Candidate Genes Research Articles

Transcriptome analysis of long non-coding RNA associated with embryonic muscle development in chickens.

1. Skeletal muscle is an important component of chicken carcass. In chickens, the number of muscle fibres is fixed during the embryonic period, and muscle development during the embryonic period determines the muscle development potential after hatching.2. Beijing-You (BY) and Cornish (CN) chickens show completely different growth rates and body types, and two breeds were used in this study to explore the role of lncRNAs in muscle development during different chicken embryonic periods. A systematic analysis of lncRNAs and mRNAs were conducted in the pectoral muscle tissues of BY and CN chickens at embryonic days 11 (ED11), 13 (ED13), 15 (ED15), 17 (ED17), and 1-day-old (D1) using RNA-seq. A total of 4,104 differentially expressed transcripts (DETs) were identified among the five stages, including 2,359 lncRNAs and 1,745 mRNAs.3. The number of DETs between the two breeds at ED17 (1,658 lncRNAs and 1,016 mRNAs) was much higher than the total number of DET at all the other stages (692 lncRNAs and 729 mRNAs), indicating that the two breeds show the largest difference in gene regulation at ED17.4. Correlation analysis was performed for all differentially expressed lncRNAs and mRNAs during the five periods. Forty-three, cis interaction pairs of lncRNA-mRNA related to chicken muscle development were predicted. The expression of four pairs was verified, and the results showed MSTRG.12395.2-FGFBP2 and MSTRG.18590.6-FMOD were significantly up-regulated in CN at ED11 compared to BY and might be important candidate genes for embryonic muscle development.

Prevalence of kidney health genetic variants in adults with sickle cell nephropathy.

The pathophysiology and genetic risk for sickle cell disease (SCD)-related chronic kidney disease (CKD) are not well understood. In 70 adults with SCD-related CKD and without APOL1 inherited in a high-risk pattern, 24 (34%) had pathogenic variants in candidate genes using KidneySeq™. A moderate impact INF2 variant was observed in 20 (29%) patients and those with 3 versus 0-2 pathogenic or moderate impact glomerular genetic variants had higher albuminuria and lower estimated glomerular filtration rate (adjusted p ≤ 0.015). Using a panel of preselected genes implicated in kidney health, we observed several variants in people with sickle cell nephropathy.

Sweet corn association panel and genome-wide association analysis reveal loci for chilling-tolerant germination

Sweet corn is highly susceptible to the deleterious effects of low temperatures during the initial stages of growth and development. Employing a 56K chip, high-throughput single-nucleotide polymorphism (SNP) sequencing was conducted on 100 sweet corn inbred lines. Subsequently, six germination indicators—germination rate, germination index, germination time, relative germination rate, relative germination index, and relative germination time—were utilized for genome-wide association analysis. Candidate genes were identified via comparative analysis of homologous genes in Arabidopsis and rice, and their functions were validated using quantitative real-time polymerase chain reaction (qRT-PCR). The results revealed 35,430 high-quality SNPs, 16 of which were significantly correlated. Within 50 kb upstream and downstream of the identified SNPs, 46 associated genes were identified, of which six were confirmed as candidate genes. Their expression patterns indicated that Zm11ΒHSDL5 and Zm2OGO likely play negative and positive regulatory roles, respectively, in the low-temperature germination of sweet corn. Thus, we determined that these two genes are responsible for regulating the low-temperature germination of sweet corn. This study contributes valuable theoretical support for improving sweet corn breeding and may aid in the creation of specific germplasm resources geared toward enhancing low-temperature tolerance in sweet corn.

