Search Results (548)

Background/Objectives: Miscanthus Andersson, a genus of perennial grasses that includes wild relatives of key crop species, remains poorly characterized in terms of genetic diversity and evolutionary relationships. The aim of this study was to elucidate the phylogenetic structure of Miscanthus through comparative genomic analysis of the chloroplast genomes of six Korean species. Methods: Complete chloroplast genomes were assembled and analyzed for six Miscanthus species. Informative nucleotide motifs and their associated gene locations were identified as potential markers, and their phylogenetic relationships with related crops were examined. Results: The chloroplast genomes exhibited a conserved quadripartite structure, with genome sizes and GC contents within typical ranges. Analysis of codon usage showed a preference for A/U-ending codons, consistent with patterns in other angiosperms. Simple sequence repeats and long repeats demonstrated non-random distributions, indicating their value as molecular markers for phylogenetic and population studies. Comparative analyses confirmed structural conservation across Miscanthus species, whereas variation in non-coding regions provided important phylogenetic signals. Phylogenetic reconstruction based on 21 chloroplast genomes revealed four major clades, corroborating previous findings and highlighting complex evolutionary relationships within Miscanthus, including close affinities between African and Himalayan species and the genus Saccharum L. Conclusions: This study provides complete chloroplast genomes of six Miscanthus species, contributing to enhanced understanding of the relationships within the subtribe Saccharinae. The findings support the inclusion of Miscanthus species in the Korea Crop Wild Relatives inventory and highlight their potential as a genetic resource for breeding programs aimed at enhancing crop resilience to environmental stress. Full article

Improving ovine reproductive efficiency is an important breeding goal that could substantially enhance economic viability in the sheep industry. The histone cell cycle regulator (HIRA) gene has been functionally validated as a reproductive regulator in model organisms such as Drosophila and murine species; however, research on the effects of HIRA on the prolificacy in sheep remains scarce. Thus, this study aimed to investigate the association between genetic variants of HIRA and litter size in sheep. In brief, we identified 15 novel exonic mutations in the Sonid sheep breed via direct sequencing. Notably, a linkage disequilibrium including the c.1521C>G, c.1572C>T, and c.1578G>A mutations on exon 14 of HIRA exhibited a significant association with litter size in Sonid sheep (p < 0.01). Meanwhile, it was predicted that mutations play a major role in enhancing the stability of the mRNA secondary structure by lowering the minimum free energy, and mutations were also thought to change the mRNA secondary structure of ovine HIRA. Therefore, these findings may provide potentially useful molecular markers for optimizing reproductive performance in Sonid sheep. Full article

Leaf rust, a devastating fungal disease caused by Puccinia triticina (Pt), severely impacts wheat quality and yield. Identifying genetic loci for wheat leaf rust resistance, developing molecular markers, and breeding resistant varieties is the most environmentally friendly and economical strategy for disease control. This study utilized a recombinant inbred line (RIL) population of Doumai and Shi4185, combined with the wheat 90 K single nucleotide polymorphisms (SNPs) chip data and maximum disease severity (MDS) of leaf rust from four environments, to identify adult plant resistance (APR) loci through linkage mapping. Additionally, kompetitive allele-specific PCR (KASP) markers suitable for breeding were developed, and genetic effects were validated in a natural population. In this study, 5 quantitative trait loci (QTL) on chromosomes 1B (2), 2A and 7B (2) were identified through inclusive composite interval mapping, and named as QLr.lfnu-1BL1, QLr.lfnu-1BL2, QLr.lfnu-2AL, QLr.lfnu-7BL1 and QLr.lfnu-7BL2, respectively, explaining 4.54–8.91% of the phenotypic variances. The resistance alleles of QLr.lfnu-1BL1 and QLr.lfnu-1BL2 originated from Doumai, while the resistance alleles of QLr.lfnu-2AL, QLr.lfnu-7BL1 and QLr.lfnu-7BL2 came from Shi4185. Among these, QLr.lfnu-1BL2, QLr.lfnu-7BL1 and QLr.lfnu-7BL2 overlapped with previously reported loci, whereas QLr.lfnu-1BL1 and QLr.lfnu-2AL are likely to be novel. Two KASP markers, QLr.lfnu-2AL and QLr.lfnu-7BL, were significantly associated with leaf rust resistance in a diverse panel of 150 wheat varieties mainly from China. Totally, 34 potential candidate genes encoded the NLR proteins, receptor-like kinases, signaling kinases and transcription factors were selected as candidate genes for the resistance loci. These findings will provide stable QTL, available breeding KASP markers and candidate genes, and will accelerate the progresses of wheat leaf rust resistance improvement through marker-assisted selection breeding. Full article

