Genetic Basis Research Articles

Genetic Markers of Spina Bifida: Enrichment of Pathogenic Variants and Variants of Uncertain Significance

ABSTRACT Introduction: The genetic diversity of the population in India, shaped by its unique history of migrations and varied ethnic landscape, suggests the possibility of genetic profiles distinct from the western populations. Objective: The objective is to investigate the genetic basis of spina bifida in the Indian cohort through whole-exome sequencing and pathway enrichment. Methods: The variants of uncertain significance (VUS) of spina bifida were identified through whole-exome sequencing in the study cohort (n = 3). The pathogenic, likely pathogenic, and VUS were analyzed for protein–protein interactions and functional associations with genes implicated in spina bifida using tools such as STRING and KEGG pathways, which were validated through a literature review. The study was focused on the Wnt/planar cell polarity signaling pathway, which is crucial for neural tube closure. Results: The study-cohort was collectively represented through 40 common VUS, including eight deleterious SNPs related to genes AP3D1, NLRP9, PCDHGA11, PRSS3, MTSS2, ENDOV, C9, and NSD3. These genes were functionally linked to neural development, immune response, and cellular processes critical for neural tube closure. Notably, interactions were observed between four genes (NLGN2, PKD1, PRSS3, and PLK1) and CTNNB1 (Wnt signaling pathway) crucial for embryonic neural tube formation. Conclusions: This study has identified novel genetic variants and pathways potentially contributing to the etiopathogenesis of spina bifida in the Indian population. Future research with larger cohorts and functional studies is necessary to validate these findings and explore their potential for clinical applications in spina bifida.

Understanding the Role of Genetics in Tumour and Cancer Biology

The interplay between genetics and cancer has been a focal point of research for decades, leading to profound understandings into the molecular mechanisms driving tumorigenesis. In this comprehensive review article, we explore the genetic basis of cancer, encompassing the diverse array of alterations that underline oncogenic transformation. From oncogenes to tumor suppressor genes, and from point mutations to chromosomal rearrangements, we delve into the molecular hallmarks of cancer and their implications for diagnosis, treatment, and prevention. Drawing on recent advancements in genomic technologies, we discuss the role of next-generation sequencing, single-cell sequencing, and computational modeling in unraveling the complexity of cancer genetics. Furthermore, we examine the clinical implications of genetic predisposition to cancer, highlighting the importance of genetic testing and counselling in cancer risk assessment and management. Through an exploration of tumor heterogeneity, clonal evolution, and therapeutic resistance, we underscore the challenges and opportunities in precision oncology. Finally, we discuss future directions in cancer genetics research, including precision prevention strategies and ethical considerations.Keywords: Cancer Genetics; Oncogenes; Tumor Suppressor Genes; Genetic Alterations; Precision Oncology; Clonal Evolution

Sensory characterization of the Ethiopian germplasm of Coffea arabica L. conserved in the Colombian Coffee Collection

The sensory quality of coffee (Coffea arabica L.) has become increasingly important and is considered the best way to increase the competitiveness and profitability of the sector. Given the narrow genetic base cultivated, the use of its genetic resources conserved in germplasm banks is particularly relevant, especially for germplasm collected in Ethiopia, the country from which coffee originated and the center of its diversity of profiles. However, the potential benefits of using these resources is unknown. Therefore, the objective of this study was to characterize the sensory quality of the Ethiopian germplasm conserved in the Colombian Coffee Collection (CCC) to determine its variability and potential for use. The sensory qualities of drinks from 378 accessions of CCC were characterized. The results showed that 34% of the accessions evaluated presented sensory descriptors different from those of the traditional varieties. For the Global Impression attribute, the highest scores were associated with citrus, spice and floral notes. Additionally, prospecting rather than the area of origin of the germplasm influenced its sensory diversity, possibly due to the established objectives of the collection. The conserved germplasm exhibited important sensory variability, which is linked to rare descriptors in traditional varieties. Characterization activities of genetic resources, such as those conducted in this study, add value and serve as an initial step toward their application in breeding. The results obtained allow the selection of genotypes with distinct sensory profiles, which can be incorporated into genetic improvement programs aimed at developing future varieties with these attributes.

Dissection of the genetic basis and molecular mechanism of ovule number per ovary in oilseed rape (Brassica napus L.)

