Search Results (4,234)

This paper examines various aspects of maize plant height. Firstly, it emphasizes that maize is a significant food and forage crop with considerable research significance, and that its plant height is influenced by multiple factors, including biotic elements such as genes and plant hormones, as well as abiotic factors such as soil, water, and climate. Secondly, the paper explores the complex relationship between maize plant height and yield, noting that moderate plant height can improve photosynthetic efficiency, reduce lodging risk, and enhance yield, although it may also affect kernel quality. Additionally, the paper reviews the application of modern biotechnological methods in maize plant height research, such as genome-wide linkage analysis, gene editing, transgenic technology, and epigenetic studies, which aid in elucidating the genetic mechanisms underlying plant height. Finally, it outlines future research directions for improving maize plant height and yield, highlighting key challenges that require urgent attention, such as the advancement of gene editing techniques, the integration of multiple biotechnologies, and strategies to address climate change, with the ultimate goal of achieving precision breeding for high-yielding, stress-resistant, and broadly adaptable maize varieties. Full article

Sex determination is a fundamental biological process governing animal reproduction. Although substantial progress has been made in elucidating its genetic basis, the genetic architecture underlying complex sex determination systems remains poorly understood. In this study, we identify sex-associated insertion–deletion (indel) variants, screen candidate genes, and compare sex-associated variation across populations with different genetic backgrounds in the Fujian oyster (Magallana angulata). Based on whole-genome resequencing data of a culture strain (designated FL), a total of 299,774 high-quality indels were identified. By integrating genome-wide association analysis (GWAS), fixation index (F_ST) analysis, and sex-biased genotype frequency comparisons, 77 overlapping sex-associated indels were identified, predominantly clustered within a 1.8 Mb (8.3–10.1 Mb) region on chromosome 9. Principal component analysis (PCA) based on the sex-associated markers and their subsets consistently separated male and female individuals in the FL strain. For two representative sex-associated indels, PCR-based genotyping methods were developed and validated. Functional annotation identified putative candidate genes for sex determination, including PKD1L1, 5-HTRL, SCP, and CCKRa. Comparative analysis of variants within PKD1L1 across wild, farmed, and selectively bred populations revealed a progressive enrichment of male-linked alleles in domesticated and selectively bred groups, particularly in male individuals. This study provides direct evidence that sex in the Fujian oyster is genetically determined and reveals that domestication and artificial selection may drive the emergence of major sex-determining loci, offering important insights into the genetic basis of sex determination in the Fujian oyster, and establishing a theoretical and practical foundation for molecular marker-assisted breeding of monosex lines for this species. Full article

Sugarcane (Saccharum spp.), a vital economic crop, suffers significant yield losses from drought. This study elucidates the genetic regulation of lignin biosynthesis—a key drought-resistance mechanism—by analyzing three contrasting accessions: drought-sensitive Saccharum officinarum (Badila), drought-resistant hybrid (XTT22), and drought-tolerant wild Saccharum spontaneum (SES-208) under progressive drought (7–21 days). Physiological analyses revealed pronounced lignin accumulation in XTT22 roots/leaves, driven by elevated coniferyl/sinapyl alcohol substrates, while Badila showed minimal deposition. Genomic characterization of cinnamyl/sinapyl alcohol dehydrogenase (CAD/SAD) families across six sugarcane genomes identified 322 genes phylogenetically clustered into three clades. Class I members (CAD1, CAD5, etc.) were critical for lignin biosynthesis, with tandem/segmental duplications driving family expansion and promoters enriched in stress-responsive cis-elements (ABA, MeJA, light). Transcriptomics and qRT-PCR confirmed strong correlations between Class I CAD expression, lignin content, and drought tolerance. These findings establish CAD Class I genes as novel molecular targets for enhancing drought resilience in sugarcane breeding programs. Full article

Sugarcane smut, caused by Sporisorium scitamineum, is a globally prevalent disease that severely impacts sugarcane yield and quality. The most cost-effective and sustainable approach to disease control is breeding for smut-resistant varieties. In this study, we conducted a genome-wide association study (GWAS) using a panel of core sugarcane parents and their derived lines to elucidate the genetic basis of smut resistance across seven different environments. We identified 68 new loci significantly associated with smut resistance across all the chromosomes. Based on functional annotations and genomic positions, 164 candidate genes were identified, many of which are related to enzymatic systems, resistance genes, transcription factors, and other pathways implicated in smut defense. Using resistance ratings and associated SNPs, we further selected ten elite parents and derivatives as potential donors for marker-assisted selection (MAS). This study provides a valuable reservoir of genetic resources for improving smut resistance in sugarcane. Full article

