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Results for “whole genome resequencing”

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At least 19 recordsLinked to original sources

PubMed2025

Construction of a Core Germplasm and Identification of Candidate SNPs Associated with Growth Performance of Epinephelus tukula by Whole-Genome Resequencing.

Epinephelus tukula is an economically important aquaculture animal, and a major parent in grouper crossbreeding. To better preserve and exploit E. tukula germplasm resources, a core collection (containing 34 individuals derived from 10 genetic groups) was first constructed based on phenotypic growth traits and whole-genome resequencing (WGS) data. The phenotypic traits of the individuals within the core collection were not significantly different from those in the original collection, suggesting effective representativeness of the core collection. Additionally, we performed genome-wide association study (GWAS) of E. tukula to identify candidate single nucleotide polymorphisms (SNPs) and genes associated with growth traits, to facilitate the improvements in the growth performance of this species. Twenty-six significant SNPs were identified, scattered among multiple chromosomes. Five SNPs were confirmed to be correlated with growth in another new group of 101 individuals. Based on the annotation results, these five SNPs were located in CCDC102A, NTRK2, CTSL, OTOF, and nestin, and were involved in cell development, differentiation and proliferation, glycolytic metabolism, neurological development, and myoblast differentiation. Our findings not only provide an effective basis for the conservation and utilization of E. tukula germplasm resources, but also promote the development of marker-assisted selection of E. tukula.

Polymorphism, Single Nucleotide↗

PubMed2026

Identification of Candidate Genes Associated with Growth Traits in Procambarus clarkii Using Whole-Genome Resequencing.

Growth is a critical economic trait in all aquaculture industries. To address issues such as germplasm degradation, a comprehensive understanding of the growth and development mechanisms, along with genetic improvement strategies, for Procambarus clarkii (P. clarkii) is urgently required. In this study, we performed whole-genome resequencing on 89 individuals from five cultured stocks to investigate growth traits (body length) and identified a total of 46,919,297 high-quality single nucleotide polymorphisms (SNPs). Based on these SNPs, we conducted principal component analysis (PCA), phylogenetic analysis, and population genetic structure analysis. Furthermore, we performed selective sweep analysis (using FST, Pi, and XP-CLR) and a genome-wide association study (GWAS) to identify genetic variants associated with growth traits. The results revealed significant genetic differentiation among the five cultured stocks, with the Ma'anshan cultured stock exhibiting the fastest linkage disequilibrium (LD) decay. Additionally, long-term aquaculture in different geographical regions resulted in distinct genetic differences among cultured stocks. Through selective sweep analysis, the intersection of FST, Pi, and XP-CLR across the five populations yielded several growth-related candidate genes: Nephrin, Somatostatin, zinc finger protein 154, and yeti. Subsequent the GWAS identified two candidate genes associated with growth traits: Cullin-associated and neddylation-dissociated protein 1 (CAND1) and Baculoviral IAP repeat-containing protein 8 (BIRC8). These genes are presumed to play pivotal roles in the growth and development of P. clarkii. Overall, our findings provide new insights into the genetic mechanisms underlying growth and development in P. clarkii, and these identified genes serve as promising candidates for further functional studies and genetic improvement of this species.

Polymorphism, Single Nucleotide↗

PubMed2025

CRISPR-Cas9-mediated knockout of OsKCS11 in rice reveals potential crosstalk between very-long-chain fatty acids and cytokinin.

