Genetic Linkage Research Articles

Genetic mapping of loci affecting seedling and adult-plant resistance to powdery mildew derived from two CIMMYT wheat lines.

PM3 and PM8 alleles carried by two CIMMYT wheat lines confer powdery mildew resistance in seedlings and/or adult plants. A stage-specific epistatic interaction was observed between PM3 and PM8. Powdery mildew is an important foliar disease of wheat. Major genes for resistance, which have been widely used in wheat breeding programs, are typically effective against only limited numbers of virulence genes of the pathogen. The main aim of this study was to map resistance loci in wheat lines 7HRWSN58 and ZWW09-149 from the International Maize and Wheat Improvement Center (CIMMYT). Doubled haploid populations (Magenta/7HRWSN58 and Emu Rock/ZWW09-149) were developed and grown in controlled environment experiments and inoculated with a composite of Blumeria graminis f.sp. tritici isolates that had been collected at various locations in Western Australia. Plants were assessed for powdery mildew symptoms (percentage leaf area diseased) on seedlings and adult plants. Populations were subjected to genotyping-by-sequencing and assayed for known SNPs in the resistance gene PM3. Linkage maps were constructed, and markers were anchored to the wheat reference genome sequence. In both populations, there were asymptomatic lines that exhibited no symptoms. Among symptomatic lines, disease severity varied widely. In the Magenta/7HRWSN58 population, most of the observed variation was attributed to the PM3 region of chromosome 1A, with the allele from 7HRWSN58 conferring resistance in seedlings and adult plants. In the Emu Rock/ZWW09-149 population, two interacting quantitative trait loci were mapped: one at PM3 and the other on chromosome 1B. The Emu Rock/ZWW09-149 population was confirmed to segregate for a 1BL·1RS translocation that carries the PM8 powdery mildew resistance gene from rye. Consistent with previous reports that PM8-derived resistance can be suppressed by PM3 alleles, the observed interaction between the quantitative trait loci on chromosomes 1A and 1B indicated that the PM3 allele carried by ZWW09-149 suppresses PM8-derived resistance from ZWW09-149, but only at the seedling stage. In adult plants, the PM8 region conferred resistance regardless of the PM3 genotype. The resistance sources and molecular markers that were investigated here could be useful in wheat breeding.

Identification and expression of gene loci underlying the quantitative trait loci of starch content in cassava

ABSTRACT In this study, a genetic linkage map was developed based on simple sequence repeat (SSR) markers to aid in the identification and expression analysis of gene loci underlying the quantitative trait loci (QTL) of starch content (SC) in cassava (Manihot esculenta). A total of 912 polymorphic loci from 4,515 tested SSRs were mapped into 18 linkage groups. QTL analysis revealed four loci with highly significant associations with starch. Gene annotation was performed, and potential genes related to starch synthesis were identified. Of these, expression of four genes related to starch synthesis (Raffinose synthase [RS], Phosphoenolpyruvate kinase [PK], Glucose-6-phosphate [G6P], and Glycogen synthase kinase 3 [GSK-3]) was investigated by real-time PCR assays. The results found a statistically significant difference (p < 0.05) at 3 months after planting (MAP) in all the tested genes, whereas a higher expression was detected in the low-SC group with specific genotypes of linked markers. A higher level of expression was observed in the RS, PK, and G6P genes at six and nine MAP, indicating that starch accumulation mainly occurs after 3 MAP, during which the root system begins to form. The potential genes identified in this study could provide a better understanding of the starch biosynthesis mechanism, and could be useful for applications in marker-assisted selection to facilitate cassava breeding programs in the future.

Seedling root system adaptation to water availability during maize domestication and global expansion.

The maize root system has been reshaped by indirect selection during global adaptation to new agricultural environments. In this study, we characterized the root systems of more than 9,000 global maize accessions and its wild relatives, defining the geographical signature and genomic basis of variation in seminal root number. We demonstrate that seminal root number has increased during maize domestication followed by a decrease in response to limited water availability in locally adapted varieties. By combining environmental and phenotypic association analyses with linkage mapping, we identified genes linking environmental variation and seminal root number. Functional characterization of the transcription factor ZmHb77 and in silico root modeling provides evidence that reshaping root system architecture by reducing the number of seminal roots and promoting lateral root density is beneficial for the resilience of maize seedlings to drought.

