Nucleotide polymorphisms of candidate genes of adaptive significance in the ural populations of Larix sibirica Ledeb

• Published in: Russian journal of genetics Vol. 53; no. 5; pp. 587 - 595
• Main Authors: Nechaeva, Yu. S., Julanov, A. A., Boronnikova, S. V., Prishnivskaya, Ya. V.
• Format: Journal Article
• Language: English
• Published: Moscow Pleiades Publishing 01-05-2017
• Subjects: Animal Genetics and Genomics; Biomedical and Life Sciences; Biomedicine; Human Genetics; Microbial Genetics and Genomics; Plant Genetics; genetic diversity; locus; SNP; Siberian larch; molecular marker
• ISSN: 1022-7954; 1608-3369
• DOI: 10.1134/S1022795417050064

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
W
= 0.015). The most selectively neutral polymorphism (
D
T
=–0.997) was attributed to locus
4CL1-363
, and polymorphism with high probability of adaptability (
D
T
=–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.