495398.2024.2329106","url":null,"abstract":"<p><p>This study analysed the genetic diversity and population structure of eight sheep breeds in Turkey and nearby countries. Moderate genetic diversity was observed, with the Sakiz (SKZ) exhibiting the highest diversity based on heterozygosity and allelic richness (AR) values. Genetic distances revealed differentiation between the populations, with the most significant divergence between the Cyprus Fat Tail (CFT) and SKZ breeds. PCA demonstrated SKZ and Chios (CHI) clustering together, indicating genetic similarity. Karakas (KRS), Norduz (NDZ), Afshari (AFS), Moghani (MOG) and others showed overlap, reflecting genetic relationships. Ancestry analysis found that KRS was predominantly inherited from the second ancestral population, while SKZ and NDZ were primarily derived from the first and second ancestral lineages. This illustrated the populations' diverse origins. Most genetic variation (96.84%) was within, not between, populations. The phi-statistic (PhiPT) indicated moderate differentiation overall. Phylogenetic analysis further demonstrated the genetic distinctiveness of the SKZ breed. ROH and FROH analyses showed that SKZ exhibited the highest homozygosity and inbreeding, while KRS displayed the lowest. This study elucidates these breeds' genetic diversity, structure and relationships. Key findings include moderate diversity, evidence of differentiation between breeds, diverse ancestral origins and distinct ROH patterns. This provides insights into the population's genetic characteristics and conservation requirements.</p>","PeriodicalId":7836,"journal":{"name":"Animal Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140142599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-01Epub Date: 2024-02-05DOI: 10.1080/10495398.2024.2309956
Long Yang, Xiaoding Lin, Yuhan Chen, Peiya Peng, Qun Lan, Heng Zhao, Hongjiang Wei, Yulong Yin, Mei Liu
SNX29 is a potential functional gene associated with meat production traits. Previous studies have shown that SNX29 copy number variation (CNV) could be implicated with phenotype in goats. However, in Diannan small-ear (DSE) pigs, the genetic impact of SNX29 CNV on growth traits remains unclear. Therefore, this study investigated the associations between SNX29 CNVs (CNV10810 and CNV10811) and growth traits in 415 DSE pigs. The results revealed that the CNV10810 mutation was significantly associated with backfat thickness in DSE pigs at 12 and 15 months old (P < 0.05), while the CNV10811 mutation had significant effects on various growth traits at 6 and 12 months old, particularly for body weight, body height, back height and backfat thickness (P < 0.05 or P < 0.001). In conclusion, our results confirm that SNX29 CNV plays a role in regulating growth and development in pigs, thus suggesting its potential application for pig breeding programmes.
SNX29 是一个与肉类生产性状相关的潜在功能基因。先前的研究表明,SNX29拷贝数变异(CNV)可能与山羊的表型有关。然而,在滇南小耳猪(DSE)中,SNX29 CNV 对生长性状的遗传影响仍不清楚。因此,本研究调查了415头DSE猪的SNX29 CNV(CNV10810和CNV10811)与生长性状之间的关联。结果表明,CNV10810 突变与 12 月龄和 15 月龄 DSE 猪的背膘厚显著相关(P P P SNX29 CNV 在猪的生长发育过程中起调控作用,因此有望应用于猪育种计划。
{"title":"Association analysis of the sorting nexin 29 (SNX29) gene copy number variations with growth traits in Diannan small-ear (DSE) pigs.","authors":"Long Yang, Xiaoding Lin, Yuhan Chen, Peiya Peng, Qun Lan, Heng Zhao, Hongjiang Wei, Yulong Yin, Mei Liu","doi":"10.1080/10495398.2024.2309956","DOIUrl":"10.1080/10495398.2024.2309956","url":null,"abstract":"<p><p><i>SNX29</i> is a potential functional gene associated with meat production traits. Previous studies have shown that <i>SNX29</i> copy number variation (CNV) could be implicated with phenotype in goats. However, in Diannan small-ear (DSE) pigs, the genetic impact of <i>SNX29</i> CNV on growth traits remains unclear. Therefore, this study investigated the associations between <i>SNX29</i> CNVs (CNV10810 and CNV10811) and growth traits in 415 DSE pigs. The results revealed that the CNV10810 mutation was significantly associated with backfat thickness in DSE pigs at 12 and 15 months old (<i>P</i> < 0.05), while the CNV10811 mutation had significant effects on various growth traits at 6 and 12 months old, particularly for body weight, body height, back height and backfat thickness (<i>P</i> < 0.05 or <i>P</i> < 0.001). In conclusion, our results confirm that <i>SNX29</i> CNV plays a role in regulating growth and development in pigs, thus suggesting its potential application for pig breeding programmes.</p>","PeriodicalId":7836,"journal":{"name":"Animal Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139690976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-01Epub Date: 2024-03-01DOI: 10.1080/10495398.2024.2314104
