LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on variant call format files

Whole-genomic comparison reveals complex population dynamics and parasitic adaptation of Echinococcus granulosus sensu stricto

Cystic echinococcosis (CE), caused by Echinococcus granulosus sensu stricto (s.s.), poses a substantial risk to both humans and domestic animals globally. Here, we compared the whole genomes of 111 E. granulosus s.s. samples from China. Genomic variation data revealed frequent cross-fertilization in the hermaphroditic E. granulosus. The G1 and G3 genotypes represent distinct mitochondrial lineages, while showing no differentiation in the nuclear genome, suggesting mito-nuclear discordance caused by historical geographic separation and subsequent fusion. Population structure, demographic history, and gene flow among populations reflected the transmission route of E. granulosus s.s. from the Middle East to Qinghai-Xizang Plateau through the migration of nomadic people, followed by introgression during secondary contact. Genomic variations highlighted selection signatures within the genome prone to balancing selection, particularly impacting genes encoding membrane-related proteins, representing a potential evolutionary strategy for adaptation to parasitic life. Balancing selection pressure on the gene-coding sodium/bile acid cotransporter led to its high level of genetic stability, which may play a crucial role in the survival and development of E. granulosus during the parasitic stage, making it a potential drug target for the treatment of CE. Meanwhile, other genomic regions under strong balancing selection may provide potential targets for protective immunity. These findings offer valuable insights into the complex dynamics and adaptive evolution of E. granulosus s.s. in China.IMPORTANCEEchinococcus granulosus sensu stricto (s.s.) is the primary cause of cystic echinococcosis (CE), a parasitic disease affecting humans and livestock with significant health and economic impacts. Previous studies on this parasite relied on mitochondrial DNA to classify its genotypes and understand its genetic diversity. However, these studies cannot capture the full complexity of its evolutionary dynamics and adaptation strategies. Our research employs comprehensive genome-wide sequencing, offering a more nuanced view of its genetic landscape. We discovered that cross-fertilization appears to be a prevalent reproductive strategy in the hermaphroditic E. granulosus, underpinning the observed deep mitochondrial divergence between genotypes G1 and G3, as well as gene flow among populations. The transmission history of E. granulosus s.s. in China and its widespread genetic mixing were likely facilitated by the migrations of nomadic peoples. Furthermore, we identified genes under balancing selection, including the gene involved in the uptake of host bile acids, which play a crucial role in the parasite's survival and development, potentially offering new targets for intervention. Our research advances the understanding of the genetic diversity and evolutionary strategies of E. granulosus, laying the foundation for improved control measures of CE.

EasyOmics: A graphical interface for population-scale omics data association, integration, and visualization

The rapid growth of population-scale whole-genome resequencing, RNA sequencing, bisulfite sequencing, and metabolomic and proteomic profiling has led quantitative genetics into the era of big omics data. Association analyses of omics data, such as genome-, transcriptome-, proteome-, and methylome-wide association studies, along with integrative analyses of multiple omics datasets, require various bioinformatics tools, which rely on advanced programming skills and command-line interfaces and thus pose challenges for wet-lab biologists. Here, we present EasyOmics, a stand-alone R Shiny application with a user-friendly interface that enables wet-lab biologists to perform population-scale omics data association, integration, and visualization. The toolkit incorporates multiple functions designed to meet the increasing demand for population-scale omics data analyses, including data quality control, heritability estimation, genome-wide association analysis, conditional association analysis, omics quantitative trait locus mapping, omics-wide association analysis, omics data integration, and visualization. A wide range of publication-quality graphs can be prepared in EasyOmics by pointing and clicking. EasyOmics is a platform-independent software that can be run under all operating systems, with a docker container for quick installation. It is freely available to non-commercial users at Docker Hub https://hub.docker.com/r/yuhan2000/easyomics.

Haplotype-resolved genomes provide insights into the origins and functional significance of genome diversity in bivalves

Bivalves are famed for exhibiting vast genetic diversity of poorly understood origins and functional significance. Through comparative genomics, we demonstrate that high genetic diversity in these invertebrates is not directly linked to genome size. Using oysters as a representative clade, we show that despite genome size reduction during evolution, these bivalves maintain remarkable genetic variability. By constructing a haplotype-resolved genome for Crassostrea sikamea, we identify widespread haplotype divergent sequences (HDSs), representing genomic regions unique to each haplotype. We show that HDSs are driven by transposable elements, playing a key role in creating and maintaining genetic diversity during oyster evolution. Comparisons of haplotype-resolved genomes across four bivalve orders uncover diverse HDS origins, highlighting a role in genetic innovation and expression regulation across broad timescales. Further analyses show that, in oysters, haplotype polymorphisms drive gene expression variation, which is likely to promote phenotypic plasticity and adaptation. These findings advance our understanding of the relationships among genome structure, diversity, and adaptability in a highly successful invertebrate group.

Integrated multi-omics analysis and functional validation uncovers RPL26 roles in regulating growth traits of Asian water buffaloes (Bubalus bubalis)

BACKGROUND

Asian water buffaloes (Bubalus bubalis) in the Yangtze River Basin of China are the important meat provider for local residents because of its outstanding body size. Several previous studies have highlighted their genetic basis of growth characteristics, but the crucial genes regulating growth traits via multi-layer omics are still rarely investigated.

RESULTS

We conducted a comprehensive multi-omics analysis integrating blood and muscle transcriptome, plasma metabolome, rumen fluid metagenome, and genome of Haizi water buffaloes. Of note, ribosomal protein L26 (RPL26) located in the evolutionary selection regions associated with body sizes is the top differentially expressed gene (DEG) in both blood and muscle tissues. Further metabolomics and metagenomics identified growth-related molecular biomarkers (myristicin and Bacteroidales) and microbiological composition (Bacteroides and Prevotella). Leveraging cattle quantitative trait loci (QTLs) and genotype-tissue expression (CattleGTEx) databases, we found the significant correlations of QTL_180979 on RPL26 and two identified cis-eQTLs in muscle tissue in the upstream of RPL26 with weight gain. The follow-up cell assay validations confirmed the regulation roles of RPL26 in cell cycle, apoptosis, and differentiation, where the low RPL26 expressions enhanced the antiapoptotic ability and promoted the differentiation of myoblasts into myotubes markedly.

CONCLUSIONS

Our study illustrates RPL26 roles in regulating growth traits via both integrated multi-omics analysis and functional validations that suggests the further applications of RPL26 for growth trait selection of water buffaloes.

A telomere-to-telomere gap-free assembly integrating multi-omics uncovers the genetic mechanism of fruit quality and important agronomic trait associations in pomegranate

Pomegranate is an important perennial fruit tree distributed worldwide. Reference genomes with gaps and limit gene identification controlling important agronomic traits hinder its functional genomics and genetic improvements. Here, we reported a telomere-to-telomere (T2T) gap-free genome assembly of the distinctive cultivar 'Moshiliu'. The Moshiliu reference genome was assembled into eight chromosomes without gaps, totalling ~366.71 Mb, with 32 158 predicted protein-coding genes. All 16 telomeres and eight centromeres were characterized; combined with FISH analysis, we revealed the atypical telomere units in pomegranate as TTTTAGGG. Furthermore, a total of 16 loci associated with 15 important agronomic traits were identified based on GWAS of 146 accessions. Gene editing and biochemical experiments demonstrated that a 37.2-Kb unique chromosome translocation disrupting the coding domain sequence of PgANS was responsible for anthocyanin-less, knockout of PgANS in pomegranate exhibited a defect in anthocyanin production; a unique repeat expansion in the promoter of PgANR may affected its expression, resulting in black peel; notably, the G → A transversion located at the 166-bp coding domain of PgNST3, which caused a E56K mutation in the PgNST3 protein, closely linked with soft-seed trait. Overexpression of PgNST3A in tomato presented smaller and softer seed coats. The E56K mutation in PgNST3 protein, eliminated the binding ability of PgNST3 to the PgMYB46 promoter, which subsequently affected the thickness of the inner seed coat of soft-seeded pomegranates. Collectively, the validated gap-free genome, the identified genes controlling important traits and the CRISPR-Cas9-mediated gene knockout system all provided invaluable resources for pomegranate precise breeding.

