Search Results (281)

Peanut (Arachis hypogaea L.) is a globally important oilseed cash crop, yet its limited genetic diversity and unique reproductive biology present persistent challenges for conventional crossbreeding. Traditional breeding approaches are often time-consuming and inadequate, mitigating the pace of cultivar development. Essential for double fertilization and programmed cell death (PCD), DUF679 membrane proteins (DMPs) represent a membrane protein family unique to plants. In the present study, a comprehensive analysis of the DMP gene family in peanuts was conducted, which included the identification of 21 family members. Based on phylogenetic analysis, these genes were segregated into five distinct clades (I–V), with AhDMP8A, AhDMP8B, AhDMP9A, and AhDMP9B in clade IV exhibiting high homology with known haploid induction genes. These four candidates also displayed significantly elevated expression in floral tissues compared to other organs, supporting their candidacy for haploid induction in peanuts. Subcellular localization prediction, confirmed through co-localization assays, demonstrated that AhDMPs primarily localize to the plasma membrane, consistent with their proposed roles in the reproductive signaling process. Furthermore, chromosomal mapping and synteny analyses revealed that the expansion of the AhDMP gene family is largely driven by whole-genome duplication (WGD) and segmental duplication events, reflecting the evolutionary dynamics of the tetraploid peanut genome. Collectively, these findings establish a foundational understanding of the AhDMP gene family and highlight promising targets for future applications in haploid induction-based breeding strategies in peanuts. Full article

The combination of Chinsurah Boro II (BT)-type cytoplasmic male sterility (CMS) and Rf1, the main fertility restorer gene (Rf) for CMS-BT, has been extensively utilized for the production of three-line commercial japonica hybrid seeds. The identification of new Rf genes holds significance for the breeding of BT-type restorer lines, aiming to enhance the heterosis level of BT-type japonica hybrids. In the present study, ‘02428’, a wide-compatibility japonica variety, was observed to partially restore fertility to BT-type CMS lines. Genetic analysis revealed that ‘02428’ carries a dominant Rf gene, Rf21(t), responsible for the fertility restoration of BT-type CMS lines. Leveraging bulked segregant analysis (BSA) resequencing technology and molecular markers, the Rf21(t) locus was identified, and mapped within a candidate interval of 6–12.5 Mb on chromosome 2. Using the iso-cytoplasmic restorer populations, Rf21(t) was ultimately mapped to an interval of approximately 77 kb, encompassing 12 predicted genes, including LOC_Os02g17360, encoding a PPR-domain-containing protein and LOC_Os02g17380 (Rf2), a cloned Rf for Lead-rice-type CMS. A comparative sequence analysis, gene expression profiling and gene knockout experiments confirmed that LOC_Os02g17360 and LOC_Os02g17380 are the most likely candidates of Rf21(t). Furthermore, Rf21(t) showed the dosage effect on the fertility restoration of BT-type CMS lines. This newly identified Rf21(t) represents a valuable genetic resource for the breeding of BT-type japonica restorer lines. Our findings offer practical insights for breeders interested in advancing BT-type japonica hybrid development. Full article

Branching is a critical agronomic trait in flowering Chinese cabbage (Brassica rapa subsp. chinensis), influencing plant architecture and yield. In this study, there was a highly significant difference between CX010 (single primary rosette branches) and BCT18 (multiple primary rosette branches). Phenotypic analysis revealed significant differences in primary rosette branch numbers, with BCT18 showing up to 15 branches and CX010 displaying only one main stem branch. Genetic analysis indicated that branching was controlled by quantitative trait loci (QTL) with a normal distribution of branch numbers. Using bulked segregant analysis coupled with sequencing (BSA-seq), we identified a candidate interval of approximately 2.96 Mb on chromosome A07 linked to branching. Fine mapping narrowed this to a 172 kb region containing 29 genes, with BraA07g032600.3C (BrTCP1) as the most likely candidate. cDNA cloning of the BrTCP1 gene revealed several variations in BCT18 compared to CX010, including a 6 bp insertion, 10 SNPs, and two single-nucleotide deletions. Expression analysis indicated that BrTCP1 was highly expressed in the rosette stems of CX010 compared to BCT18, consistent with its role as a branching suppressor. The heterologous mutants in Arabidopsis confirmed the conserved role of BrTCP1 in branch inhibition. These findings reveal that BrTCP1 might be a key regulator of branching in flowering Chinese cabbage, providing insights into the molecular mechanisms underlying this trait and offering a framework for genetic improvement in Brassica crops. Full article

