Graph pangenome advances genetic discoveries and the improvement of eggplant

Beyond single nucleotide polymorphisms (SNPs), gene presence/absence variation (PAV) plays a crucial role in elucidating species’ genetic diversity, uncovering the genetic basis of key traits, and advancing molecular marker-assisted breeding in plants. In this study, we constructed a pangenome of Liriodendron based on 24 accessions. Comparative analysis with the reference genome revealed 116 Mb of non-reference sequences and obtained 32,773 genes, including 3,558 novel genes. We subsequently employed resequencing data from 247 Liriodendron genotypes to identify PAVs, comprising 13,779 core genes and 18,179 dispensable genes. To further assess PAV applicability, a genome-wide association study (GWAS) was conducted to link gene PAVs with growth traits in hybrid Liriodendron, and identified 14 candidate genes associated with these growth traits above. Additionally, gene PAVs appeared to predominantly contribute to heterosis in growth traits, displaying a dominant expression pattern when comparing leaf, shoot, and phloem tissues of strong and weak heterotic combinations. Additionally, two key candidate genes, Litul.02G164100 and Litul.01G057400, exhibit high parental expression patterns consistent with hybrid vigor in strong heterotic combinations of leaf and shoot tissues. Altogether, this study expands the Liriodendron genomic dataset, identifies candidate genes linked to growth traits, and provides insights into their heterotic mechanisms in hybrid Liriodendron.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12870-025-07109-1.

High-quality genome assembly and pan-genome studies facilitate genetic discovery in mung bean and its improvement

Eggplant (Solanum melongena) is one of the widely known vegetables of the Solanaceae family, and is derived from the wild African species, Solanum incanum. They were domesticated in Southeast Asia, particularly in Northeast India and Southeast China, more than 2000 years ago. The study aims to influence of post-emergence herbicides and rates on the growth and yield of eggplant in Akwa Ibom State, Nigeria. A field experiment was conducted at Akwa Ibom State University Teaching and Research Farm, Obio Akpa Campus in 2023 to assess the influence of post-emergence herbicides and rates on the growth and yield of eggplant (Solanum melongena L.) in Obio Akpa. The experiment was laid out in a randomised complete block design with split plot arrangement and replicated four times. The main treatments were 2 types of herbicides Starforce 150 EC (fluazifop-P-butyl) and Bentazone-3(1-methlethyl)-1H-2,1,3-benzothiadiazin-4(3H)-one-2,2-dioxide), while the sub-treatments were 4 rates of application (1,2,3 kg a.i/ha and a control plot of no herbicide application). Data were taken on plant height(cm), number of branches, leaf area index, number of fruits per plant, length of fruit per plant(cm), fruit girth(cm), weight of fruits per plant(kg) and fruit yield (t/ha). Bentazone recorded stunted growth and the lowest fruit yield, with more yield reduction as the rate of application was increased, while Starforce showed the best growth and yield attributes. Similarly, application of 2.0 kga.i/ha favoured the growth and yield of eggplant across herbicides. To improve yield in eggplant production, proper selection of post-emergence herbicides should be one of the criteria for effective weed control despite other constraints facing its production. However, the interaction of herbicide type and rates showed Starforce at 2.0 kga.i/ha with the best growth and yield of 15.68t/ha and it is therefore recommended for weed control in eggplant production in the study area.

