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    Assessment of silage quality of phytogenic fortified feed samples in mini-silos for ruminants

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    Article Details: Received: 2019-12-04 | Accepted: 2020-02-18 | Available online: 2020-03-31https://doi.org/10.15414/afz.2020.23.01.24-28This study was conducted to assess the silage quality of Zingiber officinale fortified samples in a completely randomized design. The samples consisted of four treatments as samples: Cassava peel (65%) + Moringa leaf (15%) + PKC (20%)+ Ginger (0 g), Cassava peel (65%) + Moringa leaf (15%) + PKC (20%) + ginger (200 g), Cassava peel (65%) + Moringa leaf (15%) + PKC (20%) + ginger (300 g), Cassava peel (65%) + Moringa leaf (15%) + PKC (20%) + ginger (400 g). The physical characteristics; colour, smell, texture, pH, temperature and mould status were observed. All samples retained their original colour, had pleasant alcoholic smell with a firm texture, the pH ranged from 4.2–4.4, temperature range of 25–26 °C with sample D having the highest temperature range of 26 °C while samples A and B had the same temperature of 25.5 °C. The mould status showed absence of mould. The chemical composition revealed that dry matter ranged from 40.86% (sample B) to 54.68% (sample D). Crude protein content ranged from 13.30% to 14.88%, crude fibre content of the samples was significantly (p <0.05) different and it ranged from 14.67% to 22.14%. The mineral concentrations of the samples were higher in Zingiber officinale samples except in sample A where potassium was higher (100.40 mg 100 g-1) than in other samples. Volatile fatty acid composition showed that lactic acid (3.24–4.86%) had higher concentration than other acids. It can therefore be concluded that Zingiber officinale fortified sample showed better nutritional potential as ruminant feed.Keywords: volatile fatty acid, silage, Zingiber officinale, ruminantsReferencesAdediran , O. A, Uwalaka , E. C. and Kolapo, T.U. (2014). Antihelminthic and Anticoccidial Effects of Vernonia amygdalina in Goats. Journal of Veterinary Advances, 4(7), 610–615.Ademola, S. G., Farinu, G. O. and Babatunde , G. M. (2009). Serum lipid growth and hematological parameters of broilers fed garlic, ginger and their mixtures. World Journal of Agricultural Science, 5(1), 9–104.Aluwong , T., Kobo, P. I and Abdullahi, A. (2010). Volatile fatty acids production in ruminants and the role of monocarboxylate transporters. African Journal of Biotechnology, 9(38), 6229–6232.Ashbell, G. Z.G. et al. (2002). The effects of temperature on the aerobic stability of wheat and corn silages. J. Ind. Microbiol. Biotechnol., 28, 261–263.Association of Analytical Communities (AOAC) (1990). Official Methods of Analysis. 15th edn. Association Official Analytical Chemists, 805–845.Bilal, M.Q (2009). Effect of molasses and corn as silage additives on the characteristics of mott dwarf elephant grass silage at different fermentation periods. Pakistan Veterinary Journal, 29, 19–23.Castrillo C. (2001). The effect of crude fibre on apparent digestibility and digestible energy content of extruded dog foods. Journal of Animal physiology and Animal nutrition, 231–236.Daniel, O. A. (2015). Urban extreme weather: a challenge for a healthy Living environment in Akure, Ondo State, Nigeria. Climate, 3(4), 775–791.Ibhaze, G.A and Fajemisin , A.N. (2015). Feed intake and nitrogen metabolism by West African Dwarf does fed naturally fermented maizecob based diets. World Journal of Animal Science Research, 3(2), 1 – 8.Jenkins, T.C. and McGuire, M.A. (2006). Major Advances in Nutrition: Impact on milk composition. Journal of Dairy Science, 89(10),1302–1310.Kung, L. and Shaver, R. (2001). Interpretation and use of silage fermentation analyses reports. Focus on Forage, 3(13).Manni, G. and Caron , F. (1995). Calibration and determination of volatile fatty acids in waste leachates by gas chromatography. J. Chromatogr. A, 690, 237.Mohammed , A. A and Yusuf, M. (2011). Evaluation of ginger (Zingiber officinale) as a feed additive in broiler diets. Livestock Research for Rural Development, 23(9).Moran , J. (2005). Making quality silage. Tropical dairy farming. Feeding management for small holder dairy farmers inthe tropics. Landlinks Press.N.R.C (1984) Nutrient Requirements of sheep. National Research Council- National Academy of Sciences, Washington DC.Nhan, N.T.H., Hon, N.V., and Preston , T.R. (2009). Ensiling with or without additives to preserve pineapple residue and reduce pollution of the environment. Livestock Research for Rural Development. 21, Article #96. Retrieved November 29, 2010, from http://www.lrrd.org/lrrd21/7/nhan21096.htmNorton , B.W (2003). Studies of the nutritive of Austrialian goat : thesis (D.Agric; Sc). University of Melbourne.Pauzenga , U. (1985). Feeding Parent Stock. Zootecnica International., 22–24.SAS (2012). Statistical Analysis System. SAS Version 9.2 user’s guide. Cary, NY: SAS institute.Schroeder , J.W. (2004). Corn Silage management. Pub. AS-1253. NDSU Coop. Ext.Ser.pub. 1254.Van Soest, P.J. and Robertson , J.B. (1985). Analysis of forages and fibrous foods. Lab Manual for Animal Science no. 613. Department of Animal Science, Cornell University, Ithaca, 105–106.Weinberg , Z.G. et al. (2001). The effect of temperature on the ensiling process of corn and wheat. J Appl. Microbial., 90, 561–566

    Insects as sustainable feed and food

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    Submitted 2020-07-06 | Accepted 2020-07-31 | Available 2020-12-01https://doi.org/10.15414/afz.2020.23.mi-fpap.214-216Insects are one of the proposed responses to the increasing request of alternative feed/food productions with high production yield and low environmental impact. Insect production offers a new sustainable alternative for unexploited or underexploited resources, in accordance with the waste hierarchy principles. Insects constitute a reliable alternative or addition to feed due to their nutritional characteristics (e.g. protein content, amino acid profile and/or digestibility levels). Edible insects may be part of human foods mostly as ingredients in already well-known products or integration of insect-based foods into existing diets. In the near future research is needed to increase knowledges and support the insect industry to a considerably scale up to reach competitive price and high-quality products.Keywords: entomophagy, novel food, environment, protein, fatReferenceFinke, M. D., Rojo, S., Roos, N., van Huis, A., & Yen, A. L. (2015). The European Food Safety Authority scientific opinion on a risk profile related to production and consumption of insects as food and feed. Journal of Insects as Food and Feed, 1(4), 245–247. https://doi.org/10.3920/JIFF2015.x006Gasco, L., Biancarosa, I., & Liland, N. S. (2020). From waste to feed: A review of recent knowledge on insects as producers of protein and fat for animal feeds. Current Opinion in Green and Sustainable Chemistry. https://doi.org/10.1016/j.cogsc.2020.03.003Kroeckel, S., Harjes, A.-G. E., Roth, I., Katz, H., Wuertz, S., Susenbeth, A., & Schulz, C. (2012). When a turbot catches a fly: Evaluation of a pre-pupae meal of the Black Soldier Fly (Hermetia illucens) as fish meal substitute — Growth performance and chitin degradation in juvenile turbot (Psetta maxima). Aquaculture, 364–365, 345–352. https://doi.org/10.1016/j.aquaculture.2012.08.041Lock, E. J., Biancarosa, I., & Gasco, L. (2018). Insects as raw materials in compound feed for aquaculture. In Halloran, A. et al. (eds.) Edible Insects in Sustainable Food Systems. Springer International Publishing (pp. 263–276).Mancini, S., Moruzzo, R., Riccioli, F., & Paci, G. (2019). European consumers’ readiness to adopt insects as food. A review. Food Research International, 122, 661–678. https://doi.org/10.1016/j.foodres.2019.01.041Murefu, T. R., Macheka, L., Musundire, R., & Manditsera, F. A. (2019). Safety of wild harvested and reared edible insects: A review. Food Control, 101, 209–224. https://doi.org/10.1016/j.foodcont.2019.03.003Nischalke, S., Wagler, I., Tanga, C., Allan, D., Phankaew, C., Ratompoarison, C., Razafindrakotomamonjy, A., & Kusia, E. (2020). How to turn collectors of edible insects into mini-livestock farmers: Multidimensional sustainability challenges to a thriving industry. Global Food Security, 26, 100376. https://doi.org/10.1016/j.gfs.2020.100376Sogari, G., Amato, M., Biasato, I., Chiesa, S., & Gasco, L. (2019). The potential role of insects as feed: A multi-perspective review. Animals, 9(4), 119. https://doi.org/10.3390/ani9040119van Huis, A. (2013). Potential of insects as food and feed in assuring food security. Annual Review of Entomology, 58, 563-583. https://doi.org/10.1146/annurev-ento-120811-153704van Huis, A. (2020). Insects as food and feed, a new emerging agricultural sector: a review. Journal of Insects as Food and Feed, 6(1), 27–44. https://doi.org/10.3920/JIFF2019.0017van Huis, A., & Oonincx, D. G. A. B. (2017). The environmental sustainability of insects as food and feed. A review. Agronomy for Sustainable Development, 37(5), 43. https://doi.org/10.1007/s13593-017-0452-8van Huis, A., & Tomberlin, J. K. (2017). Insects as food and feed : from production to consumption. Wageningen: Wageningen Academic Publishers.van Huis, A., Van Itterbeeck, J., Klunder, H., Mertens, E., Halloran, A., Muir, G., & Vantomme, P. (2013). Edible insects. Future prospects for food and feed security. In FAO Forestry Paper (Vol. 171). Retrieved from http://www.fao.org/docrep/018/i3253e/i3253e.pd