Very-long-chain fatty acids (VLCFAs) play crucial roles in various physiological processes in plants. Through our investigation using a CRISPR-Cas9 knockout mutant library in rice, we identified a semi-dwarf rice mutant named CRISPR-Cas-based dwarf-1 (csd-1). This mutant displayed multiple developmental defects, such as decreased plant height, panicle length, seed size, and seed-setting rate. Whole-genome resequencing analysis revealed that a T-nucleotide insertion in β-ketoacyl-CoA synthase 11 (KCS11), responsible for the initial step in fatty acid elongation, was responsible for the observed defects in csd-1. The identity of csd-1 was confirmed through genetic complementation and CRISPR-Cas9-mediated knockout. Expression analysis indicated that OsKCS11 was present in various tissues, with differential abundance observed through RT-qPCR and promoter GUS staining, and strong localization at the node position by RNA in situ hybridization; furthermore, OsKCS11 protein was confirmed to be in the endoplasmic reticulum. Furthermore, csd-1 exhibited significantly reduced levels of linolenic acid (18:3), C24:0-OH, C28:0-alkanes, C29:0-alkanes, alpha-tocopherol, and C33:0-alkanes, while trans-nonadecenoic acid and behenic acid levels were increased. Cytokinin analysis revealed significant increases in isopentenyladenine (IPA) and cis-zeatin (cZ) levels in csd-1. Molecular investigations indicated upregulation of genes involved in cytokinin biosynthesis or signaling, suggesting a potential link between VLCFAs and cytokinin synthesis through acetyl-CoA. This study not only proposed an alternative gene mapping method based on whole-genome resequencing but also elucidated the mechanism by which VLCFAs influence cytokinin synthesis and signaling.

Oryza↗

PubMed2025

Landscape genomics analysis reveals the genetic basis underlying cashmere goats and dairy goats adaptation to frigid environments.

Understanding the genetic mechanism of cold adaptation in cashmere goats and dairy goats is very important to improve their production performance. The purpose of this study was to comprehensively analyze the genetic basis of goat adaptation to cold environments, clarify the impact of environmental factors on genome diversity, and lay the foundation for breeding goat breeds to adapt to climate change. A total of 240 dairy goats were subjected to genome resequencing, and the whole genome sequencing data of 57 individuals from 6 published breeds were incorporated. By integrating multiple approaches such as phylogenetic analysis, population structure analysis, gene flow and population history exploration, selection signal analysis, and genome-environment association analysis, an in-depth investigation was carried out. Phylogenetic analysis unraveled the genetic relationships and differentiation patterns among dairy goats and other goat breeds. Through signal analysis (θπ, FST, XP-CLR), we identified numerous candidate genes associated with cold adaptation in dairy goats (STRIP1, ALX3, HTR4, NTRK2, MRPL11, PELI3, DPP3, BBS1) and cashmere goats (MED12L, MARC2, MARC1, DSG3, C6H4orf22, CHD7, MYPN, KIAA0825, MITF). Genome-environment association (GEA) analysis confirmed the link between these genes and environmental factors. Moreover, a detailed analysis of the critical genes C6H4orf22 and STRIP1 demonstrated their significant roles in the geographical variations of cold adaptation and allele frequency differences among different breeds. This study contributes to understanding the genetic basis of cold adaptation, providing crucial theoretical support for precision breeding programs aimed at improving production performance in cold regions by leveraging adaptive alleles, thereby ensuring sustainable animal husbandry.

Environmental adaptation↗

PubMed2024

Rapid vertebrate speciation via isolation, bottlenecks, and drift.

Speciation is often driven by selective processes like those associated with viability, mate choice, or local adaptation, and "speciation genes" have been identified in many eukaryotic lineages. In contrast, neutral processes are rarely considered as the primary drivers of speciation, especially over short evolutionary timeframes. Here, we describe a rapid vertebrate speciation event driven primarily by genetic drift. The White Sands pupfish (Cyprinodon tularosa) is endemic to New Mexico's Tularosa Basin where the species is currently managed as two Evolutionarily significant units (ESUs) and is of international conservation concern (Endangered). Whole-genome resequencing data from each ESU showed remarkably high and uniform levels of differentiation across the entire genome (global FST ≈ 0.40). Despite inhabiting ecologically dissimilar springs and streams, our whole-genome analysis revealed no discrete islands of divergence indicative of strong selection, even when we focused on an array of candidate genes. Demographic modeling of the joint allele frequency spectrum indicates the two ESUs split only ~4 to 5 kya and that both ESUs have undergone major bottlenecks within the last 2.5 millennia. Our results indicate the genome-wide disparities between the two ESUs are not driven by divergent selection but by neutral drift due to small population sizes, geographic isolation, and repeated bottlenecks. While rapid speciation is often driven by natural or sexual selection, here we show that isolation and drift have led to speciation within a few thousand generations. We discuss these evolutionary insights in light of the conservation management challenges they pose.

