Quantitative Trait Loci Research Articles

Genetic dissection of flour whiteness through genome-wide association analysis in common wheat (Triticum aestivum L.)

The color of flour products has an important influence on consumer acceptance. Flour color is largely determined and measured by the index of flour whiteness (FW) in China. In this study, an association population comprising 207 wheat (Triticum aestivum) accessions originating from seven countries was used for dissection of FW-related genetic loci through genome-wide association analysis. Six quantitative trait loci (QTLs) significantly associated with FW were identified, accounting for 7.87%–16.53% of the total phenotypic variation. Four KASP markers were developed from single-nucleotide polymorphisms associated with the QTLs QFW.HAAS-1AS, QFW.HAAS-1BL, QFW.HAAS-5AL, and QFW.HAAS-7AL. The phytoene synthase-encoding gene TraesCS7A03G1357000 (TaPsyA1) was identified as a candidate gene for QFW.HAAS-7AL. Two allelic variants of TaPsyA1 (designated PsyA1-a and PsyA1-b) were differentiated on the basis of a 37bp insertion/deletion polymorphism in the second intron. PsyA1-b included the 37bp insertion, which led to a translational frameshift in the gene and was associated with higher FW. The PsyA1-a allele lacked the 37bp insertion and was classified into two haplotypes according to the number of repeated ‘TC’ units in a simple sequence repeat in the promoter region. Of the two PsyA1-a haplotypes, the Type 1 haplotype conferred higher FW, flour brightness, and flour redness, and lower yellow pigment content and flour yellowness. The KASP markers and PsyA1 polymorphic markers developed in the present study are suitable for use in molecular marker-assisted selection for improvement of wheat FW.

SFMBT2 regulates plumage color via serum metabolites in Chinese Anyi tile-like gray chickens

Plumage color is an important characteristic of chicken breeds, and molecular genetic research is significant for resource conservation and product quality control. Anyi tile-like gray chicken is a high-quality local chicken breed resource generated through long-term natural selection and artificial breeding in China. However, the molecular mechanisms underlying plumage color formation in Anyi tile-like gray chickens remain unclear. In this study, nontargeted liquid chromatography and tandem mass spectrometry (LC-MS/MS) was performed to identify serum metabolites associated with plumage color in 93 Anyi tile-like gray chickens, including 60 tile-like gray and 33 black chickens. Notably, 12 serum metabolites were significantly enriched in Anyi tile-like gray chickens, including deoxyuridine and inosine, which were the key biomarkers distinguishing tile-like gray chickens from black chickens. Additionally, nine serum metabolites were significantly enriched in black chickens. Moreover, we identified 225 significant SNPs (P < 9.71 × 10-8) on chromosomes 1, 2, 3, 4, 11, 15, and 21 that were associated with deoxyuridine, inosine, 3-hydroxybenzoic acid, and L-methionine S-oxide through metabolome genome-wide association studies (mGWAS). Importantly, chromosome 1 harbored a region, 172.79-kb, which was the most likely quantitative trait locus (QTL) interval. RNA sequencing (RNA-seq) and quantitative reverse transcription polymerase chain reaction (qRT-PCR) showed that SFMBT2 was the only differentially expressed gene in the QTL interval, and its expression was correlated with the abundance of specific serum metabolites. Conclusively, SFMBT2-mediated changes in serum metabolites contribute to plumage color development in Anyi tile-like gray chicken. This study provides important insights into the interaction between serum metabolites and host genes, and offers a theoretical basis for the breeding of Anyi tile-like gray chickens.

