Search Results (279)

Grain number per spike (GNS) is a key component of wheat yield, yet its genetic architecture remains incompletely understood. This study phenotyped 610 wheat accessions for GNS in four environments and genotyped them using 429,721 single nucleotide polymorphisms (SNPs). The phenotypes were associated with the SNPs using a three-variance multi-locus random-SNP-effect mixed linear model (3VmrMLM) to identify quantitative trait nucleotides (QTNs), as well as QTN-by-environment (QEI) and QTN-by-QTN (QQI) interactions. These genetic components and residual error explained approximately 18%, 31%, 28%, and 23% of the phenotypic variance, respectively. Two and one previously reported genes were found around QTNs and QEIs, respectively. Bioinformatics and haplotype analyses subsequently yielded 25 candidate genes, 22 gene-by-environment interactions (GEIs), and 24 gene-by-gene interactions (GGIs) around the QTNs, QEIs, and QQIs, respectively. Notably, TraesCS1D01G280000, the wheat homolog of OsRopGEF10, was located near a major QTN explaining over 10% of the total phenotypic variation. A gene interaction network constructed from all identified genes highlighted the central role of GGIs in GNS regulation. Environmental variation may reshape the regulatory network through GEIs. Furthermore, superior haplotypes of 12 candidate genes were identified, providing valuable targets for improving wheat yield. Overall, this study dissects the genetic architecture of GNS and offers practical resources for wheat molecular breeding. Full article

The evolutionary history and contemporary biogeography jointly shape the genetic architecture of marine species. This study investigates the phylogeny and population genetics of two closely related syngnathid fishes, Trachyrhamphus serratus and Trachyrhamphus longirostris. We report the first record of T. longirostris along the mainland coast of China, with samples collected from Yantai, Kenting, Zhanjiang, and Beihai. Population genetic analyses reveal genetic differentiation within T. longirostris, which exhibits low levels of genetic diversity across all sampled populations compared to T. serratus. The star-like haplotype network and significantly negative neutrality test values collectively indicate a recent population expansion event in T. longirostris. This study offers important insights into the evolutionary dynamics and biogeographic patterning of syngnathid fishes, with clear implications for their conservation and management. Full article

Postglacial expansion dynamics strongly influence the genetic structure of temperate species; however, mitochondrial data from the Baltic region are limited. To assess diversity, phylogenetic origins, and regional structuring, we analyzed mitochondrial cytochrome b (726 bp) and control region (421–422 bp) sequences of the common vole (Microtus arvalis Pallas, 1779) from Lithuania. Of the 91 cytb sequences and 70 control region sequences analyzed, five and four haplotypes were identified, respectively. Markedly low haplotype and nucleotide diversity compared with most European populations were detected. Phylogenetic Maximum Likelihood and network analyses revealed that all Lithuanian haplotypes belong to the eastern European lineage and are most closely related to Polish and central European samples, which supports recolonization from a Carpathian refugium. Despite the overall low variation, we detected two distinct mitochondrial groups: a highly differentiated western group and a second group encompassing eastern, northern, and central–southern populations. This strong regional structuring suggests limited maternal gene flow on a small geographic scale. There was no evidence of introgression from related taxa, such as Microtus obscurus. Our findings refine the phylogeographic context of Baltic M. arvalis and highlight the region’s role in shaping postglacial diversity patterns. Full article

Phosphorus (P) deficiency severely limits the growth and yield of crop plants, and anthocyanin accumulation is a key adaptive physiological response to low-P stress. However, the role of MYB transcription factors in regulating anthocyanin biosynthesis under P-deficient conditions and the application of favorable haplotypes in foxtail millet low-P tolerance breeding remain unclear. Here, we performed genome-wide identification of SiMYB genes, elucidated their evolutionary characteristics, and identified key members regulating anthocyanin accumulation under P deficiency to provide genetic resources and a theoretical basis for foxtail millet molecular breeding aimed at improving nutrient use efficiency. Specifically, a total of 229 SiMYB genes were identified in the foxtail millet genome and classified into three subgroups, with the R2R3-MYB subfamily accounting for 59.8%. Phylogenetic and synteny analyses across 15 plant species revealed diverse divergence times and complex relationships, with 29 R2R3-MYB genes showing conserved collinearity with rice and maize orthologs. Association analysis using 196 foxtail millet accessions showed that 38 single nucleotide polymorphisms (SNPs) from 16 SiMYB genes were significantly associated with leaf anthocyanin content under P deficiency (p < 0.001). Notably, the SiMYB169 gene exhibited differential tissue expression and was highly upregulated in the leaves of a P-tolerant genotype after 24 h of P deficiency treatment. Furthermore, accessions carrying the favorable G allele of SiMYB169 showed significantly higher anthocyanin accumulation under P deficiency (p < 0.01). Network prediction analysis found that SiMYB169 interacted with key genes and multiple transcription factors in the biosynthesis pathway of anthocyanin. These findings highlight SiMYB169 as an evolutionarily conserved regulator that modulated anthocyanin biosynthesis under P-deficient conditions. Full article