Growth traits are the most important economic traits in red tilapia (Oreochromis spp.) production, and are the main targets for its genetic improvement. Increasing salinity levels in the environment are affecting the growth, development, and molecular processes of aquatic animals. Red tilapia tolerates saline water to some degree. However, few credible genetic markers or potential genes are available for choosing fast-growth traits in salt-tolerant red tilapia. This work used genome-wide association study (GWAS) and RNA-sequencing (RNA-seq) to discover genes related to four growth traits in red tilapia cultured in saline water. Through genotyping, it was determined that 22 chromosomes have 12,776,921 high-quality single-nucleotide polymorphisms (SNPs). One significant SNP and eight suggestive SNPs were obtained, explaining 0.0019% to 0.3873% of phenotypic variance. A significant SNP peak associated with red tilapia growth traits was located on chr7 (chr7-47464467), and plxnb2 was identified as the candidate gene in this region. A total of 501 differentially expressed genes (DEGs) were found in the muscle of fast-growing individuals compared to those of slow-growing ones, according to a transcriptome analysis. Combining the findings of the GWAS and RNA-seq analysis, 11 candidate genes were identified, namely galnt9, esrrg, map7, mtfr2, kcnj8, fhit, dnm1, cald1, plxnb2, nuak1, and bpgm. These genes were involved in ‘other types of O-glycan biosynthesis’, ‘glycine, serine and threonine metabolism’, ‘glycolysis/gluconeogenesis’, ‘mucin-type O-glycan biosynthesis’ and ‘purine metabolism signaling’ pathways. We have developed molecular markers to genetically breed red tilapia that grow quickly in salty water. Our study lays the foundation for the future marker-assisted selection of growth traits in salt-tolerant red tilapia. Full article

4-coumarate-CoA ligase (4CL) plays a crucial role in the phenylpropanoid metabolic pathway and is a key enzyme involved in plant growth and stress responses. Black rot, caused by Xanthomonas campestris pv. campestris (Xcc) is a major bacterial disease affecting the production of global cruciferous crop-like cabbage (Brassica oleracea var. capitata). However, the role of 4CL genes in cabbage resistance to black rot remains unclear. In this study, transcriptome sequencing was conducted using resistant cabbage MY and susceptible cabbage LY at 0, 6, 24, and 48 h post-inoculation. KEGG analysis identified the enrichment of the phenylpropanoid biosynthesis pathway, and significant expression changes of 4CL genes were determined through the expression heat map. Further genome-wide analysis revealed 43 Bol4CL gene family members on the cabbage genome distributed across nine chromosomes. Gene structure and protein motif analysis revealed similarities in motifs within the same evolutionary branch, but variations in gene structure. A combination of Bol4CL gene expression profiles and differentially expressed genes (DEGs) from the transcriptome identified Bol4CL41 as a key gene for further study. Inoculation of overexpressed Bol4CL41 T₂ generation stably expressed cabbage seedlings demonstrated significantly larger lesion areas compared to wild type cabbage, indicating that Bol4CL41 negatively regulates resistance to black rot in cabbage. The analysis of multi-time point transcriptomes in cabbage and the functional study of the Bol4CL gene family enhance our understanding of the mechanisms underlying plant disease resistance. This provides compelling evidence and experimental support for elucidating the mechanisms of black rot resistance in cabbage. Full article

The family of GRAS transcription factors plays an essential role in the regulation of plant development, the transmission of hormonal signals, and the adaptation to environmental stresses seen in numerous species. However, a comprehensive analysis of the GRAS family of Hemerocallis citrina (daylily) is lacking, despite its potential to help understand the stress content and developmental processes of the monospecies. This study identified 78 GRAS genes (HcGRAS) in H. citrina, which were classified into 15 subfamilies based on chromosomal location, gene structure, conserved motifs, and expression patterns. An analysis of promoter regions indicated a significant presence of elements related to hormones and stress, showcasing these genes’ role in adapting to environmental pressures. The GO and KEGG analyses indicated that HcGRAS genes were engaged in pathways associated with developmental processes and responses to environmental stress. Notably, HcGRAS38 was identified as a key interacting protein for SHR, SCR, and DELLA subfamily members, which suggested its central role in coordinating stress response and developmental signaling. Comparative genomic mapping with seven representative monocot and dicot species underscored evolutionary conservation and divergence in functions of the GRAS family. The expression profiling of 22 HcGRAS genes across different daylily tissues provided insights into their tissue-specific roles. This research may promote the further exploration of the functional characteristics of HcGRAS genes. Full article

