Genome-wide Single Nucleotide Polymorphism Research Articles

Host-Shift Speciation Proceeded with Gene Flow in Algae Covering Shells.

AbstractHost shifts represent the advancement of a novel niche and often lead to speciation in symbionts. However, its mechanisms are not well understood. Here, we focused on the alga Pseudocladophora conchopheria growing on the shells of intertidal snails. Previous surveys have shown that the alga has host specificity-only attaching to the shell of Lunella correensis-but we discovered that the alga attaches to the shells of multiple sympatric snails. A genome-wide single-nucleotide polymorphism analysis (MIG-seq) was performed to determine whether host-associated speciation occurred in the algae. As a result, there was no gene flow or limited gene flow among the algae from different hosts, and some algae were genetically differentiated among hosts. In addition, the demographic estimate revealed that speciation with gene flow occurred between the algae from different hosts. Therefore, these results support the idea that host-shift speciation gradually proceeded with gene flow in the algae, providing insight into the early evolution of host shifts.

Angular limb deformity associated with TSPAN18, NRG3 and NOVA2 in Rambouillet rams

Angular limb deformity (ALD) affects many species of livestock and companion animals. The mechanisms of ALD development are not well understood, but previous research suggests the involvement of genetic risk factors. A case-control genome-wide association study (GWAS) was conducted with 40 ALD-affected and 302 unaffected Rambouillet rams and 40,945 single nucleotide polymorphisms (SNPs). Forelimbs of 6 ALD-affected rams were examined and diagnosed with osteochondrosis. Genome-wide or chromosome-wide significant SNPs were positioned exonic, intronic or within the 3′UTR of genes TSPAN18, NRG3 and NOVA2, respectively. These genes have previously described roles related to angiogenesis and osteoblast, osteoclast and chondrocyte proliferation and differentiation, which suggests the possibility for their involvement in the pathogenesis of osteochondrosis. Functional consequences of SNPs were evaluated through transcription factor binding site analysis, which predicted binding sites for transcription factors of known importance to bone growth, including SOX6, SOX9 and RUNX2. The identification of genetic risk factors for ALD may help to improve animal welfare and production in Rambouillet, a breed known to be at risk for ALD development. This study proposes genes TSPAN18, NRG3 and NOVA2 as targets for further research towards understanding the etiology of ALD in Rambouillet sheep.

Genome-wide association studies for phenological and agronomic traits in mungbean (Vigna radiata L. Wilczek).

Mungbean (Vigna radiata L. Wilczek) is one of the important warm-season food legumes, contributing substantially to nutritional security and environmental sustainability. The genetic complexity of yield-associated agronomic traits in mungbean is not well understood. To dissect the genetic basis of phenological and agronomic traits, we evaluated 153 diverse mungbean genotypes for two phenological (days to heading and days to maturity) and eight agronomic traits (leaf nitrogen status using SPAD, plant height, number of primary branches, pod length, number of pods per plant, seeds per pod, 100-seed weight, and yield per plant) under two environmental conditions. A wide array of phenotypic variability was apparent among the studied genotypes for all the studied traits. The broad sense of heritability of traits ranged from 0.31 to 0.95 and 0.21 to 0.94 at the Delhi and Ludhiana locations, respectively. A total of 55,634 genome-wide single nucleotide polymorphisms (SNPs) were obtained by the genotyping-by-sequencing method, of which 15,926 SNPs were retained for genome-wide association studies (GWAS). GWAS with Bayesian information and linkage-disequilibrium iteratively nested keyway (BLINK) model identified 50 SNPs significantly associated with phenological and agronomic traits. In total, 12 SNPs were found to be significantly associated with phenological traits across environments, explaining 7%-18.5% of phenotypic variability, and 38 SNPs were significantly associated with agronomic traits, explaining 4.7%-27.6% of the phenotypic variability. The maximum number of SNPs (15) were located on chromosome 1, followed by seven SNPs each on chromosomes 2 and 8. The BLAST search identified 19 putative candidate genes that were involved in light signaling, nitrogen responses, phosphorus (P) transport and remobilization, photosynthesis, respiration, metabolic pathways, and regulating growth and development. Digital expression analysis of 19 genes revealed significantly higher expression of 12 genes, viz. VRADI01G08170, VRADI11G09170, VRADI02G00450, VRADI01G00700, VRADI07G14240, VRADI03G06030, VRADI02G14230, VRADI08G01540, VRADI09G02590, VRADI08G00110, VRADI02G14240, and VRADI02G00430 in the roots, cotyledons, seeds, leaves, shoot apical meristems, and flowers. The identified SNPs and putative candidate genes provide valuable genetic information for fostering genomic studies and marker-assisted breeding programs that improve yield and agronomic traits in mungbean.