Ovule number per ovary (ONPO) determines the maximum potential of seed number per fruit that is a direct component of seed yield in crops. This study aimed to dissect the genetic basis and molecular mechanism of ONPO using a newly developed doubled haploid (DH) population in oilseed rape. In all the four investigated environments, the ONPO of 201 DH lines exhibited normal distribution with a wide variation from 22.6 to 41.8, suggesting quantitative inheritance appropriate for mapping QTL. A skeleton genetic map of 2111 markers within 19 linkage groups was developed, with a total of 1715.71 cM in length and an average of 0.82 cM between markers. Linkage mapping identified ten QTLs that were distributed on eight chromosomes and explained 7.0-15.9% of the phenotypic variance. Among these, four were identical to the reported and two were repeatedly detected with relatively large effects, highlighting their potential for marker-assisted selection. Phytohormone quantification of ovaries (at the ovule initiation stage) from two pools of high and low ONPO lines showed significant differences in the levels of nine sub-types of phytohormones, suggesting their important roles in regulating ovule number. Transcriptomic analysis identified 7689 differentially expressed genes (DEGs) between the two pools, of which nearly half were enriched into functional categories of reported genes regulating ONPO, including protein, RNA, signalling, miscellaneous, development, hormone metabolism, and tetrapyrrole synthesis. Integration of linkage QTL mapping, transcriptome sequencing and BLAST analysis identified 15 homologues of reported ovule number genes and 327 DEGs in the QTL regions, which were considered as direct and potential candidate genes. These findings propose further insights into the genetic basis and molecular mechanisms of ONPO, which will facilitate future gene cloning and genetic improvement for enhancing seed yield in oilseed rape.

Genome-wide association scan and candidate gene analysis for seed coat color in sesame (Sesamum indicum L.)

IntroductionSeed coat color in sesame is a crucial trait for breeding programs as it is closely associated with important characteristics such as oil content, protein levels, and disease resistance, which directly influence seed quality and market value.MethodsThis study investigates the genetic basis of seed coat color in 200 Sudanese sesame genotypes grown for two consecutive years through comprehensive phenotyping, genomic diversity analysis, genome-wide association studies (GWAS), and candidate gene discovery.Results and discussionPhenotypic analysis across two growing seasons revealed high heritability and significant correlations among color parameters (L*, a*, and b*), indicating strong genetic control over seed coat color. The genomic analysis identified distinct clusters among sesame accessions, with rapid linkage disequilibrium decay suggesting a high level of recombination. GWAS identified significant SNPs associated with seed coat color traits, revealing key genomic regions on chromosomes 3, 6, 9, 12, and 13. Candidate gene analysis highlighted several genes, including DOF zinc finger proteins and WRKY transcription factors, which may play essential roles in pigment biosynthesis pathways. These findings provide valuable insights for breeding programs to enhance desirable seed coat color traits in sesame.

A TTPA deletion is associated with Retinopathy with Vitamin E Deficiency (RVED) in the English Cocker Spaniel Dog.

Retinopathy with Vitamin E Deficiency (RVED) is a familial disease in the English Cocker Spaniel (ECS) dog breed. Ophthalmic abnormalities observed in RVED-affected ECS include lipofuscin granule deposition within the tapetal fundus and subsequent retinal degeneration resulting in visual deficits. Affected dogs may also exhibit neurological signs that include ataxia and hindlimb proprioceptive deficit. In all cases, circulating plasma concentrations of α-tocopherol are low. This study sought to investigate the genetic basis of RVED in the ECS breed. We undertook a genome-wide association study comprising 30 ECS with normal fundic examinations aged 6 years or older (controls) and 20 diagnosed with RVED (cases) and identified a statistically associated signal on chromosome 29 (Praw = 1.909×10-17). Whole genome sequencing (WGS) of two cases identified a 102bp deletion in exon 1 of the Alpha Tocopherol Transfer Protein gene (TTPA), truncating the protein by 34 amino acids. The c.23_124del variant segregated with RVED in a total of 30 cases and 43 controls. Variants in TTPA are causal for Ataxia with Vitamin E Deficiency (AVED) in humans which is a phenotypically similar disease to RVED. The identification of the canine variant is extremely significant as the availability of a DNA test will allow for identification of presymptomatic dogs and early therapeutic intervention which may prevent development of retinopathy and improve neurological signs. Breeders can also use the DNA test to efficiently eradicate the disease from this breed.

Signatures of natural selection may indicate a genetic basis for the beneficial effects of oily fish intake in indigenous people from coastal Ecuador.