Riptortus pedestris (Hemiptera, Alydidae) is widely distributed across East Asia, where significant genetic differentiation may occur among geographic populations. To understand the genetic structure, historical dynamics, and formation of geographic distribution patterns in China, we conducted a phylogeographic analysis using three mitochondrial genes (COI, COII, Cytb) from 35 populations. After PCR amplification, we performed genetic diversity analysis, Fst/Nm estimation, phylogenetic reconstruction (ML, BI, NJ), haplotype network, AMOVA, neutrality tests, mismatch distribution, and molecular dating. Results revealed high genetic diversity (Hd > 0.81, π > 0.011), an AT-rich base composition, and faster evolution at the first codon position. Genetic and geographic distances were significantly correlated, with high Fst values indicating strong differentiation, especially between southwestern/southern and other populations. Two main clades were identified: Clade 1 (mainly southern and southwestern China) and Clade 2 (central, northern, northwestern, and northeastern China). A star-like haplotype network and neutrality tests suggested a rapid expansion around 0.019–0.022 Ma (Last Glacial Maximum), and molecular dating estimated the main split at ~0.029 Ma. AMOVA and Gst/Nst confirmed significant phylogeographic structure with most variation among populations. This study provides initial evidence for the genetic differentiation and evolutionary history of R. pedestris in China, demonstrating that its population structure was shaped by climatic changes and geographical isolation, providing key insights into its adaptive evolution and dispersal. Full article

Background: Gametophytic self-incompatibility (GSI) controlled by a multi-allelic S-locus, is inferred to have evolved before the spilt of the Rosidae and Asteridae. In Rosaceae, molecular characterisation of the genera Prunus and Malus reveals that different numbers of genes determine GSI specificity. In Prunus, one pistil-expressed (female) gene and one pollen (male) gene encode a series of stylar RNase (S-RNase) alleles and series of S-haplotype-specific F-box (SFB) alleles, respectively, thereby determining the female and male specificity. In contrast, in Malus, GSI specificity is controlled by one pistil gene and multiple pollen genes, known as SFB-brothers (SFBBs), which encode a series of S-RNase and SFBB alleles, respectively, within the S-locus, to determine female and male specificity. Despite these advances, the molecular mechanisms of these two genera remain largely unknown, and it is still uncertain how GSI originated or which factors shape the orientation, evolution, and function of the S-locus. Methods: Therefore, in this study, we applied a holistic integrative approach combining analyses of gene distribution, phylogenetic inference, biogeographic history, selective pressures, co-evolution, and protein interaction networks across three Prunus genomes (P. dulcis, P. persica, and P. avium) to elucidate the evolutionary forces driving sexual diversity and molecular specificity of GSI within the Rosaceae. Results: Our results indicated that rapid diversification of the Prunus S-locus was due to the repeated duplication events in the SFB, SLF, and S-RNase genes producing both functional and non-functional duplicates. Conclusions: In Rosaceae, diversity of S-locus mechanisms is shaped by lineage-specific selection, functional divergence, co-evolution of pistil- and pollen-expressed components, dynamic protein-interaction networks, geological history and climatic change. Full article