Genome-wide association study revealed candidate genes associated with egg-laying time traits in layer chicken

In modern intensive caged laying hen production, variations in egg-laying time (ELT) among layers often increase the workload for egg collection, thereby raising the costs of labor or power and reducing overall efficiency. For management purpose, early and synchronized ELT is also advantageous, particularly to large-scale layer farm. However, the underlying genetic mechanisms of ELT remain unclear. In this study, through the development of video and artificial intelligence-based software, ELT records during the peak laying period (27-32 weeks) from 507 layers, and their earlier laying performance (21-32 weeks) were collected. Via whole genome sequencing data of all the individuals, the estimated heritabilities of traditional egg production traits ranged from 0.23 to 0.36, consistent with previous reports. The heritability of average egg-laying time (AELT) was estimated as 0.46. Furthermore, individuals with earlier AELT tended to exhibit superior egg production performance. Genome-wide association study revealed three SNPs associated with AELT traits, located at 170,867,650 bp on chromosome 1, at 5,548,087 and 5,817,488 bp on chromosome 9. Across the region of 5.4 to 7.0 Mb on chromosome 9, mutations were also identified to be strongly linked with the two AELT-associated SNPs. Genes located in this region may be responsible for the differences in AELT among hens. These results indicate that ELT has the potential to be integrated into the production system of caged layers. If ELT is to be included as a breeding objective in the future, its reliability needs to be validated in larger populations and over longer periods.

The role of NUDT3 in lipid accumulation and its functional variants related to backfat thickness in pigs

NUDT3 is a leading candidate gene that strongly linked to pig fatness traits, however, its function in porcine adipocytes remains poorly understood. Here, the percentage of EdU+ cells was significantly reduced when NUDT3 was knocked down, as was the expression of cell cycle repressors. NUDT3 overexpression yielded the opposite outcome. Moreover, the knockdown of NUDT3 resulted in more lipid droplets in adipocytes, whereas its enforced expression had the reverse effect. In addition, exogenous expression of NUDT3 in adipose tissue significantly reduced fat expansion triggered by a high-fat diet in mice. At molecular level, integrative RIP-seq and RNA-seq analysis revealed that genes influenced by NUDT3 overexpression or knockdown were significantly enriched in the PI3K-AKT signaling pathway, and western blot confirmed that AKT phosphorylation was significantly increased by NUDT3 knockdown, while the phosphorylation levels of PI3K, AKT, and mTOR were significantly decreased by the enforced NUDT3 expression both ex vivo and in vivo. Notably, rs694899689 was identified as a potential genetic variant for modulates NUDT3 expression and impacting backfat thickness in pigs through analysis of multi-omics data, CRISPRi (CRISPR interference) and dual luciferase reporter assays. Overall, our work established NUDT3 as a novel negative regulator of adipogenesis and lipid deposition and revealed that rs694899689 might serve as a potential molecular marker for pig breeding.

Comprehensive expression genome-wide association study of long non-coding RNAs in four porcine tissues

BACKGROUND

Long non-coding RNAs (lncRNAs), a type of non-coding RNA molecules, are known to play critical regulatory roles in various biological processes. However, the functions of the majority of lncRNAs remain largely unknown, and little is understood about the regulation of lncRNA expression. In this study, high-throughput DNA genotyping and RNA sequencing were applied to investigate genomic regions associated with lncRNA expression, commonly referred to as lncRNA expression quantitative trait loci (eQTLs). We analyzed the liver, lung, spleen, and muscle transcriptomes of 100 three-way crossbred sows to identify lncRNA transcripts, explore genomic regions that might influence lncRNA expression, and identify potential regulators interacting with these regions.

RESULT

We identified 6380 lncRNA transcripts and 3733 lncRNA genes. Correlation tests between the expression of lncRNAs and protein-coding genes were performed. Subsequently, functional enrichment analyses were carried out on protein-coding genes highly correlated with lncRNAs. Our correlation results of these protein-coding genes uncovered terms that are related to tissue specific functions. Additionally, heatmaps of lncRNAs and protein-coding genes at different correlation levels revealed several distinct clusters. An expression genome-wide association study (eGWAS) was conducted using 535,896 genotypes and 1829, 1944, 2089, and 2074 expressed lncRNA genes for liver, spleen, lung, and muscle, respectively. This analysis identified 520,562 significant associations and 6654, 4525, 4842, and 7125 eQTLs for the respective tissues. Only a small portion of these eQTLs were classified as cis-eQTLs. Fifteen regions with the highest eQTL density were selected as eGWAS hotspots and potential mechanisms of lncRNA regulation in these hotspots were explored. However, we did not identify any interactions between the transcription factors or miRNAs in the hotspots and the lncRNAs, nor did we observe a significant enrichment of regulatory elements in these hotspots. While we could not pinpoint the key factors regulating lncRNA expression, our results suggest that the regulation of lncRNAs involves more complex mechanisms.

CONCLUSION

Our findings provide insights into several features and potential functions of lncRNAs in various tissues. However, the mechanisms by which lncRNA eQTLs regulate lncRNA expression remain unclear. Further research is needed to explore the regulation of lncRNA expression and the mechanisms underlying lncRNA interactions with small molecules and regulatory proteins.

Pangenome analysis reveals structural variation associated with seed size and weight traits in peanut

Peanut (Arachis hypogaea L.) is an important oilseed and food legume crop, with seed size and weight being critical traits for domestication and breeding. However, genomic rearrangements like structural variations (SVs) underlying seed size and weight remain unclear. Here we present a comprehensive pangenome analysis utilizing eight high-quality genomes (two diploid wild, two tetraploid wild and four tetraploid cultivated peanuts) and resequencing data of 269 accessions with diverse seed sizes. We identified 22,222 core or soft-core, 22,232 distributed and 5,643 private gene families. The frequency of SVs in subgenome A is higher than in subgenome B. We identified 1,335 domestication-related SVs and 190 SVs associated with seed size or weight. Notably, a 275-bp deletion in gene AhARF2-2 results in loss of interaction with AhIAA13 and TOPLESS, reducing the inhibitory effect on AhGRF5 and promoting seed expansion. This high-quality pangenome serves as a fundamental resource for the genetic enhancement of peanuts and other legume crops.

Multiple independent MGR5 alleles contribute to a clinal pattern in leaf magnesium across the distribution of Arabidopsis thaliana

Magnesium (Mg) is a crucial element in plants, particularly for photosynthesis. Mg homeostasis is influenced by environmental and genetic factors, and our understanding of its variation in natural populations remains incomplete. We examine the variation in leaf Mg accumulation across the distribution of Arabidopsis thaliana, and we investigate the environmental and genetic factors associated with Mg levels. Using genome-wide association studies in both the widespread Eurasian population and a local-scale population in Cape Verde, we identify genetic factors associated with variation in leaf Mg. We validate our main results, including effect size estimates, using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) mutagenesis. Our findings reveal a significant association between leaf Mg and latitude of origin. In Eurasia, we find a signal at the nutrient-response regulator, RAPTOR1A, and across the species range, we find that multiple alleles of the Mg transporter, MAGNESIUM RELEASE 5 (MGR5), underlie variation in leaf Mg and contribute to the observed latitudinal cline. Overall, our results indicate that the spatial distribution of leaf Mg in A. thaliana is affected by climatic and genetic factors, resulting in a latitudinal cline. Further, they show an example of allelic heterogeneity, in which multiple alleles at a single locus contribute to a trait and the formation of a phenotypic cline.

Whole-Genome Sequencing Reveals the Role of Cis-Regulatory Elements and eQTL/sQTL in the Adaptive Selection of Hubei Indigenous Cattle

Hubei indigenous cattle have adapted to diverse environmental conditions, exhibiting unique genetic traits associated with both economic and adaptive characteristics. Understanding their adaptive selection offers insight into their evolutionary history and genetic enhancements. In this study, we analyzed whole-genome sequencing (WGS) data from five Hubei indigenous cattle breeds to identify selection signals. Selective sweep analysis revealed the candidate genes (USH2A, TMTC2, ABCC12, and SUGT1) associated with sensory perception, backfat thickness, reproduction, and immune function. The further integration of cis-regulatory elements (CREs) and expression quantitative trait loci (eQTL) highlighted regulatory variants, influencing adaptive traits. Notably, positively selected genes such as RPS6KA2, CRLS1, MGST3, GPCPD1, and LDLRAP1 were associated with lipid metabolism, meat quality, and reproductive traits, influencing aldehyde volatile organic compounds (VOCs) and fat deposition. These findings highlight the understanding of the genetic basis of adaptation and production traits in Hubei indigenous cattle and provide valuable insights for their conservation and potential breeding strategies.

GWAS study of myelosuppression among NSCLC patients receiving platinum-based combination chemotherapy

Platinum-based chemotherapy remains the mainstay for non-small cell lung cancer (NSCLC), but it frequently causes dose-limiting myelosuppression, with significant individual variability in susceptibility. However, the genetic basis of myelosuppression side effects remains elusive, greatly hindering personalized therapeutic approaches. In this study, we perform a comprehensive genome-wide association analysis on 491 NSCLC patients receiving platinum-based chemotherapy, examining 4,690,998 single-nucleotide polymorphisms (SNPs) to identify relevant genetic variants. LDBlockShow, FUMA, and MAGMA are utilized to explore linkage disequilibrium, expression quantitative trait loci (eQTLs), chromatin interaction, and conduct gene-based and gene set-based analysis of candidate SNPs. The GWAS results reveal that rs6856089 and its linked SNPs are significantly associated with platinum-based chemotherapy-induced myelosuppression. Specifically, patients with the A allele of rs6856089 have a significantly lower risk of myelosuppression (odds ratio (OR) = 0.1300, P = 7.59 × 10 -8). Furthermore, gene-based analysis reveals that EMCN ( P = 2.47 × 10 -5), which encodes endomucin, a marker for hematopoietic stem cells, might mediate myelosuppression. This study provides a scientific basis for the individual differences in platinum-based chemotherapy-induced myelosuppression.