Animals↗

PubMed2026

Zea mays Drought-Overly Sensitive1/TUBA4 Is Wilty3, and Transcriptome Co-Expression Analysis of Shoot Meristem Mutant Tissues Reveals Wilty2/TUB6:Wi3 Interactions Associated With Stem Vascular Bundle Development.

Plant vasculature is essential for the transport of water, nutrients, and signaling molecules across organs, while also providing critical mechanical support for growth and development. Disruptions in vascular bundle formation can therefore lead to severe physiological and developmental defects. In maize, ethyl methanesulfonate (EMS)-induced dominant nonallelic Wilty mutants exhibit a pronounced wilting phenotype even under well-watered conditions, indicating underlying defects in vascular function. In this study, we characterized the Wi3 mutant, identified as ZmDrought-Overly-Sensitive1/DOS1, and compared it with the previously described Wi2 mutant to uncover shared mechanisms underlying their phenotypes. We provide evidence, by bulk segregant resequencing linkage disequilibrium of SNPs adjacent to the causal Wilty SNPs in respective ß- and α-tubulin genes, for the personal communication from Gerry Neuffer that Wi2/ß-tub6 provenance is from ACR-related stock, whereas Wi3/α-tub4 allele is from Mo17, not B73 as claimed by the authors who cloned Dos1. Histochemical staining and Fourier-transform infrared (FTIR) spectroscopy of vascular bundles in Wi3 indicated apparent alterations in cellulose and lignin content consistent with those observed in Wi2. Transcriptome analysis of shoot meristems further indicated that similar sets of genes and pathways are differentially expressed in both mutants, suggesting convergence on common biological pathways. Using bulk-segregant whole-genome resequencing, we identified alpha-tubulin4 (TUA4) as the causal gene in Wi3 (ZmDOS1), harboring a C-to-T substitution within the N-terminal GTPase-binding domain. This mutation results in a glutamic acid196-to-lysine substitution. Given that α- and β-tubulin subunits heterodimerize, and in many plants and animal mutant alleles are dominant-negative gains-of-function, we infer Wi2, Wi3, and likely Wi4, based on very similar FTIR biophysical difference spectra, may act as effectors of vascular bundle cell wall deposition, potentially involving vesicle trafficking as recently shown for asymmetric cell divisions in maize stomatal development. Together, these findings highlight the functional interdependence of tubulin subunits and provide a plausible mechanistic framework for the striking biophysical, transcriptomic, and phenotypic similarities observed between Wi2, Wi3/ZmDOS1, and Wi4 mutants.

bulk segregant analysis↗

PubMed2025

Biogeographic Structure and Mitonuclear Discordance Reveal Cryptic Diversity in Pacific Herring (Clupea pallasii).

Forage fishes are biological drivers throughout the Pacific Ocean, from the Arctic to nearly subtropical latitudes. As a critical trophic link, the health and stability of Pacific herring (Clupea pallasii) populations have implications for other marine species, including several targeted by large, productive fisheries. Previous research has indicated marked divergence between Pacific herring in the Bering Sea and the Gulf of Alaska. Seeking to localize this biogeographic break, we generated low-coverage whole genome resequencing data for 120 Pacific herring from seven sites across the northern Gulf of Alaska and the eastern Bering Sea and Aleutian Islands. Single nucleotide polymorphisms across the mitogenome (267) and nuclear genome (~5.6 million) corroborate a biogeographic break in Pacific herring along the Alaska Peninsula and Aleutian Islands, as far west as Unalaska. We identified two distinct populations: one exists along the northern coasts of the Aleutian Islands and in the eastern Bering Sea; the other occupies the southern edge of the Aleutians and the Gulf of Alaska. Two mitochondrial haplogroups co-occurring across the Gulf of Alaska suggest secondary contact between two populations, likely representing glacial refugia. Our results underscore the importance of geological events to contextualize the diversification of forage fish species.

