Search Results (1,957)

Anaerobic germination (AG) is a pivotal trait for successful direct-seeded rice cultivation, encompassing rainfed and irrigated conditions. Elite rice cultivars are often vulnerable to flooding during germination, resulting in poor crop establishment. This drawback has led to the exploration of AG-tolerant rice landraces, which offer valuable insights into the genetic underpinnings of AG tolerance. Over the years, substantial progress has been made in identifying significant quantitative trait loci (QTLs) associated with AG tolerance, forming the basis for targeted breeding efforts. However, the intricate gene regulatory network governing AG tolerance remains enigmatic. This comprehensive review presents recent advances in understanding the physiological and genetic mechanisms underlying AG tolerance. It focuses on their practical implications in breeding elite rice cultivars tailored for direct-seeding systems. Full article

A unique line of Holstein cattle has been maintained without selection in Minnesota since 1964. After many generations, unselected cattle produce less milk, but have better reproductive performance and health traits when compared with contemporary cows. Comparisons between this line of unselected Holstein and those under selection provide useful insights that connect selection and complex traits in cattle. Utilizing these unique resources and sequence data, we sought to identify genome changes due to selection. We sequenced 30 unselected and 54 selected Holstein cattle and compared their sequence variants to identify selection signatures. After many years, the two populations showed completely different patterns in their genome-level population structures and linkage disequilibrium. By integrating signals from five different detection methods, we detected consensus selection signatures from at least four methods covering 14,533 SNPs and 155 protein-coding genes. An integrated analysis of selection signatures with gene annotation, pathways, and the cattle QTL database demonstrated that the genomic regions under selection are related to milk productivity, health, and reproductive efficiency. The polygenic nature of these complex traits is evident from hundreds of selection signatures and candidate genes, suggesting that long-term artificial selection has acted on the whole genome rather than a few major genes. In summary, our study identified candidate selection signatures underlying phenotypic differences between unselected and selected Holstein cows and revealed insights into the genetic basis of complex traits in cattle. Full article

Vegetable oils are essential for human nutrition and industrial applications. With growing global demand, increasing oil content in oilseed crops has become a top priority. This review synthesizes recent progress in understanding the genetic, environmental, and molecular mechanisms regulating oil content, and presents biotechnological strategies to enhance oil accumulation in major oilseed crops. Oil biosynthesis is governed by intricate genetic–environmental interactions. Environmental factors and agronomic practices significantly impact oil accumulation dynamics. Quantitative trait loci (QTL) mapping and genome-wide association studies (GWAS) have identified key loci and candidate genes involved in lipid biosynthesis pathways. Transcription factors and epigenetic regulators further fine-tune oil accumulation. Biotechnological approaches, including marker-assisted selection (MAS) and CRISPR/Cas9-mediated genome editing, have successfully generated high-oil-content variants. Future research should integrate multi-omics data, leverage AI-based predictive breeding, and apply precision genome editing to optimize oil yield while maintaining seed quality. This review provides critical references for the genetic improvement and breeding of high- and ultra-high-oil-content varieties in oilseed crops. Full article

The functional components in cereals (rice and barley), such as gamma-aminobutyric acid (GABA), resistant starch (RS), and alkaloids, play crucial roles in human health, offering benefits such as improved cardiovascular function, enhanced gut microbiota, and potential anticancer properties. Rice (Oryza sativa) and barley (Hordeum vulgare) are key dietary staples with distinct genetic architectures influencing the biosynthesis and accumulation of these bioactive compounds. In this study, we explore the interaction and divergence of gene loci associated with GABA, RS, and alkaloid pathways in rice and barley, leveraging comparative genomics to identify conserved and species-specific regulatory mechanisms. We highlight key quantitative trait loci (QTLs) and candidate genes, such as GAD (glutamate decarboxylase) for GABA synthesis, SSIIa and GBSS for RS formation, and alkaloid biosynthesis genes including CYP80G2. Additionally, we discuss the health implications of these functional components, including their roles in reducing hypertension, managing diabetes, and exhibiting neuroprotective effects. Understanding the genetic differences between rice and barley in accumulating these compounds can guide biofortification strategies to enhance nutritional quality in cereal crops, ultimately benefiting human health and dietary outcomes. Full article

