Leveraging species-wide variation and patterns of adaptation to inform pecan crop improvement efforts

bioRxiv (Cold Spring Harbor Laboratory) · 2025-12-22

The genetic basis of adaptation is a fundamental question in evolutionary biology, and understanding how species will be able to adapt to changing conditions across their range has important implications for conservation and agriculture. To accurately interrogate the genetics of adaptation and assess the adaptive capacity of a species requires also characterizing the ways other mechanisms, including geographic distance and population dynamics, shape genetic variation. Pecan is an ecologically, culturally, and economically important North American tree, and a broader understanding of the genetics of environment adaptation will aid pecan conservation, breeding, and commercial management. Here, we use an expansive set of more than 700 pecan genotypes in combination with the first haplotype-resolved genome assembly for pecan to assess species-wide genetic variation and evaluate environmental adaptation across the native distribution. We identify five gene pools in pecan, with the lowest diversity in southern gene pools, and present evidence that gene pools began differentiating during multiple glacial cycles. Using complementary genotype-environment association approaches, we infer species-wide patterns of environmental adaptation. With these results, we predict mismatches in adaptation for pecan genotypes to different environments, including future environment scenarios. We see that in all locations, present-day genotypes incur some level of predicted maladaptation to simulated future environments, but current genetic diversity may provide a valuable source of resilience to future conditions through assisted migration. These results expand the understanding of environmental adaptation in pecan and provide insight into how long-lived species will be able to adapt to future conditions.

High-density Linkage Mapping and Identification of Quantitative Trait Loci Associated with Scab Resistance in Pecan

Journal of the American Society for Horticultural Science · 2025-03-01 · 2 citations

Genetic maps are essential tools for gene positional cloning and marker-assisted breeding. A pecan ( Carya illinoinensis ) mapping population of 119 F 1 trees was developed from a cross of the widely planted cultivars ‘Pawnee’ and ‘Elliott’. Whereas ‘Pawnee’ is susceptible, ‘Elliott’ has long-standing resistance to pecan scab caused by the fungal pathogen Venturia effusa . Molecular markers were developed using genotyping by sequencing, and linkage maps were constructed for each parent following the two-way pseudo-test-cross strategy used for cross-pollinated species. The ‘Pawnee’ and ‘Elliott’ maps contain 1347 and 1050 single-nucleotide polymorphism markers spanning a genetic distance of 4493 and 3758 centimorgans, respectively. While these map lengths are likely inflated due to genotyping errors, a high level of synteny between genetic and physical distances of the markers in both parental maps was achieved. Scab resistance was evaluated through controlled inoculations in the greenhouse using two scab isolates, and a significant quantitative trait locus (QTL) for scab resistance was identified on chromosome 5 in ‘Elliott’. Candidate gene searches within the 2-logarithm of the odds interval of the scab-resistant QTL identified a number of disease resistance–related genes, including genes encoding wall-associated receptor kinases, cytochrome P450s, leucine-rich repeats receptor–like serine/threonine-protein kinases, a pectinesterase inhibitor, a cellulose synthase, a flavonol synthase, a 4-coumarate–coenzyme A ligase, caffeic acid 3- O -methyltransferase, and a myeloblastosis (MYB) domain transcription factor.

Identification of QTLs for Reduced Susceptibility to Rose Rosette Disease in Diploid Roses

Pathogens · 2022-06-08 · 16 citations

Resistance to rose rosette disease (RRD), a fatal disease of roses (Rosa spp.), is a high priority for rose breeding. As RRD resistance is time-consuming to phenotype, the identification of genetic markers for resistance could expedite breeding efforts. However, little is known about the genetics of RRD resistance. Therefore, we performed a quantitative trait locus (QTL) analysis on a set of inter-related diploid rose populations phenotyped for RRD resistance and identified four QTLs. Two QTLs were found in multiple years. The most consistent QTL is qRRV_TX2WSE_ch5, which explains approximately 20% and 40% of the phenotypic variation in virus quantity and severity of RRD symptoms, respectively. The second, a QTL on chromosome 1, qRRD_TX2WSE_ch1, accounts for approximately 16% of the phenotypic variation for severity. Finally, a third QTL on chromosome 3 was identified only in the multiyear analysis, and a fourth on chromosome 6 was identified in data from one year only. In addition, haplotypes associated with significant changes in virus quantity and severity were identified for qRRV_TX2WSE_ch5 and qRRD_TX2WSE_ch1. This research represents the first report of genetic determinants of resistance to RRD. In addition, marker trait associations discovered here will enable better parental selection when breeding for RRD resistance and pave the way for marker-assisted selection for RRD resistance.

