Sunflower Lines Research Articles

A novel sunflower broomrape race with unusual virulence potentially caused by a mutation.

The sunflower broomrape (Orobanche cumana Wallr.) gene pools of the Guadalquivir Valley and Cuenca province in Spain had predominantly race-F virulence. A new race G was observed recently in the Guadalquivir Valley potentially due to the genetic recombination of the avirulence genes of both gene pools. In this research, we have studied populations with atypical virulence from Cuenca. These populations parasitize on DEB2 sunflower line, resistant to all race-G populations evaluated. Ten populations collected in Cuenca province were evaluated with sunflower differential lines and genotyped with 67 SNP markers. Although genetic recombination with individuals of the Guadalquivir Valley gene pool has been observed in most populations, recombination of avirulence genes was discarded as the cause of the new virulence because the population with the highest degree of attack on DEB2 showed no introgression from an external gene pool. Accordingly, a point mutation is proposed as the putative cause of the new virulence. The present study provided a detailed characterization of each population, including the accurate classification of the individuals belonging to each of the classical Spanish gene pools, F1 hybrids, and those that evolved from hybridization between both gene pools. This information is essential to understand how sunflower broomrape populations are evolving in Spain, which in turn may be helpful to understand the dynamics of sunflower broomrape populations in other areas of the world and use this information to develop durable strategies for resistance breeding.

Maintainer/restorer identification for different CMS lines in sunflower (Helianthus annuus L.)

Thirty one uniform and stable germplasm accessions of economic importance of sunflower were crossed with five cytoplasmic male sterile lines viz., CMS-234A, CMS-17A, CMS-338A, CMS-851A and ARM-243A in a Line x Tester fashion to study their maintainer or restorer reaction during kharif-2012 in a Randomized Block Design in two replications. The accessions TSG-22, TSG-24, ID-7, SCG-37, RHA-464 and ID-25 acted asrestorersfor allfive CMS lines. It was found that ID-33 of the restorer for ARM-243A was maintainer for other CMS lines. The use of stable germplasm with restorer behaviour in heterosis breeding programmes and those with maintainer behaviour in the development of new CMS lines through conversion has been suggested. The identification of new restorers to the good combiner CMS sources assembled should receive priority for hybrid synthesis.

QTL mapping of oleic acid content in modern VNIIMK sunflower (Helianthus annuus L.) lines by using GBS-based SNP map.

Oleic acid is a monounsaturated fatty acid increasing oil oxidative stability. High content of oleic acid is thus a valuable trait in oilseed crops. Sunflower (Helianthus annuus L.) normally accumulates linoleic acid as a major fatty acid, but a mutant expressing a high oleic phenotype form was previously obtained by chemical mutagenesis and mapped on the sunflower genome. Several studies suggest the presence of additional genes involved in the control of the high content of oleic acid, with their expression possibly depending on the genetic background. To test this hypothesis, we performed a QTL mapping of the high oleic acid trait within two independent F2 crosses involving lines with contrasting oleic acid content from the Pustovoit All-Russia Research Institute of Oil Crops (VNIIMK) collection. We applied genotyping-by-sequencing (GBS) to construct single nucleotide polymorphism-based genetic maps and performed QTL mapping using quantitative and qualitative encoding for oleic acid content. Our results support the finding that the oleic acid content in the assessed crosses is controlled by one major effect locus. However, different dominant/recessive effects of the major locus were reported for both crosses. Additionally, a possible translocation between chromosome 7 and 14 was reported in one assessed cross. We defined a set of single nucleotide polymorphism markers for each cross which could be used for marker-assisted selection.

Registration of HA‐DM15 and HA‐DM16 oilseed sunflower germplasms with resistance to sunflower downy mildew