Peruvian Creole goats (PCGs) represent a unique genetic resource shaped by adaptation to diverse environments and traditional breeding practices. In this study, we performed a genomic analysis of six regional populations (Ancash, Ica, Lambayeque, Lima, Piura, and Tumbes) using high-density SNP genotype data. Principal component analysis revealed a moderate genetic structure, with the Ica population showing clear separation and northern populations exhibiting overlap. Runs of homozygosity were predominantly short, and specific regions on chromosome 6 were shared across populations. Inbreeding coefficients were generally low, with Ancash showing the highest values. Linkage disequilibrium decayed rapidly over genetic distance, especially in Piura, indicating higher genetic diversity. Estimates of effective population size revealed decreasing trends across populations, with Piura maintaining the largest recent population size. These findings offer valuable insights into the population structure of Peruvian Creole goats, providing guidance for conservation and sustainable breeding efforts. Full article

Nuclear Factor Y C (NF-YC) transcription factors (TFs) are central regulators of plant development and stress adaptation. However, there remains a gap in identifying NF-YC gene family members in blueberry (Vaccinium corymbosum), a globally significant fruit crop renowned for its nutritional value and good adaptability. In this study, a total of 31 NF-YC genes (designated VcNF-YC1–31) were identified in the blueberry genome, and their basic physicochemical properties, gene structures, motif patterns, and conserved domains were investigated using bioinformatic methods. The cis-acting elements in the promoters of VcNF-YCs were mainly enriched in phytohormone signaling, metabolism, and stress response. qRT-PCR analysis showed that VcNF-YCs were expressed at higher levels in leaves than in roots and stems. Transcriptional profiling revealed rapid upregulation of 24, 25, and 16 VcNF-YC genes upon ABA, salt, and cold treatments, respectively, indicating stress-specific induction patterns. The results of the yeast transformation assay revealed that VcNF-YC10 and VcNF-YC15 lacked transcription-activating activity. The results of tobacco leaf injection revealed that these two TFs were localized in the nucleus. These findings indicate the potentially important roles in abiotic stress responses of blueberry, offering potential targets for molecular breeding to enhance plant resilience. Full article

Feed efficiency is a key economic trait that affects the cost of production in broiler farming. Reducing broiler feed costs contributes to reducing excessive feed consumption and increasing the productivity of broiler breeding. Therefore, identifying genetic regions associated with feed efficiency is crucial for broiler breeding. In this study, we performed genome-wide association (GWAS) analyses of feed conversion ratio (FCR) and residual feed intake (RFI) traits for four growth cycles (72–81, 81–89, 89–113, and 113–120 days of age) using 55K single-nucleotide microarray genotypic data of 4493 Wenchang chickens from two generations. In the single-trait GWAS, a total of 59 SNPs were identified, and 36 genes were annotated within the ±50 kb regions surrounding candidate loci (including ABCC6, CLDN10, DGKB, EXT2, FOXO1, IFT140, JAG2, among others. These candidate loci explained 1.4–7.0% of the phenotypic variance explained, and applying a filtering criterion that required a deleteriousness score greater than 8, one locus-Gallus gallus chromosome (GGA) 5:3550350 (chCADD score = 12.51524) was located within intron 3 of ANOX3. In the FCR and RFI traits in the longitudinal GWAS (LONG-GWAS) model, 80 SNPs and 191 SNPs were identified, respectively, and a total of 43 genes and 121 genes were annotated. A total of 33 candidate loci were screened by combining the locus deleteriousness scores, and 25 candidate genes were annotated within the upper and lower 50 kb ranges. Through KEGG signaling pathway analysis, it was found that the candidate genes were highly enriched mainly in autophagy, mitochondrial phagocytosis, and other pathways. In conclusion, the SNPs and potential genes identified in this study will be helpful for chicken breeding and provide fundamental data for the genetic basis of chicken feed efficiency-related traits. Full article

The BBX gene family functions as a key transcription factor implicated in plant growth, development, and stress responses. However, research on this gene family in melon remains absent. In the present study, we identified 19 BBX family genes within the melon genome, distributed across chromosomes 1, 2, 3, 4, 5, 7, 8, 10, 11, and 12. Phylogenetic analysis categorized these genes into five distinct subfamilies, with notable similarities observed in gene structure and conserved motifs among members of the same subfamily. Synteny analysis revealed seven syntenic relationships among melon BBX genes, 17 between melon and Arabidopsis, and one between melon and rice. Reanalysis of transcriptome data indicated that certain BBX genes exhibit high expression levels across various tissues and developmental stages of fruits, while others display tissue specificity. Under both abiotic and biotic stress conditions, genes such as CmBBX3, CmBBX5, CmBBX2, CmBBX18, CmBBX15, and CmBBX11 demonstrated significant differential expression, highlighting their critical roles in melon growth and development. Additionally, RT-qPCR analysis was conducted to examine the expression levels of melon BBX genes at different time points under salt stress, further validating the transcriptome data. This study provides a theoretical foundation for future molecular breeding efforts in melon. Full article