Bering Sea↗

PubMed2026

Mining of important genetic loci and evaluation of genetic effects for growth traits in Baicheng You Chicken.

The Baicheng You Chicken is a precious indigenous breed in Xinjiang, China, prized for its strong disease and stress resistance and superior meat quality. However, the lack of scientific breeding and conservation has led to poor production performance, particularly in growth traits. In this study, we collected phenotypic and whole-genome resequencing data from 1,535 18-week-old Baicheng You Chickens (180 males and 1,355 females). After stringent quality control (SNP call rate > 95%, minor allele frequency > 1%), we constructed the breed's first comprehensive SNP-based genome-wide variation map, which comprised 2,020,743 high-quality SNPs across the genome. The filtered SNPs had high mapping quality (99.73% mapped to the bGalGal1.mat.broiler.GRCg7b reference genome, Q30 = 93.26%) and a reasonable Ti/Tv ratio (2.596), guaranteeing the reliability of subsequent analyses. We estimated genetic effects (SNP-based heritability and phenotypic variance explained (PVE) by individual loci) via the restricted maximum likelihood (REML) method, and performed a genome-wide association study (GWAS) using a mixed linear model (MLM) - with sex as a fixed effect and principal components to correct for population stratification - to identify significant loci and their effect sizes (Beta). All eight growth traits showed moderate to high heritability: body weight (BW) had the highest heritability (0.86±0.11), while chest width (CW, 0.41±0.08) and body slanting length (BSL, 0.43±0.09) were the lowest; keel length (KL), chest girth (CG), pelvic width (PW), chest depth (CD) and shank length (SL) had heritabilities of 0.50±0.09, 0.46±0.09, 0.54±0.09, 0.67±0.10 and 0.74±0.10, respectively. GWAS identified 145 significant SNPs, with a maximum Beta value of 0.39 and PVE ranging from 1.25% to 6.25%. We annotated 22 candidate genes, with TAPT1, IGF2BP1, ADGRB3, LDB2, NCAPG and LCORL as key candidates. These quantifiable genetic markers and effect estimates provide direct targets for marker-assisted selection (MAS) and valuable resources for future genomic selection (GS) programs, offering a practical approach to improve the breed's slow growth while preserving its unique meat quality.

Baicheng You Chicken↗

PubMed2026

Genome-wide association study of body weight and body size traits in Langya hens.

