Search Results (1,097)

Fusarium root rot, caused by Fusarium equiseti, poses a significant threat to soybean production. This study aimed to explore the genetic basis of resistance to Fusarium equiseti root rot (FERR) by evaluating the resistance phenotype of 346 soybean germplasms and conducting a genome-wide association study (GWAS) using 698,949 SNP markers obtained from soybean germplasm resequencing data. GWAS analysis identified 101 SNPs significantly associated with FERR resistance, distributed across nine chromosomes, with the highest number of SNPs on chromosomes 13 and 20. Further gene-based association and allele variation analyses identified candidate genes whose mutations are closely related to FERR resistance. To accelerate soybean FERR resistance breeding screening, we developed CAPS markers S13_14464319-CAPS1 and S15_9215524-CAPS2, targeting these SNP sites, and KASP markers based on the S15_9205620-G/A, providing an effective tool for marker-assisted selection (MAS). This study offers a valuable theoretical foundation and molecular marker resources for the functional validation of FERR resistance genes and soybean disease resistance breeding. 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

Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major threat to global rice productivity. Although hybrid rice breeding has significantly enhanced yields, persistent genetic vulnerabilities within restorer lines continue to compromise BB resistance. This study addresses this challenge by implementing functional marker-assisted selection (FMAS) to pyramid two broad-spectrum resistance (R) genes, Xa21 and Xa23, into the elite, yet BB-susceptible, restorer line K608R. To enable precise Xa23 genotyping, we developed a novel three-primer functional marker (FM) system (IB23/CB23/IR23). This system complements the established U1/I2 markers used for Xa21. This recombination-independent FMAS platform facilitates simultaneous, high-precision tracking of both homozygous and heterozygous alleles, thereby effectively circumventing the linkage drag limitations typical of conventional markers. Through six generations of marker-assisted backcrossing followed by intercrossing, we generated K608R2123 pyramided lines harboring both R genes in homozygous states, achieving a recurrent parent genome recovery rate of 96.93%, as determined by single nucleotide polymorphism (SNP) chip analysis. The pyramided lines exhibited enhanced resistance against six virulent Xoo pathogenic races while retaining parental yield performance across key agronomic traits. Our FMAS strategy overcomes the historical trade-off between broad-spectrum resistance and the preservation of elite phenotypes, with the developed lines exhibiting resistance coverage complementary to that of both introgressed R genes. This integrated approach provides breeders with a reliable molecular tool to accelerate the development of high-yielding, disease-resistant varieties, demonstrating significant potential for practical deployment in rice improvement programs. The K608R2123 germplasm represents a dual-purpose resource suitable for both commercial hybrid seed production and marker-assisted breeding programs, and it confers synergistic resistance against diverse Xoo races, thereby providing a pivotal breeding resource for sustainable BB control in epidemic regions. Full article

Microelement deficiencies, often termed “hidden hunger”, represent a significant global health challenge. Optimal human health relies on adequate dietary intake of essential microelements, including selenium (Se), zinc (Zn), copper (Cu), boron (B), manganese (Mn), molybdenum (Mo), iron (Fe), nickel (Ni), and chlorine (Cl). In recent years, there has been a growing focus on vitality and longevity, which are closely associated with the sufficient intake of essential microelements. This review focuses on these nine elements, whose bioavailability in the food chain is critically determined by their geochemical behavior in soils. There is a necessity for an understanding of the sources, soil–plant transfer, and plant uptake mechanisms of these microelements, with particular emphasis on the influence of key soil properties, including pH, redox potential, organic matter content, and mineral composition. There is a dual challenge of microelement deficiencies in agricultural soils, leading to inadequate crop accumulation, and the potential for localized toxicities arising from anthropogenic inputs or geogenic enrichment. A promising solution to microelement deficiencies in crops is biofortification, which enhances nutrient content in food by improving soil and plant uptake. This strategy includes agronomic methods (e.g., fertilization, soil amendments) and genetic approaches (e.g., marker-assisted selection, genetic engineering) to boost microelement density in edible tissues. Moreover, emphasizing the need for advanced predictive modeling techniques, such as ensemble learning-based digital soil mapping, enhances regional soil microelement management. Integrating machine learning with digital covariates improves spatial prediction accuracy, optimizes soil fertility management, and supports sustainable agriculture. Given the rising global population and the consequent pressures on agricultural production, a comprehensive understanding of microelement dynamics in the soil–plant system is essential for developing sustainable strategies to mitigate deficiencies and ensure food and nutritional security. This review specifically focuses on the bioavailability of these nine essential microelements (Se, Zn, Cu, B, Mn, Mo, Fe, Ni, and Cl), examining the soil–plant transfer mechanisms and their ultimate implications for human health within the soil–plant–human system. The selection of these nine microelements for this review is based on their recognized dual importance: they are not only essential for various plant metabolic functions, but also play a critical role in human nutrition, with widespread deficiencies reported globally in diverse populations and agricultural systems. While other elements, such as cobalt (Co) and iodine (I), are vital for health, Co is primarily required by nitrogen-fixing microorganisms rather than directly by all plants, and the main pathway for iodine intake is often marine-based rather than soil-to-crop. Full article

