Land-use changes in West Africa are threatening wildlife viability, yet their impacts on species' genetic diversity and connectivity remain poorly understood. We investigated the environmental drivers of genetic diversity and functional connectivity in the Near Threatened Guinea baboon (Papio papio) by genotyping 243 non-invasively collected faecal samples across its range and applying a landscape genetics framework. We identified distinct genetic clusters, with Gambian populations exhibiting the lowest genetic diversity and highest inbreeding. Genetic diversity was positively associated with shrublands and forest-savannah mosaics, highlighting the importance of these habitats for maintaining viable populations. Rivers, grasslands, and shrublands facilitate functional connectivity and act as dispersal corridors, whereas large waterbodies and intensive croplands serve as strong barriers. Notably, habitats constituted by mosaics of forest and croplands provide more permeable barriers to movement than strict monocultures. Our results suggest that intensive agricultural land use can reduce functional connectivity, whereas heterogeneous natural habitats and riverine networks sustain it. To ensure the long-term survival of Guinea baboons, conservation strategies must prioritize preserving riverine corridors and habitat heterogeneity. Furthermore, replacing monoculture farming with agroecological practices like agroforestry is crucial to support landscape connectivity and mitigate the adverse effects of agricultural expansion.

Drought is a major abiotic constraint on sugarcane production, but systematic multitrait evaluation of drought tolerance remains limited in genetically complex advanced backcross progenies derived from sugarcane × Tripidium arundinaceum. In this study, 100 genotypes, including 93 BC4F1 or BC5F1 progenies and seven parental or control genotypes, were evaluated under a 20 d progressive drought treatment in pots at the seven-leaf stage. Sixteen traits related to root architecture, leaf water status, gas exchange, PSII photochemistry, antioxidant activity, and lipid peroxidation were measured. Drought significantly reduced TRL, RSA, RV, RWC, Pn, Gs, Tr, ΦPSII, and ETR and significantly increased SOD activity and MDA content. Twelve traits with relatively clear and biologically interpretable relationships with drought tolerance were integrated using membership functions and trait weights to calculate an integrated D value. D values ranged from 0.078 to 0.516, and 19, 45, and 36 genotypes were classified into groups with relatively high, moderate, and low drought tolerance within this germplasm collection, respectively. Genotypes 55-109, YCE07-65, 55-43, 211-172, and 91-74 had the highest integrated D values. Within the integrated evaluation framework, higher D values were most strongly associated with RSA, RV, TRL, Pn, ΦPSII, and ETR, while PC1 was strongly correlated with the D value (r = 0.893). Maintenance of root growth and photosynthetic function therefore represented major phenotypic features associated with overall drought tolerance under the present experimental conditions. These features may provide useful criteria for screening drought-tolerant germplasm, but their utility requires validation in independent drought experiments and field environments.

This study aimed to characterize the genomic diversity, population structure, and candidate regions consistent with selection in Hamdani (HAM) sheep using high-density SNP generated by double-digest restriction site-associated DNA sequencing (ddRADseq). A total of 20 animals were sampled, and after quality filtering, 310,663 SNPs from 18 individuals were retained for downstream analyses. Genetic diversity parameters indicated a relatively high level of genomic variation within the breed (HO = 0.323 ± 0.01 and HE = 0.326 ± 0.01) and low levels of inbreeding (FHOM = 0.029 ± 0.02 and FROH = 0.008 ± 0.01), suggesting that the population has maintained substantial genetic diversity and has not experienced recent intensive inbreeding. Population structure analyses revealed that HAM sheep form a distinct genetic cluster separated from Turkish fat-tailed breeds, reflecting their unique genetic background and breeding history. Footprints of selection analyses based on runs of homozygosity (ROH) and integrated haplotype score (iHS) identified preliminary candidate genomic regions consistent with selection. After FDR correction, 12 of the 34 trait-chromosome combinations tested for the iHS-derived regions and three of the eight combinations tested for the ROH-derived regions were significantly enriched. Functional annotation highlighted biologically relevant candidate genes involved in reproductive performance (TSHR, FSHR, and LHCGR), lipid metabolism (ABCG1 and LPIN1), and environmental adaptation (LACC1 and MBOAT7). This ddRADseq-based genome-wide characterization provides preliminary information on genetic variability and candidate genomic regions consistent with selection in HAM sheep. Therefore, further studies focusing on a larger sampling strategy across multiple different sheep breeds are needed to design conservation, breeding, and future genomic selection programs.

