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Araucaria angustifolia is an endangered species with more than 97% of its natural populations extinct. Logging of the species in the few remaining natural populations is highly restricted, though not readily accepted by farmers and logging companies. Consequently, political pressures have emerged for a return to logging of the species. Assessing the sustainability of such logging requires studies of a range of impacts on the remaining populations, including their genetic viability. We investigated the effect of selective logging on genetic diversity, intrapopulation spatial genetic structure (SGS), effective population size (Ne), and pollen and seed dispersal in three A. angustifolia permanent sample blocks established in a remnant of Araucaria Forest in Brazil. In these sample blocks, three logging intensities were applied (LI: 18.4, 31.4, and 32.3% of trees). Microsatellite analysis was performed for all adult and juvenile trees pre- and post-logging saplings. After selective logging, the greatest loss of alleles and the greatest decrease in Ne were observed from the highest LI. Logging increased SGS, while the distance and patterns of pollen and seed dispersal were different for both pre- and post-logging scenarios, with pollen dispersed over greater distances than seed. Pollen dispersal distance post-logging and seed dispersal distance pre- and post-logging decreased with the increased distance between parents. After logging, Ne reduced from 27.7 (LI = 31.4%) to 28.8 (LI = 18.4%) and 39.5% (LI = 32.3%), and some alleles were lost. Despite this, the loss of these alleles may be compensated for in subsequent generations, considering that logging resulted in changes such as an increase in the rate and distance of pollen immigration. Under the conditions evaluated in this study, selective logging of A. angustifolia is not adequate. To achieve truly sustainable forest logging, new rules that combine higher minimum DBH, lower logging intensity, and longer cutting cycles must be adopted. Furthermore, extensive genetic studies must be performed before logging any individual from a natural population.

Characterisation of genetic diversity is critical to adequately exploit the potential of germplasm collections and identify important traits for breeding programs and sustainable crop improvement. Here, we characterised the phenotypic and genetic diversity of a global collection of the two cultivated buckwheat species Fagopyrum esculentum and Fagopyrum tataricum (190 and 51 accessions, respectively) using 37 agro-morphological traits and 24 SSR markers. A wide range of variation was observed in both species for most of the traits analysed. The two species differed significantly in most traits, with traits related to seeds and flowering contributing most to differentiation. The accessions of each species were divided into three major phenoclusters with no clear geographic clustering. At the molecular level, the polymorphic SSR markers were highly informative, with an average polymorphic information content (PIC) of over 0.65 in both species. Genetic diversity, as determined by Nei’s expected heterozygosity (He), was high (He = 0.77 and He = 0.66, respectively) and differed significantly between species (p = 0.03) but was homogeneously distributed between regions, confirming the lack of genetic structure as determined by clustering approaches. The weak genetic structure revealed by the phenotypic and SSR data and the low fixation indices in both species suggested frequent seed exchange and extensive cultivation and selection. In addition, 93 and 140 significant (p < 0.05) marker-trait associations (MTAs) were identified in both species using a general linear model and a mixed linear model, most of which explained >20% of the phenotypic variation in associated traits. Core collections of 23 and 13 phenotypically and genetically diverse accessions, respectively, were developed for F. esculentum and F. tataricum. Overall, the data analysed provided deep insights into the agro-morphological and genetic diversity and genetic relationships among F. esculentum and F. tataricum accessions and pointed to future directions for genomics-based breeding programs and germplasm management.

Due mainly to large genome size and prevalence of repetitive sequences in the nuclear genome of spruce (Picea Mill.), it is very difficult to develop single-copy genomic microsatellite markers. We have developed and characterized 25 polymorphic, single-copy genic microsatellites from white spruce (Picea glauca (Moench) Voss) EST sequences and determined their informativeness in white spruce and black spruce (Picea mariana (Mill.) B.S.P.) and inheritance in black spruce. White spruce EST sequences from NCBI dbEST were searched for the presence of microsatellite repeats. Forty-seven sequences containing dinucleotide, trinucleotide, tetranucleotide and compound repeats were selected to develop primers. Twenty-five of the designed primer pairs yielded scorable amplicons, with single-locus patterns, and were characterized in 20 individuals each of white spruce and black spruce. All 25 microsatellites were polymorphic in white spruce and 24 in black spruce. The number of alleles at a locus ranged from two to 18, with a mean of 8.8 in white spruce, and from one to 17, with a mean of 7.6 in black spruce. The expected heterozygosity/polymorphic information content ranged from 0.10 to 0.92, with a mean of 0.67 in white spruce, and from 0 to 0.93, with a mean of 0.59 in black spruce. Microsatellites with dinucleotide and compound repeats were more informative than those with trinucleotide and tetranucleotide repeats. Eighteen microsatellite markers polymorphic between the parents of a black spruce controlled cross inherited in a single-locus Mendelian fashion. The microsatellite markers developed can be applied for various genetics, genomics, breeding, and conservation studies and applications.