To identify the key genes conferring resistance to soybean cyst nematode race 4 (SCN4, Heterodera glycines), this study utilized 280 recombinant inbred lines (RILs) derived from the resistant cultivar Huipizhiheidou (HPD) and the susceptible cultivar Jindou23 (JD23). Through phenotypic characterization and a genome-wide association study (GWAS), a genomic region (Gm18:1,223,546–1,782,241) on chromosome 18 was mapped, yielding 14 candidate genes. GmPDH1 was validated as a critical resistance gene using reverse transcription quantitative PCR (RT-qPCR) and Kompetitive Allele Specific PCR (KASP) marker M0526. RT-qPCR revealed that GmPDH1 expression in HPD roots was upregulated 9 days post-inoculation with SCN4 compared to uninoculated controls. KASP genotyping showed that marker M0526 efficiently distinguished between resistant and susceptible plants in natural populations: 71.05% of the resistant accessions exhibited resistant or moderately resistant genotypes, whereas 81.03% of the susceptible accessions showed susceptible or highly susceptible genotypes. Functional validation demonstrated that overexpression of GmPDH1 significantly enhanced SCN4 resistance in the susceptible cultivars JD23 and Jack, whereas CRISPR/Cas9-mediated knockout of GmPDH1 in HPD attenuated its resistance. This study confirmed GmPDH1 as a key gene governing SCN4 resistance and developed an efficient molecular marker, M0526, providing theoretical insights and technical tools for dissecting nematode resistance mechanisms and advancing soybean disease-resistant breeding. Full article

The eri silkworm Samia cynthia ricini (S. ricini) is an economically and scientifically significant lepidopteran species, though its genomic resources have remained limited. Here, we present a chromosome-level genome assembly for S. ricini generated through integrated long-read, short-read, and Hi-C sequencing data. The final 456.16 Mb assembly spans 14 chromosomes, exhibiting 98.5% BUSCO completeness and a 48.51% repetitive content. Functional annotation of the 15,729 protein-coding genes against five major databases (NR, SwissProt, Pfam, GO, and KEGG) revealed a maximum annotation rate of 92.71%, demonstrating high gene set quality. Comparative genomics with B. mori uncovered conserved syntenic blocks interspersed with chromosomal fusion/fission events and inversions. We further identified 4.27 million SNPs, 1.02 million InDels, and 53,367 SVs, establishing the first comprehensive variation map for this species. These genomic variations provide a foundation for marker-assisted breeding programs and trait association studies. All the genomic resources and interactive visualization tools were integrated into the SilkMeta database. This study establishes S. ricini as a pivotal resource for comparative lepidopteran genomics and accelerates molecular breeding programs for this agriculturally valuable insect. Full article

Seed quality traits, such as seed size, oil and protein content, mineral accumulation, and morphological characteristics, are crucial for enhancing crop productivity, nutritional value, and marketability. Traditional quantitative trait loci (QTL) mapping methods, such as linkage analysis and genome-wide association studies (GWAS), have played fundamental role in identifying loci associated with these complex traits. However, these approaches often struggle with high-dimensional genomic data, polygenic inheritance, and genotype-by-environment (GXE) interactions. Recent advances in artificial intelligence (AI) and machine learning (ML) provide powerful alternatives that enable more accurate trait prediction, robust marker-trait associations, and efficient feature selection. This review presents an integrated overview of AI/ML applications in QTL mapping and seed trait prediction, highlighting key methodologies such as LASSO regression, Random Forest, Gradient Boosting, ElasticNet, and deep learning techniques including convolutional neural networks (CNNs) and graph neural networks (GNNs). A case study on soybean seed mineral nutrients accumulation illustrates the effectiveness of ML models in identifying significant SNPs on chromosomes 8, 9, and 14. LASSO and ElasticNet consistently achieved superior predictive accuracy compared to tree-based models. Beyond soybean, AI/ML methods have enhanced QTL detection in wheat, lettuce, rice, and cotton, supporting trait dissection across diverse crop species. I also explored AI-driven integration of multi-omics data—genomics, transcriptomics, metabolomics, and phenomics—to improve resolution in QTL mapping. While challenges remain in terms of model interpretability, biological validation, and computational scalability, ongoing developments in explainable AI, multi-view learning, and high-throughput phenotyping offer promising avenues. This review underscores the transformative potential of AI in accelerating genomic-assisted breeding and developing high-quality, climate-resilient crop varieties. Full article

