1. bookVolume 69 (2020): Issue 1 (January 2020)
Journal Details
License
Format
Journal
eISSN
2509-8934
First Published
22 Feb 2016
Publication timeframe
1 time per year
Languages
English
access type Open Access

Genetic structure of ural populations of Larix sibirica Ledeb. on the base of analysis of nucleotide polymorphism

Published Online: 06 Apr 2020
Volume & Issue: Volume 69 (2020) - Issue 1 (January 2020)
Page range: 20 - 28
Journal Details
License
Format
Journal
eISSN
2509-8934
First Published
22 Feb 2016
Publication timeframe
1 time per year
Languages
English
Abstract

Research on the state and dynamics of the gene pool (an important natural resource that determines the potential fitness of living organisms and, ultimately, their long-term survival) becomes an important problem in the context of increased anthropogenic environmental impact. They are especially important for key species of ecosystems of a global scale importance. Larix sibirica Ledeb., which spreads from the Western Siberia to the Russian North-West, is one of such forest tree species. We identified patterns of genetic structure of populations on the example of the species’ Western race on the Middle and Northern Urals. The analysis of nucleotide polymorphism of genes of ABA-inducible protein, MADS-box-transcription factor and of 4-kumarat: CoA ligase (a part of the gene) was used as a method. Evidences were obtained that a part of the populations previously formed a single large population. At the same time, populations with different gene pools were found. As a result, differences between populations within the region were more pronounced (fixation index FST = -0.021 – 0.260, total haplotype diversity Hd = 0.636 – 0.911; nucleotide diversity π = 0.005 – 0.009; number of mutations θW = 0.005 – 0.012) than in other parts of the race. Causes of this phenomenon are discussed. It was concluded that the larch forests with a unique gene pool and/or high genetic diversity should be objects of population-oriented forestry and conservation.

Keywords

Araki NHT, Khatab IA, G KK, Hemamali U, Inomata N, X.-R. Wang N X-R. and Szmidt AE (2008) Phylogeography of Larix sukaczewii Dyl. and Larix sibirica L. inferred from nucleotide variation of nuclear genes. Tree Genetics & Genomes: 4 (4): 611-623. https://doi.org/10.1007/s11295-008-0137-110.1007/s11295-008-0137-1Search in Google Scholar

Blanc-Jolivet C., Yanbaev Y, Kersten B, Degen B (2018) A set of SNP markers for timber tracking of Larix spp. in Europe and Russia. Forestry 91 (5): 614-628. https://doi.org/10.1093/forestry/cpy02010.1093/forestry/cpy020Search in Google Scholar

Dylis NV (1947) Siberian Larch. Moscow, Moscow Society of Naturalists (in Russian).Search in Google Scholar

Dixon DP, Skipsey M and Edwards R (2010) Roles for glutathione transferases in plant secondary metabolism. Phytochemistry 71 (№ 4): 338-350. https://doi.org/10.1016/j.phytochem.2009.12.01210.1016/j.phytochem.2009.12.01220079507Search in Google Scholar

Earl DA and vonHoldt BM (2012) STRUCTURE: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources. 4 (2): 359-361. https://doi.org/10.1007/s12686-011-9548-710.1007/s12686-011-9548-7Search in Google Scholar

Eckert AJ, Wegrzyn JL, Pande B, Jermstad KD, Lee JM, Liechty JD, Tearse BR, Krutovsky KV and Neale DB (2009) Multilocus patterns of nucleotide diversity and divergence reveal positive selection at candidate genes related to cold hardiness in coastal Douglas Fir (Pseudotsuga menziesii var. menziesii). Genetics 183 (1): 289-298. https://doi.org/10.1534/genetics.109.10389510.1534/genetics.109.103895274615219596906Search in Google Scholar

Evanno G, Regnaut S and Goudet J (2005) Detecting the number of clusters of individuals using the software structure: a simulation study. Molecular Ecology 14 (8): 2611-2620. https://doi.org/10.1111/j.1365-294x.2005.02553.x10.1111/j.1365-294X.2005.02553.x15969739Search in Google Scholar