Genomic prediction with machine learning in sugarcane, a complex highly polyploid clonally propagated crop with substantial non-additive variation for key traits.

Sugarcane has a complex, highly polyploid genome with multi-species ancestry. Additive models for genomic prediction of clonal performance might not capture interactions between genes and alleles from different ploidies and ancestral species. As such, genomic prediction in sugarcane presents an interesting case for machine learning (ML) methods, which are purportedly able to deal with high levels of complexity in prediction. Here, we investigated deep learning (DL) neural networks, including multilayer networks (MLP) and convolution neural networks (CNN), and an ensemble machine learning approach, random forest (RF), for genomic prediction in sugarcane. The data set used was 2912 sugarcane clones, scored for 26,086 genome wide single nucleotide polymorphism markers, with final assessment trial data for total cane harvested (TCH), commercial cane sugar (CCS), and fiber content (Fiber). The clones in the latest trial (2017) were used as a validation set. We compared prediction accuracy of these methods to genomic best linear unbiased prediction (GBLUP) extended to include dominance and epistatic effects. The prediction accuracies from GBLUP models were up to 0.37 for TCH, 0.43 for CCS, and 0.48 for Fiber, while the optimized ML models had prediction accuracies of 0.35 for TCH, 0.38 for CCS, and 0.48 for Fiber. Both RF and DL neural network models have comparable predictive ability with the additive GBLUP model but are less accurate than the extended GBLUP model.

Demographic history and conservation aspects of two relict shrubs (Daphnimorpha spp., Thymelaeaceae) showing disjunct and restricted distribution in the southern part of Japan

Climate relicts are of particular importance in evolutionary biology because of the strategies they may adopt for long-term survival despite climatic oscillations. However, because their current distribution is usually restricted and fragmented, many climatic relicts are at risk of extinction. Daphnimorpha (Thymelaeaceae) is a genus endemic to Japan that comprises two species (D. capitellata and D. kudoi) with a disjunct distribution in southern Japan. These two shrub species are endemic to a single mountain range. In this study, we conducted population genetic analyses using genome-wide single nucleotide polymorphisms obtained from multiplexed inter-simple sequence repeats genotyping by sequencing to reveal the phylogeographic history and obtain conservation implications for the two species. The results showed that these two species may have been isolated since the Tertiary period, supporting their status as climate relicts. In addition, D. kudoi showed clear genetic differentiation between the two mountains where it occurred (Mt. Nagata and Mt. Kuromi), with a decline in the effective population sizes inferred during the last glacial period. In contrast, D. capitellata showed no clear intraspecific genetic structure, and its effective population size was relatively stable. These differences could result in contrasting light tolerance between species. For conservation, we recommend managing these species as three evolutionarily significant units (ESUs): D. capitellata, D. kudoi population on Mt. Nagata, and D. kudoi population on Mt. Kuromi. Considering the limited gene flow among subpopulations and small population census, all ESUs require conservation attention to maintain or increase their effective population sizes.

Genome-wide association study of soluble solids content, flesh color, and fruit shape in citron watermelon.

