Intraspecific Genetic Variation Research Articles

Loss of species and genetic diversity during colonization: Insights from acanthocephalan parasites in northern European seals.

Studies on host-parasite systems that have experienced distributional shifts, range fragmentation, and population declines in the past can provide information regarding how parasite community richness and genetic diversity will change as a result of anthropogenic environmental changes in the future. Here, we studied how sequential postglacial colonization, shifts in habitat, and reduced host population sizes have influenced species richness and genetic diversity of Corynosoma (Acanthocephala: Polymorphidae) parasites in northern European marine, brackish, and freshwater seal populations. We collected Corynosoma population samples from Arctic, Baltic, Ladoga, and Saimaa ringed seal subspecies and Baltic gray seals, and then applied COI barcoding and triple-enzyme restriction-site associated DNA (3RAD) sequencing to delimit species, clarify their distributions and community structures, and elucidate patterns of intraspecific gene flow and genetic diversity. Our results showed that Corynosoma species diversity reflected host colonization histories and population sizes, with four species being present in the Arctic, three in the Baltic Sea, two in Lake Ladoga, and only one in Lake Saimaa. We found statistically significant population-genetic differentiation within all three Corynosoma species that occur in more than one seal (sub)species. Genetic diversity tended to be high in Corynosoma populations originating from Arctic ringed seals and low in the landlocked populations. Our results indicate that acanthocephalan communities in landlocked seal populations are impoverished with respect to both species and intraspecific genetic diversity. Interestingly, the loss of genetic diversity within Corynosoma species seems to have been less drastic than in their seal hosts, possibly due to their large local effective population sizes resulting from high infection intensities and effective intra-host population mixing. Our study highlights the utility of genomic methods in investigations of community composition and genetic diversity of understudied parasites.

Phenotypic variation and genomic variation in insect virulence traits reveal patterns of intraspecific diversity in a locust-specific fungal pathogen.

Intraspecific pathogen diversity is crucial for understanding the evolution and maintenance of adaptation in host-pathogen interactions. Traits associated with virulence are often a significant source of variation directly impacted by local selection pressures. The specialist fungal entomopathogen, Metarhizium acridum, has been widely implemented as a biological control agent of locust pests in tropical regions of the world. However, few studies have accounted for natural intraspecific phenotypic and genetic variation. Here, we examine the diversity of nine isolates of M. acridum spanning the known geographic distribution, in terms of (1) virulence towards two locust species, (2) growth rates on three diverse nutrient sources, and (3) comparative genomics to uncover genomic variability. Significant variability in patterns of virulence and growth was shown among the isolates, suggesting intraspecific ecological specialization. Different patterns of virulence were shown between the two locust species, indicative of potential host preference. Additionally, a high level of diversity among M. acridum isolates was observed, revealing increased variation in subtilisin-like proteases from the Pr1 family. These results culminate in the first in-depth analysis regarding multiple facets of natural variation in M. acridum, offering opportunities to understand critical evolutionary drivers of intraspecific diversity in pathogens.

An update and ecological perspective on certain sentinel helminth endoparasites within the Mediterranean Sea.

The Mediterranean Sea is recognized as a marine biodiversity hotspot. This enclosed basin is facing several anthropogenic-driven threats, such as seawater warming, pollution, overfishing, bycatch, intense maritime transport and invasion by alien species. The present review focuses on the diversity and ecology of specific marine trophically transmitted helminth endoparasites (TTHs) of the Mediterranean ecosystems, aiming to elucidate their potential effectiveness as ‘sentinels’ of anthropogenic disturbances in the marine environment. The chosen TTHs comprise cestodes and nematodes sharing complex life cycles, involving organisms from coastal and marine mid/upper-trophic levels as definitive hosts. Anthropogenic disturbances directly impacting the free-living stages of the parasites and their host population demographies can significantly alter the distribution, infection levels and intraspecific genetic variability of these TTHs. Estimating these parameters in TTHs can provide valuable information to assess the stability of marine trophic food webs. Changes in the distribution of particular TTHs species can also serve as indicators of sea temperature variations in the Mediterranean Sea, as well as the bioaccumulation of pollutants. The contribution of the chosen TTHs to monitor anthropogenic-driven changes in the Mediterranean Sea, using their measurable attributes at both spatial and temporal scales, is proposed.

Common but not connected: high genetic structure and cryptic genetic diversity in the ubiquitous biting midge Culicoides peregrinus Kieffer.