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

Nature Communications · 2021 · 110 citations

• Biology
• Genetics
• Evolutionary biology

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.

A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm

Scientific Reports · 2020 · 143 citations

• Biology
• Botany
• Horticulture

The genome of the allotetraploid species Coffea arabica L. was sequenced to assemble independently the two component subgenomes (putatively deriving from C. canephora and C. eugenioides) and to perform a genome-wide analysis of the genetic diversity in cultivated coffee germplasm and in wild populations growing in the center of origin of the species. We assembled a total length of 1.536 Gbp, 444 Mb and 527 Mb of which were assigned to the canephora and eugenioides subgenomes, respectively, and predicted 46,562 gene models, 21,254 and 22,888 of which were assigned to the canephora and to the eugeniodes subgenome, respectively. Through a genome-wide SNP genotyping of 736 C. arabica accessions, we analyzed the genetic diversity in the species and its relationship with geographic distribution and historical records. We observed a weak population structure due to low-frequency derived alleles and highly negative values of Taijma's D, suggesting a recent and severe bottleneck, most likely resulting from a single event of polyploidization, not only for the cultivated germplasm but also for the entire species. This conclusion is strongly supported by forward simulations of mutation accumulation. However, PCA revealed a cline of genetic diversity reflecting a west-to-east geographical distribution from the center of origin in East Africa to the Arabian Peninsula. The extremely low levels of variation observed in the species, as a consequence of the polyploidization event, make the exploitation of diversity within the species for breeding purposes less interesting than in most crop species and stress the need for introgression of new variability from the diploid progenitors.

New Genomic Resources for Pecan (Carya illinoinensis)

OakTrust (Texas A&M University Libraries) · 2020-01-01

Pecan (Carya illinoinensis) is a hickory tree grown for its edible seed (nut) as well as its ornamental and lumber qualities. Native to and primarily produced in Mexico and the United States, a majority of production is from graft propagated “improved” pecan cultivars. The average value of utilized in-shell production from 2017 to 2019 was approximately $535 million/year in the United States according to the NASS. The present research developed new genomic resources for the pecan breeding and research community that facilitate unprecedented resolution with which to characterize pecan germplasm. Genotyping by sequencing (GBS) was used to characterize 87,446 SNP markers across a panel of 108 pecan and Carya cultivars and accessions from the National Collection of Genetic Resources for Pecans and Hickories (NCGR-Carya). These data were used to calculate genetic relatedness, evaluate pedigree relationships, correlate genetic profiles to provenance, and perform a genome wide association study (GWAS) that identified sequences associated with flowering type (dichogamy) in pecan. Genetic linkage maps utilizing a newly-developed chromosome-scale reference genome and integrating 7,238 SNPs were created from GBS of 151 full-sibling progeny of ‘Elliott’ and ‘VC1-68’. These were used to discover four quantitative trait loci (QTL) significantly associated with budbreak and pecan scab incidence across at least two years of observation. One of the QTL explained up to 31.7% of the variation in budbreak and was found at the syntenic location of a similar major effect QTL recently identified in Juglans regia, the English walnut. Newly developed reference sequences were analyzed and compared to detect polymorphic simple sequence repeat (SSR) sequences and design primer pairs to utilize them as genetic markers. Thirty-seven of these SSR markers were identified as highly polymorphic, broadly amplifiable, and demonstrating Mendelian inheritance using a panel of 18 Carya accessions. Ninety-one accessions of pecan, phenotyped for dichogamy, were genotyped with marker KL18-027, designed from the dichogamy-associated locus, and demonstrated complete linkage to dichogamy. The resources developed here are being used to better conserve this ecologically and economically important natural resource as well as facilitate pecan improvement for human use. These resources have also informed and motivated further research into pecan genomics and flowering physiology.

Linkage mapping and QTL analysis of pecan (Carya illinoinensis) full-siblings using genotyping-by-sequencing

Tree Genetics & Genomes · 2020 · 11 citations

• Biology
• Genetics

Genotyping by sequencing (GBS) and SNP marker analysis of diverse accessions of pecan (Carya illinoinensis)

Tree Genetics & Genomes · 2019-01-05 · 28 citations