    Milk microbiome: evaluation study on the differences among cows with a different health status classified by leukocyte pattern

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    Submitted 2020-06-30 | Accepted 2020-07-25 | Available 2020-12-01https://doi.org/10.15414/afz.2020.23.mi-fpap.67-73Milk is considered not only a source of nutrient for the offspring but also a font of immunoregulatory compounds capable to predispose the naïve intestinal immune system of the new-born to react to the external environment. In the present study we evaluated the composition of milk microbiome from cows classified according to milk total and differential somatic cell counts. A total of 34, 13 and 13 milk samples of healthy, at risk and subclinical or chronic cows, respectively, were collected during the same milking from a local dairy herd. Through Next Generation Sequencing (NGS) of bacterial 16S rRNA gene, the differences of taxa in terms of relative abundances (RA) and alpha and beta biodiversity were analysed. The RA of several genera were statistically significant in the three groups, such as Arcanobacterium (p=0.001), Rhodococccus (p<0.05) and Rubrobacter (p<0.05), while at species level the presence of Propionibacterium granulosum, Pseudomonas alcaligenes and Prosthecobacter debontii were found. Shannon and Evenness indices computed at the genus level were not significant, while beta biodiversity showed a clear clusterization between groups. The results highlighted that milk microbiome is associated to a different cellular response at udder level, although more specific studies are needed to assess the source of bacteria species identified in milk microbial population of healthy animals.Keywords: milk microbiome; bovine; mastitis; differential cell countReferencesBOLYEN. E.; RIDEOUT. J.R.; DILLON. M.R.; BOKULICH. N.A.; ABNET. C.C.; AL-GHALITH. G.A.; ALEXANDER. H.; ALM. E.J.; ARUMUGAM, M.; ASNICAR. F.; et al. (2019). Reproducible. interactive. scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 37, 852-857.BOWEN, J. M.; MCCABE, M.S.; LISTER, S.J.; CORMICAN, P. AND DEWHURST, R.J. (2018). Evaluation of Microbial Communities Associated With the Liquid and Solid Phases of the Rumen of Cattle Offered a Diet of Perennial Ryegrass or White Clover. Frontiers in microbiology, 9, 2389.DERAKHSHANI, H.; FEHR, K.B.; SEPEHRI, S.; FRANCOZ, D.; DE BUCK, J.; BARKEMA, H.W.; PLAIZIER, J.C. AND KHAFIPOUR, E. (2018). Invited review: microbiota of the bovine udder: contributing factors and potential implications for udder health and mastitis susceptibility. J Dairy Sci 101, 10605-10625.GANDA, E.K.; GAETA, N.; SIPKA, A.; POMEROY, B.; OIKONOMOU, G.; SCHUKKEN, Y.H. AND BICALHO, R.C. (2017). Normal milk microbiome is reestablished following experimental infection with Escherichia coli independent of intramammary antibiotic treatment with a third-generation cephalosporin in bovines. Microbiome 5, 74.IVANOVA, N.; SIKORSKI, J.; SIMS, D.; BRETTIN, T.; DETTER, J.C.; HAN, C.; LAPIDUS, A.; COPELAND, A.; GLAVINA DEL RIO, T.; NOLAN, M.; CHEN, F.; LUCAS, S.; TICE, H.; CHENG, J.F.; BRUCE, D.; GOODWIN, L.; PITLUCK, S.; PATI, A.; MAVROMATIS, K.; CHEN, A.; PALANIAPPAN, K.; D'HAESELEER, P.; CHAIN, P.; BRISTOW, J.; EISEN, J.A.; MARKOWITZ, V.; HUGENHOLTZ, P.; GÖKER, M.; PUKALL, R.; KLENK, H.P. AND KYRPIDES, N.C. (2009). Complete genome sequence of Sanguibacter keddieii type strain (ST-74). Stand Genomic Sci 24, 1, 110-118.KEHRLI. M.E. AND HARP, J.A. (2001). Immunity in the mammary gland. Vet Clin North Am Food Anim Pract 17, 495-516.KEIKHA M. (2017). Williamsia spp. are emerging opportunistic bacteria. New Microbes New Infect 21, 88-89.KLINDWORTH. A.; PRUESSE. E.; SCHWEER. T.; PEPLIES. J.; QUAST. C.; HORN. M. AND GLOCKNER. F.O. (2013). Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 41, e1.KUEHN, J.S.; GORDEN, P.J.; MUNRO, D.; RONG, R.; DONG, Q.; PLUMMER, P.J.; WANG, C. AND PHILLIPS, G.J. (2013). Bacterial community profiling of milk samples as a means to understand culture-negative bovine clinical mastitis. PLoS ONE 13, 8, e61959.LIMA, S.F.; BICALHO, M.L.DS. AND BICALHO, R.C. (2018). Evaluation of milk sample fractions for characterization of milk microbiota from healthy and clinical mastitis cows. PLoS ONE 13, e0193671.LOZUPONE, C. AND KNIGHT, R. (2005). UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71, 8228‐8235.MACPHERSON, A.J. AND UHR, T. (2004). Induction of protective IgA by intestinal dendritic cells carrying commensal bacteria. Science 303, 1662-1665.METZGER, S.A.; HERNANDEZ, L.L.; SUEN, G. AND RUEGG, P.L. (2018). Understanding the milk microbiota. Vet Clin North Am Food Anim Pract 34, 427-438.OIKONOMOU, G.; BICALHO, M.L.; MEIRA, E.; ROSSI, R.E.; FODITSCH, C.; MACHADO, V.S.; TEIXEIRA, A.G.; SANTISTEBAN, C.; SCHUKKEN, Y.H. AND BICALHO, R.C. (2014). Microbiota of cow's milk; distinguishing healthy, sub-clinically and clinically diseased quarters. PloS one, 9(1), e85904. https://doi.org/10.1371/journal.pone.0085904 (2014) Microbiota of Cow’s Milk: Distinguishing Healthy, Sub-Clinically and Clinically Diseased Quarters. PLoS ONE 9, e85904.OIKONOMOU, G.; MACHADO, V.S.; SANTISTEBAN, C.; SCHUKKEN, Y.H. AND BICALHO, R.C. (2012). Microbial Diversity of Bovine Mastitic Milk as Described by Pyrosequencing of Metagenomic 16s DNA. PLoS ONE 7, e47671.RODRÍGUEZ, J.M. (2014). The origin of human milk bacteria: Is there a bacterial entero-mammary pathway during late pregnancy and lactation? Adv Nutr 5, 779-784.ROUX, M.E.; MCWILLIAMS, M.; PHILLIPS-QUAGLIATA, J.M.; WEISZ-CARRINGTON, P. AND LAMM, M.E. (1977). Origin of IgA-secreting plasma cells in the mammary gland. Journal of Experimental Medicine 146, 1311-1322.STOCCO, G.; SUMMER, A.; CIPOLAT-GOTET, C.; ZANINI, L.; VAIRANI, D.; DADOUSIS, D. AND A. ZECCONI (2020). Differential cell count as a novel indicator of milk quality in dairy cows. Animals 10, 1-14.TAPONEN, S.; MCGUINNESS, D.; HIITIÖ. H.; SIMOJOKI, H.; ZADOKS, R. AND PYÖRÄLÄ, S. (2019). Bovine milk microbiome: a more complex issue than expected. Vet Res 50, 44.TOLLE, A. (1980). The microflora of the udder. Factors influencing the bacteriological quality of raw milk. International Dairy Federation Bulletin Document 120, 4.VANGROENWEGHE, F.; DOSOGNE, H.; MEHRZAD, J. AND BURVENICH, C. (2001). Effect of milk sampling techniques on milk composition, bacterial contamination, viability and functions of resident cells in milk. Vet Res 32, 565-579.VERDIER-METZ, I.; GAGNE, G.; BORNES, S.; MONSALLIER, F.; VEISSEIRE, P.; DELBÈS-PAUS, C. AND MONTEL, M.C. (2012). Cow teat skin, a potential source of diverse microbial populations for cheese production. Appl Environ Microbiol 78,326-333.WEON, H.Y.; LEE, C.M.; HONG, S.B.; KIM, B.Y.; YOO, S.H.; KWON, S.W. AND GO, S.J. (2008). Kaistia soli sp. nov., isolated from a wetland in Korea. Int J Syst Evol Microbiol 58, 1522-1524.YOUNG, W.; HINE, B.C.; WALLACE, O.A.; CALLAGHAN, M. AND BIBILONI, R. (2015). Transfer of intestinal bacterial components to mammary secretions in the cow. PeerJ 3, e888.ZECCONI, A. AND PICCININI R. (2002). Intramammary infections: epidemiology and diagnosis. XXII World Buiatric Congress - Recent developments and perspectives in bovine medicine. HannoverZECCONI, A.; DELL’ORCO, F.; VAIRANI, D.; RIZZI, N.; CIPOLLA, M. AND ZANINI, L. (2020 a). Differential cell count as a marker for changes of milk composition in cows very low somatic cell counts. Animals 10, 1-14.ZECCONI, A.; ZANINI, L.; CIPOLLA, M.; STEFANON, B. (2020 b). Factors Affecting the Patterns of Total Amount and Proportions of Leukocytes in Bovine Milk. Animals 10, 992.ZECCONI, A.; HAMANN, J.; BRONZO, V.; MORONI, P.; GIOVANNINI, G. AND PICCININI, R. (2000). Relationship between teat tissue immune defences and intramammary infections. Adv Exp Med and Biol 480, 287-293.ZECCONI, A.; VAIRANI, D.; CIPOLLA, M.; RIZZI, N. AND ZANINI, L. (2019 a). Assessment of subclinical mastitis diagnostic accuracy by differential cell count in individual cow milk, Italian Journal of Animal Science 18, 460-465.ZECCONI, A.; SESANA, G.; VAIRANI, D.; CIPOLLA, M.; RIZZI, N. AND ZANINI, L. (2019 b). Somatic cell count as a decision tool for selective dry cow therapy in Italy. Italian Journal of Animal Science 18, 435-440.  

