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Díaz-Matus de la Parra M, Inostroza K, Alcalde JA, Larama G, Bravo S. Characterization of the genetic diversity, structure, and admixture of 7 Chilean chicken breeds. Poult Sci 2024; 103:103238. [PMID: 38071783 PMCID: PMC10750188 DOI: 10.1016/j.psj.2023.103238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/04/2023] [Accepted: 10/23/2023] [Indexed: 12/29/2023] Open
Abstract
The Mapuche fowl is an autochthonous breed raised in Chile and represents an important zoogenetic resource for the local economy. This study aimed at investigating the genetic diversity, relationship and population structure of 96 local Chilean chickens derived from 3 ecotype of Mapuche fowl (Kollonka, Ketro, and Kollonka de aretes), 2 ecotype Chilean (Trintre, Cogote pelado) and 2 breeds (Light Brahma and Barred Plymouth Rock) using 12 microsatellite markers. In total, 113 alleles were detected in all populations, with a mean of 7.6 alleles per population. In all population chicken breeds, the observed and expected heterozygosity ranged from 0.91 to 0.98 and from 0.69 to 0.79. Furthermore, all populations showed significant deviations from Hardy-Weinberg expectations. Across each population, the global heterozygosity deficit (FIT) was -0.174, population differentiation index (FST) was 0.073, and the global inbreeding of individuals within breed (FIS) was -0.267. The phylogenetic relationships of chickens were examined using neighbor-joining trees constructed at the level of population. The highest Nei's standard genetic distance value of 0.559 was observed between Barred Plymouth Rock and Light Brahma, whereas the minimum value (0.099) was found between Kollonka and Trintre. The neighbor-joining tree constructed at population level revealed 2 main clusters, with Light Brahma, Barred Plymouth Rock, Ketro and Kollonka de aretes in 1 cluster, and Kollonka, Trintre and Cogote pelado breeds in the second cluster. Based on the results of the STRUCTURE analysis, the most likely number of clustering of the population evaluated was at K = 3, with Light Brahma and Barred Plymouth Rock breeds forming their own distinct clusters, while Kollonka, Ketro, Kollonka de aretes, Trintre and Cogote pelado breeds clustered together. This study represents the first report of genetic diversity in these populations in Chile. These results can be used as baseline genetic information for genetic conservation program, for instance, to control inbreeding and to implement further genetic studies in local Chilean chickens.
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Affiliation(s)
| | - Karla Inostroza
- Department of Agricultural and Aquacultural Sciences, Faculty of Natural Resources, Universidad Católica de Temuco, Temuco, Chile
| | - José Antonio Alcalde
- Department of Fruit Cultivation and Enology, Faculty of Agronomy and Forest Engineering, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Giovanni Larama
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco 4811230, Chile
| | - Silvana Bravo
- Institute of Animal Production, Faculty of Agricultural and Food Sciences, Universidad Austral de Chile, Valdivia, Chile; Center for Research on Volcanic Soils, Faculty of Agricultural and Food Sciences, Universidad Austral de Chile, Valdivia, Chile.
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Naidoo L, Arumugam T, Ramsuran V. Host Genetic Impact on Infectious Diseases among Different Ethnic Groups. ADVANCED GENETICS (HOBOKEN, N.J.) 2023; 4:2300181. [PMID: 38099246 PMCID: PMC10716055 DOI: 10.1002/ggn2.202300181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/11/2023] [Indexed: 12/17/2023]
Abstract
Infectious diseases such as malaria, tuberculosis (TB), human immunodeficiency virus (HIV), and the coronavirus disease of 2019 (COVID-19) are problematic globally, with high prevalence particularly in Africa, attributing to most of the death rates. There have been immense efforts toward developing effective preventative and therapeutic strategies for these pathogens globally, however, some remain uncured. Disease susceptibility and progression for malaria, TB, HIV, and COVID-19 vary among individuals and are attributed to precautionary measures, environment, host, and pathogen genetics. While studying individuals with similar attributes, it is suggested that host genetics contributes to most of an individual's susceptibility to disease. Several host genes are identified to associate with these pathogens. Interestingly, many of these genes and polymorphisms are common across diseases. This paper analyzes genes and genetic variations within host genes associated with HIV, TB, malaria, and COVID-19 among different ethnic groups. The differences in host-pathogen interaction among these groups, particularly of Caucasian and African descent, and which gene polymorphisms are prevalent in an African population that possesses protection or risk to disease are reviewed. The information in this review could potentially help develop personalized treatment that could effectively combat the high disease burden in Africa.