Italy holds important genetic resources of small ruminant breeds. By distinguishing goat breeds at the DNA level, certification of products from specific breeds can be valorized. The aim of this study was to establish the genetic identity of Facciuta della Valnerina, a local goat population of Italy, compared with the cosmopolitan breeds, Saanen and Camosciata delle Alpi, reared in the same geographic area. A total of 116 microsatellite alleles ranging from 4 to 13 were detected at 16 loci in the three goat populations/breeds. A total of 23 private alleles with frequencies lower than 0.3 were detected in the Facciuta della Valnerina population. The mean numbers of alleles were 6.67, 4.58, and 4.92 in Facciuta della Valnerina, Camosciata delle Alpi, and Saanen, respectively. The expected heterozygosity ranged from 0.20 to 0.86. Most loci were highly polymorphic and informative (polymorphic information content ≥0.50). Factorial correspondence analysis and principal components analysis revealed very clear separation between Facciuta della Valnerina and the two reference goat breeds. Reducing the number of markers from 16 to 12 (on the basis of polymorphic information content and the number of alleles) still allowed us to distinguish the local population, indicating that microsatellite markers are capable of discriminating local livestock breeds at a low cost.

Ilex paraguariensis is a dioecious, Neotropical tree endemic to South America with wide cultural, economic and ecological signi cance. However, due to extensive fragmentation and deforestation throughout its natural area of occurrence, studies on gene ow and genetic diversity are needed to drive genetic conservation and improvement strategies. Based on the sampling of all adult and juvenile trees in two I. paraguariensis populations, we investigate the reali ed pollen and seed ow and dispersal distance, spatial genetic structure (SGS) and genetic diversity using microsatellite markers. We found limited genetic di erentiation between populations (G’ st = 0.033), but signi cant di erences in terms of genetic diversity (R: 4.7 vs 3.9, H 0 : 0.495 vs 0.371, H e : 0.445 vs 0.375), pollen (10 vs. 23.3%) and seed immigration (0 vs. 3.3%), mating among relatives (t r : 16 vs 30%) and biparental inbreeding (F r : 0.253 vs. 0.345). Within populations, the genetic diversity was similar between adults and juveniles, but adults presented signi cantly lower xation index than juveniles, suggesting selection against inbred individuals between juvenile and adult life stages. We also found similar mean pollen (255 vs. 293 m) and seed (385 vs. 323 m) dispersal distances within populations. Our results show that the studied populations are not genetically isolated and some mating occurs among related trees due to SGS; however, the frequency of biparental inbred individuals decrease over the life course due to inbreeding depression. These results contribute directly to species management and seed collection and inform in situ and ex situ conservation programs.

In the Romanian Carpathians, Silver fir covers about 5% of the forest area and is the second most important conifer species. Although there are a number of genetic studies concerning the distribution of genetic diversity of Abies alba in Europe, populations from the south-eastern limit of the distribution range have been studied less. The aim of the present study was to assess the genetic diversity and differentiation in 36 silver fir populations along the Carpathian Mountains in Romania, using seven microsatellites loci. High levels of genetic diversity (He = 0.779 to 0.834 and AR = 11.61 to 14.93) were found in all populations. Eastern Carpathians populations show higher levels of diversity, both in allelic richness and expected heterozygosity and higher degrees of genetic differentiation compared to southern populations. Bayesian clustering analysis revealed the existence of two genetically distinct groups for silver fir populations, one larger cluster which comprises the Inner Eastern Carpathians, Curvature Carpathians, South Carpathians and the Banat Mountains and the second cluster contained most of the North and Outer Eastern Carpathians population. Both AMOVA and Barrier analysis supported genetic differentiation among geographical provenance regions. The high genetic diversity of silver fir populations from the eastern limit of its distribution provide high potential to mitigate the negative effects of climate warming being valuable genetic resources in the context of global change. The distribution pattern of genetic variation at local, regional and country scale could and should be considered for the preservation of the forest genetic resources.

