Louis M Ashton, Dylan Korczynskyj, Ryan D Phillips, Stanislaw Wawrzyczek, Eddie J van Etten, Siegfried L Krauss
{"title":"Exclusion of bird pollinators impacts mating system and reduces offspring fitness in a pollination-generalist tree.","authors":"Louis M Ashton, Dylan Korczynskyj, Ryan D Phillips, Stanislaw Wawrzyczek, Eddie J van Etten, Siegfried L Krauss","doi":"10.1093/aob/mcaf168","DOIUrl":"10.1093/aob/mcaf168","url":null,"abstract":"<p><strong>Background and aims: </strong>In comparison to pollinating insects and non-flying mammals (NFMs), nectarivorous birds might display behaviours leading to greater pollen carryover. Therefore, plants pollinated by birds might display higher levels of paternal diversity and outcrossing than those pollinated by insects and NFMs, with associated fitness benefits for seeds and seedlings. Here, we test these predictions using a plant where birds, insects and NFMs are all frequent visitors to flowers.</p><p><strong>Methods: </strong>An experiment manipulating access to flowers of Banksia menziesii (Proteaceae) was conducted. Treatments applied to whole plants were: (1) open to all pollinators; (2) insect access, with birds and NFMs excluded; (3) NFM access, with insects and birds excluded; and (4) complete pollinator exclusion. Reproductive output was quantified in terms of fruit and seed production. The genetic consequences for offspring were tested using microsatellite markers to genotype individuals and quantify the mating system, and through field trials to quantify seedling vigour.</p><p><strong>Key results: </strong>When birds were excluded from flowers, maternal fitness was reduced. In comparison to open pollinated flowers, fruit set was reduced by 76 % when only NFMs could access flowers. When only insects (primarily introduced honeybees) could access flowers, the number of viable seeds per fruit was reduced by 20 % because the proportion of aborted seeds doubled, in comparison to pollination that included birds. For seedlings, heterozygosity was reduced by 22 %, outcrossing rates by 30 % and paternal diversity by 15 %, when birds were excluded. Seedling mortality was strongly associated with inbreeding, and selfing largely occurred only when birds were excluded. All parameters were lowest when only NFMs had access to flowers.</p><p><strong>Conclusions: </strong>Although honeybees were effective pollinators of B. menziesii owing to their abundance, birds were inferred to be the most effective, with their exclusion resulting in a reduction of fecundity and offspring vigour. These negative effects were largely a consequence of selection against the products of self-pollination, which was associated with pollination by insects or NFMs. Our findings highlight how a genetic component of pollination that increases offspring fitness could favour the evolution of bird pollination.</p>","PeriodicalId":8023,"journal":{"name":"Annals of botany","volume":" ","pages":"887-902"},"PeriodicalIF":3.6,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12464952/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144774577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Marinus L de Jager, Noushka Reiter, Mike Wicks, Bjorn Bohman, Gareth D Holmes, Ryan D Phillips
{"title":"Sexually deceptive orchids with distinct flower morphologies elicit different behaviours from a shared pollinator.","authors":"Marinus L de Jager, Noushka Reiter, Mike Wicks, Bjorn Bohman, Gareth D Holmes, Ryan D Phillips","doi":"10.1093/aob/mcaf234","DOIUrl":"https://doi.org/10.1093/aob/mcaf234","url":null,"abstract":"<p><strong>Background and aims: </strong>Pollination by sexual deception is one of the most specialised pollination strategies among angiosperms, with co-occurring plant species often exploiting males of different insect species. We test if the morphologically divergent orchids Caladenia cardiochila and its sympatric Endangered congener C. lowanensis are dependent on the same thynnine wasp pollinator. We further investigate the role of floral traits on pollinator behaviour and evaluate potential hybridisation risk.</p><p><strong>Methods: </strong>Pollinator sharing was tested for with DNA barcoding. Pollinator behaviour was quantified and experimental floral dissections used to determine the site of sexual attractant release. We employed GC-MS to test for the presence of sugar on orchid labella, hand crosses to assess the impact of interspecific pollen transfer on seed viability, and population monitoring to quantify natural pollination success.