Rtlp2 enhances thermotolerance in rice

The harmful effects of heat stress on agricultural production are becoming increasingly severe. Thaumatin-like proteins (TLPs) have been demonstrated to play crucial roles in regulating plant resistance to biotic and abiotic stresses. However, their involvement in plant thermotolerance is poorly understood. This study aims to investigate the major-effect gene in a key quantitative trait locus (QTL) associated with rice thermotolerance, namely Rtlp2, which encodes a rice TLP. The Rtlp2 protein was found to be localized in the endoplasmic reticulum (ER). Rice seedlings overexpressing the Rtlp2 gene showed significantly enhanced thermotolerance compared to the wild type, while rtlp2 mutant exhibited increased susceptibility to heat stress. After 48 h of heat stress treatment, rice plants overexpressing Rtlp2 exhibited reduced accumulation of hydrogen peroxide (H2O2) and cell death compared to the wild-type. Conversely, the mutant plants showed the opposite behavior. The results of gene expression level analyses revealed that Rtlp2 positively regulates rice thermotolerance through the modulation of rice heat shock transcription factors (HSFs) and heat shock proteins (HSPs) network. After undergoing natural heat stress in the field, the rice lines overexpressing Rtlp2 showed higher seed setting rate and yield per plant compared to the wild-type. In addition, Rtlp2 has also been found to positively regulate grain length and grain weight in rice. This study provides valuable resources for addressing the challenge of increasing environmental heat and promoting the breeding of heat-tolerant rice varieties.

BSA-seq and transcriptome analysis reveal GhDSA05 as a candidate gene responsible for sensitivity to defoliants in Gossypium hirsutum L.

With the development of machine-harvested cotton, the application of defoliants is a key technology that can promote defoliation and reduce impurities in cotton fibers. Therefore, sensitivity to defoliants is a very important trait in machine-harvested cotton. In this study, to uncover the genetic basis of defoliant sensitivity in cotton, bulked segregant analysis by sequencing was used with a F2 population derived from Xinluzao 57 (XLZ57, defoliant sensitive) and Nan 2 (N2, defoliant insensitive) to mapped the quantitative trait locus (QTL) to a 3.66-Mb interval at chromosome A05. Then, 284 F2 individuals were used to validate and narrow the QTL to a 1.6-Mb interval and was named qSD-A05. To identify the candidate genes, dynamic transcriptome analysis of the abscission zone (AZ) in XLZ57 and N2 after defoliant treatment was performed. A total of 132 and 142 common differentially expressed genes (DEGs) were identified at all time points in N2 and XLZ57, respectively, and were enriched in the defense response pathway and abscisic acid-activated signaling pathway. More importantly, 15 DEGs were identified in the qSD-A05 interval, among which, Ghi_A05G23601 was significantly upregulated after defoliant treatment. There were multiple variants between N2 and XLZ57, including missense and frameshift mutations. Therefore, Ghi_A05G23601 was regarded as the key candidate gene and was named GhDSA05, which encodes a Facilitator superfamily transporter protein. To verify the function of GhDSA05, virus-induced gene silencing was performed, which showed that the GhDSA05-silenced plants exhibited decreased defoliant sensitivity. Additionally, the expression of organ abscission-related genes was downregulated in the GhDSA05-silenced plants. In summary, GhDSA05 positively regulates the formation of AZ under defoliant treatment and promotes leaf abscission in cotton. The results of this study not only enhance our knowledge of the defoliation mechanism of cotton but also provide a target for the genetic improvement of defoliant sensitivity.

Integrative pan-cancer analysis reveals a common architecture of dysregulated transcriptional networks characterized by loss of enhancer methylation

Aberrant DNA methylation contributes to gene expression deregulation in cancer. However, these alterations’ precise regulatory role and clinical implications are still not fully understood. In this study, we performed expression-methylation Quantitative Trait Loci (emQTL) analysis to identify deregulated cancer-driving transcriptional networks linked to CpG demethylation pan-cancer. By analyzing 33 cancer types from The Cancer Genome Atlas, we identified and confirmed significant correlations between CpG methylation and gene expression (emQTL) in cis and trans, both across and within cancer types. Bipartite network analysis of the emQTL revealed groups of CpGs and genes related to important biological processes involved in carcinogenesis including proliferation, metabolism and hormone-signaling. These bipartite communities were characterized by loss of enhancer methylation in specific transcription factor binding regions (TFBRs) and the CpGs were topologically linked to upregulated genes through chromatin loops. Penalized Cox regression analysis showed a significant prognostic impact of the pan-cancer emQTL in many cancer types. Taken together, our integrative pan-cancer analysis reveals a common architecture where hallmark cancer-driving functions are affected by the loss of enhancer methylation and may be epigenetically regulated.