Hanfang Cai, Xin Li, Xinran Niu, Jing Li, Xianyong Lan, Chuzhao Lei, Yongzhen Huang, Huifen Xu, Ming Li, Hong Chen
Previous researches revealed a copy number variation (CNV) region in the bovine fibroblast growth factor 13 (FGF13) gene. However, its effects remain unknown. This study detected the various copy number types in seven Chinese cattle breeds and analysed their population genetic characteristics and effects on growth traits and transcription levels. Copy number Loss was more frequent in Caoyuan Red cattle and Xianan cattle than in the other breeds. Association analysis between CNV and growth traits of Qinchuan indicated that the CNV was significantly related to chest depth, hip width and hucklebone width (P < 0.05). Additionally, the growth traits of individuals with copy number Loss were significantly inferior to those with copy number Gain or Median (P < 0.05). Besides, we found two splicing isoforms, AS1 and AS2, in FGF13 gene, which resulted from alternative 5' splicing sites of intron 1. These isoforms showed varied expression levels in various tissues. Moreover, CNV was significantly and negatively associated with the mRNA expression of AS1 (r = -0.525, P < 0.05). The CNVs in bovine FGF13 gene negatively regulated growth traits and gene transcription. These observations provide new insights into bovine FGF13 gene, delivering potentially useful information for future Chinese cattle breeding programs.
{"title":"Copy number variations within fibroblast growth factor 13 gene influence growth traits and alternative splicing in cattle.","authors":"Hanfang Cai, Xin Li, Xinran Niu, Jing Li, Xianyong Lan, Chuzhao Lei, Yongzhen Huang, Huifen Xu, Ming Li, Hong Chen","doi":"10.1080/10495398.2024.2314104","DOIUrl":"10.1080/10495398.2024.2314104","url":null,"abstract":"<p><p>Previous researches revealed a copy number variation (CNV) region in the bovine fibroblast growth factor 13 (<i>FGF13</i>) gene. However, its effects remain unknown. This study detected the various copy number types in seven Chinese cattle breeds and analysed their population genetic characteristics and effects on growth traits and transcription levels. Copy number Loss was more frequent in Caoyuan Red cattle and Xianan cattle than in the other breeds. Association analysis between CNV and growth traits of Qinchuan indicated that the CNV was significantly related to chest depth, hip width and hucklebone width (<i>P</i> < 0.05). Additionally, the growth traits of individuals with copy number Loss were significantly inferior to those with copy number Gain or Median (<i>P</i> < 0.05). Besides, we found two splicing isoforms, AS1 and AS2, in <i>FGF13</i> gene, which resulted from alternative 5' splicing sites of intron 1. These isoforms showed varied expression levels in various tissues. Moreover, CNV was significantly and negatively associated with the mRNA expression of AS1 (<i>r</i> = -0.525, <i>P</i> < 0.05). The CNVs in bovine <i>FGF13</i> gene negatively regulated growth traits and gene transcription. These observations provide new insights into bovine <i>FGF13</i> gene, delivering potentially useful information for future Chinese cattle breeding programs.</p>","PeriodicalId":7836,"journal":{"name":"Animal Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139995295","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-01Epub Date: 2024-03-04DOI: 10.1080/10495398.2024.2319622
Linda George, Rani Alex, Gopal Gowane, Vikas Vohra, Pooja Joshi, Ravi Kumar, Archana Verma
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.
