Meta-analysis reveals asymmetric reduction in the genetic diversity of introduced populations of exotic insects

Factors promoting the invasion success of introduced populations have been receiving increased attention in studies of biological invasions. Previous reports have indicated that successful invasions may be attributable to reduced genetic diversity in the invasive species. However, there is large variation in the magnitude and direction of the impact of exotic species that have remained unexplained. Here, we present a structured meta-analysis of papers investigating the genetic diversity of native and introduced populations of exotic insects using nuclear microsatellites and mitochondrial DNA sequences. The results indicate that invasion by exotic insects had an overall reducing effect on the genetic diversity of the invading population, with nonzero effect sizes for the number of alleles (NA), observed heterozygosity (Ho), expected heterozygosity (He) and nucleotide diversity (Nd). However, when analyzing different orders (e.g., Lepidoptera, Hemiptera), the effect sizes of NA, Ho and Nd in Lepidoptera were found to bracket zero, as did the effect size of He in Hemiptera. These results suggest an asymmetric reduction in the genetic diversity of introduced populations of exotic insects, indicating diverse mechanisms underlying their successful invasion.     

A novel set of 223 EST-SSR markers in <Emphasis Type="Italic">Casuarina</Emphasis> L. ex Adans.: polymorphisms,cross-species transferability,and utility for commercial clone genotyping

Simple sequence repeat (SSR) markers are very useful for genetic applications in plants, but SSR resource for the important tree genus Casuarina L. ex Adans. is still limited. In this study, we report a novel set of 223 SSR markers in Casuarina developed from expressed sequence tag (EST) resource of GenBank. The 223 EST-SSR markers were polymorphic among 10 unrelated individuals of C. equisetifolia L. Johnson, with the number of alleles per locus (N_a), observed heterozygosity (H_o), expected heterozygosity (H_e), and polymorphic information content (PIC) averaging at 5.5, 0.72, 0.86, and 0.63, respectively. The rates of cross-species transferability ranged from 96.9% (C. glauca Sieber ex Sprengel) through 97.8% (C. cunninghamiana Miquel) to 99.1% (C. junghuhniana Miquel). Fifty-five C. equisetifolia clones widely planted in China were successfully genotyped with a subset of 20 EST-SSRs. These newly developed markers will have a great potential for genetic and breeding applications in Casuarina species and related taxa.     

Differential invasion success in aquatic invasive species: the role of within- and among-population genetic diversity

Despite a well-developed theoretical basis for the role of genetic diversity in the colonization process, contemporary investigations of genetic diversity in biological invasions have downplayed its importance. Observed reductions in genetic diversity have been argued to have a limited effect on the success of establishment and impact based on empirical studies; however, those studies rarely include assessment of failed or comparatively less-successful biological invasions. We address this gap by comparing genetic diversity at microsatellite loci for taxonomically and geographically paired aquatic invasive species. Our four species pairs contain one highly successful and one less-successful invasive species (Gobies: Neogobius melanostomus, Proterorhinus semilunaris; waterfleas: Bythotrephes longimanus, Cercopagis pengoi; oysters: Crassostrea gigas, Crassostrea virginica; tunicates: Bortylloides violaceous, Botryllus schlosseri). We genotyped 2717 individuals across all species from multiple locations in multiple years and explicitly test whether genetic diversity is lower for less-successful biological invaders within each species pair. We demonstrate that, for gobies and tunicates, reduced allelic diversity is associated with lower success of invasion. We also found that less-successful invasive species tend to have greater divergence among populations. This suggests that intraspecific hybridization may be acting to convert among-population variation to within-population variation for highly successful invasive species and buffering any loss of diversity. While our findings highlight the species-specific nature of the effects of genetic diversity on invasion success, they do support the use of genetic diversity information in the management of current species invasions and in the risk assessment of potential future invaders.     