    Genome sequence variation in two subspecies of western honeybee, A.m.carnica and A.m.ligustica

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    Submitted 2020-08-09 | Accepted 2020-09-21 | Available 2020-12-01https://doi.org/10.15414/afz.2020.23.mi-fpap.331-337Populations of western honeybee (Apis mellifera) show differences in morphology, physiology and behaviour as a result of adaptation to various habitats. A. m. carnica, which inhabits the South-East and Central Europe, and A. m. ligustica, which is endemic on Apennine peninsula, represent 2 closely related honeybee subspecies living in the neighbouring climatic regions. In the current study, 3,655,618 polymorphisms were identified from the whole genome sequences of 37 individual drone genomes, from A. m. carnica (n=27) and A. m. ligustica (n=10). The analysis revealed variation in genes involved in biological pathways associated with energy production and conversion, cell cycle and cytokinesis.Keywords: A. m. carnica, A. m. ligustica, genomics, honeybee, whole genome sequencingReferencesBoch, R. (1957). 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Apidologie, 38(2), 207-217. https://doi.org/10.1051/apido:2006073De la Rúa, P. et al. (2009). Biodiversity, conservation and current threats to European honeybees. Apidologie, 40(3), 263-284. https://doi.org/10.1051/apido/2009027Engel, M. S. (1999). The taxonomy of recent and fossil honey bees (Hymenoptera: Apidae; Apis). Journal of Hymenoptera Research, 8, 165-196.Gissi, C., Iannelli, F. and Pesole, G. (2008). Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species. Heredity, 101(4), 301-320. https://doi.org/10.1038/hdy.2008.62Gonzalez, A. N., Ing, N. and Rangel, J. (2018). Upregulation of antioxidant genes in the spermathecae of honey bee (Apis mellifera) queens after mating. Apidologie, 49(2), 224-234. https://doi.org/10.1007/s13592-017-0546-yHoefer, I. and Lindauer, M. (1975). Das Lernverhalten zweier Bienenrassen unter veränderten Orientierungsbedingungen. 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Metabolism and upper thermal limits of Apis mellifera carnica and A. m. ligustica. Apidologie, 45(6), 664-677. https://doi.org/10.1007/s13592-014-0284-3Kriventseva, E. V. et al. (2019). OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs. Nucleic Acids Research, 47(D1), D807-D811. https://doi.org/10.1093/nar/gky1053Kunieda, T. et al. (2006). Carbohydrate metabolism genes and pathways in insects: insights from the honey bee genome. Insect Molecular Biology, 15(5), 563-576. https://doi.org/10.1111/j.1365-2583.2006.00677.xLe Conte, Y. and Navajas, M. (2008). Climate change: impact on honey bee populations and diseases. Revue Sentifique et technique, 27(2), 485-497, 499-510.Li, H. and Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25(14), 1754-1760. https://doi.org/10.1093/bioinformatics/btp324Li, J. et al. (2007). 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    Estimation of population differentiation using pedigree and molecular data in Black Slavonian pig