Atahualpa is a rural village located in coastal Ecuador, a region that has been inhabited by people as early as 10,000 years ago. The traditional diet of their indigenous inhabitants is rich in oily fish and they have, therefore, served as a model for investigating the beneficial effects of such a diet. However, the genetic background of this population has not been studied. In this study, we sequenced the genomes of Atahualpa residents to look for variants under natural selection, which could mediate the effects of oily fish intake. DNA was extracted from 50 blood samples from randomly selected individuals recruited in the Atahualpa Project Cohort. After applying various filters, we calculated genome-wide genotype likelihoods from 33 samples, and combined data from those samples with data from other populations to investigate how the Atahualpa population is genetically related to these populations. Using selection scans, we identified signals of natural selection that may explain the above-mentioned dietary effects. The genetic ancestry in Atahualpa residents is 94.1% of indigenous American origin, but is substantially diverged from other indigenous populations in neighboring countries. Significant signatures of natural selection were found in the Atahualpa population, including a broad selection signal around the SUFU gene, which is a repressor of Hedgehog pathway signaling and associated with lipid metabolism, and another signal in the upstream region of LRP1B which encodes low-density lipoprotein (LDL) receptor related protein 1B. Our selection study reveals genes under selection in the Atahualpa population, which could mediate the beneficial effects of oily fish intake in this population.

Combined Bulked Segregant Analysis-Sequencing and Transcriptome Analysis to Identify Candidate Genes Associated with Cold Stress in Brassica napus L

Cold tolerance in rapeseed is closely related to its growth, yield, and geographical distribution. However, the mechanisms underlying cold resistance in rapeseed remain unclear. This study aimed to explore cold resistance genes and provide new insights into the molecular mechanisms of cold resistance in rapeseed. Rapeseed M98 (cold-sensitive line) and D1 (cold-tolerant line) were used as parental lines. In their F2 population, 30 seedlings with the lowest cold damage levels and 30 with the highest cold damage levels were selected to construct cold-tolerant and cold-sensitive pools, respectively. The two pools and parental lines were analyzed using bulk segregant sequencing (BSA-seq). The G’-value analysis indicated a single peak on Chromosome C09 as the candidate interval, which had a 2.59 Mb segment with 69 candidate genes. Combined time-course and weighted gene co-expression network analyses were performed at seven time points to reveal the genetic basis of the two-parent response to low temperatures. Twelve differentially expressed genes primarily involved in plant cold resistance were identified. Combined BSA-seq and transcriptome analysis revealed BnaC09G0354200ZS, BnaC09G0353200ZS, and BnaC09G0356600ZS as the candidate genes. Quantitative real-time PCR validation of the candidate genes was consistent with RNA-seq. This study facilitates the exploration of cold tolerance mechanisms in rapeseed.

Characterization of resistance to Bacillus thuringiensis toxin Cry1Ac in Crocidosema sp. (Lepidoptera: Tortricidae) from Brazil.

Crocidosema aporema (Walsingham 1914) has historically been the main bud borer species in soybean in Brazil; however, a recent study reported that this species is not C. aporema but an undescribed species. In recent seasons, injury by Crocidosema sp. has been reported in soybean expressing the Bacillus thuringiensis Berliner (Bt) toxin Cry1Ac. In this study, we investigated the genetic basis of Cry1Ac resistance and assessed the fitness costs of resistance in a field-derived Cry1Ac-resistant Crocidosema sp. strain selected through an F2 screen. The Cry1Ac-resistant strain of Crocidosema sp. developed from neonate to pupae fed on Cry1Ac soybean leaves and adults produced viable offspring. The resistance ratio to Cry1Ac in this strain was >500 000-fold relative to the susceptible strain. Results from leaf and diet-overlay bioassays indicated that the inheritance pattern of Cry1Ac resistance in Crocidosema sp. is sex-linked, with a lethal dose compensation in the F1 progeny from R♂ × S♀ (making resistance incompletely recessive), whereas the F1 progeny from R♀ × S♂ had complete mortality on Cry1Ac soybean (making resistance completely recessive). The mortality of backcrosses on Cry1Ac soybean varied significantly, suggesting that the resistance is controlled by multiple genes. Life-history results revealed that the Cry1Ac-resistant strain had lower pupal weight, reproductive performance and population growth on non-Bt soybean compared with the susceptible strain. The inheritance patterns of Cry1Ac resistance in Crocidosema sp. are sex-linked, incompletely or completely recessive depending on the direction of the reciprocal cross, polygenic and associated with fitness cost. © 2025 Society of Chemical Industry.

