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Fertility is known to be negatively affected by heat stress. Our aim was to evaluate the impact of heat stress on estimated breeding values for conception rate (CR) for Holstein cattle in the Netherlands, by modeling sire breeding values for CR within each parity as a function of THI, using a broken stick random regression model. Our results showed a clear reduction in average CR at THI levels of 70 of up to 15% for parities 1 through 3, starting after a THI threshold of 60, while no clear reduction in CR was observed for parity 0. The broken stick model estimated 2 breeding values for each sire, based on information of daughters experiencing different THI levels at the time of insemination. The first breeding value modeled the intercept, i.e., the baseline breeding value at THI values below the identified threshold, while the second breeding value modeled the slope, which reflects the change in breeding value with changes in THI above the threshold. The results revealed a clear pattern of increased genetic variance and heritability at higher THI values for parities 1 through 3, while the random regression was not significant for parity 0. Across parities 1 through 3, estimated genetic correlations between CR at THI values of 60 and 65 ranged from 0.93 to 0.97, and between THI values of 60 and 70 ranged from 0.79 to 0.88. This suggested some meaningful re-ranking between THI 60 and 70, while selection at THI values below 60 should still improve CR at high THI. In line with previously reported genetic correlations, CR in maiden heifers is clearly different from CR in lactating cows. For lactating cows, a high genetic correlation (between 0.88 and 0.96) was found between the intercepts in the different parities. Genetic correlations between the slopes suggested that the genetic component of heat stress for CR is most similar between parities 2 and 3, and between parities 1 and 2, but quite different between parities 1 and 3.

Extending functional longevity in high-producing dairy cows is important for improving economic efficiency, environmental sustainability, and animal welfare in modern dairy systems. This longitudinal controlled cohort study investigated the phenotypic expression of genomic functional longevity estimated breeding values (GFLEBV) in a stratified cohort of Holstein-Friesian cows managed under uniform conditions for more than 10 yr. Pregnant heifers were genomically classified into High-GFL_EBV (n = 18) and Low-GFL_EBV (n = 18) groups while being matched for genomic milk production estimated breeding values (GMPEBV), thereby minimizing confounding by production potential. Genomic stratification generated a 24.7-point difference in functional-longevity index between groups, corresponding to approximately 2.1 genetic standard deviations (High-GFL_EBV: 120.9 ± 6.2; Low-GFL_EBV: 96.2 ± 5.91), whereas genomic milk-production merit was comparable. Lifetime phenotypes included milk yield and milk composition traits derived from monthly standard milk performance testing, as well as reproductive performance, survival time, herd retention, and detailed veterinary diagnoses. Milk production trajectories were broadly comparable between groups across parities, indicating effective separation of functional longevity from production intensity. Across months in milk and parities 1 to 5, milk yield, energy-corrected milk, milk fat traits, lactose traits, and milk urea nitrogen showed no meaningful group differences. Milk protein percentage was greater in High-GFL_EBV cows, whereas protein yield remained similar. In contrast, somatic cell count was greater in Low-GFL_EBV cows, consistent with higher udder inflammatory burden despite similar overall lactation output. Age at first calving, lactation length, calf birth weight, and calf sex distribution were also comparable between groups, whereas High-GFL_EBV cows exhibited shorter calving intervals, indicating more favorable reproductive efficiency under similar production demands. Despite similar milk output, Low-GFL_EBV cows showed a consistently greater weighted disease burden beginning in lactation 1, characterized by mastitis clustering, transition-related disorders, and greater burdens of ketosis, digestive disorders, and infectious claw disease. This pattern progressed toward greater claw-related multimorbidity in lactation 2 and a more pronounced lameness-reproductive burden in lactation 3. Herd retention remained similar after lactation 1 (18 vs. 17 cows) but diverged thereafter; by lactations 2 to 6, the numbers of cows remaining were 18 versus 14, 17 versus 11, 14 versus 7, 10 versus 4, and 8 versus 2 for High- and Low-GFL_EBV groups, respectively. No Low-GFL_EBV cows remained beyond lactation 6, whereas High-GFL_EBV cows persisted into lactations 7 to 9. Survival analysis showed sustained separation of survival curves and longer median survival in High-GFL_EBV cows. Collectively, these findings provide long-term phenotypic evidence that GFLEBV is associated with more favorable health, reproductive, and survival outcomes under comparable milk production potential, supporting its relevance in breeding programs targeting improved lifetime performance.