The biting midge Culicoides peregrinus Kieffer is a significant pest and vector species, and knowledge of its genetic diversity and genetic structure is critically important for designing an effective control program. However, such information is limited to only small sample-size DNA barcoding studies. Therefore, in this study, we used mitochondrial cytochrome c oxidase I (COI) to examine genetic structure and diversity of C. peregrinus from northeastern Thailand. In addition, we also inferred genetic relationships between C. peregrinus from Thailand and those reported from other countries across the geographic range of the species. Maximum intraspecific genetic divergence (3.83%) within Thai specimens was relatively high compared to other Culicoides species. Genetic structure analysis revealed that 71% (32 from 45) of population comparisons were highly significantly different. A high level of genetic structure among populations, even between those in close geographic proximity (22 km geographic distance) suggested that there has been little or no movement between local populations. This is possibly due to the ability to exploit diverse types of breeding site and a generalist feeding habit which enables C. peregrinus to complete its life cycle within cattle pens. Genetic relationships between Thai C. peregrinus and those reported from other countries revealed three genetically divergent lineages (A, B and C) associated with geographic origins. Specimens from Thailand + China formed lineage A, those from Australia formed lineage B and India + Bangladesh belonged to lineage C. These genetically divergent lineages also agree with morphological variation of the wing pale marking spots. Further investigation using independent genetic loci from nuclear genes will be very useful to resolve taxonomic status of these divergent lineages.

First report and molecular identification of Chilo partellus (Swinhoe, 1885) in South-eastern Türkiye: invasion continues (Lepidoptera: Crambidae)

Chilo partellus (Swinhoe, 1885) (Lepidoptera: Crambidae), is an invasive maize pest that can cause high yield losses. The pest has recently been introduced and established in eastern Mediterranean countries such as Türkiye. However, research regarding its expansion towards other regions in Türkiye and other countries is required. This study is the first to report the presence and abundance of the pest in South-eastern Türkiye provinces, Diyarbakır, Mardin, Ranlıurfa, and Rırnak as well as the infestation rate and its contribution to the stemborer-dependent infestation rates. There were significant differences between the abundances of the pest in different counties, while the infestation rate, the contribution to the stemborer-dependent infestation rate, and the contribution to the total stemborer population were not statistically different between counties. The pest was only recorded in three southern counties of Ranlıurfa, during routine September surveys in 2022 and was absent in Diyarbakır, Mardin, and Rırnak. Specimens were morphologically diagnosed, and for molecular identification and phylogenetic analysis, nucleotide sequencing of the mitochondrial cytochrome oxidase subunit I (COI-I) gene was performed. All specimens were confirmed as C. partellus. Further, phylogenetic analysis revealed intraspecific genetic variation and the similarity of the specimens to reference sequences from Africa.

Trends of Eurasian Perch (Perca fluviatilis) mtDNA ATP6 Region Genetic Diversity within the Hydro-Systems of the Eastern Part of the Baltic Sea in the Anthropocene.

The intraspecific genetic diversity of freshwater fish inhabiting hydro-systems of the macrogeographic area spreading from the Black to Baltic Seas requires comprehensive investigation from fundamental and practical perspectives. The current study focused on the involvement of the mtDNA ATP6 region in the adaptability and microevolution of Perca fluviatilis within phylogeographic and anthropogenic contexts. We sequenced a 627 bp fragment encompassing the ATP6 region and used it for genetic analysis of 193 perch caught in Latvia, Lithuania, Belarus, and Ukraine, representing natural and anthropogenically impacted populations. We evaluated patterns of intraspecific genetic diversity in the ATP6 region and phylogeographic trends within the studied area compared with previously established D-loop trends. Evaluation of ATP6 coding sequence variability revealed that among 13 newly detected haplotypes, only two were caused by non-synonymous substitutions of amino acids of the protein. PCoA revealed three genetic groups (I-III) based on the ATP6 region that encompassed four previously described genetic groups established based on the mtDNA D-loop. The two mtDNA regions (D-loop and ATP6) have microevolved at least partially independently. Prolonged anthropogenic impacts may generate new point mutations at the ATP6 locus, but this phenomenon could be mainly concealed by natural selection and reparation processes.

Genomic and transcriptomic analyses reveal polygenic architecture for ecologically important traits in aspen (Populustremuloides Michx.).