Fruit quality traits are crucial determinants of consumers' willingness to purchase watermelon produce, making them major goals for breeding programs. There is limited information on the genetic underpinnings of fruit quality traits in watermelon. A total of 125 citron watermelon (Citrullus amarus) accessions were genotyped using single nucleotide polymorphisms (SNPs) molecular markers generated via whole-genome resequencing. A total of 2,126,759 genome-wide SNP markers were used to uncover marker-trait associations using single and multi-locus GWAS models. High broad-sense heritability for fruit quality traits was detected. Correlation analysis among traits revealed positive relationships, with the exception of fruit diameter and fruit shape index (ratio of fruit length to fruit diameter), which was negative. A total of 37 significant SNP markers associated with soluble solids content, flesh color, fruit length, fruit diameter, and fruit shape index traits were uncovered. These peak SNPs accounted for 2.1%-23.4% of the phenotypic variation explained showing the quantitative inheritance nature of the evaluated traits. Candidate genes relevant to fruit quality traits were uncovered on chromosomes Ca01, Ca03, Ca06, and Ca07. These significant molecular markers and candidate genes will be useful in marker-assisted breeding of fruit quality traits in watermelon.

Causal associations of gut microbiota and metabolites on sepsis: a two-sample Mendelian randomization study.

Sepsis stands as a dire medical condition, arising when the body's immune response to infection spirals into overdrive, paving the way for potential organ damage and potential mortality. With intestinal flora's known impact on sepsis but a dearth of comprehensive data, our study embarked on a two-sample Mendelian randomization analysis to probe the causal link between gut microbiota and their metabolites with severe sepsis patients who succumbed within a 28-day span. Leveraging data from Genome-wide association study (GWAS) and combining it with data from 2,076 European descendants in the Framingham Heart Study, single-nucleotide polymorphisms (SNPs) were employed as Instrumental Variables (IVs) to discern gene loci affiliated with metabolites. GWAS summary statistics for sepsis were extracted from the UK Biobank consortium. In this extensive exploration, 93 distinct genome-wide significant SNPs correlated with gut microbial metabolites and specific bacterial traits were identified for IVs construction. Notably, a substantial link between Coprococcus2 and both the incidence (OR of 0.80, 95% CI: 0.68-0.94, P=0.007) and the 28-day mortality rate (OR 0.48, 95% CI: 0.27-0.85, P=0.013) of sepsis was observed. The metabolite α-hydroxybutyrate displayed a marked association with sepsis onset (OR=1.08, 95% CI: 1.02-1.15, P=0.006) and its 28-day mortality rate (OR=1.17, 95% CI: 1.01-1.36, P=0.029). This research unveils the intricate interplay between the gut microbial consortium, especially the genus Coprococcus, and the metabolite α-hydroxybutyrate in the milieu of sepsis. The findings illuminate the pivotal role of intestinal microbiota and their metabolites in sepsis' pathogenesis, offering fresh insights for future research and hinting at novel strategies for sepsis' diagnosis, therapeutic interventions, and prognostic assessments.

Copy number variation analysis in 138 families with steroid-resistant nephrotic syndrome identifies causal homozygous deletions in PLCE1 and NPHS2 in two families.

Steroid-resistant nephrotic syndrome (SRNS) is the second most common cause of kidney failure in children and adults under the age of 20years. Previously, we were able to detect by exome sequencing (ES) a known monogenic cause of SRNS in 25-30% of affected families. However, ES falls short of detecting copy number variants (CNV). Therefore, we hypothesized that causal CNVs could be detected in a large SRNS cohort. We performed genome-wide single nucleotide polymorphism (SNP)-based CNV analysis on a cohort of 138 SRNS families, in whom we previously did not identify a genetic cause through ES. We evaluated ES and CNV data for variants in 60 known SRNS genes and in 13 genes in which variants are known to cause a phenocopy of SRNS. We applied previously published, predefined criteria for CNV evaluation. We detected a novel CNV in two genes in 2 out of 138 families (1.5%). The 9,673bp homozygous deletion in PLCE1 and the 6,790bp homozygous deletion in NPHS2 were confirmed across the breakpoints by PCR and Sanger sequencing. We confirmed that CNV analysis can identify the genetic cause in SRNS families that remained unsolved after ES. Though the rate of detected CNVs is minor, CNV analysis can be used when there are no other genetic causes identified. Causative CNVs are less common in SRNS than in other monogenic kidney diseases, such as congenital anomalies of the kidneys and urinary tract, where the detection rate was 5.3%. A higher resolution version of the Graphical abstract is available as Supplementary information.

