Relationship of Icelandic cattle with Northern and Western European cattle breeds,admixture and population structure     

Egill Gautason  Anna A. Schönherz  Goutam Sahana  Bernt Guldbrandtsen 《Acta Agriculturae Scandinavica, Section A - Animal Sciences》2020,69(1-2):25-38

ABSTRACT

Icelandic cattle is believed to have been brought from Norway during the settlement of Iceland around AD 870-930. Previous research on genetic relationships has indicated that Icelandic cattle is most related to northern Nordic indigenous breeds. Using single nucleotide polymorphism genotype data from Icelandic cattle and 29 Northern and Western European cattle breeds, we studied relationships and admixture among these breeds, and assessed population structure in Icelandic cattle. Population structure analysis through principal component analysis, estimation of ancestry, and analysis of patterns of population splitting and mixing revealed that Icelandic cattle are most related to three Finncattle breeds (Eastern, Northern and Western Finncattle), and Swedish Mountain cattle. Icelandic cattle has very low levels of admixture. We observed very limited population structure in Icelandic cattle. The observed structure was due to variable sire contributions. Over 1000 years of almost complete isolation has made Icelandic cattle highly genetically distinct from other cattle breeds.  相似文献   

Fine mapping of a calving QTL on Bos taurus autosome 18 in Holstein cattle          下载免费PDF全文

X. Mao  N.K. Kadri  J.R. Thomasen  D.J. De Koning  G. Sahana  B. Guldbrandtsen 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2016,133(3):207-218

Decreased calving performance not only directly impacts the economic efficiency of dairy cattle farming but also influences public concern for animal welfare. Previous studies have revealed a QTL on Bos taurus autosome (BTA) 18 that has a large effect on calving traits in Holstein cattle. In this study, fine mapping of this QTL was performed using imputed high‐density SNP chip (HD) genotypes followed by imputed next‐generation sequencing (NGS) variants. BTA18 was scanned for seven direct calving traits in 6113 bulls with imputed HD genotypes. SNP rs136283363 (BTA18: 57 548 213) was consistently the most significantly associated SNP across all seven traits [e.g. p‐value = 2.04 × 10^?59 for birth index (BI)]. To finely map the QTL region and to explore pleiotropic effects, we studied NGS variants within the targeted region (BTA18: 57 321 450–57 625 355) for associations with direct calving traits and with three conformation traits. Significant variants were prioritized, and their biological relevance to the traits was interpreted. Considering their functional relationships with direct calving traits, SIGLEC12, CD33 and CEACAM18 were proposed as candidate genes. In addition, pleiotropic effects of this QTL region on direct calving traits and conformation traits were observed. However, the extent of linkage disequilibrium combined with the lack of complete annotation and potential errors in the Bos taurus genome assembly hampered our efforts to pinpoint the causal mutation.  相似文献   

Short communication: investigation of the feasibility of genomic selection in Icelandic Cattle     

Egill Gautason  Goutam Sahana  Guosheng Su  Baldur Helgi Benjamínsson  Gumundur Jhannesson  Bernt Guldbrandtsen 《Journal of animal science》2021,99(7)

Icelandic Cattle is a local dairy cattle breed in Iceland. With about 26,000 breeding females, it is by far the largest among the indigenous Nordic cattle breeds. The objective of this study was to investigate the feasibility of genomic selection in Icelandic Cattle. Pedigree-based best linear unbiased prediction (PBLUP) and single-step genomic best linear unbiased prediction (ssGBLUP) were compared. Accuracy, bias, and dispersion of estimated breeding values (EBV) for milk yield (MY), fat yield (FY), protein yield (PY), and somatic cell score (SCS) were estimated in a cross validation-based design. Accuracy (r^) was estimated by the correlation between EBV and corrected phenotype in a validation set. The accuracy (r^) of predictions using ssGBLUP increased by 13, 23, 19, and 20 percentage points for MY, FY, PY, and SCS for genotyped animals, compared with PBLUP. The accuracy of nongenotyped animals was not improved for MY and PY, but increased by 0.9 and 3.5 percentage points for FY and SCS. We used the linear regression (LR) method to quantify relative improvements in accuracy, bias (Δ^), and dispersion (b^) of EBV. Using the LR method, the relative improvements in accuracy of validation from PBLUP to ssGBLUP were 43%, 60%, 50%, and 48% for genotyped animals for MY, FY, PY, and SCS. Single-step GBLUP EBV were less underestimated (Δ^), and less overdispersed (b^) than PBLUP EBV for FY and PY. Pedigree-based BLUP EBV were close to unbiased for MY and SCS. Single-step GBLUP underestimated MY EBV but overestimated SCS EBV. Based on the average accuracy of 0.45 for ssGBLUP EBV obtained in this study, selection intensities according to the breeding scheme of Icelandic Cattle, and assuming a generation interval of 2.0 yr for sires of bulls, sires of dams and dams of bulls, genetic gain in Icelandic Cattle could be increased by about 50% relative to the current breeding scheme.  相似文献   