Integrated multi-omics analyses provide new insights into genomic variation landscape and regulatory network candidate genes associated with walnut endocarp

Persian walnut (Juglans regia) is an economically important nut oil tree; the fruit has a hard endocarp/shell to protect seeds, thus playing a key role in its evolution, and the shell thickness is an important trait for walnut breeding. However, the genomic landscape and the gene regulatory networks associated with walnut shell development remain to be systematically elucidated. Here, we report a high-quality genome assembly of the walnut cultivar 'Xiangling' and construct a graphic structure pan-genome of eight Juglans species to reveal the genetic variations at the genome level. We re-sequence 285 accessions to characterize the genomic variation landscape. Through genome-wide association studies (GWAS), we identified 19 loci associated with more than 268 loci that underwent selection during walnut domestication and improvement. Multi-omics analyses, including transcriptomics, metabolomics, DNA methylation, and spatial transcriptomics across eleven developmental stages, revealed several candidate genes related to secondary cell biosynthesis and lignin accumulation. This integrated multi-omics approach revealed several candidate genes associated with secondary cell biosynthesis and lignin accumulation, such as UGP, MYB308, MYB83, NAC043, NAC073, CCoAOMT1, CCoAOMT7, CHS2, CESA7, LAC7, COBL4, and IRX12. Overexpression of JrUGP and JrMYB308 in Arabidopsis thaliana confirmed their roles in lignin biosynthesis and cell wall thickening. Consequently, our comprehensive multi-omics findings offer novel insights into walnut genetic variation and network regulation of endocarp development and shell thickness, which enable further genome-informed breeding strategies for walnut cultivar improvement.

Transcriptional Reprogramming and Allelic Variation in Pleiotropic QTL Regulates Days to Flowering and Growth Habit in Pigeonpea

The present study investigated the linkage between days to flowering (DTF) and growth habit (GH) in pigeonpea using QTL mapping, QTL-seq, and GWAS approaches. The linkage map developed here is the largest to date, spanning 1825.56 cM with 7987 SNP markers. In total, eight and four QTLs were mapped for DTF and GH, respectively, harbouring 78 pigeonpea orthologs of Arabidopsis flowering time genes. Corroboratively, QTL-seq analysis identified a single linked QTL for both traits on chromosome 3, possessing 15 genes bearing genic variants. Together, these 91 genes were clustered primarily into autonomous, photoperiod, and epigenetic pathways. Further, we identified 39 associations for DTF and 111 associations for GH through GWAS in the QTL regions. Of these, nine associations were consistent and constituted nine haplotypes (five late, two early, one each for super-early and medium duration). The involvement of multiple genes explained the range of allelic effects and the presence of multiple LD blocks. Further, the linked QTL on chromosome 3 was fine-mapped to the 0.24-Mb region with an LOD score of 8.56, explaining 36.47% of the phenotypic variance. We identified a 10-bp deletion in the first exon of TFL1 gene of the ICPL 20338 variety, which may affect its interaction with the Apetala1 and Leafy genes, resulting in determinate GH and early flowering. Further, the genic marker developed for the deletion in the TFL1 gene could be utilized as a foreground marker in marker-assisted breeding programmes to develop early-flowering pigeonpea varieties.

Deciphering the regulatory network of lignocellulose biosynthesis in bread wheat through genome-wide association studies

KEY MESSAGE

This study identified 46 key QTL and 17 candidate genes and developed a KASP marker, providing valuable molecular tools for enhancing lignocellulose traits, lodging resistance, and bioenergy potential in wheat. Wheat lignocellulose, composed of lignin, cellulose, and hemicellulose, plays a crucial role in strengthening plant cell walls, enhancing lodging resistance, and contributing to bioenergy production. However, the genetic basis underlying the variation in lignocellulose content in wheat remains poorly understood. The stem lignin, cellulose, and hemicellulos contents in the second stem internode of a panel of 166 wheat accessions grown in three environments were measured, combined with the genotyping data with 660 K wheat SNP chip; a genome-wide association studies (GWAS) were conducted to identify loci associated with the lignocellulose content in wheat. Significant variations in lignin, cellulose, and hemicellulose contents were observed among the wheat accessions. GWAS identified 1146 significant SNPs associated with lignin, cellulose, and hemicellulose contents, distributed across the A, B, and D sub-genomes of wheat. Joint analysis of haplotype blocks refined these associations, identifying 46 significant quantitative trait loci (QTL) regions and 17 candidate genes, primarily linked to vascular development, hemicellulose synthesis, internode elongation regulation, and lignin biosynthesis. A KASP marker (NW_CC5951) for lignocellulose was developed. These findings provide valuable molecular markers for marker-assisted selection, supporting wheat breeding for improved stem quality and lodging resistance, and offer insights into balancing grain yield with lodging resistance and lignocellulosic energy production.

Population genomic analysis identifies the complex structural variation at the fibromelanosis (FM) locus in chicken

Phenotypic diversity and its genetic basis are central questions in biology, with domesticated animals offering valuable insights due to their rapid evolution the last 10,000 years. In chickens, fibromelanosis (FM) is a striking pigmentation phenotype characterized by hyperpigmentation. A previous study identified a complex structural variant involving both two large duplications (127.4 and 170.5 kb in size) and inversions associated with upregulated expression of the Endothelin 3 (EDN3) gene. However, the detailed organization of the structural arrangements have remained unclear. In this study, we conducted a comprehensive genomic survey of 517 FM chickens representing 44 different populations. Our results elucidate the complex arrangement of the duplications and inversions at the FM locus based on the large-scale genomic survey, population level genotyping, and linkage disequilibrium analysis, providing conclusive support for one specific configuration of the two large duplications, resolving a controversy that has been unresolved for more than a decade. Our results show that the birth of this complex structural variant must have involved an interchromosomal rearrangement creating fixed heterozygosity due to sequence differences between the two copies of the 127.4 kb duplication. This study shows how population genomics can be used to understand complex structural variations that underlie phenotypic variation.

Local ancestry informed GWAS of warfarin dose requirement in African Americans identifies a novel CYP2C19 splice QTL

African Americans (AAs) are underrepresented in pharmacogenomics which has led to a significant gap in knowledge. AAs are admixed and can inherit specific loci from either their African or European ancestor, known as local ancestry (LA). A previous study in AAs identified single nucleotide polymorphisms (SNPs) located in the CYP2C cluster that are associated with warfarin dose. However, LA was not considered in this study. An IWPC cohort (N=340) was used to determine the LA-adjusted association with warfarin dose. Ancestry-specific GWAS's were conducted with TRACTOR and ancestry tracts were meta-analyzed using METAL. We replicated top associations in the independent ACCOuNT cohort of AAs (N=309) and validated associations in a warfarin pharmacokinetic study in AAs. To elucidate functional roles of top associations, we performed short-read RNA-sequencing from AA hepatocytes carrying each genotype for expression of CYP2C9 and CYP2C19. We identified 6 novel genome-wide significant SNPs (P<5E-8) in the CYP2C locus (lead SNP, rs7906871 (P=3.14E-8)). These associations were replicated (P≤2.76E-5) and validated with a pharmacokinetic association for S-Warfarin concentration in plasma (P=0.048). rs7906871 explains 6.0% of the variability in warfarin dose in AAs. Multivariate regression including rs7906871, previously associated SNPs, clinical and demographic factors explain 37% of dose variability, greater than previously reported studies in AAs. RNA-seq data in AA hepatocytes identified a significant alternate exon inclusion event between exons 6 and 7 in CYP2C19 for carriers of rs7906871. In conclusion, we have found and replicated a novel CYP2C variant associated with warfarin dose requirement and potential functional consequences to CYP2C19.

Integration of GWAS and transcriptome analysis to identify temperature-dependent genes involved in germination of rapeseed (Brassica napus L.)