Yield components are the most important breeding objectives, directly determining maize high-yield breeding. It is well known that these traits are controlled by a large number of quantitative trait loci (QTL). Therefore, deeply understanding the genetic basis of yield components and identifying key regulatory candidate genes can lay the foundation for maize marker-assisted selection (MAS) breeding. In this study, our aim was to identify the key genomic regions that regulate maize yield component formation through bioinformatic methods. Herein, 554 original QTLs related to 11 yield components, including ear length (EL), hundred-kernel weight (HKW), ear weight (EW), cob weight (CW), ear diameter (ED), cob diameter (CD), kernel row number (KRN), kernel number per row (KNR), kernel length (KL), grain weight per plant (GW), and kernel width (KW) in maize, were collected from the MaizeGDB, national center for biotechnology information (NCBI), and China national knowledge infrastructure (CNKI) databases. The consensus map was then constructed with a total length of 7154.30 cM. Approximately 80.32% of original QTLs were successfully projected on the consensus map, and they were unevenly distributed on the 10 chromosomes (Chr.). Moreover, 44 meta-QTLs (MQTLs) were identified by the meta-analysis. Among them, 39 MQTLs controlled two or more yield components, except for the MQTL4 in Chr. 1, which was associated with HKW; MQTL11 in Chr. 2, which was responsible for EL; MQTL19 in Chr. 3, which was related to KRN; MQTL26 in Chr. 5, which was involved in HKW; and MQTL36 in Chr. 7, which regulated EL. These findings were consistent with the Pearson correlation results, indicating that these traits exhibited co-linked heredity phenomena. Meanwhile, 159 candidate genes were found in all of the above MQTLs intervals, of which, 29 genes encoded E3 ubiquitin protein ligase, which was related with kernel size and weight. Other genes were involved in multiple metabolic processes, including plant hormones signaling transduction, plant growth and development, sucrose–starch synthesis and metabolism, and reproductive growth. Overall, the results will provide reliable genetic resources for high-yield molecular breeding in maize. Full article

Dioscorea polystachya (Chinese yam) is a crop valued for both medicinal and edible purposes, and exhibits rich genetic diversity. However, research into its germplasm resources remains understudied, and molecular breeding efforts lag behind. To bridge this gap, this study employed an integrated approach, combining the analysis of 23 phenotypic traits (17 qualitative and 6 quantitative) with genotyping using 19 polymorphic SSR markers. This combined strategy was applied to 53 accessions collected across 16 Chinese provinces to assess genetic diversity, population structure, and marker–trait associations. Phenotypic analysis revealed high diversity, with the Shannon diversity index (I) ranging from 0.09 to 1.15 for qualitative traits and from 1.45 to 1.79 for quantitative traits. Tuber traits exhibited the highest variability (with a CV up to 71.45%), indicating significant potential for yield improvement. Principal component analysis distilled phenotypic variation into eight principal components (accounting for 73.13% of the cumulative variance), and elite germplasm (e.g., DP24, DP52) was selected for breeding based on this analysis. Stepwise regression prioritized eight core evaluation traits (e.g., flowering rate, tuber length). SSR markers amplified 80 alleles (mean 4.211/locus), showing moderate genetic diversity (He = 0.529, PIC = 0.585). Population structure analysis divided accessions into two subpopulations, correlated with geographic origins: Group 1 (northern/southwestern China) and Group 2 (central/eastern China), reflecting adaptation to local climates and human selection. Association analysis identified 10 SSR loci significantly linked (p < 0.01) to key traits, including YM07_2 (flowering, R² = 13.94%), YM37_2 (leaf margin color, R² = 19.03%), and YM19_3 (leaf width, R² = 19.34%). This study establishes a comprehensive genetic framework for Chinese yam, offering molecular tools for marker-assisted breeding and strategies to conserve high-diversity germplasm, thereby enhancing the utilization of this orphan crop. Full article