Disruption of the OsWRKY71 transcription factor gene results in early rice seed germination under normal and cold stress conditions

Abstract Background Early seed germination in crops can confer a competitive advantage against weeds and reduce the time to maturation and harvest. WRKY transcription factors regulate many aspects of plant development including seed dormancy and germination. Both positive and negative regulators of seed germination have been reported in many plants such as rice and Arabidopsis. Using a transient expression system, we previously demonstrated that OsWRKY71 is a negative regulator of gibberellin (GA) signaling in aleurone cells and likely forms a “repressosome” complex with other transcriptional repressors. Hence, it has the potential to impact seed germination properties. Results In this study, we demonstrate that OsWRKY71, a Group IIa WRKY gene, appeared at the same time as seed-bearing plants. Rice mutants lacking OsWRKY71 have seeds and embryos that germinate earlier than wildtype controls. In oswrky71 aleurone layers, α-amylase activity was hypersensitive to stimulation by GA3 and hyposensitive to inhibition by abscisic acid (ABA). Early germination in oswrky71 intact seeds was also hyposensitive to ABA. Transcriptomic profiling during embryo germination and early post-germination growth demonstrates that OsWRKY71 influences the expression of 9–17% of genes in dry and imbibing embryos. Compared to wildtype embryos, the mutant transcriptomes have large temporal shifts at 4, 8 and 12 h after imbibition (HAI). Importantly, many genes involved in the ABA-dependent inhibition of seed germination were downregulated in oswrky71-1. This mutant also displayed altered expression of multiple ABA receptors (OsPYLs/RCARs) that control ABA signaling and the VP1-SDR4-DOG1L branch of ABA signaling that promotes seed dormancy. Association studies reveal an OsWRKY71-containing quantitative trait locus involved in low-temperature seed germinability, qLTG-2. Indeed, oswrky71 seeds germinated early at 15 °C. Conclusions Rice Group-IIa WRKY transcription factor OsWRKY71 is a master regulator of germination that influences the expression of 9–17% of genes in dry and imbibing embryos. It is also most likely the primary candidate of low-temperature seed germinability QTL, qLTG-2. We propose that knockouts of OsWRKY71 can generate rice varieties with improved germination properties under normal or low-temperature conditions.

Causal association of obesity-related anthropometric traits with myopia and the mediating role of educational attainment: a Mendelian randomization study

AIM: To study the causal relationship between obesity-related anthropometric traits and myopia and the mediating role of educational attainment (EA). METHODS: Univariable Mendelian randomization (UVMR) was performed to evaluate the causal association between body mass index (BMI), height, waist-hip ratio (WHR, adjusted for BMI), and mean spherical equivalent (MSE). BMI was divided into fat and fat-free mass and included in multivariable Mendelian randomization (MVMR) to explore the roles of different BMI components in the causal relationship between BMI and MSE. A mediation analysis based on two-step Mendelian randomization (MR) was carried out. Specifically, UVMR was conducted to estimate the causal effect of BMI on EA. The direct effect of EA on MSE was estimated from MVMR. The mediation effect of EA in the BMI-EA-MSE model was calculated by the product of coefficients method. Expression quantitative trait loci (eQTL)-MR, reverse MR, and Linkage Disequilibrium Score Regression (LDSC) were performed to assess the robustness. RESULTS: Genetically predicted higher BMI had a positive total effect on MSE (βIVW=0.26 D, 95%CI=0.14 to 0.37 D, P&amp;#x003C;0.001), whereas there was no significant association between height, WHR, and MSE. Fat mass was found to play a significant role in the effect of body mass on MSE (βIVW=0.50 D, 95%CI=0.21 to 0.78 D, P=0.001), but there was no significant association between fat-free mass and MSE. The causal effect of BMI on EA was -0.14 (95%CI=-0.16 to -0.11, P&amp;#x003C;0.001), and the direct effect of EA on MSE was -0.63 D (95%CI=-0.81 to -0.44 D, P&amp;#x003C;0.001). The mediating effect of EA in the BMI-EA-MSE model was 0.09 D (95%CI=0.06 to 0.12 D), with a mediation proportion of 33% (95%CI=22.1% to 44.6%). No reverse causal associations were detected except for BMI on EA. The results of eQTL-MR and LDSC were consistent with each MR analysis. CONCLUSION: Genetically predicted higher BMI decreases the degree of myopia with a 33% mediation proportion by EA, and fat mass provides a dominant protective role in body mass-myopia. As a supplement to previous observational studies, it provides strong evidence for the relationship between anthropometric traits and refractive errors and offers a theoretical basis for future measures to prevent and control myopia.