Rice is one of the most important staple crops in the world; therefore, the improvement of rice holds great significance for enhancing agricultural production and addressing food security challenges. Although there have been numerous studies on the role of single-nucleotide polymorphisms (SNPs) in rice improvement with the development of next-generation sequencing technologies, research on the role of presence/absence variations (PAVs) in the improvement of rice is limited. In particular, there is a scarcity of studies exploring the traits and genes that may be affected by PAVs in rice. Here, we extracted PAVs utilizing resequencing data from 148 improved rice varieties distributed in Asia. We detected a total of 33,220 PAVs and found that the number of variations decreased gradually as the length of the PAVs increased. The number of PAVs was the highest on chromosome 1. Furthermore, we identified a 6 Mb hotspot region on chromosome 11 containing 1091 PAVs in which there were 29 genes related to defense responses. By conducting a genome-wide association study (GWAS) using PAV variation data and phenotypic data for five traits (flowering time, plant height, flag leaf length, flag leaf width, and panicle number) across all materials, we identified 186 significantly associated PAVs involving 20 cloned genes. A haplotype analysis and expression analysis of candidate genes revealed that important genes might be affected by PAVs, such as the flowering time gene OsSFL1 and the flag leaf width gene NAL1. Our work investigated the pattern in PAVs and explored important PAV key functional genes associated with agronomic traits. Consequently, these results provide potential and exploitable genetic resources for rice breeding.

Eggplant (Solanum melongena) is one of the four most important Solanaceous crops, widely cultivated and consumed in Asia, the Mediterranean basin, and Southeast Europe. We studied the Genome-wide association (GWA) of historical genebank phenotypic data on a genotyped worldwide collection of 3,449 eggplant accessions. Overall, 334 significant associations for key agronomic traits were detected. Significant correlations were obtained between different types of phenotypic data, some of which were not obvious, such as between fruit size/yield and fruit color components, suggesting simultaneous anthropic selection for genetically unrelated traits. Anthropic selection of traits like leaf prickles, fruit color, and yield, acted on distinct genomic regions in the two domestication centers (India and Southeast Asia), further confirming the multiple domestication of eggplant. To discriminate anthropic from environmental selection in domestication centers, we conducted a Genotype-Environment Association (GEA) on a subset of georeferenced accessions from the Indian subcontinent. The population structure in this area revealed four genetic clusters, corresponding to a latitudinal gradient, and environmental factors explained 31% of the population structure when the effect of spatial distances was removed. GEA and outlier association (OA) identified 305 candidate regions under environmental selection, containing genes for abiotic stress responses, plant development, and flowering transition. Finally, in the Indian domestication center anthropic and environmental selection acted largely independently, and on different genomic regions. These data allow a better understanding of the different effects of environmental and anthropic selection during domestication of a crop, and the different world regions where some traits were initially selected by humans.

Gene presence/absence variation in Mytilus galloprovincialis and its implications in gene expression and adaptation

Rice is a high-silica (SiO2·nH2O) accumulator. Silicon (Si) is designated as a beneficial element associated with multiple positive effects on crops. However, the presence of high silica content is detrimental to rice straw management, hampering its use as animal feed and as raw material in multiple industries. Rice straw management is a serious concern in north-western India, and it is eventually burned in situ by farmers, contributing to air pollution. A practical solution could lie in reducing the silica content in rice while also attaining sound plant growth. A set of 258 Oryza nivara accessions along with 25 cultivated varieties of Oryza sativa was used to assess the variation in straw silica content using the molybdenum blue colorimetry method. A large continuous variation was observed for straw silica content in O. nivara accessions, ranging from 5.08% to 16%, while it varied from 6.18% to 15.81% in the cultivated varieties. The O. nivara accessions containing 43%–54% lower straw silica content than the currently prominent cultivated varieties in the region were identified. A set of 22,528 high-quality single nucleotide polymorphisms (SNPs) among 258 O. nivara accessions was used for estimating population structure and genome-wide association studies (GWAS). A weak population structure with 59% admixtures was identified among O. nivara accessions. Further, multi-locus GWAS revealed the presence of 14 marker-trait associations (MTAs) for straw silica content, with six of them co-localizing with previously reported quantitative trait loci (QTL). Twelve out of 14 MTAs showed statistically significant allelic differences. Thorough candidate gene analyses revealed the presence of promising candidate genes, including those encoding the ATP-binding cassette (ABC) transporter, Casparian thickening, multi-drug and toxin extrusion (MATE) protein, F-box, and MYB-transcription factors. Besides, ortho-QTLs among rice and maize genomes were identified, which could open ways for further genetic analysis of this trait. The findings of the study could aid in further understanding and characterizing genes for Si transport and regulation in the plant body. The donors carrying the alleles for lower straw silica content can be used in further marker-assisted breeding programs to develop rice varieties with lower silica content and higher yield potential.