Cannabis sativa L. (2n = 2x = 20) is a widely recognized species within the Cannabaceae family. Despite its utilization for medicinal, recreational, and industrial purposes, alongside its extensive historical background, the number of genetic and biotechnological studies of this plant species has decreased due to legal ramifications and prohibition campaigns associated with its use and cultivation. For many years, the development of novel varieties has been pursued solely by cultivators, as domestic growers have transitioned their work from cultivation to breeding Cannabis lineages. Recently, the application of genomics has facilitated a surge in methodologies aimed at marker-assisted selection, germplasm management, genetic differentiation, authentication of cultivated varieties or cultivars, and forensic applications such as safeguarding intellectual property rights. Nevertheless, the utilization of molecular markers for the advancement of commercial varieties through marker-assisted breeding (MAB) frameworks remains rare. This investigation was designed to evaluate a previously established informative microsatellite (SSR) array for the genotyping of drug-type Cannabis sativa cultivars derived from seeds of European origin. A total of 171 samples from 20 varieties were collected from European distributors and analyzed for genetic uniformity and population structure. The results were then compared with previously analyzed hemp samples and drug-type samples of Canadian origin, revealing the identification capabilities of our SSR genotyping method. Full article

Bacterial wilt, caused by Ralstonia solanacearum, is a major constraint to tomato production globally. To uncover resistance loci and develop efficient molecular tools for breeding, we conducted disease phenotyping over two growing seasons, which revealed consistent variation in resistance and moderate broad-sense heritability (H² = 0.22–0.28), suggesting a genetic basis. A genome-wide association study (GWAS) was performed on a diverse panel of 267 tomato accessions, evaluated against two R. solanacearum strains. A major resistance locus was identified on chromosome 12, with the strongest association observed at SNP S12_2992992, located within a gene encoding a leucine-rich repeat (LRR) receptor-like protein. Haplotype analysis indicated that the resistance-associated allele is relatively rare (~13.5%) in the population, underscoring its potential value in breeding programs. Functional validation in an F₂ population derived from a cross between the susceptible ‘Seedathip6’ and the resistant ‘Hawaii 7996’ confirmed that the TT genotype at S12_2992992 was significantly associated with enhanced resistance. A Kompetitive Allele Specific PCR (KASP) marker was developed for this SNP, facilitating cost-effective and high-throughput selection. Collectively, these findings establish S12_2992992 as a robust and functionally informative marker, offering a valuable tool for accelerating bacterial wilt resistance breeding in tomato through marker-assisted selection. Full article

Drought severely threatens wheat production. Under drought conditions, root system architecture (DRSA)-related traits in common wheat significantly affect wheat production. In China, Zhoumai16 is a high-yield winter wheat variety in the Huang-Huai wheat region. It is suitable for high-fertilizer and high-water cultivation and has moderate drought tolerance. DK171 is a newly developed high-yield and stress-tolerant variety, with higher drought tolerance. Thus, identifying genetic loci associated with DRSA-related traits from DK171 and developing available molecular markers are of great importance for enhancing wheat stress tolerance breeding. In this study, DRSA-related traits, including the total root dry weight (DDRW), total root length (DTRL), total root area (DTRA), and the number of root tips (DNRT) under drought stress, were assessed using the hydroponic system in Zhoumai16/DK171 recombinant inbred lines (RIL) population. A total of five quantitative trait loci (QTL) for DRSA-related traits were identified, e.g., QDDRW.daas-1BL, QDTRS.daas-4AL, QDNRT.daas-4DS, QDTRL.daas-3AL, and QDDRW.daas-5D, and explained 6.1% to 18.9% of the phenotypic variances, respectively. Among these, QDTRS.daas-4AL and QDTRL.daas-3AL were consistent with previous reports, whereas the QDDRW.daas-1BL, QDNRT.daas-4DS, and QDDRW.daas-5D are novel. The favorable alleles of QDTRS.daas-4AL and QDNRT.daas-4DS were inherited from Zhoumai16, whereas the favorable alleles for QDDRW.daas-1BL, QDTRL.daas-3AL, and QDDRW.daas-5D were contributed by DK171. Furthermore, five kompetitive allele-specific PCR (KASP) markers, Kasp_1BL_DTRS (QDDRW.daas-1BL), Kasp_3AL_DTRS (QDTRL.daas-3AL), Kasp_4A_DTRS (QDTRA.daas-4A), Kasp_5D_DDRW (QDDRW.daas-5D), and Kasp_4D_DNRT (QDNRT.daas-4D), were developed and validated in a diverse panel with 108 wheat varieties mainly from China. Additionally, eight candidate genes related to plant hormone regulation, ABC transporters, and calcium-dependent lipid-binding domain proteins were identified. This study offers new loci, candidate genes, and available KASP markers for wheat drought tolerance breeding and facilitating progress in developing drought-tolerant wheat cultivars. Full article