Cadmium (Cd) Tolerance and Phytoremediation Potential in Fiber Crops: Research Updates and Future Breeding Efforts

Heavy metal pollution is one of the most devastating abiotic factors, significantly damaging crops and human health. One of the serious problems it causes is a rise in cadmium (Cd) toxicity. Cd is a highly toxic metal with a negative biological role, and it enters plants via the soil–plant system. Cd stress induces a series of disorders in plants’ morphological, physiological, and biochemical processes and initiates the inhibition of seed germination, ultimately resulting in reduced growth. Fiber crops such as kenaf, jute, hemp, cotton, and flax have high industrial importance and often face the issue of Cd toxicity. Various techniques have been introduced to counter the rising threats of Cd toxicity, including reducing Cd content in the soil, mitigating the effects of Cd stress, and genetic improvements in plant tolerance against this stress. For decades, plant breeders have been trying to develop Cd-tolerant fiber crops through the identification and transformation of novel genes. Still, the complex mechanism of Cd tolerance has hindered the progress of genetic breeding. These crops are ideal candidates for the phytoremediation of heavy metals in contaminated soils. Hence, increased Cd uptake, accumulation, and translocation in below-ground parts (roots) and above-ground parts (shoots, leaves, and stems) can help clean agricultural lands for safe use for food crops. Earlier studies indicated that reducing Cd uptake, detoxification, reducing the effects of Cd stress, and developing plant tolerance to these stresses through the identification of novel genes are fruitful approaches. This review aims to highlight the role of some conventional and molecular techniques in reducing the threats of Cd stress in some key fiber crops. Molecular techniques mainly involve QTL mapping and GWAS. However, more focus has been given to the use of transcriptome and TFs analysis to explore the potential genomic regions involved in Cd tolerance in these crops. This review will serve as a source of valuable genetic information on key fiber crops, allowing for further in-depth analyses of Cd tolerance to identify the critical genes for molecular breeding, like genetic engineering and CRISPR/Cas9.

Identification of Genetic Loci Associated with Bolting Time in Radish (Raphanus sativus L.) by QTL Mapping and GWAS

Bolting time is a critical trait that affects crop yield, adaptability, and overall productivity, making its regulation vital for agricultural success. In this study, we explored the genetic mechanisms controlling flowering time in radish (Raphanus sativus) via a combination of quantitative trait locus (QTL) analysis and genome-wide association study (GWAS). By developing an F2 population from a cross between the relatively late-bolting variety ‘L432’ and the early-bolting variety ‘L285’, we identified 12 QTLs associated with bolting time. Furthermore, a GWAS performed on 60 East Asian radish accessions revealed 14 candidate genes potentially involved in flowering and bolting regulation. FLOWERING LOCUS C (FLC2) was the major candidate gene explaining the early and late bolting types. One locus was commonly detected from QTL and GWAS on chromosome 4, where CONSTANS-like (COL4) is located. To validate these findings, SNP markers were designed and applied to F2 populations, revealing a correlation between marker presence and bolting phenotypes. These results offer valuable insights into the molecular control of bolting time in radish and identify candidate genes for use in marker-assisted breeding. These findings could enhance breeding efforts for optimizing bolting time in various radish markets.

The role of the rhizobiome recruited by root exudates in plant disease resistance: current status and future directions.

Root exudates serve as a bridge connecting plant roots and rhizosphere microbes, playing a key role in influencing the assembly and function of the rhizobiome. Recent studies have fully elucidated the role of root exudates in recruiting rhizosphere microbes to enhance plant performance, particularly in terms of plant resistance to soil-borne pathogens; however, it should be noted that the composition and amount of root exudates are primarily quantitative traits regulated by a large number of genes in plants. As a result, there are knowledge gaps in understanding the contribution of the rhizobiome to soil-borne plant disease resistance and the ternary link of plant genes, root exudates, and disease resistance-associated microbes. Advancements in technologies such as quantitative trait loci (QTL) mapping and genome-wide association studies (GWAS) offer opportunities for the identification of genes associated with quantitative traits. In the present review, we summarize recent studies on the interactions of plant and rhizosphere microbes through root exudates to enhance soil-borne plant disease resistance and also highlight methods for quantifying the contribution of the rhizobiome to plant disease resistance and identifying the genes responsible for recruiting disease resistance-associated microbes through root exudates.

