Polyploidy, also known as whole genome duplication, is a major evolutionary force in plants, driving diversification and the generation of novel phenotypic variation, including superior abiotic and biotic stress tolerance. The enhanced stress resilience observed in certain polyploids is hypothesized to arise from dynamic epigenetic and genetic changes, including variations in gene content and cis-regulatory elements (CREs), that emerge following polyploidization. These changes directly impact various regulatory, signaling, and metabolic pathways associated with stress response and adaptation. Within polyploid populations, processes like gene duplications, fractionation, and homoeologous exchanges actively shape novel gene content variation, while, simultaneously, alterations in CREs (DNA sequences controlling gene expression) lead to diverse regulatory patterns. This dynamic interplay between changes in gene content and regulation further contributes to expanded phenotypic variation, including enhanced stress resilience. We discuss how advanced genomic and epigenomic techniques, such as pangenomics and single-cell assay for transposase-accessible chromatin with sequencing, are used to uncover these variations and outline new bioinformatic approaches to reveal the underlying genetics of stress resilience and adaptation. Finally, we summarize what remains poorly understood to guide future research, with the goal of unlocking the full potential for enhancing resilience in polyploid crops.

Successful establishment of a species in a new range is a useful way to understand the impact of demography and selection on the evolution of globally distributed species. In particular, introductions influence genetic diversity and population structure in the introduced range in unpredictable ways. Additionally, introgressive hybridization is often associated with successful establishment in new ranges. In this study, we explore the impact of introgressive hybridization on the polyploid Capsella bursa-pastoris in the New York City metropolitan area. We find Capsella bursa-pastoris in the New York City metropolitan area likely originated from multiple introductions from northern Eurasia, and that populations across the New York City metropolitan area are generally panmictic. As with Capsella bursa-pastoris in Eurasia, we discover evidence of introgression from the diploid Capsella rubella in this population. By evaluating ancestry in regions across the genome, we find introgressed regions are rich in gene content and contribute to genetic diversity in this population. These results suggest that introgressive hybridization before introductions may buffer species from the negative effects of population bottlenecks and allow for successful establishment.

BACKGROUND:Efforts to characterize regulatory elements in plant genomes traditionally rely on evolutionary conservation and chromatin accessibility. Recently, intergenic bi-directional nascent transcript has emerged as a putative hallmark of active enhancers. Here, we integrate these approaches to better define the cis-regulatory landscape of the rice genome. RESULTS:In juvenile leaf tissues of the Azucena rice variety, we analyze conserved noncoding sequences, intergenic bi-directional transcripts, and regions of open chromatin. These three features highlight distinct classes of regulatory targets, each exhibiting complexity and regulatory roles. Conserved noncoding sequences are associated with more complex regulatory interactions, while regions marked by chromatin accessibility or bi-directional nascent transcription tend to promote more stable regulatory activity. Some transcribed regulatory sites harbor elements linked to transposable element silencing, whereas others correlate with increased expression of nearby genes, pointing to candidate transcribed regulatory elements. We further identified molecular interactions between genic regions and intergenic transcribed regulatory elements using 3-dimensional chromatin contact data, we identify physical interactions between transcribed intergenic regions and genic regions. These interactions often co-localize with expression quantitative trait loci and coincide with increased transcription, further supporting a regulatory role. CONCLUSIONS:Our integrative analysis reveals multiple distinct classes of regulatory elements in the rice genome, with overlapping but non-identical targets and signatures. Many candidate elements share features consistent with transcriptional enhancement, though the specific criteria for defining active enhancers in plants require further characterization. These findings underscore the importance of using complementary genomic signals to discover and characterize functionally diverse regulatory elements in plant genomes.

Comprehensively identifying the loci shaping trait variation has been challenging, in part because standard approaches often miss many types of genetic variants. Structural variants (SVs), especially transposable elements (TEs), are likely to affect phenotypic variation but we lack methods that can detect polymorphic SVs and TEs using short-read sequencing data. Here, we used a whole genome alignment between two maize genotypes to identify polymorphic SVs and then genotyped a large maize diversity panel for these variants using short-read sequencing data. After characterising SV variation in the panel, we identified SV polymorphisms that are associated with life history traits and genotype-by-environment (GxE) interactions. While most of the SVs associated with traits contained TEs, only two of the SVs had boundaries that clearly matched TE breakpoints indicative of a TE insertion, while the other polymorphisms were likely caused by deletions. One of the SVs that appeared to be caused by a TE insertion had the most associations with gene expression compared to other trait-associated SVs. All of the SVs associated with traits were in linkage disequilibrium with nearby single nucleotide polymorphisms (SNPs), suggesting that the approach used here did not identify unique associations that would have been missed in a SNP association study. Overall, we have (1) created a technique to genotype SV polymorphisms across a large diversity panel using support from genomic short-read sequencing alignments and (2) connected this presence/absence SV variation to diverse traits and GxE interactions.