An evaluation of a Stenotrophomonas maltophilia outbreak due to commercial arterial blood gas collection kit

BackgroundStenotrophomonas maltophilia is a gram-negative bacterium that can cause hospital infections and outbreaks within hospitals. This study aimed to evaluate an outbreak of Stenotrophomonas maltophilia, caused by ready-to-use commercial syringes containing liquid lithium and heparin for arterial blood gas collection in a university hospital.MethodsUpon detecting an increase in Stenotrophomonas maltophilia growth in blood cultures between 15.09.2021 and 19.11.2021, an outbreak analysis and a case-control study (52 patients for the case group, 56 patients for the control group) were performed considering risk factors for bacteremia. Samples from possible foci for bacteremia were also cultured. Growing bacteria were identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The genetic linkage and clonal relationship isolates were investigated with pulsed-field gel electrophoresis (PFGE) in the reference laboratory.ResultsIn the case-control study, the odds ratio for the central venous catheter [3.38 (95% confidence interval [CI]: 1.444, 8.705 ; p = 0.006)], for surgery [3.387 (95% confidence interval [CI]: 1.370, 8.373 ; p = 0.008)] and for arterial blood gas collection history [18.584 (95% confidence interval [CI]:4.086, 84.197; p < 0.001)] were identified as significant risk factors. Stenotrophomonas maltophilia growth was found in ready-to-use commercial syringes used for arterial blood gas collection. Molecular analysis showed that the growths in the samples taken from commercial syringes and the growths from blood cultures were the same. It was decided that the epidemic occurred because the method for sterilization of heparinized liquid preparations were not suitable. After discontinuing the use of the kits with this lot number, the outbreak was brought under control.ConclusionsAccording to our results, disposable or sterile medical equipment should be included as a risk factor in outbreak analyses. The method by which injectors containing liquids, such as heparin, are sterilized should be reviewed. Our study also revealed the importance of the cooperation of the infection control team with the microbiology laboratory.

Genetic Mapping for Leaf Shape and Leaf Size in Non-Heading Chinese Cabbage by a RIL Population

Leaves are the predominant photosynthetic and edible organs in non-heading Chinese cabbage (Brassica campestris ssp. chinensis, NHCC), contributing significantly to yield, appearance, and desirability to consumers. However, the genetic basis of leaf shape and size in non-heading Chinese cabbage remains unclear. In this study, we developed a RIL population using ‘Maertou’, with slender leaves and narrow petioles, and ‘Suzhouqing’, with oval leaves and wide petioles, to construct a genetic linkage map and detect QTLs. To obtain stable and reliable QTLs, the 11 leaf-related traits, including the leaf length, leaf width, and fresh weight of the lamina and petiole and the thickness of petiole was observed on two locations—while the leaf shape, petiole shape, index of lamina/petiole length, and index of petiole fresh weight were calculated based on 7 leaf-related traits. QTL mapping illustrated that a total of 27 QTLs for leaf-related traits were preliminarily detected. The candidate genes were annotated and several genes involved in leaf development and leaf shape appeared in the overlapping regions of multiple loci, such as KRP2, GRF4, ARGOS, and SAUR9. This study lays the foundation for further exploration of the genetic mechanisms and development of effective molecular markers for leaf shape and size in NHCC.

Selective allele stacking of a novel quantitative trait locus facilitates the enhancement of seed epicatechin content in soybean (Glycine max (L.) Merr.)