Predicting cell type-specific epigenomic profiles accounting for distal genetic effects.

Understanding how genetic variants affect the epigenome is key to interpreting GWAS, yet profiling these effects across the non-coding genome remains challenging due to experimental scalability. This necessitates accurate computational models. Existing machine learning approaches, while progressively improving, are confined to the cell types they were trained on, limiting their applicability. Here, we introduce Enformer Celltyping, a deep learning model which incorporates distal effects of DNA interactions, up to 100,000 base-pairs away, to predict epigenetic signals in previously unseen cell types. Using DNA and chromatin accessibility data for epigenetic imputation, Enformer Celltyping outperforms current best-in-class approaches and generalises across cell types and biological regions. Moreover, we propose a framework for evaluating models on genetic variant effect prediction using regulatory quantitative trait loci mapping studies, highlighting current limitations in genomic deep learning models. Despite this, Enformer Celltyping can also be used to study cell type-specific genetic enrichment of complex traits.

Quantitative Trait Locus Mapping and Candidate Gene Analysis of the Contents of Three Tanshinone Components in Salvia miltiorrhiza Bunge.

Tanshinones are abietane diterpenoid quinone compounds with diverse biological activities and pharmacological effects found in Salvia miltiorrhiza. Leveraging the high-density genetic map established through our prior research endeavors, we conducted a quantitative trait locus (QTL) analysis pertaining to the concentrations of three major tanshinone components, cryptotanshinone, tanshinone I, and tanshinone IIA, in S. miltiorrhiza. This extensive investigation was conducted across three distinct planting environments, ultimately identifying a comprehensive repertoire of 27 discernible QTLs. These QTLs were mapped onto four distinct linkage groups (LG), namely LG1, LG5, LG6, and LG7, which explained 3.11%-37.85% phenotypic variation. Candidate genes were projected based on consistent QTLs detected for each active ingredient in three environments. Nineteen putative candidate genes involved in the regulation of tanshinone biosynthesis were identified. These genes participate in primary metabolic and multiple branching terpenoid biosynthesis pathways, forming a complex regulatory network. Our findings have the potential to offer novel insights into advancing the understanding of the regulatory mechanisms governing tanshinone biosynthesis. Furthermore, these results establish crucial groundwork for gene discovery, marker-assisted selection breeding, and map-based cloning of functional genes associated with tanshinone content in S. miltiorrhiza.

Whole-genome sequencing of copy number variation analysis in Ethiopian cattle reveals adaptations to diverse environments.

Genomic structural variations (GSVs), notably copy number variations (CNVs), significantly shape genetic diversity and facilitate adaptation in cattle populations. Despite their importance, the genome-wide characterization of CNVs in indigenous Ethiopian cattle breeds-Abigar, Fellata, and Gojjam-Highland remains largely unexplored. In this study, we applied a read-depth approach to whole genome sequencing (WGS) data to conduct the first comprehensive analysis of CNVs in these populations. We identified 3,893 CNV regions (CNVRs) covering 19.15Mb (0.71% of the cattle genome). These CNVRs ranged from 1.60kb to 488.0kb, with an average size of 4.92kb. These CNVRs included deletions (1713), duplications (1929), and mixed events (251) showing notable differences in distribution among the breeds. Four out of five randomly selected CNVRs were successfully validated using real time polymerase chain reaction (qPCR). Further analyses identified candidate genes associated with high-altitude adaptation (GBE1 and SOD1), heat stress adaptation (HSPA13, DNAJC18, and DNAJC8) and resistance to tick infestations (BoLA and KRT33A). In addition, variance stabilizing transformation (VST) statistics highlighted population-specific CNVRs, emphasizing the unique genetic signatures of high-altitude adaptation in the Gojjam-Highland cattle breed. Among the detected CNVRs, 4.93% (192 out of 3,893) overlapped with 520 quantitative traits loci (QTLs) associated with six economically important trait categories suggesting that these CNVRs may significantly contribute to the genetic variation underlying these traits. Our comprehensive analysis reveals significant CNVRs associated with key adaptive traits in Ethiopian cattle breeds highlighting their genetic diversity and resilience. These findings offer valuable insights into the genetic basis of adaptability and can inform sustainable breeding practices and conservation efforts. Future research should prioritize the functional validation of these CNVRs and their integration into breeding programs to enhance traits such as disease resistance and environmental adaptability.