{"title":"Weighted single step GWAS reveals genomic regions associated with economic traits in Murrah buffaloes.","authors":"Linda George, Rani Alex, Gopal Gowane, Vikas Vohra, Pooja Joshi, Ravi Kumar, Archana Verma","doi":"10.1080/10495398.2024.2319622","DOIUrl":"10.1080/10495398.2024.2319622","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":7836,"journal":{"name":"Animal Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140020805","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-01Epub Date: 2023-11-25DOI: 10.1080/10495398.2023.2286610
W Y Zhao, Q Q Zhang, Y F Zhao, C Chang, X Wang, A L Geng
Orychophragmus violaceus (OV) and chicory (Cichorium intybus L., CC) can be used as fresh or dry forage for animals. To determine whether OV and/or CC have beneficial effects on performance and egg quality, a total of 1212 28-wk-old Beijing You Chicken (BYC) laying hens with similar performance were randomly allocated to 4 groups with 3 replicate pens per group, and 101 birds per pen. The birds were fed a basal diet (control), the basal diet + OV (3.507 kg/d/pen), the basal diet + CC (2.525 kg/d/pen), and the basal diet + OV + CC (OVC, 1.7535 kg/d/pen OV + 1.2625 kg/d/pen CC) for 3 wks after one wk of adaptation. The results showed that egg-laying rate was not affected by OV, CC and OVC (p > 0.05), but weekly average egg mass was significantly increased by OV and CC (p < 0.05). The feed egg ratio in the CC group (2.82) was significantly lower than that in the other three groups (p < 0.05). The eggshell thickness (EST), albumen height (AH) and Haugh unit (HU) were decreased by OV and CC (p < 0.05); while yolk color (YC) was increased in the CC and OVC groups (p < 0.05). Egg grade was decreased by OV (p < 0.05). Sensory evaluation showed that there was a trend for increased YC in OV, CC and OVC (p = 0.089). Serum total protein was significantly lower in OV group than those in the control and CC group (p < 0.05); serum albumin content was significantly decreased in OV, CC and OVC groups (p = 0.006). Serum glutathione peroxidase activity in CC and OVC groups was significantly higher than that in the control group (p < 0.05). In conclusion, the present study suggests that CC had a better effect on the performance of the native laying hens than OV. The OV and CC affected egg quality, while YC was increased in CC and OVC groups. The OVC improved YC and serum antioxidative properties of native laying hens without affecting the performance.
堇菜(Orychophragmus violaceus, OV)和菊苣(chichorium intybus L., CC)可作为动物的鲜饲料或干饲料。为研究OV和/或CC对生产性能和蛋品质的影响,试验选用1212只28周龄性能相近的北京油鸡(BYC)蛋鸡,随机分为4组,每组3个重复栏,每个栏101只鸡。各组分别饲喂基础饲粮(对照组)、基础饲粮+ OV (3.507 kg/d/只)、基础饲粮+ CC (2.525 kg/d/只)和基础饲粮+ OV + CC (OVC, 1.7535 kg/d/只OV + 1.2625 kg/d/只CC) 3周。结果表明:OV、CC和OVC对产蛋率无显著影响(p > 0.05),但OV和CC显著提高了周平均产蛋量(p p p p p p = 0.089)。OV组血清总蛋白显著低于对照组和CC组(p p = 0.006)。CC组和OVC组血清谷胱甘肽过氧化物酶活性显著高于对照组(p
{"title":"<i>Orychophragmus violaceus</i> and/or chicory forage affects performance, egg quality, sensory evaluation and antioxidative properties in native laying hens.","authors":"W Y Zhao, Q Q Zhang, Y F Zhao, C Chang, X Wang, A L Geng","doi":"10.1080/10495398.2023.2286610","DOIUrl":"10.1080/10495398.2023.2286610","url":null,"abstract":"<p><p><i>Orychophragmus violaceus</i> (OV) and chicory (<i>Cichorium intybus L.,</i> CC) can be used as fresh or dry forage for animals. To determine whether OV and/or CC have beneficial effects on performance and egg quality, a total of 1212 28-wk-old Beijing You Chicken (BYC) laying hens with similar performance were randomly allocated to 4 groups with 3 replicate pens per group, and 101 birds per pen. The birds were fed a basal diet (control), the basal diet + OV (3.507 kg/d/pen), the basal diet + CC (2.525 kg/d/pen), and the basal diet + OV + CC (OVC, 1.7535 kg/d/pen OV + 1.2625 kg/d/pen CC) for 3 wks after one wk of adaptation. The results showed that egg-laying rate was not affected by OV, CC and OVC (<i>p</i> > 0.05), but weekly average egg mass was significantly increased by OV and CC (<i>p</i> < 0.05). The feed egg ratio in the CC group (2.82) was significantly lower than that in the other three groups (<i>p</i> < 0.05). The eggshell thickness (EST), albumen height (AH) and Haugh unit (HU) were decreased by OV and CC (<i>p</i> < 0.05); while yolk color (YC) was increased in the CC and OVC groups (<i>p</i> < 0.05). Egg grade was decreased by OV (<i>p</i> < 0.05). Sensory evaluation showed that there was a trend for