Excoffier L and Lischer HEL (2010) Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10 (3): 564-567. https://doi.org/10.1111/j.1755-0998.2010.02847.x10.1111/j.1755-0998.2010.02847.x21565059Search in Google Scholar

Hammer Ø, Harper DAT and Ryan PD (2001) PAST: Paleontological statistics software package for education and data analysis. Palaeontologia Electronica 4: 1-9.Search in Google Scholar

Hubisz MJ, Falush D, Stephens M and Pritchard JK (2009) Inferring weak population structure with the assistance of sample group information. Molecular Ecology Resources 9 (5): 1322-1332. https://doi.org/10.1111/j.1755-0998.2009.02591.x10.1111/j.1755-0998.2009.02591.x351802521564903Search in Google Scholar

Katoh K, and Standley DM (2013) MAFFT Multiple Sequence Alignment Software version 7: improvements in performance and usability. Molecular Biology and Evolution 30 (4): 772-780. https://doi.org/10.1093/molbev/mst01010.1093/molbev/mst010360331823329690Search in Google Scholar

Khatab IA, Ishiyama H, Inomata N, Wang X-R and Szmidt AE (2008) Phylogeography of Eurasian Larix species inferred from nucleotide variation in two nuclear genes. Genes & Genetic Systems 83 (1): 55-66. https://doi.org/10.1266/ggs.83.5510.1266/ggs.83.5518379134Search in Google Scholar

Kopelman NM, Mayzel J, Jakobsson M, Rosenberg NA and Mayrose I (2015) CLUMPAK: a program for identifying clustering modes and packaging population structure inferences across K. Molecular Ecology Resources 15 (5): 1179-1191. https://doi.org/10.1111/1755-0998.1238710.1111/1755-0998.12387Search in Google Scholar

Krutovsky KV (2006) From population genetics to population genomics of forest trees: Integrated population genomics approach. Russian Journal of Genetics 42 (10): 1088-1100. https://doi.org/10.1134/s102279540610002410.1134/S1022795406100024Search in Google Scholar

Krutovsky KV and Neale DB (2005) Forest genomics and new molecular genetic approaches to measuring and conserving adaptive genetic diversity in forest trees. In: Conservation and Management of Forest Genetic Resources in Europe. Arbora Publishers, Zvolen Geburek. (Eds. Th. Geburek and J. Turok). pp: 369–390.Search in Google Scholar

Leigh JW and Bryant D (2015) PopART: full-feature software for haplotype network construction. Methods in Ecology and Evolution 6 (9): 1110-1116. https://doi.org/10.1111/2041-210x.1241010.1111/2041-210X.12410Search in Google Scholar

Martinsson O and Lesinski J (2007) Siberian larch forestry and timber in a Scandinavian perspective. JiLU Jämtlands County Council Institute of Rural Development. Prinfo Accidenstryckeriet.Search in Google Scholar

Nechaeva YuS, Boronnikova SV, Prishnivskaya YaV, Chumak EI and Yusupov RR (2014) Analysis of ISSR-PCR polymorphism of markers and genetic structure of some populations of Siberian larch in the Urals. Modern problems of science and education 10 (6) (in Russian).Search in Google Scholar

Nechaeva YuS, Julanov AA, Boronnikova SV and Prishnivskaya YaV (2017) Nucleotide polymorphisms of candidate genes of adaptive significance in the Ural populations of Larix sibirica Ledeb. Russian Journal of Genetics 53 (5): 587-595. https://doi.org/10.1134/s102279541705006410.1134/S1022795417050064Search in Google Scholar

Nei M (1973) Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences of the USE 70 (12): 3321-3323. https://doi.org/10.1073/pnas.70.12.332110.1073/pnas.70.12.3321Search in Google Scholar

Nei, M (1987) Molecular evolutionary genetics. New York: Columbia University Press. https://doi.org/10.1016/0047-2484(89)90093-610.1016/0047-2484(89)90093-6Search in Google Scholar