AbstractSunflower (Helianthus L.) production ranked third in global oilseed production in 2021. Downy mildew (DM), caused by the oomycete pathogen Plasmopara halstedii (Farl.) Berl. et de Toni, is a major constraint for worldwide sunflower production, causing significant yield losses in susceptible hybrids. The search for new sources of resistance to DM is the primary objective of all sunflower breeding programs. Germplasms HA‐DM15 (Reg. no. GP‐385, PI 702359) and HA‐DM16 (Reg. no. GP‐386, PI 702360) were developed by introgressing two new DM resistance genes, Pl37 and Pl38, from the wild sunflower species H. annuus and H. praecox into oilseed sunflower, respectively. The BC1F3‐derived HA‐DM15 harboring the Pl37 gene was selected from the cross of HA 89//NMS HA 89/wild H. annuus PI 435417. The germplasm line HA‐DM16 carrying the Pl38 gene is an improved oilseed derivative of Rf PRA‐417 with DM resistance originally derived from the wild H. praecox PRA‐417 from the cross of cytoplasmic male sterile (CMS) HA89*2/wild H. praecox PRA‐417. HA‐DM15/Pl37 and HA‐DM16/Pl38 are immue to the most predominant and virulent DM races idenfied in North America and Europe. Pl37 and Pl38 have been genetically mapped to sunflower chromosomes 4 and 2, respectively, with single nucleotide polymorphism markers linked to the both genes facilitating their transfer to elite sunflower lines by marker‐assisted selection, providing new and diverse sources for sunflower DM‐resistance breeding.

Genetic diversity analysis in sunflower (Helianthus annuus L.) restorer lines using SSR markers

Sunflower is a staple oilseed crop ofthe world. Genetic diversity in the parental lines is key for hybrid breeding programmes in sunflower. In this study, genetic diversity in a set of 102 parental lines (100 restorer and twoCMS) of sunflower was assessed using 69 polymorphic SSR markers. The genetic diversity parameters: average number of alleles (3.07) per locus, gene diversity (0.356) and polymorphism information content (0.296) revealed low to moderate genetic diversity in the restorer lines. The SSR marker ORS447 located on linkage group 2 was more informative with high number of alleles (10) and high PIC value (0.89). Cluster analysis (neighbour-joining tree) revealed three major genotypic groups. Model based STRUCTURE analysis showed recognizable population structure; based on membership coefficients(>80%), 82 genotypes were classified into two populations (K=2) and the remaining 20 genotypes were classified into admixture group. The Fst value (0.278) suggested that the populations were differentiated. Analysis of molecular variance resultsshowed that maximum of genetic variation (72%) was observed between the individuals within the population suggesting that the population was weakly structured. These results would be useful for selecting SSR markers for genotype characterization as well as choosing diverse parents for hybrid development programme in sunflower.

Irradiated Pollen-Induced Parthenogenesis for Doubled Haploid Production in Sunflowers (Helianthus spp.).

Doubled haploid (DH) technology is a tool used to develop large numbers of inbred lines and increase the rate of genetic gain by shortening the breeding cycles. However, previous attempts to produce DH sunflower plants (Helianthus spp.) have resulted in limited success. In this research, we applied gamma-induced parthenogenesis to assist the production of DH sunflowers. The objectives of the study included (1) identifying optimal gamma ray doses for inducing DH sunflowers using two cytoplasmic male sterility (CMS) lines as female plants and two male pollinators with recognizable morphological markers, (2) selecting new male pollinators from wild sunflower varieties, and (3) testing the efficacy of the selected male pollinators using emasculated non-male sterile sunflower lines as female plants. In these experiments, pollen grains were irradiated with gamma ray doses ranging from 50 to 200 Gy. The optimal gamma ray dose for pollen grain irradiation and DH plant production was identified to be 100 Gy. In addition, a cultivated (G11/1440) and a wild-type (ANN1811) sunflower line can be used as common male pollinators for their distinctive morphological markers and wide capacity for DH induction by gamma-irradiated pollen grains.

Evaluation of Introgressed Lines of Sunflower (Helianthus annuus L.) under Contrasting Water Treatments

Drought stress is a major production constraint in crops globally. Crop wild relatives are important sources of resistance and tolerance for both biotic and abiotic stresses, respectively. A breeding program was initiated to introgress drought tolerance in sunflowers through hybridization between the wild species Helianthus argophyllus and the cultivated pool of H. annuus. Selection was carried out from the F2 to F5 segregating populations for the silver canopy, high cuticular wax, small leaf area, single heading and high oil content. Cuticular wax ranged between 8.72 µg g−1 and 17.19 µg g−1 in the F5 offspring. The selected F5 breeding lines were self-pollinated to obtain the F6 generation. Thereafter, this F6 was compared with the non-adapted elite sunflower germplasm in a factorial complete randomized design with different water treatments; i.e., comparing fully irrigated (100%, T0) versus 75% (T1), 50% (T2) and 25% (T3) of total irrigation. The comparison between the two types of the germplasm showed that drought-tolerant breeding lines had a comparatively lesser decrease in leaf area (0, 11, 22%) and shoot length (4, 21, 28%) than the elite germplasm, which experienced a decrease in leaf area (21%, 33% and 40%) and shoot length (17, 27 and 34%) under the various drought treatments. Moreover, drought-tolerant breeding lines had 100% more root shoot ratios than the elite germplasm (20%) in T3 when compared with control. Several drought-tolerant promising lines (D-2, D-5 and D-27) were selected due to their high leaf area, great root length and increased root to shoot ratio under T3. Some of the lines could be directly used for the development of drought-tolerant hybrids. Combining ability testing indicated that D-27 (F7) was a good general combiner for seed yield plant−1 and oil content after mating with male-line RSIN.82. Resulting hybrids could help to minimize seed yield loss due to water stress and to achieve profitable cultivation of sunflowers in arid regions of Pakistan.