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Affiliation(s)
- Lisa Naidoo
- School of Laboratory Medicine and Medical SciencesCollege of Health SciencesUniversity of KwaZulu‐NatalDurban4041South Africa
| | - Thilona Arumugam
- School of Laboratory Medicine and Medical SciencesCollege of Health SciencesUniversity of KwaZulu‐NatalDurban4041South Africa
| | - Veron Ramsuran
- School of Laboratory Medicine and Medical SciencesCollege of Health SciencesUniversity of KwaZulu‐NatalDurban4041South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA)University of KwaZulu‐NatalDurban4041South Africa
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Dukamo BH, Gedebo A, Tesfaye B, Degu HD. Genetic diversity of Ethiopian durum wheat ( T. turgidum subsp. durum) landraces under water stressed and non stressed conditions. Heliyon 2023; 9:e18359. [PMID: 37519732 PMCID: PMC10375799 DOI: 10.1016/j.heliyon.2023.e18359] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 08/01/2023] Open
Abstract
Ethiopia, being a major center of origin and diversity for durum wheat, possesses a highly variable genetic pool with diverse agroecological adaptations. Wheat landraces are an important source of genetic variation for breeding programs. This study was conducted to study the genotypic diversity of Ethiopian durum wheat genetic resources under two contrasting environments namely drought-stressed and non-stressed. It was carried out on 100 landraces and 4 local checks using an augmented design. Data were collected on 13 traits comprising yield and yield components, phenology, and canopy condition. The analysis of variance revealed significant differences between landraces for different traits with different sources of variation. Several landraces were found to outyield the checks at both environmental conditions. Intermediate to high estimates of the phenotypic coefficient of variation (PCV), genotypic coefficient of variation (GCV), heritability in a broad sense (h2b), and genetic advance in percent of the mean (GAPM) were observed for all the studied traits except for days to flowering at normal, thousands seed weight at stress, and days to maturity, leaf chlorophyll concentration measurement, and canopy temperature measurement at both conditions. The estimation of variability parameters showed that genotypic variation was higher than environmental variation for most traits. The number of tillers, spike length, kernel per spike, and grain yield indicated higher values for h2b and GAPM (74.42% and 20.86; 83.2% and 28.24; 70.79% and 28.0; and 89.54% and 74.71) at normal and (97.87% and 98.22; 71.27% and 28.51; 75.52% and 43.9; and 90.04% and 103.68) at the stressed condition, respectively. Spikelets per spike, kernel per spike, and thousands seed weight were positively correlated with grain yield. Grain yield exhibited a weak negative correlation with days to heading and days to maturity. Principal components analysis revealed that six traits were the major loadings on the first two principal components that describe 37.9% and 41.0% of the total morphological variance at normal and stressed conditions, respectively. Cluster analysis grouped the landraces into six clusters, with each cluster showing variation in performance for different traits under normal and stressed conditions. The intracluster distance was maximum in cluster I (D2 = 7.68) and (D2 = 8.19) at normal and stressed conditions respectively and the intercluster distance was found to be maximum between clusters I and IV (D2 = 11.02) and clusters I and II (D2 = 10.33) at normal and stressed conditions respectively. The presence of significant genetic variability among the evaluated durum wheat landraces suggests an opportunity for improvement of grain yield through the hybridization of genotypes from different clusters and subsequent selection. Genotypes with superior agronomic traits that outperform the best checks are identified as potential parents for yield improvement programs for moisture stress.
