Abstract
Agriculture is an essential component of the evolution of mankind. Environmental changes, human population growth, and increasing global demand for animal and vegetable food products have led to an urgent need for optimization of food production. Genomic selection is one of the most promising and safest methods for improving the genetic qualities of farm animals and plants. Genomic selection is based on the principle of using information from a large number of genetic markers distributed throughout the genome and serves to identify such diversity in this genome that is sufficient enough to predict breeding values without knowing exactly where specific genes are located. However, the effectiveness of genomic selection has currently reached a certain limit. In addition, it can be applied only within industrial breeds of animals and plant lines. The review discusses the ways to increase the effectiveness and fields of application for genomic selection, in particular, by implementing technologies from related sciences.
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REFERENCES
Yudin, N.S., Lukyanov, K.I., Voevoda, M.I., and Kolchanov, N.A., Application of reproductive technologies to improve dairy cattle genomic selection, Russ. J. Genet.: Appl. Res., 2016, vol. 6, pp. 321—329. https://doi.org/10.1134/S207905971603014X
Sirard, M.A., 40 years of bovine IVF in the new genomic selection context, Reproduction, 2018, vol. 156, no. 1, pp. 1—7. https://doi.org/10.1530/REP-18-0008
Hornak, M., Kubicek, D., Broz, P., et al., Aneuploidy detection and mtDNA quantification in bovine embryos with different cleavage onset using a next-generation sequencing-based protocol, Cytogenet. Genome Res., 2016, vol. 150, no. 1, pp. 60—67. https://doi.org/10.1159/000452923
Carvalheiro, R., Genomic selection in Nelore cattle in Brazil, Proceedings of the 10th World Congress on Genetics Applied to Livestock Production: 17—22 Aug 2014, vol.: Species Breeding Beef Cattle, Vancouver, 2014, p. 258. https://asas.org/docs/default-source/wcgalp-proceedings-oral/258_paper_10329_manuscript_1314_ 0.pdf?sfvrsn=2.
Gianola, D., Campos, G., Hill, W.G., et al., Additive genetic variability and the Bayesian alphabet, Genetics, 2009, vol. 183, no. 1, pp. 347—363. https://doi.org/10.1534/genetics.109.103952
Van Raden, P.M., Efficient methods to compute genomic predictions, J. Dairy Sci., 2008, vol. 91, pp. 4414—4423.
Strandén, I. and Christensen, O.F., Allele coding in genomic evaluation, Genet. Sel. Evol., 2011, vol. 43, no. 25. https://doi.org/10.1186/1297-9686-43-25
Legarra, A., Aguilar, I., and Misztal, I., A relationship matrix including full pedigree and genomic information, J. Dairy Sci., 2009, vol. 92, pp. 4656—4663.
Aguilar, I., Misztal, I., Johnson, D.L., et al., Hot topic: a unified approach to utilize phenotypic, full pedigree, and genomic information for genetic evaluation of Holstein final score, J. Dairy Sci., 2010, vol. 93, pp. 743—752. https://doi.org/10.3168/jds.2009-2730
Christensen, O.F. and Lund, M.S., Genomic prediction when some animals are not genotyped, Genet. Sel. Evol., 2010, vol. 42, no. 2. https://doi.org/10.1186/1297-9686-42-2
Legarra, A., Christensen, O., Aguilar, I., and Misztal, I., Single step, a general approach for genomic selection, Livestock Sci., 2014, vol. 166, pp. 54—65. https://doi.org/10.1016/j.livsci.2014.04.029
Wang, Ch., Zöllner, S., and Rosenberg, N.A., A quantitative comparison of the similarity between genes and geography in worldwide human populations, PLoS Genet., 2012. https://doi.org/10.1371/journal.pgen.1002886
Henderson, C.R., Best linear unbiased estimation and prediction under a selection model, Biometrics, 1975, vol. 31, no. 2, pp. 423—447.
Mrode, R.A., Linear Models for the Prediction of Animal Breeding Values, Wallingford: Cabi, 2014, 3rd ed.