For over 100 years, biologists have been fascinated with coevolution between mutualistic partners such as plants and their pollinators.[1][,][2][,][3][,][4][,][5] Due to the dissipating effects of species being entangled into networks of interacting species,[6][,][7][,][8] however, demonstrating reciprocal selective forces can be difficult except for strongly interdependent pairs of species.[9][,][10] Furthermore, temporal fluctuations in environmental disturbance or simple ecological shifts may result in partner swapping,[11] so that seemingly matching and coadapted species pairs may in fact have interacted only over short time frames. Here, we adopted a genomic approach[12][,][13] to scrutinize the history of the highly sex-specific and specialized mutualistic association between the purple-throated carib (Eulampis jugularis) hummingbird and its two Heliconia nectar-food plants on Dominica.[14][,][15][,][16][,][17][,][18][,][19] Notably, we investigate whether long-term coadaptation is reflected in aligned genomic signatures as linked plant and hummingbird population trajectories over evolutionary time frames. As hypothesized, our analyses indicate synchronized population size fluctuations across the three mutualistic partners, which is consistent with long-term ecological interdependence and coadaptation over millions of years. Additionally, we find evidence for the hypothesis that genetic diversity and level of inbreeding of the two plant species mirror their ecological histories with hummingbird partners: territorial purple-throated carib males promote inbreeding and low genetic diversity in H. caribaea, whereas wide-ranging, traplining females pollinate H. bihai, resulting in less inbred, more genetically diverse plants. This genomic evidence demonstrates that specialized mutualisms can leave aligned evolutionary signatures, thus highlighting the power of integrating comparative genomics with ecological context to assess the long-term persistence and consequences of species interactions across evolutionary timescales.

Early-maturing maize is vital for strengthening food security across the drought-prone agro-ecologies of Sub-Saharan Africa (SSA). Advancing genetic gain in these environments requires a clear understanding of genetic diversity and population structure patterns to support parental selection and future genomic-assisted breeding efforts. The study aimed at assessing genetic diversity and population structure of a panel of early-maturing yellow and orange kernel maize inbred lines, classify the inbred lines into putative heterotic groups, and identify a core set of elite, genetically divergent lines suitable for use in hybrid breeding and long-term genetic improvement. A panel of 376 elite early-maturing yellow and orange maize inbred lines from four source populations were genotyped using the DArTag SNP markers. After quality filtering, 1,954 high-quality SNP markers retained exhibited moderate diversity with an average polymorphic information content (PIC) of 0.38 and minor allele frequency (MAF) of 0.28. Linkage disequilibrium analysis showed a mean r2 of 0.046, with rapid LD decay across the genome, indicating substantial historical recombination and suggesting potential utility of the panel for future association studies. The Admixture analysis and discriminant analysis of principal components (DAPC) consistently resolved the panel into two major subpopulations with overlapping membership. Phylogenetic clustering also resolved the panel into two broad molecular clusters corresponding to putative heterotic groups. Analysis of molecular variance (AMOVA) revealed that most genetic variation occurred within groups (86%), with moderate differentiation among groups (14%). A core set representing 20% of the collection was identified using an allelic-richness-based greedy algorithm, offering valuable insights to accelerate breakthrough hybrid development for SSA farming systems. The study provides a comprehensive genomic characterization of early-maturing maize germplasm, providing genomic insights that may support future hybrid development and germplasm management efforts for SSA maize breeding programs.