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Affiliation(s)
- Bantewalu Hailekidan Dukamo
- Hawassa University, College of Natural and Computational Sciences, Ethiopia
- Hawassa University, College of Agriculture, Ethiopia
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Moraiti CA, Verykouki E, Papadopoulos NT. Chill coma recovery of Ceratitis capitata adults across the Northern Hemisphere. Sci Rep 2022; 12:17555. [PMID: 36266456 PMCID: PMC9585097 DOI: 10.1038/s41598-022-21340-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 09/26/2022] [Indexed: 01/13/2023] Open
Abstract
The Mediterranean fruit fly, Ceratitis capitata (Diptera: Tephritidae), is an invasive pest, that is currently expanding its geographic distribution from the Mediterranean coasts to more temperate areas of Europe. Given that low temperature is a primary determinant of insect species' range boundaries especially in the Northern Hemisphere with pronounced seasonality, we used chill coma recovery time for assessing latitudinal clines in basal chill tolerance of C. capitata adults. We selected six populations obtained from areas with broad climatic variability based on the main bioclimatic variables of temperature and precipitation, spanning a latitudinal range of about 19° from Middle East to Central Europe. Adults were exposed to 0 °C for 4 h, and time to regain the typical standing position of a fly at 25 °C were recorded. The post-stress survival after a period of 8 days was also recorded. Results revealed that adults from Israel and Austria were less chill tolerant than those from Greece, resulting in curvilinear trends with latitude. Analysis of macroclimatic conditions revealed combined effects of latitude (as a proxy of photoperiod) and macroclimatic conditions on chill coma recovery time. Nonetheless, there was not a deleterious effect on post-recovery survival, except for flies obtained from the northern most point (Vienna, Austria). Overall, it seems that evolutionary patterns of basal chill coma recovery time of C. capitata adults are driven mainly by local climatic variability.
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Affiliation(s)
- Cleopatra A Moraiti
- Laboratory of Entomology and Agricultural Zoology, Department of Agriculture Crop Production and Rural Environment, School of Agricultural Sciences, University of Thessaly, Fytokou St., 38446, Volos, Magnesia, Greece
| | - Eleni Verykouki
- Laboratory of Entomology and Agricultural Zoology, Department of Agriculture Crop Production and Rural Environment, School of Agricultural Sciences, University of Thessaly, Fytokou St., 38446, Volos, Magnesia, Greece
| | - Nikos T Papadopoulos
- Laboratory of Entomology and Agricultural Zoology, Department of Agriculture Crop Production and Rural Environment, School of Agricultural Sciences, University of Thessaly, Fytokou St., 38446, Volos, Magnesia, Greece.
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Yirgu M, Kebede M, Feyissa T, Lakew B, Woldeyohannes AB. Morphological variations of qualitative traits of barley ( Hordeum vulgare L.) accessions in Ethiopia. Heliyon 2022; 8:e10949. [PMID: 36262303 PMCID: PMC9573889 DOI: 10.1016/j.heliyon.2022.e10949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/16/2022] [Accepted: 09/29/2022] [Indexed: 11/17/2022] Open
Abstract
Ethiopian barley germplasm is a potential source of useful traits to fight the production challenges of barley farming and to enhance yield productivity in favorable and marginal environments. A study was carried out to assess the distribution and patterns of 17 qualitative trait variations among 85 Ethiopian barley accessions using an alpha lattice design with two replications. The Shannon-Weaver diversity (H') index was used to estimate morphological diversity. Fifteen morphological traits of barley accessions originating from various regions of origins and altitude ranges were polymorphic. However, two traits including stem branching and lemma awn were monomorphic. The highest (0.94) overall mean of H' was obtained for glume colour, kernel row and kernel shape. The estimated H' ranged from 0.41 to 0.99 across regions, and 0.52 to 0.99 across altitude ranges with an overall mean of 0.76. The analysis of variance of H' showed significant variation for most studied traits. Principal components analysis revealed that eight traits were the major loading on the first two principal components that describe 38.3% of the total morphological variance. Heat map analysis based on morphological traits of barley accessions was also grouped into three distinct clusters. Thus, the present finding confirmed that the Ethiopian barley accessions showed vast morphological variations across the region of origins and altitude ranges. Based on the result, further evaluation is ongoing to exploit specific gene variations through phenotyping and genotyping trait association.
