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.

The components that define cereal-grain yield potential have not been well defined. The objective of this study was to collect many differing biological measurements from a long-term winter wheat (Triticum aestivum L.) study in an attempt to better define yield potential. Four treatments were sampled that annually received 0, 45, 90, and 135 kg N ha −1 at fixed rates of phosphorus (P) (30 kg ha −1 ) and potassium (K) (37 kg ha −1 ). Mid-season measurements of leaf color, chlorophyll, normalized difference vegetative index (NDVI), plant height, canopy temperature, tiller density, plant density, soil moisture, soil NH 4 -N, NO 3 -N, organic carbon (C), total nitrogen (N), pH, and N mineralization potential were collected. In addition, soil texture and bulk density were determined to characterize each plot. Correlations and multiple linear-regression analyses were used to determine those variables that can predict final winter wheat grain yield. Both the correlation and regression analyses suggested mid-season NDVI, chlorophyll content, plant height, and total N uptake to be good predictors of final winter wheat grain yield. Keywords

Pecan (Carya illinoinensis) leaf elemental concentrations are the industry standard to guide fertility programs. To provide meaningful information, a standard index tissue collected at a specific development stage is required along with established elemental sufficiency ranges. We report pecan leaf elemental sufficiency ranges used in Oklahoma that were developed based on research in Oklahoma and elsewhere. In addition, fertilizer recommendations, based on various leaf elemental concentrations, are included.

This study provides a method with broad applicability for PCR detection of Salmonella in complex sample matrices. This method has a potential for its application in different research arenas and diagnostic laboratories.

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