Induction of haploid plants for speed-up breedıng in sunflower (Helianthus annuus L.) by pollen irradiation

The creation of homozygous plants is essential for both genetic studies and the production of hybrid seeds, particularly in plants that were pollinated by an alien species. Dihaploid (DH) technology is an important application in obtaining homozygous lines used to plant speed breeding programs. The generation of haploid embryos by pollen irradiation and pollination of female flowers with irradiated pollen has been successfully applied. The influence of irradiated pollen on the induction of haploids in sunflower (Helianthus annuus L.) has been evaluated on 16 different sunflower lines from Turkey’s National Sunflower Breeding Program. In this study, pollen grains were irradiated with varying dosages of Gamma rays (500-1000 Gy) to generate parthenogenetic haploid embryos in oilseed sunflowers. At a period of 12–20 days following the process of pollination, embryos were plated into modified MS culture media under a 16/8 h photoperiod and a temperature of 25◦C. Parthenogenetic 18457 embryos at different developmental stages were rescued in vitro and 650 were germinated. The ploidy analysis of regenerants was made with chromosome count and flow cytometry. Except for 500 Gy, all dosages were effective for inducing embryos and haploid plants. Obtained results indicate that parthenogenetic haploid embryos can be produced in K3AD SN:8, IMI 069, and IMI 044 sunflower genotypes by selecting the appropriate Gamma ray dose and embryonic developmental stage. This study was focused to recover sunflower doubled haploids to accelerate the production of non-segregating lines for breeding.

Similar Transcriptomic Responses to Early and Late Drought Stresses Produce Divergent Phenotypes in Sunflower (Helianthus annuus L.).

Cultivated sunflower (Helianthus annuus L.) exhibits numerous phenotypic and transcriptomic responses to drought. However, the ways in which these responses vary with differences in drought timing and severity are insufficiently understood. We used phenotypic and transcriptomic data to evaluate the response of sunflower to drought scenarios of different timing and severity in a common garden experiment. Using a semi-automated outdoor high-throughput phenotyping platform, we grew six oilseed sunflower lines under control and drought conditions. Our results reveal that similar transcriptomic responses can have disparate phenotypic effects when triggered at different developmental time points. Leaf transcriptomic responses, however, share similarities despite timing and severity differences (e.g., 523 differentially expressed genes (DEGs) were shared across all treatments), though increased severity elicited greater differences in expression, particularly during vegetative growth. Across treatments, DEGs were highly enriched for genes related to photosynthesis and plastid maintenance. A co-expression analysis identified a single module (M8) enriched in all drought stress treatments. Genes related to drought, temperature, proline biosynthesis, and other stress responses were overrepresented in this module. In contrast to transcriptomic responses, phenotypic responses were largely divergent between early and late drought. Early-stressed sunflowers responded to drought with reduced overall growth, but became highly water-acquisitive during recovery irrigation, resulting in overcompensation (higher aboveground biomass and leaf area) and a greater overall shift in phenotypic correlations, whereas late-stressed sunflowers were smaller and more water use-efficient. Taken together, these results suggest that drought stress at an earlier growth stage elicits a change in development that enables greater uptake and transpiration of water during recovery, resulting in higher growth rates despite similar initial transcriptomic responses.

Разработка ДНК-маркеров признака устойчивости подсолнечника к расе G заразихи (Orobanche cumana Wallr.)