Intraspecific genetic variation in foundation species such as aspen (Populus tremuloides Michx.) shapes their impact on forest structure and function. Identifying genes underlying ecologically important traits is key to understanding that impact. Previous studies, using single-locus genome-wide association (GWA) analyses to identify candidate genes, have identified fewer genes than anticipated for highly heritable quantitative traits. Mounting evidence suggests that polygenic control of quantitative traits is largely responsible for this "missing heritability" phenomenon. Our research characterized the genetic architecture of 30 ecologically important traits using a common garden of aspen through genomic and transcriptomic analyses. A multilocus association model revealed that most traits displayed a highly polygenic architecture, with most variation explained by loci with small effects (likely below the detection levels of single-locus GWA methods). Consistent with a polygenic architecture, our single-locus GWA analyses found only 38 significant SNPs in 22 genes across 15 traits. Next, we used differential expression analysis on a subset of aspen genets with divergent concentrations of salicinoid phenolic glycosides (key defense traits). This complementary method to traditional GWA discovered 1243 differentially expressed genes for a polygenic trait. Soft clustering analysis revealed three gene clusters (241 candidate genes) involved in secondary metabolite biosynthesis and regulation. Our work reveals that ecologically important traits governing higher-order community- and ecosystem-level attributes of a foundation forest tree species have complex underlying genetic structures and will require methods beyond traditional GWA analyses to unravel.

Applying molecular genetic data at different scales to support conservation assessment of European Habitats Directive listed species: A case study of Eurasian otter in Austria.

Evaluating intraspecific genetic structure and diversity is fundamental to assessing a species' conservation status, but direct incorporation of such information into legal frameworks such as the EU's Habitats Directive is surprisingly rare. How genetic structure aligns with EU member state boundaries or biogeographic regions may be very important in designing management plans or achieving legislative goals. The Eurasian fish otter experienced a sharp population decline during the 20th century but is currently re-expanding in several countries. The species is listed under Annex II and IV of the European Habitats Directive, and member states are obliged to assess the species separately across different biogeographic regions. We genotyped 2492 otter spraints across four provinces in Austria, collected between 2017 and 2021. A total of 384 different genotypes were identified, supporting densities along river habitats from 0.1 to 0.47 otters per river km (mean: 0.306), with a resampling-based simulation supporting limited density overestimation at survey lengths of 20 km or more. Three distinct genetic clusters were revealed, two of them presumably reflecting two relict populations whereas the source of the third cluster is unknown. The geographic extent of the three clusters does not coincide with provincial or biogeographic boundaries, both relevant for assessment and management within existing national or European legislative frameworks. We advocate more consideration of genetic structure in the assessment and conservation management planning of species listed in the European Habitats Directive.

Comparative genomics of Lactobacillus johnsonii reveals extensive intraspecific genetic variation

Lactobacillus johnsonii, as a microorganism widely presenting in the intestinal tract of mammals, dairy products, and poultry, possesses various probiotic characteristics. Currently, many research focused on the probiotic functions and industrial applications of L. johnsonii. In this study, 98 strains of L. johnsonii were subjected to comparative genomic analyses to explore its genetic diversity. The results indicated that based on ANI values, d-DDH values, phylogenetic analysis, and whole-genome comparison, the 98 strains of L. johnsonii were classified into two phylogenetic clusters. The carbohydrate utilization genes, bacteriocin operon, extracellular polysaccharide gene cluster, and bile salt hydrolase encoding genes in L. johnsonii shared common features and exhibited systematic differences based on phylogenetic clustering. The main reason for the high intra-species gene diversity of L. johnsonii might be differences in phages and other mobile genetic elements. This study provides new insights into the genomic features and functional genes of L. johnsonii.

Cryptic diversity and phylogeographic patterns of <italic>Plocamium telfairiae</italic> and <italic>P. cartilagineum</italic> (Plocamiales, Rhodophyta) in the Northwest Pacific

