Accurate variant calling is critical for identifying the genetic basis of complex traits, yet filters used in variant detection may inadvertently exclude valuable genetic information. In this study, we compare common sequencing depth filters, used to eliminate error-prone variants associated with repetitive regions and technical issues, with a biologically relevant filtering approach that targets expected Mendelian segregation. The resulting variant sets were evaluated in the context of nectar volume quantitative trait loci (QTL) mapping in sunflower (Helianthus annuus L.). Our previous research failed to detect an interval containing a strong candidate gene for nectar production (HaCWINV2). We removed hard filters and implemented a chi-square goodness-of-fit test to retain variants that segregate according to expected genetic ratios. We demonstrate that biologically relevant filtering retains more significant QTL and candidate genes, including HaCWINV2, while removing variants due to technical errors more effectively, and accounted for 48.55% of nectar production phenotypic variation. In finding nine putative homologs of Arabidopsis genes with nectary function within QTL regions, we demonstrate that this filtering strategy has a higher power of true variant detection in QTL mapping than the commonly used variant depth filtering strategy. Future research will adapt the technique to multiple population contexts, such as genomic selection.

The sunflower (Helianthus annuus) pericarp protects the seed within from both abiotic and biotic stresses. Achenes with stronger pericarps are less susceptible to damage from insect feeding. Complicating the genetic improvement of pericarp strength is the negative correlation between pericarp thickness (a component of strength) and oil content. As breeding efforts have increased oil content, there has been a concomitant decrease in pericarp thickness. One breeding goal is to improve oil content while preserving pericarp strength through genetic mechanisms independent of the tradeoffs with pericarp thickness. To determine the genetic basis of oil content, pericarp strength, and thickness, we identified QTL in two populations: the Sunflower Association Mapping panel (Mandel et al. in Theor Appl Genet 123:693–704, 2011) and a recombinant inbred line (RIL) population derived from a thin pericarp oilseed inbred (HA 467) crossed to a thick pericarp open-pollinated variety from Türkiye (PI 170415). A region on chromosome 15 was associated with neighboring QTL for banded moth resistance, oil content, and pericarp thickness, partially underlying the trade-offs among these traits. Additional QTL on chromosome 5 and 14 for pericarp strength provide fewer trade-offs with oil content. QTL for pericarp strength on chromosome 5 and pericarp thickness on chromosome 16 were associated with large structural variants on chromosome 5 and putative structural variation on chromosome 16, with candidate gene presence/absence variation between the haplotypes on chromosome 5. Understanding the origin and nature of phenotypic tradeoffs is beneficial to plant biologists and sunflower breeders as they seek to understand the origin and genetic architecture of adaptive and maladaptive traits.

Abstract. The expansive range of Lewis flax (Linum lewisii), an herbaceous perennial, exposes the species to a diversity of climatic conditions. As interest in the domestication and adoption of perennial crop alternatives grows and interest in this species for natural area restoration continues, the assurance of a commercial plant variety's ability to endure the full range of possible climatic extremes is paramount. This study examines the freezing tolerance of a geographically representative sampling of 44 Lewis flax accessions at winter temperature extremes experienced in the northern Great Plains of the USA. Survival analysis models were adapted to include temperature exposure, in replacement of ordinal time typically used in such models, to produce statistics evaluating reactions to extreme temperatures that Lewis flax would encounter in our field environments. Our results revealed Lewis flax is more freezing tolerant than previously reported, and revealed four accessions with significantly superior genetic freezing tolerance than the released 'Maple Grove' cultivar. Furthermore, regrowth analyses indicate variation among accessions not associated with survival, which could lead to improving regrowth rate and survival simultaneously. These findings and their methodology expand the understanding of Lewis flax adaptation for winter hardiness and offer an efficient, new model that can be used to evaluate freezing tolerance at ordinal temperatures without requiring extensive prior physiological knowledge for a species.

Host-microbe interactions are increasingly recognized as important drivers of organismal health, growth, longevity and community-scale ecological processes. However, less is known about how genetic variation affects hosts' associated microbiomes and downstream phenotypes. We demonstrate that sunflower (Helianthus annuus) harbours substantial, heritable variation in microbial communities under field conditions. We show that microbial communities co-vary with heritable variation in resistance to root infection caused by the necrotrophic pathogen Sclerotinia sclerotiorum and that plants grown in autoclaved soil showed almost complete elimination of pathogen resistance. Association mapping suggests at least 59 genetic locations with effects on both microbial relative abundance and Sclerotinia resistance. Although the genetic architecture appears quantitative, we have elucidated previously unexplained genetic variation for resistance to this pathogen. We identify new targets for plant breeding and demonstrate the potential for heritable microbial associations to play important roles in defence in natural and human-altered environments.