Integrating meta‐analysis of genome‐wide association study with Pig Genotype‐Tissue Expression resources uncovers the genetic architecture for age at first farrowing in pigs

AbstractAge at first farrowing (AFF) is a reproductive trait with low heritability and high importance in the pig industry. To enhance the statistical power of genome‐wide association study (GWAS) and further explore the genetic nature of AFF, we first conducted GWAS meta‐analysis using three Yorkshire populations, and then integrated the Pig Genotype‐Tissue Expression (PigGTEx) resources to interpret their potential regulatory mechanism. Additionally, we compared the AFF in pig with the age at first birth (AFB) of human using GWAS summary statistics. We detected 18 independent variants in GWAS meta‐analysis and 8 genes in gene‐based association analysis significantly associated with AFF. By integrating the PigGTEx resource, we conducted transcriptome‐wide association study (TWAS) and colocalization analysis on 34 pig tissues. In TWAS, we detected 18 significant gene‐tissue pairs, such as DCAF6 in uterus and CREG1 in blood. In colocalization, we found 111 potential candidate tissue‐gene pairs, such as GJD4 and LYPLAL1. We found that the homologous gene, CHST10, might be the potential candidate gene between humans in AFB and pigs in AFF. In conclusion, integrating GWAS meta‐analysis and PigGTEx resources is a meaningful way to decipher the genetic architecture of complex traits. We found that DCAF6, CREG1, GJD4, and LYPLAL1 are candidate genes with high reliability for AFF in swine. The comparative analysis showed that CHST10 might play a potentially critical role in AFB/AFF across human and pigs.

Molecular characterization of positively selected genes contributing aquatic adaptation in marine mammals.

Marine mammals, which have evolved independently into three distinct lineages, share common physiological features that contribute to their adaptation to the marine environment. To identify positively selected genes (PSGs) for adaptation to the marine environment using available genomic data from three taxonomic orders: cetaceans, pinnipeds, and sirenians. Based on the genomes within each group of Artiodactyla, Carnivora and Afrotheria, we performed selection analysis using the branch-site model in CODEML. Based on the branch-site model, 460, 614, and 359 PSGs were predicted for the cetaceans, pinnipeds, and sirenians, respectively. Functional enrichment analysis indicated that genes associated with hemostasis were positively selected across all lineages of marine mammals. We observed positive selection signals for the hemostasis and coagulation-related genes plasminogen activator, urokinase (PLAU), multimerin 1 (MMRN1), gamma-glutamyl carboxylase (GGCX), and platelet endothelial aggregation receptor 1 (PEAR1). Additionally, we found out that the sodium voltage-gated channel alpha subunit 9 (SCN9A), serine/arginine repetitive matrix 4 (SRRM4), and Ki-ras-induced actin-interacting protein (KRAP) are under positive selection pressure and are associated with cognition, neurite outgrowth, and IP3-mediated Ca2 + release, respectively. This study will contribute to our understanding of the adaptive evolution of marine mammals by providing information on a group of candidate genes that are predicted to influence adaptation to aquatic environments, as well as their functional characteristics.

Natural variant of Rht27, a dwarfing gene, enhances yield potential in wheat.

Discovery of Rht27, a dwarf gene in wheat, showed potential in enhancing grain yield by reducing plant height. Plant height plays a crucial role in crop architecture and grain yield, and semi-dwarf Reduced Height (Rht) alleles contribute to lodging resistance and were important in "Green Revolution." However, the use of these alleles is associated with some negative side effects in some environments, such as reduced coleoptile length, low nitrogen use efficiency, and reduced yield. Therefore, novel dwarf gene resources are needed to pave an alternative route to overcome these side effects. In this study, a super-dwarf mutant rht27 was obtained by the mutagenesis of G1812 (Triticum urartu, the progenitor of the A sub-genome of common wheat). Genetic analysis revealed that the dwarf phenotype was regulated by a single recessive genetic factor. The candidate region for Rht27 was narrowed to a 1.55Mb region on chromosome 3, within which we found two potential candidate genes that showed polymorphisms between the mutant and non-mutagenized G1812. Furthermore, the natural variants and elite haplotypes of the two candidates were investigated in a natural population of common wheat. The results showed that the natural variants affect grain yield components, and the dwarf haplotypes show the potential in improving agronomic traits and grain yield. Although the mutation in Rht27 results in severe dwarf phenotype in T. urartu, the natural variants in common wheat showed desirable phenotype, which suggests that Rht27 has the potential to improve wheat yield by utilizing its weak allelic mutation or fine-tuning its expression level.