P-20 EARLY ZOLEDRONIC ACID TREATMENT IN A PEDIATRIC CASE OF OSTEOGENESIS IMPERFECTA TYPE V: CLINICAL OUTCOMES AND THE ROLE OF IFITM5 (BRIL) MUTATION

Abstract Introduction Osteogenesis imperfecta (OI) is a rare genetic disorder characterized by bone fragility, low bone mass, and frequent fractures. OI is typically associated with mutations in the COL1A1 and COL1A2 genes, but a subset of cases, such as OI type V, is linked to mutations in the IFITM5 gene, also known as BRIL (bone-restricted IFITM-like). Clinical Case This report presents a case of a 2-year-old boy diagnosed with OI type V, a rare form of the disease caused by a mutation in BRIL. The patient exhibited multiple recurrent bone fractures beginning in infancy, though there was no family history of bone disease or consanguineous marriage. Physical examination revealed that the patient was of normal weight and height for his age, with neurodevelopmental milestones met. Laboratory tests showed elevated alkaline phosphatase (ALP) levels, indicative of increased bone turnover, while other values were within normal ranges. Radiological evaluations confirmed an active fracture in the left tibia but showed no additional pathological involvement. Genetic testing identified a de novo C>T variant in the IFITM5 gene, confirming the diagnosis of OI type V. The patient was treated with intravenous zoledronic acid (ZA), a bisphosphonate therapy, which is currently being tested in infants and toddlers for OI treatment. The treatment led to a significant reduction in fracture recurrence and a decrease in ALP levels, demonstrating its efficacy in managing the disease. Despite these positive outcomes, certain hallmark features of OI type V, such as hyperplastic callus formation and new periosteal bone growth, were not observed during follow-up, possibly due to the early initiation of ZA therapy. OI type V is distinguished from other forms of OI by hyperplastic callus formation and increased osteoblast activity, often accompanied by elevated ALP levels. Radiographic and histological findings specific to this type include periosteal bone growth and a reticular lamellation pattern in the bone matrix. Although ZA has shown promise in reducing fracture risk and improving clinical outcomes, its long-term efficacy in preventing other disease manifestations, such as intramembranous ossification, remains uncertain. The underlying pathological mechanisms of OI type V, particularly the role of BRIL, are not yet fully understood. Further research into the activation of BRIL in osteoblasts could lead to the development of targeted therapies that address the root cause of the disease. While ZA therapy has been effective in managing the immediate symptoms of OI type V, a deeper understanding of the disease's genetic and molecular basis is crucial for improving long-term treatment outcomes. In conclusion, the IFITM5 (BRIL) mutation is recognized as the genetic cause of OI type V. Early intervention with ZA has shown positive effects in managing the disease, but further research is needed to fully understand the pathological mechanisms and to develop treatments that can address all aspects of the disease.Table 1:Lab workout (age 2)ALP = alkaline phosphatase; AST = aspartate transaminase; BUN = blood urea nitrogen; GGT = gamma-glutamyl transferase; CBC: complete blood count

Identification and functional validation of a new gene conferring resistance to Soybean Mosaic Virus strains SC4 and SC20 in soybean

Soybean Mosaic Virus (SMV) poses a serious threat to soybean production, often resulting in considerable yield losses or complete crop failure, particularly if infection occurs during early growth stages. While several SMV resistance genes have been identified, the genetic basis of resistance to certain strains remains poorly understood. Among the 22 SMV strains, SC4 and SC20 are considered pathogenic in Central China. Dominant genes resistant to SC4 (Rsc4) on Chr.14 in Dabaima and to SC20 (Rsc20) on Chr.13 in Qihuang-1 have been identified. Kefeng-1 is resistant to SC4 and SC20. This study aimed to determine whether the resistance to SC4 and SC20 in Kefeng-1 was identical and whether Rsc4 and Rsc20 in Dabaima and Qihuang-1 are also present in Kefeng-1 due to translocation. Mendelian experiments using F1, F2, and recombinant inbred lines (RIL3:8) of Kefeng-1 (resistant) and NN1138-2 (susceptible) indicated a single dominant gene inheritance pattern in SC4 and SC20, respectively. Linkage mapping showed two loci for SC4 and SC20 in neighboring single nucleotide polymorphism linkage disequilibrium blocks (SNPLDB) marker regions of 253 kb and 375 kb, respectively, in Kefeng-1. Association between SNPs in possible gene regions of Kefeng-1 and resistance data showed SNP11692903 jointly as the most significant SNP, exhibiting the highest χ2 value. By comparing SNP11692903 to possible gene sequences in the coding region, Glyma02g13380 was identified as a joint candidate gene. The results were validated using qRT-PCR, virus induced gene silencing (VIGS), and gene-sequence. Therefore, the two Mendelian genes on chromosome 2 in Kefeng-1 responsible for SC4 and SC20 resistance are unique genes, different from Rsc4 in Dabaima and Rsc20 in Qihuang-1. Hence, one gene is involved in resistance toward two SMV strains resistance. This result challenged our previous hypothesis of a single dominant gene responsible for resistance against a single strain and underscored the potential for using multiple resistance sources aimed at enhancing SMV resistance in breeding practices.