Broomrape (Orobanche cumana Wallr.) is an obligatory parasite which is able to decrease significantly sunflower yields. The race G is the most spread and virulence broomrape race in the Russian Federation. Cultivation of genetically resistance sunflower varieties and hybrids is the most ecologic and economically efficient method to control this parasite plant. Usage of DNA-markers when selecting the resistant plants increases significantly the effectiveness of a breeding process. To mark the sunflower resistance to broomrape race G, using bioinformative approaches, we developed new DNA-markers: four SCAR (sequence characterized amplified region) and ten SSR (simple sequence repeat). These markers were tested on 20 lines and hybrids of sunflower. Due to the results of this testing, all SSR- and two SCAR-markers were eliminated by steps. SCAR-marker RORS1 was characterized with the presence of an amplified DNA fragment with a length ≈ 168 bps and showed association with a trait of resistance, and SORS1 with a fragment length ≈ 322 bps had a relation with a sus-ceptible phenotype. These markers composed a marker system for a multiplex PCR, which allowed distinguishing resistant and susceptible lines and hybrids, except a line VK678 and F1 hybrids developed using this line as parental one. To eliminate faults of the marker system, seven SCAR-markers analogous to SORS1 were created. Due to estimation result, we selected a marker SORS9 characterized with the presence an amplified DNA fragment with a length ≈ 217 bps in susceptible phenotypes. The new system of markers RORS1/SORS9 for a multiplex PCR was validated on 70 sunflower lines and hybrids. The susceptible lines and hybrids were characterized with amplification of only marker SORS9, resistant lines – only marker RORS1, and resistant hybrids – both markers. The developed marker system allowed distinguishing all susceptible lines and hybrids from the resistant sunflower genotypes.

Transcriptional activity of mitochondrial genes in intraspecific and interspecific sunflower hybrids

Relevance. The genetic structure of plant cells implies the coordinated work of three genomes: nuclear, plastid, and mitochondrial. Hybridization between genetically heterogeneous parents can lead to changes in the established nuclear-cytoplasmic balance, which in turn can affect the level and consistency of their gene expression. Changes in the transcriptional activity of organelle genes (in particular, mitochondria) during distant (interspecific) hybridization remain poorly understood. Results. The present study employed the qPCR technique to evaluate the transcriptional activity level of the mitochondrial genes atp1, atp4, atp6, atp9, nad3, nad6, cox1, and cox3 in intra- and interspecific sunflower hybrids and their parental forms from the VIR collection. According to the analyzed transcriptional activity of mitochondrial genes, they can be divided into three groups: genes with a relatively high level of expression – atp1, atp6, and nad6, those with a medium level of expression – atp4, cox1, cox3, and genes with a low level of expression – atp9 and nad3. Comparative analysis showed no significant difference (P<0.05) between maternal lines and hybrids. However, the expression of the nad6 gene in the case of Helianthus argophyllus (Torr. & A. Gray) was 2.6 times higher than in the cultivated sunflower lines. Conclusion. The absence of substantial changes in the expression of mitochondrial genes both in intra- and interspecific hybrids indicates the lack of significant changes in the regulation of nuclear-cytoplasmic interactions in these hybrids.

Assessment of stableness for male sterility in newly developed CMS lines in sunflower (Helianthus annuus L.)

Assessment of stableness for male sterility in newly developed CMS lines in sunflower (Helianthus annuus L.)

Assessment of parental lines, F1 and F2 sunflower hybrids to Septoria leaf spot infection and some inheritance patterns

Abstract The foliar fungal disease Septoria leaf spot is economically important for sunflowers. It develops most intensively during the wet and warm season. However, the genetic nature of sunflower resistance to Septoria leaf spot is still not clear. The purpose of our work was to identify some inheritance patterns of sunflower resistance to this disease based on the assessment of lines and hybrids of the first and second generations. The studied material was sown in 2020 and 2021 and subsequently grown on a stationary artificial infectious plot enriched with Septoria helianthi pathogen. The frequency of infection and the severity of infection of each sample were taken into account. The two-factor variance analysis revealed a significant influence of genotype on the frequency of infection in six sunflower lines and confirmed the effect of individuality of the response of individual genotypes to disease damage. It was shown that about 65 % of the total variation of the trait is due to the genetic nature of the line, and only a little more than 20 % and about 11 % – to the influence of the environment and the “genotype × environment” interaction respectively. Based on disease damage data in 2020 and 2021, the lines were classified as susceptible, moderately susceptible, moderately resistant and resistant. Differentiation of lines according to sensitivity to Septoria leaf spot made it possible to obtain hybrids with different manifestations of the trait in their parents. The nature of inheritance of infection frequency in F1 sunflower hybrids was determined by the degree of dominance. As a result, it was revealed intermediate inheritance, as well as positive and negative overdominance of the trait. The severity of infection by S. helianthi pathogen in F1 hybrids was inherited according to the type of parental form with greater resistance to the disease. F2 populations were found to inherit infection frequency from the more resistant parent, showing a proportion of infected plants similar to that of the more resistant line from a given cross combination. It has been shown that the frequency of infection of the F2 population with Septoria leaf spot can be affected by the severity of infection of F1 plant with the pathogen S. helianthi.