Okonechnikov K, Golosova O and Fursov M (2012) Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 28 (8): 1166-1167. https://doi.org/10.1093/bioinformatics/bts09110.1093/bioinformatics/bts09122368248Search in Google Scholar

Oreshkova NV, Belokon MM and Jamiyansuren S (2013) Genetic diversity, population structure, and differentiation of Siberian larch, Gmelin larch, and Cajander larch on SSR-marker data. Russian Journal of Genetics 49 (2): 178-186. https://doi.org/10.1134/s102279541212009510.1134/S1022795412120095Search in Google Scholar

Petit R.J, El Mousadik A and Pons O (2008) Identifying populations for conservation on the basis of genetic markers. Conservation Biology 12 (4): 844–855. https://doi.org/10.1111/j.1523-1739.1998.96489.x10.1111/j.1523-1739.1998.96489.xSearch in Google Scholar

Polezhaeva MA, Lascoux M and Semerikov VL (2010) Cytoplasmic DNA variation and biogeography of Larix Mill. in Northeast Asia. Molecular ecology 19 (6): 1239-1252. https://doi.org/10.1111/j.1365-294x.2010.04552.x10.1111/j.1365-294X.2010.04552.x20163546Search in Google Scholar

Putenikhin VP, Farukshina GG and Shigapov ZKh (2004) Larix Sukaczewii in the Urals: variability and population-genetic structure. Nauka, Moscow (in Russian).Search in Google Scholar

Rellstab C, Zoller S, Walthert L, Lesur I, Pluess AR, Graff R, Bodenez C, Sperisen C, Kremer A and Gugerli F (2016) Signatures of local adaptation in candidate genes of oaks (Quercus spp.) with respect to present and future climatic conditions. Molecular Ecology 25 (23): 5907-5924. https://doi.org/10.1111/mec.1388910.1111/mec.1388927759957Search in Google Scholar

Rogers SO and Bendich AJ (1985) Extraction of DNA from milligram amounts of fresh, herbarium and mummified plant tissues. Plant Molecular Biology 5 (2): 69-76. https://doi.org/10.1007/bf0002008810.1007/BF0002008824306565Search in Google Scholar

Rozas J, Ferrer-Mata A, Sanchez-DelBarrio JC, Guirao S, Librado P, Ramos-Onsins SE and Sanches-Gracia A (2017) DnaSP 6: DNA sequence polymorphism analysis of large data sets. Molecular Biology and Evolution 34 (12): 3299-3302. https://doi.org/10.1093/molbev/msx24810.1093/molbev/msx24829029172Search in Google Scholar

Semerikov VL and Lascoux M (2003) Nuclear and cytoplasmic variation within and between Eurasian Larix (Pinaceae) species. American Journal of Botany 90 (8): 1113-1123. https://doi.org/10.3732/ajb.90.8.111310.3732/ajb.90.8.111321659211Search in Google Scholar

Semerikov VL, Iroshnikov AI and Lascoux M (2007) Mitochondrial DNA variation pattern and postglacial history of the Siberian larch (Larix sibirica Ledeb.). Russian Journal of Ecology 38 (3): 147-154. https://doi.org/10.1134/s106741360703001010.1134/S1067413607030010Search in Google Scholar

Semerikov VL, Semerikova SA and Polezhaeva MA (2013) Nucleotide diversity and linkage disequilibrium of adaptive significant genes in Larix (Pinaceae). Russian Journal of Genetics 49 (9): 915-923. https://doi.org/10.1134/s102279541309007x10.1134/S102279541309007XSearch in Google Scholar

Svetlakova TN, Boronnikova SV and Yanbaev YuA (2014) Genetic diversity and differentiation in Ural populations of the aspen, Populus tremula L., as revealed by inter-simply sequence repeat (ISSR) markers. Silvae Genetica 63 (1-6): 39-41. https://doi.org/10.1515/sg-2014-000610.1515/sg-2014-0006Search in Google Scholar

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