Generalized functional varying-index coefficient model for dynamic synergistic gene-environment interactions with binary longitudinal traits.

The genetic basis of complex traits involves the function of many genes with small effects as well as complex gene-gene and gene-environment interactions. As one of the major players in complex diseases, the role of gene-environment interactions has been increasingly recognized. Motivated by epidemiology studies to evaluate the joint effect of environmental mixtures, we developed a functional varying-index coefficient model (FVICM) to assess the combined effect of environmental mixtures and their interactions with genes, under a longitudinal design with quantitative traits. Built upon the previous work, we extend the FVICM model to accommodate binary longitudinal traits through the development of a generalized functional varying-index coefficient model (gFVICM). This model examines how the genetic effects on a disease trait are nonlinearly influenced by a combination of environmental factors. We derive an estimation procedure for the varying-index coefficient functions using quadratic inference functions combined with penalized splines. A hypothesis testing procedure is proposed to evaluate the significance of the nonparametric index functions. Extensive Monte Carlo simulations are conducted to evaluate the performance of the method under finite samples. The utility of the method is further demonstrated through a case study with a pain sensitivity dataset. SNPs were found to have their effects on blood pressure nonlinearly influenced by a combination of environmental factors.

Genome‐wide association studies on body weight in Loumen ducks

AbstractBody weight is an important trait associated with meat production in the poultry industry. To better understand the genetic basis of body weights in ducks, we estimated genetic parameters and performed a genome‐wide association study. The phenotypic values of body weights at ages 0 weeks (bw0) and 8 weeks (bw8) were collected individually from 199 Loumen ducks, and their genotypes were assayed with whole genome re‐sequencing. The heritability of bw0 and bw8 are 0.32 and 0.43, respectively, and the genetic correlation of bw0 and bw8 was very low (−7.256e‐5). The genome‐wide association study results identified eight SNPs significantly associated with bw0 and bw8. The two and nine genes nearest to the significant SNPs were selected as candidate genes: PIK3R5 and MYH10 for bw0, and LOC119717016, RHOJ, PPP2R5E, BRF1, LOC106018961, NUDT14, JAG2, CEP170B, and AKT1 for bw8. Together, the SNPs and candidate genes identified in this study advance understanding of the complex genetic architecture of bw0 and bw8, and provide important clues for future implementation of a genomic selection program in Loumen ducks.

Natural variation of CTB5 confers cold adaptation in plateau japonica rice

During cold acclimation in high-latitude and high-altitude regions, japonica rice develops enhanced cold tolerance, but the underlying genetic basis remains unclear. Here, we identify CTB5, a homeodomain-leucine zipper (HD-Zip) transcription factor that confers cold tolerance at the booting stage in japonica rice. Four natural variations in the promoter and coding regions enhance cold response and transcriptional regulatory activity, enabling the favorable CTB5KM allele to improve cold tolerance. CTB5 interacts with OsHox12 and targets gibberellin (GA) metabolism genes to promote GAs accumulation in anthers and facilitate tapetum development under cold stress. Moreover, CTB5 directly regulates PYL9 and improves cold tolerance at the seedling stage by reducing reactive oxygen species (ROS) accumulation. The CTB5KM allele is selected during the cold acclimation of japonica rice to plateau habitats in Yunnan Province. Our findings provide insights into the mechanisms underlying cold adaptation in plateau japonica rice and offer potential targets for breeding cold-tolerant rice varieties.