</p><p><strong>Key results: </strong>We found that C. cardiochila and C. lowanensis both employ sexual deception of Phymatothynnus aff. nitidus wasps as pollination strategy. However, the behaviour they elicit differs with wasps attempting to mate with the insectiform labellum in C. cardiochila and the glandular sepal tips in C. lowanensis, which are the respective sources of sexual attractant. Unlike most sexually deceptive orchids, C. lowanensis secretes minute amounts of sugar from its labellum. While wasps interacted more frequently with the labellum in C. cardiochila, placing them closer to its reproductive structures, both species exhibited comparable pollination success and pollen transfer efficiency. Experimental crosses revealed that hybrid seed has high viability.</p><p><strong>Conclusions: </strong>Sexual deception of the same pollinator by orchids varying in the location of sexual attractant and flower morphology highlights the considerable flexibility of this pollination strategy. Given their overlapping distributions and the viability of hybrid seed, pollinator sharing poses a hybridisation risk that needs to be considered in the management of wild C. lowanensis populations and future conservation translocations.</p>","PeriodicalId":8023,"journal":{"name":"Annals of botany","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Loïc Pittet, Piotr Kosiński, Natascha D Wagner, Elvira Hörandl
{"title":"Niche expansion of polyploid cytotypes shaped the phylogeographical history of the Salix retusa complex in the European Alpine System.","authors":"Loïc Pittet, Piotr Kosiński, Natascha D Wagner, Elvira Hörandl","doi":"10.1093/aob/mcaf163","DOIUrl":"10.1093/aob/mcaf163","url":null,"abstract":"<p><strong>Background and aims: </strong>Alpine plants exhibit diverse postglacial recolonization patterns following the last glacial periods. Polyploidization may have impacted these dynamics by introducing ecological and physiological novelties that facilitate adaptation to changing environments. However, consistent trends in the recolonization, niche optima and dynamics of polyploids and their related diploids remain elusive. In this study, we investigate the biogeographical history of the Salix retusa polyploid complex in the European Alpine System. By comparing genetic patterns and their climatic and edaphic niche optima, we explore how polyploidization shaped species' geographical distributions by influencing their ecological adaptation.</p><p><strong>Methods: </strong>RAD sequencing was used to reconstruct the biogeographical history and genetic structure of two related willow species. High-resolution edaphic and climatic data were used to compare the niche optima, breadth and dynamics between the species.</p><p><strong>Key results: </strong>The distribution of the polyploid species overlaps with more peripheral refugial areas, which correlates with its broader geographical range in the European Alpine System. However, genetic analyses suggest more potential peripheral glacial refugia within the Alps for the diploid. Our findings indicate niche conservatism within the S. retusa complex, with the polyploid species having a broader niche but the diploid being adapted to a more extreme niche.</p><p><strong>Conclusions: </strong>In our study species, polyploidy is associated with a higher genetic diversity and geographical structure, which might be due to a broader ecological niche and distribution. However, it did not appear to facilitate adaptation or confer a survival advantage during the last glaciation.</p>","PeriodicalId":8023,"journal":{"name":"Annals of botany","volume":" ","pages":"903-917"},"PeriodicalIF":3.6,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12464947/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144706068","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Stronger transgenerational plasticity in clonal compared to sexual offspring of Fragaria vesca: effects of drought, elevated temperature and CO2.","authors":"Iris Sammarco, Zofia Szlachtowska, Gerson Beltrán-Torres, Zuzana Münzbergová, Vít Latzel","doi":"10.1093/aob/mcaf136","DOIUrl":"10.1093/aob/mcaf136","url":null,"abstract":"<p><strong>Background and aims: </strong>Climate change threatens plant species, potentially exceeding their adaptive capacities. Plants may adapt to rapid environmental changes through transgenerational plasticity (TGP), where adaptive traits are passed to their offspring via proteins, hormones and epigenetic modifications such as DNA methylation. The extent of TGP and its ecological implications may differ between sexual and clonal reproductive modes due to differences in the inheritance of DNA methylation and provisioning. However, it remains unclear whether TGP differs between these reproductive modes and the role of DNA methylation. Addressing this gap is crucial, as higher TGP in clonal propagation could compensate for low genetic variation and help these plants in adapting to rapid environmental changes.</p><p><strong>Methods: </strong>We assessed the adaptive potential of woodland strawberry (Fragaria vesca), a widely distributed herb with both clonal and sexual reproduction, in response to environmental conditions expected by the end of the 21st century: a temperature rise of 4 °C, a 400 ppm rise in atmospheric CO2 and periodic droughts. We quantified ecologically relevant phenotypic traits and examined whole-genome DNA methylation patterns in parents and their clonal and sexual offspring.