Certain specialist herbivorous insects have evolved elegant mechanisms to manipulate the physiology of their host plants, including the ability to redirect the fate of plant cells toward the creation of a novel, tumor-like organ, called 'galls'. While some plants have evolved resistance to gall-inducing insects, the underlying genetic mechanisms remain poorly understood. In this study, we focused on the chalcid gall-inducing wasp, Hemadas nubilipennis (Ormyridae) and its host plant, highbush blueberry Vaccinium corymbosum (Ericaceae). To identify the genetic basis of resistance to gall induction in blueberry, we developed a genetic mapping population derived from the susceptible 'Liberty' and resistant 'Draper' cultivars. We identified four quantitative trait loci (QTLs) associated with galling resistance, with candidate genes in these regions associated with plant defense, biotic stress response, and phytohormone metabolism. Furthermore, we analyzed gene expression on days one through seven post-oviposition in both susceptible and resistant genotypes, compared to controls, to identify genes and pathways that may contribute to galling resistance. Gene expression analyses, including genes within the four identified QTL regions, revealed a robust early defense response in the resistant genotype, marked by upregulation of defense, stress, and immunity genes following oviposition, ultimately leading to insect death. Conversely, the susceptible genotype exhibited a delayed and weaker response, allowing gall development and insect survival. We expect these results to serve as a resource that will enable breeding programs to employ molecular approaches for selection of resistant cultivars, while also guiding future research aimed at studying the evolution of galling resistance.

Fertilization is a fundamental process that triggers seed and fruit development, but the molecular mechanisms underlying fertilization-induced seed development are poorly understood. Previous research has established AGamous-Like62 (AGL62) activation and auxin biosynthesis in the endosperm as key events following fertilization in Arabidopsis (Arabidopsis thaliana) and wild strawberry (Fragaria vesca). To test the hypothesis that epigenetic mechanisms are critical in mediating the effect of fertilization on the activation of AGL62 and auxin biosynthesis in the endosperm, we first identified and analyzed imprinted genes from the endosperm of wild strawberries. We isolated endosperm tissues from F1 seeds of 2 wild strawberry F. vesca subspecies, generated endosperm-enriched transcriptomes, and identified candidate Maternally Expressed and Paternally Expressed Genes (MEGs and PEGs). Through bioinformatic analyses, we identified 4 imprinted genes that may be involved in regulating the expression of FveAGL62 and auxin biosynthesis genes. We conducted functional analysis of a maternally expressed gene FveMYB98 through CRISPR-knockout and over-expression in transgenic strawberries as well as analysis in heterologous systems. FveMYB98 directly repressed FveAGL62 at stage 3 endosperm, which likely serves to limit auxin synthesis and endosperm proliferation. These results provide an inroad into the regulation of early-stage seed development by imprinted genes in strawberries, suggest the potential function of imprinted genes in parental conflict, and identify FveMYB98 as a regulator of a key transition point in endosperm development. Identification of imprinted genes from strawberry endosperm reveals a maternally expressed gene that negatively regulates auxin synthesis in the endosperm and thereby limits seed size.

Subgenome dominance has been reported in diverse allopolyploid species, where genes from one subgenome are preferentially retained and are more highly expressed than those from other subgenome(s). However, the molecular mechanisms responsible for subgenome dominance remain poorly understood. Here, we develop genome-wide map of accessible chromatin regions (ACRs) in cultivated strawberry (2 n = 8 x = 56, with A, B, C, D subgenomes). Each ACR is identified as an MNase hypersensitive site (MHS). We discover that the dominant subgenome A contains a greater number of total MHSs and MHS per gene than the submissive B/C/D subgenomes. Subgenome A suffers fewer losses of MHS-related DNA sequences and fewer MHS fragmentations caused by insertions of transposable elements. We also discover that genes and MHSs related to stress response have been preferentially retained in subgenome A. We conclude that preservation of genes and their cognate ACRs, especially those related to stress responses, play a major role in the establishment of subgenome dominance in octoploid strawberry.