Sandfish generations: Loss of genetic diversity due to hatchery practices in the sea cucumber Holothuria (Metriatyla) scabra

Hatcheries are indispensable for seed production of many commercial aquaculture species. However, for mass-spawning species in particular, they can be capricious environments where genetic diversity among progeny may be lost due to small effective broodstock population sizes, variable parental contributions and differential family survival. Understanding the genetic impacts of hatchery production is therefore important for addressing these problems and optimising propagation methods. We used 6051 genome-wide Single Nucleotide Polymorphisms (SNPs) to analyse genetic diversity, parental contributions and offspring kinship during a commercial-scale hatchery production run of sandfish (Holothuria scabra), a high-value sea cucumber grown in mariculture operations across the Indo-Pacific region. Broodstock contributions were highly skewed, with up to 26% of the parent pool contributing and kinship analyses determined that just two parents sired between 44.4 and 67.5% of all offspring genotyped. Effective population sizes were reduced as expected between broodstock and offspring groups (NeLD = 1121.2 vs. 19.4, respectively), while losses of allelic diversity but not overall heterozygosity were apparent. Numbers of families surviving (13–16) to the juvenile stage were low, suggesting low effective population sizes among offspring cohorts is an issue for sandfish hatchery operations. To address variability in family compositions and broodstock contributions, pedigree tracking and batch spawning may be used to optimize broodstock management and hatchery protocols, to ensure production of genetically diverse offspring for routine culture and restocking operations. As many sandfish broodstock remain wild-sourced, maintenance of healthy wild populations as reservoirs of genetic diversity is important, along with selection for spawning of genetically diverse individuals which are as distantly-related as possible.

Genome-wide association study in 404,302 individuals identifies 7 significant loci for reaction time variability

Reaction time variability (RTV), reflecting fluctuations in response time on cognitive tasks, has been proposed as an endophenotype for many neuropsychiatric disorders. There have been no large-scale genome-wide association studies (GWAS) of RTV and little is known about its genetic underpinnings. Here, we used data from the UK Biobank to conduct a GWAS of RTV in participants of white British ancestry (n = 404,302) as well as a trans-ancestry GWAS meta-analysis (n = 44,873) to assess replication. We found 161 genome-wide significant single nucleotide polymorphisms (SNPs) distributed across 7 genomic loci in our discovery GWAS. Functional annotation of the variants implicated genes involved in synaptic function and neural development. The SNP-based heritability (h2SNP) estimate for RTV was 3%. We investigated genetic correlations between RTV and selected neuropsychological traits using linkage disequilibrium score regression, and found significant correlations with several traits, including a positive correlation with mean reaction time and schizophrenia. Despite the high genetic correlation between RTV and mean reaction time, we demonstrate distinctions in the genetic underpinnings of these traits. Lastly, we assessed the predictive ability of a polygenic score (PGS) for RTV, calculated using PRSice and PRS-CS, and found that the RTV-PGS significantly predicted RTV in independent cohorts, but that the generalisability to other ancestry groups was poor. These results identify genetic underpinnings of RTV, and support the use of RTV as an endophenotype for neurological and psychiatric disorders.

Familial Mesial Temporal Lobe Epilepsy: Clinical Spectrum and Genetic Evidence for a Polygenic Architecture.