(-)-Epicatechin (EC), a primary form of flavan-3ol and a building block of proanthocyanidins, has health benefits as it is a potent antioxidant. So far, no quantitative trait loci (QTLs) associated with EC have yet been identified in soybean. In this study, QTLs for EC and hilum color were identified in recombinant inbred lines (RILs) derived from the varieties Jinpung and IT109098 using high-resolution single nucleotide polymorphism linkage mapping. This revealed two major QTLs for EC content, qEC06 and qEC08. qEC06 spanned the Tawny (T) locus encoding flavonoid 3′-hydroxylase. qEC08, located near the Inhibitor (I) locus on Chr08, was also a major QTL for hilum color; however, allelic stacking of qEC08 and I revealed no relationship between I and EC content. RILs with IT109098 alleles at both qEC06 and qEC08 had higher EC content than other lines. These results will enable the production of soybean varieties with high EC content via marker-assisted selection.

Understanding genome structure facilitates the use of wild lentil germplasm for breeding: A case study with shattering loci.

Plant breeders are generally reluctant to cross elite crop cultivars with their wild relatives to introgress novel desirable traits due to associated negative traits such as pod shattering. This results in a genetic bottleneck that could be reduced through better understanding of the genomic locations of the gene(s) controlling this trait. We integrated information on parental genomes, pod shattering data from multiple environments, and high-density genetic linkage maps to identify pod shattering quantitative trait loci (QTLs) in three lentil interspecific recombinant inbred line populations. The broad-sense heritability on a multi-environment basis varied from 0.46 (in LR-70, Lens culinaris × Lens odemensis) to 0.77 (in LR-68, Lens orientalis × L. culinaris). Genetic linkage maps of the interspecific populations revealed reciprocal translocations of chromosomal segments that differed among the populations, and which were associated with reduced recombination. LR-68 had a 2-5 translocation, LR-70 had 1-5, 2-6, and 2-7 translocations, and LR-86 had a 2-7 translocation in one parent relative to the other. Segregation distortion was also observed for clusters of single nucleotide polymorphisms on multiple chromosomes per population, further affecting introgression. Two major QTL, on chromosomes 4 and 7, were repeatedly detected in the three populations and contain several candidate genes. These findings will be of significant value for lentil breeders to strategically access novel superior alleles while minimizing the genetic impact of pod shattering from wild parents.

Genomic loci associated with grain yield under well-watered and water-stressed conditions in multiple bi-parental maize populations

Smallholder maize farming systems in sub-Saharan Africa (SSA) are vulnerable to drought-induced yield losses, which significantly impact food security and livelihoods within these communities. Mapping and characterizing genomic regions associated with water stress tolerance in tropical maize is essential for future breeding initiatives targeting this region. In this study, three biparental F3 populations composed of 753 families were evaluated in Kenya and Zimbabwe and genotyped with high-density single nucleotide polymorphism (SNP) markers. Quantitative trait loci maping was performed on these genotypes to dissect the genetic architecture for grain yield (GY), plant height (PH), ear height (EH) and anthesis-silking interval (ASI) under well-watered (WW) and water-stressed (WS) conditions. Across the studied maize populations, mean GY exhibited a range of 4.55–8.55 t/ha under WW and 1.29–5.59 t/ha under WS, reflecting a 31–59% reduction range under WS conditions. Genotypic and genotype-by-environment (G × E) variances were significant for all traits except ASI. Overall broad sense heritabilities for GY were low to high (0.25–0.60). For GY, these genetic parameters were decreased under WS conditions. Linkage mapping revealed a significant difference in the number of QTLs detected, with 93 identified under WW conditions and 41 under WS conditions. These QTLs were distributed across all maize chromosomes. For GY, eight and two major effect QTLs (&amp;gt;10% phenotypic variation explained) were detected under WW and WS conditions, respectively. Under WS conditions, Joint Linkage Association Mapping (JLAM) identified several QTLs with minor effects for GY and revealed genomic region overlaps in the studied populations. Across the studied water regimes, five-fold cross-validation showed moderate to high prediction accuracies (−0.15–0.90) for GY and other agronomic traits. Our findings demonstrate the polygenic nature of WS tolerance and highlights the immense potential of using genomic selection in improving genetic gain in maize breeding.