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    Submitted 2020-07-17 | Accepted 2020-08-24 | Available 2020-12-01https://doi.org/10.15414/afz.2020.23.mi-fpap.241-249The aim of the study was to investigate the genetic differentiation of the Black Slavonian pig population. Two parallel analyses were performed using genealogical records and molecular data. Pedigree information of 6,099 pigs of the Black Slavonian breed was used to evaluate genetic variability and population structure. Additionally, 70 pigs were genotyped using 23 microsatellite markers. Genealogical data showed shrinkage in genetic diversity parameters with effective population size of 23.58 and inbreeding of 3.26%. Expected and observed heterozygosity were 0.685 and 0.625, respectively, and the average number of alleles per locus was 7.826. Bayesian clustering algorithm method and obtained dendrograms based on pedigree information and molecular data revealed the existence of four genetic clusters within the Black Slavonian pig. Wright’s FIS, FST and FIT from pedigree records were 0.017, 0.006, and 0.024, respectively, and did not prove significant population differentiation based on the geographical location of herds, despite the natural mating system. Obtained results indicate that despite the increased number of animals in the population, genetic diversity of Black Slavonian pig is low and conservation programme should focus on strategies aimed at avoiding further loss of genetic variability. Simultaneous use of genealogical and molecular data can be useful in conservation management of Black Slavonian pig breed.Keywords: autochthonous pig breed, microsatellite, genealogical data, genetic structuringReferencesBarros, E. A., Brasil, L. H. de A., Tejero, J. P., Delgado-Bermejo, J. V. & Ribeiro, M. N. (2017). Population structure and genetic variability of the Segureña sheep breed through pedigree analysis and inbreeding effects on growth traits. Small Ruminant Research, 149, 128-133.Belkhir, K. (2004). GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations. http://www. genetix. univ-montp2. fr/genetix/genetix. htm.Boichard, D., Maignel, L. & Verrier, E. (1997). The value of using probabilities of gene origin to measure genetic variability in a population. Genetics Selection Evolution, 29, 5.Caballero, A. & Toro, M. A. (2000). Interrelations between effective population size and other pedigree tools for the management of conserved populations. Genetics Research, 75, 331-343.Casellas, J., Ibanez-escriche, N., Varona, L., Rosas, J. P. & Noguera, J. L. (2019). Inbreeding depression load for litter size in Entrepelado and Retinto Iberian pig varieties. Journal of Animal Science, 97(5), 1979–1986.Cortés, O., Martinez, A. M., Cañon, J., Sevane, N., Gama, L. T., Ginja, C., Landi, V., Zaragoza, P., Carolino, N., Vicente, A., Sponenberg, P. & Delgado, J. V. for the BioPig Consortium. (2016). 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Rome: Food and Agriculture Organization.Francis, R. M. (2017). Pophelper: an R package and web app to analyse and visualize population structure. Molecular Ecology Resources, 17(1), 27-32.Goyache, F., Gutiérrez, J. P., Fernández, I., Gomez, E., Alvarez, I., Díez, J. & Royo, L. J. (2003). Using pedigree information to monitor genetic variability of endangered populations: the Xalda sheep breed of Asturias as an example. Journal of Animal Breeding and Genetics, 120, 95-105.Gutiérrez, J. P. & Goyache, F. (2005). A note on ENDOG: a computer program for analysing pedigree information. Journal of Animal Breeding and Genetics, 122, 172-176.Gvozdanović, K., Margeta, V., Margeta, P., Djurkin Kušec, I., Galović, D., Dovč, P. & Kušec, G. (2019). Genetic diversity of autochthonous pig breeds analyzed by microsatellite markers and mitochondrial DNA D-loop sequence polymorphism. Animal Biotechnology, 30(3), 242-251.Gvozdanović, K., Djurkin Kušec, I., Margeta, P., Salajpal, K., Džijan, S., Bošnjak, Z. & Kušec, G. (2020). Multiallelic marker system for traceability of Black Slavonian pig meat. Food Control, 109, 106917.International Society for Animal Genetics (ISAG)/Food and Agricultural Organization (FAO) (2011). Molecular genetic characterization of animal genetic resources. Rome: FAO Animal Production and Health Guidelines.Jombart, T. (2008). adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics, 24, 1403–1405.Jombart, T., Devillard, S. & Balloux, F. (2010). Discriminant analysis of principal components: A new method for the analysis of genetically structured populations. BMC Genetics, 11(1), 94.Kramarenko, S. S., Lugovoy, S. I., Kharzinova, V. R., Lykhach, V. Y., Kramarenko, A. S. & Lykhach, A. V. (2018). Genetic diversity of Ukrainian local pig breeds based on microsatellite markers. Regulatory Mechanisms in Biosystems, 9(2), 177-182.Lacy, R. C. (1987). Loss of genetic diversity from managed populations: interacting effects of drift, mutation, immigration, selection, and population subdivision. Conservation Biology, 1, 143-158.Lemus-Flores, C., Ulloa-Arvizu, R., Ramos-Kuri, M., Estrada, F. J. & Alonso, R. A. (2001). Genetic analysis of Mexican hairless pig populations. Journal of Animal Science, 79(12), 3021-3026.Lukić, B., Smetko, A., Mahnet, Ž., Klišanić, V., Špehar, M., Raguž, N. & Kušec, G. (2015). Population genetic structure of autochthonous Black Slavonian Pig. Poljoprivreda, 21(1), 28-32.Ma, L., Ya-Jie J. & Zhang, D. X. (2015). Statistical measures of genetic differentiation of populations: Rationales, history and current states. Current Zoology, 61(5): 886–897.Margeta, P., Margeta, V. & Budimir, K. (2013). How black is really Black Slavonian pig? Acta Agriculturae Slovenica, Suppl. 4, 25-28.Margeta, P., Margeta, V., Gvozdanović, K., Galović, D., Djurkin Kušec, I. & Kušec, G. (2016). Microsatellite multiplex method for potential use in Black Slavonian pig breeding. Acta Agriculturae Slovenica, 5, 66-70.Margeta, P., Gvozdanovic, K., Djurkin Kušec, I., Radišić, Ž., Kusec, G. & Margeta, V. (2018). Genetic analysis of Croatian autochthonous pig breeds based on microsatellite markers. Archivos de Zootecnia, 1, 13-16.Mariani, E., Summer, A., Ablondi, M. & Sabbioni, A. (2020). Genetic variability and management in Nero di Parma swine breed to preserve local diversity. Animals, 10(3), 538.Meuwissen, T. H. E. & Luo, Z. (1992). Computing inbreeding coefficients in large populations. Genetics Selection Evolution, 24, 305.Muñoz, M., Bozzi, R., García-Casco, J., Núñez, Y., Ribani, A., Franci, O., García, F., Škrlep, M., Schiavo, G., Bovo, S., Utzeri, V. J., Charneca, R., Martins, J. M., Quintanilla, R., Tibau, J., Margeta, V., Djurkin-Kušec, I., Mercat, M. J., Riquet, J., Estellé, J., Zimmer, C., Razmaite, V., Araujo, J. P., Radović, Č., Savić, R., Karolyi, D., Gallo, M., Čandek-Potokar, M., Fernández, A. I., Fontanesi, L. & Óvilo, C. (2019). Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip. Scientific Reports, 9(1), 13546.Nei, M. (1973). Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences, 70(12), 3321-3323.Nei, M., Tajima, F. & Tateno, Y. (1983). Accuracy of estimated phylogenetic trees from molecular data. Journal of Molecular Evolution, 19(2), 153-170.Nei, M., (1987). Molecular Evolutionary Genetics. Columbia University Press, New York, 512 pp.Pritchard, J. K., Stephens, M. & Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155, 945–959.Posta, J., Szabó, P. & Komlósi, I. (2016). 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Genetics Selection Evolution, 49(1), 71.Zhang, J., Jiao, T. & Zhao, S. (2016). Genetic diversity in the mitochondrial DNA D-loop region of global swine (Sus scrofa) populations. Biochemical and Biophysical Research Communications, 473(4), 814-820.

    Predicted Feed Efficiency index applied to Italian Holstein Friesian cattle population