Cryptochromes (CRYs), as essential blue-light photoreceptors, play pivotal roles in modulating plant growth, development, and stress responses. Although CRY-mediated light signaling has been extensively studied in model species, their functions remain limited in wheat. In this work, a comprehensive analysis of the TaCRY gene family was performed in wheat, identifying 12 TaCRY members localized to distinct chromosomes 2, 6, and 7. TaCRYs contain the conserved PHR and CCT domains and diverse gene structures. Collinearity relationships indicated their dynamic evolution patterns during polyploidization. Cis-acting elements of TaCRY members associated with light responsiveness, phytohormone signaling, and abiotic stress were also identified. Transcriptome analysis revealed that the differential expression patterns of TaCRY members under seed vigor process. This study expands our understanding of TaCRY diversity and provides valuable molecular information for marker-assisted selection in wheat improvement. 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

Background: Rheumatoid arthritis (RA) is a chronic autoimmune disorder that predominantly affects synovial joints, leading to inflammation, pain, and progressive joint damage. Despite therapeutic advancements, the molecular basis of established RA remains poorly defined. Methods: In this study, we conducted an untargeted plasma proteomic analysis using two-dimensional differential gel electrophoresis (2D-DIGE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) in samples from RA patients and healthy controls in the discovery phase. Results: Significantly (ANOVA, p ≤ 0.05, fold change > 1.5) differentially abundant proteins (DAPs) were identified. Notably, upregulated proteins included mitochondrial dicarboxylate carrier, hemopexin, and 28S ribosomal protein S18c, while CCDC124, osteocalcin, apolipoproteins A-I and A-IV, and haptoglobin were downregulated. Receiver operating characteristic (ROC) analysis identified CCDC124, osteocalcin, and metallothionein-2 with high diagnostic potential (AUC = 0.98). Proteins with the highest selected frequency were quantitatively verified by multiple reaction monitoring (MRM) analysis in the validation cohort. Bioinformatic analysis using Ingenuity Pathway Analysis (IPA) revealed the underlying molecular pathways and key interaction networks involved STAT1, TNF, and CD40. These central nodes were associated with immune regulation, cell-to-cell signaling, and hematological system development. Conclusions: Our combined proteomic and bioinformatic approaches underscore the involvement of dysregulated immune pathways in RA pathogenesis and highlight potential diagnostic biomarkers. The utility of these markers needs to be evaluated in further studies and in a larger cohort of patients. Full article

Nightlily (Hemerocallis citrina Baroni) is mainly cultivated for bud consumption with medicinal, nutritional, and economic value. Enhancing nightlily yield is one of the most significant breeding goals of modern agriculture of H. citrina breeding objective, but it also faces great challenges. In this study, an intraspecific hybridization population crossed between two varieties, ‘Liuyuehua’ and ‘Datong Huanghua’ of Hemerocallis, was used to establish 715 F₁ individuals. Phenotypic data for eight floral traits, including scape number, bud number, scape length, scape diameter, bud length, bud diameter, fresh flower bud weight, and dry flower bud weight, were collected from 715 F₁ individuals over a three-year period (2022, 2023, and 2024). The Simple Repeat Sequence (SSR) markers were validated to genotype the 116 random F₁ individuals and to construct a linkage map. The intraspecific hybridization map contained 11 linkage groups. A total of 169 SSR markers were used to construct a linkage map, spanning a total map length of 1605.3 cM, with an average marker interval of 9.50 cM. The linkage map revealed 11 floral QTLs from 7.21% to 24.29% of phenotypic variation. Through collinearity analysis, it was found that 122 markers could be aligned to the published genome sequence of H. citrina. A total of five candidate genes for floral traits were predicted. The linkage map is essential for mapping and marker-assisted progeny selection that will accelerate the pace of nightlily breeding. Full article

