Significant Genetic Differences Research Articles

Melanism in the Saw-scaled Viper, Echis carinatus (Schneider, 1801) from Sheedvar Island, Persian Gulf, Iran

Melanism in Echis carinatus has been observed on Sheedvar Island in the Persian Gulf. A comparative analysis between melanistic and non-melanistic individuals showed no significant morphological or genetic differences. The evolution of melanism in E. carinatus may serve as camouflage or aid in predator avoidance, similar to other nocturnal viper species. However, a deeper understanding of the ecological role of melanism in nocturnal vertebrates, including E. carinatus, requires further investigation to clarify its broader significance.

Metabolic and hormonal profiling in polycystic ovarian syndrome: insights into INSR gene variations.

Polycystic Ovary Syndrome (PCOS) is a hormonal disorder characterized by irregular periods, excess androgen levels, and polycystic ovaries, affecting many women of reproductive age. This study employed statistical and molecular analyses to compare hormone and metabolic markers between PCOS patients and controls. Sanger sequencing identified two INSR gene variants linked to high insulin and pre-diabetic conditions. Statistically, no significant age differences were detected (p = 0.492) between the overall PCOS patient pool and controls. However, a substantial variation in Vitamin D levels was observed within PCOS patients compared to controls (p = 0.0006), suggesting an association with PCOS. Correlations between Vitamin D and insulin, as well as HbA1c levels (R2 = 0.141 and 0.143, respectively), suggest Vitamin D's potential impact on glycemic control. Significant differences were found in HbA1c (p < 0.0001), insulin (p < 0.0001), and LDL (p = 0.0004) levels between PCOS patients and controls, highlighting marked disparities in these metabolic markers. LH levels also showed a significant contrast (p < 0.0001), while progesterone levels displayed a notable difference (p = 0.007) between the two groups. Correlation analyses within PCOS patients demonstrated associations among LDL, HbA1c, and insulin, with no such correlations observed in control cases. Additionally, Sanger sequencing identified two INSR gene variants, c.3614C > T (p.Pro1205Leu) and c.3355C > T (p.Arg1119Trp), associated with high insulin, LH, and pre-diabetic conditions. These amino acid changes may trigger metabolic imbalances and hormonal irregularities, potentially contributing to the development of PCOS. The findings highlight the multifaceted nature of PCOS, revealing significant metabolic, hormonal, and genetic differences compared to controls. These insights may inform tailored interventions and management strategies for the complex associations characteristic of PCOS.

Morphological and Transcriptomic Analyses Reveal the Involvement of Key Metabolic Pathways in Male Sterility in Chimonanthus praecox (L.) Genotypes.

Chimonanthus praecox (Calycanthaceae family) is a unique ornamental and economic flowering tree in China, and after thousands of years of cultivation, it has produced several varieties and varietal types. Notably, male sterility is common in flowering plants and is an important tool for the genetic improvement in plants and optimization using hybrid plant technology; however, there have been no reports on male-sterile material or related studies on C. praecox. To our knowledge, this is the first time that C. praecox male sterility is dissected unveiling the involvement of key metabolic pathways. Notably, male sterility in C. praecox was observed during the budding period and likely occurred during the premature stage of pollen cell maturation. Additionally, differentially expressed genes in the starch and sucrose metabolism pathway and the plant hormone signal transduction pathway showed regular expression trends. This study reports on significant genetic differences that contribute to male sterility in C. praecox and provides a basis for further research and breeding strategies.

Yellow Dwarf Virus Resistance in Barley: Phenotyping, Remote Imagery, and Virus-Vector Characterization.