Previous high-throughput screening studies have indicated that trans-eQTLs tend to be tissue-specific. This study investigates whether this feature can be used to identify tissue-specific gene regulatory networks. eQTL data for 19,960 genes were obtained from the eQTLGen study. Next, eQTLs displaying both cis- and trans-regulatory effects (p < 5 × 10⁻⁸) were selected, and the association between their corresponding genes was examined by Mendelian randomization. The findings were further validated using eQTL data from the INTERVAL study. The trans-regulatory impact of 138 genes on 342 genes was detected (p < 5 × 10⁻⁸). The majority of the identified gene-pairs were aggregated into networks with scale-free topology. An examination of the function of genes indicates they are involved in immune processes. The hub genes primarily shared transcription regulation activity and were associated with blood cell traits. The hub gene, DDAH2, impacted several metabolic and autoimmune disorders. On average, a gene in the network was under the regulatory control of 34 cis-eQTLs and 6 trans-eQTLs, and genes with higher heritabilities tended to exert higher regulatory impacts. This study reports tissue-specific gene regulatory networks can be detected by investigating their genomic underpinnings. The identified networks displayed scale-free topology, indicating that hub genes within a network could be targeted to correct abnormalities. Full article

Osteoporosis is a multifactorial, polygenic disease characterized by reduced bone mineral density (BMD) and increased fracture risk. Genome-wide association studies (GWASs) have identified numerous loci associated with BMD and/or bone fractures, but functional characterization of these target genes is essential to understand the biological mechanisms underlying osteoporosis. This review focuses on current methodologies and key examples of successful functional studies aimed at evaluating gene function in osteoporosis research. Functional evaluation typically follows a multi-step approach. In silico analyses using omics datasets expression quantitative trait loci (eQTLs), protein quantitative trait loci (pQTLs), and DNA methylation quantitative trait loci (mQTLs) help prioritize candidate genes and predict relevant biological pathways. In vitro models, including immortalized bone-derived cell lines and primary mesenchymal stem cells (MSCs), are used to explore gene function in osteogenesis. Advanced three-dimensional culture systems provide additional physiological relevance for studying bone-related cellular processes. In situ analyses of patient-derived bone and muscle tissues offer validation in a disease-relevant context, while in vivo studies using mouse and zebrafish models enable comprehensive assessment of gene function in skeletal development and maintenance. Integration of these complementary methodologies helps translate GWAS findings into biological insights and supports the identification of novel therapeutic targets for osteoporosis. Full article

Wheat is one of the three major staple crops globally. The wheat spike serves as the primary structure bearing wheat grains. Spike architectures of wheat have a direct impact on the number of grains per spike, and thus the grain yield per spike. The development of wheat spike morphology is conserved to some extent in cereal crops, yet also exhibits differences, being strictly regulated by photoperiod and temperature. This paper compiles QTLs and genes related to wheat spike traits that have been published over the past two decades, summarizes the photoperiod and vernalization pathways influencing the transition from vegetative to reproductive growth, and organizes the key regulatory networks controlling spikelet and floret development. Additionally, it anticipates advancements in wheat gene cloning methods, challenges in optimizing wheat spike architecture for high yield and future directions in wheat spike trait research. Full article

Fruit size is an important agronomic trait affecting the yield and commercial value of melon and a key trait selected for during domestication. In this study, two respective melon accessions (large-fruited M202008 and small-fruited M202009) were crossed, and developed biparental mapping populations of the F₂ generation (160 and 382 plants) were checked across two subsequent experimental years (2023 and 2024). The phenotypic characterization and genetic inheritance analysis showed that melon fruit size is modulated by quantitative genetics. Bulked segregant sequencing analysis (BSA-seq) identified a stable and effective quantitative trait locus (QTL, named Cmfs) controlling fruit size, localized to a 3.75 Mb region on chromosome 9. To better delineate the main-effect Cmfs locus, co-dominant polymorphic molecular markers were developed in this genetic interval, and genotyping was performed within the F₂ mapping populations grown across two years. QTL analysis of the phenotypic and genotypic datasets delimited the major-effect Cmfs locus interval for fruit length [2023: logarithm of odds (LOD) value = 6.16, 16.20% phenotypic variation explained (PVE); 2024: LOD = 5.44, 6.35% PVE] and fruit diameter (2023: LOD value = 5.48, 14.59% PVE; 2024: LOD = 6.22, 7.22% PVE) to 1.88 and 2.20 Mb intervals, respectively. The annotation analysis across the melon genome and comparison of resequencing data from the two parental lines led to the preliminary identification of MELO3C021600.1 (annotated as cytochrome P450 724B1) as a candidate gene related to melon fruit size. These results provide a better understanding for further fine mapping and functional gene analysis related to melon fruit size. Full article