</p><p><strong>Key results: </strong>We found evidence for TGP induced by the parental environment, with a stronger overall effect observed in clonal compared to sexual offspring. Specifically, parental exposure to current temperature and CO2 conditions prompted adaptive TGP, particularly in clonal offspring. Additionally, adaptive TGP was observed exclusively in clonal offspring in response to a combination of elevated parental temperature and drought conditions. Finally, we found a higher inheritance of DNA methylation marks in clonal than in sexual offspring.</p><p><strong>Conclusions: </strong>These results suggest that while TGP via DNA methylation can influence clonal plant adaptation to future conditions, it remains uncertain whether this influence will consistently result in adaptive outcomes. Moreover, TGP would probably be more important in clonal than in sexual reproduction.</p>","PeriodicalId":8023,"journal":{"name":"Annals of botany","volume":" ","pages":"769-782"},"PeriodicalIF":3.6,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12464940/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144493727","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Avian taxi drivers? A commentary on 'Diversity of fungi attached to birds corresponds to the habitat ecologies of their avian dispersal vectors'.","authors":"Marcos V Caiafa","doi":"10.1093/aob/mcaf137","DOIUrl":"10.1093/aob/mcaf137","url":null,"abstract":"","PeriodicalId":8023,"journal":{"name":"Annals of botany","volume":" ","pages":"i-ii"},"PeriodicalIF":3.6,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12464938/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144504733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Astrid de Mestier, Banessa Falcón-Hidalgo, Thomas Borsch
{"title":"Plastid phylogenomics of the parietal clade of Malpighiales: ancestral genome synteny and congruent signal across exons, introns and spacers in support of Salicaceae relationships.","authors":"Astrid de Mestier, Banessa Falcón-Hidalgo, Thomas Borsch","doi":"10.1093/aob/mcaf148","DOIUrl":"10.1093/aob/mcaf148","url":null,"abstract":"<p><strong>Background and aims: </strong>The parietal clade is one of the major lineages of the angiosperm order Malpighiales. Several nodes in the phylogenetic trees inferred from concatenated chloroplast genes exhibited low support, and various Malpighiales genera were found to have highly altered plastid genomes.</p><p><strong>Methods: </strong>Here we newly generated seven complete plastid genomes to represent the major lineages of the pantropical genus Casearia using genome skimming. Together with published genome sequences of various sources, we comparatively analysed the genome structure of all major lineages of the Salicaceae and their putative relatives across the parietal clade.</p><p><strong>Key results: </strong>All plastid genomes, including those of the Rhizophoraceae outgroup, were syntenous, with the exception of Passifloraceae, which exhibited accelerated pseudogenization, gene loss and major structural rearrangements. Although rpl32 is absent from all Salicaceae, this is not a synapomorphy for the family, due to other losses in genera such as Hydnocarpus and Viola. Apart from the exons, we found sequences of all introns and most spacers to be alignable, except short and hypervariable stem-loop elements. We could therefore explore the phylogenetic signal of complete plastid genomes.</p><p><strong>Conclusions: </strong>All three partitions, exons, introns and spacers, presented congruent topologies with maximum support for the Samydoideae being sister to a clade of Salicoideae and Scyphostegioideae within the monophyletic Salicaceae. Our results underscore the potential of complete plastid genomes to further explore the evolutionary diversification of the Malpighiales.</p>","PeriodicalId":8023,"journal":{"name":"Annals of botany","volume":" ","pages":"837-850"},"PeriodicalIF":3.6,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12464943/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144615974","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cristina Pop, Irene Terry, Laurence A Mound, Casper J van der Kooi
