Sex-specific polymorphism of MET1 and ARR17 genes in Populus × sibirica

• Published in: Biochimie Vol. 162; pp. 26 - 32
• Main Authors: Melnikova, Nataliya V., Kudryavtseva, Anna V., Borkhert, Elena V., Pushkova, Elena N., Fedorova, Maria S., Snezhkina, Anastasiya V., Krasnov, George S., Dmitriev, Alexey A.
• Format: Journal Article
• Language: English
• Published: France Elsevier B.V 01.07.2019
• Subjects: Alleles; ARR17; Base Sequence; Deep sequencing; DNA (Cytosine-5-)-Methyltransferases - genetics; DNA-Binding Proteins - genetics; Genes, Y-Linked - genetics; Genome, Plant; Genotype; High-Throughput Nucleotide Sequencing - methods; MET1; Polymorphism, Single Nucleotide - genetics; Populus; Populus - genetics; Sequence Analysis, DNA - methods; Sex; SNP; Transcription Factors - genetics; Deep sequencing; MET1; Populus; SNP; ARR17; Sex
• ISSN: 0300-9084; 1638-6183
• DOI: 10.1016/j.biochi.2019.03.018

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. •Deep sequencing of sex-associated regions was performed in Populus × sibirica.•11 and 6 sex-specific SNPs were identified in MET1 and ARR17 genes respectively.•In sex-specific SNP sites, females were homozygous and males were heterozygous.•Our results confirmed the XY sex-determination system in poplars.•The developed HRM-based approach enabled sex identification in Populus × sibirica.