Isopentenyltransferase (IPT) is the rate-limiting enzyme in cytokinin biosynthesis and plays a critical role in plant acclimation to abiotic stress. To explore soybean IPT genes, we performed genome-wide identification, bioinformatics analysis, and molecular experimental validation to systematically characterize the features and functions of the soybean IPT (GmIPT) gene family. We identified 15 GmIPT genes in the soybean genome, which are unevenly distributed across 12 chromosomes; their evolutionary expansion is primarily driven by whole-genome duplication events. Phylogenetic analysis of soybean IPT proteins with those from Arabidopsis, rice and maize clustered them into four groups, exhibiting lineage-specific functional specialization. GmIPT genes exhibit significant variations in conserved motifs, gene structure, and cis-acting elements; their promoter regions are enriched in light-responsive, abiotic stress-responsive, and hormone-responsive elements, indicating their involvement in complex transcriptional regulatory networks. Tissue expression profiling revealed that GmIPT7 and GmIPT10 are highly expressed in various tissues, whereas GmIPT14 shows specific expression in flowers and the shoot apical meristem. Transcriptomic analysis and qRT-PCR validation demonstrated that GmIPT7, GmIPT10 and GmIPT15 respond differentially to drought, salt and low-temperature stress, with GmIPT15 exhibiting a transient upregulation at 3 h (p < 0.01) followed by a gradual decline to levels close to the pre-treatment control at 6–12 h under low-temperature stress. We further performed haplotype analysis of GmIPT15 and identified a putative elite haplotype (hap1) associated with cold tolerance based on low-temperature germination index assessment. This study provides useful insights for the future functional characterization of plant IPT genes and offers potential genetic resources and molecular markers that may support molecular-assisted breeding for soybean abiotic stress tolerance. Full article

Hybridization is considered an important process in plant evolution, especially in the origins of domesticated plant taxa, with many crop species being the result of interspecific hybridization events. There are several unidentified lineages of Spondias in the northeastern region of Brazil known only by vernacular names such as ‘cajaguela’, ‘umbu-cajá’, and ‘umbuguela’. These taxa are often regarded as being of hybrid origin, based on supposedly intermediate morphological features. However, the morphology-based hypotheses of hybrid origin and parentage of these Spondias taxa remain largely untested experimentally. We collected 355 accessions of Spondias, including S. bahiensis, other putative hybrid taxa, and both native (S. mombin, S. tuberosa, and S. venulosa) and introduced (S. purpurea) species believed to be the parental taxa. We then reconstructed phylogenies of plastid and nuclear markers and haplotype networks in order to ascertain the genetic affinities between putative hybrids and other Spondias species. All taxa with intermediate morphology were confirmed as hybrids between their putative parental species. All hybrids involving S. purpurea (native to Mexico) appear to be F₁ generation. The recently described S. bahiensis is shown to have originated from hybridization between S. tuberosa and S. venulosa. The other ‘umbu-cajá’ taxon found in Northeastern Brazil is revealed to be the result of hybridization between S. mombin and S. tuberosa. Both the northern ‘umbu-cajá’ taxon and S. bahiensis appear to be well-established hybrid lineages and not early-generation hybrids. Additionally, some introgression and backcrossing processes between S. bahiensis and one of the parents was also observed. Our findings confirm the hybrid origins of the domesticated Spondias taxa found in Northeastern Brazil. Full article

Correct species identification is essential for understanding biodiversity and managing ecosystems. The bisexual Brine Shrimp Artemia tibetiana and Artemia sorgeloosi represent two regional endemic taxa on the Tibetan Plateau, yet the taxonomic status of several populations remains unresolved. In particular, the Artemia population from Kyêbxang Co (Tibet, China) has been inconsistently assigned to either A. tibetiana or A. sorgeloosi in recent ecological and genomic studies, lacking formal taxonomic evaluation. To resolve this ambiguity, we conducted a precise biosystematic assessment based on DNA analyses: In this study, we performed a taxonomic reassessment of the Kyêbxang Co Artemia population, based on complete mitochondrial genome sequences and mitochondrial gene COI haplotype analyses. Phylogenetic analysis consistently positioned the Kyêbxang Co population within the A. sorgeloosi clade, clearly separated from the polyphyletic A. tibetiana lineage. Genetic distance values corroborated this placement, revealing minimal divergence from A. sorgeloosi (0.31%) but substantial divergence from A. tibetiana (9.07%). The COI haplotype network further indicated an exclusive maternal gene pool shared with topotypic A. sorgeloosi. Collectively, these results provide conclusive molecular evidence that the Brine Shrimp population of Kyêbxang Co belongs to A. sorgeloosi, not A. tibetiana. Full article