{"title":"Tiny but significant: on the importance of thrips as pollinators.","authors":"Cristina Pop, Irene Terry, Laurence A Mound, Casper J van der Kooi","doi":"10.1093/aob/mcaf069","DOIUrl":"10.1093/aob/mcaf069","url":null,"abstract":"<p><strong>Background: </strong>Thrips (Thysanoptera) are minute plant and flower visitors in ecosystems across the world but are commonly viewed as notorious pests and too small to effect pollination. The role of thrips as pollinators is thus largely neglected. We provide an overview of the number of plant taxa that are pollinated by thrips, the floral traits of thrips-pollinated plants, and discuss why thrips can be effective pollinators.</p><p><strong>Main findings: </strong>Thrips pollination occurs in almost half of all seed plant orders, 53 families and 102 plant genera. In many taxa, thrips are the primary or only pollinator. Thrips effectiveness as pollen vectors is enhanced by enormous thrips population sizes in inflorescences, pollen loads of up to >100 grains per individual, and the ability to travel in wind streams. A meta-analysis shows that thrips can significantly contribute to seed and fruit set compared with open pollination controls. A review of the floral traits of thrips-pollinated plants suggests that there is no universal 'thripophily' pollination syndrome. One plant trait that stands out is a floral architecture that limits access to larger pollinators and gives thrips a refuge, such as globose or disc-like structures with small or slit-like openings. Some specialist systems exhibit characteristic floral or cone odours that attract thrips; however, too few systems have been studied in detail to cast a general description. Together, our results suggest that pollination by thrips is more common than has been historically perceived, and thrips should not be overlooked in pollination studies and as agents of selection of floral traits.</p>","PeriodicalId":8023,"journal":{"name":"Annals of botany","volume":" ","pages":"669-682"},"PeriodicalIF":3.6,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12464953/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143961294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Allelic value in gene regulation-implications for gene editing.","authors":"Mazahar Moin, Mayank Rai, Wricha Tyagi","doi":"10.1093/aob/mcaf072","DOIUrl":"10.1093/aob/mcaf072","url":null,"abstract":"<p><strong>Background: </strong>Gene editing has emerged as the most precise trait modification tool in plant breeding. However, an understanding of what to target and in which genetic background to obtain the intended phenotype is still emerging. This perspective presents an analytical overview of traits targeted, particularly in tomato and rice, where extensive data on gene editing are available in the public domain.</p><p><strong>Scope: </strong>The available gene editing data on allelic values for a given molecular pathway in crops like tomato and rice are revisited. The phenotypes of edits generated across genetic backgrounds were assessed and compared with available resequencing and phenotypic data. The traits evaluated in the current perspective were de novo domestication, grain quality, fruit colour, yield-related traits and stress tolerance to check whether the data available give significant leads to address these traits via editing in other crops. The rationale for editing a particular gene lies in the understanding of the diverse alleles generated, and in this perspective we attempt to discern both the advancements made and the bottlenecks encountered.</p><p><strong>Conclusions: </strong>The effectiveness of gene editing relies significantly on the roles of alleles generated in regulating specific genetic pathways. It is essential to conduct functional validation of the targeted allele across multiple distinct genetic backgrounds to ascertain its utility. The influence an allele exerts on a given trait is contingent upon factors like the nature of the trait, the position of the gene within a given pathway, and the genetic background in which it has been/will be tested. This perspective highlights how editing has led to a range of phenotypic variations influenced by the genetic background, with certain lines achieving the desired phenotype alongside pleiotropic effects, whereas others do not manifest the expected phenotype. This challenge may be addressed by prioritizing the identification of the right candidate and specific motifs in the regulatory regions as potential targets rather than directly intervening in coding sequences.</p>","PeriodicalId":8023,"journal":{"name":"Annals of botany","volume":" ","pages":"683-697"},"PeriodicalIF":3.6,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12464954/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143959595","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Vitor M Costa-Silva, Iasmim De-Freitas, Kleber Del-Claro, Xoaquín Moreira