Chili peppers (Capsicum spp.) are among the most widely cultivated horticultural crops worldwide due to the high demand for their pungent fruits. Despite Colombia's high diversity of Capsicum species and varieties, its genetic resources remain underrepresented in international markets and scientific studies. This study aims to characterize the genetic diversity and population structure of Capsicum accessions from southwestern Colombia. Accessions were collected through field surveys in local markets and protected natural areas and genotyped using DArTseq platform. A total of 69 accessions representing seven species were genotyped using 3681 high quality DArT-SNP markers. Standard genetic diversity metrics and population structure analyses were performed. The analysis revealed low observed heterozygosity (mean 1%) and high inbreeding coefficients (FIS: 0.24). However, expected heterozygosity values indicate that these accessions still retain substantial genetic variability, highlighting their potential for breeding and genetic improvement programs. Population structure analysis revealed clear genetic differentiation between Andean and domesticated Capsicum species. Moreover, Silico-DArT markers could discriminate between wild and domesticated accessions within C. annuum and C. frutescens. This study represents the first genome wide assessments of Andean Capsicum species using DArTseq genotyping. These findings contribute to the understanding and conservation of Capsicum genetic resources of Southwestern Colombian and provide valuable information for future breeding programs.

Charcot-Marie-Tooth (CMT) is a group of inherited neuromuscular disorders with diverse clinical features such as muscle weakness and atrophy of the distal regions, foot deformities, sensory loss and decreased or absent reflexes. With the diverse inheritance patterns including dominant, recessive, and X-linked, it exhibits significant genetic heterogeneity often overlapping with other neurological disorders. Whole exome sequencing (WES) has emerged as favorable diagnostic tool for such challenging disease entities. We recruited five Pakistani families that consisted of 14 affected individuals exhibiting representative symptoms of CMT such as severe muscle weakness of the lower limbs, muscles atrophy, claw hands and feet deformities. WES data analysis revealed two novel and two already reported homozygous missense variants in GDAP1 (NM_018972) c.1A > G (p. Met1Val), c.683A > G (p. Glu228Gly), c.734C > T (p. Thr245Ile) and c.811G > A (p. Gly271Arg) in families A-D, respectively. While a novel homozygous SBF2 variant c.2746G > C, p. (Gly916Arg) was identified in family E. Sanger sequencing confirm the segregation of all candidate variants in their respective pedigrees. Moreover, molecular modeling supports the destabilizing effect of these variants on final protein product of both GDAP1 and SBF2 by inducing modifications in overall conformation of the protein. The present study expands the mutation spectrum of the GDAP1 and SBF2 genes, with possible implications for improved understanding of disease pathophysiology. Furthermore, the current study highlights the importance of NGS, particularly WES, in achieving rapid and precise molecular genetic diagnosis for clinical purposes, especially in neuromuscular disorders of heterogeneous nature.

The Guinan toad-headed lizard, Phrynocephalus guinanensis, is a small reptilian species restricted only to the Mugetan Desert on the northeastern corner of the Qinghai-Xizang Plateau. This species faces endangerment due to its extremely narrow distribution range, combined with progressively increasing human activities recently. However, a conservation genomic assessment of P. guinanensis remains uninvestigated, thus resulting in a limited understanding of the genetic diversity of this species. Here, we assembled a high-quality reference genome for P. guinanensis using HiFi sequencing technology and conducted a comprehensive assessment of its population genetic diversity by integrating data from 191 individuals across 14 populations. The updated genome size was 1.84 Gb with a scaffold N50 of 133.2 Mb, and 21 884 coding genes were annotated. The lower genetic diversity (meanπ = 1.0253 × 10[-3], meanheterozygosity = 8.8150 × 10[-4]), higher inbreeding levels (meanF ROH = 0.0778), and an elevated mutation load (meanMissense = 0.5660, meanLOF = 0.5689) were detected in P. guinanensis. Based on the demographic simulation, this species has experienced a significant decrease in effective population size. Our results indicated that P. guinanensis is undergoing severe genetic erosion, which may compromise its adaptive potential and increase its extinction risk. We therefore propose prioritizing genetically diverse populations as a source for captive breeding and long-term field monitoring to ensure the viability of P. guinanensis. Our study enriches the understanding of the Guinan toad-headed lizard's genetic diversity, providing useful genomic resources for conservation strategies on this species.

