Background Pecan ( Carya illinoinensis ) and Chinese hickory ( C. cathayensis ) are important commercially cultivated nut trees in the genus Carya (Juglandaceae), with high nutritional value and substantial health benefits. Results We obtained >187.22 and 178.87 gigabases of sequence, and ∼288× and 248× genome coverage, to a pecan cultivar (“Pawnee”) and a domesticated Chinese hickory landrace (ZAFU-1), respectively. The total assembly size is 651.31 megabases (Mb) for pecan and 706.43 Mb for Chinese hickory. Two genome duplication events before the divergence from walnut were found in these species. Gene family analysis highlighted key genes in biotic and abiotic tolerance, oil, polyphenols, essential amino acids, and B vitamins. Further analyses of reduced-coverage genome sequences of 16 Carya and 2 Juglans species provide additional phylogenetic perspective on crop wild relatives. Conclusions Cooperative characterization of these valuable resources provides a window to their evolutionary development and a valuable foundation for future crop improvement.

Sandal et al. MPMI 4 INTRODUCTIONGenetic analysis and application of genetic approaches in the model legume Lotus japonicus (Handberg and Stougaard 1992) has progressed rapidly. Several key genes important for symbiosis with mycorrhizal fungi, root nodule development and other developmental processes have been identified using molecular genetics. The developmental regulators Nin (Schauser et al. 1999) and Pfo (Zhang et al. 2002) were isolated by transposon tagging while map-based cloning led to the molecular characterisation of Har1, SymRK, Nfr1, Nfr5, Castor and Pollux involved in autoregulation, Nod-factor signal perception or signal transduction (Schauser et al. 1999, Krusell et al. 2002 Nishimura et al. 2002a;Stracke et al. 2002;Radutoiu et al. 2003;Madsen et al. 2003; Imaizumi-Anraku et al. 2005). Genetic loci required for the early stages of endosymbiosis have attracted particular interest. Diallelic crosses together with phenotypical studies defined seven loci, SymRK, Nup133, Castor, Pollux, Sym6, Sym15,Sym24, in the common pathway required for both rhizobial and mycorrhizal symbiosis (Kistner et al. unpublished data) and map-based cloning of these loci has been accomplished or is advancing rapidly. A similar interest and effort is now emerging for genetic dissection of nodule organogenesis and function using the Fix -mutants arrested at various stages of nodule development or impaired in nodule function. Cloning of the Sst1 sulfate transporter required in functional root nodules is a first example (Krusell et al. 2005).Continuous isolation of new plant mutant lines is important for completing the genetic dissection of symbiosis and so far six independent mutant populations have been obtained by chemical (EMS) mutagenesis (Perry et al. 2003;Szczyglowski et al. 1998; Webb et al. unpublished data; Gresshoff et al. unpublished data), four populations after T-DNA or transposon insertion mutagenesis (Thykjaer et al. 1995;Schauser et al. 1998;Webb et al. 2000; Gresshoff et al. unpublished data), one population made with fast neutrons (Gresshoff et al. unpublished Umehara and Kouchi (unpublished data). All in all more than 400 symbiotic Lotus mutant lines were identified by screening in these populations and more are likely to follow. Assignment to complementation groups is next logical step in order to determine the number of loci involved, identify all alleles that contribute to phenotypic characterisation of mutants and genotyping of loci. However, diallelic crossing is a relatively slow process where progress is determined by generation time and slowed by a continuously increasing number of individual crosses necessary to keep up with mutant isolation programs. Given the number of symbiotic mutant lines already available and considering the time used to define seven complementation groups with a total of 26 alleles constituting the common pathway (Kistner et al. unpublished data), this approach is unlikely to encompass all alleles in near future. Detection of alleles in already cloned genes ...

The evolution of glyphosate resistance in weedy species places an environmentally benign herbicide in peril. The first report of a dicot plant with evolved glyphosate resistance was horseweed, which occurred in 2001. Since then, several species have evolved glyphosate resistance and genomic information about nontarget resistance mechanisms in any of them ranges from none to little. Here, we report a study combining iGentifier transcriptome analysis, cDNA sequencing, and a heterologous microarray analysis to explore potential molecular and transcriptomic mechanisms of nontarget glyphosate resistance of horseweed. The results indicate that similar molecular mechanisms might exist for nontarget herbicide resistance across multiple resistant plants from different locations, even though resistance among these resistant plants likely evolved independently and available evidence suggests resistance has evolved at least four separate times. In addition, both the microarray and sequence analyses identified non–target-site resistance candidate genes for follow-on functional genomics analysis.