increased YC in OV, CC and OVC (<i>p</i> = 0.089). Serum total protein was significantly lower in OV group than those in the control and CC group (<i>p</i> < 0.05); serum albumin content was significantly decreased in OV, CC and OVC groups (<i>p</i> = 0.006). Serum glutathione peroxidase activity in CC and OVC groups was significantly higher than that in the control group (<i>p</i> < 0.05). In conclusion, the present study suggests that CC had a better effect on the performance of the native laying hens than OV. The OV and CC affected egg quality, while YC was increased in CC and OVC groups. The OVC improved YC and serum antioxidative properties of native laying hens without affecting the performance.</p>","PeriodicalId":7836,"journal":{"name":"Animal Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138440221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
At various stages of ovarian follicular development, more than 99% of follicles will be eliminated through a degenerative process called atresia. The regulatory mechanisms of atresia have been elucidated to some extent, involving hormones, growth factors, cytokines, and other factors. However, the stimuli initiating atresia in follicular granulosa cells remain unknown. In this study, we isolated the granulosa cells from porcine ovarian follicles (3-5 mm diameter) divided into healthy follicles (HFs) and early atretic follicles (EAFs). We applied high-throughput RNA sequencing to identify and compare differentially expressed genes (DEGs) between HFs and EAFs. A total of 31,694 genes were detected, of which 21,806 were co-expressed in six samples, and 243 genes (p < 0.05; FDR < 0.05) were differentially expressed (DEGs), including 123 downregulated and 120 upregulated in EAFs. GO analysis highlighted hormone metabolism, plasma membrane localization, and transporter activity. The pathway analysis indicated that 51 DEGs, involved in steroidogenesis, cell adhesion molecules, and TGF-beta signaling pathways, were highly related to atresia. Additionally, the interaction network of DEGs (p < 0.01; FDR < 0.05) using STRING highlighted LHR, ACACB, and CXCR4 as central nodes. In summary, this transcriptome analysis enriched our knowledge of the shifted mechanisms in granulosa cells during early atresia and provided novel perspectives into the atresia initiation.
{"title":"Comparative transcriptome profile analysis of granulosa cells from porcine ovarian follicles during early atresia.","authors":"Jinbi Zhang, Xinxin Qin, Caixia Wang, Yuge Zhang, Yizhe Dou, Shiyong Xu, Jingge Liu, Zengxiang Pan","doi":"10.1080/10495398.2023.2282090","DOIUrl":"10.1080/10495398.2023.2282090","url":null,"abstract":"<p><p>At various stages of ovarian follicular development, more than 99% of follicles will be eliminated through a degenerative process called atresia. The regulatory mechanisms of atresia have been elucidated to some extent, involving hormones, growth factors, cytokines, and other factors. However, the stimuli initiating atresia in follicular granulosa cells remain unknown. In this study, we isolated the granulosa cells from porcine ovarian follicles (3-5 mm diameter) divided into healthy follicles (HFs) and early atretic follicles (EAFs). We applied high-throughput RNA sequencing to identify and compare differentially expressed genes (DEGs) between HFs and EAFs. A total of 31,694 genes were detected, of which 21,806 were co-expressed in six samples, and 243 genes (<i>p</i> < 0.05; FDR < 0.05) were differentially expressed (DEGs), including 123 downregulated and 120 upregulated in EAFs. GO analysis highlighted hormone metabolism, plasma membrane localization, and transporter activity. The pathway analysis indicated that 51 DEGs, involved in steroidogenesis, cell adhesion molecules, and TGF-beta signaling pathways, were highly related to atresia. Additionally, the interaction network of DEGs (<i>p</i> < 0.01; FDR < 0.05) using STRING highlighted LHR, ACACB, and CXCR4 as central nodes. In summary, this transcriptome analysis enriched our knowledge of the shifted mechanisms in granulosa cells during early atresia and provided novel perspectives into the atresia initiation.</p>","PeriodicalId":7836,"journal":{"name":"Animal Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138440223","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-01Epub Date: 2023-12-23DOI: 10.1080/10495398.2023.2290528