Advances in Breeding for Oil Quality Enhancement in Indian Mustard (Brassica spp. L.): Achievements, Challenges, and Research Opportunities

Major objectives in oil crop improvement are enhancement of seed and oil yield, quality of oil according to its use, i.e. edible or industrial uses, breeding of varieties that fit in different cropping systems and breeding biotic and abiotic stress resistant/tolerant varieties. Despite traditional breeding approaches, including pure line breeding, yielding only modest gains in productivity, recent advancements in mustard breeding have led to significant breakthroughs in both productivity and oil quality. This review discusses the innovative breeding strategies that have contributed to these advancements, with a focus on hybrid development, oil quality enhancement, and biotechnological approaches. To enhance productivity, researchers at the University of Delhi have developed hybrid seed production techniques using transgenic Barnase-barstar systems and cytoplasmic male sterility (CMS) systems. These systems enable large-scale hybrid seed production, with field trials demonstrating significant yield heterosis ranging from 31% to 55% compared to national check varieties. In addition to productivity, improving oil and meal quality has been a key objective. By integrating genes from canola-quality mustard lines, breeders have achieved reductions in erucic acid and glucosinolates, enhancing the health profile and industrial applicability of mustard oil. A high-density linkage map developed using an F1 double haploid mapping population has facilitated the marker-assisted backcross breeding of desirable traits, enabling precise transfer of key quality traits. Transgenic approaches, such as antisense RNA technology, have led to the development of high-oleic, low-linoleic mustard lines with improved fatty acid profiles. These advancements reflect a strategic combination of conventional and biotechnological methods, demonstrating a clear pathway for boosting mustard yields while enhancing oil quality. Molecular markers reported for genetic diversity assessment, mapping and tagging genes/QTLs for different qualitative and quantitative traits and their use in marker-assisted selection have been presented. This progress not only addresses current challenges but also sets the stage for future research aimed at further optimizing productivity, oil quality, and resistance to pests and diseases in mustard cultivation.

Unraveling the genetic basis of superior traits in Gossypium barbadense: From phenotype to genotype

G. barbadense is renowned for its high-quality fiber and is highly regarded as a natural material in the textile industry. However, research on cotton has mainly focused on G. hirsutum, and progress in sea island cotton has been relatively slow. There was limited understanding of the genetic loci and transcriptional regulatory mechanisms of important traits, and the genetic basis for the development of superior traits remains unclear. In this study, a recombinant inbred line (RIL) population was constructed using two sea island cotton parents from different cotton regions. The phenotypic characteristics of the two parents and the RIL population, as well as the phenotypic correlations, heritability, and genetic models of the RIL population, were comprehensively analyzed. The RIL population was genotyped using whole-genome resequencing technology, and a high-density intraspecific linkage map was constructed, consisting of 5295 bin markers and a total genetic map distance of 2721.79 centimorgans (cM). Phenotypic data collected from five different environments were used to detect 169 quantitative trait loci (QTLs) using the composite interval mapping method. Among these QTLs, 30 were related to agronomic traits, 61 were related to yield traits, and 78 were related to fiber quality traits. Additionally, 17 QTL clusters were detected, and the additive effects of these clusters explained the correlation between different phenotypic traits. Candidate genes for stable QTLs related to agronomic and yield traits were identified through variant annotation and functional prediction. Two bin markers associated with lint percentage (LP) were validated as potential breeding markers. Furthermore, using RNA-seq data of cotton fiber from the RIL population parents, the dynamic changes in gene expression during different developmental stages of cotton fiber were revealed, and important differentially expressed genes in the secondary cell wall development and metabolism network of fibers were identified. Importantly, through the combined analysis of fiber trait QTLs and transcriptomes, eight candidate genes involved in regulating fiber quality traits were predicted, and the genetic basis of the excellent allele site qFL_D04_1 in the breeding history of Chinese sea island cotton was elucidated. In summary, this study provides new genetic resources and potential breeding markers for cotton variety improvement, valuable theoretical information for understanding the genetic basis of important traits in sea island cotton, and effectively promotes the development of cotton biotechnology breeding.