Yellow dwarf viruses (YDVs) spread by aphids are some of the most economically important barley (Hordeum vulgare) virus-vector complexes worldwide. Detection and control of these viruses are critical components in the production of barley, wheat, and numerous other grasses of agricultural importance. Genetic control of plant diseases is often preferable to chemical control to reduce the environmental and economic cost of foliar insecticides. Accordingly, the objectives of this work were to (i) screen a barley population for resistance to YDVs under natural infection using phenotypic assessment of disease symptoms, (ii) implement drone imagery to further assess resistance and test its utility as a disease screening tool, (iii) identify the prevailing virus and vector types in the experimental environment, and (iv) perform a genome-wide association study to identify genomic regions associated with measured traits. Significant genetic differences were found in a population of 192 barley inbred lines regarding their YDV symptom severity, and symptoms were moderately to highly correlated with grain yield. The YDV severity measured with aerial imaging was highly correlated with on-the-ground estimates (r = 0.65). Three aphid species vectoring three YDV species were identified with no apparent genotypic influence on their distribution. A quantitative trait locus impacting YDV resistance was detected on chromosome 2H, albeit undetected using aerial imaging. However, quantitative trait loci for canopy cover and mean normalized difference vegetation index were successfully mapped using the drone. This work provides a framework for utilizing drone imagery in future resistance breeding efforts for YDVs in cereals and grasses, as well as in other virus-vector disease complexes.

Identification and characterisation of carbapenem-resistant Streptococcus nidrosiense sp. nov. isolated from blood culture

BackgroundThis study aimed to investigate a highly resistant strain of Streptococcus sp. isolated from a patient with bloodstream infection and determine its taxonomic classification. MethodsThe strain was isolated from blood culture from a 65-year-old male patient admitted to St. Olavs University hospital, Trondheim, Norway, in 2023. Antimicrobial susceptibility testing as well as phenotypic and biochemical characterization were performed. Whole genome sequencing was conducted and genomic comparison to Streptococcus type strains was carried out. ResultsThe strain was initially identified as Streptococcus mitis/oralis but showed significant genetic differences, suggesting that it belonged to an undescribed species within the Streptococcus genus. Phenotypic and biochemical characterization identified the strain as a non-motile, facultative anaerobic bacterium with α-hemolysis. Antimicrobial susceptibility testing showed resistance to all beta-lactams tested. Genomic analyses confirmed the classification of the strain as a novel species, which was designated Streptococcus nidrosiense. ConclusionThis study combines conventional phenotypic tests with whole genome sequencing for accurate taxonomic classification of a bacterial strain isolated from blood culture. The identification of a novel species within the Streptococcus genus contributes to the understanding of microbial diversity and antibiotic resistance of the Streptococcus genus in clinical settings.

Mitochondrial DNA of the Arabian Camel Camelus dromedarius.

The Camelidae family, ranging from southwest Asia to north Africa, South America, and Australia, includes key domesticated species adapted to diverse environments. Among these, the Arabian camel (Camelus dromedarius) is vital to the cultural and economic landscape of the Arabian Peninsula. This review explores the mitochondrial DNA of the dromedary camel, focusing on the D-loop region to understand its genetic diversity, maternal inheritance, and evolutionary history. We aim to investigate the unique characteristics of Arabian camel mtDNA, analyze the D-loop for genetic diversity and maternal lineage patterns, and explore the implications of mitochondrial genomic studies for camel domestication and adaptation. Key findings on mtDNA structure and variation highlight significant genetic differences and adaptive traits. The D-loop, essential for mtDNA replication and transcription, reveals extensive polymorphisms and haplotypes, providing insights into dromedary camel domestication and breeding history. Comparative analyses with other camelid species reveal unique genetic signatures in the Arabian camel, reflecting its evolutionary and adaptive pathways. Finally, this review integrates recent advancements in mitochondrial genomics, demonstrating camel genetic diversity and potential applications in conservation and breeding programs. Through comprehensive mitochondrial genome analysis, we aim to enhance the understanding of Camelidae genetics and contribute to the preservation and improvement of these vital animals.

Stability of population genetic structure in large yellow croaker (Larimichthys crocea): Insights from temporal, geographical factors, and artificial restocking processes.