Low temperature germination (LTG) is one of crucial agronomic traits for field-grown rapeseed in the Yangtze River Basin, where delayed sowing frequently exposes germination to cold stress. Because of its importance, the genetic basis underlying rapeseed germination under different temperatures has been continuously focused. By long-term field observation, we screened out two cultivars with significantly different LTG performance (JY1621 and JY1605) in field and lab conditions, which therefore were further used for the transcriptome sequencings at three key timepoints under normal and low temperatures. Comparative analysis among multiple groups of differentially expressed genes (DEGs) revealed a set of either early or late temperature response germination (ETRG or LTRG) genes, as well as cold-tolerant (CDT) and temperature-insensitive (TPI) candidate regulators at different germination stages. Furthermore, we performed a genome-wide association study (GWAS) using germination index of 273 rapeseed accessions and identified 24 significant loci associated with germination potential under normal temperatures. Through integrated analysis of transcriptome sequencing and GWAS, we identified a series of candidate genes involved in temperature-dependent germination. Based on the comprehensive analysis, we hypothesized that BnaA3.CYP77A4 and BnaA3.NAC078 could be important candidate genes for LTG due to their expression patterns and haplotype distributions. This study performed the multi-omics analysis on temperature-dependent germination and provided potential genetic loci and candidate genes required for robust germination, which could be further considered for low-temperature germination breeding of rapeseed.

Single-nucleotide polymorphisms and copy number variations drive adaptive evolution to freezing stress in a subtropical evergreen broad-leaved tree: Hexaploid wild Camellia oleifera

Subtropical evergreen broad-leaved trees are usually vulnerable to freezing stress, while hexaploid wild Camellia oleifera shows strong freezing tolerance. As a valuable genetic resource of woody oil crop C. oleifera, wild C. oleifera can serve as a case for studying the molecular bases of adaptive evolution to freezing stress. Here, 47 wild C. oleifera from 11 natural distribution sites in China and 4 relative species of C. oleifera were selected for genome sequencing. "Min Temperature of Coldest Month" (BIO6) had the highest comprehensive contribution to wild C. oleifera distribution. The population genetic structure of wild C. oleifera could be divided into two groups: in cold winter (BIO6 ≤ 0 °C) and warm winter (BIO6 > 0 °C) areas. Wild C. oleifera in cold winter areas might have experienced stronger selection pressures and population bottlenecks with lower N e than those in warm winter areas. 155 single-nucleotide polymorphisms (SNPs) were significantly correlated with the key bioclimatic variables (106 SNPs significantly correlated with BIO6). Twenty key SNPs and 15 key copy number variation regions (CNVRs) were found with genotype differentiation > 50% between the two groups of wild C. oleifera. Key SNPs in cis-regulatory elements might affect the expression of key genes associated with freezing tolerance, and they were also found within a CNVR suggesting interactions between them. Some key CNVRs in the exon regions were closely related to the differentially expressed genes under freezing stress. The findings suggest that rich SNPs and CNVRs in polyploid trees may contribute to the adaptive evolution to freezing stress.

Tissue-specific expression, functional analysis, and polymorphism of the KRT2 gene in sheep horn

Horn is a defensive weapon of sheep, consisting of a horny sheath and a bony core. The KRT2 gene is related to keratinization of the epidermis, so it is likely to be one of the contributor genes affecting horn type in sheep. In this study, we first analyzed the species-specific and tissue-specific expression of the KRT2 gene using transcriptome sequencing data. Then, by comparing the protein sequences of 20 species, we identified 28 specific amino acid sites in Artiodactyla animals, constructed a phylogenetic tree of the KRT2 gene, and predicted its three-dimensional protein structure. Finally, whole genome sequencing data was used and mined 4 functional SNP sites of KRT2 gene, and use KASP assay to verify the loci. In addition, we explored the relationship between the KRT2 gene and the evolution of Artiodactyla animals, and predicted the possible mechanism by which the KRT2 gene affects the horn type of sheep.

Genome-Wide Association Study Identifies the Serine/Threonine Kinase ClSIK1 for Low Nitrogen Tolerance in Watermelon Species

Plants have evolved multiple complex mechanisms enabling them to adapt to low nitrogen (LN) stress via increased nitrogen use efficiency (NUE) as nitrogen deficiency in soil is a major factor limiting plant growth and development. However, the adaptive process and evolutionary roles of LN tolerance-related genes in plants remain largely unknown. In this study, we resequenced 191 watermelon accessions and examined their phenotypic differences related to LN tolerance. A major gene ClSIK1 encoding a serine/threonine protein kinase involved in the response to LN stress was identified on chromosome 11 using genome-wide association study and RNA-Seq analysis. According to a functional analysis, ClSIK1 overexpression can increase the root area, total biomass, NUE and LN tolerance by manipulating multiple nitrogen-metabolized genes. Interestingly, the desirable LN-tolerant haplotype ClSIK1HapC was detected in only one wild relative (Citrullus mucosospermus) and likely gradually lost during watermelon domestication and improvement. This study clarified the regulatory effects of ClSIK1 on NUE and adaptations to LN stress, which also identifying valuable haplotypes-resolved gene variants for molecular design breeding of 'green' watermelon varieties highly tolerant to LN stress.

Neolithic introgression of IL23R-related protection against chronic inflammatory bowel diseases in modern Europeans

BACKGROUND

The hypomorphic variant rs11209026-A in the IL23R gene provides significant protection against immune-related diseases in Europeans, notably inflammatory bowel diseases (IBD). Today, the A-allele occurs with an average frequency of 5% in Europe.

METHODS

This study comprised 251 ancient genomes from Europe spanning over 14,000 years. In these samples, the investigation focused on admixture-informed analyses and selection scans of rs11209026-A and its haplotypes.

FINDINGS

rs11209026-A was found at high frequencies in Anatolian Farmers (AF, 18%). AF later introduced the allele into the ancient European gene-pool. Subsequent admixture caused its frequency to decrease and formed the current southwest-to-northeast allele frequency cline in Europe. The geographic distribution of rs11209026-A may influence the gradient in IBD incidence rates that are highest in northern and eastern Europe.

INTERPRETATION

Given the dramatic changes from hunting and gathering to agriculture during the Neolithic, AF might have been exposed to selective pressures from a pro-inflammatory lifestyle and diet. Therefore, the protective A-allele may have increased survival by reducing intestinal inflammation and microbiome dysbiosis. The adaptively evolved function of the variant likely contributes to the high efficacy and low side-effects of modern IL-23 neutralisation therapies for chronic inflammatory diseases.

FUNDING

German Research Foundation (EXC 2167 390884018 and EXC 2150 390870439).

Association mapping and genomic prediction for processing and end-use quality traits in wheat (Triticum aestivum L.)

End-use and processing traits in wheat (Triticum aestivum L.) are crucial for varietal development but are often evaluated only in the advanced stages of the breeding program due to the amount of grain needed and the labor-intensive phenotyping assays. Advances in genomic resources have provided new tools to address the selection for these complex traits earlier in the breeding process. We used association mapping to identify key variants underlying various end-use quality traits and evaluate the usefulness of genomic prediction for these traits in hard red spring wheat from the Northern United States. A panel of 383 advanced breeding lines and cultivars representing the diversity of the University of Minnesota wheat breeding program was genotyped using the Illumina 90K single nucleotide polymorphism array and evaluated in multilocation trials using standard assessments of end-use quality. Sixty-three associations for grain or flour characteristics, mixograph, farinograph, and baking traits were identified. The majority of these associations were mapped in the vicinity of glutenin/gliadin or other known loci. In addition, a putative novel multi-trait association was identified on chromosome 6AL, and candidate gene analysis revealed eight genes of interest. Further, genomic prediction had a high predictive ability (PA) for mixograph and farinograph traits, with PA up to 0.62 and 0.50 in cross-validation and forward prediction, respectively. The deployment of 46 markers from GWAS to predict dough-rheology traits yielded low to moderate PA for various traits. The results of this study suggest that genomic prediction for end-use traits in early generations can be effective for mixograph and farinograph assays but not baking assays.

Genetically predicted inflammatory proteins mediate the association between gut microbiota and renal cell carcinoma

BACKGROUND

Studies have indicated a potential relationship between gut microbiota and renal cell carcinoma. However, the causal relationship between various types of gut microbiota and renal cell carcinoma, as well as the role of inflammatory protein as mediators, remains unclear.

METHODS

This study aimed to identify the relationship between gut microbiota, inflammatory protein, and renal cell cancer through a large-scale genome-wide association study (GWAS) utilizing pooled data. We employed Mendelian randomization (MR) to investigate the causal relationship among these variables. Inverse variance weighting (IVW) was utilized as the primary statistical method. Furthermore, we examined the mediating role of inflammatory protein in the pathway through which gut microbiota influences the development of renal cell cancer.

RESULTS

The analysis revealed 12 positive causal relationships and 15 negative causal relationships between the genetic liability of gut microbiota and renal cell cancer. Furthermore, there were three positive causal relationships and one negative causal relationship between inflammatory proteins and renal cell cancer. There were two axes of relationships in which gut microbiota promote the development of renal cell cancer. through inflammatory proteins acting as mediators.

CONCLUSIONS

Gut microbiota and inflammatory protein were causally related to renal cell cancer, and inflammatory protein were intermediary factors in the pathway between gut microbiota and renal cell cancer.