Cryptic diversity refers to two or more distinct species classified as a single species due to lack of morphological difference. Although Plocamium Lamouroux has potential applications in biotechnology, several phylogenetic studies suggest the presence of cryptic diversity within the genus that requires further phylogenetic evaluation. Here, we investigated two species of Plocamium, P. “cartilagineum” and P. “telfairiae”, in the Northwest (NW) Pacific. The aims of this study are to identify potential cryptic species by analyzing the genetic differences between the species from their type localities and specimens from the NW Pacific, to characterize their population genetic diversity and structure, and to find potential hotspots with high intraspecific genetic diversity in Korea. A reconstructed phylogenetic tree based on mitochondrial 5′ region of cytochrome c oxidase subunit I (COI-5P) and plastid ribulose-1,5-bisphosphate carboxylase / oxygenase large subunit (rbcL) with molecular delimitation methods revealed significant differences as distinct species in the genus Plocamium. Comparison with specimens from their type localities indicated the presence of two cryptic species in the NW Pacific, including Plocamium luculentum sp. nov. The phylogeographic study for both species showed low genetic differences among populations, demonstrating genetic connectivity within the NW Pacific. These findings could promote the discovery of other morphologically and ecologically similar but phylogenetically different Plocamium species worldwide, which is essential for conservation assessments.

Inter- and Intraspecific Genetic Variation of Native Hawthorn (Crataegus spp.) Genotypes Grown in the Çoruh Valley in Türkiye

Inter- and Intraspecific Genetic Variation of Native Hawthorn (Crataegus spp.) Genotypes Grown in the Çoruh Valley in Türkiye

Morphology, molecular phylogeny and biogeography revealed two new Pseudo‐nitzschia (Bacillariophyceae) species in Chinese waters

AbstractPseudo‐nitzschia is a group of widely distributed planktonic diatoms. Some species produce the neurotoxin domoic acid. Herein, two new Pseudo‐nitzschia species were described from Chinese coastal waters and the South China Sea after combining morphological and molecular data, together with biogeographical traits. Pseudo‐nitzschia punctionis sp. nov. was similar to Pseudo‐nitzschia bipertita morphologically, but differed in poroid structure, which was undivided in P. punctionis but divided in two sectors in P. bipertita. This difference corresponded to the presence of two hemicompensatory base changes (HCBCs) in the secondary structure of internal transcribed spacer 2. Pseudo‐nitzschia polymorpha sp. nov. was sister to Pseudo‐nitzschia limii phylogenetically, but distinct by the various shapes of perforations on the valve and copula, which was supported by four HCBCs. In a metabarcoding analysis, multiple new ribotypes were identified within the two new species, and intraspecific genetic divergences were analyzed. Metabarcoding data revealed that P. punctionis had a broader temperature range (12.9–30.5 °C) than P. polymorpha (22.3–30.5 °C). Within the two new species, different traits were found among the amplicon sequence variants regarding temperature and biogeography, representing different microevolutionary directions under environmental selection. The two new species had different biogeographical traits when compared to their closely related species. Domoic acid was detected in strains of P. punctionis at a concentration of 13.5–17.7 fg/cell, but the toxin was not found in strains of P. polymorpha. A combination of characters based on laboratory strains and field metabarcoding data provided more data for delimiting Pseudo‐nitzschia species and gave new insights into their diversity and biogeography.

Single-cell transcriptomics supports presence of cryptic species and reveals low levels of population genetic diversity in two testate amoebae morphospecies with large population sizes.

The enormous population sizes and wide biogeographical distribution of many microbial eukaryotes set the expectation of high levels of intraspecific genetic variation. However, studies investigating protist populations remain scarce, mostly due to limited 'omics data. Instead, most genetics studies of microeukaryotes have thus far relied on single loci, which can be misleading and do not easily allow for detection of recombination, a hallmark of sexual reproduction. Here, we analyze >40 genes from 72 single-cell transcriptomes from two morphospecies - Hyalosphenia papilio and Hyalosphenia elegans - of testate amoebae (Arcellinida, Amoebozoa) to assess genetic diversity in samples collected over four years from New England bogs. We confirm the existence of cryptic species based on our multi-locus dataset, which provides evidence of recombination within and high levels of divergence between the cryptic species. At the same time, total levels of genetic diversity within cryptic species are low, suggesting that these abundant organisms have small effective population sizes, perhaps due to extinction and repopulation events coupled with efficient modes of dispersal. This study is one of the first to investigate population genetics in uncultivable heterotrophic protists using transcriptomics data and contributes towards understanding cryptic species of non-model microeukaryotes.