The Pacific oyster (Magallana gigas) is a widely cultivated species, and its commercial value has been significantly enhanced by the widespread adoption of triploid oysters. Since triploid offspring inherit two chromosome sets from tetraploid males, this suggests that genetic improvement of tetraploid oysters is essential. The induction of the dark-shelled tetraploid 'Haida No. 3' line from selected diploid lines of Pacific oysters has been achieved. However, the genetic parameters of growth and shell color traits in this line remain unclear. This study involved analyzing the genetic parameters of 42 tetraploid full-sibling families using the restricted maximum-likelihood (REML) method, with a tetraploid inverse additive relationship matrix constructed by the polyAinv package. These results indicated that the heritability of growth traits was moderate, with values ranging from 0.19 ± 0.05 for shell width to 0.45 ± 0.09 for whole weight. For shell color traits, the heritability values for color L*, color a*, color b*, and ΔE were 0.42 ± 0.09, 0.46 ± 0.09, 0.55 ± 0.10, and 0.63 ± 0.12, respectively. The genetic correlations ([Formula: see text]) between color L* and growth traits (excluding shell width) were moderate, ranging from 0.32 ± 0.15 to 0.42 ± 0.15. The low ΔE values observed across the tetraploid 'Haida No. 3' families indicate that the shell color purification has achieved the desired level of phenotypic consistency. Therefore, growth was identified as the primary breeding objective, with shell color regarded as secondary for the subsequent breeding program. The results provide useful information into selective breeding of fast-growing, black-shelled tetraploid oysters in aquaculture.

Understanding the agro-climatic structure of morphological diversity is essential for the effective utilization and improvement of drumstick (Moringa oleifera Lam.), a multipurpose tree species of high nutritional and economic value. The present study aimed to evaluate morphological diversity and phenotypic variation of M. oleifera across ten agro-climatic zones of Rajasthan, India, and to identify key traits and morphotypes relevant for breeding, conservation, and climate-resilient cultivation. A total of 367 accessions were characterized using 17 morphological traits, including eight quantitative and nine qualitative descriptors. Quantitative traits were analyzed using non-parametric statistics and Principal Component Analysis (PCA), while qualitative traits were evaluated through Multiple Correspondence Analysis (MCA). An integrated approach using Factor Analysis of Mixed Data (FAMD) was employed to assess overall variation, followed by hierarchical and FAMD-based clustering. Correlation analysis was conducted to identify relationships among traits. The results revealed significant variations among agro-climatic zones for all quantitative traits (Kruskal-Wallis, p&#x2009;<&#x2009;0.01), with moderate to high effect sizes (&#x3b5;&#xb2; = 0.07-0.26). PCA indicated that the first two components explained 56.9% of total variance, primarily driven by stem girth and leaf-related traits. MCA showed that qualitative variation was largely influenced by stem morphology, canopy size, and branching density. FAMD further confirmed the integration of qualitative and quantitative traits, with the first two dimensions explaining 56.4% of total variability. Correlation analysis demonstrated strong positive associations among leaf traits, indicating a coordinated leaf development system. Clustering analysis grouped the accessions into distinct morphotypes, with substantial overlap across agro-climatic zones, suggesting that morphological variation is governed by both environmental factors and inherent genetic diversity. Two major groups identified through FAMD represented broadly adapted and high growth morphotypes. From an applied perspective, accessions with larger canopy and higher leaf area are recommended for biomass-oriented breeding and cultivation in favourable environments, while stable, moderate-growth accessions are suitable for arid and semi-arid regions. The study also highlights leaf traits as reliable selection indices and emphasizes the need for stratified germplasm conservation across agro-climatic zones. This study provides a robust framework for understanding morphological diversity in M. oleifera and offers practical insights for its genetic improvement, conservation and climate-resilient utilization.