Familial mesial temporal lobe epilepsy (FMTLE) is an important focal epilepsy syndrome; its molecular genetic basis is unknown. Clinical descriptions of FMTLE vary between a mild syndrome with prominent déjà vu to a more severe phenotype with febrile seizures and hippocampal sclerosis. We aimed to refine the phenotype of FMTLE by analyzing a large cohort of patients and asked whether common risk variants for focal epilepsy and/or febrile seizures, measured by polygenic risk scores (PRS), are enriched in individuals with FMTLE. We studied 134 families with ≥ 2 first or second-degree relatives with temporal lobe epilepsy, with clear mesial ictal semiology required in at least one individual. PRS were calculated for 227 FMTLE cases, 124 unaffected relatives, and 16,077 population controls. The age of patients with FMTLE onset ranged from 2.5 to 70 years (median = 18, interquartile range = 13-28 years). The most common focal seizure symptom was déjà vu (62% of cases), followed by epigastric rising sensation (34%), and fear or anxiety (22%). The clinical spectrum included rare cases with drug-resistance and/or hippocampal sclerosis. FMTLE cases had a higher mean focal epilepsy PRS than population controls (odds ratio = 1.24, 95% confidence interval = 1.06, 1.46, p = 0.007); in contrast, no enrichment for the febrile seizure PRS was observed. FMTLE is a generally mild drug-responsive syndrome with déjà vu being the commonest symptom. In contrast to dominant monogenic focal epilepsy syndromes, our molecular data support a polygenic basis for FMTLE. Furthermore, the PRS data suggest that sub-genome-wide significant focal epilepsy genome-wide association study single nucleotide polymorphisms are important risk variants for FMTLE. ANN NEUROL 2023;94:825-835.

Causal Relationship Between Body Mass Index and Risk of Otitis Media with Effusion in Children: A Mendelian Randomization Study

BackgroundBody mass index(BMI) in children appears to be associated with Otitis media with effusion(OME) in observational studies, but the causal relationship is not clear.MethodsA two-sample Mendelian randomization (MR) study was used to explore the causal relationship between childhood BMI and OME in people of European ancestry. Genome-wide association studies (GWAS) of childhood BMI were used as exposures (n = 61,111), while GWAS of OME were used as outcomes (n = 429,290). The weighted inverse variance method (IVW) was used as a baseline method to test for causality. In addition, MR-Egger, simple mode analysis, weighted median, and weighted mode were used as complementary methods.MR-PRESSO analysis, MR-Egger intercept analysis, and Cochran’s Q statistical analysis were also used to detect possible directional heterogeneity and polymorphism. To assess this association, we used ratios (OR) with 95% confidence intervals (ci). All statistical analyses were performed in R.ResultsWe selected 22 genome-wide significant single nucleotide polymorphisms (SNPs) from GWAS as instrumental variables (IVW). the IVW approach showed evidence supporting a causal relationship between BMI and OME in children (β = 0.265, SE = 0.113, P = 0.018). MR-Egger regression showed that targeted polymorphisms were unlikely to bias the results bias (intercept=-0.022; P = 0.488), but there was no causal relationship between BMI and OME (β = 0.584, SE = 0.465, P = 0.224). Although the results of the IVW and MR Egger analyses were not consistent, the IVW analysis maintained higher precision, and the Cochran Q test, heterogeneity and polymorphism tests showed no heterogeneity, no directionality and no polymorphism.ConclusionsMR studies suggest that genetically predicted body mass index in childhood is associated with an increased risk of OME. Notably, given the limitations of this study, the mechanism of association between body mass index and OME in childhood needs further investigation. These results support the importance of effective management of obesity, which may reduce OME occurrence and decrease OME recurrence.