Genetic Diversity, Linkage Disequilibrium, and Population Structure in a Common Bean Reference Collection

An in-depth understanding of the extent and pattern of genetic diversity and population structure in crop populations is of paramount importance for any crop improvement program to efficiently promote the translation of genetic diversity into genetic gain. A reference collection of 150 common bean genotypes selected from the International Center for Tropical Agriculture’s global core collection was evaluated using single-nucleotide polymorphism (SNP) markers to quantify the amount of genetic diversity, linkage disequilibrium, and population structure. The cultivars and landraces of the collection were diverse and originated from 14 countries, and wild accessions were used as controls for each gene pool. The collection was genotyped using an SNP array, generating a total of 5398 locus calls distributed across the entire bean genome. The SNP data quality was checked, and two datasets were generated. The first dataset (Dataset_1) comprised a set of 5108 SNPs and 150 genotypes after filtering for 10% missing alleles and an MAF &lt; 0.05. The second dataset (Dataset_2) comprised a set of 2300 SNPs that remained after removing any null-allele SNPs and LD pruning for a criterion of r2 &lt; 0.2. Dataset_1 was used for a principal coordinate analysis (PCoA), phylogenetic relationship determination, an analysis of molecular variance (AMOVA), and a discriminant analysis of principal components. Dataset_2 was used for a population structure analysis using STRUCTURE software and is proposed for a genome-wide association study (GWAS). The population structure analysis split the reference collection into two subpopulations according to an Andean or Mesoamerican gene pool. The Mesoamerican populations displayed higher genetic differentiation and tended to split into more groups that were somewhat aligned with common bean races. Andean beans were characterized by a larger average LD but lower LD percentage, a small average genetic distance between members of the population, and a higher major allele frequency, which suggested narrower genetic diversity compared to the Mesoamerican gene pool. In conclusion, the results indicated the presence of high genetic diversity, which is useful for a GWAS. However, the presence of significant linkage disequilibrium requires that genetic distance be considered as a co-factor for any further genetic studies. Overall, the molecular variation observed in the genotypes shows that this reference collection is valuable as a genebank-derived diversity panel which is useful for marker trait association studies.

The impact of maternal smoking during pregnancy and the age of smoking initiation on incident dementia: A prospective cohort study.

The impact of early-life tobacco exposure on dementia has remained unknown. Using the UK Biobank, the associations of maternal smoking during pregnancy (MSDP) and age of smoking initiation (ASI) with the onset time of all-cause dementia were estimated with accelerated failure time models. The effects of MSDP and ASI on brain structure and their genetic correlation to Alzheimer's disease (AD) were analyzed. A Mendelian randomization (MR) analysis was conducted. The time ratios for smokers starting in childhood, adolescence, and adulthood (vs never smokers) were 0.87 (0.76 to 0.99), 0.92 (0.88 to 0.96), and 0.95 (0.89 to 1.01). MSDP and smoking in adolescence altered many brain regions, including the hippocampus. In genetic analysis, MSDP was genetically and causally linked to AD, and a younger ASI was genetically correlated to a higher AD risk. Early-life smoking accelerated dementia onset and was genetically correlated to AD. MSDP demonstrated genetic and causal linkage to AD risks. Unlike the commonly used Cox proportional hazards model, this article uses a parametric survival analysis method - the accelerated failure model - to explore the relationship between exposure to onset time. It can be used as an alternative method when the proportional hazards assumption is not met. Genetic analyses including genetic correlation study and MR analysis and brain structure analyses were conducted to support our findings and explore the potential mechanisms. The study reveals the relationship between different smoking initiation periods and the onset time of dementia and shows that earlier smoking exposure has a more significant impact on dementia. It emphasizes the importance of preventing early smoking. In the future, more research focusing on the relationship between early exposure and dementia is called for to provide more detailed prevention measures for dementia that cover all age groups.