The Finnish Ayrshire cattle belong to the Nordic Red breeds. The basis of selection in Nordic Red breeds shifted from traditional pedigree-based breeding values to genomic breeding values between 2011 and 2014. Joint genetic evaluation and admixture among the Nordic Red breeds have led to the formation of a composite Nordic Red population; consequently, contemporary Finnish Ayrshire represents an admixed population. We identified recent selection signatures in the Finnish Ayrshire genome using two complementary approaches: the Hudson estimator of Wright's fixation index (FST) and generation proxy selection mapping (GPSM). Hudson FST quantifies population-differentiation between groups, whereas GPSM detects selection signatures within a single population by regressing birth year on SNP genotypes. The aim of this study was to identify temporal allele frequency changes in SNPs consistent with selection during the genomic era and to evaluate their associations with milk production and fertility traits in Finnish Ayrshire. Genotypes were available for 64,160 cows across 46,914 SNPs, and phenotypic data on milk production and fertility traits were available for 49,417 genotyped individuals. Based on Hudson FST, 56 SNPs showed genetic differentiation between cows selected using pedigree-based and genomic information. In addition, 54 SNPs exhibited temporal allele frequency changes consistent with selection according to GPSM. Overall, 11 SNPs were identified by both methods. Of the 54 SNPs, thirteen were associated with the interval from first to last insemination in Finnish Ayrshire heifers. These results suggest that a substantial proportion of SNPs exhibiting temporal allele frequency changes during genomic selection are associated with heifer fertility.

Streptococcus agalactiae infection remains a major constraint on the productivity of Nile tilapia (Oreochromis niloticus), a species of considerable economic importance in global aquaculture. Although selective breeding programs have successfully produced tilapia strains with enhanced resistance to this pathogen, the B cell-mediated immune mechanisms underlying this resistance remain unclear. In this study, we systematically investigated differences in IgM+ B cell mediated immune responses between S. agalactiae-resistant and susceptible Nile tilapia. Transcriptomic analysis of splenic leukocytes revealed that genes associated with immunoglobulin production and B cell differentiation were markedly upregulated in resistant tilapia following infection. Consistent with these findings, flow cytometry further demonstrated a more pronounced expansion of splenic IgM+ B cells in resistant tilapia, which was primarily driven by significantly increased proliferative activity. Importantly, this expansion coincided with elevated activation induced apoptosis, suggesting an accelerated B cell turnover that could facilitate the selection and maintenance of functionally competent cells during the immune response. Functionally, IgM+ B cells from resistant tilapia exhibited sustained enhancement of antigen processing capacity following infection. Meanwhile, macrophage-mediated phagocytosis of S. agalactiae increased progressively and became particularly evident at later stages of infection. Moreover, IgM+ B cells in resistant tilapia maintained relatively stable intracellular ROS levels, whereas susceptible tilapia exhibited persistent oxidative stress. Collectively, these findings indicate that resistance to S. agalactiae infection in Nile tilapia is closely associated with coordinated functional remodeling of IgM+ B cells, characterized by efficient proliferation, functional maturation, and stringent homeostatic regulation. This refined B cell-mediated immunity likely contributes to the effective pathogen clearance and provides an immunological basis for the evaluation and selective breeding of disease-resistant tilapia strains.

The present investigation was conducted during 2023-2025 to evaluate the performance and variability of ten genotypes along with the standard cultivar Allison for flowering, vegetative, fruit quality and biochemical traits. Significant differences among genotypes were observed for all studied parameters, indicating substantial genetic variability. UHF-9 recorded the longest flowering duration (24.44&#xa0;days), whereas Allison produced the highest number of flowers per shoot (42.78). Enhanced vegetative growth was observed in UHF-6, which exhibited maximum leaf area (227.23 cm2), while Allison recorded larger leaf dimensions. Fruit morphological evaluation revealed that Allison produced the longest fruits (91.57&#xa0;mm) with the highest fruit length/width ratio (1.807), whereas UHF-7 recorded maximum fruit weight (181.58&#xa0;g) and fruit width (61.58&#xa0;mm). Superior biochemical quality traits were observed in UHF-3 for total soluble solids (19.19&#xb0;B), UHF-6 for total sugars (7.55%) and UHF-5 for ascorbic acid (163.70&#xa0;mg/100&#xa0;g) and sugar-acid ratio (23.09). Genotypes UHF-7, UHF-8 and UHF-9 exhibited comparatively higher phenol and carotenoid contents, indicating enhanced antioxidant potential. Principal component analysis revealed that the first two principal components contributed 61.32 per cent and 20.68 per cent of the total variation, respectively, accounting for 82.00 per cent of the cumulative variability among genotypes. Hierarchical cluster analysis grouped the genotypes into distinct clusters according to flowering, vegetative, fruit and biochemical traits, demonstrating clear phenotypic divergence. Several genotypes, particularly UHF-5, UHF-6, UHF-7, UHF-8 and UHF-9, exhibited performance comparable or superior to the standard cultivar Allison for important horticultural and nutritional attributes. The findings indicate the potential utility of these genotypes for varietal selection, quality improvement and future breeding programmes.