Identification and validation of two quantitative trait loci showing pleiotropic effect on multiple grain-related traits in bread wheat (Triticum aestivum L.).

QKl/Tgw/Gns.yaas-2D associates with KL, TGW, and GNS, and QKl/Tgw.yaas-5A associates with KL and TGW. Significantly pleiotropic and additive effects of these two QTL were validated. The YM5 allele both at QKl/Tgw/Gns.yaas-2D and QKl/Tgw.yaas-5A was proved to be the best allelic combination for improving yield potential. Kernel length (KL), kernel width (KW), thousand grain weight (TGW), and grain number per spike (GNS) play important roles in the yield improvement of wheat. In this study, one recombinant inbred line (RIL) derived from a cross between Yangmai 5 (YM5) and Yanzhan 1 (YZ1) was used to identify quantitative trait loci (QTL) associated with KL, KW, TGW, and GNS across three years. Two pleiotropic QTL namely QKl/Tgw/Gns.yaas-2D and QKl/Tgw.yaas-5A were located in two genomic regions on chromosomes 2D and 5A, respectively. Breeder-friendly Kompetitive Allele-Specific PCR (KASP) markers for QKl/Tgw/Gns.yaas-2D and QKl/Tgw.yaas-5A were developed and validated in a set of 246 wheat cultivars/lines. Analysis of allelic combinations indicated that the YM5 allele both at QKl/Tgw/Gns.yaas-2D and QKl/Tgw.yaas-5A is probably the best one to promote TGW, GNS, and grain weight per spike. Based on the analysis of gene annotation, sequence variations, expression patterns, and GO enrichment, twenty-five and twenty-four candidate genes of QKl/Tgw/Gns.yaas-2D and QKl/Tgw.yaas-5A, respectively, were identified. These results provide the basis of fine-mapping the target QTL and marker-assisted selection in wheat yield-breeding programs.

Quantitative trait locus mapping and OsFLOq12 identification for rice grain hardness: towards improved rice flour for wheat substitution.

Recent shifts in consumer dietary preferences have led to a significant decline in rice consumption in Korea, resulting in surplus rice production. To address this issue, rice flour has been proposed as a substitute for wheat flour. However, the physical, chemical and structural differences between rice and wheat, particularly in grain hardness, pose challenges in using rice flour as an alternative. Understanding the genetic factors that influence rice grain hardness is crucial for improving the milling process and producing high-quality rice flour suitable for wheat flour substitution. In this study, various grain traits, including length, width, thickness, length-to-width ratio and hardness, were measured in a population of brown and milled rice. Quantitative trait locus (QTL) analysis revealed a significant association between grain hardness and thickness, with QTLs for grain hardness mapped on chromosomes 1 and 12 for brown and milled rice, respectively. A total of 20 candidate genes related to grain hardness were identified through QTL analysis. Among them, OsFLOq12 (LOC_Os12g43550) was identified as a key gene influencing grain hardness, which encodes a Ras small GTPase. Phenotypic analysis showed differences in endosperm appearance and particle size between lines with low and high grain hardness. The genetic analysis of OsFLOq12 revealed a single nucleotide polymorphism associated with grain hardness. This study provides valuable insights into the genetic background of grain hardness, offering a foundation for breeding rice varieties optimized for flour production as a viable substitute for wheat flour. © 2024 Society of Chemical Industry.

Ferroptosis regulates hemolysis in stored murine and human red blood cells.