Langya chicken is a Chinese indigenous chicken breed with high genetic diversity. To systematically analyse the genetic basis of body size traits, eight traits (including BW, comb shape, and body size) of 2 952 Langya hens were measured at 130 days of age and at first egg of age. A total of 9 708 856 high-quality single-nucleotide polymorphisms (SNPs) were obtained through whole-genome resequencing and used for subsequent genetic parameter estimation and genome-wide association study (GWAS). The results of genetic parameter analysis revealed significant differences in the SNP heritability of different body size traits, with an overall range of 0.13-0.64. In particular, BW, comb length, comb height, and tibia length exhibited moderate-to-high heritability (0.34-0.64) during both developmental stages. GWAS revealed significantly associated SNP loci distributed across multiple chromosomal regions, indicating that body size traits have a complex multilocus genetic regulatory structure and that some chromosomal regions recur for different body size traits and during different developmental stages, showing potential pleiotropic effects or shared genomic regions. Notably, multiple stable body size trait-associated regions were identified on Gallus gallus autosome (GGA) 1, 4, and 27, including genomic regions on GGA1 (167.56-178.18 Mb), GGA4 (68.24-81.17 Mb), and GGA27 (5.22-6.73 Mb), in which significantly associated signals were repeatedly detected for multiple body size traits, such as BW and tibia length. The significant SNPs in the above regions were characterised by strong linkage disequilibrium and were associated with multiple body size traits, indicating that these SNPs may serve as important genetic hotspots for the regulation of chicken body shape and structure. Candidate genes annotated in these core regions include NCAPG, KPNA3, LDB2, PPARGC1A, FNDC3A, SOST, RB1, STON2, and TARP; the functions of these genes are involved mainly in the regulation of cell proliferation, energy metabolism, bone development, and tissue growth. NCAPG was consistently associated with multiple traits at both developmental stages. Functional enrichment analysis further revealed that these candidate genes were significantly enriched in the phosphatidylinositol, GnRH, energy metabolism, skeletal development and protein biosynthesis signalling pathways. The genetic characteristics of Langya chicken body size traits during the growth stage at the genome-wide level and the underlying molecular mechanisms were systematically revealed in this study. The findings provide important candidate gene resources and a theoretical basis for the screening of molecular markers for body size traits and the genomic breeding of regional chicken breeds.

Candidate genes↗

PubMed2025

Genomic insights into the population history of fat-tailed sheep and identification of two mutations that contribute to fat tail adipogenesis.

INTRODUCTION: Since their domestication, domestic sheep (Ovis aries) have been culturally and economically significant farming animals worldwide. Fat-tailed sheep serve as a unique genetic resource for understanding adipogenesis and adaptive evolution in livestock. OBJECTIVES: Several genomic analyses have been conducted on various sheep breeds to elucidate the genome and regulation mechanism of the fat tail trait, prior genomic studies have failed to reconcile conflicting evidence about the genetic basis of tail morphology, particularly regarding the roles of PDGFD and BMP2. METHODS: Here, we conducted whole-genome resequencing of 283 sheep, encompassing 66 domestic breeds and 5 wild ovine species, to investigate the domestication history and selection signatures of fat-tailed sheep. Additionally, we performed transcriptome sequencing on adipose tissue to identify differentially expressed genes and cellular assays to validate these results. RESULTS: Demographic analysis revealed that domestic sheep descended from Asiatic mouflon and fat-tailed sheep began to diverge from thin-tailed sheep approximately 4.4-7.5 thousand years ago in East Asia. Chinese indigenous sheep were classified into Mongolian, Kazakh, Tibetan, and Yunnan populations. The Yunnan population may have experienced more recent genetic introgression from wild species, rather than an independent domestication event. Moreover, many potential regions associated with the fat-tailed phenotype (DDI1, PDGFD, and BMP2) were identified by selective sweep and genome-wide association analyses. Additionally, a fine-scale analysis of fat-tailed and thin-tailed sheep revealed two novel mutations: a G/A missense variant of PDGFD (Chr15: 3900312) and a C/T missense variant of BMP2 (Chr13: 48462350), both of which were significantly associated with tail adiposity. Functional validation demonstrated that mutant A-PDGFD significantly activated PFGFD expression and reduced fat deposition compared to wildtype. The C-BMP2 mutant activated BMP2 expression and promoted preadipocyte fat deposition. CONCLUSION: Our study provides the first evidence that these genes jointly regulate fat tail development through complementary mechanisms: PDGFD promotes adipose expansion, whereas BMP2 modulates energy partitioning. These findings offer new insights into the evolutionary history of fat-tailed sheep and identify potential targets for precision breeding in small ruminants.

Animals↗

PubMed2025

Genomic resequencing unravels species differentiation and polyploid origins in the aquatic plant genus Trapa.