Identification of potential candidate genes for the Houyan trait in developing Wulong goose embryos by transcriptomic analysis

ABSTRACT 1. The Wulong goose is a Chinese breed and a source of high-quality meat and eggs. A characteristic of the Wulong goose is that a proportion of the birds do not have eyelids, known as the Huoyon trait. 2. Wulong geese exhibiting the Huoyan trait at embryonic stages of 9 days (E9), 12 days (E12) and 14 days (E14) were selected alongside those with normal eyelids for comprehensive transcriptome sequencing. Differentially expressed gene (DEG) and functional enrichment analyses were performed and finally, eight DEG were chosen to verify the accuracy of qPCR sequencing. 3. Overall, 466, 962 and 550 DEG were obtained from the three control groups, D9 vs. N9, D12 vs. N12 and D14 vs. N14, respectively, by differential analysis (p < 0.05). CDKN1C, CRH, CROCC and TYSND1 were significantly expressed in the three groups. Enrichment analysis revealed the enrichment of CROCC and TYSND1 in pathways of cell cycle process, endocytosis, microtubule-based process, microtubule organising centre organisation, protein processing and protein maturation. CDKN1C and CRH were enriched in the cell cycle and cAMP signalling pathway. 4. Some collagen family genes were detected among the DEGs, including COL3A1, COL4A5, COL4A2 and COL4A1. FREM1 and FREM2 genes were detected in both Huoyan and normal eyelids. There was a significant difference (p < 0.01) in FREM1 expression between ED9 and ED14 in female embryos, but this difference was not observed in male embryos.

R2R3-MYB transcription factor CsMYB60 controls mature fruit skin color by regulating flavonoid accumulation in cucumber.

Skin color is an important trait that determines the cosmetic appearance and quality of fruits. In cucumber, the skin color ranges from white to brown in mature fruits. However, the genetic basis for this important trait remains unclear. We conducted a genome-wide association study of natural cucumber populations, along with map-based cloning techniques, on an F2 population resulting from a cross between Pepino (with yellow-brown fruit skin) and Zaoer-N (with creamy fruit skin). We identified CsMYB60 as a candidate gene responsible for skin coloration in mature cucumber fruits. In cucumber accessions with white to pale yellow skin color, a premature stop mutation (C to T) was found in the second exon region of CsMYB60, whereas light yellow cucumber accessions exhibited splicing premature termination caused by an intronic mutator-like element insertion in CsMYB60. Transgenic CsMYB60c cucumber plants displayed a yellow-brown skin color by promoting accumulation of flavonoids, especially hyperoside, a yellow-colored flavonol. CsMYB60c encodes a nuclear protein that primarily acts as a transcriptional activator through its C-terminal activation motif. RNA sequencing and DNA affinity purification sequencing assays revealed that CsMYB60c promotes skin coloration by directly binding to the YYTACCTAMYT motif in the promoter regions of flavonoid biosynthetic genes, including CsF3'H, which encodes flavonoid 3'-hydroxylase. The findings of our study not only offer insight into the function of CsMYB60 as dominantly controlling fruit coloration, but also highlight that intronic DNA mutations can have a similar phenotypic impact as exonic mutations, which may be valuable in future cucumber breeding programs.