This study identifies and classifies resistance gene analogues (RGAs) in the genomes of Brassica nigra, Sinapis arvensis and Sinapis alba using the RGAugury pipeline. RGAs were categorised into four main classes: receptor-like kinases (RLKs), receptor-like proteins (RLPs), nucleotide-binding leucine-rich repeat (NLR) proteins and transmembrane-coiled-coil (TM-CC) genes. A total of 4499 candidate RGAs were detected, with species-specific proportions. RLKs were the most abundant across all genomes, followed by TM-CCs and RLPs. The sub-classification of RLKs and RLPs identified LRR-RLKs, LRR-RLPs, LysM-RLKs, and LysM-RLPs. Atypical NLRs were more frequent than typical ones in all species. Atypical NLRs were more frequent than typical ones in all species. We explored the relationship between chromosome size and RGA count using regression analysis. In B. nigra and S. arvensis, larger chromosomes generally harboured more RGAs, while S. alba displayed the opposite trend. Exceptions were observed in all species, where some larger chromosomes contained fewer RGAs in B. nigra and S. arvensis, or more RGAs in S. alba. The distribution and density of RGAs across chromosomes were examined. RGA distribution was skewed towards chromosomal ends, with patterns differing across RGA types. Sequence hierarchical pairwise similarity analysis revealed distinct gene clusters, suggesting evolutionary relationships. The study also identified homologous genes among RGAs and non-RGAs in each species, providing insights into disease resistance mechanisms. Finally, RLKs and RLPs were co-localised with reported disease resistance loci in Brassica, indicating significant associations. Phylogenetic analysis of cloned RGAs and QTL-mapped RLKs and RLPs identified distinct clusters, enhancing our understanding of their evolutionary trajectories. These findings provide a comprehensive view of RGA diversity and genomics in these Brassicaceae species, providing valuable insights for future research in plant disease resistance and crop improvement. Full article

Background/Objectives: Cardiovascular diseases are a global health issue with an increasing burden and are exacerbated by hypertension. High blood pressure is partly attributed to genetic variants that are generally not well understood or extensively studied in sub-Saharan African populations. Variants linked to blood pressure have been found through genome-wide association studies (GWASs), which were mostly conducted among European ancestry populations; however, limited research has been undertaken in Africa. The current study evaluated single-nucleotide polymorphisms (SNPs) of PCSK9, ABCA1, LPL, and PON1 in relation to blood pressure measurements of 1839 Ghanaian adults. Methods: Genotypes were extracted from data generated by the H3Africa SNP array. After adjusting for sex, age, smoking, and body mass index (BMI), inferential statistics were used to investigate the relationships between SNPs and blood pressure (BP) indices. Additionally, Bonferroni correction was used to adjust for multiple testing. Results: Diastolic blood pressure (DBP) and the minor allele T of the PCSK9 variant (rs17111557) were positively associated at p = 0.006 after covariate adjustments. Although this novel DBP-associated variant is located in the 3′ untranslated region (3′ UTR) of the PCSK9 gene, in silico functional prediction suggests it is an expression quantitative trait locus (eQTL) that may change the binding site of transcription factors, potentially altering the rate of transcription and impacting DBP in this Ghanaian population. Conclusions: Our findings highlight the role of genetics in hypertension risk and the potential of discovering new therapies targeting isolated diastolic blood pressure in this rural African population. Full article

Enhancing quality traits is a primary objective in silage maize breeding programs. The use of genome-wide association studies (GWAS) for quality traits, in combination with the integration of genetic resources, presents an opportunity to identify crucial genomic regions and candidate genes influencing silage maize quality. In this study, a GWAS was conducted on 580 inbred lines of silage maize, and a meta-analysis was performed on 477 quantitative trait loci (QTLs) from 34 studies. The analysis identified 27 significant single nucleotide polymorphisms (SNPs) and 87 consensus QTLs (cQTLs), with 7 cQTLs associated with multiple quality traits. By integrating the SNPs identified through association mapping, one SNP was found to overlap with the cQTL interval related to crude protein, neutral detergent fiber, and starch content. Furthermore, enrichment analysis predicted 300 and 5669 candidate genes through GWAS and meta-analysis, respectively, highlighting pathways such as cellular metabolism, the biosynthesis of secondary metabolites, ribosome function, carbon metabolism, protein processing in the endoplasmic reticulum, and amino acid biosynthesis. The examination of 13 candidate genes from three co-located regions revealed Zm00001d050977 as a cytochrome P450 family gene, while the other 2 genes primarily encode proteins involved in stress responses and other biological pathways. In conclusion, this research presents a methodology combining GWAS and meta-analysis to identify genomic regions and potential genes influencing quality traits in silage maize. These findings serve as a foundation for the identification of significant QTLs and candidate genes crucial for improving silage maize quality. Full article

