Development of microsatellite genetic markers in Siberian larch (Larix sibirica Ledeb.) based on the de novo whole genome sequencing

Abstract

geneticist Yuri Petrovich Altukhov, who paid much attention in his research to the development of molecular genetic markers for population studies. Over the past time markers and methods of their development have undergone significant change. Thanks to modern methods of whole genome sequencing, it has become possible to develop markers of very different types-selectively neutral, as well as functional. Among them, microsatellite markers remain the most informative, convenient, reproducible, relatively inexpensive, and polymorphic. Whole genome sequencing greatly facilitates their Göttingen, the Department for Monitoring of Forest Genetic Resources of the Forest Protection Center of the Krasnoyarsk Territory, and the Laboratory of Forest Genetics and Selection of the V. N. Sukachev Institute of Forest of the Siberian Branch of the Russian Academy of Sciences within the framework of the project "Genomics of the key boreal forest conifer species and their major phytopathogens in the Russian Federation" funded by the Government of the Russian Federation (grant no. 14.Y26.31.0004).

Postgenomic technologies in practical forestry: development of genome-wide markers for timber origin identification and other applications

“…To develop new highly informative microsatellite genetic markers for Siberian larch and Siberian stone pine using their whole genome assemblies a computer search for microsatellite loci with high repetitive simple motifs was done in the genomic DNA sequences, oligonucleotide primers were developed, synthesized and tested for the selected loci. ------------------------------------------------------------------ A preliminary estimate of allelic diversity was made on two test samples of a Siberian larch population collected in the Republic of Khakassia (Russian Federation) and several Siberian stone pine populations [9,10].…”

“…The most promising markers were selected, and multiplex genotyping panels were designed for Siberian larch and tested for fragment analysis using the ABI 3130xl Genetic Analyzer with capillary electrophoresis [10].…”

“…As a result, 59 primers pairs were designed and tested. Needle samples collected from 100 individ-ual Siberian larch trees in 2014 in two populations (50 trees per population) in the Republic of Khakassia were used in this study [10]. The one population is located in the Shirinsky District of Khakassia near the Shira-Berenjak highway (larch forest with pine on a gentle slope), anothernear the Efremkino Village (larch on a steep slope and at its foot).…”

Development of Nuclear Microsatellite Markers with Long (Tri-, Tetra-, Penta-, and Hexanucleotide) Motifs for Three Larch Species Based on the de novo Whole Genome Sequencing of Siberian Larch (Larix sibirica Ledeb.)

“…Given the large size of conifer genomesfrom 10 to 30 billion nucleotide bases (Gbp), this task becomes particularly difficult. However, the development of new generation sequencing (NGS) technologies has greatly simplified the process, making it also faster and cheaper [8][9][10].…”

“…Among species in the genus Larix, microsatellite markers have been developed for Japanese [11,12], European [13], Alpine [14], Western [14,15], and Siberian [9] larch. In early studies, the measurement of genetic diversity and the assessment of population structure of Siberian, Gmelin, and Cajander larch were carried out using SSR markers developed for other larch species [16,17].…”