Muhammad Munir Khan, Syed Muhammad Suhail, Hafiz Abdul Majid, Ijaz Ahmad, Umer Sadique, Rajwali Khan, Iftikhar Ahmad, Asim Ijaz, Khalid Khan, Farhad Ali, Muhammad Saeed Khan, Ahmed A El-Mansi
The present study was designed with the aim to study morphometric characterization as well as phylogeny and diversity of the local Surguli goat at their breeding tract district Kohat through mitochondrial DNA region, i.e., Cytochrome C Oxidase Subunit One (CO1) gene. Morphometric data and blood samples were collected from thirty (30) pure goats. Morphometric analysis showed that sex had significant effect (p < 0.05) on body weight, body length, hearth girth and horn length while no significant effect (p > 0.05) was observed for other characteristics. The results also indicated that age had significant effect (p < 0.05) on height at rump, ear length, horn length and tail length while no significant effect (p > 0.05) was observed for other characteristics. The phylogenetic analysis through CO1 nucleotide sequences within nucleotide range 1-767 showed nine polymorphic sites segregating into eight haplotypes. The mean intraspecific diversity and mean interspecific diversity were calculated as 0.23 and 2.36%, respectively. Phylogenetic tree revealed that Capra Ibex and native Surguli goat have common ancestors. The morphometric and molecular results obtained from the present study can be exploited as a selection tool for breeding and overall improvement.
本研究旨在通过线粒体 DNA 区域,即细胞色素 C 氧化酶亚基一(CO1)基因,研究库哈特(Kohat)地区当地苏古利山羊的形态特征以及系统发育和多样性。采集了三十(30)只纯种山羊的形态数据和血液样本。形态分析表明,性别对其他特征有显著影响(p p > 0.05)。结果还表明,年龄对其他特征也有显著影响(p p > 0.05)。通过核苷酸范围为 1-767 的 CO1 核苷酸序列进行的系统进化分析表明,9 个多态位点分离成 8 个单倍型。计算得出的种内平均多样性和种间平均多样性分别为 0.23% 和 2.36%。系统发育树显示,山羊和本地苏尔古丽山羊有共同的祖先。本研究获得的形态计量学和分子结果可作为育种和整体改良的选育工具。
{"title":"Morpometric and molecular characterization of Surguli goat through CO1 gene in district Kohat.","authors":"Muhammad Munir Khan, Syed Muhammad Suhail, Hafiz Abdul Majid, Ijaz Ahmad, Umer Sadique, Rajwali Khan, Iftikhar Ahmad, Asim Ijaz, Khalid Khan, Farhad Ali, Muhammad Saeed Khan, Ahmed A El-Mansi","doi":"10.1080/10495398.2023.2290528","DOIUrl":"10.1080/10495398.2023.2290528","url":null,"abstract":"<p><p>The present study was designed with the aim to study morphometric characterization as well as phylogeny and diversity of the local Surguli goat at their breeding tract district Kohat through mitochondrial DNA region, i.e., Cytochrome C Oxidase Subunit One (CO1) gene. Morphometric data and blood samples were collected from thirty (30) pure goats. Morphometric analysis showed that sex had significant effect (<i>p</i> < 0.05) on body weight, body length, hearth girth and horn length while no significant effect (<i>p</i> > 0.05) was observed for other characteristics. The results also indicated that age had significant effect (<i>p</i> < 0.05) on height at rump, ear length, horn length and tail length while no significant effect (<i>p</i> > 0.05) was observed for other characteristics. The phylogenetic analysis through CO1 nucleotide sequences within nucleotide range 1-767 showed nine polymorphic sites segregating into eight haplotypes. The mean intraspecific diversity and mean interspecific diversity were calculated as 0.23 and 2.36%, respectively. Phylogenetic tree revealed that Capra Ibex and native Surguli goat have common ancestors. The morphometric and molecular results obtained from the present study can be exploited as a selection tool for breeding and overall improvement.</p>","PeriodicalId":7836,"journal":{"name":"Animal Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139032048","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The inducing activation event of secondary hair follicle (SHF)-stem cells is considered a key biological process in the SHF regeneration, and the morphogenesis of cashmere fiber in cashmere goats. The miR-361-5p was essentially implicated in the induced activation of SHF-stem cells of cashmere goats, but its functional mechanisms are unclear. Here, we confirmed miR-361-5p was significantly downregulated in anagen SHF bugle of cashmere goats compared with that at telogen, and miR-361-5p expression was significantly lower in SHF-stem cells after activation than its counterpart before activation. Further, we found that miR-361-5p could negatively regulate the induced activation event of SHF-stem cells in cashmere goats. Mechanistically, through dual-luciferase reporter assays, miR-361-5p specifically bound with FOXM1 mRNA in SHF-stem cells of cashmere goats and negatively regulated the expression of FOXM1 gene. Also, through overexpression/knockdown analysis of FOXM1 gene, our results indicated that FOXM1 upregulated the expression of Wnt/β-catenin pathway related genes in SHF-stem cells. Moreover, based on TOP/FOP-flash Wnt report assays, the knockdown of miR-361-5p promotes the Wnt/β-catenin pathway activation through upregulating the FOXM1 expression in SHF-stem cells. Finally, we demonstrated that miR-361-5p negatively regulated the induced activation of SHF-stem cells through FOXM1 mediated Wnt/β-catenin pathway in cashmere goats.