Despite concerns about overfishing and the potential impact of release programs on wild populations, our study of 3116 individuals from 13 wild populations and 2787 individuals from two cultured populations in Zhejiang and Fujian provinces spanning 2008 to 2023 reveals a relatively stable genetic diversity in Larimichthys crocea. Surprisingly, the genetic diversity of wild large yellow croaker populations has remained consistent over the years, suggesting minimal influence from population declines due to overfishing. With the exception of populations in Sansha Bay and Luoyuan Bay, no significant genetic differences were observed among wild populations, indicating a single panmictic genetic population across the East and South China seas. Notably, significant genetic differentiation exists between cultured and wild populations, suggesting a possible limited genetic adaptation of cultured-released individuals to the wild environment. The genetic differences observed between the Sansha Bay, with its adjacent Luoyuan Bay populations, and other wild populations underscore the dual effects of habitat environment and farming activities on the genetic structure of large yellow croaker. Our findings suggest that, despite declines in population numbers due to overfishing and expands extensive cultured releases, the genetic diversity of L. crocea populations remains largely unaffected. Moreover, the L. crocea population along the Chinese coast appears to form a single panmictic population with considerable genetic diversity.

Genetic variations and clinical features associated with burning sensation due to topical tacrolimus in patients with atopic dermatitis

AbstractBackgroundTopical tacrolimus has been used as one of the treatment options for atopic dermatitis (AD). A burning sensation is the most common side effect of topical tacrolimus.ObjectivesThis study was designed to identify genetic variations and clinical features to predict burning sensation by topical tacrolimus in patients with AD.MethodsPatients with AD who had applied topical tacrolimus were classified according to the presence of a burning sensation. We compared the patients' demographics and blood test results, including serum eosinophil, serum immunoglobulin E and multiple allergen simultaneous test. Furthermore, the frequency of variations in barrier‐ (KLK7, FLG 3321delA, FLG K4022X, SPINK5 1156, SPINK5 1188, SPINK5 2475) and immune response‐ (DEFB1, KDR, CDKAL1, IL‐5RA, IL‐9, IL‐12RB1, IL‐12RB2, IL‐17RA) related genes was compared between two groups by reverse blot hybridization assay of the buccal mucosa.ResultsAmong 206 patients with AD using topical tacrolimus, 34 (16.5%) complained of a burning sensation. The burning sensation was associated with severe AD and a family history of atopic disease. Furthermore, with statistical significance, a heterozygous mutation in the filaggrin gene (FLG K4022X) was more frequent in AD patients with a burning sensation due to topical tacrolimus. However, no other significant genetic differences were observed between them.ConclusionsA burning sensation caused by topical tacrolimus can be expected in AD patients with severe symptoms, a family history of atopy and a genetic variation such as FLG K4022X.

Ecological displacement in a Rocky Mountain hybrid zone informs management of North American martens (Martes)

ContextParapatric sister species are ideal for tests of ecological interactions. Pacific (Martes caurina) and American pine (M. americana) martens are economically and culturally valuable furbearers that hybridize in the north-central Rocky Mountains. Despite preliminary evidence of biased introgression, the hybrid zone has been geographically stable for 70 years, but interspecific ecological interactions have yet to be examined in detail.ObjectivesWe test whether ecological interactions may influence the outcome of hybridization in this system. To that end, we estimate the fundamental niche of each species and gauge how suitability landscapes change when the two species are in contact.MethodsWe genotyped > 400 martens from the Rocky Mountain hybrid zone to diagnose individuals to species-level and identify putative hybrids. We then built range-wide ecological niche models for each species, excluding individuals in the hybrid zone, to approximate their respective fundamental niches. Those models were projected into the hybrid zone and compared with niche models trained on individuals within the hybrid zone to assess how niche dynamics change when the species are in sympatry.ResultsThe fundamental niche of each species differed significantly, while the hybrid zone was equally suitable for both. Niches of each species based on models built within the hybrid zone showed that Pacific martens utilized significantly less suitable habitat than expected based on their range-wide fundamental niche, suggesting that species interactions shape local hybridization. We detected few admixed individuals (12%), with no evidence of directional (sex or species) biases. Interstate-90 further acts as a major dispersal barrier.ConclusionsNorth American martens are currently managed as a single species by some state agencies, yet significant ecological and genetic differences indicate they should be managed separately. The observed ecological displacement of Pacific martens by American pine martens may partially explain the mixed success of historical, mixed-species wildlife translocations and cautions such translocations in the future. Landscape-scale consideration of ecological dynamics, in addition to molecular compatibility, will be essential to the success of future translocations.