Large-scale transcriptomic and genomic analyses reveal a novel functional gene SERPINB6 for chicken carcass traits

BackgroundCarcass traits are crucial indicators of meat production efficiency. However, the molecular regulatory mechanisms associated with these traits remain unclear.ResultsIn this study, we conducted comprehensive transcriptomic and genomic analyses on 399 Tiannong partridge chickens to identify key genes and variants associated with carcass traits and to elucidate the underlying regulatory mechanisms. Based on association analyses with the elastic net (EN) model, we identified 12 candidate genes (AMY1A, AP3B2, CEBPG, EEF2, EIF4EBP1, FGFR1, FOXD3, GOLM1, LOC107052698, PABPC1, SERPINB6 and TBC1D16) for 4 carcass-related traits, namely live weight, dressed weight, eviscerated weight, and breast muscle weight. SERPINB6 was identified as the only overlapping gene by 3 analyses, EN model analysis, weighted gene co-expression network analysis and differential expression analysis. Cell-level experiments confirmed that SERPINB6 promotes the proliferation of chicken DF1 cells and primary myoblasts. Further expression genome-wide association study and association analysis indicated that rs317934171 is the critical site that enhances SERPINB6 expression. Furthermore, a dual-luciferase reporter assay proved that gga-miR-1615 targets the 3′UTR of SERPINB6.ConclusionsCollectively, our findings reveal that SERPINB6 serves as a novel gene for chicken carcass traits by promoting fibroblast and myoblast proliferation. Additionally, the downstream variant rs317934171 regulates SERPINB6 expression. These results identify a new target gene and molecular marker for the molecular mechanisms of chicken carcass traits.

Single nucleotide polymorphisms in the KRT82 promoter region modulate irregular thickening and patchiness in the dorsal skin of New Zealand rabbits

BackgroundWhile rabbits are used as models in skin irritation tests, the presence of irregular patches and thickening on the dorsal skin can affect precise evaluation. In this study, genes associated with patchiness or non-patchiness on the dorsal skin of New Zealand rabbits were investigated to identify potential regulators of the patchiness phenotype.ResultsThe results showed that parameters associated with hair follicles (HFs), such as HF density, skin thickness, and HF depth, were augmented in rabbits with the patchiness phenotype relative to the non-patchiness phenotype. A total of 592 differentially expressed genes (DEGs) were identified between the two groups using RNA-sequencing. These included KRT72, KRT82, KRT85, FUT8, SOX9, and WNT5B. The functions of the DEGs were investigated by GO and KEGG enrichment analyses. A candidate gene, KRT82, was selected for further molecular function verification. There was a significant positive correlation between KRT82 expression and HF-related parameters, and KRT82 overexpression and knockdown experiments with rabbit dermal papilla cells (DPCs) showed that it regulated genes related to skin and HF growth and development. Investigation of single nucleotide polymorphisms (SNPs) in the exons and promoter region of KRT82 identified four SNPs in the promoter region but none in the exons. The G.-631G > T, T.-696T > C, G.-770G > T and A.-873 A > C alleles conformed to the Hardy − Weinberg equilibrium, and three identified haplotypes showed linkage disequilibrium. Luciferase reporter assays showed that the core promoter region of KRT82 was located in the − 600 to − 1200 segment, in which the four SNPs were located.ConclusionsThe morphological characteristics of the patchiness phenotype were analyzed in New Zealand rabbits and DEGs associated with this phenotype were identified by RNA-sequencing. The biological functions of the gene KRT82 associated with this phenotype were analyzed, and four SNPs were identified in the promoter region of the gene. These findings suggest that KRT82 may be a potential biomarker for the breeding of experimental New Zealand rabbits.

Analysis and validation of biomarkers of immune cell-related genes in postmenopausal osteoporosis: An observational study.