{"title":"Knockdown of miR-361-5p promotes the induced activation of SHF-stem cells through FOXM1 mediated Wnt/β-catenin pathway in cashmere goats.","authors":"Ruqing Xu, Man Bai, Yixing Fan, Yubo Zhu, Zeying Wang, Taiyu Hui, Qi Zhang, Xingwang Liu, Jialiang Zhang, Jincheng Shen, Wenlin Bai","doi":"10.1080/10495398.2024.2356110","DOIUrl":"https://doi.org/10.1080/10495398.2024.2356110","url":null,"abstract":"<p><p>The inducing activation event of secondary hair follicle (SHF)-stem cells is considered a key biological process in the SHF regeneration, and the morphogenesis of cashmere fiber in cashmere goats. The miR-361-5p was essentially implicated in the induced activation of SHF-stem cells of cashmere goats, but its functional mechanisms are unclear. Here, we confirmed miR-361-5p was significantly downregulated in anagen SHF bugle of cashmere goats compared with that at telogen, and miR-361-5p expression was significantly lower in SHF-stem cells after activation than its counterpart before activation. Further, we found that miR-361-5p could negatively regulate the induced activation event of SHF-stem cells in cashmere goats. Mechanistically, through dual-luciferase reporter assays, miR-361-5p specifically bound with <i>FOXM1</i> mRNA in SHF-stem cells of cashmere goats and negatively regulated the expression of <i>FOXM1</i> gene. Also, through overexpression/knockdown analysis of <i>FOXM1</i> gene, our results indicated that <i>FOXM1</i> upregulated the expression of Wnt/β-catenin pathway related genes in SHF-stem cells. Moreover, based on TOP/FOP-flash Wnt report assays, the knockdown of miR-361-5p promotes the Wnt/β-catenin pathway activation through upregulating the <i>FOXM1</i> expression in SHF-stem cells. Finally, we demonstrated that miR-361-5p negatively regulated the induced activation of SHF-stem cells through <i>FOXM1</i> mediated Wnt/β-catenin pathway in cashmere goats.</p>","PeriodicalId":7836,"journal":{"name":"Animal Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141157832","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cattle are sensitive to temperature fluctuations but adapt well to inclement weather conditions. When environmental temperatures exceed specific thresholds, heat stress becomes a critical concern for cattle. The TRPM2 gene, which resides on cattle chromosome 1 encodes a TRP channel protein, holding a unique capacity to sense temperature changes and facilitate rapid response to avoid heat stress. Here, we utilized the Bovine Genome Variation Database (BGVD) (http://animal.omics.pro/code/index.php/BosVar), and identified a missense mutation site, c.805A > G: p. Met269Val (rs527146862), within the TRPM2 gene. To elucidate the functional assessment of this mutation in temperature adaptation attributes of Chinese cattle, we genotyped 407 samples from 20 distinct breeds representing diverse climatic zones across China. The association analysis incorporates three temperature parameters and revealed compelling insights in terms of allele frequency. Interestingly, the prevalence of the wild-type allele A was notably higher among northern cattle breeds and this trend diminished gradually as observed in southern cattle populations. Conversely, the mutant-type allele G demonstrated a contrasting trend. Moreover, southern cattle exhibited markedly higher frequencies of GG and GA genotypes (P < 0.01). The presence of heterozygous and homozygous mutations appears to confer an enhanced capacity for adaptation to elevated temperatures. These results provide unequivocal correlation evidence between TRPM2 genotypes (AA, GA, GG) and environmental temperature parameters and comprehend the genetic mechanisms governing temperature adaptation in cattle. This provides valuable insights for strategic breed selection across diverse climatic regions, thereby aiding livestock production amid evolving climate challenges.