Genetic Structure of Domesticated Reindeer (Rangifer tarandus) Populations in the Central Siberian Plateau and Adjacent Areas

On the basis of 16 microsatellite markers, the genetic structure of the domesticated reindeer of two breeds, Evenk and Even, bred on the territory of the Central Siberian Plateau and adjacent territories, was studied. Genetic flows between modern domesticated reindeer populations of two breeds were analyzed. Significant differences were found between the Evenk taiga and Even breeds of domestic deer. Using a historical sample from the middle of the last century, a high degree of stability in time of the gene pool of domesticated populations was revealed. It has been established that genetic flows between wild and domesticated forms in the study area are insignificant. Statistically significant genetic differences between wild and domesticated reindeer populations are shown.

QTL analysis of divergent floral morphology traits between Gilia yorkii and G. capitata.

Speciation is a complex process typically accompanied by significant genetic and morphological differences between sister populations. In plants, divergent floral morphologies and pollinator differences can result in reproductive isolation between populations. Here, we explore floral trait differences between two recently diverged species, Gilia yorkii and G. capitata. The distributions of floral traits in parental, F1, and F2 populations are compared, and groups of correlated traits are identified. We describe the genetic architecture of floral traits through a quantitative trait locus analysis using an F2 population of 187 individuals. While all identified quantitative trait locus were of moderate (10-25%) effect, interestingly, most quantitative trait locus intervals were non-overlapping, suggesting that, in general, traits do not share a common genetic basis. Our results provide a framework for future identification of genes involved in the evolution of floral morphology.

Whole-genome resequencing revealed the population structure and selection signal of 4 indigenous Chinese laying ducks

The assessment of animal genetic structure had significant importance for the preservation and breeding of animal germplasm resources. Selection signals are genotype markers generated during the process of biological evolution, and the detection of selection signals could reveal the direction of species evolution. The aim of this study was to generate a whole-genome resequencing data from Jinding duck, Shanma duck, Youxian Partridge duck, and Taiwan Brown tsaiya duck to reveal their population structure and selection signals. The population structure analysis revealed significant genetic differences among the 4 indigenous laying ducks, indicating their independent lineage. Specifically, Shanma duck and Youxian partridge duck were closely and likely originated from a common ancestor. In addition, selection sweep analysis was performed using the population genetic differentiation coefficient (Fst) and nucleotide diversity ratio (π ratio). The top 5% was used as the threshold for the Fst and π ratio, and the 2 thresholds were combined to identify selected genomic regions. In the selected regions of the 3 comparison groups, 136, 143, and 268 candidate genes were detected. Further screening of all candidate genes revealed that 35 candidate genes appeared simultaneously in 3 comparative groups, with 16 genes annotated. The 16 genes were analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. The results revealed 5 functional genes (AQP3, PIK3C3, NOL6, RPP25, and DCTN3) that may be related to important economic traits in laying ducks and involved mainly invasopressin-regulated water reabsorption, ribosome biogenesis, and the PI3K signaling pathway. The results provide insights into the protection and exploitation of genetic resources of Chinese indigenous laying ducks.

Pathological and Molecular Diagnosis of Uveal Melanoma.