Trapa L. is a non-cereal aquatic crop with significant economic and ecological value. However, debates over its classification have caused uncertainties in species differentiation and the mechanisms of polyploid speciation. This study employed whole-genome resequencing together with the fruit morphology of 229 Trapa accessions (153 Asian and 76 North American samples) to elucidate species differentiation and polyploidization events in Trapa. For the species with AA genome and large fruits, clear genetic differentiation was found between two clades with different geographic origins, that is, from the Yangtze River and Amur River basins. The invasive AA species in North America (T. natans) was identified as originating from the Amur River based on genetic and morphological similarities, while all the cultivated accessions were AA species originating from the Yangtze River with severe genetic impoverishment. The separation of the two BB species with small seeds, that is, T. incisa and T. maximowiczii, was strongly supported by both morphological and genetic evidence. For the tetraploids, Asian and North American tetraploids were revealed to have distinct evolutionary origins. Asian allotetraploids (AABB) originated through hybridization between AA diploids from the Yangtze River Basin and BB diploids T. maximowiczii, supported by nuclear and chloroplast evidence. In contrast, the invasive North American tetraploids (T. bispinosa var. iinumai) exhibited an AACC-like genome, suggesting an independent polyploidization involving an unknown "CC" diploid. These findings provide critical insights into Trapa's complex evolutionary history, polyploidizations, and invasive origins, offering a genomic foundation for the conservation and sustainable utilization of the underutilized aquatic crop amid global environmental challenges.

Polyploidy↗

PubMed2026

Genome-Wide Identification of SSR and InDel Markers and Experimental Validation of SSR Markers for Distinguishing Cold-Tolerant and Cold-Sensitive Lily Cultivars.

In this study, whole-genome resequencing was performed on the cold-tolerant variety ND-6 and the cold-sensitive variety 'Sorbonne'. After evaluation, the Lilium davidii var. unicolor reference genome was selected to analyze SSR distribution characteristics. Whole-genome InDel identification and comparative analysis were conducted for the two varieties, yielding 34,812,909 and 24,497,857 InDels, respectively. Short InDels were predominant, with deletions slightly outnumbering insertions, mostly located in intergenic regions. Twenty pairs of SSR primers were screened and synthesized. Among them, 10 pairs amplified clearly, with a polymorphism rate of 82.6%, effectively distinguishing the two cultivars examined in this study. This study provides systematic data and a reliable marker resource for the analysis of lily genomic variation, laying a foundation for the identification of cold-tolerant germplasm; validation across additional cultivars and individuals will be required to extend their utility to broader germplasm.

cold resistant lilies↗

PubMed2026

Exploratory identification and cellular functional characterization of ppiabl as a candidate gene associated with growth traits in Paralichthys olivaceus.

The Japanese flounder (Paralichthys olivaceus) is an important mariculture species. However, the genetic mechanisms underlying its growth traits remain poorly understood. To explore the genetic basis of growth variation, whole-genome resequencing was performed in a cultured cohort of 60 individuals, followed by exploratory genome-wide association analysis and candidate-gene prioritization. The results revealed heritability estimates of 0.40 for body weight and 0.24 for body length, with substantial overlap in associated loci between the two traits. Exploratory association and variant-annotation analyses prioritized ppiabl, which carries a nonconservative missense variant, as a candidate gene for further investigation. Tissue expression analysis showed that ppiabl was highly expressed in muscle tissue. This gene encodes a protein belonging to the conserved peptidyl-prolyl cis-trans isomerase family. In Japanese flounder primary muscle cells, ppiabl knockdown was associated with altered expression of growth-related genes and an increased G1-phase fraction, whereas overexpression produced changes in the opposite direction. In line with this, fast-growing individuals were found to have significantly larger muscle fiber areas than slow-growing ones. These findings suggest that ppiabl may be involved in muscle-related cellular processes associated with growth variation in Japanese flounder, although its contribution to whole-animal growth requires further validation. Overall, this exploratory study prioritizes ppiabl as a candidate gene potentially associated with growth-related cellular processes in Japanese flounder, although validation in larger independent populations and in vivo models is required.