Land-use change driven by agricultural intensification is a major contributor to insect declines globally. As a result of population decline and subdivision, species lose genetic diversity, reducing adaptive potential and increasing genetic load. We examine how genetic diversity has changed over the past century in three focal and five additional Polyommatinae butterfly species in Sweden by sequencing specimens from museum collections. Based on 59 historical and 90 contemporary genomes, we document a 6% decline in heterozygosity in the grassland specialist Cyaniris semiargus, driven by division into small, isolated populations. In contrast, generalist Polyommatus icarus and heathland specialist Plebejus argus have maintained genetic diversity and connectivity. Reduced heterozygosity in Cy. semiargus reflects increases in runs of homozygosity, increasing the homozygosity of derived mutations at missense and conserved positions. While genomic erosion is currently relatively mild, it is expected to lag demographic change. We infer that demographic decline in Cy. semiargus is considerably larger than declines in genetic diversity to date. We use simulations to demonstrate that only mild losses of genetic diversity are expected at the early stages of demographic decline, leaving populations with substantial genetic extinction debt. We detect similar reductions in genetic diversity in two of five additional species, underscoring the need for restoring habitat connectivity and gene flow to limit further genomic erosion in specialist grassland insects. This study illustrates how incorporation of genetic monitoring into conservation planning can identify where demographic decline has left populations with a genetic extinction debt even after they stabilize.

Covariances between relatives, between traits evaluated in the same environment, and between the values for the same trait in different environments have long been exploited in plant and animal breeding. An assumption underlying these covariances is that individuals belong to a single population or that populations have homogeneous covariances. This assumption is routinely violated, yet a framework for defining and estimating the covariance between populations is lacking. Our objective was to develop and validate a framework for estimating the genetic covariance between plant biparental populations via their molecular marker effects. We derived an analytical method to estimate variances and covariances between such populations, then validated it in simulated datasets and in a maize (Zea mays L.) dataset from a commercial breeding program. The simulated populations confirmed the method's expected behavior, whereas the maize dataset showed trait- and population-specific patterns in (co)variance. Our method requires the following inputs that can all be estimated or approximated: marker effects for each population; a linkage map; linkage phase information; and the inbreeding coefficient of the populations. The covariance between populations has potential applications not only in genomewide prediction, but also in non-breeding fields such as ecology and domestication.

Wheat production faces severe yield threats globally and regionally in India from rust diseases caused by Puccinia species. Genetic resistance breeding is the most sustainable approach to mitigate these losses, but traditional phenotypic selection is often constrained by environmental fluctuations and rapid pathogen evolution. Here we utilized marker-assisted backcross breeding (MABB) to introgress broad-spectrum yellow rust resistance genes, Yr10 and Yr15, from the donor genetic stock PBW703 into the elite, high-yielding wheat cultivar DBW88 to develop two high-yielding rust-resistant genotypes DBW476 and DBW477. Foreground selection was executed using gene-linked molecular markers PSP3000 (Yr10) and Xbarc8 (Yr15). Background selection with 107 polymorphic simple sequence repeat (SSR) markers accelerated recurrent parent genome recovery up to 95% within just two backcross generations, significantly outperforming conventional breeding timelines. Seedling resistance tests and adult plant resistance evaluations confirmed that the introgressed lines exhibited a high degree of immune response and comprehensive resistance against virulent Puccinia striiformis pathotypes, including 238S119 and 110S119. Multi-year agronomic testing across multiple environments demonstrated that the improved near-isogenic lines achieved equal or superior grain yield performance compared to their recurrent parents and commercial checks. These findings indicate successful gene introgression without any associated linkage drag or yield penalties. These advanced, stable lines were nominated for multi-location varietal trials, presenting a strategically superior asset for sustainable rust management and food security in the rust-prone environments of India.