Low light intensity is a major abiotic stress that severely affects rice yields, particularly in India and Southeast Asia, causing yield reductions of 35–40% during the wet season compared to the dry season. Tolerant rice genotypes exhibit adaptive changes at anatomical, physiological, biochemical, and molecular levels under low-light stress, enabling higher yields compared to susceptible varieties. Our study identified 20 novel QTLs associated with grain yields and nine related traits under low-light and control (normal)-light conditions, using a recombinant inbred line (RIL) population derived from the cross between the low-light-tolerant variety Swarnaprabha and the low-light-susceptible variety IR8. Across the Kharif seasons of 2019 and 2021, 33 stable QTLs were identified, with 11, 13, and 9 QTLs specific to low-light, normal-light, and both conditions, respectively. Of these, Swarnaprabha contributed 28 QTLs, while five were contributed by IR8. Notably, the study identified 11 and 9 novel QTLs under low-light and both conditions, respectively. Three hotspot regions on chromosomes 1, 4, and 8 were identified. These regions harbored 10 novel QTLs and revealed twenty candidate genes, out of which three key hub genes, OsAUX1, OsSBDCP1, and OsNPF5.16, were identified. These hub genes are involved in hormone signaling, starch metabolism, and nitrogen metabolism, respectively. A comprehensive expression analysis of these genes indicated that they are linked to low-light tolerance, offering deeper insights into the genetic and molecular mechanisms underlying low-light resilience. These findings provide valuable genomic resources and potential markers for breeding programs for improving rice productivity under low-light conditions. Full article

To identify molecular markers associated with wool traits in fine-wool sheep, we examined genetic polymorphisms in the NOTCH2 and CD1A genes in 944 Subo Merino sheep in this study. Subsequently, we performed association analyses between mutation sites in the NOTCH2 and CD1A genes and wool traits using SAS 9.4 software, followed by linkage disequilibrium (LD) analysis of different mutation sites using Haploview 4.2 software. Additionally, bioinformatics tools were employed to predict the potential impacts of missense mutations on protein secondary and tertiary structures. Finally, quantitative PCR (qPCR) was used to assess the expression levels of the NOTCH2 and CD1A genes. Genetic analysis revealed six polymorphic sites in NOTCH2 and CD1A, all of which were missense mutations. Two SNPs in NOTCH2 (SNP1 and SNP2) showed significant associations with the coefficient of variation of fibre diameter, and SNP1 was also associated with greasy fleece weight. Four SNPs in CD1A (SNP3–SNP6) were significantly associated with fibre diameter standard deviation, and SNP3, SNP4, and SNP5 were additionally associated with crimp number. LD analysis revealed that SNP3, SNP4, and SNP5 were closely linked. Bioinformatics analysis indicated that the mutations caused alterations in the secondary and tertiary structures of the NOTCH2 and CD1A proteins. qPCR results showed that the CD1A gene was highly expressed in the fine wool fibre group compared with the ultra-fine wool fibre group. In conclusion, this study revealed a genetic association between NOTCH2 and CD1A and wool traits. The results are expected to provide a theoretical foundation for breeding wool traits in Subo Merino sheep, thereby enhancing the economic value of fine wool. Full article