{"title":"The complex dynamics of ant-plant mutualisms: exploring the roles of plant-provided resources and bird predation on ants in shaping plant performance.","authors":"Vitor M Costa-Silva, Iasmim De-Freitas, Kleber Del-Claro, Xoaquín Moreira","doi":"10.1093/aob/mcaf156","DOIUrl":"10.1093/aob/mcaf156","url":null,"abstract":"<p><strong>Background and aims: </strong>Protection mutualisms involve plants receiving defence against herbivores from predators, such as ants and insectivorous birds, in exchange for food resources. Ants can reduce herbivory by actively patrolling plants with extrafloral nectaries (EFNs) or by tending trophobiotic insects that provide them with food rewards. Insectivorous birds also contribute to herbivore suppression but might simultaneously reduce ant activity through predation. Although both ants and birds can enhance plant performance, few studies have explored how the availability of multiple ant-associated resources influences herbivore suppression, or how bird predation on ants affects these ant-plant mutualisms. These gaps limit our understanding of the dynamics in complex multitrophic interactions.</p><p><strong>Methods: </strong>We investigated how the availability of multiple food resources for ants and the predation exerted by insectivorous birds on ants influence the performance of the tropical shrub Banisteriopsis malifolia. To address this, we conducted two field experiments. The first manipulated the individual and combined presence of mutualistic ant resources (EFNs, myrmecophilous caterpillars and treehoppers). The second experiment manipulated the presence or absence of both ants and birds to assess their interactive effects. Plant performance was evaluated by measuring leaf herbivore damage, the number of fruits and fruit weight.</p><p><strong>Key results: </strong>Our findings show that B. malifolia plants offering a full complement of mutualistic food resources for ants, including EFNs and trophobiotic insects, experienced significantly lower leaf herbivory and higher fruit production in comparison to plants lacking these resources. Bird exclusion resulted in increased herbivore damage and reduced fruit output, with these negative effects being even more pronounced when both birds and ants were excluded.</p><p><strong>Conclusions: </strong>Our findings highlight the complexity of multitrophic interactions in ant-plant mutualisms. They emphasize the importance of considering multiple trophic levels in plant defence strategies and underscore the cascading effects of predator interactions within natural ecosystems.</p>","PeriodicalId":8023,"journal":{"name":"Annals of botany","volume":" ","pages":"877-886"},"PeriodicalIF":3.6,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12464946/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144648385","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dongryung Lee, Byeong Yong Jeong, Backki Kim, Seong-Gyu Jang, Yuting Zeng, Ah-Rim Lee, Junghyun Gong, Soon-Wook Kwon, Joohyun Lee
{"title":"Genome-wide association analysis identifies natural allelic variants associated with leaf rolling in rice (Oryza sativa L.).","authors":"Dongryung Lee, Byeong Yong Jeong, Backki Kim, Seong-Gyu Jang, Yuting Zeng, Ah-Rim Lee, Junghyun Gong, Soon-Wook Kwon, Joohyun Lee","doi":"10.1093/aob/mcaf153","DOIUrl":"10.1093/aob/mcaf153","url":null,"abstract":"<p><strong>Background and aims: </strong>Leaf rolling in rice affects plant architecture, light interception and photosynthetic efficiency. This study aims to identify the genetic basis of adaxial leaf rolling using a genome-wide association study (GWAS) in a diverse panel of rice accessions.</p><p><strong>Methods: </strong>A GWAS was performed using 1.5 million single nucleotide polymorphisms (SNPs) across 113 rice accessions. The analysis included population structure, linkage disequilibrium, haplotype patterns and expression correlation. To validate the identified association, an additional panel of japonica inbred lines was analyzed, supporting the link between the SNP and adaxial leaf rolling.</p><p><strong>Key results: </strong>A japonica-specific quantitative trait locus, qALR1, was identified on chromosome 1. A putative causal SNP was located within a shared cis-regulatory motif (RAV1-B) upstream of two candidate genes, LOC_Os01g72370 and LOC_Os01g72380. Previous studies suggest that variation in this motif can influence gene expression, supporting the hypothesis that regulatory divergence in these genes may underlie variation in leaf rolling. Validation with an expanded panel of japonica inbred lines revealed its enrichment in breeding germplasm, indicating possible historical selection.</p><p><strong>Conclusions: </strong>This study identifies a subspecies-specific regulatory mechanism underlying adaxial leaf rolling in rice. The putative causal SNP may affect transcription factor binding and gene regulation, ultimately influencing leaf morphology. These findings offer valuable targets for optimizing canopy architecture and enhancing photosynthetic performance through molecular breeding.</p>","PeriodicalId":8023,"journal":{"name":"Annals of botany","volume":" ","pages":"851-864"},"PeriodicalIF":3.6,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12464949/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144681902","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}