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Affiliation(s)
- Mihret Yirgu
- Department of Applied Biology, School of Applied Natural Science, Adama Science and Technology University, P.O. Box 1888, Adama, Ethiopia
- Department of Plant Science, College of Agriculture and Natural Resource, Madda Walabu University, P.O. Box 247, Robe, Oromia, Ethiopia
- Corresponding author.
| | - Mulugeta Kebede
- Department of Plant Biology and Biodiversity Management, College of Natural and Computational Sciences, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Tileye Feyissa
- Institute of Biotechnology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Berhane Lakew
- Holetta Agricultural Research Center, Ethiopian Institute of Agricultural Research, Holetta, Ethiopia
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Halvarsson P, Baltrušis P, Kjellander P, Höglund J. Parasitic strongyle nemabiome communities in wild ruminants in Sweden. Parasit Vectors 2022; 15:341. [PMID: 36167594 PMCID: PMC9516825 DOI: 10.1186/s13071-022-05449-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/26/2022] [Indexed: 11/10/2022] Open
Abstract
Background Wildlife hosts may serve as reservoirs for strongyles, which can be transmitted to domestic livestock. Therefore, studies evaluating nemabiome compositions in wildlife ruminants are of great use in assessing the possibility of transmission of important nematode pathogens to domestic sheep in Sweden. Methods First, fecal samples were collected from roe deer (n = 125), fallow deer (n = 106), red deer (n = 18) and mouflon (n = 13) in south central Sweden during the hunting season in 2019. Second, after fecal examination samples were cultured and the larvae were harvested, followed by DNA extractions. Third, all samples were barcoded and processed for sequence analysis on the PacBio platform. Finally, bioinformatic sequence analysis was conducted with DADA2, while species diversity and richness, as well as interactions between the different hosts, were calculated and analyzed in R. Results Nematode ITS2 sequences were found in 225 of 262 (86%) samples. In total, 31 taxa were identified, among which 26 (86%) to the species level. These were found in different combinations, among which 24 (77%) occurred in roe deer, 19 (61%) in fallow deer, 20 (65%) in red deer and 10 (32%) in mouflon. Five of the species found are known to be associated with livestock (Chabertia ovina, Haemonchus contortus, Oesophagostomum venulosum, Teladorsagia circumcincta and Trichostrongylus axei). However, in the present study the relative abundance and prevalence of most of these species were low. The most striking exception was T. axei, which was relatively abundant in all wildlife hosts. Mostly a wide range of wildlife specific nematodes such as Ostertagia leptospicularis and Spiculopteragia spp. were identified including the invasive nematode Spiculopteragia houdemeri, which was found for the first time in red deer, fallow deer, and mouflon in Sweden. The difference in the number of shared species between mouflon and all cervids (n = 6) was less than among all three cervids (n = 8). Conclusion In this study, we investigated the community structure of parasitic intestinal nematodes in four wildlife hosts, and we found that the majority of the parasite species identified were wildlife specific. We also found a new, potentially invasive species not reported before. After comparing the nemabiome of the wildlife hosts in this study with a previous study in sheep from the same geographical region, we conclude that the horizontal transmission potential appears to be relatively low. Still, cross-infections of nematodes between game and sheep cannot be completely ignored. Graphical Abstract ![]()
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Affiliation(s)
- Peter Halvarsson
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, 7036, 750 05, Uppsala, Sweden.