Camelina (Camelina sativa), an allohexaploid species, is an emerging aviation biofuel crop that has been the focus of resurgent interest in recent decades. To guide future breeding and crop improvement efforts, the community requires a deeper comprehension of subgenome dominance, often noted in allopolyploid species, "alongside an understanding of the genetic diversity" and population structure of material present within breeding programs. We conducted population genetic analyses of a C. sativa diversity panel, leveraging a new genome, to estimate nucleotide diversity and population structure, and analyzed for patterns of subgenome expression dominance among different organs. Our analyses confirm that C. sativa has relatively low genetic diversity and show that the SG3 subgenome has substantially lower genetic diversity compared to the other two subgenomes. Despite the low genetic diversity, our analyses identified 13 distinct subpopulations including two distinct wild populations and others putatively representing founders in existing breeding populations. When analyzing for subgenome composition of long non-coding RNAs, which are known to play important roles in (a)biotic stress tolerance, we found that the SG3 subgenome contained significantly more lincRNAs compared to other subgenomes. Similarly, transcriptome analyses revealed that expression dominance of SG3 is not as strong as previously reported and may not be universal across all organ types. From a global analysis, SG3 "was only significant higher expressed" in flower, flower bud, and fruit organs, which is an important discovery given that the crop yield is associated with these organs. Collectively, these results will be valuable for guiding future breeding efforts in camelina.

Anthracnose fruit rot (AFR), caused by the fungal pathogen Colletotrichum fioriniae, is among the most destructive and widespread fruit disease of blueberry, impacting both yield and overall fruit quality. Blueberry cultivars have highly variable resistance against AFR. To date, this pathogen is largely controlled by applying various fungicides; thus, a more cost-effective and environmentally conscious solution for AFR is needed. Here we report three quantitative trait loci associated with AFR resistance in northern highbush blueberry (Vaccinium corymbosum). Candidate genes within these genomic regions are associated with the biosynthesis of flavonoids (e.g. anthocyanins) and resistance against pathogens. Furthermore, we examined gene expression changes in fruits following inoculation with Colletotrichum in a resistant cultivar, which revealed an enrichment of significantly differentially expressed genes associated with certain specialized metabolic pathways (e.g. flavonol biosynthesis) and pathogen resistance. Using non-targeted metabolite profiling, we identified a flavonol glycoside with properties consistent with a quercetin rhamnoside as a compound exhibiting significant abundance differences among the most resistant and susceptible individuals from the genetic mapping population. Further analysis revealed that this compound exhibits significant abundance differences among the most resistant and susceptible individuals when analyzed as two groups. However, individuals within each group displayed considerable overlapping variation in this compound, suggesting that its abundance may only be partially associated with resistance against C. fioriniae. These findings should serve as a powerful resource that will enable breeding programs to more easily develop new cultivars with superior resistance to AFR and as the basis of future research studies.

Supplementary Table S2 from Hu/Mu ProtIn Oligonucleotide Microarray: Dual-Species Array for Profiling Protease and Protease Inhibitor Gene Expression in Tumors and Their Microenvironment

Supplementary Figure S1 from Hu/Mu ProtIn Oligonucleotide Microarray: Dual-Species Array for Profiling Protease and Protease Inhibitor Gene Expression in Tumors and Their Microenvironment

Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s, respectively, and in part owing to their flavors and health-promoting benefits are now cultivated and consumed worldwide. The industry continues to face a wide variety of production challenges (e.g. disease pressures) as well as a demand for higher-yielding cultivars with improved fruit quality characteristics. Unfortunately, molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value crops. Here, we describe the construction and analysis of the first pangenome for both blueberry and cranberry. Our analysis of these pangenomes revealed both crops exhibit great genetic diversity, including the presence-absence variation of 48.4% genes in highbush blueberry and 47.0% genes in cranberry. Auxiliary genes, those not shared by all cultivars, are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites, including compounds previously associated with improving fruit quality traits. The discovery of thousands of genes, not present in the previous reference genomes for blueberry and cranberry, will serve as the basis of future research and as potential targets for future breeding efforts. The pangenome, as a multiple-sequence alignment, as well as individual annotated genomes, are publicly available for analysis on the Genome Database for Vaccinium - a curated and integrated web-based relational database. Lastly, the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.