Variance in Female Reproductive Success Differentially Impacts Effective Population Size in the Short-Nosed Fruit Bat, <Emphasis Type="Italic">Cynopterus sphinx</Emphasis>

Effective population size (N _e) quantifies the effects of micro-evolutionary processes and the rate of loss of genetic diversity in a population. Several demographic and mating parameters reduce N _e. Theoretical studies elucidate the impacts of various demographic and mating system parameters on N _e, while empirical studies illustrate realized N _e for species with differing life histories and mating systems. However, effect of intra-specific variation in mating system on effective size remains largely unexplored. In this paper we investigated the effect of promiscuous and polygynous mating on N _e in two wild populations of the short-nosed fruit bat, Cynopterus sphinx. N _e/N (ratio of effective population size to census size) was lower than unity in both populations, and much lower for the polygynous population compared to promiscuous population. Elasticity analyses reveal that N _e/N was sensitive to deviations in the sex ratio. Variance in female reproductive success had a higher impact on N _e compared to variance in male reproductive success in the promiscuous population. However, for the polygynous population, impact of variance in male reproductive success on N _e was higher than that of variance in female reproductive success. Our results suggest that depending on mating system, different populations of the same species could have alternate evolutionary trajectories. The rate of loss of genetic diversity would be lower for the promiscuous population compared to the polygynous population. Our study is the first to highlight which parameters would most significantly impact population specific N _e under different mating systems.     

Candidate gene sequencing and validation of SNP markers linked to carotenoid content in cassava (<Emphasis Type="Italic">Manihot esculenta</Emphasis> Crantz)

Cassava is a widely grown staple in Sub-Saharan Africa and consumed as a cheap source of calories, but the crop is deficient in micronutrients including pro-vitamin A carotenoids. This challenge is currently being addressed through biofortification breeding that relies on phenotypic selection. Gene-based markers linked to pro-vitamin A content variation are expected to increase the rate of genetic gain for this critical trait. We sequenced four candidate carotenoid genes from 167 cassava accessions representing the diversity of elite breeder lines from IITA. Total carotenoid content was determined using spectrophotometer and total β-carotene was quantified by high-performance liquid chromatography. Storage root yellowness due to carotenoid pigmentation was assessed. We carried out candidate gene association analysis that accounts for population structure and kinship using genome-wide single nucleotide polymorphisms (SNPs) generated through genotyping-by-sequencing. Significant SNPs were used to design competitive allele-specific PCR assays and validated on the larger population for potential use in marker-assisted selection breeding. Candidate gene sequencing of the genes β-carotene hydroxylase (crtRB), phytoene synthase (PSY2), lycopene epsilon cyclase (lcyE), and lycopene beta cyclase (lcyB) yielded a total of 37 SNPs. Total carotenoid content, total β-carotene, and color parameters were significantly associated with markers in the PSY2 gene. The SNPs from lcyE were significantly associated with color while those of lcyB and crtRB were not significantly associated with carotenoids or color parameters. These validated and breeder-friendly markers have potential to enhance the efficiency of selection for high β-carotene cassava, thus accelerating genetic gain.     

Genetic diversity of Nubian ibex in comparison to other ibex and domesticated goat species

Capra nubiana is a wild ibex species that is in danger of extinction. This study aimed at assessing the genetic diversity and population structure of Nubian ibex (Capra nubiana, n?=?8) in comparison to Alpine ibex (Capra ibex, n?=?8), Bezoar ibex (Capra aegagrus, n?=?4), and domesticated Taggar goats (Capra aegagrus hircus, n?=?24). All animals were genotyped with the 50K goat SNP chip. Since commercial SNP chips are not designed for wild species, data analysis was done in two ways: (1) using all callable SNPs (33,698) and (2) with a reduced set of SNPs segregating within three out of four populations (662). Using these two sets of SNPs, the observed heterozygosity in Nubian ibex ranged from 0.02 to 0.44, in Alpine ibex from 0.01 to 0.38, and in Bezoar ibex from 0.13 to 0.38, when analyzing 33,698 or 662 SNPs, respectively. In domesticated Taggar goats, the values for the observed heterozygosity using all 33,698 callable SNPs and the reduced set of 662 SNPs were similar (0.40–0.41). Pairwise F_ST values for the differentiation between species ranged from 0.17–0.35 (Bezoar ibex vs. Taggar goats) to 0.47–0.91 (Bezoar vs. Alpine ibex), and was 0.33–0.90 between Bezoar and Nubian ibex, respectively, to the two sets of SNPs. The analysis of molecular variance among all animals revealed that 74–78% can be explained by differences between species, while the residual 22–26% result from differences among individuals, respectively. Cluster analysis of Nei’s genetic distance allowed to detected two distinct clusters comprising Nubian and Alpine ibex on one hand and Taggar goats and Bezoar ibex on the other hand, and clear separation of all four breeds. Principal component (PC) analysis confirmed and further refined the clusters. SNPs that contributed most to PC1 allowed us to identify genomic regions accounting for the distances between species. These regions contain known milk protein genes. The identification of milk protein genes as contributors to the differentiation between species provides insights into the domestication of wild Capra breeds.     