| | - Paulius Baltrušis
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, 7036, 750 05, Uppsala, Sweden
| | - Petter Kjellander
- Department of Ecology, Swedish University of Agricultural Sciences, Grimsö Wildlife Research Station, 739 93, Riddarhyttan, Sweden
| | - Johan Höglund
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, 7036, 750 05, Uppsala, Sweden
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Hajar CGN, Md Akhir S, Zefarina Z, Riffin NSM, Tuan Mohammad TH, Hassan MN, Aziz MY, Pati S, Chambers GK, Kari ZA, Edinur HA, Che Mat NF. Distribution of 22 Single Nucleotide Polymorphisms in 13 Cytokine Genes in Malays, Chinese, and Indians in Peninsular Malaysia. Genet Test Mol Biomarkers 2022; 26:449-456. [PMID: 36166739 DOI: 10.1089/gtmb.2022.0107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Introduction: Cytokines are cell signaling glycoproteins that are particularly important in immunity and inflammatory responses. Therefore, variations, such as single nucleotide polymorphisms (SNPs), in genes encoding for cytokines may have important consequences for their roles in health. Materials and Methods: A total of 222 unrelated, healthy, and un-admixed Malays (n = 97), Chinese (n = 77), and Indians (n = 48) with a median age of 30 years old (range 21-50) were typed for 22 cytokine gene SNPs: IL-1α -889 T/C, IL-1β (-511 T/C, +3962 T/C), IL-1R pst1 1970 T/C, IL-1RA mspa1 11100 T/C, IL-4Rα +1902 G/A, IL-12 - 1188 C/A, IFN-γ +874 A/T, TGF-β (cdn 10 C/T, cdn 25 G/C), TNF-α (-308 A/G, -238 A/G) IL-2 (+166 G/T, -330 T/G), IL-4 (-1098 T/G, -590 T/C, -33 T/C), IL-6 (-174 C/G, nt565 G/A), and IL-10 (-1082 G/A, -819 C/T, -592 A/C). This involved using well-established polymerase chain reaction procedures with sequence-specific primers and restriction fragment length polymorphism methods. Results: The majority of the screened cytokine gene SNPs are polymorphic in all three ethnicities. Exceptions include TGF-β cdn 25 (G/C), IL-1β +3962 (T/C), and TNF-α -238 (A/G), which were all observed to be monomorphic in Malays, Chinese and Indians. Many of the analyzed cytokine gene SNP genotypes deviated from Hardy-Weinberg equilibrium and the three ethnic study groups were all well-separated from reference Asian, African and European populations in a principal component analysis plot. Conclusion: We successfully typed 22 SNPs in 13 cytokine genes from genetic material collected from unrelated and un-admixed Malay, Chinese and Indian individuals in Peninsular Malaysia. These new cytokine gene population datasets reveal interesting contrasts with other populations.
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Affiliation(s)
- Che Ghazali Norul Hajar
- Forensic Science Programme, School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
- Transfusion Medicine Unit, Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Suhaida Md Akhir
- Biomedicine Science Programme, School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Zulkafli Zefarina
- Transfusion Medicine Unit, Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kelantan, Malaysia
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | | | | | - Mohd Nazri Hassan
- Transfusion Medicine Unit, Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kelantan, Malaysia
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Mohd Yusmaidie Aziz
- Integrative Medicine Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | | | | | - Zulhisyam Abdul Kari
- Faculty of Agro Based Industry, Universiti Malaysia Kelantan, Kelantan, Malaysia
| | - Hisham Atan Edinur
- Forensic Science Programme, School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
- Transfusion Medicine Unit, Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Nor Fazila Che Mat
- Transfusion Medicine Unit, Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kelantan, Malaysia
- Biomedicine Science Programme, School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
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Huang JH, Zeng FJ, Guo JF, Huang JY, Lin HC, Lo CT, Chou WM. Purification, identification and characterization of Nag2 N-acetylglucosaminidase from Trichoderma virens strain mango. BOTANICAL STUDIES 2022; 63:14. [PMID: 35578140 PMCID: PMC9110600 DOI: 10.1186/s40529-022-00344-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND N-acetylglucosaminidase (NAGase) could liberate N-acetylglucosamine (GlcNAc) from GlcNAc-containing oligosaccharides. Trichoderma spp. is an important source of chitinase, particularly NAGase for industrial use. nag1 and nag2 genes encoding NAGase, are found in the genome in Trichoderma spp. The deduced Nag1 and Nag2 shares ~ 55% homology in Trichoderma virens. Most studies were focus on Nag1 and nag1 previously. RESULTS The native NAGase (TvmNAG2) was purified to homogeneity with molecular mass of ~ 68 kDa on SDS-PAGE analysis, and identified as Nag2 by MALDI/MS analysis from an isolate T. virens strain mango. RT-PCR analyses revealed that only nag2 gene was expressed in liquid culture of T. virens, while both of nag1 and nag2 were expressed in T. virens cultured on the plates. TvmNAG2 was thermally stable up to 60 °C for 2 h, and the optimal pH and temperature were 5.0 and 60-65 °C, respectively, using p-nitrophenyl-N-acetyl-β-D-glucosaminide (pNP-NAG) as substrate. The hydrolytic product of colloidal chitin by TvmNAG2 was suggested to be GlcNAc based on TLC analyses. Moreover, TvmNAG2 possesses antifungal activity, inhibiting the mycelium growth of Sclerotium rolfsii. And it was resistant to the proteolysis by papain and trypsin. CONCLUSIONS The native Nag2, TvmNAG2 was purified and identified from T. virens strain mango, as well as enzymatic properties. To our knowledge, it is the first report with the properties of native Trichoderma Nag2.