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    Submitted 2020-08-02 | Accepted 2020-09-21 | Available 2020-12-01https://doi.org/10.15414/afz.2020.23.mi-fpap.326-330Feed efficiency has a major influence on farm profitability and environmental stewardship in the dairy industry. The aim of this study was to describe a new selection index adopted by the Italian Holstein and Jersey Association (ANAFIJ, Cremona, Italy) to improve feed efficiency using data recorded by the official dairy recording system. Predicted dry matter intake (pDMI) was derived from milk yield, fat content, and estimated cow body weight. Fat-protein corrected milk (FPCM) was derived from milk yield corrected for fat, protein, and a fixed coefficient for lactose content (4.80%). Therefore, the predicted feed efficiency (pFE) was estimated as ratio between FPCM and pDMI. Average pFE was 1.27±0.18 (kg.d-1) with heritability of 0.32. Predicted Feed Efficiency index (pFEi), traditional and genomic, has been implemented in the Italian Holstein Friesian evaluation system. Results suggest that pFEi may be a new breeding objective for Italian Friesians. The official selection index (PFT), in use since 2002, is positively correlated with pFEi. However, the introduction of pFEi will improve the positive feed efficiency trend. This approach will permit the Italian Holstein Friesian breeders to improve feed efficiency, without increasing costs of recording system. However, to avoid the risk of selecting animals with an excessive negative energy balance after calving, it would be useful to include in the pFE a correction for body condition score and reproductive performances. Meanwhile, in order to increase the accuracy of the predicted phenotype, an Italian consortium is creating a consistent phenotypic critical mass of individual data for dry matter intake in cows, heifers and young bulls.Keywords: feed efficiency, cattle breeding, dry matter intake, breeding value estimationReferencesCassandro, M. (2020). Animal breeding and climate change, mitigation and adaptation. Journal of Animal Breeding and Genetics, 137(2), 121-122. https://doi.org/10.1111/jbg.12469Cassandro, M. et al. (2010). Genetic parameters of predicted methane production in Holstein Friesian cows. Proceedings of the 9th World Congress on Genetics Applied to Livestock Production, Leipzig, Germany.Cassandro, M., Mele, M. and Stefanon, B. (2013). Genetic aspects of enteric methane emission in livestock ruminants. Italian Journal of Animal Science, 12(3), 450-458.De Haas, Y. et al. (2012). Improved accuracy of genomic prediction for dry matter intake of dairy cattle from combined European and Australian data sets. Journal of Dairy Science, 95(10), 6103-6112.De Vries, M. and Veerkamp, R. (2000). Energy balance of dairy cattle in relation to milk production variables and fertility. Journal of Dairy Science, 83(1), 62-69.Finocchiaro, R. et al. (2017). Body weight prediction in Italian Holstein cows. ICAR Technical Series, 22, 95-98.Hegarty, R. et al. (2007). Cattle selected for lower residual feed intake have reduced daily methane production. Journal of Animal Science, 85(6), 1479-1486.Hurley, A. M. et al. (2018). Characteristics of feed efficiency within and across lactation in dairy cows and the effect of genetic selection. Journal of Dairy Science, 101(2), 1267-1280. https://doi.org/https://doi.org/10.3168/jds.2017-12841Meuwissen, T. H., Hayes, B. J. and Goddard, M. E. (2001). Prediction of total genetic value using genome-wide dense marker maps. Genetics, 157(4), 1819-1829.National Research Council. (2001). Nutrient Requirements of Dairy Cattle: Seventh Revised Edition, 2001. The National Academies Press. http://www.nap.edu/catalog.php?record_id=9825Pryce, J. et al. (2014). Genomic selection for feed efficiency in dairy cattle. Animal, 8(1), 1-10.Sjaunja, L. et al. (1990). A Nordic proposal for an energy corrected milk formula. Proceedings of the 2nd Session of Committee for Recording and Productivity of Milk Animal, Paris, p. 156.Veerkamp, R. et al. (2000). Genetic correlation between days until start of luteal activity and milk yield, energy balance, and live weights. Journal of Dairy Science, 83(3), 577-583.Verbyla, K. et al. (2010). Predicting energy balance for dairy cows using high-density single nucleotide polymorphism information. Journal of Dairy Science, 93(6), 2757-2764.Wall, E., Coffey, M. and Brotherstone, S. (2007). The relationship between body energy traits and production and fitness traits in first-lactation dairy cows. Journal of Dairy Science, 90(3), 1527-1537.Wallace, R. J. et al. (2019). A heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions. Science Advances, 5(7), eaav8391

    Morphological characteristics as a key attribute for a successful determination of selected Cotoneaster species

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    Article Details: Received: 2019-12-17 | Accepted: 2019-01-24 | Available online: 2020-03-31 https://doi.org/10.15414/afz.2020.23.01.15-23In this paper, morphological features, such as the number of pyrenes in pome and the number of pomes in infructescence, were used for determination of closely related tetraploid Cotoneaster species. Samples were collected from various localities in the Western Carpathians. The collection of samples, designed for counting of pyrenes in pome, included 2353 pomes of >130  individuals. Number of pyrenes in pome ranged from 1 to 5. Statistical analysis revealed a significant difference in pyrenes per pome mean values between C. integerrimus (3.01), C. melanocarpus agg. (2.46; including C. matrensis) and C. tomentosus (3.93). The collection of samples, designed for counting of pomes in infructescence, included 1019 infructescences of 141 individuals. Number of pomes in infructescence ranged from 1 to 5. Statistical analysis also revealed a significant difference in pomes per infructescence mean values between C. integerrimus (1.14) and C. melanocarpus agg. (1.54; including C. matrensis), and between C. integerrimus and C. tomentosus (1.50).Keywords: pyrenes, pomes, infructescence, Cotoneaster, Western CarpathiansReferences:Baranec, T. (1992). Cotoneaster Medicus. In Bertová, L. (Ed.) Flora of Slovakia IV/3. Bratislava: Veda (pp. 452–462). In Slovak.Baranec, T. and Eliáš ml., P. (2004). Taxonomy and chorology of genus Cotoneaster Medicus in the territory of Nízke Tatry Mts. In Jasík, M. et al. (Eds.) Nature of Low Tatras. Banská Bystrica: State Nature Conservancy of the Slovak Republic, The Administration of the National Park Low Tatras (pp. 101–106). In Slovak.Bartha, D. (2009). Cotoneaster Medik. In Király, G. (Ed.) New Hungarian Herbal. The Vascular Plants of Hungary. Identification key. Jósvafő: Aggteleki Nemzeti Park Igazgatóság (pp. 229). In Hungarian.Bartish, I. V. et al. (2001). RAPD analysis of interspecific relationships in presumably apomictic Cotoneaster species. Euphytica, 120(2), 273–280.Dickoré, W. B. and Kasperek, G. (2010). Species of Cotoneaster (Rosaceae, Maloideae) indigenous to, naturalising or commonly cultivated in Central Europe. Willdenowia, 40, 13–45.Ďurišová, Ľ. and Baranec, T. (2016). The evidence of apomixis in Cotoneaster matrensis. In Bačkor, M. and Valachovič, M. (Eds.) Bulletin of Slovak Botanical Society 38, Supplement 1. Bratislava: Slovak Botanical Society (pp. 25–33). In Slovak.Ďurišová, Ľ. et al. (2016). Population and reproductive biology of Cotoneaster matrensis Domokos. In Brindza, J. and Klymenko, S. (Eds.) Agrobiodiversity for improving nutrition, health and life quality, PART. Nitra: Slovak University of Agriculture (pp. 134–138). In Slovak.Hajrudinović, A. et al. (2015). When sexual meets apomict: genome size, ploidy level and reproductive mode variation of Sorbus aria s.l. and S. austriaca (Rosaceae) in Bosnia and Herzegovina. Annals of Botany, 116(2), 301–312.Kicel, A. et al. (2019). Polyphenolic profile, antioxidant activity, and pro-inflammatory enzymes inhibition of leaves, flowers, bark and fruits of Cotoneaster integerrimus: A comparative study. Phytochemistry Letters, 30, 349–355.Kovanda, M. (1992). Cotoneaster Med. In Hejný, S. et al. (Eds.) Flora of the Czech Republic 3. Praha: Academia (pp. 485– 487). In Czech.Kšiňan, S. et al. (2019). Identification of autochthonous West-Carpathian Cotoneaster species by using a flow cytometry method. In Eliáš ml., P. (Ed.) Book of Abstracts of 11th Congress of Slovak Botanical Society. Nitra: Slovak Botanical Society & Slovak University of Agriculture. In Slovak.Kurtto, A. et al. (2013). Atlas Florae Europaeae. Distribution of Vascular Plants in Europe. 16. Rosaceae (Cydonia to Prunus, excl. Sorbus). Helsinki: The Committee for Mapping the Flora of Europe & Societas Biologica Fennica Vanamo.Macková, L. et al. (2017). Hybridization success is largely limited to homoploid Prunus hybrids: a  multidisciplinary approach. Plant Systematics and Evolution, 303(4), 481–495.Macková, L. et al. (2018). Insight into the cytotype and reproductive puzzle of Western Carpathian Cotoneaster integerrimus. In Štěpánková, R. (Ed.) Systematics, ecology and floristics in the light of flow cytometry. Praha: Czech Botanical Society. In Czech.Marhold, K. and Hindák, F. (1998). Checklist of nonvascular and vascular plants of Slovakia. Bratislava: Veda.Potter, D. et al. (2007). Phylogeny and classification of Rosaceae. Plant Systematics and Evolution, 266, 5–43.QGIS Development Team (2018). QGIS Geographic Information System. Open Source Geospatial Foundation Project. Retrieved December 17, 2019 from https://www.qgis.org/en/site/Rohrer, J. R. et al. (1991). Variation in Structure Among Fruits of Maloideae (Rosaceae). American Journal of Botany, 78(12), 1617–1635.Rothleutner, J. J. et al. (2016). Ploidy Levels, Relative Genome Sizes, and Base Pair Composition in Cotoneaster. Journal of the American Society for Horticultural Science, 141(5), 457–466.Thiers, B. (2019). Index Herbariorum: A global directory of public herbaria and associated staff. New York Botanical Garden‘s Virtual Herbarium, New York. Retrieved December 17, 2019 from http://sweetgum.nybg.org/ih/Uysal, A. et al. (2016). Chemical and biological insights on Cotoneaster integerrimus: A new (-)- epicatechin source for food and medicinal applications. Phytomedicine, 23(10), 979–988.Žabka, M. et al. (2018). Genome size and ploidy level among wild and cultivated Prunus taxa in Slovakia. Biologia, 73(2), 121–128