Identifying SNP markers tightly associated with six major genes in peach [<Emphasis Type="Italic">Prunus persica</Emphasis> (L.) Batsch] using a high-density SNP array with an objective of marker-assisted selection (MAS)

One of the applications of genomics is to identify genetic markers linked to loci responsible for variation in phenotypic traits, which could be used in breeding programs to select individuals with favorable alleles, particularly at the seedling stage. With this aim, in the framework of the European project FruitBreedomics, we selected five main peach fruit characters and a resistance trait, controlled by major genes with Mendelian inheritance: fruit flesh color Y, fruit skin pubescence G, fruit shape S, sub-acid fruit D, stone adhesion-flesh texture F-M, and resistance to green peach aphid Rm2. They were all previously mapped in Prunus. We then selected three F₁ and three F₂ progenies segregating for these characters and developed genetic maps of the linkage groups including the major genes, using the single nucleotide polymorphism (SNP) genome-wide scans obtained with the International Peach SNP Consortium (IPSC) 9K SNP array v1. We identified SNPs co-segregating with the characters in all cases. Their positions were in agreement with the known positions of the major genes. The number of SNPs linked to each of these, as well as the size of the physical regions encompassing them, varied depending on the maps. As a result, the number of useful SNPs for marker-assisted selection varied accordingly. As a whole, this study establishes a sound basis for further development of MAS on these characters. Additionally, we also discussed some limitations that were observed regarding the SNP array efficiency.     

A novel set of EST-InDel markers in <Emphasis Type="Italic">Eucalyptus</Emphasis> L’Hérit.: polymorphisms,cross-species amplification,physical positions and genetic mapping

Insertion/deletion (InDel) markers are valuable for genetic applications in plant species, and the public databases of expressed sequence tags (ESTs) have facilitated the development of genic InDel markers. In this study, we developed a novel set of 144 InDel markers in an important tree genus Eucalyptus L’Hérit. using the ESTs of GenBank. Amplicon sequencing against two parents of a mapping population (Eucalyptus urophylla S. T. Blake × E. tereticornis Smith) revealed that the InDel size ranged from 2 to 44 bases, and the dinucleotide type was the most abundant (37.3 %). The cross-species/subgenus amplification rate ranged from 62.5 % in E. tessellaris F. Muell. (subgenus Blakella) to 99.3 % in E. grandis Hill ex Maiden (subgenus Symphyomyrtus) with an average of 85.4 %. There were 121 EST-InDels (84.0 %) polymorphic among 12 individuals of E. grandis, and the mean number of alleles per polymorphic locus (N _a), observed heterozygosity (H _o), expected heterozygosity (H _e) and polymorphic information content (PIC) were 4.0, 0.278, 0.538 and 0.465, respectively. Physical positions of 143 EST-InDels were predicted on the E. grandis genome sequence. A total of 81 EST-InDels were incorporated into prior dense genetic maps of E. urophylla and E. tereticonis, and extensive synteny and colinearity were observed between E. grandis genome sequence and the mapped EST-InDel markers. These EST-InDels will provide a valuable resource of functional markers for genetic diversity evaluation, genome comparison, QTL mapping and marker-assisted breeding in Eucalyptus.     