The Ariadne (ARI) gene family belongs to RBR-type E3 ubiquitin ligases and regulates plant growth, development, and abiotic stress responses. However, a systematic genome-wide analysis of the ARI family has not been reported in wheat. In this study, we identified 21 TaARI genes that were unevenly distributed on 12 chromosomes. The phylogenetic analysis showed that ARI proteins were divided into A, B, and C subfamilies. Most TaARIs existed in subfamilies A and B, and only TaARI7-D belonged to subfamilies C. TaARIs with closer phylogenetic relationships had similar gene structures and conserved motifs. Promoter cis-acting element analysis revealed that stress-responsive elements were the most abundant in the promoter of TaARIs. Expression profiling demonstrated that most TaARIs were preferentially expressed in roots, and induced by PEG-simulated drought or salt stress, with TaARI2, TaARI3, TaARI4, TaARI5 and TaARI6 as candidate stress regulators for drought and salt stresses. A total of 72 upstream transcription factors of TaARIs belonging to 24 transcription factor families were determined, with MYB-related, bZIP, and ERF transcription factors being the most abundant. Protein interaction prediction indicated that TaARIs interact with E3 ubiquitin-protein ligase RBX1 and ubiquitin-40&#xa0;S ribosomal protein S27a, suggesting that TaARIs might participate in the ubiquitin-proteasome pathway. Haplotype analysis suggested that TaARI6-D-Hap I could be a superior drought-resistant haplotype with higher gene expression and seedling survival under drought stress. In conclusion, our results provided crucial insights into the functions and molecular mechanisms of TaARI genes under drought and salt stress, and provided a gene resource for molecular breeding to stress&#x2011;resistant wheat varieties.

Plasma membrane (PM) H+-ATPases are pivotal for plant adaptation to abiotic stresses; however, the specific function of the rice (Oryza sativa L.) PM H+-ATPase isoform OSA2 in salt stress responses remains elusive. In this study, using the Zhonghua 11 (ZH11) cultivar, we created an OSA2 knockout mutant (osa2-9) via CRISPR/Cas9 technology and generated OSA2 overexpression lines (OSA2OE). Subcellular localization assays confirmed that OSA2 protein is specifically localized to the cell plasma membrane. Physiological and biochemical analyses under 150&#x202f;mM NaCl revealed that the survival rate of osa2-9 was significantly higher than that of OSA2OE, albeit slightly lower than the wild type (WT). Salt stress induced a marked elevation in catalase (CAT) and peroxidase (POD) activities in WT plants, effectively mitigating malondialdehyde (MDA) accumulation. Conversely, OSA2OE plants exhibited suppressed CAT activity, excessive MDA accumulation, and exacerbated oxidative damage. Furthermore, quantitative real-time PCR (qRT-PCR) demonstrated that OSA2 overexpression significantly repressed the transcription of salt tolerance- and reactive oxygen species (ROS) metabolism-related genes, such as OsHKT1 and OsodCc1, in the roots. Collectively, our findings identify OSA2 as a negative regulator that compromises salt tolerance in rice seedlings, likely by perturbing PM H+ transport and disrupting antioxidant homeostasis. This study provides a theoretical framework for elucidating the molecular mechanisms underlying rice salt tolerance and for the breeding of salt-resilient cultivars.

