Biology subjects

Pincot, D. D. A.

Publications and source records attributed to Pincot, D. D. A..

5 recordsLinked to original sources

bioRxiv2025

The PERPETUAL FLOWERING Locus: Necessary But Insufficient for Genomic Prediction of Runnerless and Other Asexual Reproduction Phenotypes in Strawberry

Strawberry (Fragaria x ananassa) reproduces sexually through seeds and asexually through stolons. The ability to cost-effectively clonally propagate hybrid individuals on a large scale has profoundly shaped strawberry breeding and production practices. Despite the technical and economic importance of clonal propagation, little is known about the genetic regulation of runnering in strawberry, other than the photoperiod-dependent pleiotropic effects of PERPETUAL FLOWERING (PF), a dominant, yield-doubling gene introgressed from a wild relative that knocks out temperature-dependent photoperiod sensitivity and partially suppresses runnering. Herewe showthat runnering phenotypes are highly variable and heritable, ranging from runnerless to prolific and unrestrained in both short-day (pfpf) and day-neutral (PF_) plants. We physically mapped the PF locus to Mb 26.4-27.3 on chromosome 4B using high-density SNP haplotypes and historical recombination among 932 individuals. PF was the only runneringassociated locus uncovered by genome-wide association studies among diverse clonal genetic resources and progeny from narrow and wide crosses (1,537 individuals). However, PF explained only 22% of the genetic variance for runnering. Genomic-estimated breeding values for runnering were accurately estimated especially among runnerless to near-runnerless individuals. Genomic prediction accuracies were greater within than between populations, increased when corrected for PF, and are sufficient for implementing genomic selection. These results pave the way for enhancing the productivity of strawberry by creating runnerless cultivars for seed-propagation and near-runnerless and reduced runnering cultivars for clone-propagation through phenotypic or genomic selection. 1 CORE IDEASO_LIGenetic variation for runnering is substantial and heritable C_LIO_LIThe dominant PERPETUAL FLOWERING (PF) allele does not uniformly or ubiquitously suppress asexual reproduction C_LIO_LISubstantial wild donor DNA has persisted in day-neutral and summer-plant cultivars carrying the Wasatch PF allele C_LIO_LIThe accuracy of PF-corrected breeding values for runnering are sufficient for implementing genomic selection C_LIO_LIStrawberry productivity can be improved by introducing cultivars with runnerless or near-runnerless phenotypes C_LI

genetics↗

bioRxiv2024

Genomic Architecture of the Resistance to Phytophthora Cactorum 2 (RPc2) Locus in Strawberry (Fragaria x ananassa)

Phytophthora crown rot (PhCR), caused by Phytophthora cactorum, is a soilborne disease with broad impacts to cultivated strawberries in the United States and worldwide. While a resistance locus, RPc2, has been identified in octoploid strawberries, the underlying genomic architecture and mechanism remain unclear. Here, we fine-mapped the RPc2 region to 546 kb, containing 92 genes, and constructed a chromosome-scale haplotype-phased genome of resistant breeding selection FL 16.33-8. Comparative genome analyses with high-quality octoploid reference genomes, Florida Brilliance (FaFB1) and Royal Royce (FaRR1), identified two candidate genes, Wall Associated Kinase 1 (WAK1) and Cyclic Nucleotide Gated Channel 1 (CNGC1). Gene functions were validated using an Agrobacterium-mediated transient expression assay. Furthermore, by leveraging the population structure of the RPc2 locus among genetically diverse breeding populations, we unveiled the complexity of genetic architecture and recent selective sweeps associated with RPc2. Notably, the predominant resistant haplotype (RPc2-H3) is prevalent in most commercial strawberry varieties in the US. The findings from this study are facilitating the advancement of genome-assisted breeding strategies for resistance to PhCR in strawberries. SummaryO_LIPhytophthora crown rot (PhCR), caused by the soilborne pathogen Phytophthora cactorum, is a disease with broad impacts to cultivated strawberries worldwide. The Resistance to Phytophthora Cactorum 2 (RPc2) locus is widespread in important cultivars and is a target of selection in breeding programs. Despite its importance, the genomic architecture and mechanisms of RPc2 remain poorly characterized. C_LIO_LIWe performed fine-mapping and delimited the genomic region to a 546 kb segment containing 92 genes. We developed a chromosome-scale haplotype-phased genome from an elite resistant line, FL16.33-8, and made comparisons to reference genomes of Florida Brilliance (FaFB1) and Royal Royce (FaRR1) to uncover gene sequence and structural variants in resistant accessions. C_LIO_LIThrough comparative genomics and transcriptome profiling, we identified three candidate genes, Wall Associated Kinase 1 (WAK1) and Cyclic Nucleotide Gated Channel 1 (CNGC1) and CNGC2. The functions of these genes were validated using a simplified Agrobacterium-mediated transformation method for transient gene expression in strawberry crowns and roots. C_LIO_LIAn examination of the population structure of the RPc2 locus among genetically diverse accessions (N=1029) revealed that the predominant H3 resistant haplotype is widespread in breeding accessions in the US, supporting the findings of a previous study on recent selective sweeps associated with RPc2. Results from this study are advancing genome-assisted breeding strategies for enhancing resistance to PhCR in strawberry. C_LI

plant biology↗

bioRxiv2021

Novel Fusarium Wilt Resistance Genes Uncovered in the Wild Progenitors and Heirloom Cultivars of Strawberry