Genome-Wide Association Study Reveals Growth-Related SNPs and Candidate Genes in Largemouth Bass (Micropterus salmoides) Adapted to Hypertonic Environments

Sustainable development of the largemouth bass industry is hindered by limited freshwater resources. Consequently, the expansion of farming space by brackish and saline water aquaculture has become imperative. Largemouth bass is an economically important freshwater fish species. However, there is presently a lack of germplasm resources with the capacity to adapt to hypertonic environments and maintain rapid growth. A genome-wide association study is a technique used for the detection of genetic variants associated with specific phenotypic traits. In this study, we firstly applied this technique to explore the potential single-nucleotide polymorphism (SNP) locus and candidate genes associated with rapid growth and adaptation to the hypertonic environment of largemouth bass. A total of 10 potential growth-related SNPs were obtained on chromosome 16, and SNP16:4120214 was a significant SNP peak. Based on these SNPs, 23 candidate genes were annotated in the genome, including Nkcc1, Mapkap1, Hmgcs1, Slc27a6, and Shroom3. Shroom3 expression was significantly higher in individuals enriched for the most growth-advantageous genotypes. Shroom3 upregulation is beneficial for fish growth in hyperosmotic environments. This study provides insight into the genetic basis of rapid growth in hypertonic environments and foundational information for the future breeding of salt-tolerant largemouth bass.

The ZNF717-rs2918520 genotype contributes to COVID-19 severity: a Taiwanese cohort study

BACKGROUND

Coronavirus disease 2019 (COVID-19) has been a challenging pandemic since late 2019 and patients with COVID-19-related severe respiratory failure associated with high mortality rates worldwide. Genetic information such as single nucleotide polymorphisms (SNPs) serves as a predictor or prognostic factor in disease development and cancer progression. This study aimed to explore the clinical associations of SNPs with mild and severe COVID-19 symptoms in the Taiwanese population.

METHODS

SARS-CoV-2-infected patients in pilot cohort study (cohort 1, n = 39) and validation cohort (cohort 2, n = 71) were enrolled. The clinical significance of SNPs in those patients with mild and severe symptoms was investigated by whole exon sequencing, polymerase chain reaction and Sanger sequencing.

RESULTS

The current study investigated Taiwanese patients with COVID-19. We found that clinical parameters such as age, aspartate aminotransferase, blood urea nitrogen, C-reactive protein, ferritin, and segment were positively associated with severe COVID-19 symptoms but that albumin, lymphocytes, and basophils correlated negatively with severe symptoms in two independent cohorts. By conducting whole-exome sequencing, we identified a novel SNP, ZNF717-rs2918520, the GG genotype of which was significantly associated with severe symptoms in COVID-19 patients.

CONCLUSIONS

Our findings highlight that the ZNF717-rs2918520 GG genotype may serve as a predictor for evaluating the severity of COVID-19 in Taiwan.

Whole genome re-sequencing in 437 tobacco germplasms identifies plant height candidate genes

Tobacco is one of the most important model plants. Plant height is one of the most important agronomic traits in tobacco. To better understand the population genetic structure and the genetic basis of plant height in tobacco, 437 tobacco germplasms were whole genome re-sequencing in this study. A total of 2,263,775 high-quality single nucleotide polymorphisms were identified. The analysis of the population genetic structure showed that tobacco germplasm could be divided into 8 clusters. In addition, gene flow was found between flue-cured tobacco and ustic tobacco, as well as between oriental tobacco and air-cured tobacco. Three genes associated with plant height were identified as candidate genes by genome-wide association study. This study provides valuable genetic resources for population structure analysis and elucidation of the genetic basis of various traits. It helps to improve the efficiency of molecular breeding.

Genome-Wide Association Study Pinpoints Novel Candidate Genes Associated with the Gestation Length of the First Parity in French Large White Sows

Gestation length (GL) is a critical indicator of reproductive performance in sows and is closely associated with other reproductive traits, such as total number born (TNB) and number born alive (NBA). Despite its importance, the genetic mechanisms underlying GL and its impact on reproductive traits remain poorly understood. In this study, we investigated the relationship between GL and reproductive traits using 7013 farrowing records and conducted an imputed whole-genome sequence-based genome-wide association study (GWAS) for GL in first-parity sows, involving 3005 French Large White sows. Our findings revealed that the heritability of GL ranged from 0.22 to 0.26. Both excessively short and long GLs were associated with negative impacts on TNB, NBA, and other reproductive traits. A total of 64 SNPs exceeded the significance threshold, leading to the identification of two novel quantitative trait loci (QTLs) on chromosome 5 (QTL-1: 15.29-15.39 Mb and QTL-2: 12.86-12.94 Mb) and three promising candidate genes: TROAP, RFX4, and ADCY6. Gene ontology and KEGG pathway enrichment analyses revealed that these candidate genes are enriched in key biological processes, including ovarian steroidogenesis, the GnRH signaling pathway, and the regulation of cAMP biosynthesis, all of which are crucial for gestation and pregnancy maintenance. These findings improve our understanding of the genetic architecture of GL in sows and offer valuable genetic markers for enhancing reproductive efficiency in breeding programs.

Multi-omics analysis reveals the allelic variation in JrWDRC2A9 and JrGPIAP conferring resistance against anthracnose (Colletotrichum gloeosporioides) in walnut (Juglans regia)

Walnut anthracnose induced by Colletotrichum gloeosporioides is a devastating disease that seriously threatens walnut cultivation. Screening novel resistance genes and exploring the molecular mechanisms are essential for disease-resistant genetic improvement of walnut. We conducted a genome-wide association studies of disease resistance traits based on the relative resistance index and single nucleotide polymorphisms (SNPs) obtained from 182 resequenced walnut accessions and 10 loci and corresponding candidate genes associated with resistance against C. gloeosporioides were identified. Then, through combined transcriptome analysis during C. gloeosporioides infection and qRT-PCR, we identified JrWDRC2A9 in SNP Chr13_36265784 loci and JrGPIAP in SNP Chr07_10106470 loci as two walnut anthracnose resistance genes. The validation of the disease resistance function of transgenic strains indicated that both JrWDRC2A9 and JrGPIAP promote walnut resistance to anthracnose. SNP Chr13_36265784 (A>G) is located in the coding region of JrWDRC2A9 causing a glutamine (JrWDRC2A9HapI) to arginine (JrWDRC2A9HapII). Allelic variation in the WD domain attenuates JrWDRC2A9-mediated resistance against C. gloeosporioides and the binding affinity of JrWDRC2A9 for JrTLP1. On the contrary, the allelic variation caused by SNP Chr07_10106470 (T>G) increased the walnut accessions resistance to C. gloeosporioides by promoting the expression level of JrGPIAP. Functional genomics revealed that JrGPIAP binds to the promoter of JrPR1L and activates its transcription, which is strengthened by the interaction between JrGPIAP and JrEMP24. These findings reveal the allelic variation in JrWDRC2A9 and JrGPIAP conferring resistance against C. gloeosporioides, providing a genetic basis for walnut disease resistance breeding in the future.

Genomic selection and genetic architecture of agronomic traits during modern flowering Chinese cabbage breeding

Flowering Chinese cabbage is a type of leafy vegetable that belongs to the Brassica genus. Originally native to South China, it is now widely cultivated and consumed across the globe, particularly in Asian countries. The recent cultivation and regional expansion of flowering Chinese cabbage provides a valuable opportunity to elucidate the genomic basis underlying environmental adaptation and desired traits during a short-term artificial selection process. Here, we investigate the genetic variation, population structure, and diversity of a diverse germplasm collection of 403 flowering Chinese cabbage accessions. Our investigation seeks to elucidate the genomic basis that guides the selection of adaptability, yield, and pivotal agronomic traits. We further investigated breeding improvement associated with stem development by integrating transcriptome data. Genome-wide association analysis identified 642 loci and corresponding candidate genes associated with 11 essential agronomic traits, including plant architecture and yield. Furthermore, we uncovered a significant disparity in the allele frequency distribution of nonsynonymous mutations in these candidate genes throughout the improvement stages. Our results shed light on the genetic basis of improvement and crucial agronomic traits in flowering Chinese cabbage, offering invaluable resources for upcoming genomics-assisted breeding endeavors.

