Single nucleotide polymorphism (SNP) characterization of drought-responsive genes to estimate genetic variation ofPopulus tremulavar.davidianaand eight otherPopulusspecies

Abstract

To reveal the genetic mechanisms behind drought tolerance, we attempted to identify the drought-responsive genes in Populus tremula var. davidiana (Dode) C.K. Schneid. and eight other species of Populus. Nine drought-responsive genes were assayed by single nucleotide polymorphism (SNP) genotyping using TaqMan probe-based real-time PCR. A total of 346 SNPs were found from the 101 sequences of the nine genes. Among them, 57 primers were selected for SNP genotyping and haplotype determination. For the SNP genotyping, 56 assays were applicable to section Leuce Duby, 53 to section Aigeiros Duby, 50 to Populus maximowiczii Henry, and 52 to Populus simonii Carrière. The expectation maximization algorithm was implemented to determine haplotypes among species and sections. A total of 78 haploid types were estimated from nine drought-responsive gene loci, and the average number of haploid types per locus was 8.67. The analysis of genetic diversity revealed that P. tremula var. davidiana had substantial levels of genetic variation for the nine drought-responsive genes, which was higher than the eight other species. The means of observed number of alleles (NA) and heterozygosity (Ho) were 5.33 and 0.6609, respectively. Analysis of the genetic differentiation of P. tremula var. davidiana showed that 7.52% of genetic variation was among populations and the remaining was within a population.

Neutral and adaptive genetic diversity in plants: An overview

“…For instance, researchers can estimate genetic diversity parameters based on genetic markers linked to genes involved with adaptive traits [Le Corre and Kremer, 2003; or quantitative trait loci which are genomic regions at which AGV is associated with a particular quantitative trait and identified by using statistical associations between neutral genetic markers and phenotypic traits (Falconer and Mackay, 1996;Caballero, 2020; Figure 1)]. Typically, researchers measure H e-A , π A , S A , p S-A , and F ST-A (e.g., Toro and Caballero, 2005;Jeffries et al, 2016;Fischer et al, 2017;Kim et al, 2018; hereafter " A " indicates adaptive). For the calculation of S A and p S-A , L is the same as when calculated with all site parameters.…”

“…As for conservation and restoration efforts, π A and θ W-A are based on adaptive loci screened from candidate genes or genome-wide loci (e.g., SNPs), and many of them which underlay adaptive traits have recently been studied for signatures of selection at single sites (Eveno et al, 2008;Eckert et al, 2009;Gailing et al, 2009;Derory et al, 2010;Ekblom et al, 2018;Kim et al, 2018;Supple and Shapiro, 2018). Quantification of AGV, as well as transcriptomics and epigenetics, constitute important and promising potential approaches for developing future conservation strategies for rare and endangered plant species (Figure 1; Eckert et al, 2009;Gailing et al, 2009;Nichols and Neale, 2010;Ouborg et al, 2010;Harrisson et al, 2014;He et al, 2016;Anderson and Song, 2020;Hohenlohe et al, 2020).…”

Analysis of the genetic diversity and population structure of Salix psammophila based on phenotypic traits and simple sequence repeat markers

“…Molecular markers such as restriction fragment length polymorphisms (Brunner et al, 2001; Thormann, Myrholm & Mallett, 2001; Tsarouhas, Gullberg & Lagercrantz, 2002), amplified fragment length polymorphisms (Chen et al, 2016; Hu, Lv & Lu, 2011), simple sequence repeats (SSRs) (He et al, 2015; Perdereau et al, 2014; Cortés et al, 2014) and single nucleotide polymorphisms (Kim et al, 2018) have been widely used in Salix genome analyses. SSRs have a high rate of polymorphism, good reproducibility, and codominant inheritance, and are evenly distributed in coding and non-coding regions of the plant genome, making them ideal markers for studying genetic diversity and population structure (Kalia et al, 2010).…”

Future Climate Change Will Have a Positive Effect on Populus davidiana in China

“…The P. davidiana forest covers about 21,600 km 2 in China, which is substantially less than the potential/historical extent [18]. At present, most research regarding P. davidiana mainly focuses on the following aspects: Physiological ecology [19][20][21], genetic variation [22,23], genetic expression [24,25], tissue culture [26,27], and spatial structure [28]. All these provide a basis for the protection and utilization of P. davidiana.…”