Genome-enabled biotechnologies have the potential to accelerate breeding efforts in long-lived perennial crop species. Despite the transformative potential of molecular tools in pecan and other outcrossing tree species, highly heterozygous genomes, significant presence–absence gene content variation, and histories of interspecific hybridization have constrained breeding efforts. To overcome these challenges, here, we present diploid genome assemblies and annotations of four outbred pecan genotypes, including a PacBio HiFi chromosome-scale assembly of both haplotypes of the ‘Pawnee’ cultivar. Comparative analysis and pan-genome integration reveal substantial and likely adaptive interspecific genomic introgressions, including an over-retained haplotype introgressed from bitternut hickory into pecan breeding pedigrees. Further, by leveraging our pan-genome presence–absence and functional annotation database among genomes and within the two outbred haplotypes of the ‘Lakota’ genome, we identify candidate genes for pest and pathogen resistance. Combined, these analyses and resources highlight significant progress towards functional and quantitative genomics in highly diverse and outbred crops.

This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium dahliae, Wasmannia auropunctata, and Zygochlamys patagonica. These loci were cross-tested on the following species: Chaetodon baronessa, Falco columbarius, Falco eleonorae, Falco naumanni, Falco peregrinus, Falco subbuteo, Didelphis aurita, Gracilinanus microtarsus, Marmosops paulensis, Monodelphis Americana, Odontesthes hatcheri, Podocarpus grayi, Podocarpus lawrencei, Podocarpus smithii, Portunus pelagicus, Syngnathus acus, Syngnathus typhle,Uroteuthis (Photololigo) edulis, Uroteuthis (Photololigo) duvauceli and Verticillium albo-atrum. This article also documents the addition of nine sequencing primer pairs and sixteen allele specific primers or probes for Oncorhynchus mykiss and Oncorhynchus tshawytscha; these primers and assays were cross-tested in both species.

Twelve simple sequence repeat (SSRs) loci were used to evaluate genetic diversity of 109 isolates of Macrophomina phaseolina collected from different geographical regions and host species throughout the United States (US). Genetic diversity was assessed using Nei's minimum genetic distance, and the usefulness of each locus was determined by calculating the polymorphism information content (PIC). A total of 98 alleles were detected and of these 31 were unique to individual genotypes. Eight of twelve loci were highly informative with PIC values greater than 0.50. The majority of pairwise comparisons of genetic distance were greater than 0.60 indicating moderate to high genetic diversity. Dendrograms based on the genetic dissimilarities were created for the 109 isolates of which 79 were from soybean. Some clustering by host and geography was noted, but, the dendrograms generally grouped isolates independent of host or geography. Additionally, sequencing of the internal transcribed spacer region (ITS) for 10 isolates revealed that all of these isolates were 99% similar. Three SSR loci from M. phaseolina were cross amplified in other genera in the Botryosphaeriaceae. This was the first study of genotyping and assessing genetic diversity of M. phaseolina isolates collected from a widespread host and geographic range across the US with SSRs. With an additional 34 loci publically available for M. phaseolina, the results indicate that previously developed SSRs from one species can be used in future population, ecological, and genetic studies of M. phaseolina and other genera within the Botryosphaeriaceae.

The sugarcane aphid (Melanaphis sacchari) has become a serious pest causing severe economic losses to sorghum [Sorghum bicolor (L.) Moench] grown in the southern United States. Since its original detection in four states in 2013, M. sacchari on sorghum has now, in 2016, spread to 19 states. The presence of one or multiple genotypes on sorghum in the United States has not yet been established. In this study, genome sequencing of M. sacchari was used to develop microsatellite markers. A total of 8,665,267 reads and 1.44 Gb of nucleotide sequences were generated, and 79.6% of the reads were from M. sacchari. Melanaphis sacchari DNA from 46 samples from 17 locations across seven states and one US territory was polymerase chain reaction (PCR) amplified using 38 newly created microsatellite markers, as well as 14 published microsatellite markers. Genotyping with the 52 microsatellite markers indicated that the samples of M. sacchari on sorghum were all one genotype, with the exception of a single sample collected from Sinton, TX, which had the predominant genotype as well as another genotype. Genotyping of the aphid samples with 12 microsatellite markers for Buchnera aphidicola, the obligate aphid symbiont, had nearly identical results. The invasive M. sacchari on sorghum appears to be spreading in the United States on sorghum as primarily one asexual clone.

A type 2 metallothionein gene, SsMT2, was cloned from Suaeda salsa, a salt- and alkali-tolerant plant, which is dominant species on the saline/alkali soil of northeast China. The SsMT2 gene was expressed in all organs except the flower and its expression was induced by various stresses such as CdCl2, NaCl, NaHCO3, and H2O2 treatments. SsMT2-transgenic yeast (Saccharomyces cerevisiae) and plants (Arabidopsis thaliana) showed significantly increased resistance to metal, salt and oxidant stresses. These transgenics accumulated more Cd2+, but less Na+ than their wild type counterparts. SsMT2 transgenic Arabidopsis maintained lower level of H2O2 than wild type plants did in response to the stress treatments. These results demonstrated that the SsMT2 gene plays an important role in reactive oxygen species scavenging and confers enhanced metal and oxidant tolerance to plants.