Postmenopausal osteoporosis (PMOP) is a common metabolic inflammatory disease. In conditions of estrogen deficiency, chronic activation of the immune system leads to a hypo-inflammatory phenotype and alterations in its cytokine and immune cell profile, although immune cells play an important role in the pathology of osteoporosis, studies on this have been rare. Therefore, it is important to investigate the role of immune cell-related genes in PMOP. PMOP-related datasets were downloaded from the Gene Expression Omnibus database. Immune cells scores between high bone mineral density (BMD) and low BMD samples were assessed based on the single sample gene set enrichment analysis method. Subsequently, weighted gene co-expression network analysis was performed to identify modules highly associated with immune cells and obtain module genes. Differential analysis between high BMD and low BMD was also performed to obtain differentially expressed genes. Module genes are intersected with differentially expressed genes to obtain candidate genes, and functional enrichment analysis was performed. Machine learning methods were used to filter out the signature genes. The receiver operating characteristic (ROC) curves of the signature genes and the nomogram were plotted to determine whether the signature genes can be used as a molecular marker. Gene set enrichment analysis was also performed to explore the potential mechanism of the signature genes. Finally, RNA expression of signature genes was validated in blood samples from PMOP patients and normal control by real-time quantitative polymerase chain reaction. Our study of PMOP patients identified differences in immune cells (activated dendritic cell, CD56 bright natural killer cell, Central memory CD4 T cell, Effector memory CD4 T cell, Mast cell, Natural killer T cell, T follicular helper cell, Type 1 T-helper cell, and Type 17 T-helper cell) between high and low BMD patients. We obtained a total of 73 candidate genes based on modular genes and differential genes, and obtained 5 signature genes by least absolute shrinkage and selection operator and random forest model screening. ROC, principal component analysis, and t-distributed stochastic neighbor embedding down scaling analysis revealed that the 5 signature genes had good discriminatory ability between high and low BMD samples. A logistic regression model was constructed based on 5 signature genes, and both ROC and column line plots indicated that the model accuracy and applicability were good. Five signature genes were found to be associated with proteasome, mitochondria, and lysosome by gene set enrichment analysis. The real-time quantitative polymerase chain reaction results showed that the expression of the signature genes was significantly different between the 2 groups. HIST1H2AG, PYGM, NCKAP1, POMP, and LYPLA1 might play key roles in PMOP and be served as the biomarkers of PMOP.

PE (Prickly Eggplant) encoding a cytokinin-activating enzyme responsible for the formation of prickles in eggplant

Abstract Eggplant is one of the most important vegetables worldwide, with some varieties displaying prickles. These prickles, present on the leaves, stems, and fruit calyxes, pose challenges during cultivation, harvesting, and transportation, making them an undesirable agronomic trait. However, the genetic mechanisms underlying prickle morphogenesis in eggplant remain poorly understood, impeding genetic improvements. In this study, genetic analyses revealed that prickle morphogenesis is governed by a single dominant nuclear gene, termed PE (Prickly Eggplant). Subsequent bulk segregant RNA-sequencing (BSR-seq) and linkage analysis preliminarily mapped PE to chromosome 6. This locus was then fine mapped to a 9,233-bp interval in a segregating population of 1109 plants, harboring only one candidate gene, SmLOG1, which encodes a LONELY GUY (LOG)-family cytokinin biosynthetic enzyme. Expression analyses via transcriptome and qRT-PCR demonstrate that SmLOG1 is predominantly expressed in immature prickles. CRISPR-Cas9 knockout experiments targeting SmLOG1 in prickly parental line 'PI381159' abolished prickles across all tissues, confirming its critical role in prickle morphogenesis. Sequence analysis of SmLOG1 pinpointed variations solely within the non-coding region. We developed a CAPS marker from a distinct SNP located at -735-bp within the SmLOG1 promoter, finding significant association with prickle variation in 190 eggplant germplasms. These findings enhance our understanding of the molecular mechanisms governing prickle development in eggplant and facilitate the use of marker-assisted selection (MAS) for breeding prickleless cultivars.

Clpf encodes pentatricopeptide repeat protein (PPR5) and regulates pink flesh color in watermelon (Citrullus lanatus L.).

