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Genetical genomics, or genetic analysis applied to gene expression data, has not been widely used in plants. We used quantitative cDNA-AFLP to monitor the variation in the expression level of cotton fiber transcripts among a population of inter-specific Gossypium hirsutum × G. barbadense recombinant inbred lines (RILs). Two key fiber developmental stages, elongation (10 days post anthesis, dpa), and secondary cell wall thickening (22 dpa), were studied. Normalized intensity ratios of 3,263 and 1,201 transcript-derived fragments (TDFs) segregating over 88 RILs were analyzed for quantitative trait loci (QTL) mapping for the 10 and 22 dpa fibers, respectively. Two-thirds of all TDFs mapped between 1 and 6 eQTLs (LOD> 3.5). Chromosome 21 had a higher density of eQTLs than other chromosomes in both data sets and, within chromosomes, hotspots of presumably trans-acting eQTLs were identified. The eQTL hotspots were compared to the location of phenotypic QTLs for fiber characteristics among the RILs, and several cases of co-localization were detected. Quantitative RT-PCR for 15 sequenced TDFs showed that 3 TDFs had at least one eQTL at a similar location to those identified by cDNA-AFLP, while 3 other TDFs mapped an eQTL at a similar location but with opposite additive effect. In conclusion, cDNA-AFLP proved to be a cost-effective and highly transferable platform for genome-wide and population-wide gene expression profiling. Because TDFs are anonymous, further validation and interpretation (in silico analysis, qPCR gene profiling) of the eQTL and eQTL hotspots will be facilitated by the increasing availability of cDNA and genomic sequence resources in cotton.

Wheat dwarf virus, transmitted by the leafhopper Psammotettix alienus in a persistent, non-propagative manner, infects numerous species from the Poaceae family. Data associated with wheat dwarf virus (WDV) suggest that some isolates preferentially infect wheat while other preferentially infect barley. This allowed to define the wheat strain and the barley strain. There are contradictory results in the literature regarding the ability of each of these two strains to infect its non-preferred host. To improve knowledge on the interactions between WDV strains and barley and wheat, transmission experiments were carried out using barcoded P. alienus and an experimental design based on single/sequential acquisitions of WDV strains and on transmissions to wheat and barley. Results showed that (I) WDV strains are transmitted with similar efficiencies by P. alienus males, females and larvae, (II) WDV wheat and barley strains do not infect barley and wheat plants, respectively, and (III) a functional transcomplementation between the wheat and barley strains allows a mixed infection of barley and wheat. The described ability of each WDV strain to infect a non-host plant in the presence of the other viral strain must be considered to analyze data available on WDV host range.Viruses 2020, 12, 34 2 of 15The WDV genome also contains two non-coding sequences (the long and short intergenic regions (LIR and SIR, respectively)) which contain sequences important for viral replication and for the regulation of gene expression [7]. Phylogenetic studies carried out with complete WDV genomic sequences obtained from isolates sampled on different host species evidenced two main groups, including, respectively, the originally described wheat (noted WDV-W in this study) and barley (WDV-B in this study) strains [8,9]. The WDV genetic diversity has been further categorized into clades (A to E) based on sequence similarity and phylogenetic relationships [10]: the WDV-W group includes clades C, D and E, whereas WDV-B includes clades A (subdivided into A1 and A2 [11]) and B. WDV-B and WDV-W strains show 83-84% nucleotide identity [12], LIR and SIR being the most variable genomic regions [13]. Nucleotide identity is above 94% between WDV-B isolates and above 98% between WDV-W isolates [13][14][15][16][17].WDV is transmitted from plant to plant in a persistent, non-propagative manner [18] by leafhoppers from the genus Psammotettix (Hemiptera, Cicadellidae, Deltocephalinae), a Holartic species commonly found in cereal fields and in grassland [19,20]. Morphological characteristics of these insects can be used to assign leafhoppers to the genus Psammotettix [21,22]. However, the accurate identification of Psammotettix species requires a morphological description of the male genitalia (i.e., aedeagus), which does not allow the assignment of females to the Psammotettix species. Due to the complex taxonomy of the Psammotettix spp., criteria used to identify leafhoppers species are poorly described in WDV studies. This could lead to some conflicting resul...