Morkhor 60-3 is an upland rice variety primarily cultivated in northeastern Thailand. This glutinous rice is valued for its adaptability and rich aroma but remains susceptible to significant diseases, particularly blast and bacterial blight. Using resistant varieties represents the most cost-effective approach to address this limitation. This study incorporated the QTLs/genetic markers qBl1, qBl2, and xa5 from Morkhor 60-1 through marker-assisted backcrossing. From the BC₁F₃ population, ten lines were selected based on their parentage and evaluated for blast resistance using a spray inoculation method with 12 isolates of Pyricularia oryzae, and for bacterial blight (BB) resistance using a leaf-clipping method with nine isolates of Xanthomonas oryzae pv. oryzae. Broad-spectrum resistance (BSR) was also assessed in the lines for both diseases. Subsequently, BC₁F₄ lines were evaluated for field performance, including agronomic traits and aroma. Results identified three superior lines, BC₁F₄ 22-7-140-4, BC₁F₄ 22-7-322-5, and BC₁F₄ 22-7-311-9, that demonstrated resistance to both BB and blast pathogens with average BSR values of 0.61 and 1.00, 0.66 and 1.00, and 0.55 and 0.87, respectively. These lines also exhibited enhanced performance in flowering date, plant height, panicle number per plant, grain number per plant, and grain weight. These findings demonstrate the effectiveness of marker-assisted selection (MAS) for gene pyramiding in rice improvement. Full article

The transforming growth factor-beta (TGF-β) superfamily plays a crucial role in regulating female reproductive traits, particularly litter size, in small ruminants, such as sheep and goats. This review comprehensively examines the molecular mechanisms through which TGF-β superfamily members—including bone morphogenetic proteins (BMPs), growth differentiation factor 9 (GDF9), inhibin (INHA and INHB), and associated signaling genes—influence ovarian follicular development, ovulation rate, and ultimately, litter size. We synthesize recent findings on polymorphisms in key genes, such as BMPR1B, BMP15, GDF9, inhibins and SMADs family genes, across diverse sheep and goat breeds worldwide. The manuscript highlights how specific mutations in these genes create an intricate signaling network that modulates granulosa cell proliferation, follicular sensitivity to FSH, and the prevention of dominant follicle selection. These molecular interactions result in increased ovulation rates and larger litter sizes in prolific breeds. The gene dosage effects observed in heterozygous versus homozygous mutation carriers further illuminate the complex nature of these reproductive regulations. This improved the understanding of the genetic basis for prolificacy provides valuable insights for marker-assisted selection strategies aimed at enhancing reproductive efficiency in small ruminant breeding programs, with significant implications for improving livestock productivity and economic outcomes. Full article

The large yellow croaker (Larimichthys crocea) is one of China’s most economically important marine fish species, with its cage culture production leading the nation for many years. However, the rapid expansion of aquaculture has brought challenges such as germplasm degradation, reduced disease resistance, inconsistent product quality, and low adoption of improved strains, which have hindered the sustainable development of the industry. The primary objective of this review is to summarize the current practices and challenges in seedling selection for L. crocea. The secondary objectives include discussing the influence of genetic, physiological, and environmental factors on growth performance and proposing future research directions for sustainable breeding programs. This review covers key topics including morphological screening, growth performance evaluation, genetic diversity conservation, disease resistance improvement, and adaptation to environmental stress. It also explores the application of modern technologies such as marker-assisted selection, intelligent monitoring, environmental control, precision feeding, and disease prevention. Moreover, it highlights core issues in current breeding practices, such as over-reliance on single-trait selection and insufficient integration of environmental adaptability and disease resistance. Finally, future trends are discussed, emphasizing the integration of genomic tools with artificial intelligence to promote intelligent, precise, and sustainable breeding approaches. These insights aim to enhance aquaculture productivity while supporting long-term ecological balance and industry sustainability. Full article