Background: Xianan cattle, the first cross-bred beef cattle developed in China, are recognized for their rapid growth, tolerance to rough feed, and high meat yield. These characteristics make them a valuable model for studies aimed at improving beef production traits. Methods: In this study, two complementary gene mapping strategies, selection signature analysis and association analysis, were employed to identify candidate genes associated with body weight. The analyses utilized resequencing data comprising 16,250,950 high-quality single nucleotide polymorphisms (SNPs). Twenty independent variables showed significant correlations with body weight, with effect sizes ranging from 239 kg to 629.37 kg, while controlling for a false discovery rate (FDR) of less than 0.5. Results: The most prominent signal was identified in the 54.24–54.39 MB region on chromosome 9, which contains the MANEA gene. Furthermore, we investigated the functional role of the MANEA gene at the cellular level. siRNA-mediated knockdown of MANEA resulted in significant alterations in the expression of downstream genes, notably MGAT1, MGAT3, FUT8, and HK1. Among these, the expression of MGAT1 was markedly increased, showing an increase of up to 600-fold compared to the control. Conclusions: These results offer critical insights into the molecular mechanisms underlying body weight regulation and provide a foundation for developing strategies to enhance economically important production traits in beef cattle. Full article

Bacterial leaf streak (BLS) is one of the internationally significant quarantine diseases in rice. Effectively utilizing BLS resistance genes from wild rice (Oryza rufipogon Griff.) to breed new varieties offers a fundamental solution for BLS control. This study focused on the fine mapping of the BLS resistance gene bls2 and the development of closely linked molecular markers for breeding BLS-resistant lines. Using a Guangxi common wild rice accession DY19 (carrying bls2) as the donor parent and the highly BLS-susceptible indica rice variety 9311 as the recipient parent, BLS-resistant rice lines were developed through multiple generations of backcrossing and selfing, incorporating molecular marker-assisted selection (MAS), single nucleotide polymorphism(SNP) chip genotyping, pathogen inoculation assays, and agronomic trait evaluation. The results showed that bls2 was delimited to a 113 kb interval between the molecular markers ID2 and ID5 on chromosome 2, with both markers exhibiting over 98% accuracy in detecting bls2. Four stable new lines carrying the bls2 segment were obtained in the BC₅F₄ generation. These four lines showed highly significant differences in BLS resistance compared with 9311, demonstrating moderate resistance or higher with average lesion lengths ranging from 0.69 to 1.26 cm. Importantly, no significant differences were observed between these resistant lines and 9311 in key agronomic traits, including plant height, number of effective panicles, panicle length, seed setting rate, grain length, grain width, length-to-width ratio, and 1000-grain weight. Collectively, two molecular markers closely linked to bls2 were developed, which can be effectively applied in MAS, and four new lines with significantly enhanced resistance to BLS and excellent agronomic traits were obtained. These findings provide technical support and core germplasm resources for BLS resistance breeding. Full article

Leaf rust (LR) is a devastating foliar disease that impacts common wheat (Triticum aestivum L.) globally. For optimal disease protection, wheat cultivars should possess adult plant resistance (APR) to leaf rust. In the current study, the objective was to map quantitative trait loci (QTL) related to leaf rust resistance. This was achieved by using 193 recombinant inbred line (RIL) populations which were developed from the cross between N. Strampelli and Huixianhong. Four trials were conducted in China (three in Baoding, Hebei province, and one in Zhoukou, Henan province) to assesses the leaf rust response of the RILs and parental lines. The wheat 660K SNP array and additional SSR markers were used to genotype the RIL populations. Through inclusive composite interval mapping (ICIM), three QTL related to leaf rust (LR) resistance were detected. ICIM was also employed to reevaluate previously published data in order to identify QTL with pleiotropic effects. To determine the physical positions, the flanking sequences of all SNP probes were compared against the Chinese Spring wheat reference sequence through BLAST searches. Three leaf rust resistance loci, two on chromosome 2A and 5B, were contributed by N. Strampelli. QLr.hbau-2AL.1 was detected in three leaf rust environments with phenotypic variance explained (PVE of 12.2–17%); QLr.hbau-2AL.2 was detected in two environments with 12.5–13.2% of the PVE; and QLr.hbau-5BL was detected in all leaf rust environments with phenotypic variance explained (PVE) of 17.8–19.1%. QLr.hbau-5BL exhibited potentially pleiotropic responses to multiple diseases. The QTL and the associated flanking markers discovered in this study could prove valuable for purposes such as fine mapping, the exploration of candidate genes, and marker-assisted selection (MAS). Full article