Linum lewisii , a perennial blue flax native to North America, holds potential as a sustainable perennial crop for oilseed production due to its ecological adaptability, upright harvestable structure, nutritious seeds, and low insect and disease issues. Its native distribution spans a large geographic range, from the Pacific Coast to the Mississippi River, and from Alaska to Baja California. Tolerant to cold and drought conditions, this species is also important for native ecosystem rehabilitation. Its enhancement of soil health, support for pollinators, and carbon sequestration underscore its agricultural relevance.This study presents a high-quality, chromosome-scale assembly of the L. lewisii (2n = 2x = 18) genome, derived from PacBio HiFi and Dovetail Omni-C sequencing of the “Maple Grove” variety. The initial assembly contained 642,903,787 base pairs across 2,924 scaffolds. Following HiRise scaffolding, the final assembly contained 643,041,835 base pairs, across 1,713 scaffolds, yielding an N50 contig length of 66,209,717 base pairs. Annotation of the assembly revealed 38,808 genes, including 37,599 protein-coding genes and 7,108 putative transposable elements. Analysis of synteny with other flax species revealed a striking number of chromosomal rearrangements. We also found an intriguing absence of the single-copy TSS1 gene in the L. lewisii genome, potentially linked to its transition from heterostyly to homostyly.Taken together, these findings represent a significant advancement in our understanding of the Linum genus and provide a resource for future domestication efforts and basic research on Lewis flax.### Competing Interest StatementThe authors have declared no competing interest.

De novo domestication has received recent attention because of the potential to produce new crop species with additional agroecosystem functions and useful products for climate-resilient agricultural systems of the future. However, there are often traits in wild species that make them difficult to domesticate. One key domestication trait selected by early farmers and modern plant breeders in many crops is the ability to self-pollinate. Benefits include higher seed set and more reliable seed production, as well as more efficient selection during breeding because it allows for unmasking of recessive traits and enforcement of favorable gene interactions. Similarly, interspecific hybridization has been used to add to the genetic diversity of many crop species. We evaluated self-pollination and interspecific hybridization in Silphium integrifolium and S. perfoliatum to learn the extent of possible gene flow between the species and its usefulness in cultivar development and the potential for fixation of favorable domestication genes by self-pollination. Our results indicate that Silphium interspecific hybrids can be easily developed, potentially facilitating movement of otherwise invariable traits from one species to another. Further, we showed, for the first time, that self-pollination is also possible in both species and their interspecific hybrids, but the rate varies among genotypes. This has profound implications in optimizing plant breeding methods for the study and improvement of these species and adds more evidence to our understanding of mating systems in Asteraceae, an underutilized family of plants with great potential for additional domesticated species.

Sclerotinia diseases and Phomopsis stem canker, among the most serious diseases threatening the success of sunflower (Helianthus annuus L.) production across the world, have been of increasing concern in recent history, and there is a need for additional inbred lines with resistance to these diseases. While breeding new lines capable of thriving in agricultural landscapes riddled with these widespread diseases, it is essential that lines also exhibit other desirable traits such as high yield potential, satisfactory fatty acid composition (e.g., high oleic acid), and herbicide tolerance (e.g., to imidazolinones), along with overall agronomic performance suitable to the northern Great Plains climate in the United States, and similar climates across other continents. A maintainer inbred germplasm line, HA 482 (Reg. no. GP‐364, PI 690015), and two restorer inbred germplasms, RHA 483 (Reg. no. GP‐365, PI 690016) and RHA 484 (Reg. no. GP‐366, PI 690017), have been developed with the pedigree breeding method, evaluated through the use of testcross hybrid trials for both disease resistance and agronomic traits, and released by the USDA–ARS, Fargo, ND. All three lines have high oleic acid composition in the seed oil and exhibit resistance to Sclerotinia and Phomopsis stem canker, and both RHA 483 and RHA 484 are imidazolinone tolerant.