Phenotypic diversity and population structure of Pecan (Carya illinoinensis) collections reveals geographic patterns.

Pecan (Carya illinoinensis) is an economically important nut crop known for its genetic diversity and adaptability to various climates. Understanding the growth variability, phenological traits, and population structure of pecan populations is crucial for breeding programs and conservation. In this study, plant growth and phenological traits were evaluated over three consecutive seasons (2015-2017) for 550 genotypes from 26 provenances. Significant variations in plant height, stem diameter, and budbreak were observed among provenances, with Southern provenances exhibiting faster growth and earlier budbreak compared to Northern provenances. Population structure analysis using SNP markers revealed eight distinct subpopulations, reflecting genetic differentiation among provenances. Notably, Southern Mexico collections formed two separate clusters, while Western collections, such as 'Allen 3', 'Allen 4', and 'Riverside', were distinguished from others. 'Burkett' and 'Apache' were grouped together due to their shared maternal parentage. Principal component analysis and phylogenetic tree analysis further supported subpopulation differentiation. Genetic differentiation among the 26 populations was evident, with six clusters highly in agreement with the subpopulations identified by STRUCTURE and fastSTRUCTURE. Principal components analysis (PCA) revealed distinct groups, corresponding to subpopulations identified by genetic analysis. Discriminant analysis of PCA (DAPC) based on provenance origin further supported the genetic structure, with clear separation of provenances into distinct clusters. These findings provide valuable insights into the genetic diversity and growth patterns of pecan populations. Understanding the genetic basis of phenological traits and population structure is essential for selecting superior cultivars adapted to diverse environments. The identified subpopulations can guide breeding efforts to develop resilient rootstocks and contribute to the sustainable management of pecan genetic resources. Overall, this study enhances our understanding of pecan genetic diversity and informs conservation and breeding strategies for the long-term viability of pecan cultivation.

Consumer Hedonic Ratings and Associated Sensory Characteristics and Emotional Responses to Fourteen Pecan Varieties Grown in Texas.

Pecan is one of the top five most widely consumed tree nuts, and pecan nut quality is a major factor for consideration in breeding better pecan cultivars for use by producers. However, the pecan industry faces a hurdle to evaluate its nutmeat taste, and there has so far been limited evaluation of consumer attitudes toward pecan nutmeat. This study aimed to investigate the consumer (n = 198) hedonic rating, diagnostic sensory attribute intensity, and emotional response for 14 pecan samples, consisting of native/seedling and improved varieties. The results showed all kernels received positive hedonic scores (>5, 9-point hedonic scale) for overall acceptance and the acceptability of size, interior color, typical-pecan flavor, and raw-nut flavor. The primary sensory attributes (intensities > 5.0, 0−10 line scale) were typical-pecan and raw-nut flavors, followed by buttery flavor, sweetness, and astringency. Kernel off-flavors were not perceived in general. For 20 emotion-associated terms, the intensity of the satiating effect was medium, while the energizing effect was lower. The major emotional responses were healthy, satisfied, and comfort, followed by calm, interested, premium, and relaxed. Kernel variety difference was significant (p ≤ 0.05) for all these measured variables. Consumer overall acceptance toward pecan kernels was driven by the acceptability of flavor and interior color, flavor intensities, no off-flavors, and positive emotional responses; kernel size was not an impactful factor. The six most preferred varieties were 86TX2-1.5, Pawnee, Barton, 1997-09-0012, 1991-01-0026, and Harris Super. This study is the first to use consumer input to assess nut quality and consumption preference and will be foundational to ongoing breeding programs to develop new pecan cultivars that will better meet consumer preferences and expectations, and therefore will be accepted by the processing industry and growers.

Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding.

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.