Potato (Solanum sp., family Solanaceae) is the most important noncereal food crop globally. It has over 100 wild relatives in the Solanum section Petota, which features species with both sexual and asexual reproduction and varying ploidy levels. A pangenome of Solanum section Petota composed of 296 accessions was constructed including diploids and polyploids compared via presence/absence variation (PAV). The Petota core (genes shared by at least 97% of the accessions) and shell genomes (shared by 3 to 97%) are enriched in basic molecular and cellular functions, while the cloud genome (genes present in less than 3% of the member accessions) showed enrichment in transposable elements (TEs). Comparison of PAV in domesticated vs. wild accessions was made, and a phylogenetic tree was constructed based on PAVs, grouping accessions into different clades, similar to previous phylogenies produced using DNA markers. A cladewise pangenome approach identified abiotic stress response among the core genes in clade 1+2 and clade 3, and flowering/tuberization among the core genes in clade 4. The TE content differed between the clades, with clade 1+2, which is composed of species from North and Central America with reproductive isolation from species in other clades, having much lower TE content compared to other clades. In contrast, accessions with in vitro propagation history were identified and found to have high levels of TEs. Results indicate a role for TEs in adaptation to new environments, both natural and artificial, for Solanum section Petota.

Cannabis sativa is a crop which has been cultivated since ancient times, with important cultural and industrial value. Due to its substantial economic impact, cannabis has attracted widespread scientific attention. A pan-genome is a significant tool for breeding, because it provides a comprehensive representation of genetic diversity. To provide a valuable tool for Cannabis breeding, we constructed a Cannabis pan-genome based on 113 accessions. A total of 24,679,380 bp of non-reference-genome sequences were assembled, identifying 1313 protein-coding genes. Using pan-genome analyses, a total of 32,428 gene presence/absence variations (PAVs) were obtained, and gene loss was recovered during the domestication of Cannabis. By partitioning the pan-genome using PAVs, a total of 23,309 core genes were identified, accounting for 71.88% of all genes in the pan-genome. In particular, there were 7148 flexible genes, making up 22.05% of the pan-genome. The flexible genes were associated with adaptive traits, including stress resistance and disease resistance in Cannabis. Population genetic analysis presented gene distribution, gene flow, and gene specificity on a pan-genome level. These results provide important genetic basis, functional genes, and guidance for Cannabis breeding.

Effect of NPK Mutiara and Cow Manure Fertilizers on the Growth and Yield of Eggplant ( Solanum melongena L.) Objective of the research was (1) to study the effect of NPK Mutiara and cow manure fertilizers, as well as their interaction on the growth and yield of purple eggplant; and (2) to find out the proper NPK Mutiara dan cow manure fertilizers dosage that affect high yield. The research was carried out in Melapeh Baru Village, Linggung Bigung Sub Disctrict of West Kutai District, East Kalimantan Province. It lasted for four months (February 2013 to May 2013). The Randomised Completely Block Design was employed for this research with factorial 4 x 4 and 3 replications. The first factor was NPK Mutiara fertilizer (M), consisted of 4 levels: no NPK Mutiara application (m0), 20 gr per plant (m1), 40 gr per plant (m2) ,and 60gr per plant(m3). And the second factor was cow manure fertilizer (P) consisted of 3 levels : no NPK Pelangi application (p0), 500 gr per plant(p1), 750gr per plant (p2) ,and1000 gr per plant (p3). Results of the research indicated that: The application of NPK Mutiara fertilizer affected significantly on plant height at 30 and 45 days after sowing, number of fruits per plant, length of fruit, heavy fruit per crop, and weight per piece. The highest heavy fruit per crop was attained on 20 gr per plant NPK Mutiara application with 1587,78 gr per plant, meanwhile the lowest one was found on no NPK Mutiara application with only 825 gr per plant. The application of cow manure fertilizer affected very significantly on plant height at 15, 30, and 45 days after sowing, number of fruits per plant, length of fruit, heavy fruit per crop, and weight per piece. The highest production of heavy fruit per crop was attained on 500 gr per plant cow manure application with 1644 gr per plant, meanwhile the lowest one was found on no cow manure application with only 425,16 gr per plant; and The interaction effect between NPK Mutiara and cow manure fertilizers application was significant on number of fruits per plant, length of fruit, heavy fruit per crop, and weight per piece, and not significant on plant height at 15 days after sowing, and fruit diameter.