The genus Vaccinium L. (Ericaceae) contains premium berryfruit crops, including blueberry, cranberry, bilberry, and lingonberry. Consumption of Vaccinium berries is strongly associated with various potential health benefits, many of which are attributed to the relatively high concentrations of flavonoids, including the anthocyanins that provide the attractive red and blue berry colors. Because these phytochemicals are increasingly appealing to consumers, they have become a crop breeding target. There has been substantial recent progress in Vaccinium genomics and genetics together with new functional data on the transcriptional regulation of flavonoids. This is helping to unravel the developmental control of flavonoids and identify genetic regions and genes that can be selected for to further improve Vaccinium crops and advance our understanding of flavonoid regulation and biosynthesis across a broader range of fruit crops. In this update we consider the recent progress in understanding flavonoid regulation in fruit crops, using Vaccinium as an example and highlighting the significant gains in both genomic tools and functional analysis.

Teleost fishes, which are the largest and most diverse group of living vertebrates, have a rich history of ancient and recent polyploidy. Previous studies of allotetraploid common carp and goldfish (cyprinids) reported a dominant subgenome, which is more expressed and exhibits biased gene retention. However, the underlying mechanisms contributing to observed ‘subgenome dominance’ remains poorly understood. Here we report high-quality genomes of twenty-one cyprinids to investigate the origin and subsequent subgenome evolution patterns following three independent allopolyploidy events. We identify the closest extant relatives of the diploid progenitor species, investigate genetic and epigenetic differences among subgenomes, and conclude that observed subgenome dominance patterns are likely due to a combination of maternal dominance and transposable element densities in each polyploid. These findings provide an important foundation to understanding subgenome dominance patterns observed in teleost fishes, and ultimately the role of polyploidy in contributing to evolutionary innovations.

Summary Understanding chromosome recombination behavior in polyploidy species is key to advancing genetic discoveries. In blueberry, a tetraploid species, the line of evidences about its genetic behavior still remain poorly understood, owing to the inter‐specific, and inter‐ploidy admixture of its genome and lack of in depth genome‐wide inheritance and comparative structural studies. Here we describe a new high‐quality, phased, chromosome‐scale genome of a diploid blueberry, clone W85. The genome was integrated with cytogenetics and high‐density, genetic maps representing six tetraploid blueberry cultivars, harboring different levels of wild genome admixture, to uncover recombination behavior and structural genome divergence across tetraploid and wild diploid species. Analysis of chromosome inheritance and pairing demonstrated that tetraploid blueberry behaves as an autotetraploid with tetrasomic inheritance. Comparative analysis demonstrated the presence of a reciprocal, heterozygous, translocation spanning one homolog of chr‐6 and one of chr‐10 in the cultivar Draper. The translocation affects pairing and recombination of chromosomes 6 and 10. Besides the translocation detected in Draper, no other structural genomic divergences were detected across tetraploid cultivars and highly inter‐crossable wild diploid species. These findings and resources will facilitate new genetic and comparative genomic studies in Vaccinium and the development of genomic assisted selection strategy for this crop.

Rice (Oryza sativa) was domesticated around 10,000 years ago and has developed into a staple for half of humanity. The crop evolved and is currently grown in stably wet and intermittently dry agro-ecosystems, but patterns of adaptation to differences in water availability remain poorly understood. While previous field studies have evaluated plant developmental adaptations to water deficit, adaptive variation in functional and hydraulic components, particularly in relation to gene expression, has received less attention. Here, we take an evolutionary systems biology approach to characterize adaptive drought resistance traits across roots and shoots. We find that rice harbors heritable variation in molecular, physiological, and morphological traits that is linked to higher fitness under drought. We identify modules of co-expressed genes that are associated with adaptive drought avoidance and tolerance mechanisms. These expression modules showed evidence of polygenic adaptation in rice subgroups harboring accessions that evolved in drought-prone agro-ecosystems. Fitness-linked expression patterns allowed us to identify the drought-adaptive nature of optimizing photosynthesis and interactions with arbuscular mycorrhizal fungi. Taken together, our study provides an unprecedented, integrative view of rice adaptation to water-limited field conditions.