Prevalence and molecular characterization of colistin resistance in Pseudomonas aeruginosa isolates: insights from a study in Ardabil hospitals

BackgroundPseudomonas aeruginosa is a common cause of nosocomial infections. However, the emergence of multidrug-resistant strains has complicated the treatment of P. aeruginosa infections. While polymyxins have been the mainstay for treatment, there is a global increase in resistance to these antibiotics. Therefore, our study aimed to determine the prevalence and molecular details of colistin resistance in P. aeruginosa clinical isolates collected between June 2019 and May 2023, as well as the genetic linkage of colistin-resistant P. aeruginosa isolates.ResultsThe resistance rate to colistin was 9% (n = 18) among P. aeruginosa isolates. All 18 colistin-resistant isolates were biofilm producers and carried genes associated with biofilm formation. Furthermore, the presence of genes encoding efflux pumps, TCSs, and outer membrane porin was observed in all colistin-resistant P. aeruginosa strains, while the mcr-1 gene was not detected. Amino acid substitutions were identified only in the PmrB protein of multidrug- and colistin-resistant strains. The expression levels of mexA, mexC, mexE, mexY, phoP, and pmrA genes in the 18 colistin-resistant P. aeruginosa strains were as follows: 88.8%, 94.4%, 11.1%, 83.3%, 83.3%, and 38.8%, respectively. Additionally, down-regulation of the oprD gene was observed in 44.4% of colistin-resistant P. aeruginosa strains.ConclusionThis study reports the emergence of colistin resistance with various mechanisms among P. aeruginosa strains in Ardabil hospitals. We recommend avoiding unnecessary use of colistin to prevent potential future increases in colistin resistance.

Recycling carbonated hydrous sediments into the mantle source of carbonatite-associated rare-earth-element deposits

Decoding the petrogenesis of carbonatites is of great importance for our understanding of the Earth’s deep carbon cycling and formation of rare-earth-element (REE) deposits. Among global carbonatites, the Cenozoic Mianning-Dechang (MD) carbonatites in the western Yangtze Craton are unique because of their development in a post-collisional zone and host numerous giant-large REE deposits. However, most of previous studies have focused on the late magmatic to hydrothermal stages, while the nature of the mantle source and early-stage magmatic evolution remain largely unexplored. Here we present a combined petrographic, chemical and Sr-Nd-Pb isotopic study on the MD lamprophyres to address these issues. A genetic linkage is revealed between these lamprophyres and the MD carbonatites and syenites by their geochemical similarities and close spatial and temporal associations. Our data suggest a phlogopite-rich carbonated subcontinental lithospheric mantle (SCLM) source metasomatized by subducted carbonated hydrous sediment-derived melts/fluids. Significant fractional crystallization of olivine, clinopyroxene and biotite (±Ti-Fe oxides) from hydrous, K-rich and carbonated primary melts caused the carbonate–silicate liquid immiscibility in the highly evolved melts and thus formation of the MD carbonatites and syenites at shallow depths. Melting of subducted carbonated hydrous sediments not only provides carbonatitic liquids for the SCLM carbonation, but also supplies sufficient water and alkalis that are critical for accumulating and transporting REE in carbonatitic fluids. Post-collisional lithospheric thinning also played a critical role in the formation of carbonatites via triggering the melting of the carbonated SCLM. This study provides new insights into the formation of carbonatites and associated REE deposits in post-collisional zones related to melting of subducted carbonated hydrous sediments.

Identification of novel SNPs and candidate genes significantly affecting growth in grass carp (Ctenopharyngodon idella) through GWAS analysis