Mutation and sequencing-based cloning and functional studies of a rust resistance gene in sunflower (Helianthus annuus).

Rust, caused by the fungus Puccinia helianthi Schwein., is one of the most devastating diseases of sunflower (Helianthus annuus L.), affecting global production. The rust R gene R11 in sunflower line HA-R9 shows broad-spectrum resistance to P. helianthi virulent races and was previously mapped to an interval on sunflower chromosome 13 encompassing three candidate genes annotated in the XRQr1.0 reference genome assembly. In the current study, we combined ethyl methane sulfonate (EMS) mutagenesis with targeted region capture and PacBio long-read sequencing to clone the R11 gene. Sequencing of a 60-kb region spanning the R11 locus from the R11 -HA-R9 rust-resistant line and three EMS-induced susceptible mutants facilitated the identification of R11 and definition of induced mutations. The R11 gene is predicted to have a single 3996-bp open reading frame and encodes a protein of 1331 amino acids with CC-NBS-LRR domains typical of genes conferring plant resistance to biotrophic pathogens. Point mutations identified in the R11 rust-susceptible mutants resulted in premature stop codons, consistent with loss of function leading to rust susceptibility. Additional functional studies using comparative RNA sequencing of the resistant line R11 -HA-R9 and R11 -susceptible mutants revealed substantial differences in gene expression patterns associated with R11 -mediated resistance at 7 days post-inoculation with rust, and uncovered the potential roles of terpenoid biosynthesis and metabolism in sunflower rust resistance.

Genetic diversity of the Russian sunflower breeding lines revealed by microsatellite loci analysis

The breeding of high-yielding sunflower varieties and hybrids requires the use of parent material with considerable genetic diversity. It can be identified using molecular genetic markers. The purpose of this study was the genotyping of sunflower lines bred by V. S. Pustovoit All-Russian Research Institute of Oil Crops (VNIIMK), developed in different ecological areas of cultivation, and to evaluate their genetic diversity using microsatellite loci. For the studies conducted in 2020-2022, there were used 23 lines from the Central experimental base (СEB), 17 lines from L.A. Zhdanov Don experimental station (DES), and 10 lines from the Armavir experimental station (AES). DNA was isolated from seedlings by the CTAB method. Samples were genotyped using 12 SSR markers. PCR products were separated in 8 % denaturing polyacrylamide gel or by capillary electrophoresis in a genetic analyzer. The main indicators of genetic diversity for all collections did not differ significantly from each other, and were moderate and increased in the collections of VNIIMK: AES – DES – CEB -the joint collection. In total there have been identified 37 alleles, an average 3.083 alleles per locus. The effective number of alleles ranged from 1.094 to 3.290 with an average value of 2.154. The values of the polymorphic information content (PIC) index ranged from 0.084 to 0.651, with an average of 0.434. The values of observed and expected heterozygosity ranged from zero to 0.071, 0.030, on average, and from 0.086 to 0.696, 0.500, on average, respectively. The number of shared alleles between different collections was 23. Molecular variation analysis revealed that most of the total variance (91 %) was due to differences between lines within each collection and 3 % to differences between collections. According to the results of the cluster analysis, the maternal lines from the collections of the CEB, DES, and AES of VNIIMK were mostly grouped into a cluster or subcluster separate from the paternal ones. The obtained results indicate a moderate genetic diversity of the studied sunflower lines of the breeding of VNIIMK and the existence of small differences between the collections.