Red blood cell (RBC) metabolism regulates hemolysis during aging in vivo and in the blood bank. However, the genetic underpinnings of RBC metabolic heterogeneity and extravascular hemolysis at population scale are incompletely understood. Based on the breeding of 8 founder strains with extreme genetic diversity, the Jackson laboratory diversity outbred population can capture the impact of genetic heterogeneity in like fashion to population-based studies. RBCs from 350 outbred mice, either fresh or stored for 7 days, were tested for post-transfusion recovery, as well as metabolomics and lipidomics analyses. Metabolite and lipid Quantitative Trait Loci (QTL) mapped >400 gene-metabolite associations, which we collated into an online interactive portal. Relevant to RBC storage, we identified a QTL hotspot on chromosome 1, mapping on the region coding for the ferrireductase Steap3, a transcriptional target to p53. Steap3 regulated post-transfusion recovery, contributing to a ferroptosis-like process of lipid peroxidation, as validated via genetic manipulation in mice. Translational validation of murine findings in humans, STEAP3 polymorphisms were associated with RBC iron content, lipid peroxidation and in vitro hemolysis in 13,091 blood donors from the Recipient Epidemiology and Donor Evaluation Study. QTL analyses in humans identified a network of gene products (FADS1/2, EPHX2, LPCAT3, SLC22A16, G6PD, ELOVL, PLA2G6) associated with lower levels of oxylipins. These polymorphisms were prevalent in donors of African descent and were linked to allele frequency of hemolysis-linked polymorphisms for Steap3 or p53. These genetic variants were also associated with lower hemoglobin increments in thousands of single-unit transfusion recipients from the vein-to-vein database.

Identification of a novel locus qGW12/OsPUB23 regulating grain shape and weight in rice (Oryza sativa L.).

Key message A major quantitative trait locus (qGW12) for grain shape and weight has been isolated in rice, corresponding to LOC_Os12g17900/OsPUB23, and its encoded protein interacts with OsMADS1. Grain shape in rice is an important trait that influences both yield and quality. The primary determinants of grain shape are quantitative trait loci (QTLs) inherited from natural variation in crops. In recent years, much attention has been paid to the molecular role of QTLs in regulating grain shape and weight. In this study, we report the cloning and characterization of qGW12, a major QTL regulating grain shape and weight in rice, using a series of chromosome fragment substitution lines (CSSLs) derived from Oryza sativa indica cultivar 9311 (acceptor) and Oryza rufipogon Griff (donor). One CSSL line, Q187, harboring the introgression of qGW12, exhibited a significant decrease in grain-shape-related traits (including grain length and width) and thousand-grain weight compared to the cultivar 9311. Subsequent backcrossing of Q187 with 9311 resulted in the generation of secondary segregating populations, which were used to fine-map qGW12 to a 24-kb region between markers Seq-44 and Seq-48. Our data indicated that qGW12 encodes a previously unreported U-box type E3 ubiquitin ligase, designated OsPUB23, which exhibited E3 ubiquitin ligase activity. Overexpression of OsPUB23 in rice resulted in higher plant yield than the wild type due to an increase in grain size and weight. Conversely, loss of OsPUB23 function resulted in the opposite tendency. Yeast two-hybrid screening and split luciferase complementation assays revealed that OsPUB23 interacts with OsMADS1. The functional characterization of OsPUB23 provides new genetic resources for improving of grain yield and quality in crops.

Genome-wide association of an organic naked barley diversity panel identified quantitative trait loci for disease resistance.

Foliar fungal diseases are a major limitation in organic naked barley (Hordeum vulgare L.) production. The lack of conventional fungicides in organic systems increases reliance on genetic resistance. We evaluated the severity of barley stripe rust (Puccinia striiformis f.sp. hordei Westend), leaf rust (Puccina hordei sp. hordei), spot blotch (Cochliobolus sativus, anamorph Bipolaris sorokiniana (S. Ito & Kurib.) Drechsler ex Dastur), and scald (Rhynchosporium commune Zaffarano, McDonald and Linde sp. November) on a naked barley diversity panel of 350 genotypes grown in 13 environments to identify quantitative trait loci associated with disease resistance. Genome-wide association analyses across and within environments found 10 marker trait associations for barley stripe rust, four marker trait associations for leaf rust, one marker trait association for scald, and five marker trait associations for spot blotch. Structure analysis identified six Ward groups based on genotypic diversity. Resistance to susceptible allele ratios were high for stripe rust and spot blotch, moderate for leaf rust, and low for scald. Combined phenotypic analysis values for each disease overlayed by a principal component analysis found distinct resistance and susceptibility patterns for barley stripe rust and scald. Most significant marker trait associations were previously identified in the literature, providing confirmation and potential new sources of disease resistance for genetic improvement of naked barley germplasm.

