Genetic structure and geographical differentiation of Siberian Larch (Larix sibirica Ledeb.) populations based on genome genotyping by sequencing
S. V. NOVIKOVA1,2, N. V. ORESHKOVA1,2,3, V. V. SHAROV1,2, V. L. SEMERIKOV4, K. V. KRUTOVSKY1,5,6,7
1Siberian Federal University, Krasnoyarsk, Russia
2Federal Research Center “Krasnoyarsk Science Center of the SB RAS”, Krasnoyarsk, Russia
3V. N. Sukachev Institute of Forest SB RAS, Krasnoyarsk, Russia
4Institute of Plant and Animal Ecology UB RAS, Yekaterinburg, Russia
5Georg-August University of Göttingen, GÖttingen, Germany
6N. I. Vavilov Institute of General Genetics RAS, Moscow, Russia
7Voronezh State University of Forestry and Technologies named after G. F. Morozov, Voronezh, Russia
Keywords: population, genetic structure, Larix sibirica, adaptation, climatic variables, conifers, ddRADseq, SNP
Abstract
The genetic differentiation of Siberian larch (Larix sibirica Ledeb.) populations in the latitudinal gradient of climatic conditions was studied based on high-throughput double digest restriction-site associated DNA sequencing (ddRADseq) data. We studied the correlation of five main climatic variables with the variability of 47,929 single nucleotide polymorphisms (SNPs). A total of 125 trees were studied: 61 trees in four populations along the western geographic transect and 64 trees in four populations along the eastern geographic transect. 21 SNPs with signatures of selection were identified, including 9 outlier SNPs whose variability cannot be explained by selectively neutral processes, and 12 SNPs whose variability correlated with the environmental factors. Seven SNPs are located in the introns of mitochondrial genes, three are located relatively close to the mitochondrial genes encoding NAD2 and ribosomal proteins S7 and S11, one is located at a distance from the nuclear gene encoding a protein homologous to the microtubule-associated futsch-like protein of Arabidopsis thaliana, two in the protein genes of an unknown nature and three in contigs containing no genes, and for which no homologous sequences were found in the NCBI GenBank.
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