Animals↗

PubMed2025

Analysis of genetic differences underlying chilling stress tolerance using whole genome Re-Sequencing in walnut (Juglans regia L.).

Walnut (Juglans regia L.) is prized worldwide for both its nutritional value and economic importance, yet it remains vulnerable to cold stress, with significant differences in tolerance among varieties. This study combined physiological analyses with whole-genome resequencing (WGS) to evaluate the cold stress responses of two varieties, ‘Qingxiang’ and ‘Liaoning No.8’. Under chilling stress (0 °C), we measured electrolyte leakage and antioxidant enzyme activity, applying both exogenous methyl jasmonate (MeJA) and the jasmonate inhibitor DIECA. Genomic variations were analyzed using WGS. Results showed that ‘Liaoning No.8’ exhibited superior cold tolerance. Application of MeJA reduced electrolyte leakage by 37% and MDA accumulation by 52% on average, whereas DIECA exacerbated stress-related damage. WGS achieved 16.24–16.26× coverage and identified 2.73–2.78 million SNPs, 378–382k InDels, 25–26k SVs, and 7.2–7.9k CNVs. Twenty genes containing sequence variants showed transcriptional responses under cold stress that were significantly correlated with mutation density (r = 0.62, P < 0.01). One gene, XM_018985465.2, which lacked SNPs in ‘Liaoning No.8’, was expressed 4.2 times more in this variety, suggesting cis-regulatory influence. These findings highlight the role of jasmonic acid signaling in enhancing cold tolerance in walnut and offer genomic insights into its underlying adaptive mechanisms.

Juglans↗

PubMed2026

Transposable Element Dynamics Drive the Genomic Evolution and Phenotypic Diversification of Allotetraploid Common Carp.

An important question in evolutionary biology is how polyploidization generates raw material for phenotypic diversification. Transposable elements (TEs) represent an underestimated source of genetic variation in eukaryotic genomes. By integrating 516 whole-genome resequencing datasets and 236 transcriptomes from common carp (Cyprinus carpio), a representative allotetraploid fish, we constructed the first population-scale landscape of TE insertions in teleosts. TE insertions are widespread in the carp genome and preferentially associated with stress-responsive genes, with DNA transposons as major contributors. Relaxed purifying selection and TE burst events coexist, generating abundant variation for subsequent subspecies differentiation. Compared with a closely related diploid species, carp exhibits more exonic TE insertions and shorter TE-gene distances, and multiple TE superfamilies expanded during tetraploidization. Genome-wide association analyses uncovered intragenic TE variants underlying domesticated traits missed by SNPs, including DNA transposon deletions associated with scale reduction and altered body shape. Notably, lighter-colored individuals harbor homozygous deletions of LTR and DNA transposons within mdfic2, whose knockout in zebrafish reduces pigmentation. Most trait-associated variants reflect lineage-specific loss of ancient TE insertions rather than recent transposition. Overall, these findings highlight the distinct role of TEs in polyploid genome evolution and phenotypic diversification, providing new insights into TE dynamics in vertebrates.

allotetraploidization↗

PubMed2026

A multi-model genome-wide association study identifies genetic variants underlying resistance to Largemouth Bass Ranavirus (LMBV) in Micropterus salmoides.