Phytophthora fruit rot caused by Phytophthora capsici is a devastating disease in many solanaceous vegetables, resulting in tremendous yield and economic losses. However, the underlying resistance or susceptibility to P. capsici in eggplant remains obscure. In this study, the transcriptomic analysis was performed between the resistant (G42) and susceptible (EP28) eggplant genotypes at 0, 1, 3 and 5 days post-inoculation (dpi). Taking 0 dpi as the control, a total of 4111, 7496 and 7325 DEGs were expressed at 1, 3 and 5 dpi, respectively, in G42 and 5316, 12675 and 12048 DEGs were identified at 1, 3 and 5 dpi, respectively, in EP28. P. capsici infection induced substantial transcriptional changes in the inoculated fruits. The analysis of the Kyoto Encyclopedia of Genes and Genomes (KEGG) identified defense-related pathways including ‘plant-pathogen interactions’, ‘mitogen-activated protein kinase (MAPK)’ and ‘hormone biosynthesis and signal transduction’. The hormone-related genes encompassing ethylene, abscisic acid, auxins and gibberellins showed differential expression between G42 and EP28 eggplant genotypes, signifying their important roles in plant disease resistance. P. capsici infection induced the expression of major transcription factors such as MYB, NAC/NAM, bHLH, WRK, HSF, HD-ZIPAP2/ERF and Mad-box. qRT-PCR validation of the selected genes corroborates with RNA-seq, depicting the precision and consistency of the transcriptomic data. According to qRT-PCR and RNA-seq analyses, the expression of the pathogenesis-related gene transcriptional activator, SmPTI6 (Smechr0603020), is upregulated in G42 and downregulated in EP28. This differential expression suggests a potential role in the resistance to P. capsici. Functional analysis via a virus-induced gene silencing (VIGS) system found that silencing SmPTI6 in G42 enhanced infection by P. capsici, indicating that SmPTI6 performs a critical role in response to pathogen attack. The comprehensive results obtained in this study provide a valuable resource for understanding the molecular mechanisms underlying eggplant resistance to P. capsici and for establishing breeding resistant eggplant genotypes to P. capsici. Full article

The convergence of genomic selection and artificial intelligence (AI) is redefining precision breeding in dairy cattle, enabling earlier, more accurate, and multi-trait selection for health, fertility, climate resilience, and economic efficiency. This review critically examines how advanced genomic tools—such as genome-wide association studies (GWAS), genomic breeding values (GEBVs), machine learning (ML), and deep learning (DL) models to accelerate genetic gain for complex, low heritability traits. Key applications include improved resistance to mastitis and metabolic diseases, enhanced thermotolerance, reduced enteric methane emissions, and increased milk yield. We discuss emerging computational frameworks that combine sensor-derived phenotypes, omics datasets, and environmental data to support data-driven selection decisions. Furthermore, we address implementation challenges related to data integration, model interpretability, ethical considerations, and access in low-resource settings. By synthesizing interdisciplinary advances, this review provides a roadmap for developing AI-augmented genomic selection pipelines that support sustainable, climate-smart, and economically viable dairy systems. Full article

Background: The chloroplast genome provides rich genetic information for plant evolutionary studies. This study aimed to assemble, annotate, and analyze the complete chloroplast genome of flax cultivar ‘Longya 15’ (Linum usitatissimum L.) and clarify its phylogenetic relationships with other Linaceae species. Methods: We assembled and annotated the chloroplast genome of ‘Longya 15’ and retrieved chloroplast genomes of related species (e.g., Linum grandiflorum NC_058845.1, Linum lewisii NC_058799.1) from the NCBI database for phylogenetic analysis. Results: The chloroplast genome of ‘Longya 15’ was a 157,074-bp quadripartite structure with 37.42% GC content, encoding 128 genes (83 mRNAs, 37 tRNAs, 8 rRNAs) without pseudogenes. It showed codon bias for leucine (28 codons with RSCU > 1, ending in A/U), 260 dispersed repeats, and 240 SSRs. Ka/Ks analysis revealed purifying selection for most genes, while rps18 and ycf2 had positive selection. ycf1 was identified as the hypervariable region (pi = 0.25024). Phylogenetically, it clustered closest with Linum grandiflorum, followed by L. lewisii and L. perenne, and was related to Hypericum species. Conclusions: This is the first fine assembly and annotation of ‘Longya 15’ chloroplast genome, confirming no pseudogenes in flax chloroplast. It elucidates flax chloroplast genome conservation and evolutionary dynamics, enriches the database, and provides a foundation for Linaceae phylogenetics, germplasm development, and stress-resistant breeding. Full article