(1) Background: Uveal melanoma (UM) is a common malignant intraocular tumor that presents with significant genetic differences to cutaneous melanoma and has a high genetic burden in terms of prognosis. (2) Methods: A systematic literature search of several repositories on uveal melanoma diagnosis, prognosis, molecular analysis, and treatment was conducted. (3) Results: Recent genetic understanding of oncogene-initiation mutations in GNAQ, GNA11, PLCB4, and CYSLTR2 and secondary progression drivers of BAP1 inactivation and SF3B1 and EIF1AX mutations offers an appealing explanation to the high prognostic impact of adding genetic profiling to clinical UM classification. Genetic information could help better explain peculiarities in uveal melanoma, such as the low long-term survival despite effective primary tumor treatment, the overwhelming propensity to metastasize to the liver, and possibly therapeutic behaviors. (4) Conclusions: Understanding of uveal melanoma has improved step-by-step from histopathology to clinical classification to more recent genetic understanding of oncogenic initiation and progression.

Genetic diversity, heritability, and estimated breeding values for growth of domesticated Asian seabass Latescalcarifer from Thailand

To establish a new breeding program, genetic diversity of five domesticated populations and two commercial stocks of Asian seabass (Lates calcarifer) were examined. Moderate levels of genetic diversity based on microsatellite polymorphism were found. The number of alleles per locus (NA) was 3.429–11.571. Observed (Ho) and expected (He) heterozygosities were 0.416–0.772 and 0.423–0.805. FST and genetic heterogeneity analysis revealed significant genetic differences of most pairwise comparisons (P < 0.001). Genetic distance between populations was 0.000–0.703. Phylogenetic analysis divided examined populations to two genetic stocks; A: DOF-Chachoengsao 2, DOF-Songkhla, and DOF-Trang and B: Commercial Farm 1 (Phuket) and Commercial Farm 2 (Chachengsao), DOF-Chachoengsao 1 and DOF-Krabi. The base population (G0, 51 families) was established from crosses between these founder populations. Heritability and estimated breeding values (EBVs) for growth in G0 families were evaluated at 519 day post hatch (dph, mean body weight = 616.64 ± 266.80 g, N = 1655). The heritability (h2) for growth of L. calcarifer in this study was 0.386 ± 0.020. The additive genetic coefficient of variation was 28% indicating high potential of genetic improvement for growth in this population. The distribution of EBVs showed high variation both between and within families. Fish exhibiting high EBVs (SATREPS-DOF-G0-hEBVs) clustered with a phylogenetic clade A while the SATREPS-DOF-G0-lEBVs group was phylogenetically allocated to clade B. Genetic selection with +1SD criteria is expected to achieve genetic gain of 28.5% per generation. The information on genetic diversity and EBVs estimates allows efficient implementation of our ongoing breeding program of L. calcarifer.

Species divergence in valleys: the phylogeny of Phrynocephalus forsythii complex and description of a new species.

Geographic isolation caused by high-altitude valleys promotes the formation of geographic segregation of species, leading to species differentiation. The subgenus Oreosaura contains viviparous species from the Tibetan Plateau and the vicinity of the Tarim Basin, which can be divided into three species complexes according to their geographical distribution: Phrynocephalus vlangalii, Phrynocephalus theobaldi, and Phrynocephalus forsythii. However, molecular data for the P. forsythii complex are limited and the diversity of this species complex has been greatly underestimated. Therefore, this study aimed to explore the species diversity of Oreosaura and species differentiation within the P. forsythii complex. We analysed the species diversity of Oreosaura by combining previous data, constructed a phylogenetic tree of the subgenus based on cytochrome c oxidase subunit I and 16S sequences, and estimated the divergence time. The results suggest significant genetic differences between the Tarim Basin populations and adjacent mountain valley populations of the P. forsythii complex and that the combination of deep valley landscapes in the high mountains and ice-age events have contributed to the differentiation of the viviparous toad-headed agama lizard, which is a key factor in the phylogenetics of the P. forsythii complex. Furthermore, we identified a population collected from Wuqia County, Xinjiang, as a new species, Phrynocephalus kangsuensis sp. nov. The results will provide data for phylogenetic studies following the P. forsythii complex and help demonstrate that valleys promote the formation of Phrynocephalus species.