    The effect of zinc application on annual ryegrass (Lolium multiflorum) under drought stress

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    Article Details: Received: 2020-09-28 | Accepted: 2020-10-14 | Available online: 2020-12-31https://doi.org/10.15414/afz.2020.23.04.198-204 The aim of the vegetation pot experiment observed the effect of zinc foliar application in combination with nitrogen fertilization on annual ryegrass plant ability to deal with drought stress. Experiment with two irrigation regimes was established and the rate of drought stress was evaluated by determination of abscisic acid (ABA) content in above-ground part of ryegrass, dry matter weight and nutrient content in plant were also determined. Foliar Zn application had statistically significant effect (P <0.05) on decrease of ABA content in comparison to variants without Zn fertilization which implies that zinc contributed to better plant dealing with drought stress. Foliar application of higher Zn dose (1.25 g l-1) under drought stress was found the strongest decreased of ABA in comparison with variant without Zn fertilization (about 50.1%). Zinc supported also the growth of above-ground part regardless to irrigation, we found the highest dry matter weight on variant with higher nitrogen dose (0.5 g pot-1) and higher Zn dose (1.25 g l-1). Graded levels of zinc application significantly effected of Zn content in plant.Keywords: annual ryegrass, foliar zinc application, drought stress, abscisic acid contentReferences ALVES, A. A. C. and SETTER, T. L. (2000). Response of cassava to water deficit: Leaf area growth and abscisic acid. Crop Science, 40, 131–137. https://doi.org/10.1093/aob/mch179AMANUEL, B. A. et al. (2015). Forage yield and quality response of annual ryegrass (Lolium multiflorum) to different water and nitrogen levels. African Journal of Range & Forage Science, 32(2), 125–131. https://doi.org/10.2989/10220119.2015.1056228ASHKAN, A. et al. (2020). Effects of foliar zinc application on yield and oil quality of rapeseed genotypes under drought stress. Journal of Plant Nutrition, 43(11), 1594–1603. https://doi.org/10.1080/01904167.2020.1739299BANO, A. et al. (2012). Role of abscisic acid and drought stress on the activities of antioxidant enzymes in wheat. Plant, Soil and Environment, 58, 181–185. https://doi.org/10.17221/210/2011-PSEBOOMINATHAN, P. et al. (2004). Long term transcript accumulation during development of dehydration adaptation in Cicer arietinum. Plant Physiology, 135, 1608–1620. https://doi.org/10.1104/pp.104.043141BOWEN, H. J. M. (1979). Environmental chemistry of the elements. New York: Academic Press.BRAMBILLA, D. M. et al. (2012). Impact of nitrogen fertilization on the forage characteristics and beef calf performance on native pasture overseeded with ryegrass. Revista Brasileira de Zootecnia, 41(3), 528–536. https://doi.org/10.1590/S1516-35982012000300008CAKMAK, I. (2000). Possible roles of zinc in protecting plant cells from damage by reactive oxygen species. New Phytologist, 146, 185–205. http://dx.doi. org/10.1046/j.1469-8137.2000.00630.xCAO, W. X., WANG, Z. L. and DAI, T. B. (2000). Changes in levels of endogenous plant hormones during floret development in wheat genotypes of different spike sizes. Acta Botanica Sinica, 42(10), 696–700. https://doi.org/10.1007/s00299-019-02430-0CINAR, S., OZKURT, M. and CETIN, R. (2020). Effects of nitrogen fertilization rates on forage yield and quality of annual ryegrass (Lolium multiflorum L.) in central black sea climatic zone in Turkey. Applied Ecology and Environmental Research, 18(1), 417–432. https://doi.org/10.15666/aeer/1801_417432CLARKE, N. D. and BERG, J. M. (1998). Zinc fingers in Caenorhabditis elegans: finding families and probing pathways. Science, 282, 2018–2022.CONTI, S. et al. (1994). Genetic and environmental effects on abscisic acid accumulation in leaves of field-grown maize. Euphytica, 78, 81–89. https://doi.org/10.1007/BF00021401DIMKPA, C. O. et al. (2019). Zinc oxide nanoparticles alleviate drought-induced alterations in sorghum performance, nutrient acquisition, and grain fortification. Science of The Total Environment, 688, 926–934. https://doi.org/10.1016/j.scitotenv.2019.06.392GRZEBISZ, W. et al. (2008). Effect of zinc foliar application at an early stage of maize growth on patterns of nutrients and dry matter accumulation by the canopy: Part II. Nitrogen uptake and dry matter accumulation patterns. Journal of Elementology, 13, 29–40.HAVLIN, J. L. et al. (1999). Soil Fertility and Fertilizers – an introduction to nutrient management. 6th ed. New Jersey: Prentice Hall.HUANG, B., Da COSTA, M. and JIANG, Y. (2014). Research advances in mechanisms of grass tolerance to abiotic stresses: From physiology to molecular biology. Critical Reviews in Plant Sciences, 33(2–3), 141–189. https://doi.org/10.1080/07352689.2014.870411HUSSAIN, S. et al. (2020). 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Development of a DTPA Soil Test for Zinc, Iron, Manganese, and Copper. Soil Science Society of America Journal, 42, 421–428.MA, D. et al. (2017). Physiological responses and yield of wheat plants in zinc-mediated alleviation of drought stress. Frontiers in plant science, 8, 1–12. https://doi.org/10.3389/fpls.2017.00860MATHPAL, B. et al. (2015). Zinc enrichment in wheat genotypes under various methods of zinc application. Plant, Soil and Environment, 61, 171–175. https://doi.org/10.17221/41/2015-PSEMONJEZI, F. et al. (2013). Effects of iron and zinc spray on yield and yield components of wheat (Triticum aestivum L.) in drought stress. Cercetări Agronomice în Moldova, 46(1), 23–32. https://doi.org/10.2478/v10298-012-0072-zLINDSAY, W.L. and NORVELL, W.A. (1978). Development of a DTPA soil test for zinc, iron, manganese and copper. Soil Science Society America Journal, 42, 421–428. http://dx.doi.org/10.2136/sssaj1978.03615995004200030009xPOBLACIONES, M. J., DAMON, P. and RENGEL, Z. 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    Use of High-density SNP analyses to develop a long-term strategy for conventional populations to prevent loss of diversity - review