牛对温度波动很敏感,但对恶劣天气条件的适应能力很强。当环境温度超过特定阈值时,热应激就会成为牛的一个重要问题。位于牛 1 号染色体上的 TRPM2 基因编码一种 TRP 通道蛋白,具有感知温度变化的独特能力,可促进快速反应以避免热应激。在此,我们利用牛基因组变异数据库(BGVD)(http://animal.omics.pro/code/index.php/BosVar),在 TRPM2 基因中发现了一个错义突变位点,即 c.805A > G: p. Met269Val (rs527146862)。为了阐明该突变在中国牛温度适应属性中的功能评估,我们对代表中国不同气候区的 20 个不同品种的 407 个样本进行了基因分型。关联分析结合了三个温度参数,并从等位基因频率方面揭示了令人信服的见解。有趣的是,在北方牛种中,野生型等位基因 A 的流行率明显较高,而在南方牛种中,这一趋势逐渐减弱。相反,突变型等位基因 G 则呈现出相反的趋势。此外,南方牛的 GG 和 GA 基因型(P TRPM2 基因型(AA、GA、GG)和环境温度参数)频率明显较高,这有助于理解牛的温度适应遗传机制。这为不同气候地区的战略品种选择提供了宝贵的见解,从而在不断变化的气候挑战中帮助畜牧业生产。
{"title":"Temperature adaptation patterns in Chinese cattle revealed by <i>TRPM2</i> gene mutation analysis.","authors":"Dekai Liu, Yifan Yang, Zhefu Chen, Yijie Fan, Jianyong Liu, Yibing Xu, Zulfiqar Ahmed, Jicai Zhang, Fuqiang Li, Xingshan Qi, Weiru Song, Kaixia Zhu, Jiangcai Gongque, Guomei Li, Bizhi Huang, Chuzhao Lei","doi":"10.1080/10495398.2023.2299944","DOIUrl":"10.1080/10495398.2023.2299944","url":null,"abstract":"<p><p>Cattle are sensitive to temperature fluctuations but adapt well to inclement weather conditions. When environmental temperatures exceed specific thresholds, heat stress becomes a critical concern for cattle. The <i>TRPM2</i> gene, which resides on cattle chromosome 1 encodes a TRP channel protein, holding a unique capacity to sense temperature changes and facilitate rapid response to avoid heat stress. Here, we utilized the Bovine Genome Variation Database (BGVD) (http://animal.omics.pro/code/index.php/BosVar), and identified a missense mutation site, c.805A > G: p. Met269Val (rs527146862), within the <i>TRPM2</i> gene. To elucidate the functional assessment of this mutation in temperature adaptation attributes of Chinese cattle, we genotyped 407 samples from 20 distinct breeds representing diverse climatic zones across China. The association analysis incorporates three temperature parameters and revealed compelling insights in terms of allele frequency. Interestingly, the prevalence of the wild-type allele A was notably higher among northern cattle breeds and this trend diminished gradually as observed in southern cattle populations. Conversely, the mutant-type allele G demonstrated a contrasting trend. Moreover, southern cattle exhibited markedly higher frequencies of GG and GA genotypes (P < 0.01). The presence of heterozygous and homozygous mutations appears to confer an enhanced capacity for adaptation to elevated temperatures. These results provide unequivocal correlation evidence between <i>TRPM2</i> genotypes (AA, GA, GG) and environmental temperature parameters and comprehend the genetic mechanisms governing temperature adaptation in cattle. This provides valuable insights for strategic breed selection across diverse climatic regions, thereby aiding livestock production amid evolving climate challenges.