Background/Objetives: Sea lice (Caligus rogercresseyi) pose a major threat to Atlantic salmon (Salmo salar) aquaculture by compromising fish health and reducing production efficiency. While genetic variation in parasite load has been reported, the molecular mechanisms underlying this variation remain unclear. Methods: two sea lice challenge trials were conducted, achieving high infestation rates (47.5% and 43.5%). A total of 85 fish, selected based on extreme phenotypes for lice burden (42 low, 43 high), were subjected to transcriptomic analysis. Differential gene expression was integrated with allele-specific expression (ASE) analysis to uncover cis-regulatory variation influencing host response. Results: Sixty genes showed significant ASE (p < 0.05), including 33 overexpressed and 27 underexpressed. Overexpressed ASE genes included Keratin 15, Collagen IV/V, TRIM16, and Angiopoietin-1-like, which are associated with epithelial integrity, immune response, and tissue remodeling. Underexpressed ASE genes such as SOCS3, CSF3R, and Neutrophil cytosolic factor suggest individual variation in cytokine signaling and oxidative stress pathways. Conclusions: several ASE genes co-localized with previously identified QTLs for sea lice resistance, indicating that cis-regulatory variants contribute to phenotypic differences in parasite susceptibility. These results highlight ASE analysis as a powerful tool to identify functional regulatory elements and provide valuable candidates for selective breeding and genomic improvement strategies in aquaculture. Full article

Background: Prolactin receptor (PRLR) signaling affects breastfeeding and potentially breast cancer treatment response. Methods: The prognostic impact of 20 PRLR single nucleotide polymorphisms (SNPs) in relation to adjuvant treatment groups in patients with primary breast cancer (n = 1701, 2002–2016, Sweden) was evaluated. Genomic DNA was genotyped on Illumina OncoArray, and survival analyses with up to 15-year follow-up were performed. Interaction models, adjusted for potential confounders, were created with different adjuvant treatment modalities: chemotherapy, radiotherapy, tamoxifen, and aromatase inhibitors. Results: Five SNPs (rs7734558, rs6860397, rs2962101, rs7732013, and rs4703503) showed interactions with radiotherapy and were utilized to create seven combined genotypes: six unique and one ‘rare’. Patients carrying combined genotype AG/GG/TT/CC/TC or ‘rare’ combinations derived greater benefits from radiotherapy than other patient groups (both HR_adj ≤ 0.29, Bonferroni-adjusted P_int ≤ 0.039). Expression Quantitative Trait Loci (eQTL) analysis revealed that three PRLR SNPs were associated with decreased PRLR expression. To explore potential SNP-associated effects, gene expression and transcriptional networks were analyzed in the METABRIC cohort and indicated that PRLR-low tumors were associated with reduced DNA repair signaling and enhanced anti-tumoral immunity. Conclusions: PRLR merits further evaluation as a putative pharmacogenomic biomarker in relation to radiotherapy for breast cancer patients. Full article

Wheat leaf rust (Lr), caused by Puccinia triticina Eriks. (Pt), is one of the most important diseases affecting wheat production worldwide. Using resistant wheat cultivars is the most economic and environmentally friendly way to control leaf rust. The Chinese wheat cultivar Xinong1163-4 has shown good resistance to Lr in field trials. To identify the genetic basis of Lr resistance in Xinong1163-4, 195 recombinant inbred lines (RILs) from the Xinong1163-4/Thatcher cross were phenotyped for Lr severity in three environments: the 2017/2018, 2018/2019, and 2019/2020 growing seasons in Baoding, Hebei Province. Bulked segregant analysis and simple sequence repeat markers were then used to identify the quantitative trait loci (QTLs) for Lr adult plant resistance (APR) in the population. As a result, six QTLs were detected, designated as QLr.hbau-1BL.1, QLr.hbau-1BL.2, and QLr.hbau-1BL.3. These QTLs were predicted to be novel. QLr.hbau-4BL, QLr.hbau-4BL.1, and QLr.hbau-3A were identified at similar physical positions to previously reported QTLs. Based on chromosome positions and molecular marker testing, QLr.hbau-1BL.3 shares similar flanking markers with Lr46. Lr46 is a non-race-specific APR gene for leaf rust, stripe rust, and powdery mildew. Similarly, QLr.hebau-4BL showed resistance to multiple diseases, including leaf rust, stripe rust, Fusarium head blight, and powdery mildew. The QTLs identified in this study, as well as their closely linked markers, can potentially be used for marker-assisted selection in wheat breeding. Full article

The intergenic SNP (single-nucleotide polymorphism) rs80860411A>C was identified as a major QTL for drip loss measured on semimembranosus muscle (SM) in pigs. The SNP is located near the GALNT15. The purpose of this study was to analyze the association between rs80860411A>C and fattening, slaughter, and quality traits of Polish pigs. This study was conducted on 235 individuals belonging to two breeds, Polish Large White (n = 187) and Pulawska (n = 48). The rs80860411 genotypes were determined using the PCR-RFLP method. Association analysis was performed for each breed separately. It was shown that rs80860411A>C had a significant effect on fattening performance traits, on several slaughter performance traits, including width of the loin eye and carcass meat content (p ≤ 0.01, p ≤ 0.05), as well as on meat color—redness (a*) (p ≤ 0,05) in Pulawska breed. The obtained results indicate that the studied SNP has the potential to be a QTN and could be included in pig selection programs, especially in Pulawska pigs. Full article