Eggplant relatives as sources of variation for developing new rootstocks: Effects of grafting on eggplant yield and fruit apparent quality and composition

No Evidence in a Large UK Collection for Celiac Disease Risk Variants Reported by a Spanish Study

Hypomesus nipponensis a commercially valuable fish within the Osmeriformes order, is naturally found in northeastern Asia and has been extensively introduced for commercial purposes across eastern Asia. To investigate the taxonomic status and evolutionary history of Hypomesus nipponensis within the Osmeridae family, we first performed a de novo genome assembly using PacBio HiFi reads and CLR (Continuous Long Read) reads. Subsequently, we leveraged synteny information from closely related species to further refine the assembly and construct a chromosome-level genome. The final assembly spans 507.8 Mb, with a scaffold N50 of 20Mb, achieving chromosome-level contiguity. It comprises 164Mb of repetitive sequences and encodes 27,876 protein-coding genes. Compared to previous assembly, the H. nipponensis genome is notably more contiguous and complete. Notably, it contains an unusually high proportion of tandem repeats, which likely contributed to the assembly challenges encountered in earlier efforts. We also observed the transposons of H. nipponensis have expanded significantly in recent times, and paralogous gene families have expanded during the same period. Our analysis estimates that H. nipponensis, Osmerus eperlanus, and Hypomesus transpacificus diverged from a common ancestor approximately 24.1 million years ago, with significant chromosomal segment recombination events occurring during their divergence. Additionally, we compared the genomes of O. eperlanus and Hypomesus and found that most of the genes in the Presence/Absence Variants (PAVs) of O. eperlanus were associated with immune response. Our efforts significantly enhance the genome's integrity and continuity for this ecologically and commercially important fish, providing a chromosome-level genome draft that supports fundamental biological research while offering insights into the evolutionary relationships and genomic diversity within the Osmeriformes order. This advancement has profound implications for understanding the evolutionary history and adaptive strategies of H. nipponensis.

Presence-absence variations (PAVs) are important structural variations, wherein a genomic segment containing one or more genes is present in some individuals but absent in others. While PAVs have been extensively studied in plants, research in cattle remains limited. This study identified PAVs in 173 Holstein bulls using whole-genome sequencing data and assessed their associations with 46 economically important traits. Out of 28,772 cattle genes (from the longest transcripts), a total of 26,979 (93.77%) core genes were identified (present in all individuals), while variable genes included 928 softcore (present in 95-99% of individuals), 494 shell (present in 5-94%), and 371 cloud genes (present in <5%). Cloud genes were enriched in functions associated with hormonal and antimicrobial activities, while shell genes were enriched in immune functions. PAV-based genome-wide association studies identified associations between gene PAVs and 16 traits including milk, fat, and protein yields, as well as traits related to health and reproduction. Associations were found on multiple chromosomes, illustrating important associations on cattle chromosomes 7 and 15, involving olfactory receptor and immune-related genes, respectively. By examining the PAVs at the population level, the results of this research provided crucial insights into the genetic structures underlying the complex traits of Holstein cattle.

Genome-wide presence/absence variation discovery and its application in Peach (Prunus persica)