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Affiliation(s)
- Jheng-Hua Huang
- Department of Biotechnology, National Formosa University, Yunlin, 632 Taiwan, ROC
| | - Feng-Jin Zeng
- Department of Biotechnology, National Formosa University, Yunlin, 632 Taiwan, ROC
| | - Jhe-Fu Guo
- Department of Biotechnology, National Formosa University, Yunlin, 632 Taiwan, ROC
| | - Jian-Yuan Huang
- Department of Biotechnology, National Formosa University, Yunlin, 632 Taiwan, ROC
| | - Hua-Chian Lin
- Department of Biotechnology, National Formosa University, Yunlin, 632 Taiwan, ROC
| | - Chaur-Tsuen Lo
- Department of Biotechnology, National Formosa University, Yunlin, 632 Taiwan, ROC
| | - Wing-Ming Chou
- Department of Biotechnology, National Formosa University, Yunlin, 632 Taiwan, ROC
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Identification of functional features underlying heat stress response in Sprague-Dawley rats using mixed linear models. Sci Rep 2022; 12:7671. [PMID: 35538164 PMCID: PMC9090733 DOI: 10.1038/s41598-022-11701-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 04/25/2022] [Indexed: 11/11/2022] Open
Abstract
Since global temperature is expected to rise by 2 °C in 2050 heat stress may become the most severe environmental factor. In the study, we illustrate the application of mixed linear models for the analysis of whole transcriptome expression in livers and adrenal tissues of Sprague–Dawley rats obtained by a heat stress experiment. By applying those models, we considered four sources of variation in transcript expression, comprising transcripts (1), genes (2), Gene Ontology terms (3), and Reactome pathways (4) and focussed on accounting for the similarity within each source, which was expressed as a covariance matrix. Models based on transcripts or genes levels explained a larger proportion of log2 fold change than models fitting the functional components of Gene Ontology terms or Reactome pathways. In the liver, among the most significant genes were PNKD and TRIP12. In the adrenal tissue, one transcript of the SUCO gene was expressed more strongly in the control group than in the heat-stress group. PLEC had two transcripts, which were significantly overexpressed in the heat-stress group. PER3 was significant only on gene level. Moving to the functional scale, five Gene Ontologies and one Reactome pathway were significant in the liver. They can be grouped into ontologies related to DNA repair, histone ubiquitination, the regulation of embryonic development and cytoplasmic translation. Linear mixed models are valuable tools for the analysis of high-throughput biological data. Their main advantages are the possibility to incorporate information on covariance between observations and circumventing the problem of multiple testing.
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Hussain S, Habib M, Ahmed Z, Sadia B, Bernardo A, Amand PS, Bai G, Ghori N, Khan AI, Awan FS, Maqbool R. Genotyping-by-Sequencing Based Molecular Genetic Diversity of Pakistani Bread Wheat ( Triticum aestivum L.) Accessions. Front Genet 2022; 13:772517. [PMID: 35464861 PMCID: PMC9019749 DOI: 10.3389/fgene.2022.772517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 01/07/2022] [Indexed: 11/29/2022] Open
Abstract
Spring wheat (Triticum aestivum L.) is one of the most imperative staple food crops, with an annual production of 765 million tons globally to feed ∼40% world population. Genetic diversity in available germplasm is crucial for sustainable wheat improvement to ensure global food security. A diversity panel of 184 Pakistani wheat accessions was genotyped using 123,596 high-quality single nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing with 42% of the SNPs mapped on B, 36% on A, and 22% on D sub-genomes of wheat. Chromosome 2B contains the most SNPs (9,126), whereas 4D has the least (2,660) markers. The mean polymorphic information content, genetic diversity, and major allele frequency of the population were 0.157, 0.1844, and 0.87, respectively. Analysis of molecular variance revealed a higher genetic diversity (80%) within the sub-population than among the sub-populations (20%). The genome-wide linkage disequilibrium was 0.34 Mbp for the whole wheat genome. Among the three subgenomes, A has the highest LD decay value (0.29 Mbp), followed by B (0.2 Mbp) and D (0.07 Mbp) genomes, respectively. The results of population structure, principal coordinate analysis, phylogenetic tree, and kinship analysis also divided the whole population into three clusters comprising 31, 33, and 120 accessions in group 1, group 2, and group 3, respectively. All groups were dominated by the local wheat accessions. Estimation of genetic diversity will be a baseline for the selection of breeding parents for mutations and the genome-wide association and marker-assisted selection studies.