Probiotic efficiency of Bacillus sp. in Labeo rohita challenged by Aeromonas hydrophila: assessment of stress profile,haemato‐biochemical parameters and immune responses          下载免费PDF全文

Ankita Nandi  Goutam Banerjee  Suhas Kumar Dan  Koushik Ghosh  Arun Kumar Ray 《Aquaculture Research》2017,48(8):4334-4345

Fish are always susceptible to a wide variety of deadly pathogens which cause a huge loss in aquaculture industries. In this investigation, we have demonstrated the in vivo probiotic efficiency of Bacillus sp. MVF1 (GenBank Acc. No. KP256503) in Labeo rohita challenged with pathogenic strain of Aeromonas hydrophila (MTCC 1739). To check the probiotic potential of the selected bacterial strain, fish were divided into four groups: control, D1, D2 and D3. A total of 100 days (70 days probiotic feeding + 71th day sampling and 28 days challenged test + 29th day sampling) of feeding trial was conducted. To establish the probiotic potential of Bacillus sp. MVF1, certain haematological parameters (haemoglobin, total erythrocyte and leucocyte count), serum biochemical parameters (total protein, albumin and globulin), immune parameters (serum lysozyme and total IgM levels) and hepatic stress profile (malondialdehyde production, superoxide dismutase and catalase activity) have been measured. Our results demonstrated that red blood cell number, white blood cell number and haemoglobin content were much higher in D2 group fish compared to other groups and control fish. Similarly, total protein contents, albumin concentration, globulin concentration, lysozyme activity and IgM production were also recorded to be highest in D2 group fish. This finding clearly indicated the probiotic potential of Bacillus sp. MVF1 in L. rohita. Furthermore, our results also demonstrated that 1 × 10⁷ CFU g^?1 feed (D2) provides better immunity compared to 1 × 10⁵ (D1) and 1 × 10⁹ (D3). Due to beneficial effects, the bacterium Bacillus sp. MVF1 might be useful in aquaculture industries to reduce the disease susceptibility.  相似文献   

Genome‐wide association studies revealed candidate genes for tail fat deposition and body size in the Hulun Buir sheep     

Tongyu Zhang  Hongding Gao  Goutam Sahana  Yanjun Zan  Hongying Fan  Jiaxin Liu  Liangyu Shi  Hongwei Wang  Lixin Du  Lixian Wang  Fuping Zhao 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2019,136(5):362-370

Fat‐tailed sheep have a unique characteristic of depositing fat in their tails. In the present study, we conducted genome‐wide association studies (GWAS) on traits related to tail fat deposition and body size in the Hulun Buir sheep. A total number of 300 individuals belonging to two fat‐tailed lines of the Hulun Buir sheep breed genotyped with the Ovine Infinium HD SNP BeadChip were included in the current study. Two mixed models, one for continuous and one for binary phenotypic traits, were employed to analyse ten traits, that is, body length (BL), body height (BH), chest girth (CG), tail length (TL), tail width (TW), tail circumference (TC), carcass weight (CW), tail fat weight (TF), ratio of CW to TF (RCT) and tail type (TT). We identified 7, 6, 7, 2, 10 and 1 SNPs significantly associated with traits TF, CW, RCT, TW, TT and CG, respectively. Their associated genomic regions harboured 42 positional candidate genes. Out of them, 13 candidate genes including SMURF2, FBF1, DTNBP1, SETD7 and RBM11 have been associated with fat metabolism in sheep. The RBM11 gene has already been identified in a previous study on signatures of selection in this specific sheep population. Two more genes, that is, SMARCA5 and GAB1 were associated with body size in sheep. The present study has identified candidate genes that might be implicated in tail fat deposition and body size in sheep.  相似文献   

Identification and Pathogenicity of Pseudomonas aeruginosa DJ1990 on Tail and Fin Rot Disease in Spotted Snakehead          下载免费PDF全文

Dibya J. Saikia  Pritam Chattopadhyay  Goutam Banerjee  Bandita Talukdar  Dandadhar Sarma 《Journal of the World Aquaculture Society》2018,49(4):703-714

Tail and fin rot disease (TFRD) is a big issue in the production of spotted snakehead, Channa punctata Bloch. The aims of the present study were to isolate and identify the bacterial pathogen causing TFRD, to detect histopathological changes in tissues (fin, tail, liver, and kidney), and to ascertain the antibiotic sensitivity pattern of the isolate. Out of six bacterial isolates, only the isolate DJ1990 was found to be the causal candidate of TFRD in C. punctata. Identical histopathological changes were detected in tail, fin, liver, and kidney under light and scanning electron microscope in both collected diseased fish and artificially infected fish. The isolate was identified as Pseudomonas aeruginosa strain DJ1990 (National Center for Biotechnology Information Ace. No. KX709967) based on the biochemical characterization tests and 16S rDNA sequence‐based phylogeny analysis. Artificial challenge test demonstrated that the strain DJ1990 was highly virulent (100% mortality at 48 h of postinjection period at the concentration of 1.5 × 10⁷ CFU/g of body weight) for C. punctata. The isolate exhibited sensitivity to the broad‐spectrum antibiotics but was resistant against aztreonum. To the best of our knowledge, this is the first report of P. aeruginosa as a TFRD‐causing candidate in C. punctata.  相似文献   