Fusarium wilt, a soilborne disease caused by Fusarium oxysporum f. sp. fragariae, poses a significant threat to strawberry (Fragaria x ananassa) production in many parts of the world. This pathogen causes wilting, collapse, and death in susceptible genotypes. We previously identified a dominant gene (FW1) on chromosome 2B that confers resistance to race 1 of the pathogen and hypothesized that gene-for-gene resistance to Fusarium wilt was widespread in strawberry. To explore this, a genetically diverse collection of heirloom and modern cultivars and wild octoploid ecotypes were screened for resistance to Fusarium wilt races 1 and 2. Here we show that resistance to both races is widespread and that resistance to race 1 is mediated by dominant genes (FW1, FW2, FW3, FW4, and FW5) on three non-homoeologous chromosomes (1A, 2B, and 6B). The resistance proteins encoded by these genes are not yet known; however, plausible candidates were identified that encode pattern recognition receptor or other proteins known to mediate gene-for-gene resistance in plants. High-throughput genotyping assays for SNPs in linkage disequilibrium with FW1-FW5 were developed to facilitate marker-assisted selection and accelerate the development of race 1 resistant cultivars. This study laid the foundation for identifying the genes encoded by FW1-FW5, in addition to exploring the genetics of resistance to race 2 and other races of the pathogen, as a precaution to averting a Fusarium wilt pandemic. Key MessageSeveral race-specific resistance genes were identified and rapidly deployed via marker-assisted selection to develop strawberry cultivars resistant to Fusarium wilt, a devastating soil-borne disease.

plant biology↗

bioRxiv2021

Genomic Prediction of Strawberry Resistance to Postharvest Fruit Decay Caused by the Fungal Pathogen Botrytis cinerea

Gray mold, a disease of strawberry (Fragaria x ananassa) caused by the ubiquitous necrotroph Botrytis cinerea, renders fruit unmarketable and causes economic losses in the postharvest supply chain. To explore the feasibility of selecting for increased resistance to gray mold, we undertook genetic and genomic prediction studies in strawberry populations segregating for fruit quality and shelf life traits hypothesized to pleiotropically affect susceptibility. As predicted, resistance to gray mold was heritable but quantitative genetically complex. While every individual was susceptible, the speed of symptom progression and severity differed. Narrow-sense heritability ranged from 0.38-0.71 for lesion diameter (LD) and 0.39-0.44 for speed of emergence of external mycelium (EM). Even though significant additive genetic variation was genome wide observed for LD and EM, the phenotypic ranges were comparatively narrow and genome-wide analyses did not identify any large effect loci. Genomic selection accuracy ranged from 0.28-0.59 for LD and 0.37-0.47 for EM. Additive genetic correlations between fruit quality and gray mold resistance traits were consistent with prevailing hypotheses: LD decreased as titratable acidity increased, whereas EM increased as soluble solid whole genome content decreased and firmness increased. We concluded that phenotypic and genomic selection could be regression effective for reducing LD and increasing EM, especially in long shelf life populations, but that a significant fraction of the genetic variation for resistance to gray mold was caused by the pleiotropic effects of fruit quality traits that differ among market and shelf life classes.

genetics↗

bioRxiv2020

Social Network Analysis of the Genealogy of Strawberry: Retracing the Wild Roots of Heirloom and Modern Cultivars

The widely recounted story of the origin of cultivated strawberry (Fragaria x ananassa) oversimplifies the complex interspecific hybrid ancestry of the highly admixed populations from which heirloom and modern cultivars have emerged. To develop deeper insights into the three century long domestication history of strawberry, we reconstructed the genealogy as deeply as possible--pedigree records were assembled for 8,851 individuals, including 2,656 cultivars developed since 1775. The parents of individuals with unverified or missing pedigree records were accurately identified by applying exclusion analysis to array-genotyped single nucleotide polymorphisms. We identified 187 wild octoploid and 1,171 F. x ananassa founders in the genealogy, from the earliest hybrids to modern cultivars. The pedigree networks for cultivated strawberry are exceedingly complex labyrinths of ancestral interconnections formed by diverse hybrid ancestry, directional selection, migration, admixture, bottlenecks, overlapping generations, and recurrent hybridization with common ancestors that have unequally contributed allelic diversity to heirloom and modern cultivars. Fifteen to 333 ancestors were predicted to have transmitted 90% of the alleles found in country-, region-, and continent-specific populations. Using parent-offspring edges in the global pedigree network, we found that selection cycle lengths over the last 200 years of breeding have been extraordinarily long (16.0-16.9 years/generation) but decreased to a present-day range of 6.0-10.0 years/generation. Our analyses uncovered conspicuous differences in the ancestry and structure of North American and European populations and shed light on forces that have shaped phenotypic diversity in F. x ananassa.

plant biology↗