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Affiliation(s)
- Shabbir Hussain
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Madiha Habib
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Zaheer Ahmed
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Bushra Sadia
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Amy Bernardo
- USDA, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, United States
| | - Paul St Amand
- USDA, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, United States
| | - Guihua Bai
- USDA, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, United States
| | - Nida Ghori
- USDA, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, United States
| | - Azeem I Khan
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Faisal S Awan
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Rizwana Maqbool
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
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Sharko FS, Khatib A, Prokhortchouk EB. Genomic Estimated Breeding Value of Milk Performance and Fertility Traits in the Russian Black-and-White Cattle Population. Acta Naturae 2022; 14:109-122. [PMID: 35441049 PMCID: PMC9013432 DOI: 10.32607/actanaturae.11648] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/14/2022] [Indexed: 11/20/2022] Open
Abstract
A breakthrough in cattle breeding was achieved with the incorporation of animal genomic data into breeding programs. The introduction of genomic selection has a major impact on traditional genetic assessment systems and animal genetic improvement programs. Since 2010, genomic selection has been officially introduced in the evaluation of the breeding and genetic potential of cattle in Europe, the U.S., Canada, and many other developed countries. The purpose of this study is to develop a system for a genomic evaluation of the breeding value of the domestic livestock of Black-and-White and Russian Holstein cattle based on 3 milk performance traits: daily milk yield (kg), daily milk fat (%), and daily milk protein content (%) and 6 fertility traits: age at first calving (AFC), calving interval (CI), calving to first insemination interval (CFI), interval between first and last insemination (IFL), days open (DO), and number of services (NS). We built a unified database of breeding animals from 523 breeding farms in the Russian Federation. The database included pedigree information on 2,551,529 cows and 69,131 bulls of the Russian Holstein and Black-and-White cattle breeds, as well as information on the milk performance of 1,597,426 cows with 4,771,366 completed lactations. The date of birth of the animals included in the database was between 1975 and 2017. Genotyping was performed in 672 animals using a BovineSNP50 v3 DNA Analysis BeadChip microarray (Illumina, USA). The genomic estimated breeding value (GEBV) was evaluated only for 644 animals (427 bulls and 217 cows) using the single-step genomic best linear unbiased prediction - animal model (ssGBLUP-AM). The mean genetic potential was +0.88 and +1.03 kg for the daily milk yield, -0.002% for the milk fat content, and -0.003 and 0.001% for the milk protein content in the cows and bulls, respectively. There was negative genetic progress in the fertility traits in the studied population between 1975 and 2017. The reliability of the estimated breeding value (EBV) for genotyped bulls ranged from 89 to 93% for the milk performance traits and 85 to 90% for the fertility traits, whereas the reliability of the genomic estimated breeding value (GEBV) varied 54 to 64% for the milk traits and 23 to 60% for the fertility traits. This result shows that it is possible to use the genomic estimated breeding value with rather high reliability to evaluate the domestic livestock of Russian Holstein and Black-and-White cattle breeds for fertility and milk performance traits. This system of genomic evaluation may help bring domestic breeding in line with modern competitive practices and estimate the breeding value of cattle at birth based on information on the animal's genome.