Thoroughbreds are maintained under a closed studbook and have undergone intense selection for racing performance, potentially reducing genetic diversity and increasing inbreeding. As inbreeding can adversely affect fitness, monitoring inbreeding levels and conserving genetic diversity are essential. In this study, we assessed the temporal changes in genomic diversity and genomic inbreeding in Japanese Thoroughbreds using high-density single nucleotide polymorphism (SNP) genotyping. We genotyped 96 foals born in each of the years 2000, 2018, and 2022 using a 670 K Axiom Equine Genotyping Array, excluding two samples due to insufficient genotypic information. After quality control, we retained 363,301 autosomal SNPs for downstream analysis. Per-locus expected heterozygosity (mean ± standard deviation [SD]) revealed only a slight decline across the cohorts: 0.309 ± 0.156, 0.305 ± 0.158, and 0.304 ± 0.159 for 2000, 2018, and 2022, respectively, with a statistically significant but negligible effect size (η[2]=0.00019). Runs of homozygosity (ROH) covered approximately 27.5%, 28.5%, and 29.0% of the autosomal genome in the three cohorts. Genomic inbreeding, estimated from the mean ROH-based inbreeding, increased from 0.276 ± 0.021 in 2000 to 0.286 ± 0.023 and 0.290 ± 0.024 in 2018 and 2022, respectively. The per-generation increase (assuming an 11-year generation interval) was higher in 2018-2022 (1.10 percentage points/generation) than in 2000-2018 (0.611 percentage points/generation), driven mainly by increased long ROH (≥5 Mb) length. Our results indicate a modest reduction in genome-wide diversity and recently accelerated genomic inbreeding in the Japanese Thoroughbred population, supporting the need for continued SNP genotyping-based monitoring.

Inbreeding depression is a major threat to the long-term viability of small populations. Although captive breeding and genetic rescue are the main alternative in conservation, their genomic impacts are largely unknown, and the unintended effects of these approaches may intensify the depression by introducing new deleterious mutations. Based on whole-genome sequencing data from 247 critically endangered Chinese alligators, we constructed a high-resolution genetic variation map and identified three distinct genetic populations, clarifying their demographic history and further supporting the independent origin of the American population. Comparisons between captive and semi-wild populations revealed that captive management outperforms semi-wild management in reducing inbreeding and increasing genetic diversity, while simultaneously elevating the accumulation of deleterious mutations, which may result from relaxed purifying selection. Although the inbreeding coefficient in this species is notably higher than in other endangered species, purging has likely played a significant role in reducing the amount of recessive deleterious mutations. Forward-in-time simulations indicated that mixing populations can mitigate the risk of demographic decline, yet current populations still remain vulnerable to future environmental changes. These findings provide valuable genomic evidence to guide balanced and effective conservation strategies for the Chinese alligator.

Reindeer and caribou (Rangifer tarandus) play key ecological, cultural, and economical roles across Arctic and Subarctic regions. However, genome-wide patterns of genetic diversity and population structure in semi-domesticated reindeer from Norway remain insufficiently characterized. Here we generated a high-quality chromosome-level genome assembly (GCA_965153185.1) for Norwegian semi-domesticated Eurasian tundra reindeer (Rangifer tarandus tarandus). The genome spans 2.54 Gb, with a scaffold N50 of 75.6 Mb, 96.1% complete BUSCOs, and 39,855 predicted protein-coding genes. Using this reference, we performed whole-genome resequencing of 175 individuals from five reindeer populations from Norway and 28 individuals from Iceland, identifying ~19.9 million genetic variants. Genetic differentiation was low among Norwegian populations (FST = 0.005-0.011), but substantially higher between Norway and Iceland (FST = 0.140-0.161). Populations from Norway exhibited similar levels of nucleotide diversity (π = 1.39-1.62 × 10-3), whereas the Icelandic population showed reduced diversity (π = 0.99 × 10-3) and approximately half as many segregating variants. Analyses of runs of homozygosity (ROH) and genome-wide heterozygosity indicated low levels of recent inbreeding across all populations, with long ROHs (>8 Mb) being rare. Despite reduced genetic diversity, the Icelandic population showed limited evidence of recent inbreeding. These patterns are consistent with contrasting demographic histories, with gene flow maintaining diversity among populations from Norway, while founder effects combined with long-term isolation have shaped the Icelandic population.