Genomic surveillance is a cornerstone of pandemic response; it has helped guide public health interventions worldwide. However, North Africa stands between limited surveillance resources and efforts to address the data gap in this strategic geographic region that links sub-Saharan Africa and Europe. In this study, we present the first comprehensive evolutionary investigation of Algerian SARS-CoV-2 genomes, revealing their phylogeny, continuous phylogeography within the country, mutation analysis, and a super-spreading event through haplotype network analysis. We characterized the genetic diversity and unique mutation pattern of 449 Algerian sequences, revealing multiple independent introductions into the country since the first reported case on the 25th of February 2020 followed by numerous local transmissions that facilitated the virus’s rapid propagation. This study highlights both the importance of molecular epidemiology and equitable access to resources in implementing genomic epidemiology and in increasing sequencing efforts to strengthen pandemic preparedness. Full article

Bats are hosts to many diseases that emerge in humans and livestock. Knowledge about the diversity and circulation of paramyxoviruses in European bat populations, despite their recognized importance, remains limited. Here, we present data on the first detection of paramyxoviruses in Poland in the new bat species of Cnephaeus serotinus and Cnephaeus nilsonii, which have never been previously recognized as paramyxovirus hosts, as well as in Myotis daubentonii and two unknown bat species. Viral RNA was detected in fecal and intestinal samples using the semi-nested RT-PCR protocol followed by Sanger sequencing. A widespread comprehensive phylogenetic study supported by haplotype network analyses of 376 nt sequences of paramyxoviruses detected in bats worldwide revealed that paramyxoviruses are closely related to the host and strongly correlate to the area of origin. Full article

Background/Objectives: Arctic foxes (Vulpes lagopus) exemplify the vulnerability of Arctic species to global warming and anthropogenic impacts, including habitat loss, interspecific competition with temperate species, pollution (chemical and biological), and declining prey abundance. Despite their ecological importance, the evolutionary and demographic history of the species is still incompletely understood, and the colonization history of isolated island populations, such as the one on Iceland, remains unresolved. Methods: We analyzed 80 mitochondrial genomes from across the Holarctic, including 22 Icelandic individuals. We combined phylogenetic reconstruction, coalescence-dating, haplotype network analysis, and diversity metrics to infer matrilineal relationships and colonization history. Results: Seven distinct haplogroups (Hg.1–Hg.7) were identified, which diverged ≥65 thousand years ago (kya). Two haplogroups were broadly distributed across Fennoscandia, Russia, Iceland, and Canada, while others were region-specific: two in eastern Russia (respectively diverging ~171 kya and ~89 kya), one in central Russia (~66 kya), and two in Iceland (~95 kya and ~66 kya). Three haplogroups were detected in Iceland, and at least four unrelated founding females are required to explain the current matrilineal diversity. One haplogroup contained sufficient representatives for molecular dating, yielding a minimum colonization age of ~5600 years, assuming in situ diversification. Observed matrilineal diversity in Iceland does not uniquely identify a single geographic source. Conclusions: Arctic foxes’ distribution and diversity reflect repeated cycles of isolation and expansion as circumpolar environments shifted. Broader sampling across the Nearctic is critical to clarify the timing, sources, and routes of Iceland’s colonization, as Nearctic sampling was limited to a single Canadian mitogenome. Full article

Tick-borne viral infections, including severe fever with thrombocytopenia syndrome virus (SFTSV), are increasingly recognized as a significant threat to global public health owing to their rapid dissemination and high mortality rates. While isolated outbreaks within single species have been documented, reports of multi-host cluster cases remain scarce. This study describes a consecutive, cross-species outbreak of severe fever with thrombocytopenia syndrome disease between April and May 2024 on a remote island in Nagasaki Prefecture that involved four cats and four humans. An interdisciplinary investigation integrating molecular phylogenetic analysis of viral genomes—including previously identified Nagasaki strains of SFTSV—and haplotype network analysis provided insights into the infection dynamics. Despite the absence of confirmed direct contact between cats and humans, four animals and one patient succumbed to the infection. Genomic analyses demonstrated high similarity to circulating Nagasaki strains, whereas haplotype analysis indicated multiple viral introduction events and complex transmission pathways, reflecting diverse sources. These findings underscore the critical need for a One Health approach—integrating human, animal, and vector surveillance—to effectively monitor, understand, and control tick-borne viruses globally, in both endemic and emerging regions. Full article