Buffaloes are a vital genetic resource for dairy production, yet advancements in improving milk production have been somewhat limited. In this study, we performed an integrated analysis of genomic sequencing data from 78 water buffaloes and their milk production traits, with a focus on 305-day milk yield (MY). Leveraging advancements in sequencing technology alongside genome-wide association study (GWAS) methods such as cBLUP, GMATs, and BayesR, we aimed to identify genetic factors that could facilitate the breeding of high-quality buffaloes. Our analysis revealed two significant SNPs associated with milk production traits. Based on these markers, four candidate genes were identified within the surrounding genomic regions. These genes showed significant enrichment in lactation-related pathways, including the prolactin signaling pathway (mitogen-activated protein kinase 10, MAPK10), IL-17 signaling pathway (MAPK10), MAPK signaling pathway (MAPK10), and adipocytokine signaling pathway (MAPK10). The identification of these candidate genes, particularly MAPK10, provides a robust theoretical basis for molecular breeding strategies aimed at enhancing milk production in buffaloes. This work paves the way for more targeted and effective breeding programs in the future. Full article

As severe selection and declining population numbers in many breeds have resulted in losses in the worldwide livestock genetic biodiversity, human concern about the situation of genetic variety in livestock breeds and their conservation has grown. In this context, genomic techniques now allow for more exact monitoring of adaptive traits and inbreeding, while reproductive techniques such as somatic cell nuclear transfer and IVF (In Vitro Fertilization) help to preserve and recover rare genetic lines. AI-powered (Artifficial Inteligence) risk assessment models and digital herdbooks contribute to data-driven reproductive strategies, particularly in smallholder settings. Nonetheless, these advances face persistent hurdles, including a lack of legislative frameworks, high costs, limited accessibility in low-resource settings, and unresolved ethical problems. The findings highlight the importance of a balanced, interdisciplinary strategy that combines new biotechnologies with traditional knowledge, collaborative practices, and strong policy to assist in preserving the long-term viability of livestock genetic resources. This review intends to assess modern and traditional methods for the preservation of livestock breeds, analyzing references published between 2019 and the present. Full article

As a crucial aspect of epigenetic research, DNA methylation is fundamental to genomic stability, gene transcription regulation, and chromatin remodeling. Rice is a staple food source for roughly half of the world’s population. Therefore, optimizing rice yield and stress tolerance is vital for global food security. With the continuous advancement of DNA methylation detection technologies, studies have shown that DNA methylation regulates various rice growth and development processes, including root differentiation and grain development, through the dynamic equilibrium of de novo methylation, maintenance methylation, and demethylation. Furthermore, DNA methylation is crucial in the plant’s response to environmental stressors like high or low temperature, drought and salinity. The patterns of DNA methylation modifications are also closely linked to rice domestication and heterosis formation. Therefore, a comprehensive investigation of the DNA methylation regulatory network holds significant theoretical value for rice genetic improvement and molecular breeding. This review offers a systematic analysis of the molecular mechanisms and detection technologies of DNA methylation, as well as its regulatory roles in rice growth and development, stress responses, and other biological processes, aiming to provide a theoretical foundation for rice genetic improvement research. Full article

The Dof (DNA binding with one finger) protein is one of the unique transcription factors in plants, and it plays an important role in plant growth and stress response. Sesame is an oil-bearing crop with high oil content and rich nutrition. In this study, 34 Dof genes were identified in the sesame genome using bioinformatics technology, and their physicochemical properties, gene structure, conserved motifs, tissue-specific expression and functions in fatty acid synthesis were preliminarily analyzed. The results showed that although there were differences in sequence length, molecular weight and isoelectric point, SiDofs all contained a conservative zinc finger structure, which could be divided into three categories in phylogeny. All 34 SiDof genes contain 1–2 exons, and the conserved motifs among subfamilies are similar. Tissue-specific expression analysis showed that the expression levels of SiDof8, SiDof10 and SiDof34 were the highest in seeds 24 days after pollination. Overexpression of SiDof8, SiDof10 and SiDof34 could significantly increase the contents of C18:0, C18:1, C18:2 and C18:3, and all of them are located in the nucleus. There were Dof DNA binding elements in the promoter region of fatty acid synthesis genes. These results provide a theoretical basis for further study on the function of the sesame Dof genes and biological breeding. Full article