The gene controlling pink flesh in watermelon was finely mapped to a 55.26-kb region on chromosome 6. The prime candidate gene, Cla97C06G122120 (ClPPR5), was identified through forward genetics. Carotenoids offer numerous health benefits; while, they cannot be synthesized by the human body. Watermelon stands out as one of the richest sources of carotenoids. In this study, genetic generations derived from parental lines W15-059 (red flesh) and JQ13-3 (pink flesh) revealed the presence of the recessive gene Clpf responsible for the pink flesh (pf) trait in watermelon. Comparative analysis of pigment components and microstructure indicated that the disparity in flesh color between the parental lines primarily stemmed from variations in lycopene content, as well as differences in chromoplast number and size. Subsequent bulk segregant analysis (BSA-seq) and genetic mapping successfully narrowed down the Clpf locus to a 55.26-kb region on chromosome 6, harboring two candidate genes. Through sequence comparison and gene expression analysis, Cla97C06G122120 (annotated as a pentatricopeptide repeat, PPR) was predicted as the prime candidate gene related to pink flesh trait. To further investigate the role of the PPR gene, its homologous gene in tomato was silenced using a virus-induced system. The resulting silenced fruit lines displayed diminished carotenoid accumulation compared with the wild-type, indicating the potential regulatory function of the PPR gene in pigment accumulation. This study significantly contributes to our understanding of the forward genetics underlying watermelon flesh traits, particularly in relation to carotenoid accumulation. The findings lay essential groundwork for elucidating mechanisms governing pigment synthesis and deposition in watermelon flesh, thereby providing valuable insights for future breeding strategies aimed at enhancing fruit quality and nutritional value.

Deciphering genetic factors contributing to enhanced resistance against Cercospora leaf blight in soybean (Glycine max L.) using GWAS analysis

Cercospora leaf blight (CLB), caused by Cercospora cf. flagellaris, C. kikuchii, and C. cf. sigesbeckiae, is a significant soybean [Glycine max (L.) Merr.] disease in regions with hot and humid conditions causing yield loss in the United States and Canada. There is limited information regarding resistant soybean cultivars, and there have been marginal efforts to identify the genomic regions underlying resistance to CLB. A Genome-Wide Association Study was conducted using a diverse panel of 460 soybean accessions from maturity groups III to VII to identify the genomic regions associated to the CLB disease. These accessions were evaluated for CLB in different regions of the southeastern United States over 3 years. In total, the study identified 99 Single Nucleotide Polymorphism (SNPs) associated with the disease severity and 85 SNPs associated with disease incidence. Across multiple environments, 47 disease severity SNPs and 23 incidence SNPs were common. Candidate genes within 10 kb of these SNPs were involved in biotic and abiotic stress pathways. This information will contribute to the development of resistant soybean germplasm. Further research is warranted to study the effect of pyramiding desirable genomic regions and investigate the role of identified genes in soybean CLB resistance.

A time-resolved multi-omics atlas of transcriptional regulation in response to high-altitude hypoxia across whole-body tissues

High-altitude hypoxia acclimatization requires whole-body physiological regulation in highland immigrants, but the underlying genetic mechanism has not been clarified. Here we use sheep as an animal model for low-to-high altitude translocation. We generate multi-omics data including whole-genome sequences, time-resolved bulk RNA-Seq, ATAC-Seq and single-cell RNA-Seq from multiple tissues as well as phenotypic data from 20 bio-indicators. We characterize transcriptional changes of all genes in each tissue, and examine multi-tissue temporal dynamics and transcriptional interactions among genes. Particularly, we identify critical functional genes regulating the short response to hypoxia in each tissue (e.g., PARG in the cerebellum and HMOX1 in the colon). We further identify TAD-constrained cis-regulatory elements, which suppress the transcriptional activity of most genes under hypoxia. Phenotypic and transcriptional evidence indicate that antenatal hypoxia could improve hypoxia tolerance in offspring. Furthermore, we provide time-series expression data of candidate genes associated with human mountain sickness (e.g., BMPR2) and high-altitude adaptation (e.g., HIF1A). Our study provides valuable resources and insights for future hypoxia-related studies in mammals.