The grapevine (Vitis vinifera L.) is one of the most important horticultural crops, with thousands of varieties cultivated worldwide. In this study, we analyzed chloroplast SNV markers using a whole-genome shotgun sequencing approach to investigate the genetic diversity and phylogeny of 409 cultivated V. vinifera accessions originating from nine countries across Southeast and Central Europe, as well as a heterogeneous set of additional accessions maintained by INRAE. Shotgun sequencing allowed high coverage, enabling the detection of 93 SNVs across 24 chloroplast genes, including 11 non-synonymous variants. The ycf1 gene showed the highest variability, consistent with its role in species differentiation. Haplotype analysis revealed 102 distinct haplotypes, with clear geographic structuring: ATT predominated in the eastern Mediterranean, ATA in western Europe, and GTA mainly in a heterogeneous group of varieties from a French collection. To validate the shotgun approach, seven SNV markers were analyzed using target capture sequencing, confirming the accuracy of detected variants with only minimal discrepancies, which is mostly attributable to homopolymeric regions and low-frequency alleles. Phylogenetic analyses using both trees and networks delineated three major haplotype clusters, reflecting human-mediated dispersal of grapevine cultivars through historical viticultural practices. This study represents the largest chloroplast genome analysis of cultivated V. vinifera to date, providing a large cpDNA resource for assessing chloroplast diversity and maternal haplotype structure in cultivated grapevine. The results highlight the power of combining high-throughput sequencing and chloroplast genomics for population-level studies in perennial crops. Full article

Hypera postica (Gyllenhal) is a major pest of alfalfa. We combined mitochondrial COI and CytB gene sequences to characterize the genetic diversity of 20 geographic populations of H. postica across Xinjiang, China, and to elucidate their lineage relationships at both regional and global scales. We found that Nucleotide diversity (Pi) was markedly higher in western Xinjiang populations (Pi > 0.016), specifically Wusu (0.023), Tekes (0.023), Jinghe (0.023), Wenquan (0.021), Bole (0.021), Habahe (0.020), Nilka (0.020), Tacheng (0.019), Toli (0.018), Altay (0.017), Emin (0.016), Xinyuan (0.016), and Zhaosu (0.016), whereas central Xinjiang populations exhibited substantially lower diversity (Pi < 0.014), including Shawan (0.014), Qitai (0.011), Jimsar (0.007), Urumqi (0.004), Hutubi (0.003), Fukang (0.001), and Manas (0.001). Pairwise F_ST analysis revealed pronounced genetic divergence between the western Xinjiang group (Altay, Bole, Wenquan, Tacheng, Emin, Toli, Nilka, Xinyuan, Tekes, Zhaosu) and the central Xinjiang group (Qitai, Urumqi, Fukang, Habahe, Hutubi, Jimsar, Shawan, Manas). At the global level, H. postica can be divided into two major phylogroups: the Western and Eastern lineages. All Xinjiang populations belong to the Eastern lineage. Haplotype network analysis identified two distinct sublineages, western and central Xinjiang, with H2 and H26 as their respective dominant shared haplotypes; both are unique to China. Both maximum likelihood (ML) and Bayesian phylogenetic trees robustly support the central Xinjiang lineage as a distinct clade. Neutrality tests provided strong evidence of recent demographic expansion across the Xinjiang H. postica population as a whole (Fu’s Fs = −21.987, p < 0.05), with particularly pronounced signals in Hutubi (HTB: Tajima’s D = −1.966, Fu’s Fs = −0.781, p < 0.05), Jimsar (JMSE: Tajima’s D = −2.176, Fu’s Fs = −0.962, p < 0.01), and Wenquan (WQ: Fu’s Fs = −11.159, p < 0.01). Our results reveal a clear phylogeographic split within Xinjiang H. postica populations, comprising western and central sub-lineages, with the western sub-lineage likely representing ancestral lineage. The western Xinjiang sub-lineage appears to be shaped primarily by mountainous topography, whereas the central Xinjiang sub-lineage likely results from the combined effects of piedmont plain geography and infection with the endosymbiont Wolbachia strain wHypera4. Full article