Misztal, I., Legarra, A., and Aguilar, I., Using recursion to compute the inverse of the genomic relationship matrix, J. Dairy Sci., 2014, vol. 97, pp. 3943—3952. https://doi.org/10.3168/jds.2013-7752
Misztal, I. and Legarra, A., Invited review: efficient computation strategies in genomic selection, Animal, 2017, vol. 11, no. 5, pp. 731—736. https://doi.org/10.1017/S1751731116002366
Tsuruta, Sh., Misztal, I., and Strandén, I., Use of the preconditioned conjugate gradient algorithm as a generic solver for mixed-model equations in animal breeding applications, J. Anim. Sci., 2001, vol. 79, pp. 1166—1172. https://doi.org/10.2527/2001.7951166x
Masuda, Yu., Aguilar, I., Tsuruta, Sh., and Misztal, I., Acceleration of computations in AI REML for single-step GBLUP models, Proceedings of the 10th World Congress on Genetics Applied to Livestock Production, 2014. https://doi.org/10.13140/2.1.1655.7760
Masuda, Yu., Aguilar, I., Tsuruta, S., and Misztal, I., Technical note: acceleration of sparse operations for average-information REML analyses with supernodal methods and sparse-storage refinements, J. Anim. Sci., 2015, vol. 93, no. 10, pp. 4670—4674. https://doi.org/10.2527/jas.2015-9395
Andersson, L., Bottema, C., Archibald, A.L., and Brauning, R., Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project, Genome Biol., 2015, vol. 16, pp. 57—63. https://doi.org/10.1186/s13059-015-0622-4
Villar, D., Berthelot, C., Aldridge, S., et al., Enhancer evolution across 20 mammalian species, Cell, 2015, vol. 160, no. 3, pp. 554—566. https://doi.org/10.1016/j.cell.2015.01.006
Zhou, Y., Bickhart, D.M., Xu, L., et al., Reduced representation bisulphite sequencing of ten bovine somatic tissues reveals DNA methylation patterns and their impacts on gene expression, BMC Genomics, 2016, vol. 17. https://doi.org/10.1186/s12864-016-3116-1
Khansefid, M., Pryce, J.E., Bolormaa, S., et al., Comparing allele specific expression and local expression quantitative trait loci and the influence of gene expression on complex trait variation in cattle, BMC Genomics, 2018, vol. 19, no. 1. https://doi.org/10.1186/s12864-018-5181-0
Sun, Z., Wang, M., Han, S., et al., Production of hypoallergenic milk from DNA-free beta-lactoglobulin (BLG) gene knockout cow using zinc-finger nucleases mRNA, Sci. Rep., 2018, vol. 8, no. 1. https://doi.org/10.1038/s41598-018-32024-x
Van Eenennaam, A.L., Genetic modification of food animals, Curr. Opin. Biotechnol., 2017, vol. 44, pp. 27—34. https://doi.org/10.1016/j.copbio.2016.10.007
Lillico, S., Proudfoot, Ch., Carlson, D., et al., Live pigs produced from genome edited zygotes, Sci. Rep., 2013, vol. 3, p. 2847. https://doi.org/10.1038/srep02847
Qian, L., Tang, M., Yang, J., et al., Targeted mutations in myostatin by zinc-finger nucleases result in double-muscled phenotype in Meishan pigs, Sci. Rep., 2015, vol. 5, p. 14435. https://doi.org/10.1038/srep14435
Mueller, M.L., Cole, J.B., Sonstegard, T.S., and Van Eenennaam, A.L., Comparison of gene editing versus conventional breeding to introgress the POLLED allele into the US dairy cattle population, J. Dairy Sci., 2019, vol. 102, no. 5, pp. 4215—4226. https://doi.org/10.3168/jds.2018-15892
Jenko, J., Gorjanc, G., Cleveland, M.A., et al., Potential of promotion of alleles by genome editing to improve quantitative traits in livestock breeding programs, Genet. Sel. Evol., 2015, vol. 47. https://doi.org/10.1186/s12711-015-0135-3
Saji, N., Niida, S., Murotani, K., et al., Analysis of the relationship between the gut microbiome and dementia: a cross-sectional study conducted in Japan, Sci. Rep., 2019, vol. 9, no. 1. https://doi.org/10.1038/s41598-018-38218-7
Sasson, G., Kruger Ben-Shabat, S., Seroussi, E., et al., Heritable bovine rumen bacteria are phylogenetically related and correlated with the cow’s capacity to harvest energy from its feed, MBio, 2017, vol. 8, no. 4. https://doi.org/10.1128/mBio.00703-17
Wang, H., Zheng, H., Browne, F., et al., Integrated metagenomic analysis of the rumen microbiome of cattle reveals key biological mechanisms associated with methane traits, Methods, 2017, vol. 15, no. 124, pp. 108—119. https://doi.org/10.1016/j.ymeth.2017.05.029
Wang, M., Pryce, J.E., Savin, K., and Hayes, B.J., Prediction of residual feed intake from genome and metagenome profiles in first lactation Holstein-Friesian dairy cattle, Proc. Assoc. Adv. Breed. Sci. Rep., 2019, vol. 9, no. 1. https://doi.org/10.1038/s41598-018-38218-7
Kondrat’ev, M.N., Budarin, S.N., and Larikova, Yu.S., Physiological and ecological mechanisms of invasive penetration of Sosnowsky hogweed (Heracleum sosnowskyi Manden.) into unused agroecosystems, Izv. Timiryazevsk. S.-kh.Akad., 2015, vol. 2, pp. 36—39.
Stolpovskiy, Yu.A. and Zakharov-Gezekhus, I.A., The problem of conservation of gene pools of domesticated animals, Vavilovskii Zh. Genet. Sel., 2017, vol. 21, no. 4, pp. 477—486. https://doi.org/10.18699/VJ17.266
Ventura, R., Larmer, S., Schenkel, F.S., et al., Genomic clustering helps to improve prediction in a multibreed population, J. Anim. Sci., 2016, vol. 94, no. 5, pp. 1844—1856. https://doi.org/10.2527/jas.2016-0322
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This work was supported by a grant of the Russian Science Foundation, project no. 19-76-20061.
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The authors declare no conflict of interest. This article does not contain any studies carried out with animals as objects. This article does not contain any studies carried out with people as objects.
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Translated by M. Bibov
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Stolpovsky, Y.A., Svishcheva, G.R. & Piskunov, A.K. Genomic Selection. II. Latest Trends and Future Trajectories. Russ J Genet 56, 1155–1161 (2020). https://doi.org/10.1134/S1022795420100129
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DOI: https://doi.org/10.1134/S1022795420100129