Narrow-sense heritability and <Emphasis Type="Italic">P</Emphasis><Subscript>ST</Subscript> estimates of DNA methylation in three <Emphasis Type="Italic">Populus nigra</Emphasis> L. populations under contrasting water availability

In a context of climate change and forest decline, a better understanding of the sources of tree flexibility involved in phenotypic plasticity and adaptation is needed. These last years, the role of epigenetics in the response to environmental variations has been established in several model plants at the genotype level but little is known at the level of natural populations grown in pedoclimatic sites. Here, we focused on three French natural populations of black poplar, a key pioneer tree from watersheds, planted in common garden and subjected to controlled variations of water availability. We estimated common genetic parameters such as narrow-sense heritability (h²), phenotypic differentiation index (P_ST), and the overall genetic differentiation index (F_ST) from genome-wide SNPs to evaluate the extent of epigenetic variations. Indeed, global DNA methylation levels from individuals exposed to drought or irrigated in a common garden were used. We found that the three populations were not distinguished by their levels of DNA methylation. However, a moderate drought was associated to a significant decrease in DNA methylation in the populations. Narrow-sense heritability and P_ST estimates of DNA methylation were similar to those found for biomass productivity. Heritability and P_ST were higher when trees were subjected to drought than in control condition. Negative genetic correlations between global DNA methylation and height or biomass were detected in drought condition only. Altogether, our data highlight that global DNA methylation acts as a genetic marker of natural population differentiation under drought stress in a pedoclimatic context.     

Development of cost-effective single nucleotide polymorphism marker assays for genetic diversity analysis in <Emphasis Type="Italic">Brassica rapa</Emphasis>

Competitive allele-specific PCR (KASPar) assay is a user-friendly system that provides flexibility in the numbers of single nucleotide polymorphisms (SNPs) and genotypes. Based on Illumina-GA-IIx genomic data from 10 genotypes with a broad genetic background, 3183 SNPs were selected for KASPar assays development, and 568 were finally converted and selected for Brassica rapa germplasm characterization (17.8%) on the basis of reproducibility, missing data rate, and uniform genetic distribution. High levels of polymorphism of these markers across 231 B. rapa genotypes were verified, illustrating by high polymorphic information content (averaged 0.34), minor allele frequency (0.37), genetic diversity (0.45), and the low observed heterozygosity (0.10). Based on the SNP dataset, structure and principal coordinates analysis, and neighbor-joining phylogenetic methods were used to examine the population structure and gave highly consistent results. The 231 accessions were divided into the four primary subspecies, representing 99 accessions from B. rapa ssp. pekinensis, 85 from B. rapa ssp. chinensis, 30 from B. rapa ssp. rapifera, and 17 from B. rapa ssp. oleifera and were further subdivided into 12 lower-order clusters according to different morphotypes. The genetic variability and pairwise fixation index analysis revealed that the ssp. pekinensis accessions possess the most extensive genetic variation among the four subspecies. The KASPar system is highly useful for validating SNPs and will be valuable for genetics research and breeding applications in B. rapa.     

Isolation of Polymorphic RAPD-SSR Markers from Xinjiang Arctic Grayling (<Emphasis Type="Italic">Thymallus arcticus grubei</Emphasis>) and a Test of Cross-Species Amplification

A total of 18 polymorphic microsatellite loci were isolated and characterized from RAPD products in the Xinjiang Arctic Grayling (Thymallus arcticus grubei). The number of alleles (N_a) per locus varied from 2 to 10. Observed (H_o) and expected (H_e) heterozygosities ranged from 0.64 to 0.92, and from 0.63 to 0.88, respectively. Considerable differences were found among HBH, FH and FY populations in the number of alleles, effective number of alleles, number of genotypes at all of these loci. These new RAPD-SSR markers have provided a helpful tool for genetic analyses and resources conservation of T. arcticus grubei. Five additional fish species, Amur grayling (Thymallus grubii), Taimen (Hucho taimen), Sea perch (Lateolabrax japonicus), Lenok (Brachymystax lenok) and Red seam bream (Pagrosomus major) were assessed for cross-species amplification. Three of the five species showed at least one polymorphic locus. In addition, seven loci were found to be polymorphic in at least one species.     