A cross-tissue transcriptome-wide association study identifies new susceptibility genes for benign prostatic hyperplasia

Benign prostatic hyperplasia (BPH) is a prevalent urinary system disorder. Despite evidence of a significant genetic component from previous studies, the specific pathogenic genes and biological mechanisms are still largely unknown. The study utilized the FinnGen R10 dataset, encompassing 177,901 individuals (36,601 cases and 141,300 controls), and the GTEx v8 EQTLs files to conduct single-tissue and cross-tissue transcriptome-wide association studies (TWAS). FUSION method was utilized to validate the findings in specific tissues. Gene Analysis and Multi-marker Analysis of Genomic Annotation (MAGMA) were used to identify potential susceptibility genes. The intersection genes of the above results were analyzed by Mendelian randomization (MR), summary data-based MR (SMR) and colocalization studies. Fine-mapping of causal gene sets (FOCUS) software was employed to accurately locate risk genes. Gene Expression Omnibus (GEO) analysis explores the differential expression of genes. Finally, The GeneMANIA tool was utilized to further understand the functional roles of these susceptibility genes. The cross-tissue TWAS analysis revealed 28 genes associated with BPH susceptibility. Single-tissue TWAS and MAGMA further refined eight genes, and subsequent MR, SMR, FOCUS and colocalization analysis pinpointed INO80B as the key gene. The differential expression of this result was verified by GEO. INO80B may help prevent excessive prostatic cell proliferation by regulating cell cycle-related gene expression. Our research identified the INO80B gene, whose predicted expression is associated with BPH risk and hence provided a new insight into the genetic basis of this disease. However, further functional studies are necessary to elucidate the potential biological activity of these significant signals.

Polygenic diseases

Background: Recent advances in molecular genetics have revolutionized our understanding of hereditary diseases, particularly polygenic (multifactorial) conditions. This comprehensive review examines the genetic basis of common polygenic diseases, including diabetes, preeclampsia, breast cancer, and factors influencing athletic performance. Material and Methods: Analysis of current literature covering genetic aspects of polygenic diseases, focusing on gene polymorphisms, single nucleotide polymorphisms (SNPs), and their role in disease development. The review encompasses nutrigenetics, sports genomics, and genetic markers associated with athletic performance and injury risk. Results: Gene polymorphisms significantly impact disease susceptibility and progression. For type 2 diabetes, over 600 candidate genes have been identified. In preeclampsia, multiple genes influence maternal-fetal interactions and vascular function. Breast cancer involves complex interactions between high and moderate penetrance genes, with over 300 SNPs identified. Athletic performance is influenced by both genetic factors (approximately 66%) and environmental conditions, with specific genetic markers associated with endurance, strength, and injury risk. Conclusions: Polygenic diseases result from complex interactions between multiple genes and environmental factors. Understanding these interactions enables more effective personalized approaches to prevention, diagnosis, and treatment. Integration of genetic testing into clinical practice offers opportunities for improved patient outcomes through targeted interventions and personalized medicine strategies.

Transcriptional time-course analysis during ash dieback infection revealed different responses in tolerant and susceptible Fraxinus excelsior genotypes

Hymenoscyphus fraxineus, the causal agent of Ash Dieback (ADB), has been introduced to eastern Europe in the 1990s from where it spread causing decline in European ash populations. However, the genetic basis of the molecular response in tolerant and susceptible ash trees to this disease is still largely unknown. We performed RNA-sequencing to study the transcriptomic response to the disease in four ash genotypes (ADB-tolerant FAR3 and FS36, and ADB-susceptible UW1 and UW2), during a time-course of 7, 14, 21, and 28 days post-inoculation, including mock-inoculated trees as control samples for each sampling time point. The analysis yielded 395 and 500 Differentially Expressed Genes (DEGs) along the response for ADB-tolerant FAR3 and FS36, respectively, while ADB-susceptible UW1 and UW2 revealed 194 and 571 DEGs, respectively, with most DEGs found exclusively in just one of the genotypes. DEGs shared between tolerant genotypes FAR3 and FS36, included genes involved in the production of phytoalexins and other secondary metabolites with roles in plant defense. Moreover, we identified an earlier expression of genes involved in both pattern- and effector-triggered immunity (PTI and ETI) in ADB-tolerant genotypes, while in ADB-susceptible genotypes both responses were delayed (late response). Overall, these results revealed different transcriptomic expression patterns not only between ADB-tolerant and ADB-susceptible genotypes, but also within these two groups. This hints to individual responses in the natural tolerance to ADB, possibly revealing diversified strategies across ash genotypes.