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    Article Details: Received: 2020-09-10 | Accepted: 2020-10-30 | Available online: 2020-12-31https://doi.org/10.15414/afz.2020.23.04.236-240The aim was to review obtained results related to molecular-genetic analyses by high-density SNP chips and mtDNA in farm and wild populations within the project APVV-17-0060 Genomic Indicators of extranuclear DNA as a source of Diversity for Animal Breeding. Continuous human activity and subsequent socioeconomic and climatic changes of the environment significantly affect the genetic diversity of livestock on both intra- and inter-population levels. Concerning the conservation of local livestock populations and thus animal genetic resources (AnGR) for future generations is, therefore, necessary to monitor and look for new “more precise“ tools to measure the amount of genetic diversity. The expected result will be the identification of SNP markers and spot mutations with a significant effect on the process of development resp. variability of traits. In the case of the dog, identification of regions related to fitness, health, and trainability will be the primary objective. Keywords: Genetic diversity, economically important breeds, Animal genetic resources, SlovakiaReferencesCURIK, I., FERENČAKOVIĆ, M. and SÖLKNER, J. (2014). Inbreeding and runs of homozygosity: a possible solution to an old problem. Livestock Science, 166, 26–34.ENGELSMA, K.A., VEERKAMP, R.F., CALUS, M.P., BIJMA, P. and WINDIG, J.J. (2012). Pedigree and marker-based methods in the estimation of genetic diversity in small groups of Holstein cattle. Journal of Animal Breeding and Genetics, 129, 195–205.FERENČAKOVIĆ, M., BANADINOVIĆ, M., MERCVAJLER, M., KHAYATZADEH, N., MÉSZÁROS, G., CUBRIC-CURIK, V., CURIK, I. and SÖLKNER, J. (2016) Mapping of heterozygosity rich regions in Austrian Pinzgauer cattle. Acta argiculturae Slovenica, Supplement 5, 41–44.KASARDA, R., KADLEČÍK, O., TRAKOVICKÁ, A. and MORAVČÍKOVÁ, N. (2019d). Genomic and pedigree-based inbreeding in Slovak Spotted cattle. In AGROFOR, 4(1), 102–110.KASARDA, R., Kadlečík, O., Trakovická, A. and Moravčíková, N. (2019f). Genomic and pedigree-based inbreeding in Slovak spotted cattle. In AGROFOR International Journal.KASARDA, R., MORAVČÍKOVÁ, N., HALO, M., HORNÝ, M., LEHOCKÁ, K., OLŠANSKÁ, B., BUJKO, J. and CANDRÁK, J. (2019a). Trend vývoja genomického inbrídingu v populácii plemena lipican. In Aktuálne smerovanie v chove koní. Nitra : Slovenská poľnohospodárska univerzita, p. 32–36.KASARDA, R., MORAVČÍKOVÁ, N., KADLEČÍK, O., TRAKOVICKÁ, A., HALO, M. and CANDRÁK, J. (2019b). Level of inbreeding in Norik of Muran horse: pedigree vs. genomic data. Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis, 67(6), 1457–1463.KASARDA, R., MORAVČÍKOVÁ, N., KADLEČÍK, O., TRAKOVICKÁ, A., ŽITNÝ, J., TERPAJ, V. P., MINDEKOVÁ, S. and MLYNEKOVÁ, L. (2019c). Common origin of local cattle breeds in western region of Carpathians. Danubian animal genetic resources, 4, 84–90.KASARDA, R., MORAVČÍKOVÁ, N., ŽIDEK, R., TRAKOVICKÁ, A. and KADLEČÍK, O. (2019e). Gene flow and diversity in local red deer populations. In 15th International Arctic Ungulate conference. 1st ed. 83 p. Arctic Ungulate conference. Uppsala : Swedish University of Agricultural Sciences, pp. 61.KASARDA, R., MORAVČÍKOVÁ, N., TRAKOVICKÁ, A., KRUPOVÁ, Z. and KADLEČÍK, O. (2017) Genomic variation across cervid species in respect to the estimation of Red deer diversity. Acta Veterinaria, 67(1), 43–56.KASARDA, R., MORAVČÍKOVÁ, N., ŽIDEK, R., MÉSZÁROS, G., KADLEČÍK, O., TRAKOVICKÁ, A. and POKORÁDI, J. (2015) Investigation of the genetic distances of bovids and cervids using BovineSNP50k BeadChip. Archiv Tierzucht, 58, 57–63.KASARDA, R., MORAVČÍKOVÁ, N., KUKUČKOVÁ, V., KADLEČÍK, O., TRAKOVICKÁ, A. and MÉSZÁROS, G. (2016). Evidence of selective sweeps through haplotype structure of Pinzgau cattle. Acta agriculturae Slovenica, 107(Suppl. 5), 160–164.KUKUČKOVÁ, V., MORAVČÍKOVÁ, N., CURIK, I., SIMČIČ, M., MÉSZÁROS, G. and KASARDA, R. (2018). Genetic diversity of local cattle. Acta Biochimica Polonica, 65(3), 421–424.KUKUČKOVÁ, V., MORAVČÍKOVÁ, N., FERENČAKOVIĆ, M., SIMČIČ, M., MÉSZÁROS, G., SÖLKNER, J., TRAKOVICKÁ, A., KADLEČÍK, O., CURIK, I. and KASARDA, R. (2017). Genomic characterization of Pinzgau cattle: genetic conservation and breeding perspectives. Conservation Genetics, 18(4), 893–910.LEHOCKÁ, K., KASARDA, R., TRAKOVICKÁ, A., KADLEČÍK, O. and MORAVČÍKOVÁ, N. (2019). Genomic diversity and level of admixture in the Slovak Spotted cattle. In AgroSym 2019. AgroSym. Bosna : University of East Sarajevo, pp. 1607–1612. LU, D. (2012) Applications of the Illumina BovineSNP50 BeadChip in Genetic Improvement of Beef Cattle. Guelph, Ontario, Canada, 1.MILUCHOVÁ, M., GÁBOR, M., CANDRÁK, J. and TRAKOVICKÁ, A. (2018). Bovine beta-casein and complex traits – The impact of the A2 variant of the CSN2 gene in the Slovak Holstein cow population on production traits. 2 THETA : Český Tešín. 96 p.MORAVČÍKOVÁ, N., KADLEČÍK, O., TRAKOVICKÁ, A. and KASARDA, R. (2018b). Autozygosity island resulting from artificial selection in slovak spotted cattle. In Agriculture & Forestry, 64(4), 21–28.MORAVČÍKOVÁ, N., KASARDA, R., HALO, M., KADLEČÍK, O., TRAKOVICKÁ, A., LEHOCKÁ, K., OLŠANSKÁ, B. and CANDRÁK, J. (2020a). Genome-wide distribution of autozygosity islands in Slovak Warmblood horse. In AGROFOR. in press.MORAVČÍKOVÁ, N., KASARDA, R., HALO, M., LEHOCKÁ, K., OLŠANSKÁ, B. and CANDRÁK, J. (2019b). Vplyv selekcie na genóm slovenského teplokrvníka. In Aktuálne smerovanie v  chove koní. Nitra : Slovenská poľnohospodárska univerzita, p. 48–52.MORAVČÍKOVÁ, N., KASARDA, R., KADLEČÍK, O., TRAKOVICKÁ, A., HALO, M. and CANDRÁK, J. (2019c). Runs of homozygosity as footprints of selection in the norik of muran horse genome. Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis, 67(5), 1165–1170.MORAVČÍKOVÁ, N., KASARDA, R., VOSTRÝ, L., KRUPOVÁ, Z., KRUPA, E., LEHOCKÁ, K., OLŠANSKÁ, B., TRAKOVICKÁ, A., NÁDASKÝ, R., ŽIDEK, R., BELEJ, Ľ. and GOLIAN, J. (2019a). Analysis of selection signatures in the beef cattle genome. Czech journal of animal science, 64(12), 491–503.MORAVČÍKOVÁ, N., KASARDA, R., ŽIDEK, R., TRAKOVICKÁ, A. and KADLEČÍK, O. (2019e). Genetic variation of family Cervidae based on cross-species SNPs genotyping. In 15th  International  Arctic Ungulate conference. 1st ed. 83 p. Arctic Ungulate conference. Uppsala : Swedish University of Agricultural Sciences, pp. 60.MORAVČÍKOVÁ, N., KASARDA, R., ŽITNÝ, J., TRAKOVICKÁ, A. and KADLEČÍK, O. (2018a). Validation of bovine 50k SNP chip transferability into non-model wild animals. Slovak Journal of Animal Science, 51(4), 180.MORAVČÍKOVÁ, N., SIMONOVÁ, D. and KASARDA, R. (2019d). Traces of Carpathanian wolf in genome of dogs. In Book of Abstracts of the 70th Annual Meeting of the European Federation of Animal Science. Annual meeting of the European federation of animal science. Wageningen : Wageningen Academic Publishers, pp. 462.MORAVČÍKOVÁ, N., KASARDA, R. and KADLEČÍK, O. (2017) The degree of genetic admixture within species from genus cervus. Agriculture and Forestry, 63(1), 137–143.MORAVČÍKOVÁ, N., KASARDA, R., KUKUČKOVÁ, V., VOSTRÝ, L. and KADLEČÍK, O. (2016) Genetic diverzity of old Kladruber and Nonius horse populations through microsatellite variation analysis. Acta agriculturae Slovenica, 107, 45–49.MORAVČÍKOVÁ, N., TRAKOVICKÁ, A., KADLEČÍK, O. and KASARDA, R. (2019f). Genomic signatures of selection in cattle throught variation of allele frequencies and linkage disequilibrium. Journal of Central European Agriculture, 20(2), 576–580.MORAVČÍKOVÁ, N., ŽIDEK, R., KASARDA, R., JAKABOVÁ, D., GENČÍK, M., POKORÁDI, J. and FERIANCOVÁ, E. (2020b). Identification of genetic families based on mitochondrial D-loop sequence in population of the Tatra chamois (Rupicapra rupicapra tatrica). Biologia, 75(1), 121–128.TRAKOVICKÁ, A., LEHOCKÁ, K., KASARDA, R., KADLEČÍK, O. and MORAVČÍKOVÁ, N. (2019). Effective population size and genomic inbreeding of Slovak Spotted cattle. In Book of Abstracts of the 70th Annual Meeting of the European Federation of Animal Science. Annual meeting of the European federation of animal science. Wageningen : Wageningen Academic Publishers, pp. 112