Genome-wide association analysis of key genes for feed efficiency in Qingyuan Partridge chickens

Qingyuan Partridge chickens represent a notable breed of high-quality, slow-growing chickens. The cost of feed constitutes 65-70 % of the total breeding expense for Qingyuan Partridge chickens. Enhancing feed utilization efficiency and reducing feed consumption are crucial for the advancement of Qingyuan Partridge chickens and the broader poultry industry. To investigate the key candidate genes associated with feed efficiency in Qingyuan Partridge chickens for genome selection, the genome-wide association study (GWAS) was performed in this study. Genetic parameters estimation results indiated that the heritability of 12-17 feed conversion ratio was 0.19, with the highest genetic correlation observed with 17 body weight (-0.96). Additionally, the heritability of 12-17 residual feed intake was 0.09, with the highest genetic correlation with 12-14 average daily feed intake (0.93). GWAS results revealed 28 significant SNPs associated with body weight, feed intake, metabolic weight, weight gain, feed conversion ratio, and residual feed intake. The multiple genes are significantly enriched in the aromatic compound biosynthetic process, heterocycle biosynthetic process, and nucleobase-containing compound biosynthetic process. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis showed that the expression levels of four genes-exocyst complex component 4(EXOC4), fibrosin like 1(FBRSL1), methionine adenosyltransferase 2 non-catalytic beta subunit (MAT2B), and cytidine/uridine monophosphate kinase 1(CMPK1)-related to significant SNPs exhibited significant differences in the liver tissues of high residual feed intake group compared with low residual feed intake group. These findings contribute to a better understanding of the molecular mechanisms underlying chicken feed efficiency traits, enabling further genetic improvement of Qingyuan Partridge chickens, and improving industrial efficiency.

Genetic Variation in a Crossing Population of Camellia oleifera Based on ddRAD Sequencing and Analysis of Association with Fruit Traits

Tea oil is an important high-quality edible oil derived from woody plants. Camellia oleifera is the largest and most widely planted oil-producing plant in the Camellia genus in China, and its seeds are the most important source for obtaining tea oil. In current research, improving the yield and quality of tea oil is the main goal of oil tea genetic breeding. The aim of this study was to investigate the degree of genetic variation in an early crossing population of C. oleifera and identify single nucleotide polymorphisms (SNPs) and genes significantly associated with fruit traits, which can provide a basis for marker-assisted selection and gene editing for achieving trait improvement in the future. In this study, we selected a crossing population of approximately 40-year-old C. oleifera with a total of 330 samples. Then, ddRAD sequencing was used for SNP calling and population genetic analysis, and association analysis was performed on fruit traits measured repeatedly for two consecutive years. The research results indicate that over 8 million high-quality SNPs have been identified, but the vast majority of SNPs occur in intergenic regions. The nucleotide polymorphism of this population is at a low level, and Tajima's D values are mostly greater than 0, indicating that the change in this population was not suitable for the model of central evolution. The population structure analysis shows that the population has seven theoretical sources of genetic material and can be divided into seven groups, and the clustering analysis results support the population structure analysis results. Association analysis identified significant SNPs associated with genes related to the seed number of a single fruit and seed kernel oil content. Our findings provide a basis for molecular breeding and future genetic improvement of cultivated oil tea.

Significance of KLK7 expression, polymorphisms, and function in sheep horn growth

BACKGROUND

Sheep horns play a critical role in the survival and reproduction of sheep. Research on sheep horns not only aids in comprehending their biological roles but is also vital for developing hornless breeds. Although previous studies have suggested that KLK7 may be associated with keratin growth, there are few studies that have focused on the role of KLK7 in sheep horns. This study aims to elucidate the relationship between KLK7 and sheep horns by analyzing the expression, genetic polymorphisms, and potential functions of KLK7 in sheep horns.

RESULTS

This study utilized RNA sequencing (RNA-Seq) data to analyze the expression levels of the KLK7 gene across different species, as well as among different breeds, tissue types, and genders in sheep. Potential functional sites of KLK7 were explored using whole-genome sequencing (WGS) data. Allele specific expression sites in the KLK7 gene sequence were identified. Finally, the WGS data were linked with sheep horn length for association analysis, and significantly different single-nucleotide polymorphisms (SNPs) were detected and validated by Kompetitive Allele Specific PCR (KASP) genotyping.

CONCLUSION

Our results demonstrate that KLK7 was highly expressed in soft horn and skin tissues, and its expression was significantly higher in small-horned sheep than it was in large-horned sheep, suggesting that KLK7 may have an inhibitory effect on horn growth. By comparing the amino acid sequence of KLK7 with KLK7 sequences in other species, we discovered eight amino acids at specific positions in the KLK7 protein sequence that may have regulatory functions in determining the size of horns in ruminant animals. Thirteen SNPs with F-statistic value (Fst) > 0.15 were identified. By integrating RNA-Seq and WGS data, we discovered two SNPs (g.56695395 T > C and g.56695484A > C) with allele specific expression between the large- and small-horned sheep. The two SNPs were validated and were found to have significantly different (P < 0.05) effects on horn length. Our findings suggest a strong association between KLK7 and sheep horn length, indicating the potential role of KLK7 in inhibiting horn growth and providing novel insights into the functionality of KLK7.

Genome-wide association studies with prolapsed gland of the third eyelid in dogs

Cherry eye, the common name for the prolapse of the third eyelid gland in dogs, is a widespread ophthalmic disease affecting dogs of various breeds. This condition severely affects the quality of life of affected dogs, and its underlying cause remains unresolved. In this study, 170K SNP microarray data were collected from 653 brachycephalic dogs and 788 brachycephalic and mesocephalic dogs. These two datasets were analyzed separately in genome-wide association studies (GWAS) involving 12 dog breeds affected by cherry eye. The GWAS analysis of 653 short-headed dogs revealed that four SNPs in the CFA3:15627075-15983629 bp region exceeded the genome-level significance threshold. Association analysis of this region also indicated that these four SNPs were strongly associated. Gene annotation showed that the region contained genes such as KIAA0825, FAM172A, and NR2F1, of which NR2F1 was associated with eye development. The results showed that GWAS analysis performed on 788 short- and medium-headed dogs identified five SNPs in the CFA22:15627075-15983629 bp region that exceeded the genome-level significance threshold, and association analysis was performed in this region, which showed that these five SNPs were strongly associated. In addition, 104 annotated genes were identified in both GWAS. To explore the genes involved in cherry eyes, we performed GO functional enrichment analysis. The genes involved in the high pathway were DIO3 and TTC8. In addition, an in-depth analysis revealed 33 genes associated with eye development and diseases. Our study provides new perspectives for further understanding cherry eye in dogs.

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.

SoyOD: An Integrated Soybean Multi-omics Database for Mining Genes and Biological Research

Soybean is a globally important crop for food, feed, oil, and nitrogen fixation. A variety of multi-omics studies have been carried out, generating datasets ranging from genotype to phenotype. In order to efficiently utilize these data for basic and applied research, a soybean multi-omics database with extensive data coverage and comprehensive data analysis tools was established. The Soybean Omics Database (SoyOD) integrates important new datasets with existing public datasets to form the most comprehensive collection of soybean multi-omics information. Compared to existing soybean databases, SoyOD incorporates an extensive collection of novel data derived from the deep-sequencing of 984 germplasms, 162 novel transcriptomic datasets from seeds at different developmental stages, 53 phenotypic datasets, and more than 2500 phenotypic images. In addition, SoyOD integrates existing data resources, including 59 assembled genomes, genetic variation data from 3904 soybean accessions, 225 sets of phenotypic data, and 1097 transcriptomic sequences covering 507 different tissues and treatment conditions. Moreover, SoyOD can be used to mine candidate genes for important agronomic traits, as shown in a case study on plant height. Additionally, powerful analytical and easy-to-use toolkits enable users to easily access the available multi-omics datasets, and to rapidly search genotypic and phenotypic data in a particular germplasm. The novelty, comprehensiveness, and user-friendly features of SoyOD make it a valuable resource for soybean molecular breeding and biological research. SoyOD is publicly accessible at https://bis.zju.edu.cn/soyod.

Graph pangenome reveals the regulation of malate content in blood-fleshed peach by NAC transcription factors

BACKGROUND

Fruit acidity and color are important quality attributes in peaches. Although there are some exceptions, blood-fleshed peaches typically have a sour taste. However, little is known about the genetic variations linking organic acid and color regulation in peaches.

RESULTS

Here, we report a peach graph-based pangenome constructed from sixteen individual genome assemblies, capturing abundant structural variations and 82.3 Mb of sequences absent in the reference genome. Pangenome analysis reveals a long terminal repeat retrotransposon insertion in the promoter of the NAC transcription factor (TF) PpBL in blood-fleshed peaches, which enhances PpBL expression. Genome-wide association study identifies a significant association between PpBL and malate content. Silencing PpBL in peach fruit and ectopic overexpression of PpBL in tomatoes confirm that PpBL is a positive regulator of malate accumulation. Furthermore, we demonstrate that PpBL works synergistically with another NAC TF, PpNAC1, to activate the transcription of the aluminum-activated malate transporter PpALMT4, leading to increased malate content.

CONCLUSIONS

These findings, along with previous research showing that PpBL and PpNAC1 also regulate anthocyanin accumulation, explain the red coloration and sour taste in blood-fleshed peach fruits.