Fluorescence resonance energy transfer (FRET)-based technique for tracking of endophytic bacteria in rice roots     

Avishek Banik  Subhra Kanti Mukhopadhaya  Animesh Sahana  Debasis Das  Tushar Kanti Dangar 《Biology and Fertility of Soils》2016,52(2):277-282

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Transcriptional profile of endometrial TLR4 and 5 genes during the estrous cycle and uterine infection in the buffalo (Bubalus bubalis)     

Ganesan Ajevar  Sankar Muthu  Mihir Sarkar  Harendra Kumar  Goutam Kumar Das  Narayanan Krishnaswamy 《Veterinary research communications》2014,38(2):171-176

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Cytotoxicity of Senecio in macrophages is mediated via its induction of oxidative stress     

Samiran Bandyopadhyay  Goutam Mandal  Piu Saha  Mihir Sarkar 《Research in veterinary science》2009,87(1):85-90

In Arunachal Pradesh and other sub-Himalayan areas of India, accidental consumption of Senecio plants by yaks is often fatal as the plant contains toxic alkaloids like Seneciophylline. The present investigation was undertaken to demonstrate the pro-oxidant effects of an ethanolic extract of Seneciochrysanthemoides (S-EtOH). S-EtOH impaired viability in macrophages, the IC₅₀ being 13.8 ± 1.11 μg/mL. The effect of S-EtOH (1 μg/mL) on generation of reactive oxygen species (ROS) in macrophages was measured by flow cytometry using 2′,7′-dichlorofluorescein diacetate (H₂DCFDA) where it caused a significant increase in the mean fluorescence channel (MFC) from 8.55 ± 0.03 to 47.32 ± 2.25 (p < 0.001). S-EtOH also effected a 3.8-fold increase in extracellular nitric oxide (NO) generation from 4.90 ± 0.72 μM to 18.79 ± 0.32 μM (p < 0.001), a 2.2-fold increase in intracellular NO production, the MFC increasing from 14.95 ± 0.48 to 33.34 ± 1.66 (p < 0.001), and concomitantly depleted non protein thiols as analyzed by flow cytometry using mercury orange, with a reduction in MFC from 632.5 ± 49.44 to 407.4 ± 12.61 (p < 0.01). Additionally, S-EtOH (14 μg/mL, 24 h) caused apoptosis as evident by increased Annexin V binding and terminal deoxynucleotidyl transferase mediated dUTP DNA nick end labeling. Taken together, the cytotoxicity of S-EtOH can be partly attributed to its capacity to inflict oxidative damage via generation of both reactive oxygen and nitrogen species culminating in apoptosis.  相似文献   

Effects of an emulsifier on the performances of Khaki Campbell ducks added with different sources of fats     

Zosangpuii  Amlan Kumar Patra  Goutam Samanta  Kaushik Pal 《Frontiers of Agriculture in China》2011,5(4):605-611

An experiment was conducted to assess the effects of different sources of fats added with an external emulsifier (lecithin) on the performances of Khaki Campbell Ducks in an eight-week trial. Ducks were grouped into five dietary groups with three replicates (n = 10) in each group. The ducks were fed with a basal diet supplemented with 3% soybean oil and without emulsifier (C1), 3% palm oil without emulsifier (C2), 3% soybean oil with emulsifier (T1), 3% palm oil with emulsifier (T2) and 3% lard with emulsifier (T3). The growth performance of ducks did not vary (P > 0.1) among the dietary treatments. Feed intakes by ducks were also similar (P > 0.1) among treatments within the periods. Similarly, feed intake to gain ratios were not affected by any dietary treatments. The metabolizability of dry matter, crude protein and nitrogen free extract also did not change (P > 0.1) due to various dietary treatments. However, the metabolizability of fats in all the emulsifier added groups (T1, T2 and T3) was greater (P < 0.05) than the dietary groups without emulsifier (C1 and C2). Various carcass traits such as percentages of hot carcass, breast, legs, lungs, hearts, gizzard, giblets weights relative to bodyweights did not vary (P > 0.1) among the groups. The carcass yield tended (P = 0.06) to be greater in the T1 than in the C1 group. The moisture, fats, protein and ash composition of meat (percent on fresh basis) was similar (P > 0.1) among treatments. In conclusion, supplementation of lecithin as an emulsifier to the diets containing different sources of fats (3%) appears to have no major impact on the overall performances of Khaki Campbell ducks in their grower phase.  相似文献