The Influence of Macroclimatic Drivers on the Macrophyte Phylogenetic Diversity in South African Estuaries

The geographical distribution of plants is influenced by macroclimate and dispersal limitations, which have led to lineage isolation and subsequent diversification within and across various environmental gradients. Macroclimatic variables in coastal wetlands influence plant species and lineages across biogeographical boundaries. This study aimed to determine the influence of macroclimatic variables on species and phylogenetic richness in South African estuaries. Open-source chloroplast DNA barcoding sequences, species distribution and climatic data layers were used to determine the relationship between species richness, MPD, MNTD and each bioclimatic variable individually. Temperate species richness and phylogenetic diversity were positively correlated with temperature bioclimatic variables whereas subtropical and tropical species were associated with increases in precipitation. Phylogenetic niche conservatism is evident in malvids and rosids which are restricted to tropical and subtropical regions due to their physiological adaptations to tropical climates. Caryophylales was mostly associated with temperate regions. Poales and Alismatales showed wide distributions that is likely attributed to traits related to wind pollination and hydrochory, rapid, clonal, and high reproductive output, tolerance to stressful conditions, and intraspecific genetic diversity. The findings highlight the importance of considering macroclimate and phylogenetic factors in understanding the distribution and diversity of coastal wetland plants.

Integrative taxonomy of coastal Adota Casey (Coleoptera: Staphylinidae: Aleocharinae) with descriptions of two new species in Korea

A taxonomic review of Adota Casey on Korean seacoasts is presented based on morphological and molecular characters (COI and 28S). Five species are recognized, two of which are new species (Adota namhae Lee and Ahn sp. nov. and Adota sinanensis Lee and Ahn sp. nov.). Detailed morphological characters and molecular analyses support the validity of all species including two new species. Intraspecific genetic divergence of COI using uncorrected p-distance among individuals of Korean Adota species ranged from 0% to 0.63%, while interspecific divergence among five species ranged from 7.14% to 12.22%. All the five species were each supported as a single lineage based on COI and 28S on both parsimony and maximum likelihood trees. A key, descriptions, habitus photographs, and illustrations of diagnostic characters of these two new species are provided to facilitate identification. urn:lsid:zoobank.org:pub:538ED6AC-8B68-4677-9658-849A67FD315A

Soil Biota in a Nonnative Range has a Net Positive Effect on the Perennial Herb Lupinus polyphyllus

Invasive species can have detrimental effects on the health of local ecosystems. Lupinus polyphyllus is an herb native to western and northeast North America, but the species has become invasive worldwide. In northeastern Ohio, United States, the species is nonnative, but not invasive and not spreading rapidly. Because physical distance is not a barrier, there are other reasons behind the inability of the species to become locally invasive. Here, the net effect of the local soil biota on the range expansion of the species was tested to explore 2 alternative, non-mutually exclusive, hypotheses. First, if belowground enemies limit this species range, thenet effect of the soil biota would be negative. Alternatively, soil mutualists might have a relatively greater net effect on plant fitness. A greenhouse experiment was conducted with 3 populations of seeds from the invasive range across 2 experimental treatments: a general fungicide (ZeroTol®) treatment and a water-control treatment. Fungicide treatment reduced total biomass in 2 out of 3 populations, consistent with limitations by the abundance of belowground mutualists. Fungicide treatment also changed root structure by reducing the number of nodules, root length, and diameter, while increasing root tissue density. Although the fungicidetreatment hindered the growth of lupines overall, the changes in root structure indicate that the treated individuals were able to partially compensate by shifting to more of an outsourcing method of resource acquisition. The results suggest that in addition to belowground mutualistic interactions, phenotypic plasticity and intraspecific genetic variation may also contribute to the success of L. polyphyllus in its nonnative ranges.

Evolutionary dynamics of Euphorbia carniolica suggest a complex Plio-Pleistocene history of understorey species of deciduous forest in southeastern Europe.

Deciduous forests form the dominant natural vegetation of Europe today, but were restricted to small refugia during Pleistocene cold stages, implying an evolutionary past shaped by recurrent range contractions and expansions. Cold-stage forest refugia were probably widespread in southern and central Europe, with the northwestern Balkan Peninsula being of particular importance. However, the actual number and location of deciduous forest refugia, as well as the connections between them, remain disputed. Here, we address the evolutionary dynamics of the deciduous forest understorey species Euphorbia carniolica as a proxy for past forest dynamics. To do so, we obtained genomic and morphometric data from populations representing the species' entire range, investigated phylogenetic position and intraspecific genetic variation, tested explicit demographic scenarios and applied species distribution models. Our data support two disjoint groups linked to separate refugia on the northwestern and central Balkan Peninsula. We find that genetic differentiation between groups started in the early Pleistocene via vicariance, suggesting a larger distribution in the past. Both refugia acted as sources for founder events to the southeastern Alps and the Carpathians; the latter were likely colonised before the last cold stage. In line with traditional views on the pre-Pleistocene origin of many southeastern European deciduous forest species, the origin of E. carniolica was dated to the late Pliocene. The fact that E. carniolica evolved at a time when a period of continuous forestation was ending in much of Eurasia provides an interesting biogeographical perspective on the past links between Eurasian deciduous forests and their biota.