Development of species diagnostic SNP markers for quality control genotyping in four rice (<Emphasis Type="Italic">Oryza</Emphasis> L.) species

Species misclassification (misidentification) and handling errors have been frequently reported in various plant species conserved at diverse gene banks, which could restrict use of germplasm for correct purpose. The objectives of the present study were to (i) determine the extent of genotyping error (reproducibility) on DArTseq-based single-nucleotide polymorphisms (SNPs); (ii) determine the proportion of misclassified accessions across 3134 samples representing three African rice species complex (Oryza glaberrima, O. barthii, and O. longistaminata) and an Asian rice (O. sativa), which are conserved at the AfricaRice gene bank; and (iii) develop species- and sub-species (ecotype)-specific diagnostic SNP markers for rapid and low-cost quality control (QC) analysis. Genotyping error estimated from 15 accessions, each replicated from 2 to 16 times, varied from 0.2 to 3.1%, with an overall average of 0.8%. Using a total of 3134 accessions genotyped with 31,739 SNPs, the proportion of misclassified samples was 3.1% (97 of the 3134 accessions). Excluding the 97 misclassified accessions, we identified a total of 332 diagnostic SNPs that clearly discriminated the three indigenous African species complex from Asian rice (156 SNPs), O. longistaminata accessions from both O. barthii and O. glaberrima (131 SNPs), and O. sativa spp. indica from O. sativa spp. japonica (45 SNPs). Using chromosomal position, minor allele frequency, and polymorphic information content as selection criteria, we recommended a subset of 24 to 36 of the 332 diagnostic SNPs for routine QC genotyping, which would be highly useful in determining the genetic identity of each species and correct human errors during routine gene bank operations.     

A genome-wide association study on growth traits in orange-spotted grouper (<Emphasis Type="Italic">Epinephelus coioides</Emphasis>) with RAD-seq genotyping

The orange-spotted grouper, Epinephelus coioides, is one of the most popular fish in China and Southeast Asian countries because of its important economic value. However, molecular mechanism underlying the growth of orange-spotted grouper has never been fully understood. Herein, we performed a genome-wide association study (GWAS) on a natural population of 198 individuals aiming to screen the whole genome of orange-spotted grouper for identification of growth-related loci by restrictionsite associated DNA sequencing. In this research, 261,366 single nucleotide polymorphisms (SNPs) were developed, in which 110 SNPs were identified to be correlated with growth and 20 SNPs were further confirmed to be associated with both body weight and total length. From these identified SNPs, we annotated a total of 34 genes, including adgrb2, csnkza1, cers5, col22a1, creb5, dnd1, dzank1, dnai1, npy2r, fat3, lrrk2, lrp5, map3k9, and so on. Among these candidate genes, npy2r (neuropeptide Y receptor Y2) was reported to play a critical role in growth of the orange-spotted grouper. In addition, population structure, principal component analysis, kinship matrix and linkage disequilibrium were examined to verify the accuracy and reliability of our GWAS results. Our data will also provide a valuable genetic resource for further marker-assisted selection program to improve growth quality in groupers.     

No genetic association between attention-deficit/hyperactivity disorder (ADHD) and Parkinson’s disease in nine ADHD candidate SNPs