Human activities are intensifying heatwaves and droughts, threatening forest ecosystems worldwide. However, understanding intraspecific variation in physiological traits that confer resistance to hotter drought is critical for predicting tree responses to climate change. In Pinus taeda L., long-term geographic isolation across the Mississippi River Valley after the last glacial maximum has resulted in distinct population genetic structures, likely reflecting historical adaptation to contrasting climatic conditions in western and eastern refugia. However, it remains unclear whether contemporary populations retain meaningful variation in traits that confer tolerance to hotter and drier conditions, such as hydraulic vulnerability and water-use regulation, which are critical for predicting responses to future climate extremes. Here, in a common garden of adult P. taeda L. trees planted in 2010, we characterized intraspecific variability in 22 physiological traits related to resistance to hotter droughts across 10 provenances originating from either west or east of the Mississippi River Valley. Key traits included xylem vulnerability to embolism, leaf and bark residual conductance, and leaf turgor loss point. We used an integrated indicator, time to hydraulic failure (THF), predicted by a mechanistic hydraulic model, SurEau, to assess how trait combinations contribute to tree resistance to hotter droughts. While we hypothesized that western provenances would be more adapted to hotter drought, we found that THF was lower in western than eastern provenances. The THF values were negatively correlated with residual transpiration and leaf mass per area. These patterns suggest physiological differentiation between populations, although not one strictly determined by drought resistance alone. Overall, our findings demonstrate that intraspecific variation in physiological traits can inform forest management and breeding strategies, underscoring the complex interplay of hydraulic and residual transpiration traits in shaping drought resilience and emphasizing the need to integrate multiple physiological processes when predicting forest responses to climate change.

Expression of sugar-related genes downregulated while hormone-related genes upregulated during the later stages of fiber development is related to the superior fiber quality but low fiber yield of G. barbadense. Compared to Gossypium hirsutum, G. barbadense exhibits superior fiber quality but relatively lower fiber yield. Exploring the genetic basis of yield-related traits could facilitate yield improvement in G. barbadense. Here, we conducted a genome-wide association study (GWAS) on two yield components, boll weight and lint percentage, using 246 G. barbadense accessions. We identified a total of 272 main-effect quantitative trait loci (qtls) and 34 QTL-by-environment interaction loci (qtlEs) for these traits, among which 57 qtls and 3 qtlEs overlapped with previously reported loci. To explore the potential mechanism between yield and fiber quality, we extracted the genes located within these loci and compared their expression patterns between G. barbadense accessions with extreme differences in fiber quality or yield traits. Gene ontology analysis of differentially expressed genes revealed that sugar- and hormone-related genes were antagonistically expressed during the later stages of fiber development, correlating with high yield and superior fiber quality, respectively. Local association analysis further identified 67 candidate genes associated with the two yield components, 20 of which were located within two introgression segments (ISs) from G. hirsutum into G. barbadense. Among them, A10-1-Y IS reduced the yield of G. barbadense, while D08-1-Y IS increased the yield of G. barbadense. Finally, we demonstrated that two haplotypes of the gene GB_A06G0815 (encoding beta-galactosidase 1), GB_A06G0815C and GB_A06G0815-, with a 1-bp insertion/deletion of C/- in the 10th exon, were significantly associated with fiber yield. Overexpression of GB_A06G0815C in Arabidopsis resulted in longer roots, larger leaves, higher yield, and more vigorous growth and development compared to the control. Our findings provide novel insight into the negative correlation between fiber quality and yield traits and offer potential genetic loci for high-yield breeding in G. barbadense.

Potato is a critical staple crop, and enhancing its carotenoid content is a promising strategy to improve its nutritional value. However, the synergistic mechanisms underlying carotenoid accumulation, superior nutritional traits, and the role of the endophytic microbiome remain unclear. Using an integrated multi-omics strategy, we systematically analyzed two high-zeaxanthin/lutein hybrids and four commercial cultivars. The hybrids accumulated significantly higher levels of zeaxanthin, lutein, and minerals, while exhibiting superior processing traits (e.g., higher dry matter/starch, lower reducing sugars). Integrated metabolomic and transcriptomic profiling revealed a coordinated upregulation of carotenoid and phenylpropanoid biosynthesis, alongside enrichment of stress-responsive phenolic acids. Notably, the endophytic microbiome in high-carotenoid tubers was distinct, dominated by Firmicutes and Proteobacteria, with genera like Bacillus and Latilactobacillus positively correlating with carotenoid content. Weighted gene co-expression network analysis identified a core regulatory module containing key genes (e.g., CCD4, BCH2) and novel transcription factors. Our findings elucidate a synergistic network linking metabolism, gene regulation, and the endophytic microbiome that collectively is associated with carotenoid accumulation and tuber quality. This provides critical targets for breeding nutritionally enhanced potatoes with desirable agronomic performance, supporting nutritional security and sustainable agriculture.