Mining genomic regions associated with stomatal traits and their candidate genes in bread wheat through genome-wide association study (GWAS)

KEY MESSAGE

112 candidate quantitative trait loci (QTLs) and 53 key candidate genes have been identified as associated with stomatal traits in wheat. These include bHLH, MADS-box transcription factors, and mitogen-activated protein kinases (MAPKs). Stomata is a common feature of the leaf surface of plants and serve as vital conduits for the exchange of gases (primarily CO₂ and water vapor) between plants and the external environment. In this study, a comprehensive genome analysis was conducted by integrating genome-wide association study (GWAS) and genome prediction to identify the genomic regions and candidate genes of stomatal traits associated with drought resistance and water-saving properties in a panel of 184 diverse bread wheat genotypes. There were significant variations on stomatal traits in the wheat panel across different environmental conditions. GWAS was conducted with the genotypic data from the wheat 660 K single-nucleotide polymorphism (SNP) chip, and the stomatal traits conducted across three environments during two growing seasons. The final GWAS identified 112 candidate QTLs that exhibited at least two significant marker-trait associations. Subsequent analysis identified 53 key candidate genes, including 13 bHLH transcription factor, 2 MADS-box transcription factors, and 4 mitogen-activated protein kinase genes, which may be strongly associated with stomatal traits. The application of Bayesian ridge regression for genomic prediction yielded an accuracy rate exceeding 60% for all four stomatal traits in both SNP matrices, with stomatal width achieving a rate in excess of 70%. Additionally, three Kompetitive allele-specific PCR markers were developed and validated, representing a significant advancement in marker-assisted prediction. Overall, these results will contribute to a more comprehensive understanding of wheat stomatal traits and provide a valuable reference for germplasm screening and innovation in wheat germplasm with novel stomatal traits.

A genome-wide association study identified candidate regions and genes for commercial traits in a Landrace population

Backfat thickness (BFT) and feed conversion ratio (FCR) are important commercial traits in the pig industry. With the increasing demand for human health and meat production, identifying functional genomic regions and genes associated with these commercial traits is critical for enhancing production efficiency. In this research, we conducted a genome-wide association study (GWAS) on a Landrace population comprising 4,295 individuals with chip data for BFT and FCR. Our analysis revealed a total of 118 genome-wide significant signals located on chromosomes SSC1, SSC2, SSC7, SSC12, and SSC13, respectively. Furthermore, we identified 10 potential regions associated with the two traits and annotated the genes within these regions. In addition, enrichment analysis was also performed. Notably, candidate genes such as SHANK2, KCNQ1, and ABL1 were found to be associated with BFT, whereas NAP1L4, LSP1, and PPFIA1 genes were related to the FCR. Our findings provide valuable insights into the genetic architecture of these two traits and offer guidance for future pig breeding efforts.

iDog: a multi-omics resource for canids study

iDog (https://ngdc.cncb.ac.cn/idog/) is a comprehensive public resource for domestic dogs (Canis lupus familiaris) and wild canids, designed to integrate multi-omics data and provide data services for the worldwide canine research community. Notably, iDog 2.0 features a 15-fold increase in genomic samples, including 29.55 million single nucleotide polymorphisms (SNPs) and 16.54 million insertions/deletions (InDels) from 1929 modern samples and 29.09 million SNPs from 111 ancient Canis samples. Additionally, 43487 breed-specific SNPs and 530 disease/trait-associated variants have been identified and integrated. The platform also includes data from 141 BioProjects involving gene expression analyses and a single-cell transcriptome module containing data from 105 057 Beagle hippocampus cells. iDog 2.0 also includes an epignome module that evaluates DNA methylation patterns across 547 samples and chromatin accessibility across 87 samples for the analysis of gene expression regulation. Additionally, it provies phenotypic data for 897 dog diseases, 3207 genotype-to-phenotype (G2P) pairs, and 349 dog disease-associated genes, along with two newly constructed ontologies for breed and disease standardization. Finally, 13 new analytical tools have been added. Given these enhancements, the updated iDog 2.0 is an invaluable resource for the global cannie research community.

Allelic variation in the promoter of WRKY22 enhances humid adaptation of Arabidopsis thaliana

Submergence stress tolerance is a complex trait governed by multiple loci. Because of its wide distribution across arid and humid regions, Arabidopsis thaliana offers an opportunity to explore the genetic components and their action mechanisms underlying plant adaptation to submergence stress. In this study, using map-based cloning we identified WRKY22 that activates RAP2.12, a locus previously identified to contribute to the submergence stress response, to regulate plant humid adaptation possibly through ethylene signal transduction in Arabidopsis. WRKY22 expression is inhibited by ARABIDOPSIS RESPONSE REGULATORs (ARRs) but activated by the WRKY70 transcription factor. In accessions from humid environments, a two-nucleotide deletion in the WRKY22 promoter region prevents binding of phosphorylated ARRs, thereby maintaining its high expression. Loss of the ARR-binding element in the WRKY22 promoter underwent strong positive selection during colonization of A. thaliana in the humid Yangtze River basin. However, the WRKY70-binding motif in the WRKY22 promoter shows no variation between accessions from humid and arid regions. These findings together establish a novel signaling axis wherein WRKY22 plays a key role in regulating the adaptive response that enables A. thaliana to colonize contrasting habitats. Notably, we further showed functional conservation of this locus in Brassica napus, suggesting that modulating this axis might be useful in the breeding of flood-tolerant crop varieties.

Examination of MGMT as a risk gene for dementia in the Amish

INTRODUCTION

Recently, the O-6-methylguanine-DNA methyltransferase (MGMT) locus was proposed as influencing the risk of Alzheimer's disease (AD) in women who did not carry the apolipoprotein E ε4 allele. We examined an Amish founder population for any influence of genetic variation in and around the MGMT locus on the risk for dementia.

METHODS

Genetic association was performed for single nucleotide polymorphisms (SNPs) surrounding the MGMT locus. A total of 946 individuals of Amish descent between the ages of 76 and 95 who were classified as cognitively impaired or cognitively unimpaired were included. Multiple statistical models were applied to test for replication.

RESULTS

The results for the previously associated individual SNPs were not significant. However, a different SNP (rs7909468) generated significant results under a model different from the previous report.

DISCUSSION

The MGMT locus may influence the risk of AD, although its genetic mechanisms remain unclear and warrant further study.

HIGHLIGHTS

Association analyses around the O-6-methylguanine-DNA methyltransferase (MGMT) locus showed a study-significant single nucleotide polymorphism (SNP), rs7909468, in a female cognitively impaired group lacking the apolipoprotein E ε4 genotype. Functional implications of rs7909468 are relatively unexplored, but in silico analyses indicate it may regulate MGMT expression. rs7909468 was not in linkage disequilibrium with other SNPs found to be significant in this region and appears as a distinct novel association.

OsWRKY49 on qAT5 positively regulates alkalinity tolerance at the germination stage in Oryza sativa L. ssp. japonica

KEY MESSAGE

Integrated genome-wide association study and linkage mapping revealed genetic basis of alkalinity tolerance during rice germination. The key gene OsWRKY49 was further verified in transgenic plants. With the widespread use of the rice direct seeding cultivation model, improving the tolerance of rice varieties to salinity-alkalinity at the germination stage has become increasingly important. However, as previous studies have concentrated on neutral salt stress, understanding of alkalinity tolerance is still in its infancy, and the genetic resource data is scarce. Here, we used a natural population composed of 295 japonica rice varieties and a recombinant inbred population including 189 lines derived from Caidao (alkali-sensitive) and WD20342 (alkali-tolerant) to uncover the genetic structure of alkalinity tolerance during rice germination. A total of 15 lead SNPs and six QTLs related to relative germination potential (RGP) and relative germination index (RGI) were detected by genome-wide association study and linkage mapping. Of which, Chr5_28094966, a lead SNP was located in the interval of the mapped major QTL qAT5, that was significantly associated with both RGP and RGI in the two populations. According to the LD block analysis and QTL interval, a 425 kb overlapped region was obtained for screening the candidate genes. After haplotype analysis, qRT-PCR and parental sequence analysis, LOC_Os05g49100 (OsWRKY49) was initially considered as the candidate gene. Having studied the characteristics of rice lines with OsWRKY49 knockout and overexpression, we established that OsWRKY49 could be a positive regulator of alkalinity tolerance in rice at the germination stage. Subcellular localization showed that green fluorescent protein-tagged OsWRKY49 was localized in the nucleus. The application of OsWRKY49 could be useful for increasing alkalinity tolerance of rice direct seeding.