Novel candidate genes and genetic basis analysis of kernel starch content in tropical maize

BackgroundStarch is the most abundant carbohydrate in maize grains, serving as a primary energy source for both humans and animals, and playing a crucial role in various industrial applications. Increasing the starch content of maize grains is beneficial for improving the grain yield and quality. To gain insight into the genetic basis of starch content in maize kernels, a multiparent population (MPP) was constructed and evaluated for starch content in three different environments.ResultsThe integration of QTL mapping and genome-wide association analysis (GWAS) identified two SNPs, 8_166371888 and 8_178656036, which overlapped the QTL interval of qSC8-1, identified in the tropical maize line YML46. The phenotypic variance explained (PVE) by the QTL qSC8-1 was12.17%, while the SNPs 8_166371888 and 8_178656036 explained 10.19% and 5.72% of the phenotypic variance. Combined GWAS and QTL analyses led to the identification of two candidate genes, Zm00001d012005 and Zm00001d012687 located on chromosome 8.ConclusionsThe candidate geneZm00001d012005 encodes histidine kinase, which is known to play a role in starch accumulation in rice spikes. Related histidine kinases, such as AHK1, are involved in endosperm transfer cell development in barley, which affects grain quality. Zm00001d012687 encodes triacylglycerol lipase, which reduces seed oil content. Since oil content in cereal kernels is negatively correlated with starch content, this gene is likely involved in regulating the starch content in maize kernels. These findings provide insights into the genetic mechanisms underlying kernel starch content and establish a theoretical basis for breeding maize varieties with high starch content.

Genetic diversity and environmental adaptation in Ethiopian tef.

Orphan crops serve as essential resources for both nutrition and income in local communities and offer potential solutions to the challenges of food security and climate vulnerability. Tef [Eragrostis tef (Zucc.)], a small-grained allotetraploid, C4 cereal mainly cultivated in Ethiopia, stands out for its adaptability to marginal conditions and high nutritional value, which holds both local and global promise. Despite its significance, tef is considered an orphan crop due to limited genetic improvement efforts, reliance on subsistence farming, and its nutritional, economic, and cultural importance. Although pre-Semitic inhabitants of Ethiopia have cultivated tef for millennia (4000-1000 BCE), the genetic and environmental drivers of local adaptation remain poorly understood. To address this, we resequenced a diverse collection of traditional tef varieties to investigate their genetic structure and identify genomic regions under environmental selection using redundancy analysis, complemented by differentiation-based methods. We identified 145 loci associated with abiotic environmental factors, with minimal geographic influence observed in the genetic structure of the sample population. Overall, this work contributes to the broader understanding of local adaptation and its genetic basis in tef, providing insights that support efforts to develop elite germplasms with improved environmental resilience.

Analysis of the genetic basis of fiber-related traits and flowering time in upland cotton using machine learning.

Cotton is an important crop for fiber production, but the genetic basis underlying key agronomic traits, such as fiber quality and flowering days, remains complex. While machine learning (ML) has shown great potential in uncovering the genetic architecture of complex traits in other crops, its application in cotton has been limited. Here, we applied five machine learning models-AdaBoost, Gradient Boosting Regressor, LightGBM, Random Forest, and XGBoost-to identify loci associated with fiber quality and flowering days in cotton. We compared two SNP dataset down-sampling methods for model training and found that selecting SNPs with an Fscale value greater than 0 outperformed randomly selected SNPs in terms of model accuracy. We further performed machine learning quantitative trait loci (mlQTLs) analysis for 13 traits related to fiber quality and flowering days. These mlQTLs were then compared to those identified through genome-wide association studies (GWAS), revealing that the machine learning approach not only confirmed known loci but also identified novel QTLs. Additionally, we evaluated the effect of population size on model accuracy and found that larger population sizes resulted in better predictive performance. Finally, we proposed candidate genes for the identified mlQTLs, including two argonaute 5 proteins, Gh_A09G104100 and Gh_A09G104400, for the FL3/FS2 locus, as well as GhFLA17 and Syntaxin-121 (Gh_D09G143700) for the FSD09_2/FED09_2 locus. Our findings demonstrate the efficacy of machine learning in enhancing the identification of genetic loci in cotton, providing valuable insights for improving cotton breeding strategies.