In cytogenetics, the ability to perform FISH (Fluorescence In Situ Hybridization) experiments using probes that map very closely together depends on the capacity to produce sufficiently long chromosomes. Traditionally, colcemid is the chemical agent used to obtain metaphase spreads. However, various substances have been reported to arrest cells in an earlier stage of mitosis than the metaphase, potentially providing longer chromosomes. In this study, we tested seven substances different from colcemid, which, according to the literature, have this capability: Vinblastine, Combretastatin A-4, Podophyllotoxin, Org9935, Nocodazole, Paclitaxel, and Griseofulvin. All substances were tested on lymphocyte cultures derived from whole blood at the same concentration: 0.1 µg/mL. Among these, Org9935 and Griseofulvin were confirmed to have the ability to produce metaphases with longer chromosomes compared to those obtained with colcemid. Full article

The APETALA2/Ethylene-Responsive Factor (AP2/ERF) superfamily is one of the largest transcription factor families in plants, playing diverse roles in development, stress response, and metabolic regulation. Despite their ecological and economic importance, AP2/ERF genes remain uncharacterized in marigold (Tagetes erecta), a valuable ornamental and medicinal plant in the Asteraceae family known for its unique capitulum-type inflorescence with distinct ray and disc florets. Here, we conducted a comprehensive genome-wide analysis of the AP2/ERF superfamily in marigold and identified 177 AP2/ERF genes distributed across 11 of the 12 chromosomes. Phylogenetic analysis revealed their classification into the AP2 (28 genes), ERF (143 genes), RAV (4 genes), and Soloist (2 genes) families based on domain architecture. Gene structure and motif composition analyses demonstrated group-specific patterns that correlated with their evolutionary relationships. Chromosome mapping and synteny analyses revealed that segmental duplications significantly contributed to AP2/ERF superfamily gene expansion in marigold, with extensive collinearity observed between marigold and other species. Expression profiling across different tissues and developmental stages indicated distinct spatio-temporal expression patterns, with several genes exhibiting tissue-specific expression in Asteraceae-specific structures. In floral organs, TeAP2/ERF145 exhibited significantly higher expression in ray floret corollas compared to disc florets, while TeAP2/ERF103 showed stamen-specific expression in disc florets. Protein interaction network analysis revealed AP2 as a central hub with extensive predicted interactions with MADS-box and TCP family proteins. These findings suggest that AP2 family genes may collaborate with MADS-box and CYC2 genes in regulating the characteristic floral architecture of marigold, establishing a foundation for future functional studies and molecular breeding efforts to enhance ornamental and agricultural traits in this economically important plant. Full article

Barley (Hordeum vulgare L.) is one of the most important cereal crops in the world, and its production is important to humans. Barley spike morphology is highly correlated with yield and is also a complex multigene-controlled quantitative trait. To date, a considerable number of spike-related quantitative trait loci (QTLs) have been reported in barley, but the large physical distances between most of them and the lack of follow-up studies have made it difficult to use them in molecular-assisted breeding in barley. To explore more novel and yield-enhancing spike QTLs, in this study, a high-density genetic linkage map was developed based on a population of 172 F_2:12 recombinant inbred lines (RILs) developed from a cross between the barley variety Yongjiabaidamai (YJ) and Hua 30 (H30), and used to map the spike length (SL), rachis node number (SRN), and spike density (SD). A total of 50 additive QTLs (LOD > 3) were mapped in four environments, four of them being stable and major QTLs. The qSL2-5 overlaps with the zeo1 gene, comparing the gene sequences of both parents and combining with previous studies, zeo1 was determined to be the SL regulatory gene in qSL2-5. The qSRN2-1 overlaps with vrs1, but it has not been previously reported that vrs1 affects SRN. Notably, two novel QTLs, one each on chromosomes 2H (qSL2-1) and 5H (qSL5-1), respectively, were first identified in this study. The qSL2-1 has only 0.06 Mb and contains three high-confidence genes. In addition, this study explored the relationship between three spike traits, and found that SL was affected by both SRN and SD, while there was almost no relationship between SRN and SD. We also explored the effect of these QTLs on grain weight per spike (GWPS) to assess their effect on yield and found that qSRN2-1 and qSL5-1 had a greater effect on GWPS, suggesting that they are potential loci to increase yield. Full article