Transcriptional Landscape and Dynamics Involved in Sugar and Acid Accumulation during Apple Fruit Development.

In fleshy fruit, sugars and acids are central components of fruit flavor and quality. To date, the mechanisms underlying transcriptional regulation of sugar and acid during fruit development remain largely unknown. Here, we combined ATAC-seq with RNA-seq to investigate the genome-wide chromatin accessibility and to identify putative transcription factors related to sugar and acid accumulation during apple (Malus domestica) fruit development. By integrating the differentially accessible regions (DARs) and differentially expressed genes (DEGs), we generated a global dataset of promoter-accessibility- and expression-increased genes (PEIGs). Using this strategy, we constructed a transcriptional regulatory network enabling screening for key transcription factors and target genes involved in sugar and acid accumulation. Among these transcription factors, five fruit-specific Dof (DNA binding with one finger) genes were selected to confirm their regulatory effects, and our results showed that they could affect sugar or acid concentration by regulating the expression of sugar or acid metabolism-related genes in apple fruits. Our transcriptional regulatory network provides a suitable platform to identify candidate genes that control sugar and acid accumulation. Meanwhile, our dataset will aid in analyzing other characteristics of apple fruit that have not been illuminated previously. Overall, these findings support a better understanding of the regulatory dynamics during apple fruit development and lay a foundation for quality improvement of apple.

Potential role of CTNNA3 and FRMPD4 in vascular tumorous thrombosis of colon adenocarcinoma.

Vascular tumorous thrombosis is a crucial pathological feature of malignant tumors that is closely associated with lymph node metastasis and is considered a form of tumor micrometastasis. Two downregulated genes, catenin alpha 3 (CTNNA3) and FERM and PDZ domain-containing 4 (FRMPD4), were selected by analyzing the differential expression of vascular tumorous thrombus in colon adenocarcinoma and paracancerous tissues. Further investigation revealed their potential role in the development of vascular tumorous thrombosis in colon adenocarcinomas. Candidate genes for vascular tumorous thrombosis in colon adenocarcinoma were screened using GSE127069, and pan-cancer verification and immune infiltration analysis were performed. The relationship between gene expression and vascular tumorous thrombosis was analyzed based on the level of gene mutations using cBioPortal. Finally, the collected clinical samples were used to verify expression. CTNNA3 and FRMPD4 were expressed at low levels in the vascular tumorous thrombosis of colon adenocarcinoma and positively correlated with microsatellite instability. They are also closely related to the immune microenvironment and the infiltration of immune cell subtypes. Based on gene mutation analysis, gene deletion is suggested to be related to vascular invasion indicators. Finally, protein and messenger ribonucleic acid (mRNA) expression of CTNNA3 and FRMPD4 were downregulated in the vascular tumorous thrombosis samples of colon adenocarcinoma compared to normal glands from paracancerous tissues. Our study suggests that CTNNA3 and FRMPD4 could be promising biomarkers for vascular tumorous thrombosis in colon adenocarcinoma, potentially enabling the identification of micrometastases in this type of cancer. These findings suggest a novel strategy for the detection and management of colon adenocarcinomas.