Improvement of triterpenoid production in mycelia of Antrodia camphorata through mutagenesis breeding and amelioration of CCl4-induced liver injury in mice

Due to the scarcity of wild fruiting bodies, submerged fermentation of the medicinal fungus Antrodia camphorata is attracting much attention, but the production of bioactive triterpenoids is low. Therefore, there is an urgent need to improve the triterpenoid yield of submerged fermentation. Here, the A. camphorata mutant E3-64 was generated from strain AC16101 through random mutagenesis breeding, producing 172.8 mg triterpenoid per gram of dry mycelia. Further optimization of culture parameters resulted in a yield of 255.5 mg/g dry mycelia (i.e., an additional >1.4-fold increase), which is the highest reported yield thus far. Notably, mutant E3-64 produced 94% and 178% more of the triterpenoid components antcin A and antcamphin A, respectively, while it produced 52% and 15% less antcin B and G, respectively. Mutant E3-64 showed increased expression of key genes involved in triterpenoid biosynthesis, as well as different genome-wide single-nucleotide polymorphisms as compared with AC16101. Triterpenoids of the E3-64 mycelia exhibited remarkably protective activity against acute CCl4-induced liver injury in mice. This study shows the potential of A. camphorata for scientific research and commercial application.

CSF metabolites associated with biomarkers of Alzheimer's disease pathology.

Metabolomics technology facilitates studying associations between small molecules and disease processes. Correlating metabolites in cerebrospinal fluid (CSF) with Alzheimer's disease (AD) CSF biomarkers may elucidate additional changes that are associated with early AD pathology and enhance our knowledge of the disease. The relative abundance of untargeted metabolites was assessed in 161 individuals from the Wisconsin Registry for Alzheimer's Prevention. A metabolome-wide association study (MWAS) was conducted between 269 CSF metabolites and protein biomarkers reflecting brain amyloidosis, tau pathology, neuronal and synaptic degeneration, and astrocyte or microglial activation and neuroinflammation. Linear mixed-effects regression analyses were performed with random intercepts for sample relatedness and repeated measurements and fixed effects for age, sex, and years of education. The metabolome-wide significance was determined by a false discovery rate threshold of 0.05. The significant metabolites were replicated in 154 independent individuals from then Wisconsin Alzheimer's Disease Research Center. Mendelian randomization was performed using genome-wide significant single nucleotide polymorphisms from a CSF metabolites genome-wide association study. Metabolome-wide association study results showed several significantly associated metabolites for all the biomarkers except Aβ42/40 and IL-6. Genetic variants associated with metabolites and Mendelian randomization analysis provided evidence for a causal association of metabolites for soluble triggering receptor expressed on myeloid cells 2 (sTREM2), amyloid β (Aβ40), α-synuclein, total tau, phosphorylated tau, and neurogranin, for example, palmitoyl sphingomyelin (d18:1/16:0) for sTREM2, and erythritol for Aβ40 and α-synuclein. This study provides evidence that CSF metabolites are associated with AD-related pathology, and many of these associations may be causal.

Genetic characterisation of the Connemara pony and the Warmblood horse using a within-breed clustering approach

BackgroundThe Connemara pony (CP) is an Irish breed that has experienced varied selection by breeders over the last fifty years, with objectives ranging from the traditional hardy pony to an agile athlete. We compared these ponies with well-studied Warmblood (WB) horses, which are also selectively bred for athletic performance but with a much larger census population. Using genome-wide single nucleotide polymorphism (SNP) and whole-genome sequencing data from 116 WB (94 UK WB and 22 European WB) and 36 CP (33 UK CP and 3 US CP), we studied the genomic diversity, inbreeding and population structure of these breeds.ResultsThe k-means clustering approach divided both the CP and WB populations into four genetic groups, among which the CP genetic group 1 (C1) associated with non-registered CP, C4 with US CP, WB genetic group 1 (W1) with Holsteiners, and W3 with Anglo European and British WB. Maximum and mean linkage disequilibrium (LD) varied significantly between the two breeds (mean from 0.077 to 0.130 for CP and from 0.016 to 0.370 for WB), but the rate of LD decay was generally slower in CP than WB. The LD block size distribution peaked at 225 kb for all genetic groups, with most of the LD blocks not exceeding 1 Mb. The top 0.5% harmonic mean pairwise fixation index (FST) values identified ontology terms related to cancer risk when the four CP genetic groups were compared. The four CP genetic groups were less inbred than the WB genetic groups, but C2, C3 and C4 had a lower proportion of shorter runs of homozygosity (ROH) (74 to 76% < 4 Mb) than the four WB genetic groups (80 to 85% < 4 Mb), indicating more recent inbreeding. The CP and WB genetic groups had a similar ratio of effective number of breeders (Neb) to effective population size (Ne).ConclusionsDistinct genetic groups of individuals were revealed within each breed, and in WB these genetic groups reflected population substructure better than studbook or country of origin. Ontology terms associated with immune and inflammatory responses were identified from the signatures of selection between CP genetic groups, and while CP were less inbred than WB, the evidence pointed to a greater degree of recent inbreeding. The ratio of Neb to Ne was similar in CP and WB, indicating the influence of popular sires is similar in CP and WB.

