Comparative analysis of flax (Linum usitatissimum L.) genomes and transcriptomes

Poster (download) Elena Pushkova1, George Krasnov2, Roman Novakovskiy3, Liubov Povkhova4, Artemy Beniaminov5, Nadezhda Bolsheva6, Tatiana Rozhmina7, Alexey Dmitriev8, Nataliya Melnikova91Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, pushkova18@gmail.com2Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, gskrasnov@mail.ru3Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, 0legovich46@mail.ru4Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia; Moscow Institute of Physics and Technology, Dolgoprudny, Russia, povhova.lv@phystech.edu5Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, abeniaminov@mail.ru6Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, nlbolsheva@mail.ru7Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia; Federal Research Center for Bast Fiber Crops, Torzhok, Russia, tatyana_rozhmina@mail.ru8Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, alex_245@mail.ru9Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, mnv-4529264@yandex.ru Flax (Linum usitatissimum L.) is an agriculturally important plant that has a wide range of applications in industry, and the direction of cultivar application is determined by its genetic characteristics. The present work aimed to obtain high-quality sequences of flax genomes and transcriptomes for genetically diverse cultivars and lines, which have breeding value and different direction of use. Six cultivars/lines (LM98, #3896, Diplomat, Atlant, Universal, Alizee) were selected for the present work. We have developed an optimal method for the extraction of pure high-molecular-weight DNA from flax plants and performed genome and transcriptome sequencing. From 6 to 10 Gb was obtained for each of the studied flax cultivars/lines on the Oxford Nanopore platform and 20-25 million reads on the Illumina platform. Transcriptome sequencing of different flax tissues was also performed. Genome assembly using Flye resulted in the N50 value from 200 kb to 1 Mb depending on the genotype. Genome annotation was then performed. The obtained genome assemblies are the basis for molecular genetic studies in flax and allow assessment of the differences in L. usitatissimum cultivars/lines at the genome-wide level.

Read More

Molecular markers based on SNPs in FAD3 genes for determination of linolenic acid content in flax seed

Poster (download) Liubov Povkhova1, Parfait Kezimana2, Tatiana Rozhmina3, Elena Pushkova4, Roman Novakovskiy5, George Krasnov6, Alexey Dmitriev7, Nataliya Melnikova81Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia; Moscow Institute of Physics and Technology, Dolgoprudny, Russia, povhova.lv@phystech.edu2Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia; RUDN University, Moscow, Russia, k1par@mail.ru3Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia; Federal Research Center for Bast Fiber Crops, Torzhok, Russia, tatyana_rozhmina@mail.ru4Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, pushkova18@gmail.com5Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, 0legovich46@mail.ru6Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, gskrasnov@mail.ru7Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, alex_245@mail.ru8Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, mnv-4529264@yandex.ru Flax is grown for seeds in many countries. Depending on the ratio of fatty acids, seeds are used in pharmaceutical, food, feed, or polymer production. It is known that genes of FAD3 family responsible for the desaturation of linoleic (LIO) into linolenic (LIN) fatty acid and some alleles of these genes are associated with a certain composition of flax oil. However, the development of the marker-assisted selection of flax is complicated due to a lack of methods for the identification of these polymorphisms. In the present study, we used 84 flax cultivars/lines with diverse content of LIO and LIN to search for fatty acid associated SNPs and then developed HRM-based system for identification of these SNPs that can increase the efficiency of breeding by obtaining pure improved cultivars with the targeted LIO and LIN content.

Read More