Effects of tooth loss on behavioral and psychological symptoms of dementia in app knock-in mice

ObjectivesMany patients with Alzheimer's disease (AD) experience behavioral and psychological symptoms of dementia (BPSD), which significantly affect their quality of life. It is known that 5-Hydroxytryptamine (5-HT) plays a crucial role in the development of BPSD. While the relationship between tooth loss and AD symptoms has been acknowledged, the aspect of aggression has not been focused on until now. Despite the established importance of 5-HT in BPSD, how tooth loss is related to the exacerbation of AD symptoms, especially in terms of aggression, remains largely unexplored. Although nutritional status is known to influence the progression of dementia, the specific effect of tooth loss on peripheral symptoms, notably aggression, is not well understood. MethodsIn our study, we conducted maxillary molar extractions in aged C57BL/6J and AppNL-G-F mice and observed their condition over a 3-month period. During this time, we documented significant behavioral and genetic differences between mice in the control groups and mice that underwent tooth extraction. Notably, mice that underwent tooth extraction exhibited a considerable decline in cognitive function and increased in aggression 3 months after tooth extraction compared with the control groups (C57BL/6J and AppNL-G-Fmice). ResultsOur findings suggest that molar loss may lead to reduced 5-HT levels in the hippocampus, possibly mediated by the trigeminal nerve, contributing to the development of aggression and BPSD in AD. ConclusionThis study sheds light on the intricate relationships between oral health, 5-HT, and AD symptoms, offering valuable insights into potential therapeutic avenues for managing BPSD in patients with dementia.

Parasite and genetic diversity of big-scale sand smelt (Atherina boyeri Risso, 1810) populations in their natural and expansion ranges in Ukraine.

The big-scale sand smelt (Atherina boyeri) is an Atlanto-Mediterranean amphidromous fish species found within the Black Sea. Here, we assess differences in the parasite fauna of big-scale sand smelt populations from their natural range in the northwestern Black Sea and from their expansion range in the Lower and Middle River Dnipro. In addition, we undertook a microsatellite analysis to assess the genetic similarity of fish from the different locations. We found that the parasite community of fish in their natural range was wider than that from their expansion range. While the Gulf of Odesa was most distant from all other localities by parasite community composition and the Dnipro Reservoir was characterised by an absence of parasites (newest and most distant expansion locality), only fish from the Danube Delta showed a significant genetic difference. Our results suggest that the parasite community of big-scale sand smelt is primarily influenced by environmental factors, such as habitat type, water salinity and/or prey composition. Both microsatellite analysis and parasite community species composition (e.g. the presence of the marine Telosentis exiguus in the Kakhovka Reservoir and freshwater Raphidascaris sp. in the Gulf of Odesa) confirmed that populations in the River Dnipro reservoirs had, at some time, been connected with native marine populations, thus also confirming the species' amphidromous nature.

Bases to inform a genetic line of whiteleg shrimp Penaeus (Litopenaeus) vannamei of Mexican origin

The whiteleg shrimp Penaeus (Litopenaeus) vannamei is one of the most relevant aquaculture species in Latin America and globally. Among several elements, the improvement of its production depends on the larval genetic quality produced in commercial hatcheries. A strategy for achievement is setting up a long-term management plan that includes the genetic settlement of a breeding population with broad genetic variability and reduced inbreeding levels and the design of adequate management and crossbreeding schemes. The settlement of the breeding population requires a detailed characterization of the genetic composition and diversity of the breeding line(s) that are being managed. The present study evaluated the genetic composition of six wild populations from the southern and northern coasts of the Mexican Pacific (Oaxaca, Guerrero, Nayarit, and Sinaloa) and 56 breeding lots maintained in commercial hatcheries. The genetic profiles of a low-density SNP marker panel (171 and 152 loci for the wild and hatchery-reared groups, respectively) were used to estimate genetic diversity and differentiation within and among samples. The wild population presented significant genetic differences between southern and northern Pacific locations. Although these populations showed higher diversity levels than the cultivated stocks, the genetic pool of the total 56 lots was highly variable with low inbreeding levels. The genetic characteristics of the analyzed populations and cultivated stocks warrant the constitution of a Mexican-origin breeding line with future potential for selection to the environmental conditions of the northwestern region of Mexico.