Matching an Old Marine Paradigm: Limitless Connectivity in a Deep-Water Fish over a Large Distance.

Investigations of population structuring in wild species are fundamental to complete the bigger picture defining their ecological and biological roles in the marine realm, to estimate their recovery capacity triggered by human disturbance and implement more efficient management strategies for fishery resources. The Blackspot Seabream (Pagellus bogaraveo, Brünnich 1768) is a commercially valuable deep-water fish highly exploited over past decades. Considering its exploitation status, deepening the knowledge of intraspecific variability, genetic diversity, and differentiation using high-performing molecular markers is considered an important step for a more effective stock assessment and fishery management. With one of the largest efforts conceived of and completed by countries overlooking the Atlantic and Mediterranean coasts in recent years, a total of 320 individuals were collected from different fishing grounds in the Mediterranean Sea and Atlantic Ocean and analysed using 29 microsatellite loci. We applied multiple statistical approaches to investigate the species' connectivity and population structure across most of its described distribution area. Considering the incomplete knowledge regarding the migratory behaviour of adults, here we suggest the importance of egg and larval dispersal in sustaining the observed genetic connectivity on such a large geographical scale.

More geckos, fewer gaps: diversity and distribution of Hemidactylus geckos (Squamata: Gekkonidae) in Jordan

Until relatively recently, the gecko species Hemidactylus turcicus was believed to be the only member of the genus to occur in Jordan. Later taxonomic treatments confirmed the presence of another two species in the country – H. dawudazraqi and H. mindiae. It has been more than 10 years now since the last study on species of the genus Hemidactylus in Jordan was published and the distribution limits of the different species remain unknown. To shed light on the geographic and genetic boundaries between the species and different populations we collected material from across Jordan and sequenced each sample for two mitochondrial genes to provide identification by means of DNA barcoding. The results of phylogenetic analyses of species that occur in Jordan and neighbouring countries allowed us to assess the level of inter- and intraspecific genetic diversity of Hemidactylus in the region. Based on our results we confirm the presence of two species that were previously not known from the country – H. granosus and H. lavadeserticus. We also found another genetic lineage to be present in Jordan, implying that there may be yet another undescribed species of Hemidactylus present in Jordan. The results of this study will help to clarify the distribution of Hemidactylus species in Jordan and enable better delineation of the boundaries between the individual species.

Genome-wide association analysis identifies natural allelic variants associated with panicle architecture variation in African rice, Oryza glaberrima Steud.

African rice (Oryza glaberrima Steud), a short-day cereal crop closely related to Asian rice (Oryza sativa L.), has been cultivated in Sub-Saharan Africa for ∼ 3,000 years. Although less cultivated globally, it is a valuable genetic resource in creating high-yielding cultivars that are better adapted to diverse biotic and abiotic stresses. While inflorescence architecture, a key trait for rice grain yield improvement, has been extensively studied in Asian rice, the morphological and genetic determinants of this complex trait are less understood in African rice. In this study, using a previously developed association panel of 162 O. glaberrima accessions and new SNP variants characterized through mapping to a new version of the O. glaberrima reference genome, we conducted a genome-wide association study of four major morphological panicle traits. We have found a total of 41 stable genomic regions that are significantly associated with these traits, of which 13 co-localized with previously identified QTLs in O. sativa populations and 28 were unique for this association panel. Additionally, we found a genomic region of interest on chromosome 3 that was associated with the number of spikelets and primary and secondary branches. Within this region was localized the O. sativa ortholog of the PHYTOCHROME B gene (Oglab_006903/OgPHYB). Haplotype analysis revealed the occurrence of natural sequence variants at the OgPHYB locus associated with panicle architecture variation through modulation of the flowering time phenotype, whereas no equivalent alleles were found in O. sativa. The identification in this study of genomic regions specific to O. glaberrima indicates panicle-related intra-specific genetic variation in this species, increasing our understanding of the underlying molecular processes governing panicle architecture. Identified candidate genes and major haplotypes may facilitate the breeding of new African rice cultivars with preferred panicle traits.