Phenolic compounds are important targets in olive breeding due to their health benefits and impact on fruit and oil quality. Fruit phenolic profiling enables efficient screening of large germplasm collections without oil extraction, but environmental variability, especially year-to-year differences, affects their expression. The aim of this study was to assess the genotypic influence on fruit phenolic composition, based on a three-year evaluation of 10 wild olive genotypes and 75 cultivars from an olive core collection. Each genotype was sampled in at least two seasons, with 1 to 3 trees analyzed annually. Variance analysis revealed significant genetic variation among cultivars and notable genotype-by-year interactions for certain phenolics. Broad-sense heritability was generally high for most compounds, although some, such as ligstroside and ligstroside aglycone, showed greater environmental sensitivity. Best linear unbiased predictions (BLUPs) were highly correlated with average relative phenotypic values. Clustering analyses identified strong associations among key phenolic compounds and highlighted distinct metabolic profiles separating wild and cultivated genotypes, reflecting differences in phenolic accumulation patterns. These findings demonstrate the genetic and environmental influences on olive fruit phenolics and provide reliable estimates to support future marker-assisted selection studies aimed at developing useful tools in olive breeding programs. Full article

Vernalization genes (Vrn) play a key role in plant adaptation to various geographic locations and their allelic diversity can have fundamental importance for breeding programs. In the current study, 340 barley genotypes were studied, including germplasm accessions and advanced breeding lines. For phenotype evaluation in South-Eastern Kazakhstan, the transition of barley plants from vegetative to reproductive stages was estimated in field trials with spring- and winter-sown seeds. For molecular analysis, 10 previously described molecular markers were studied in three barley vernalization loci: Vrn-H1, Vrn-H2 and Vrn-H3. The comparison between molecular results and phenotypes for plant development confirmed 211 spring genotypes, 56 winter and 28 facultative. Vrn-H1 haplotypes 1A and recessive allele vrn-H3 were in the majority. Best spring and winter high-yielding advanced breeding lines were identified. Based on Vrn allele combination, a breeding line 76/13-4 with facultative type development showed superior results in both winter and spring sowings, presenting a new prospective barley cultivar that can be grown equally either in spring or winter sowing conditions. The presented results can be used for barley marker-assisted selection predicting crosses with favourable combinations of Vrn alleles for prospective breeding line development. Full article

Grass carp (Ctenopharyngodon idella), a globally important aquaculture species, exhibits protein-dependent growth plasticity, requiring genetic improvement for sustainable production. This study integrates genome-wide association analysis (GWAS) and genomic selection (GS) to unravel the genetic architecture of four growth traits, body weight, body length, body height, and body depth, in grass carp fed with diets of varying protein levels (20%, 25%, 30%, and 35%). Using a 21K liquid SNP array, we identified 62,736 high-quality SNPs across 24 chromosomes, with 90 SNPs significantly associated with growth traits. Notably, three SNPs (SLG14_24417024, SLG14_24417039, SLG24_30276273) exhibited pleiotropic effects on multiple traits. Functional annotation of 276 candidate genes near significant SNPs revealed enrichment in keratinocyte development, septin cytoskeleton organization, and heat acclimation pathways. Genomic prediction achieved accuracies up to 0.79 for body weight traits using 1533 optimal markers. This study provides the first comprehensive SNP resource for grass carp growth traits with different dietary treatments, bridging GWAS and genomic prediction to accelerate marker-assisted selection. Our findings not only advance genetic breeding strategies but also inform protein diet optimization, minimizing economic and environmental costs in aquaculture. Full article

The optimal exploitation of genetic variability is essential for the success of breeding programs and for identifying quantitative trait loci (QTLs) in genetic association studies. These benefit from populations with a high number of individuals; however, they are expensive since extensive plant maintenance, characterization, and evaluation are required. Core collections offer a practical solution by reducing the number of individuals while representing the original diversity of the population. This study aimed to construct a core collection for Japanese plum to serve as pre-breeding material and enable genetic association studies for traits that are difficult to evaluate. Starting from a population of 1062 individuals genotyped by sequencing, genetic distance and allele coverage metrics were applied to construct several core collections. Genetic parameters and phenotype distribution comparisons allowed for the selection of a core collection of 108 individuals that maximized genetic variability while representative of the original population, confirmed by linkage disequilibrium and population structure analyses. Its usefulness was validated by successfully mapping flowering and maturity dates through marker–trait association. The core collection constructed here will help in the study of fruit quality traits and biotic and abiotic responses, ultimately generating molecular markers to assist the crop’s molecular breeding. Full article