Hybridization generates inter-genomic interactions, which may result in unique traits not seen in either parent species. Here we explore the genetic basis of both carotenoid and anthocyanin floral pigmentation in hybrids between monkeyflower species Mimulus cupreus and M. luteus var. variegatus. Mimulus cupreus has abundant yellow carotenoid pigmentation in its petal lobes, while M. l. variegatus has a derived reduction in carotenoid intensity. Thus, as expected, carotenoid intensity segregates in an F2 hybrid population. More surprisingly, both species appear to have petal lobes solidly and identically covered in magenta anthocyanin pigment (which, when overlaid on the bright yellow carotenoid background, leads to an orange color in M. cupreus ), yet F1 and F2 hybrids exhibit novel and complex spatial patterns of anthocyanin spotting. A rare yellow morph of M. cupreus , which lacks petal anthocyanins, also generates spatially patterned offspring when hybridized with M. l. variegatus . We use this cross, together with newly developed high-quality genome assembly of M. l. luteus and image analysis tools, to investigate the genetic architecture of color and pattern variation in an F2 hybrid population. We report a single QTL, containing the Beta-carotene hydroxylase ( BCH ) gene, associated with the non-patterned carotenoid reduction in M. l. variegatus . HPLC shows that relative beta-carotene abundance differs between dark yellow and light yellow petals, supporting a causal role for BCH . The presence versus absence of petal lobe anthocyanin segregates in a 3:1 ratio, and we report (as expected) an associated QTL encompassing the anthocyanin activator MYB5a/NEGAN which has previously been shown to be both necessary and sufficient to activate petal lobe anthocyanins in M. l. variegatus . Anthocyanin patterning was more complex, with seven QTLs associated with five quantitative patterning traits on the upper petals; 11 on the lower petals; and three qualitative whole-flower patterning traits. Although power was too limited to effectively test for epistatic interactions in this cross, the QTLs provide candidate genomic regions for further investigating the molecular mechanisms of spatially complex floral color patterning, and multiple candidate genes are identified including anthocyanin activators and an anthocyanin repressor. ### Competing Interest Statement The authors have declared no competing interest.

Background Plant genomes encode transcripts that require spatio-temporal regulation for proper cellular function, and a large fraction of the regulators can be found in intergenic regions. In animals, distal intergenic regions described as enhancer regions are actively transcribed as enhancer RNAs (eRNAs); the existence of eRNAs in plants has only been fairly recently documented. In this study, we evaluated with high sensitivity the synthesis of eRNAs that arise at genomic elements both distal and proximal to genes by combining PRO-seq with chromatin accessibility, histone modification, and methylation profiles in rice. Results We found that regions defined as transcribed intergenic regions are widespread in the rice genome, and many likely harbor transcribed regulatory elements. In addition to displaying evidence of selective constraint, the presence of these transcribed regulatory elements are correlated with an increase in nearby gene expression. We further identified molecular interactions between genic regions and intergenic transcribed regulatory elements using 3D chromosomal contact data, and found that these interactions were both associated with eQTLs as well as promoting transcription. We also compared the profile of accessible chromatin regions to our identified transcribed regulatory elements, and found less overlap than expected. Finally, we also observed that transcribed intergenic regions that overlapped partially or entirely with repetitive elements had a propensity to be enriched for cytosine methylation, and were likely involved in TE silencing rather than promoting gene transcription. Conclusion The characterization of eRNAs in the rice genome reveals that many share features of enhancers and are associated with transcription regulation, which could make them compelling candidate enhancer elements.

Plastic phenotypic responses to environmental change are common, yet we lack a clear understanding of the fitness consequences of these plastic responses. Here, we use the evolution of herbicide resistance in the common morning glory (Ipomoea purpurea) as a model for understanding the relative importance of adaptive and maladaptive gene expression responses to herbicide. Specifically, we compare leaf gene expression changes caused by herbicide to the expression changes that evolve in response to artificial selection for herbicide resistance. We identify a number of genes that show plastic and evolved responses to herbicide and find that for the majority of genes with both plastic and evolved responses, plastic responses appear to be adaptive. We also find that selection for herbicide response increases gene expression plasticity. Overall, these results show the importance of adaptive plasticity for herbicide resistance in a common weed and that expression changes in response to strong environmental change can be adaptive.

Fragaria vesca is one of the putative diploid progenitors and donor of subgenome A in the octoploid genome of the economically important cultivated strawberry (Fragaria x ananassa). With its small genome size, short generation time, and wellestablished transformation system, F. vesca is an ideal model species for Fragaria and other rosaceous crops. The F. vesca genome was first sequenced in 2011 and since then, with the availability of other molecular genetics and genomic resources, the assembly and annotation of the draft genome were further improved. The F. vesca draft genome has been an invaluable resource to the strawberry research community, with numerous studies using it as reference genome to identify candidate genes related to agronomically important traits. It has led to the generation of a 90 K array, metabolic pathways database, and various other new genetic resources. The strawberry genome also has been used in comparative genomics studies that elucidated the relationship among members of the Rosaceae family and identified genes and genomic signals across several rosaceous species. Altogether, the discoveries made with this genome will provide potential ways to improve cultivated strawberry and expand on our understanding of the Rosaceae family.