Grass carp (Ctenopharyngodon idella) is one of the most important cultivated fish species in the global freshwater aquaculture with fast growth, low cost of production and delicious meat. A breeding program to improve economically important growth traits in grass carp would benefit from effective molecular markers. Although a genetic linkage map of grass carp has been constructed, and quantitative trait loci (QTL) mapping and a genome-wide association study (GWAS) have been conducted, the effective number of SNP markers and genes currently available for breeding is still very limited. In this study, we conducted a GWAS based on re-sequencing of individuals to identify genomic regions and candidate genes potentially associated with various growth traits of grass carp, including body weight (BW), body length (BL) and body height (BH). A total of 4,854,366 high-quality SNPs were identified and located on 24 chromosomes. Among them, 31 SNPs were identified as being associated with growth traits, including 8 SNPs on chromosomes 1, 2, 10, 13, 14, 17 and 22 associated with BW, 21 SNPs on chromosomes 2, 4, 5, 8, 10, 13, 14, 15, 17, 23 and 24 correlated with BL, and 18 SNPs on chromosomes 2, 9, 10, 13, 14, 17, 23 and 24 related to BH. In addition, 13 of these SNPs were simultaneously associated with two or three growth traits. Within a 48 kb range upstream and downstream of these significant SNPs, 120 candidate genes were identified to be associated with the QTLs. Most of these genes were related to growth and development, fat metabolism, bone mineralization and differentiation, vascular development, or feeding regulation. Notably, the genes pwp1, cers5, chrebp, lsr, ctnnbip1, smoc2, ano6 and cckrb were specifically associated with growth, fat, bone formation and feeding. Our findings would provide a foundation for molecular marker-assisted selection, genomic selection, and functional analysis of growth traits in grass carp.

Co-localization and analysis of miR477b with fiber length quantitative trait loci in cotton.

Cotton is an important cash crop for the textile industry. However, the understanding of natural genetic variation of fiber elongation in relation to miRNA is lacking. A miRNA gene (miR477b) was found to co-localize with a previously mapped fiber length (FL) quantitative trait locus (QTL). The miR477b was differentially expressed during fiber elongation between two backcross inbred lines (BILs) differing in FL and its precursor sequences. Bioinformatics and qRT-PCR analysis were further used to analyse the miRNA genes, which could produce mature miR477b. Cotton plants with virus-induced gene silencing (VIGS) constructs to over-express the allele of miR477b from the BIL with longer fibers had significantly longer fibers as compared with negative control plants, while the VIGS plants with suppressed miRNA expression had significantly shorter fibers. The expression level of the target gene (DELLA) and related genes (RDL1 and EXPA1 for DELLA through HOX3 protein) in the two BILs and/or the VIGS plants were generally congruent, as expected. This report represents one of the first comprehensive studies to integrate QTL linkage mapping and physical mapping of small RNAs with both small and mRNA transcriptome analysis, followed by VIGS, to identify candidate small RNA genes affecting the natural variation of fiber elongation in cotton.

The role of dietary preferences in osteoarthritis: a Mendelian randomization study using genome-wide association analysis data from the UK Biobank.

To understand the impact of individual preferences for specific dietary items on OA, and to help inform the development of effective and targeted OA prevention and management strategies, we performed a Mendelian randomization analysis between dietary preferences and osteoarthritis. This study utilized genetic data from the UK Biobank to investigate the association between OA and 21 different common dietary items. Instrumental variables representing European populations were carefully selected based on their genetic significance and linkage disequilibrium. In cases where a dietary item had few relevant genetic markers, a more lenient selection threshold was applied. To prevent bias, the analysis excluded single nucleotide polymorphisms (SNPs) associated with factors such as body mass index (BMI) and cholesterol. Using inverse-variance weighting (IVW) and Mendelian randomization, significant associations were detected between certain dietary items and OA. Using Mendelian randomization to examine the relationship between 21 different dietary items and OA, significant associations were found for coffee, peas, watercress, and cheese, where the first two had a promoting effect and the last two an inhibiting effect on OA. Due to heterogeneity in the test results for cheese, a random IVW representation was used. The results of sensitivity analysis showed no significant heterogeneity or horizontal pleiotropy in the selected SNPS, demonstrating the reliability of Mendelian randomization analysis. This study identified coffee, peas, watercress, and cheese as food items that may have significant dietary effects on osteoarthritis. This information may be useful to consider in the development of OA management strategies.