From chip to SNP: Rapid development and evaluation of a targeted capture genotyping-by-sequencing approach to support research and management of a plaguing rodent.

The management of invasive species has been greatly enhanced by population genetic analyses of multilocus single-nucleotide polymorphism (SNP) datasets that provide critical information regarding pest population structure, invasion pathways, and reproductive biology. For many applications there is a need for protocols that offer rapid, robust and efficient genotyping on the order of hundreds to thousands of SNPs, that can be tailored to specific study populations and that are scalable for long-term monitoring schemes. Despite its status as a model laboratory species, there are few existing resources for studying wild populations of house mice (Mus musculus spp.) that strike this balance between data density and laboratory efficiency. Here we evaluate the utility of a custom targeted capture genotyping-by-sequencing approach to support research on plaguing house mouse populations in Australia. This approach utilizes 3,651 hybridization capture probes targeting genome-wide SNPs identified from a sample of mice collected in grain-producing regions of southeastern Australia genotyped using a commercially available microarray platform. To assess performance of the custom panel, we genotyped wild caught mice (N = 320) from two adjoining farms and demonstrate the ability to correctly assign individuals to source populations with high confidence (mean >95%), as well as robust kinship inference within sites. We discuss these results in the context of proposed applications for future genetic monitoring of house mice in Australia.

Integrated statolith and genomic analysis reveals high connectivity in the nektonic squid Illex argentinus: implications for management of an international cephalopod fishery

Abstract The neritic-oceanic squid Illex argentinus supports one of the largest fisheries in the Southwest Atlantic. It is characterized by extensive migrations across the Patagonian Shelf and complex population structure comprising distinct seasonal spawning groups. To address uncertainty as to the demographic independence of these groups that may compromise sustainable management, a multidisciplinary approach was applied integrating statolith ageing with genome-wide single-nucleotide polymorphism (SNP) analysis. To obtain complete coverage of the spawning groups, sampling was carried out at multiple times during the 2020 fishing season and covered a large proportion of the species’ range across the Patagonian Shelf. Statolith and microstructure analysis revealed three distinct seasonal spawning groups of winter-, spring-, and summer-hatched individuals. Subgroups were identified within each seasonal group, with statolith microstructure indicating differences in environmental conditions during ontogeny. Analysis of &amp;gt;10 000 SNPs reported no evidence of neutral or non-neutral genetic structure among the various groups. These findings indicate that I. argentinus across the Patagonian Shelf belong to one genetic population and a collaborative management strategy involving international stakeholders is required. The connectivity among spawning groups may represent a “bet-hedging” mechanism important for population resilience.

Rapid sperm length divergence in a polygynandrous passerine: a mechanism of cryptic speciation?