Genomic structure analysis and construction of DNA fingerprint for four sheep populations

The Yongdeng Qishan sheep (QS) is a sheep population found locally in China. To gain in-depth knowledge of its population characteristics, three control groups were chosen, comprising the Lanzhou fat-tailed sheep (LFT), TAN sheep (TAN), and Minxian black fur sheep (MBF), inhabiting the nearby environments. This study genotyped a total of 120 individuals from four sheep populations: QS, LFT, TAN, and MBF. Using Specific-Locus Amplified Fragment Sequencing, we conducted genetic diversity, population structure, and selective sweep analysis, and constructed the fingerprint of each population. In total, there were 782 535 single nucleotide polymorphism (SNP) variations identified, with most being situated within regions that are intergenic or intronic. The genetic diversity analysis revealed that the QS population exhibited lower genetic diversity compared to the other three populations. Consistent results were obtained from the principal component, phylogenetic tree, and population structure analysis, indicating significant genetic differences between QS and the other three populations. However, a certain degree of differentiation was observed within the QS population. The linkage disequilibrium (LD) patterns among the four populations showed clear distinctions, with the QS group demonstrating the most rapid LD decline. Kinship analysis supported the findings of population structure, dividing the 90 QS individuals into two subgroups consisting of 23 and 67 individuals. Selective sweep analysis identified a range of genes associated with reproduction, immunity, and adaptation to high-altitude hypoxia. These genes hold potential as candidate genes for marker-assisted selection breeding. Additionally, a total of 86 523 runs of homozygosity (ROHs) were detected, showing non-uniform distribution across chromosomes, with chromosome 1 having the highest coverage percentage and chromosome 26 the lowest. In the high-frequency ROH islands, 79 candidate genes were associated with biological processes such as reproduction and fat digestion and absorption. Furthermore, a DNA fingerprint was constructed for the four populations using 349 highly polymorphic SNPs. In summary, our research delves into the genetic diversity and population structure of QS population. The construction of DNA fingerprint profiles for each population can provide valuable references for the identification of sheep breeds both domestically and internationally.

Whole-Genome Scanning for Selection Signatures Reveals Candidate Genes Associated with Growth and Tail Length in Sheep.

Compared to Chinese indigenous sheep, Western sheep have rapid growth rate, larger physique, and higher meat yield. These excellent Western sheep were introduced into China for crossbreeding to expedite the enhancement of production performance and mutton quality in local breeds. Here, we investigated population genetic structure and genome-wide selection signatures among the Chinese indigenous sheep and the introduced sheep based on whole-genome resequencing data. The PCA, N-J tree and ADMIXTURE results showed significant genetic difference between Chinese indigenous sheep and introduced sheep. The nucleotide diversity (π) and linkage disequilibrium (LD) decay results indicated that the genomic diversity of introduced breeds were lower. Then, Fst & π ratio, XP-EHH, and de-correlated composite of multiple signals (DCMS) methods were used to detect the selection signals. The results showed that we identified important candidate genes related to growth rate and body size in the introduced breeds. Selected genes with stronger selection signatures are associated with growth rate (CRADD), embryonic development (BVES, LIN28B, and WNT11), body size (HMGA2, MSRB3, and PTCH1), muscle development and fat metabolism (MSTN, PDE3A, LGALS12, GGPS1, and SAR1B), wool color (ASIP), and hair development (KRT71, KRT74, and IRF2BP2). Thus, these genes have the potential to serve as candidate genes for enhancing the growth traits of Chinese indigenous sheep. We also identified tail-length trait-related candidate genes (HOXB13, LIN28A, PAX3, and VEGFA) in Chinese long-tailed breeds. Among these genes, HOXB13 is the main candidate gene for sheep tail length phenotype. LIN28A, PAX3, and VEGFA are related to embryonic development and angiogenesis, so these genes may be candidate genes for sheep tail type traits. This study will serve as a foundation for further genetic improvement of Chinese indigenous sheep and as a reference for studies related to growth and development of sheep.