CgSSR marker based trait associations for Sitotroga cerealella (Olivier) resistance in stored paddy rice

Rice is stored for a longer time and many primary and secondary insect pests attack grains, causing both quantitative and qualitative losses. Physicochemical characteristics of grain influence stored grain insect susceptibility and resistance. Identification of gene/Quantitative Trait Loci (QTLs) and introgression in the cultivars would provide the desired solution for varietal resistance against S. cerealella. A group of 80 rice varieties was used for genetic analysis for the identification of candidate genes responsible for Sitotroga cerealella resistance. Heat maps derived from values in the kinship matrix were used to group the varieties into three subpopulations. The largest subpopulation has 34 varieties, while the lowest had 19. The first three principal components (PCs) explained 16, 9, and 6 percent of total variation, respectively, as indicated by the Principal Component Analysis (PCA). The PCA results complemented the heat map results in defining population structure. Genome-wide association mapping can detect marker-trait associations/QTLs in a heterogeneous population of breeding lines, despite population structure and unequal family relatedness. As shown by the Genomic Association and Prediction Integrated Tool (GAPIT) heat map, there are three subpopulations in the association mapping panel. Two cgSSR markers, related to gene SDG725 and FLO2, were linked to the attributes and responsible for conferring resistance against S. cerealella infestation. This is the first report of association and that would help in the development of cultivar with S. cerealella resistance.

Assessment of genotypic variability and genome‐wide association analysis of cooking time and canning quality traits in common bean (Phaseolus vulgaris L.)

AbstractDeveloping improved common bean varieties with short cooking time (CT) and good canning quality traits (CQTs) is very key for accelerating bean consumption among the urban and middle‐class population. The objective of this study was to assess the genotypic variability and identify single nucleotide polymorphism (SNP) markers associated with CT and CQTs in common bean. A total of 250 common bean accessions were evaluated under field conditions for two seasons using alpha lattice design with two replications. Three months post‐harvest, the dry bean grains were evaluated for CT and CQTs. Significant variation was observed among the 250 common bean accessions tested for both traits. CT ranged from 51 to 215 min, with 11 genotypes cooking in less than 60 min. The percentage total CQTs' score ranged from 41% to 84% with 31 genotypes scoring 76% and above. Forty‐seven significant GWAS signals were detected for CT on chromosomes Pv01, Pv04, Pv05 and Pv11 and CQTs on Pv01, Pv02, Pv03, Pv04, Pv05, Pv06, Pv07, Pv08, Pv10 and Pv11, respectively. Positional candidate genes including Phvul.005G161200 on chromosome Pv05, Phvul.007G2803001 and Phvul.007G280700 on chromosome Pv07 were associated with seed coat colour retention of the canned beans. Besides their usefulness in breeding research, the identified bean genotypes with shorter CT and good CQTs could enhance bean consumption and processing industries.

The first high-quality genome assembly and annotation of Lantana camara, an important ornamental plant and a major invasive species

This study presents the first annotated, haplotype-resolved, chromosome-scale genome of Lantana camara, a flowering shrub native to Central America and known for its dual role as an ornamental plant and an invasive species. Despite its widespread cultivation and ecological impact, the lack of a high-quality genome has hindered the investigation of traits of both ornamental and invasive. This research bridges the gap in genomic resources for L. camara, which is crucial for both ornamental breeding programs and invasive species management. Whole-genome and transcriptome sequencing were utilized to elucidate the genetic complexity of a diploid L. camara breeding line UF-T48. The genome was assembled de novo using HiFi and Hi-C reads, resulting in two phased genome assemblies with high Benchmarking Universal Single-Copy Orthologs (BUSCO) scores of 97.7%, indicating their quality. All 22 chromosomes were assembled with pseudochromosomes averaging 117 Mb. The assemblies revealed 29 telomeres and an extensive presence of repetitive sequences, primarily long terminal repeat transposable elements. The genome annotation identified 83,775 protein-coding genes, with 83% functionally annotated. In particular, the study mapped 42 anthocyanin and carotenoid candidate gene clusters and 12 herbicide target genes to the assembly, identifying 38 genes spread across the genome that are integral to flower color development and 53 genes for herbicide targeting in L. camara. This comprehensive genomic study not only enhances the understanding of L. camara’s genetic makeup but also sets a precedent for genomic research in the Verbenaceae family, offering a foundation for future studies in plant genetics, conservation, and breeding.