</p>","PeriodicalId":7836,"journal":{"name":"Animal Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139073061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In this study, we investigated the effects of supplemental Glycyrrhiza polysaccharide (GCP) on growth performance and intestinal health of weaned piglets. Ninety piglets weaned at 28 days of age were randomly allocated to three groups with five replicates per treatment. Piglets were fed the following diets for 28 days: (1) CON (control group), basal diet; (2) G500, CON + 500 mg/kg GCP; (3) G1000, CON + 1000 mg/kg GCP. The results showed that supplementation with 1000 mg/kg GCP increased the average daily gain (ADG) and decreased the feed-to-gain ratio (F/G) (P < 0.05). Serum diamine oxidase (DAO) and D-lactic acid (DL-A) levels were lower in the G1000 group (P < 0.05). Dietary GCP 1000 mg/kg improved mucosal trypsin activity in the duodenum, jejunum and ileum and increased lipase and amylase activity in the jejunum (P < 0.05). Moreover, in the G1000 group, ZO-1, claudin 1 and occludin levels were increased in the jejunum mucosa, whereas interleukin-1β (IL-1β) and IL-6 levels were decreased (P < 0.05). The 16S rRNA gene analysis indicated that dietary 1000 mg/kg GCP altered the jejunal microbial community, with increased relative abundances of beneficial bacteria. In conclusion, dietary GCP 1000 mg/kg can improve growth performance, digestive enzyme activity, intestinal immunity, barrier function and microbial community in weaned piglets.
本研究调查了补充甘草多糖(GCP)对断奶仔猪生长性能和肠道健康的影响。90 头 28 日龄断奶仔猪被随机分配到三个组,每个处理有五个重复。仔猪饲喂以下日粮 28 天:(1) CON(对照组),基础日粮;(2) G500,CON + 500 mg/kg GCP;(3) G1000,CON + 1000 mg/kg GCP。结果表明,添加 1000 毫克/千克 GCP 可提高平均日增重(ADG),降低料增重比(F/G)(P P P P P
{"title":"Effects of supplemental <i>Glycyrrhiza</i> polysaccharide on growth performance and intestinal health in weaned piglets.","authors":"Xueying Wang, Pengli Zhao, Cai Zhang, Chenxu Li, Yanbo Ma, Shucheng Huang","doi":"10.1080/10495398.2024.2362640","DOIUrl":"https://doi.org/10.1080/10495398.2024.2362640","url":null,"abstract":"<p><p>In this study, we investigated the effects of supplemental <i>Glycyrrhiza</i> polysaccharide (GCP) on growth performance and intestinal health of weaned piglets. Ninety piglets weaned at 28 days of age were randomly allocated to three groups with five replicates per treatment. Piglets were fed the following diets for 28 days: (1) CON (control group), basal diet; (2) G500, CON + 500 mg/kg GCP; (3) G1000, CON + 1000 mg/kg GCP. The results showed that supplementation with 1000 mg/kg GCP increased the average daily gain (ADG) and decreased the feed-to-gain ratio (F/G) (<i>P</i> < 0.05). Serum diamine oxidase (DAO) and D-lactic acid (DL-A) levels were lower in the G1000 group (<i>P</i> < 0.05). Dietary GCP 1000 mg/kg improved mucosal trypsin activity in the duodenum, jejunum and ileum and increased lipase and amylase activity in the jejunum (<i>P</i> < 0.05). Moreover, in the G1000 group, ZO-1, claudin 1 and occludin levels were increased in the jejunum mucosa, whereas interleukin-1β (IL-1β) and IL-6 levels were decreased (<i>P</i> < 0.05). The 16S rRNA gene analysis indicated that dietary 1000 mg/kg GCP altered the jejunal microbial community, with increased relative abundances of beneficial bacteria. In conclusion, dietary GCP 1000 mg/kg can improve growth performance, digestive enzyme activity, intestinal immunity, barrier function and microbial community in weaned piglets.</p>","PeriodicalId":7836,"journal":{"name":"Animal Biotechnology","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141299842","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}