Association Mapping for Yield Attributing Traits and Yellow Mosaic Disease Resistance in Mung Bean [Vigna radiata (L.) Wilczek]

Mung bean [Vigna radiata (L.) Wilczek] is an important short-duration grain legume widely known for its nutritional, soil ameliorative, and cropping system intensification properties. This study aims at evaluating genetic diversity among mung bean genotypes and detecting genomic regions associated with various yield attributing traits and yellow mosaic disease (YMD) resistance by association mapping. A panel of 80 cultivars and advanced breeding lines was evaluated for 10 yield-related and YMD resistance traits during kharif (monsoon) and summer seasons of 2018–2019 and 2019–2020. A total of 164 genome-wide simple sequence repeat (SSR) markers were initially screened, out of which 89 were found polymorphic which generated 317 polymorphic alleles with an average of 3.56 alleles per SSR locus. The number of alleles at each locus varied from 2 to 7. The population genetic structure analysis grouped different genotypes in three major clusters and three genetically distinct subpopulations (SPs) (i.e., SP-1, SP-2, and SP-3) with one admixture subpopulation (SP-4). Both cluster and population genetic structure analysis categorized the advanced mung bean genotypes in a single group/SP and the released varieties in other groups/SPs, suggesting that the studied genotypes may have common ancestral history at some level. The population genetic structure was also in agreement with the genetic diversity analysis. The estimate of the average degree of linkage disequilibrium (LD) present at the genome level in 80 mung bean genotypes unveiled significant LD blocks. Over the four seasons, 10 marker-trait associations were observed significant for YMD and four seed yield (SY)-related traits viz., days to flowering, days to maturity, plant height, and number of pods per plant using the mixed linear model (MLM) method. These associations may be useful for marker-assisted mung bean yield improvement programs and YMD resistance.

Genetic Diversity in Populations of Mediterranean Fruit Flies in North-Eastern Brazil

This study aimed at determining the population genetic structure of Mediterranean fruit flies (Ceratitis capitata) in North-eastern Brazil, so as to improve our understanding of the viability of the inter-simple sequences repeat (ISSR) markers in Brazilian populations, along with inferences on population genetic composition which can be used in management programs. For this, ISSR markers were used in groups collected from four municipalities in this region. Primers were polymorphic, revealing moderate expected heterozigosity, with 80% of the variation occurring within populations and moderate structure. Bayesian analysis revealed K = 3, consistent with pairwise FST and indicating low structure between Barra do Choça and Planalto, and moderate structure between Caraíbas and Planalto. Data indicated high diversity, suggesting two interpretations: the analyzed populations arose from a single population and are now under structuring processes, or populations had different origins, but are currently connected by gene flow. Thus, ISSR primers were affective in obtaining information about genetic structure of C. capitata populations in North-eastern Brazil, as evidenced by high polymorphism and separation or grouping of populations according to their allelic compositions. Furthermore, this paper provides useful information for understanding the genetic diversity, population structure and gene flow of C. capitata populations in this region and developing regional strategies for the control and management of the species.

Life Cycle and Phylogeography of True Truffles

True truffle (Tuber spp.) is one group of ascomycetes with great economic importance. During the last 30 years, numerous fine-scale population genetics studies were conducted on different truffle species, aiming to answer several key questions regarding their life cycles; these questions are important for their cultivation. It is now evident that truffles are heterothallic, but with a prevalent haploid lifestyle. Strains forming ectomycorrhizas and germinating ascospores act as maternal and paternal partners respectively. At the same time, a number of large-scale studies were carried out, highlighting the influences of the last glaciation and river isolations on the genetic structure of truffles. A retreat to southern refugia during glaciation, and a northward expansion post glaciation, were revealed in all studied European truffles. The Mediterranean Sea, acting as a barrier, has led to the existence of several refugia in different peninsulas for a single species. Similarly, large rivers in southwestern China act as physical barriers to gene flow for truffles in this region. Further studies can pay special attention to population genetics of species with a wide distribution range, such as T. himalayense, and the correlation between truffle genetic structure and the community composition of truffle-associated bacteria.