Construction of a high-density genetic map based on large-scale marker development in Coix lacryma-jobi L. using specific-locus amplified fragment sequencing (slaf-seq)

Coix lacryma-jobi L. is one of the most economically and medicinally important corns. This study constructed a high-density genetic linkage map of C. lacryma-jobi based on a cross between the parents 'Qianyi No. 2' × 'Wenyi No. 2' and their F2 progeny through high-throughput sequencing and the construction of a specific-locus amplified fragment (SLAF) library. After pre-processing, 325.49 GB of raw data containing 1628 M reads were obtained. A total of 22,944 high-quality SLAFs were identified, among which 3952 SLAFs and 3646 polymorphic markers met the requirements for the construction of a genetic linkage map. The integrated map contained 3605 high-quality SLAFs, which were grouped into ten genetic linkage groups. The total length of the map was 1620.39 cM, with an average distance of 0.45 cM and an average of 360.5 markers per linkage group. This report presents the first high-density genetic map of C. lacryma-jobi. This map was constructed using an F2 population and SLAF-seq approach, which allows the development of a large number of polymorphic markers in a short period. These results provide a platform for precise gene/quantitative trait locus (QTL) mapping, map-based gene separation, and molecular breeding in C. lacryma-jobi. They also help identify a target gene for tracking, splitting quantitative traits, and estimating the phenotypic effects of each QTL for QTL mapping. They are of great significance for improving the efficiency of discovering and utilizing excellent gene resources of C. lacryma-jobi.

Genome-wide QTL and eQTL mapping reveal genes associated with growth rate trait of the Pacific white shrimp (Litopenaeus vannamei)

BackgroundGrowth rate is a crucial economic trait for farmed animals, but the genetic regulation of this trait is largely unknown in non-model organisms such as shrimp.ResultsIn this study, we performed genome-wide phenotypic quantitative trait loci (QTL) and expression quantitative trait loci (eQTL) mapping analyses to identify genes affecting the growth rate of Pacific white shrimp (Litopenaeus vannamei), which is the most commercially-farmed crustacean worldwide. We used RNA-sequencing of 268 individuals in a mapping population, and subsequently validated our findings through gene silencing and shrimp growth experiments. We constructed a high-density genetic linkage map comprising 5533 markers spanning 44 linkage groups, with a total distance of 6205.75 cM and an average marker interval of 1.12 cM. Our analyses identified 11 QTLs significantly correlated with growth rate, and 117,525 eQTLs. By integrating QTL and eQTL data, we identified a gene (metalloreductase STEAP4) highly associated with shrimp growth rate. RNA interference (RNAi) analysis and growth experiments confirmed that STEAP4 was significantly correlated with growth rate in L. vannamei.ConclusionsOur results indicate that the comprehensive analysis of QTL and eQTL can effectively identify genes involved in complex animal traits. This is important for marker-assisted selection (MAS) of animals. Our work contributes to the development of shrimp breeding and available genetic resources.

Identification of Quantitative Trait Loci Controlling Root Morphological Traits in an Interspecific Soybean Population Using 2D Imagery Data.

Roots are the hidden and most important part of plants. They serve as stabilizers and channels for uptaking water and nutrients and play a crucial role in the growth and development of plants. Here, two-dimensional image data were used to identify quantitative trait loci (QTL) controlling root traits in an interspecific mapping population derived from a cross between wild soybean 'PI366121' and cultivar 'Williams 82'. A total of 2830 single-nucleotide polymorphisms were used for genotyping, constructing genetic linkage maps, and analyzing QTLs. Forty-two QTLs were identified on twelve chromosomes, twelve of which were identified as major QTLs, with a phenotypic variation range of 36.12% to 39.11% and a logarithm of odds value range of 12.01 to 17.35. Two significant QTL regions for the average diameter, root volume, and link average diameter root traits were detected on chromosomes 3 and 13, and both wild and cultivated soybeans contributed positive alleles. Six candidate genes, Glyma.03G027500 (transketolase/glycoaldehyde transferase), Glyma.03G014500 (dehydrogenases), Glyma.13G341500 (leucine-rich repeat receptor-like protein kinase), Glyma.13G341400 (AGC kinase family protein), Glyma.13G331900 (60S ribosomal protein), and Glyma.13G333100 (aquaporin transporter) showed higher expression in root tissues based on publicly available transcriptome data. These results will help breeders improve soybean genetic components and enhance soybean root morphological traits using desirable alleles from wild soybeans.