Cucumber is a globally significant vegetable crop whose production and market value are affected by fruit quality and resilience to diverse environmental stressors. Despite the identification of numerous Quantitative Trait Loci (QTL) over the last two decades, their direct application in breeding has been hindered by inconsistent genomic positions and broad confidence intervals. In this study, we conducted a comprehensive Meta-QTL (mQTL) analysis by integrating 647 initial QTLs from 40 independent studies published between 2003 and 2024. Using a high-density consensus map containing 9,299 markers, we projected 531 QTLs, identifying 38 robust mQTLs associated with fruit quality, biotic and abiotic stress tolerance. The identified mQTLs exhibited a significant reduction in the average confidence interval (CI) by 5.3-fold, compared to the average CI of the original QTLs and phenotypic variance explained values reaching up to 49.81% (mQTL 6.8). Our results identifying specific genomic hotspots on chromosomes 1, 3, 5, and 6 that harbor high-confidence candidate genes responsible for stress tolerance and fruit quality. Comparative analysis with seven independent genome-wide association studies validated 16 mQTL regions, confirming their stability across diverse genetic backgrounds. Biotic stress resilience was linked to immune regulators such as LRK10L2 and MLO-like protein 12, while abiotic stress tolerance was anchored by genes like NCED5 (cold), ClpB1 (heat), and MYB44-like (waterlogging). Furthermore, we identified key drivers of fruit quality, including Expansin-A4 and CNR2 for dimensions, CsWOX9 for epidermal spine initiation, and Hd3a for flowering phenology. Transcriptomic profiling provided robust expression support for these prioritized candidate genes within the target mQTL intervals. The markers linked to these genes serve as robust tools for marker-assisted selection and fine mapping, offering precise targets for the development of climate-resilient, high-quality cucumber cultivars.

The soybean plant (Glycine max L.) is an important crop for valuable food source because of its high levels of protein and oil, thus contributing greatly to a sustainable system for producing food through biological nitrogen fixation. Recent research supports the theory that the soybean-associated microbiome located in the rhizosphere is a crucial regulatory mechanism governing plant growth, nutrient acquisition, and stress tolerance. Additionally, advances in metagenomics, metatranscriptomics, metabolomics, and root exudate profiling via LC&#x2012;MS have shown that soybean roots alter the microbial communities found in their rhizosphere by utilizing dynamic chemical signaling and targeted microbial recruitment, thereby enhancing the ecological interpretation of the processes that drive microbiome assembly. Microbial consortia (AMF & PGPR) assess cycling through nutrients, phytohormones, suppressing diseases, as well as having a legacy effects on the productivity of agroecosystems. Factors such as plant genotype, physical and chemical soil properties, and environmental conditions greatly affect the assembly and functioning of the soybean microbiome, thus this is difficult to transfer this information to field applications. Unlike previous reviews focused primarily on biological nitrogen fixation, this review integrates recent advances in multi-omics technologies, species-level microbiome characterization, root exudate chemistry, microbiome-assisted breeding, and translational microbiome engineering approaches to provide a systems-level perspective of soybean-microbiome interactions. while also identifying significant knowledge gaps and future areas of research within this aspect of agriculture.

Bumblebees (Bombus spp.) are important pollinators that are widely used for greenhouse crop pollination and are produced annually by commercial breeding facilities. In this study, we used the commercially important bumblebee species Bombus terrestris Linnaeus (Hymenoptera: Apidae: Bombini) to evaluate the effects of artificial box stocking density on the reproductive performance of newly eclosed females under commercial rearing conditions. Newly eclosed gynes and workers were artificially held in separate wooden boxes at different stocking densities (1 to 150 individuals per box for gynes and 1 to 50 individuals per box for workers) before mating tests, ovarian development assessments, or oviposition observations. Higher box stocking density reduced mating success in both gynes and workers, whereas worker ovarian development and oviposition occurred earlier as worker box stocking density increased. At worker stocking densities of 30 individuals per box or higher, workers began to lay eggs on day 6, and oviposition was concentrated between days 6 and 9. These findings show that artificial box stocking density is an important management factor during commercial bumblebee rearing and can be adjusted according to whether the production goal is to maximize female mating success or promote earlier worker-derived male production.

