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Genome sequencing methods and assembly tools have improved dramatically since the 2013 publication of draft genome assemblies for the mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae). We conducted proximity ligation library sequencing and scaffolding to improve contiguity, and then used linkage mapping and recent bioinformatic tools for correction and further improvement. The new assemblies have dramatically improved contiguity and gaps compared to the originals: N50 values increased 26- to 36-fold, and the number of gaps were reduced by half. Ninety per cent of the content of the assemblies is now contained in 12 and 11 scaffolds for the female and male assemblies, respectively. Based on linkage mapping information, the 12 largest scaffolds in both assemblies represent all 11 autosomal chromosomes and the neo-X chromosome. These assemblies now have nearly chromosome-sized scaffolds and will be instrumental for studying genomic architecture, chromosome evolution, population genomics, functional genomics, and adaptation in this and other pest insects. We also identified regions in two chromosomes, including the ancestral-X portion of the neo-X chromosome, with elevated differentiation between northern and southern Canadian populations., (© 2021 Her Majesty the Queen in Right of Canada Molecular Ecology Resources © 2021 John Wiley & Sons Ltd.)

Verticillium wilt (VW) of alfalfa is a devastating disease that causes forage yield reductions of up to 50% in the northern United States and Canada. The most effective method for controlling the disease is through the development and use of resistant varieties. To identify quantitative trait loci (QTL) for VW resistance in alfalfa, we used a full-sib population segregating for VW resistance. High-density linkage maps for both resistant and susceptible parents were constructed using single-dose alleles of single-nucleotide polymorphism markers generated by genotyping-by-sequencing. Five QTL associated with VW resistance were identified and they were in four linkage groups (4D, 6B, 6D, and 8C). Of those, three QTL ( qVW-6D-1, qVW-6D-2 , and qVW-8C ) had higher logarithm of odds. Two putative candidates of nucleotide-binding site leucine-rich repeat disease resistance genes were identified in the QTL intervals of qVW-6D-2 and qVW-8C , respectively. The result agreed with our previous studies, in which similar resistance loci were identified in an association panel using genome-wide association. The results provide insight into the quantitative resistance to VW in alfalfa. The resistance loci and closely linked markers identified in the present study can be used in developing new alfalfa varieties with enhanced resistance to VW.