Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow, 119991, Russia.
Biochimie. 2019 Jul;162:26-32. doi: 10.1016/j.biochi.2019.03.018. Epub 2019 Mar 29.
The genus Populus is an effective model in tree genetics. This genus includes dioecious species and, recently, whole genome resequencing of P. trichocarpa and P. balsamifera enabled the identification of sex-linked regions and sex-associated single nucleotide polymorphisms (SNPs). These results created new opportunities to study sex determination in poplars. In the present work, we performed deep sequencing of genes encoding METHYLTRANSFERASE1 (MET1) and homolog of ARABIDOPSIS RESPONSE REGULATOR 17 (ARR17), which are localized in a sex-linked region of Populus genome and contain a number of sex-associated SNPs. Amplicon libraries for 38 samples of P. × sibirica (19 males and 19 females) were sequenced on MiSeq Illumina (300 nt paired-end reads) and approximately 4000× coverage was obtained for each sample. In total, from 80 to 179 SNPs were detected in poplar individuals for MET1, and from 16 to 49 SNPs were detected for ARR17. We identified 17 sex-specific SNPs (11 in MET1 and 6 in ARR17) - they were present in all males but absent in all females. For identified sex-specific SNP sites, females were homozygous, while males were heterozygous. Moreover, colocation of sex-specific SNPs confirming the XY sex-determination system of poplars was revealed: in one allelic variant, males had the same nucleotides as females, while in the other, sex-specific SNPs were present. Based on the data obtained, we developed and successfully applied a high-resolution melting-based approach for sex identification in poplars. The developed molecular markers are useful for distinguishing between male and female poplars in scientific research and can also be applied to select male-only genotypes for use in city landscaping and production of paper, pulp, and biofuel.
杨属是树木遗传学中的有效模式生物。该属包含雌雄异株物种，最近对 P. trichocarpa 和 P. balsamifera 的全基因组重测序，使得鉴定出性连锁区域和与性相关的单核苷酸多态性（SNP）成为可能。这些结果为研究杨树的性别决定提供了新的机会。在本工作中，我们对 METHYLTRANSFERASE1（MET1）和 ARABIDOPSIS RESPONSE REGULATOR 17（ARR17）的编码基因进行了深度测序，这些基因位于杨树基因组的性连锁区域，并且包含许多与性相关的 SNP。使用 MiSeq Illumina 对 38 个 P. ×sibirica 样本（19 个雄性和 19 个雌性）的扩增子文库进行测序（300nt 配对末端读取），每个样本的覆盖度约为 4000×。总共在杨树个体中检测到 MET1 中有 80 到 179 个 SNP，ARR17 中有 16 到 49 个 SNP。我们鉴定到 17 个性别特异性 SNP（MET1 中有 11 个，ARR17 中有 6 个），它们存在于所有雄性中，但不存在于所有雌性中。对于鉴定到的性别特异性 SNP 位点，雌性是纯合的，而雄性是杂合的。此外，揭示了性连锁 SNP 的共定位，证实了杨树的 XY 性别决定系统：在一个等位基因变体中，雄性与雌性具有相同的核苷酸，而在另一个等位基因变体中，存在性别特异性 SNP。基于获得的数据，我们开发并成功应用了一种基于高分辨率熔解的杨树性别鉴定方法。开发的分子标记可用于区分科研中的雄性和雌性杨树，也可用于选择雄性纯合基因型，用于城市景观美化和纸浆、纸和生物燃料的生产。