    Homozygosity indicators in canine MHC region of the Standard Poodle and Leonberger populations

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    Submitted 2020-06-15 | Accepted 2020-08-04 | Available 2020-12-01https://doi.org/10.15414/afz.2020.23.mi-fpap.29-37Dog breeds are the leading examples of artificial selection, with sometimes extreme changes between the wolf-like phenotypes and current breeds. This increased selection pressure manifest in increased homozygosity throughout the genome, including the major histocompatibility complex (MHC) with large influence on the immune system. The MHC region in 98 Leonberger and 37 Standard Poodle dogs was examined using single nucleotide polymorphism (SNP) data. The overall homozygosity levels and via the runs of homozygosity (ROH) were calculated as indicators to assess the MHC regions, compared to other random parts of the dog genome. High proportion of homozygosity was observed in all examined chromosomes, ranging from 58 to 78%. The ROH was preferred to the overall level of homozygosity, as it showed the variability within the MHC regions. The homozygosity was even lower at the locations of the genes with a known effect on the immune response, confirming previous findings.Keywords: Run of homozygosity, SNP, Dog, Dog leukocyte antigenReferencesBarth, S.M., Schreitmüller, C.M., Proehl, F., Oehl, K., Lumpp, L.M., Kowalewski, D.J., Marco, M.D., Sturm, T., Backert, L., Schuster, H., Stevanović, S., Rammensee, H.-G., Planz, O. (2016). Characterization of the Canine MHC Class I DLA-88*50101 Peptide Binding Motif as a Prerequisite for Canine T Cell Immunotherapy. PLOS ONE 11, e0167017. https://doi.org/10.1371/journal.pone.0167017Biniok, J. (2008). The Poodle, Our Best Friends. Pittsburgh: Eldorado Ink.Brown T, Borgia G, Sullivan J, Willis M, Appleton S. (2019). Artificial Selection. Natl. Geogr. Educ., Encyclopedia Entry.Burnett, R.C., DeRose, S.A., Wagner, J.L., Storb, R. (1997). Molecular analysis of six dog leukocyte antigen class I sequences including three complete genes, two truncated genes and one full-length processed gene. Tissue Antigens 49, 484–495. https://doi.org/10.1111/j.1399-0039.1997.tb02783.xBurnett, R.C., Geraghty, D.E. (1995). Structure and expression of a divergent canine class I gene. J. Immunol. 155, 4278–4285.Ceballos, F.C., Hazelhurst, S., Ramsay, M. (2018). Assessing runs of Homozygosity: a comparison of SNP Array and whole genome sequence low coverage data. BMC Genomics 19, 106. https://doi.org/10.1186/s12864-018-4489-0Chang, C.C., Tellier, L.C.A.M., Vattikuti, S., Purcell, S.M., Lee, J.J. (2015). Second-generation PLINK: rising to the challenge of larger and richer datasets. GigaScience 4. https://doi.org/10.1186/s13742-015-0047-8Debenham, S.L., Hart, E.A., Ashurst, J.L., Howe, K.L., Quail, M.A., Ollier, W.E.R., Binns, M.M. (2005). Genomic sequence of the class II region of the canine MHC: comparison with the MHC of other mammalian species. Genomics 85, 48–59. https://doi.org/10.1016/j.ygeno.2004.09.009Graumann, M.B., DeRose, S.A., Ostrander, E.A., Storb, R. (1998). Polymorphism analysis of four canine MHC class I genes. Tissue Antigens 51, 374–381. https://doi.org/10.1111/j.1399-0039.1998.tb02976.xKennedy, L. (2009). Major Histocompatibility Complex Diversity in Dogs & Disease Associations. Tufts Canine Feline Breed. Genet. Conf. 2009.Kennedy, L.J., Angles, J.M., Barnes, A., Carter, S.D., Francino, O., Gerlach, J.A., Happ, G.M., Ollier, W.E.R., Thomson, W., Wagner, J.L. (2001).Nomenclature for factors of the dog major histocompatibility system (DLA), 2000: Second report of the ISAG DLA Nomenclature Committee. Tissue Antigens 58, 55–70. https://doi.org/10.1034/j.1399-0039.2001.580111.xKennedy, L.J., Randall, D.A., Knobel, D., Brown, J.J., Fooks, A.R., Argaw, K., Shiferaw, F., Ollier, W.E.R., Sillero-Zubiri, C., Macdonald, D.W., Laurenson, M.K. (2011). Major histocompatibility complex diversity in the endangered Ethiopian wolf (Canis simensis). Tissue Antigens 77, 118–125. https://doi.org/10.1111/j.1399-0039.2010.01591.xKhatib, H. (2015). Molecular and Quantitative Animal Genetics. New York: John Wiley & Sons.Klein, J. (1986). Natural history of the major histocompatibility complex. Cell Biochem. Funct. 6, 222–222. https://doi.org/10.1002/cbf.290060321Meyermans, R., Gorssen, W., Buys, N., Janssens, S. (2020). How to study runs of homozygosity using PLINK? A guide for analyzing medium density SNP data in livestock and pet species. BMC Genomics 21, 94. https://doi.org/10.1186/s12864-020-6463-xMillstein, R.L. (2017). Genetic Drift, in: Zalta, E.N. (Ed.), The Stanford Encyclopedia of Philosophy. Metaphysics Research Lab, Stanford University.R Core Team (2013). A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.Rebelato, A.B., Caetano, A.R., Rebelato, A.B., Caetano, A.R. (2018). Runs of homozygosity for autozygosity estimation and genomic analysis in production animals. Pesqui. Agropecuária Bras. 53, 975–984. https://doi.org/10.1590/s0100-204x2018000900001Rodenburg, T.B., Turner, S.P. (2012). The role of breeding and genetics in the welfare of farm animals. Anim. Front. 2, 16–21. https://doi.org/10.2527/af.2012-0044Safra, N., Pedersen, N.C., Wolf, Z., Johnson, E.G., Liu, H.W., Hughes, A.M., Young, A., Bannasch, D.L. (2011). Expanded dog leukocyte antigen (DLA) single nucleotide polymorphism (SNP) genotyping reveals spurious class II associations. Vet. J. Lond. 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