Identification of ALOX12B Gene Expression, Evolution, and Potential Functional Sites in Horn Development of Sheep

The growth and development of horns are primarily controlled by the skin. The ALOX12B gene is crucial for epidermal barrier function and may have a significant impact on horn growth. The purpose of this study was to investigate the expression of ALOX12B across different sheep breeds and tissues by utilizing RNA sequencing. Additionally, potential functional sites were identified in conjunction with whole genome sequencing. Our findings revealed that ALOX12B was highly expressed in the scurred horn group as opposed to the normal horn group (SHE). ALOX12B expression was also notably high in the skin across several species. Eight loci that may influence horn size were indicated in this study. Through the alignment of the ALOX12B protein sequence from 16 species, 15 amino acid sites were identified specifically expressed in horned animals. In conclusion, this study established a connection between ALOX12B and horn size and identified a series of functional sites that may serve as molecular markers for reducing the presence of horns in Chinese sheep breeds.

Identification of genetic loci and candidate genes regulating photosynthesis and leaf morphology through genome-wide association study in Brassica napus L

Rapeseed (Brassica napus L.) is a major agricultural crop with diverse applications, particularly in the production of seed oil for both culinary use and biodiesel. However, its photosynthetic efficiency, a pivotal determinant of yield, remains relatively low compared with other C3 plants such as rice and soybean, highlighting the necessity of identifying the genetic loci and genes regulating photosynthesis in rapeseed. In this study, we investigated 5 photosynthesis traits and 5 leaf morphology traits in a natural population of rapeseed, and conducted a genome-wide association study (GWAS) to identify significantly associated loci and genes. The results showed that the gas-exchange parameters of the dark reactions in photosynthesis exhibited a significant positive correlation with the chlorophyll content, whereas they showed a weaker negative correlation with the leaf area. By GWAS, a total of 538 quantitative trait nucleotides (QTNs) were identified as significantly associated with traits related to both leaf morphology and photosynthesis. These QTNs were classified into 84 QTL clusters, of which, 21 clusters exhibited remarkable stability across different traits and environmental conditions. In addition, a total of 3,129 potential candidate genes were identified to be significantly associated with the above-mentioned 10 traits, most of which were shared by certain traits, further indicating the reliability of the findings. By integrating GWAS data with GO enrichment analysis and gene expression analysis, we further identified 8 key candidate genes that are associated with the regulation of photosynthesis, chlorophyll content, leaf area, and leaf petiole angle. Taken together, this study identified key genetic loci and candidate genes with the potential to improve photosynthetic efficiency in rapeseed. These findings provide a theoretical framework for breeding new rapeseed varieties with enhanced photosynthetic capabilities.

Revealing genes related teat number traits via genetic variation in Yorkshire pigs based on whole-genome sequencing

BACKGROUND

Teat number is one of the most important indicators to evaluate the lactation performance of sows, and increasing the teat number has become an important method to improve the economic efficiency of farms. Therefore, it is particularly important to deeply analyze the genetic mechanism of teat number traits in pigs. In this study, we detected Single Nucleotide Ploymorphism (SNP), Insertion-Deletion (InDel) and Structural variant (SV) by high-coverage whole-genome resequencing data, and selected teat number at birth and functional teat number as two types of teat number traits for genome-wide association study (GWAS) to reveal candidate genes associated with pig teat number traits.

RESULTS

In this study, we used whole genome resequencing data from 560 Yorkshire sows to detect SNPs, InDels and SVs, and performed GWAS for the traits of born teat number and functional teat number, and detected a total of 85 significant variants and screened 214 candidate genes, including HEG1, XYLT1, SULF1, MUC13, VRTN, RAP1A and NPVF. Among them, HEG1 and XYLT1 were the new candidate genes in this study. The co-screening and population validation of multiple traits suggested that HEG1 may have a critical effect on the born teat number.

CONCLUSION

Our study shows that more candidate genes associated with pig teat number traits can be identified by GWAS with different variant types. Through large population validation, we found that HEG1 may be a new key candidate gene affecting pig teat number traits. In conclusion, the results of this study provide new information for exploring the genetic mechanisms affecting pig teat number traits and genetic improvement of pigs.

Comparative Whole-Genome Analysis of Production Traits and Genetic Structure in Baiyu and Chuanzhong Black Goats

Natural selection and artificial breeding are crucial methods for developing new animal groups. The Baiyu black goats and Chuanzhong black goats are indigenous goat breeds from distinct ecological regions in Sichuan Province, with dramatically different growth and reproductivity. This study aimed to systematically elucidate the differences in production performance and genetic traits between Baiyu black goats and Chuanzhong black goats. We quantified growth and reproductive attributes for both breeds. Furthermore, we conducted a comprehensive analysis of genetic diversity, population structure, and selection signatures using whole-genome resequencing data. This dataset included 30 individuals from the Baiyu black goat breed, 41 from the Chuanzhong black goat breed, and an additional 59 individuals representing Chengdu grey goats, Tibetan cashmere goats, and Jianchang black goats, totaling 130 individuals across five goat breeds. The comparative analysis of production performance revealed that the weight and body size of Chuanzhong black goats were significantly higher than those of Baiyu black goats (p < 0.01). At the same time, the average kidding rate and kid-weaning survival rate of Chuanzhong black goats were also notably superior to those of Baiyu black goats (p < 0.01). The Baiyu black goats exhibited a more abundant genetic diversity and distinct genetic differences compared to the Chuanzhong black goat, according to an analysis grounded on genomic variation. The Baiyu black goats are more closely related to Tibetan cashmere goats, whereas Chuanzhong black goats share a closer genetic relationship with Chengdu grey goats. Additionally, we employed the π, Fst, and XP-EHH methodologies to identify genes related to immunity (TRIM10, TRIM15, TRIM26, and TRIM5), neurodevelopment (FOXD4L1, PCDHB14, PCDHB4, PCDHB5, PCDHB6, and PCDHB7), reproduction (BTNL2 and GABBR1), body size (NCAPG, IBSP, and MKNK1), and meat quality traits (SUCLG2 and PGM5). These results provide a theoretical basis for further resource conservation and breeding improvement of the Baiyu black goat and Chuanzhong black goat.

Genome-Wide Association Study of Birth Wool Length, Birth Weight, and Head Color in Chinese Tan Sheep Through Whole-Genome Re-Sequencing

The Chinese Tan sheep is a unique breed of sheep that is typical throughout China, mainly used for fur and meat production. They are widely distributed in northwestern China and are famous for their lambskin and shiny white curly wool. In this study, the phenotypic traits of wool length, birth weight, and head coat color were evaluated in 256 Chinese Tan sheep breeds. Whole genome sequencing generated 23.67 million high-quality SNPs for genome-wide association studies (GWAS). We identified 208 significant SNPs associated with birth wool length, implicating RAD50, MACROD2, SAMD5, SASH1, and SPTLC3 as potential candidate genes for this trait. For birth weight, 1056 significant SNPs, with 76.89% of them located on chromosome 2, were identified by GWAS, and XPA, INVS, LOC121818504, GABBR2, LOC101114941, and LOC106990096 were identified as potential candidate genes for birth weight. The GWAS for head coat color identified 1424 significant SNPs across three chromosomes, with 99.65% on chromosome 14, and SPIRE2, TCF25, and MC1R as candidate genes were found to be possibly involved in the development of the black-headed coat color in sheep. Furthermore, we selected head coat color as a representative trait and performed an independent test of our GWAS findings through multiplex PCR SNP genotyping. The findings validated five mutation sites in chromosome 14 (14,251,947 T>A, 14,252,090 G>A, 14,252,158 C>T, 14,252,329 T>G, and 14,252,464 C>T) within the exon1 of the MC1R gene (517 bp), as identified by GWAS in an additional 102 Tan sheep individuals, and revealed that black-headed sheep predominantly exhibited heterozygous genotypes, possibly contributing to their color change. Our results provide a valuable foundation for further study of these three economically important traits, and enhance our understanding of genetic structure and variation in Chinese Tan sheep.

Candidate genes for alkali tolerance identified by genome-wide association study at the seedling stage in rice (Oryza sativa L.)

Alkali stress is one of the most serious abiotic stresses limiting crop yield and it has become an increasingly serious global problem in recent years. Alkalinity tolerance (AT) at the seedling stage is one of the determinant factors for establishment of rice population under alkaline stress condition. Here, we evaluated and measured seven traits related to AT of 528 diverse rice accessions at the seedling stage. Xian accessions were generally more alkali-tolerant than Geng accessions. GJ-tmp accessions showed the most alkali tolerance in the Geng subgroups and XI-1B accessions had the weakest alkali tolerance in the Xian subgroups. A total of 121 QTLs were identified for AT by genome-wide association study (GWAS), and five important candidate genes, LOC_Os01g19800, LOC_Os01g20160, LOC_Os01g52500, LOC_Os01g67370 and LOC_Os03g03900, were selected by gene function annotation, haplotype analysis, and qRT-PCR. Pyramiding of multiple AT advanced candidate genes is a favorable strategy for improving AT of rice varieties. Our study has screened alkali-tolerant germplasm resources and provided valuable genetic information for alkali-tolerant rice breeding.