Background: High-temperature stress is one of the major abiotic stresses limiting cotton production. Identifying genetic loci and genes for heat tolerance is crucial for breeding heat-tolerant varieties. Methods: Given the complexity of heat tolerance phenotypes in cotton, this study, which focused on resource materials, identified an A/C SNP mutation at position 5486185 on chromosome D06 within the heat tolerance interval through genome-wide association studies (GWAS) of natural Gossypium hirsutum populations. Results: A total of 308 resource materials were identified and evaluated for their heat tolerance phenotypes over two years of field research. Kompetitive allele-specific PCR (KASP) molecular markers were developed on the basis of the D06-5486185 SNP to characterize the heat tolerance phenotypes of these 308 resource materials. Genotyping for heat tolerance-related traits and agronomic traits was also performed. Materials with the C/C haplotype at position D06-5486185 presented increased heat tolerance (higher pollen viability (PV), leaf area (LA), chlorophyll (Chl) and number of bolls on the third fruit branch (FB3) and a lower number of dry buds (DBs) and drop rate (DR)) without negatively impacting key yield traits. This locus is located in the intergenic region of two adjacent bZIP transcription factor genes (GH_D06G0408 and GH_D06G0409). Expression analysis revealed that the expression levels of these two genes were significantly greater in heat-tolerant accessions (C/C type) than in sensitive accessions and that their expression levels were significantly correlated with multiple heat-tolerant phenotypes. Conclusions: In summary, this study developed a Kompetitive Allele Specific PCR (KASP) marker associated with heat tolerance in G. hirsutum and identified two key heat tolerance candidate genes. These results provide an efficient marker selection tool and important genetic resources for the molecular breeding of heat-tolerant G. hirsutum, laying an important foundation for further establishing a molecular marker-assisted breeding system for heat tolerance in G. hirsutum. Full article

Excessive abdominal fat deposition accompanying rapid growth in broiler chickens seriously affects production efficiency. Using divergently selected broiler lines from Northeast Agricultural University, we integrated transcriptome sequencing, whole-genome resequencing, and three-dimensional genomic data to identify key SNPs affecting abdominal fat deposition. From 3,850,758 initial SNPs, 22,721 high-quality SNPs were selected (|ΔAF| ≥ 0.9) and validated to obtain 7341 reliable SNPs. GWAS identified 16 SNPs significantly associated with abdominal fat weight, while LD analysis revealed 22 highly linked SNPs, finally determining 2302 candidate SNPs. Transcriptome analysis identified 825 differentially expressed genes (p ≤ 0.05, |FC| ≥ 1.5). Functional annotation revealed 201 SNPs located in differentially expressed gene regions, including 8 coding SNPs and 193 non-coding SNPs, with an additional 15 SNPs potentially regulating through long-range chromatin interactions. Mechanistic analysis showed that coding SNPs regulate gene expression by altering codon translation rates or mRNA stability, while non-coding SNPs regulate transcription by affecting transcription factor binding. Phenotypic association analysis demonstrated that all 213 SNPs can cause ≥2-fold differences in abdominal fat weight, with 182 SNPs causing ≥3-fold differences. This study successfully identified 213 functional SNPs affecting abdominal fat deposition in broilers and revealed their molecular basis for regulating fat metabolism through multiple mechanisms, providing important genetic markers for low-fat breeding in broilers. Full article

The wool of sheep consists of structurally intricate natural fibres that can be processed and manufactured into a range of products. It is prized for its insulation, moisture-buffering capability, flame resistance, and biodegradability. These features arise from its unique fibre architecture and specialised protein composition, which set it apart from most other natural and synthetic fibres. However, despite these novel characteristics, wool fibre variation hampers its uses and reduces its ability to compete with other fibres. This review summarises our current knowledge of wool fibre biology. It begins with a description of wool’s functional properties and performance attributes, then explores the structural foundations of these properties, the molecular basis of fibre trait variation, and prospects for improving fibre quality using genetic approaches. Particular attention is given to the wool keratin and keratin-associated protein genes, their spatiotemporal expression patterns, and genetic polymorphism that may influence fibre characteristics. Opportunities for the genetic improvement of sheep are discussed, including the use of genetic modification and marker-assisted selection. Challenges in interpreting gene–trait associations, particularly from high-throughput omics studies, are highlighted, along with the need for functionally validated genetic markers. Potential trade-offs between wool characteristics and other production and reproductive traits are considered, emphasising the need for balanced breeding approaches. By integrating insights from structural biology, molecular genetics, and breeding strategies, this review provides a foundation for wool fibre improvement. Full article