Genetic Dissection of Milled Rice Grain Shape by Using a Recombinant Inbred Line Population and Validation of qMLWR11.1 and qMLWR11.2

Grain shape in rice (Oryza sativa L.) is a complex trait governed by multiple quantitative trait loci (QTLs). To dissect the genetic basis of rice shape, QTL analysis was conducted for milled rice grain width (MGW), milled rice grain length (MGL), and milled rice length-to-width ratio (MLWR) using a recombinant inbred line (RIL) population of F10 and F11 generations derived from a cross between Yuexiangzhan and Shengbasimiao. A high-density genetic map consisting of 2412 bins was constructed by sequencing 184 RILs, spanning a total length of 2376.46 cM. A total of 19 QTLs related to MGL, MGW, and MLWR were detected under two environments. The range of phenotypic variation attributed to individual QTL ranged from 1.67% to 32.08%. Among those, a novel locus for MGL, MGW and MLWR, designated as qMLWR3.2, was pinpointed within a specific ~0.96-Mb region. Two novel loci for MGW and MLWR, qMLWR11.1 and qMLWR11.2, were verified within ~1.22-Mb and ~0.52-Mb regions using three RIL-developed populations, respectively. These findings lay the foundation for further map-based cloning and molecular design breeding in rice.

QTL mapping and genome-wide association analysis reveal genetic loci and candidate gene for resistance to gray leaf spot in tropical and subtropical maize germplasm.

Using QTL mapping and GWAS, two candidate genes (Zm00001d051039 and Zm00001d051147) were consistently identified across the three different environments and BLUP values. GWAS analysis identified the candidate gene, Zm00001d044845. These genes were subsequently validated to exhibit a significant association with maize gray leaf spot (GLS) resistance. Gray leaf spot (GLS) is a major foliar disease of maize (Zea mays L.) that causes significant yield losses worldwide. Understanding the genetic mechanisms underlying gray leaf spot resistance is crucial for breeding high-yielding and disease-resistant varieties. In this study, eight tropical and subtropical germplasms were crossed with the temperate germplasm Ye107 to develop a nested association mapping (NAM) population comprising 1,653 F2:8 RILs, consisting of eight recombinant inbred line (RIL) subpopulations, using the single-seed descent method. The NAM population was evaluated for GLS resistance in three different environments, and genotyping by sequencing of the NAM population generated 593,719 high-quality single-nucleotide polymorphisms (SNPs). Linkage analysis and genome-wide association studies (GWASs) were conducted to identify candidate genes regulating GLS resistance in maize. Both analyses identified 25 QTLs and 149 SNPs that were significantly associated with GLS resistance. Candidate genes were screened 20Kb upstream and downstream of the significant SNPs, and three novel candidate genes (Zm00001d051039, Zm00001d051147, and Zm00001d044845) were identified. Zm00001d051039 and Zm00001d051147 were located on chromosome 4 and co-localized in both linkage (qGLS4-1 and qGLS4-2) and GWAS analyses. SNP-138,153,206 was located 0.499kb downstream of the candidate gene Zm00001d051039, which encodes the protein IN2-1 homolog B, a homolog of glutathione S-transferase (GST). GSTs and protein IN2-1 homolog B scavenge reactive oxygen species under various stress conditions, and GSTs are believed to protect plants from a wide range of biotic and abiotic stresses by detoxifying reactive electrophilic compounds. Zm00001d051147 encodes a probable beta-1,4-xylosyltransferase involved in the biosynthesis of xylan in the cell wall, enhancing resistance. SNP-145,813,215 was located 2.69kb downstream of the candidate gene. SNP-5,043,412 was consistently identified in three different environments and BLUP values and was located 8.788kb downstream of the candidate gene Zm00001d044845 on chromosome 9. Zm00001d044845 encodes the U-box domain-containing protein 4 (PUB4), which is involved in regulating plant immunity. qRT-PCR analysis showed that the relative expression levels of the three candidate genes were significantly upregulated in the leaves of the TML139 (resistant) parent, indicating that these three candidate genes could be associated with resistance to GLS. The findings of this study are significant for marker-assisted breeding aimed at enhancing resistance to GLS in maize and lay the foundation for further elucidation of the genetic mechanisms underlying resistance to gray leaf spot in maize and breeding of new disease-resistant varieties.