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Affiliation(s)
- F. S. Sharko
- Laboratory of vertebrate genomics and epigenomics, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Moscow, 119071 Russia
| | - A. Khatib
- Laboratory I-Gene, ZAO “Genoanalytica”, Moscow, 119234 Russia
- Department of biotechnology, faculty of Biology, Lomonosov Moscow State University, Moscow, 119234 Russia
- Atomic Energy Commission of Syria (AECS), Department of Agriculture, Damascus, 6091 Syria
| | - E. B. Prokhortchouk
- Laboratory of vertebrate genomics and epigenomics, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Moscow, 119071 Russia
- Laboratory I-Gene, ZAO “Genoanalytica”, Moscow, 119234 Russia
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Rezaei Topraggaleh T, Numan Bucak M, Shahverdi M, Koohestani Y, Furkan Batur A, Rahimizadeh P, Ili P, Gul M, Ashrafzade AM, Kazem-Allilo A, Garip M, Shahverdi A. Functional and Flow Cytometric Analysis of Buffalo Cryopreserved Spermatozoa: Comparison of Different Breeds and Incubation Times. INTERNATIONAL JOURNAL OF FERTILITY & STERILITY 2021; 15:252-257. [PMID: 34913292 PMCID: PMC8530219 DOI: 10.22074/ijfs.2021.521116.1057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/15/2021] [Indexed: 11/18/2022]
Abstract
BACKGROUND The purpose of this research was to compare the functional parameters of frozen-thawed Iranian Azari buffalo spermatozoa with imported semen samples of Italian Mediterranean buffalo (IMB) after the thawing process and 4 hours of incubation. MATERIALS AND METHODS In this experimental study, a total of twenty-four ejaculates from four Iranian Azari buffalo bulls were collected. Semen samples were diluted in AndroMed extender at a concentration of 50×106 spermatozoa/ ml. The diluted samples were filled in 0.5 ml straws and were frozen in a programmable freezer. For imported semen samples, twenty-four samples of four IMB were used, which were diluted in AndroMed extender and frozen by the same procedure. Frozen-thawed sperm motion patterns, mitochondrial activity, membrane integrity, DNA integrity, reactive oxygen species (ROS), and apoptosis status were evaluated immediately after thawing and 4 hours of incubation. RESULTS Post-thawed sperm motility, progressive motility (PM), mitochondrial activity, membrane integrity were significantly higher in imported semen samples in compare with Iranian Azari buffalo. After 4 hours of incubation, sperm velocity patterns were superior in Iranian Azari semen samples. Moreover, the percentage of sperm cells with un-damaged DNA was higher in Iranian semen samples compared to imported samples at the time 0 of incubation. Following 4 hours of incubation, a significant increase in intracellular ROS level leads to reduced membrane integrity, mitochondrial activity, and DNA integrity in both buffalo breeds. At time 4, Iranian samples showed significantly lower apoptosis and higher dead spermatozoa compared to imported semen samples. CONCLUSION Our study showed that the post-thawed quality of Iranian Azari buffalo semen was comparable with imported samples after 4 hours of incubation. Further investigations are recommended to assess the in vitro and in vivo fertility rate of both buffalo breeds.
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Affiliation(s)
- Tohid Rezaei Topraggaleh
- Department of Anatomical Sciences, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Mustafa Numan Bucak
- Department of Reproduction and Artificial Insemination, Faculty of Veterinary Medicine, Selcuk University, Konya, Turkey
| | - Maryam Shahverdi
- Department of Embryology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Yegane Koohestani
- Department of Anatomical Sciences, Faculty of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Ali Furkan Batur
- Department of Urology, Selcuk University School of Medicine, Konya, Turkey
| | - Pegah Rahimizadeh
- Department of Embryology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Pinar Ili
- Department of Medical Services and Techniques, Denizli Vocational School of Health Services, Pamukkale University, Denizli, Turkey
| | - Murat Gul
- Department of Urology, Selcuk University School of Medicine, Konya, Turkey
| | - Amir Mahdi Ashrafzade
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | | | - Mustafa Garip
- Department of Animal Science, Faculty of Veterinary Medicine, Selcuk University, Konya, Turkey
| | - Abdolhossein Shahverdi
- Department of Embryology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran,Reproductive Epidemiology Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran,P.O.Box: 16635-148Department of EmbryologyReproductive Biomedicine Research CenterRoyan Institute for Reproductive BiomedicineACECRTehranIran
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