A Differential Phytohormone Profile in the Aerial Part and Roots as a Response to Water Stress Underlying Morphophysiological and Biochemical Changes in Two Inbred Sunflower Lines at Early Growth Stage

A Differential Phytohormone Profile in the Aerial Part and Roots as a Response to Water Stress Underlying Morphophysiological and Biochemical Changes in Two Inbred Sunflower Lines at Early Growth Stage

Screening of Sunflower Genotypes for Reaction to Alternaria Leaf Blight Disease across Multi-environments using Pooled Analysis

Sunflower (Helianthus annuus L.) is an oilseed crop with potential health benefits as a source of oil and dietary fiber. The productivity of sunflower is hampered by both biotic and abiotic stresses caused due to climate changes. So far, the available gene pool is having moderately resistant lines. In the present study, we evaluated two screening methods by artificially challenging the plants with the causative agent A. helianthi. Significant changes in disease severity have been observed across 160 pre-breeding lines of sunflower, including the susceptible check, Morden in three different seasons. Among the160 pre-breeding lines derived from a mutant population of sunflower cv. Morden, 6.25 and 5.63 % of lines showed less leaf blight disease incidence under in vivo and in vitro environments respectively. Moreover, 44.38 % of the sunflower pre breeding lines demonstrated field tolerance with disease severity in the scale of 5. The promising accessions evaluated in our studies by whole plant assay method and detached leaf technique includes KSFI 19, KSFI 24, KSFI 147, KSFI 56, KSFI 120, KSFI 88, KSFI 152, KSFI 51 and KSFI 115. Therefore, these sunflower lines, could be employed for introgression of resistance genes against leaf blight disease in sunflower cultivars through marker assisted breeding strategies.

Correlation and path analysis studies in maintainer and restorer lines of sunflower (Helianthus annuus L.)

Correlation and path analysis studies in maintainer and restorer lines of sunflower (Helianthus annuus L.)

Influence of climatic conditions on infection of sunflower lines by phoma black stem

The purpose of the research was to analyze three year observations (2018–2020) for the climate changes effect on infection of the breeding sunflower lines (Helianthus annuus L.) by a Phoma black stem pathogen Plenodomus lindquistii (Frezzi) Gruyter, Aveskamp & Verkley in the central zone of the Krasnodar region. The disease was monitored on fields of V.S. Pustovoit All-Russian Research Institute of Oil Crops, Krasnodar. Analysis of climatic factors in years of the research resulted that heavy rainfalls (119.2?134.6 mm) exceeding multi-year averages (60.0 mm) by two times and the optimal average daily temperature 23.0?26.4 ?С in July are favorable for stem infection by Plenodomus lindquistii in the second half of the summer, in a phase of sunflower flowering – maturing. In 2018, the moisture deficit in June (11.0 mm) and August (6.8 mm) was a factor suppressing the viability of an infectious matter of a fungus that led to a low frequency of Phoma black stem on the sunflower lines (in average 20.3%). In 2019 and 2020, prevalence (P) and development (R) of Phoma black stem in average on sunflower lines were equal 23.3?29.9% and 21.4?28.1%, respectively. A line L 107 demonstrated a stable resistance to Plenodomus lindquistii infection during three years: amount of infected plants was within 5.7?8.3%, development was 3.8?8.3% at the infection level of 1–2 points. A susceptible line L 116 was selected (P: 47.5?62.8%, and R: 38.0?40.0%). Among the studied breeding lines, the sample VK 900 was the most susceptible to weather conditions of the year: prevalence of the Phoma black stem varied within 21.1?45.5% at the infection level of 1?3 points.

The genomics of linkage drag in inbred lines of sunflower

Crop wild relatives represent valuable sources of alleles for crop improvement, including adaptation to climate change and emerging diseases. However, introgressions from wild relatives might have deleterious effects on desirable traits, including yield, due to linkage drag. Here, we analyzed the genomic and phenotypic impacts of wild introgressions in inbred lines of cultivated sunflower to estimate the impacts of linkage drag. First, we generated reference sequences for seven cultivated and one wild sunflower genotype, as well as improved assemblies for two additional cultivars. Next, relying on previously generated sequences from wild donor species, we identified introgressions in the cultivated reference sequences, as well as the sequence and structural variants they contain. We then used a ridge-regression best linear unbiased prediction (BLUP) model to test the effects of the introgressions on phenotypic traits in the cultivated sunflower association mapping population. We found that introgression has introduced substantial sequence and structural variation into the cultivated sunflower gene pool, including >3,000 new genes. While introgressions reduced genetic load at protein-coding sequences, they mostly had negative impacts on yield and quality traits. Introgressions found at high frequency in the cultivated gene pool had larger effects than low-frequency introgressions, suggesting that the former likely were targeted by artificial selection. Also, introgressions from more distantly related species were more likely to be maladaptive than those from the wild progenitor of cultivated sunflower. Thus, breeding efforts should focus, as far as possible, on closely related and fully compatible wild relatives.