Genetic linkage maps of Populus nigra L. including AFLPs, SSRs, SNPs, and sex trait

Abstract

Black poplar (Populus nigra L.) is a tree of ecological and economic interest. A better knowledge of P. nigra genome is needed for an effective protection and use of its genetic resources. The main objective of this study is the construction of a highly informative genetic map of P. nigra species including genes of adaptive and economic interest. Two genotypes originated from contrasted natural Italian populations were crossed to generate a F 1 mapping pedigree of 165 individuals. Amplification fragment length polymorphism (AFLP), simple sequence repeat (SSR), and single nucleotide polymorphism (SNP) markers were used to genotype 92 F 1 individuals, and the pseudo-test-cross strategy was applied for linkage analysis. The female parent map included 368 markers (274 AFLPs, 91 SSRs, and 3 SNPs) and spanned 2,104 cM with 20 linkage groups, and the male parent map, including 317 markers (205 AFLPs, 106 SSRs, 5 SNPs, and sex trait), spanned 2,453 cM with 23 main linkage groups. The sex, as morphological trait, was mapped on the linkage group XIX of the male parent map. The generated maps are among the most informative in SSRs when compared to the Populus maps published so far and allow a complete alignment with the 19 haploid chromosomes of Populus sequence genome. These genetic maps provide informative tools for a better understanding of P. nigra genome structure and genetic improvement of this ecologically and economically important European tree species.

Patterns of genetic diversity and differentiation in resistance gene clusters of two hybridizing European Populus species

“…This difference might be explained by balancing selection on chromosome III, whereas both balancing and divergent selection were detected on chromosome XIX. Indications for divergent selection in BayeScan analyses of both species (Table 4) accumulate especially in the chromosome part closer to the sex determination region of European species (Gaudet et al 2008;Yin et al 2008;Paolucci et al 2010;Pakull et al 2011;Tuskan et al 2012). These patterns support the hypothesis that the evolution of NBS-LRR genes on chromosome XIX is, directly or indirectly, linked to the evolution of sex determination.…”

“…This chromosomal region is not only particular regarding its genetic diversity but also regarding its genomic architecture. Despite high levels of synteny among Populus genomes, the location of the gender determination locus appears to be variable in position along chromosome XIX in different sections of the Populus genus (Gaudet et al 2008;Yin et al 2008;Pakull et al 2011;Kersten et al 2014). In P. alba and P. tremula, sex determination appears to have a centromeric localization rather than the peritelomeric localization described for Populus trichocarpa (Tuskan et al 2012).…”

The obscure events contributing to the evolution of an incipient sex chromosome in Populus: a retrospective working hypothesis

“…This reproductive habit in Populus, along with the ubiquitous vegetative reproduction via root suckering, air layering, and/or cladoptosis, evolved proximally to or simultaneously with the advent of this family 65 million years ago, as nearly all members of the Salicaceae family displays these habits (Karrenberg et al 2002;Eckenwalder 1996). Dioecy in Populus is strongly genetically controlled, and a region of the genome located on chromosome XIX appears to contain a gene (genes) that controls gender determination, though there are noted examples of gender reversion and hermaphroditic plants in most species (Rottenberg et al 2000;Markussen et al 2007;Gaudet et al 2008;Pakull et al 2009Pakull et al , 2011Paolucci et al 2010). The peritelomeric region on chromosome XIX in female Populus trichocarpa genotypes contains approximately 1 Mb of DNA that is not found in male genotypes and appears to have a region of suppressed and/or reduced recombination that extends 3-4 Mb beyond the hemizygous segment in females (Yin et al 2004a).…”

“…One generalized hypothesis is that sex chromosomes originate from autosomes, and dioecy almost certainly evolves from ancestral hermaphrodites that lacked sex chromosomes (Muller 1914;Liu et al 2004). Based on genetic mapping results, evidence of sex chromosomes has been reported in various species by Gaudet et al (2008), Yin et al (2008), Pakull et al (2009Pakull et al ( , 2011, and Paolucci et al (2010). Yin et al (2008) described genetic and genomic features in the peritelomeric region of chromosome XIX that suggested this region of the Populus genome is in the process of developing characteristics of a sex chromosome.…”

“…Yin et al (2008) described genetic and genomic features in the peritelomeric region of chromosome XIX that suggested this region of the Populus genome is in the process of developing characteristics of a sex chromosome. A provocative feature of chromosome XIX is the location of a gender determination locus, which maps to alternate positions on chromosome XIX, depending upon the Populus species (Gaudet et al 2008;Pakull et al 2009Pakull et al , 2011Yin et al 2008;Paolucci et al 2010) (Fig. 2), with a peritelomeric localization in members of the Aigeiros and Tacamahaca subgenera and a centromeric localization in Leuce.…”