When populations become geographically isolated, they begin to diverge in various traits and at variable rates. The dynamics of such trait divergences are relevant for understanding evolutionary processes such as local adaptation and speciation. Here we examine divergences in sperm and body structures in a polygynandrous songbird, the alpine accentor (Prunella collaris) between two allopatric high-altitude populations, in Morocco and Spain. The populations diverged around 82,000 years ago, as estimated with a coalescence-based phylogenetic analysis of genome-wide single-nucleotide polymorphisms. We found that birds in the two areas had nonoverlapping sperm lengths, which suggests adaptation to divergent female reproductive tract environments. Sperm length also showed an exceptionally low coefficient of among-male variation, a signal of strong stabilizing selection imposed by sperm competition. The evolutionary rate of sperm length was almost twice the rates for the most divergent morphological traits and more than three times higher than expected from literature data over a similar generational timescale. This rapid evolution of a key reproductive trait has implications for reproductive isolation and ultimately for speciation. Strong selection for different sperm length optima in allopatry predicts conspecific sperm precedence and disruptive selection in sympatry, hence a possible postcopulatory prezygotic barrier to gene flow.

Construction of a High-Density Genetic Linkage Map Based on Bin Markers and Mapping of QTLs Associated with Fruit Size in Jujube (Ziziphus jujuba Mill.)

Jujube (Ziziphus jujuba Mill.) is a fruit tree that is gaining increasing importance in drought-affected regions worldwide. The fruit size is an important quantitative agronomic trait that affects not only the fruit yield and attractiveness but also consumer preference. Genetic enhancement of fruit appearance is a fundamental goal of jujube breeding programs. The genetic control of jujube fruit size traits is highly quantitative, and development of high-density genetic maps can facilitate fine mapping of quantitative trait loci (QTLs) and gene identification. However, studies regarding the construction of high-density molecular linkage maps and identification of quantitative trait loci (QTLs) targeting fruit size in jujube are limited. In this study, we performed whole-genome resequencing of the jujube cultivars “JMS2” and “Xing16” and their 165 F1 progenies to identify genome-wide single-nucleotide polymorphism (SNP) markers and constructed a high-density bin map of jujube that can be used to assist in the selection of multiple traits in jujube breeding. This analysis yielded a total of 116,312 SNPs and a genetic bin map of 2398 bin markers spanning 1074.33 cM with an average adjacent interval of 0.45 cM. A quantitative genetic analysis identified 15 QTLs related to fruit size and the observed phenotypic variation associated with a single QTL ranged from 9.5 to 13.3%. Through the screening of overlapping and stable QTL regions, we identified 113 candidate genes related to fruit size. These genes were ascertained to be involved in cell division, cell wall metabolism, synthesis of phytohormones (ABA, IAA, and auxin), and encoding of enzymes and transcription factors. These candidate genomic regions will facilitate marker-assisted breeding of fruits with different sizes and shapes and lay a foundation for future breeding and manipulation of fruit size and shape in jujube.

Genetic differentiation and evolution of broad-leaved evergreen shrub and tree varieties of Daphniphyllum macropodum (Daphniphyllaceae).

Tree form evolution is an important ecological specialization for woody species, but its evolutionary process with adaptation is poorly understood, especially on the microevolutionary scale. Daphniphyllum macropodum comprises two varieties: a tree variety growing in a warm temperate climate with light snowfall and a shrub variety growing in a cool temperate climate with heavy snowfall in Japan. Chloroplast DNA variations and genome-wide single-nucleotide polymorphisms across D. macropodum populations and D. teijsmannii as an outgroup were used to reveal the evolutionary process of the shrub variety. Population genetic analysis indicated that the two varieties diverged but were weakly differentiated. Approximate Bayesian computation analysis supported a scenario that assumed migration between the tree variety and the southern populations of the shrub variety. We found migration between the two varieties where the distributions of the two varieties are in contact, and it is concordant with higher tree height in the southern populations of the shrub variety than the northern populations. The genetic divergence between the two varieties was associated with snowfall. The heavy snowfall climate is considered to have developed since the middle Quaternary in this region. The estimated divergence time between the two varieties suggests that the evolution of the two varieties may be concordant with such paleoclimatic change.