Largemouth bass (Micropterus salmoides) is an economically important freshwater aquaculture species, yet recurrent outbreaks of Largemouth Bass Ranavirus (LMBV) continue to impair production and cause substantial losses. The genetic basis of host variation in LMBV resistance remains insufficiently characterized. Here, we applied a multi-model genome-wide association study (GWAS) to identify loci associated with resistance following a controlled challenge with the LMBV-23PY strain. Whole-genome resequencing was performed for 146 phenotyped fish, including 72 susceptible and 74 resistant individuals. After stringent quality control, 877,262 high-quality variants were retained and tested using six GWAS models. Across binary survival status and survival time phenotypes, 32 shared suggestive variants were consistently detected across models, representing suggestive loci for LMBV-23PY resistance. Genes within ±50 kb of these loci were annotated, and functional enrichment highlighted immune- and redox-related biological processes. Three prioritized candidates-GSTT3L (glutathione S-transferase theta-3-like), CGRP2 (calcitonin gene-related peptide 2), and NPPC (natriuretic peptide C)-were associated with pathways involved in oxidative stress responses and immune regulation. Collectively, these results provide insight into the genetic architecture of LMBV-23PY resistance in largemouth bass and identify suggestive variants and associated candidate genes for downstream validation, functional interrogation, and the development of marker-assisted and genome-enabled breeding strategies.

Animals↗

PubMed2026

Development and identification of KASP-SNP markers correlated with Aeromonas hydrophila resistance traits in blunt snout bream (Megalobrama amblycephala).

The blunt snout bream (Megalobrama amblycephala) is an economically important freshwater fish species. However, it is highly susceptible to Aeromonas hydrophila infection, especially in intensive pond aquaculture in China. Molecular marker-assisted selection provides an efficient approach for breeding disease-resistant varieties; however, the key genes or molecular markers linked to A. hydrophila resistance remain scarce in this species. A 436 differential SNP sites with disease-resistant were screened on basis of whole-genome resequencing. Then, a high-throughput genomic KASP genotyping technique was utilized to discover favorable genes and SNP sites associated with A. hydrophila resistance. A total of 46 KASP markers were successfully developed with an accuracy of 92 %. These markers were used to genotyping 120 blunt snout bream individuals. Through trait correlation analysis and general linear models (GLM), five SNPs significantly (P < 0.05) associated with resistance to A. hydrophila were identified and mapped to five candidate genes (btnl2, cfhr2, slc47a1, neu3, nlrp1). Survival rate of individuals carrying the dominant genotype demonstrated an average survival rate of 81.39 %, which represents a 69.35 % increase in comparison with that of 48 % in total population. This effect was validated in an external population of 100 fish. These findings identify key genetic markers associated with A. hydrophila resistance and provide a direction for elucidating the underlying molecular immune mechanisms, thus establishing a genetic foundation for future breeding strategies.

Cyprinidae↗

PubMed2026

Metabolome-based genome-wide association study provides genetic insights into the andrographolide accumulation in Andrographis paniculata.

Andrographis paniculata is a distinctive medicinal plant that produces andrographolide-related metabolites, a class of diterpenoid compounds with potent anti-inflammatory activities. To elucidate the genetic mechanisms underlying the biosynthesis of these compounds, we perform comprehensive metabolic profiling and whole-genome resequencing on a natural population of A. paniculata. Population structure analysis reveals four distinct subgroups characterized by low intra-group genetic diversity but significant inter-group differentiation. Through metabolome-based genome-wide association study, we identify a significant locus associated with 14-deoxyandrographolide content. This locus harbors the candidate gene ApNB-ARC25 (CXN00004106), which encodes an NB-ARC domain-containing resistance protein. Functional characterization using virus-induced gene silencing shows that silencing of ApNB-ARC25 significantly reduces andrographolide accumulation and downregulates expressions of key genes in the andrographolide biosynthetic pathway. Heterologous overexpression of ApNB-ARC25 in rice not only improves resistance to blast disease but also enhances diterpenoid phytoalexin production. Our findings reveal that ApNB-ARC25 promotes diterpenoid accumulation and andrographolide biosynthesis by upregulating key genes involved in terpenoid backbone formation and diterpenoid synthesis. This work not only expands the functional understanding of the ApNB-ARC gene family but also provides a genetic resource for enhancing valuable compound accumulation in medicinal plants, offering important insights into the molecular regulation of medicinal metabolite biosynthesis.

Diterpenes↗