The Indonesian Local Ettawah Goat (ILEG) exhibits substantial genetic variation, suggesting its potential for high productivity and promote sustainable practices in farm animal breeding. This study aimed to investigate the molecular characteristics of prolific ILEG by identifying potential candidate genes through polymerase chain reaction (PCR) analysis of the bone morphogenetic protein receptor type 1B (BMPR1B) gene with two variants: alleles G and A. The research involved PCR amplification and sequencing of the BMPR1B A allele, followed by a combined PCR approach integrating both A and G alleles for genotyping. Blood samples were collected from 73 does with documented prolificacy history and 358 does without prolificacy histories, sourced from seven village breeding operations in East Java. PCR amplification yielded fragments of 556–1181 base pairs in all samples. Haplotype analysis revealed 15 unique haplotypes with a diversity of 0.94 and a mutation frequency of 27.15%. Integration of the BMPR1B alleles G and A revealed polymorphic prolific traits. Polymorphism analysis of 385 ILEGs demonstrated allele frequencies of 0.55 for allele A and 0.45 for the allele G. Average fecundity rates associated with the BMPR1B polymorphism were 1.49 offspring for the homozygous AA, 1.60 for the heterozygous GA, and 1.89 for the homozygous GG. While overall differences among genetic groups were approached statistically significantly (Kruskal–Wallis, p = 0.056), pairwise comparison (Mann–Whitney test) revealed that homozygous GG was significantly associated with higher prolificacy compare to the heterozygous GA (p = 0.029) and homozygous AA (p = 0.040). Similar results were also obtained from data without documented history. These findings suggest that the GG polymorphism of BMPR1B may increase prolificacy in ILEG. Furthermore, the higher frequency of allele G highlights the importance of considering prolificacy traits in breeding selection strategies to enhance sustainable genetic improvement and increase litter size in ILEG. It is recommended to apply dual-primer specific amplification and fragment size differentiation as key molecular approaches for polymorphism of the BMPR1B gene and prolificacy, since these methods can highlight genetic variation and provide valuable markers for breeding programs of the Indonesian Local Etawah Goat. Full article

Lignocellulosic biomass may play a major role in the production of biofuels, bioplastics, sugar, paper, and various other industrial products. In addition, it is a key trait in plants due to its contribution to lodging resistance. Fiber also shows a significant negative correlation with most yield traits and all sugar traits. As the most harvested crop globally by tonnage, sugarcane is an important resource for both sugar and bioenergy production. In this study, a panel of sugarcane clones was utilized to investigate the fiber content. This panel included 17 core parental lines derived from 11 countries involved in sugarcane cultivation and breeding. It represented the genetic base of commercial sugarcane breeding programs in China and other countries. The objective of this research was to identify molecular markers and candidate genes associated with fiber content in sugarcane using genome-wide association studies (GWASs). By integrating 5,964,084 high-quality single-nucleotide polymorphisms (SNPs) with phenotypic data collected across five different environments, a total of 69 SNPs spanning 41 quantitative trait loci (QTLs) were identified. Based on functional annotations and genomic positions, these QTLs contained 52 candidate genes. These candidate genes encoded the ultraviolet-B receptor (UVR8), leucine-rich repeat receptor-like kinases (LRR-RLKs), serine/threonine kinases (STKs), cellulose synthase (CESA), vegetative cell wall protein glycoproteins1 (gp1), F-box protein, MYB transcription factor, and so on. These genes could directly or indirectly influence the fiber content in sugarcane. Furthermore, according to previous studies, among these candidate genes, five located in four QTL regions were proposed to be the most critical. They included Sspon.02G0041160-2C, encoding CESA; Sspon.03G0039010-1C and Sspon.03G0039030-1C, both encoding gp1; Sspon.06G0023090-1B, encoding an F-box protein; and Sspon.07G0019440-2C, encoding a MYB transcription factor. The genetic basis of the fiber content was explored using elite breeding lines and their derivatives from the Chinese sugarcane breeding program. These candidate genes represent promising targets for future functional studies and may contribute to the development of different types of sugarcane varieties with correspondingly suitable fiber content through marker-assisted selection. Full article