Multi-environment genome-wide association study (GWAS) and haplotype analysis identified a height-reducing WAK4 (SETIT_033071mg) haplotype as a promising target for plant height improvement in foxtail millet. Plant height is pivotal for plant architecture, harvestability, and yield potential in foxtail millet (Setaria italica). Here, we evaluated plant height in 209 diverse Shanxi local foxtail millet landraces in three field environments in Jinzhong, Shanxi, during 2020-2022, and performed whole-genome resequencing of these accessions at a mean depth of approximately 38&#x2009;&#xd7;. After standard filtering, 833,157 high-quality single nucleotide polymorphisms (SNPs) were retained. Neighbor-joining and principal component analysis consistently resolved four genetic groups with minor differences in sample assignment. GWAS using EMMAX, complemented by MLMM, identified four loci associated with plant height, including two loci not previously reported. Comparative genomics with rice and Arabidopsis shortlisted ten candidate genes, among which SETIT_033071mg was prioritized for further haplotype analysis based on its genomic location and functional annotation. Haplotype analysis of SETIT_033071mg in our GWAS panel (209 accessions evaluated across three environments) and an expanded diversity panel (313 accessions evaluated across five field environments) resolved multiple major haplotypes, among which H2 was consistently associated with reduced plant height across environments. These findings refine the genomic basis of plant height in foxtail millet and provide useful targets for marker development in plant height-related breeding.

Sexual dimorphism in growth is a major factor affecting the economic efficiency of fish aquaculture; however, its molecular underpinnings remain incompletely elucidated. We combined comparative liver transcriptomics with genome-wide screening to identify growth-related genes in female and male S. hollandi. We identified 1063 differentially expressed genes (DEGs), with 869 being significantly upregulated in females. KEGG enrichment analysis revealed key growth-related pathways, including Growth hormone synthesis, secretion and action, mTOR, insulin and MAPK signaling pathway were significantly enriched. Furthermore, we identified seven core IGF system components at the genomic level: four ligands (igf1, igf2a, igf2b, igf3) and three receptors (igf1ra, igf1rb, igf2r). Phylogenetic and protein structure analyses indicated high conservation of these genes among teleosts. Multi-tissue expression profiling revealed marked tissue specificity and sexual dimorphism for several IGF members. Notably, hepatic expression levels of igf1, igf2a, igf2b, and igf1ra were significantly higher in females than in males. This expression pattern correlates with the faster female growth phenotype. Here, we present the first systematic characterization of the IGF/IGFR gene family in S. hollandi and based on comparative hepatic transcriptomics targeting growth-related pathways, suggesting that sexually dimorphic activity of the hepatic IGF system may serve as a central regulatory mechanism at the transcriptional level driving growth dimorphism. These findings offer novel theoretical insights and candidate genes for understanding the molecular mechanisms of sexual growth differences in fish and for advancing molecular breeding.

Sesame (Sesamum indicum L., 2n&#x2009;=&#x2009;26) is one of the oldest oilseed crops and is often called the 'queen of oilseeds' due to its high content of unsaturated fatty acids and natural antioxidants. Despite its long history, the origin and global spread of cultivated sesame remain unresolved. We assembled a telomere-to-telomere (T2T), high-quality reference genome of sesame (cv. Yuzhi11) to investigate sequence differences between genomes and its origin and the local adaptation evolution of flowering time (DF). We generated a 305&#x2009;Mb T2T sesame reference genome (cv. Yuzhi11) with >&#x2009;99.99% base-level accuracy, identifying 31&#x2009;063 protein-coding genes. Repetitive elements accounted for 52.03% of the genome. Population genomic analysis of 927 accessions from 14 regions identified four major groups. Integrative analyses of linkage disequilibrium decay (LD), nucleotide diversity (&#x3c0;), and fixation index (FST) support East Africa as the center of origin, with subsequent migration through the Middle East, to South Asia, South-East Asia, East Asia and ultimately to other parts of the world. Genome-wide association studies (GWAS) and selection scans identified 30 genes associated with flowering time. SiUBP16 is a candidate associated with 7.6% of DF variation. Early-flowering accessions carried up to 225 favourable alleles. A flowering time prediction model for high-latitude regions achieved 96% accuracy. We present a high-quality T2T reference genome for cultivated sesame, shedding light on its origin, evolutionary history, and regional flowering time adaptation. This genome insights valuable tools for breeding programs aimed at improving yield and environmental adaptation in sesame and related crops.