The annual yield of matsutake mushrooms (Tricholoma matsutake) has consistently decreased in Japan over the past few decades. We used 15 polymorphic and codominant simple sequence repeat (SSR) markers, developed using next-generation sequencing, to carry out genetic analyses of 10 populations in Nagano, Japan. Using the SSRs, we identified 223 genotypes, none of which was observed in more than one population. The mean expected heterozygosity and standardized allelic richness values were 0.67 and 4.05, respectively. Many alleles appeared in only one of the 10 populations; 34 of these private alleles were detected with a mean number per population of 3.4. The fixation index (FST) and standardized genetic differentiation (G′ST) values were 0.019 and 0.028, respectively. Analysis of molecular variance (AMOVA) showed that the contribution of among population, among genets within a population, and within genets variation to the total variation was 2.91%, 11.62%, and 85.47%, respectively, with genetic differentiation being detected for all sources. Twenty-eight of 45 pairwise FST values were significantly larger than zero, and no pattern of isolation by distance was detected among the 10 populations. Bayesian-based clustering did not show clear differences among populations. These results suggest that reestablishment of a colony would be best accomplished by transplantation within a field; if this is not possible, then transplantation from within several dozen kilometers will cause little damage to the original population genetic structure.

The petiole of Colocasia gigantea (Blume) Schott is an important agricultural and biological organ, which contains high dietary fiber, pyridoxine, and nicotinamide. However, available genomic resources of C. gigantea are scarce, and this restricts further genetic diversity research, linkage map construction, and marker-assisted selection in C. gigantea. A large-scale genomic DNA study of C. gigantea was conducted using the 454 sequencing technology to develop simple sequence repeats (SSRs). We identified 31 069 putative genomic C. gigantea SSRs, and 100 primers were randomly selected to validate their usefulness in 10 C. gigantea samples. The specificity of six primers yielded amplification products with expected sizes and exhibited polymorphism. The number of alleles per locus ranged from 3 to 7 alleles and the polymorphic information content (PIC) ranged from 0.561 to 0.756. The newly developed SSRs in this study should be useful tools for assessing genetic diversity, understanding population structure, and conserving and using C. gigantea effectively.

The objective of this work was to map QTL for agronomic traits in a Brazilian soybean population. For this, 207 F2:3 progenies from the cross CS3035PTA276-1-5-2 x UFVS2012 were genotyped and cultivated in Viçosa-MG, using randomized block design with three replications. QTL detection was carried out by linear regression and composite interval mapping. Thirty molecular markers linked to QTL were detected by linear regression for the total of nine agronomic traits. QTL for SWP (seed weight per plant), W100S (weight of 100 seeds), NPP (number of pods per plant), and NSP (number of seeds per plant) were detected by composite interval mapping. Four QTL with additive effect are promising for marker-assisted selection (MAS). Particularly, the markers Satt155 and Satt300 could be useful in simultaneous selection for greater SWP, NPP, and NSP.

Pterocarpus is a genus of trees mainly distributed in tropical Asia, Africa, and South America. Some species of Pterocarpus are rosewood tree species, having important economic value for timber, and for some species, medicinal value as well. Up to now, information about this genus with regard to the genomic characteristics of the chloroplasts has been limited. Based on a combination of next-generation sequencing (Illumina Hiseq) and long-read sequencing (PacBio), the whole chloroplast genomes (cp genomes) of five species (rosewoods) in Pterocarpus (Pterocarpus macrocarpus, P. santalinus, P. indicus, P. pedatus, P. marsupium) have been assembled. The cp genomes of five species in Pterocarpus have similar structural characteristics, gene content, and sequence to other flowering plants. The cp genomes have a typical four-part structure, containing 110 unique genes (77 protein coding genes, 4 rRNAs, 29 tRNAs). Through comparative genomic analysis, abundant simple sequence repeat (SSR)loci (333–349) were detected in Pterocarpus, among which A /T single nucleotide repeats accounted for the highest proportion (72.8–76.4%). In the five cp genomes of Pterocarpus, eight hypervariable regions, including trnH-GUG_psbA, trnS-UGA_psbC, accD-psaI, ndhI-exon2_ndhI-exon1, ndhG_ndhi-exon2, rpoC2-exon2, ccsA, and trnfM-CAU, are proposed for use as DNA barcode regions. In the comparison of gene selection pressures (P. santalinus as the reference genome), purifying selection was inferred as the primary mode of selection in maintaining important biological functions. Phylogenetic analysis shows that Pterocarpus is a monophyletic group. The species P. tinctorius is resolved as early diverging in the genus. Pterocarpus was resolved as sister to the genus Tipuana.