ISSN 1022-7954, Russian Journal of Genetics, 2017, Vol. 53, No. 5, pp. 587–595. © Pleiades Publishing, Inc., 2017.
Original Russian Text © Yu.S. Nechaeva, A.A. Julanov, S.V. Boronnikova, Ya.V. Prishnivskaya, 2017, published in Genetika, 2017, Vol. 53, No. 5, pp. 591–600.
Nucleotide Polymorphisms of Candidate Genes of Adaptive
Significance in the Ural Populations of Larix sibirica Ledeb.
Yu. S. Nechaeva
*, A. A. Julanov
, S. V. Boronnikova
, and Ya. V. Prishnivskaya
Perm State National Research University, Perm, 614990 Russia
Natural Sciences Institute, Perm State National Research University, Perm, 614990 Russia
Received July 1, 2016
Abstract⎯The objectives of conservation and sustainable forest management require in depth study of
genomes of woody plants and definition of their intraspecific genetic diversity. In recent years, an approach
was developed based on the study of “candidate genes” that can potentially be involved in the formation of
adaptive traits. In this study, we investigated nucleotide polymorphism of several adaptive candidate genes in
the populations of Siberian larch (Larix sibirica Ledeb.) in the Urals. Representatives of this genus are among
the most valuable and widely distributed forest tree species in Russia. From ten selected gene loci in the
genome of L. sibirica, we isolated and investigated three loci, one of which (ABA-WDS) was sequenced in
L. sibirica for the first time. The total length of the analyzed sequence in each individual amounted to 2865 bp.
The length of locus alignment was from 360 bp to 1395 bp. In total, we identified 200 polymorphic positions.
The most conservative is locus 4CL1-363, and the most polymorphic is locus sSPcDFD040B03103-274. The
studied populations of L. sibirica are characterized by a high level of nucleotide polymorphism in comparison
with other species and genuses (Picea, Pinus, Pseudotsuga, Abies) conifers plants (Hd = 0.896; π = 0.007; θ
0.015). The most selectively neutral polymorphism (D
= –0.997) was attributed to locus 4CL1-363, and
polymorphism with high probability of adaptability (D
= –1.807) was determined for the ABA-WDS locus.
We identified 54 SNP markers, only five of which were nonsynonymous (9.26%) replacements. The average
frequency of SNPs in the three studied loci of L. sibirica was one SNP in 53 bp. We detected unique SNP
markers for eight populations, which could potentially be used to identify populations. Populations that are
characterized by the highest number of unique SNP markers can be recommended for selection in order to
preserve the gene pool of the species.
Keywords: genetic diversity, locus, molecular marker, SNP, Siberian larch
Development of modern molecular genetic meth-
ods of research opened up new possibilities for the
studies of distribution patterns of genetic variation, as
well the maintenance of equilibrium processes in pop-
ulations of woody plants to enhance their stability .
The search for alleles that underlie adaptation of spe-
cies to a heterogeneous environment is one of the
urgent problems of modern genetics , including for
coniferous species of plants [3, 4].
Genomic studies distinguish an integrative system
approach, in the course of which variability is investi-
gated at the level of the whole genome or a large num-
ber of genes and markers [5, 6]. In woody plant spe-
cies, genomic analysis revealed a relationship between
allelic genetic variability and variation of important
adaptive phenotypic traits essential for selection, such
as growth rate, wood quality, and resistance to disease,
low temperatures, drought, etc. [6, 7]. In addition,
identification of genetic mechanisms of adaptation of
local populations is very important for the develop-
ment of scientifically solid programs and approaches
for forest protection, seed-bearing and reforestation
. Comprehensive genomic analysis can enable iso-
lation of the adaptive structures of the populations and
aid in understanding of molecular evolution of
important genes and identification of alleles under the
influence of various forms of selection [3, 9, 10]. How-
ever, the large size of genomes of coniferous plant spe-
cies (more than 10 Gb) makes it challenging to execute
a whole genome sequencing for these organisms to
study the “genotype–trait” associations . In this
regard, an approach was developed based on the study
of candidate genes potentially involved in the forma-
tion of adaptive characteristics . Investigations of
nucleotide diversity and its association with adaptive
features of candidate genes were carried out for conifer
species Pseudotsuga [3, 7], Pinus [13–16], and Picea
[17, 18]. Comprehensive studies of the main conifer
species of plants of European forests were conducted