Population genetic structure and conservation management of hill pigeons (Columba rupestris) recently endangered in South Korea

Background Hill pigeons (Columba rupestris) are close to local extinction (ca. less than 100 individuals) in South Korea where a variety of conservation management procedures are urgently required. Objective This study was aimed at determining the conservation direction of captive propagation and reintroduction of hill pigeons using genetic information based on mitochondrial DNA. We also evaluated the extent of hybridization between hill pigeons and cohabiting domestic pigeons. Methods We used 51 blood samples of hill pigeons from Goheung (GH), Gurye (GR), and Uiryeong (UR), and domestic pigeons cohabiting with hill pigeon populations. Genetic diversity, pairwise Fst, analysis of molecular variance, and haplotype network analysis were used to examine the genetic structure of hill pigeons. Results Hill pigeons that inhabited South Korea were not genetically distinct from Mongolian and Russian populations and showed relatively low genetic diversity compared with other endangered species in Columbidae. The GR population that exhibited the largest population size showed lower genetic diversity, compared to the other populations, although the pairwise Fst values of the three populations indicated low genetic differentiation. The GH and GR populations were confirmed to lack hybridization, relatively, whereas the UR population was found to exhibit some degrees of hybridization. Conclusion To conserve hill pigeons with low genetic diversity and differentiation in South Korea, the conservation process of captive propagation and reintroduction may require artificial gene flows among genetically verified populations in captivity and wildness. The introduction of foreign individuals from surrounding countries is also considered an alternative strategy for maintaining genetic diversity.

Pharmacogenetics of HIV therapy: challenges for tailoring treatment in genetically complex populations

Tweetable abstract Pharmacogenetic tests are a promising strategy to improve safety and effectiveness of HIV therapy. However, implementation can be challenging in populations with complex genetic structure.

Phylogeography of Nasutitermes ephratae (Termitidae: Nasutitermitinae) in Neotropical region

The neotropical region ranks third in the number of termites with five different families. Of these, Termitidae is the most diverse and includes the species Nasutitermes ephratae and is common in the neotropics. To date, only one study has been published about phylogeographic issues in neotropical termites (N. corniger). Here, we aimed to investigate and analyze the population genetic patterns of N. ephratae and then evaluated the phylogeographical processes involved in the evolutionary history of the species. We used the mitochondrial genes 16S rRNA and COII as molecular markers: These were sequenced for 128 samples of N. ephratae. We estimated the genetic diversity and divergence time as well as the demographic and genetic structure analyses. We also produced ancestral area reconstruction and a haplotype network. The results showed high genetic variability, recent demographic expansion, and strong genetic structure. We also inferred a dispersal route for the species that occurred in both directions between South and Central America. The results emphasize a temporary separation between the South and Central America population that affected the origin of the current Central America populations. These were formed form different phylogeographic histories.

Teasing apart the joint effect of demography and natural selection in the birth of a contact zone

Vast population movements induced by recurrent climatic cycles have shaped the genetic structure of plant species. This is especially true in Scandinavia that was repeatedly glaciated. During glacial periods trees were confined to refugia, south and east of the ice sheet, from which they recolonized Scandinavia as the ice melted away. This multi-pronged recolonization led to large contact zones in most species. We leverage large genomic data from 5000 trees to reconstruct the demographic history of Norway spruce (Picea abies) and test for the presence of natural selection during the recolonization process and the establishment of the contact zone. Sweden is today made up of two large genetic clusters, a southern one originating from the Baltics and a Northern one originating from Northern Russia. The contact zone delineating these two clusters closely matches the limit between two major climatic regions. This suggests that natural selection contributed to the establishment and the maintenance of the contact zone. To test this hypothesis we first used Approximate Bayesian Computation; an Isolation-with migration model with genomewide linked selection fits the data better than a purely neutral one. Secondly, we identified loci characterized by both extreme allele frequency differences between geographic regions and association to the variables defining the climatic zones. These loci, many of which are related to phenology, form clusters present on all linkage groups. Altogether, the current genetic structure reflects the joint effect of climatic cycles, recolonization and selection on the establishment of strong local adaptation and con-tact zones.

The genetic structure of a wild wheat population has remained associated with microhabitats over 36 years

Wild progenitors of major crops can help us understand domestication, and may also provide the genetic resources needed for ensuring food security in the face of climate change. We examined the genetic structure of a wild emmer wheat population, sampled over 36 years while both temperature and CO2 concentration increased significantly. The genotypes of 832 individuals revealed high genetic diversity over scales of tens of meters and were clustered spatially into ecological microhabitats. This pattern was remarkably stable over time. Simulations indicate that neutral processes alone are unlikely to fully explain the spatial and temporal stability of the population. These results are consistent with a role for local adaptation in shaping the fine-scale structure of plant populations, which is relevant for in-situ conservation strategies of biodiversity in nature.