Attention-deficit/hyperactivity disorder (ADHD) and Parkinson’s disease (PD) involve pathological changes in brain structures such as the basal ganglia, which are essential for the control of motor and cognitive behavior and impulsivity. The cause of ADHD and PD remains unknown, but there is increasing evidence that both seem to result from a complicated interplay of genetic and environmental factors affecting numerous cellular processes and brain regions. To explore the possibility of common genetic pathways within the respective pathophysiologies, nine ADHD candidate single nucleotide polymorphisms (SNPs) in seven genes were tested for association with PD in 5333 cases and 12,019 healthy controls: one variant, respectively, in the genes coding for synaptosomal-associated protein 25 k (SNAP25), the dopamine (DA) transporter (SLC6A3; DAT1), DA receptor D4 (DRD4), serotonin receptor 1B (HTR1B), tryptophan hydroxylase 2 (TPH2), the norepinephrine transporter SLC6A2 and three SNPs in cadherin 13 (CDH13). Information was extracted from a recent meta-analysis of five genome-wide association studies, in which 7,689,524 SNPs in European samples were successfully imputed. No significant association was observed after correction for multiple testing. Therefore, it is reasonable to conclude that candidate variants implicated in the pathogenesis of ADHD do not play a substantial role in PD.     

Species delimitation and conservation genetics of the Canarian endemic <Emphasis Type="Italic">Bethencourtia</Emphasis> (Asteraceae)

Bethencourtia Choisy ex Link is an endemic genus of the Canary Islands and comprises three species. Bethencourtia hermosae and Bethencourtia rupicola are restricted to La Gomera, while Bethencourtia palmensis is present in Tenerife and La Palma. Despite the morphological differences previously found between the species, there are still taxonomic incongruities in the group, with evident consequences for its monitoring and conservation. The objectives of this study were to define the species differentiation, perform population genetic analysis and propose conservation strategies for Bethencourtia. To achieve these objectives, we characterized 10 polymorphic SSR markers. Eleven natural populations (276 individuals) were analyzed (three for B. hermosae, five for B. rupicola and three for B. palmensis). The results obtained by AMOVA, PCoA and Bayesian analysis on STRUCTURE confirmed the evidence of well-structured groups corresponding to the three species. At the intra-specific level, B. hermosae and B. rupicola did not show a clear population structure, while B. palmensis was aggregated according to island of origin. This is consistent with self-incompatibility in the group and high gene flow within species. Overall, the genetic diversity of the three species was low, with expected heterozygosity values of 0.302 (B. hermosae), 0.382 (B. rupicola) and 0.454 (B. palmensis). Recent bottleneck events and a low number of individuals per population are probably the causes of the low genetic diversity. We consider that they are naturally rare species associated with specific habitats. The results given in this article will provide useful information to assist in conservation genetics programs for this endemic genus.     

Identification of <Emphasis Type="Italic">Pm58</Emphasis> from <Emphasis Type="Italic">Aegilops tauschii</Emphasis>

Key message

A novel powdery mildew-resistance gene, designated Pm58, was introgressed directly from Aegilops tauschii to hexaploid wheat, mapped to chromosome 2DS, and confirmed to be effective under field conditions. Selectable KASP? markers were developed for MAS.

Abstract

Powdery mildew caused by Blumeria graminis (DC.) f. sp. tritici (Bgt) remains a significant threat to wheat (Triticum aestivum L.) production. The rapid breakdown of race-specific resistance to Bgt reinforces the need to identify novel sources of resistance. The d-genome species, Aegilops tauschii, is an excellent source of disease resistance that is transferrable to T. aestivum. The powdery mildew-resistant Ae. tauschii accession TA1662 (2n?=?2x?=?DD) was crossed directly with the susceptible hard white wheat line KS05HW14 (2n?=?6x?=?AABBDD) followed by backcrossing to develop a population of 96 BC₂F₄ introgression lines (ILs). Genotyping-by-sequencing was used to develop a genome-wide genetic map that was anchored to the Ae. tauschii reference genome. A detached-leaf Bgt assay was used to screen BC₂F_4:6 ILs, and resistance was found to segregate as a single locus (χ?=?2.0, P value?=?0.157). The resistance gene, referred to as Pm58, mapped to chromosome 2DS. Pm58 was evaluated under field conditions in replicated trials in 2015 and 2016. In both years, a single QTL spanning the Pm58 locus was identified that reduced powdery mildew severity and explained 21% of field variation (P value?<?0.01). KASP? assays were developed from closely linked GBS-SNP markers, a refined genetic map was developed, and four markers that cosegregate with Pm58 were identified. This novel source of powdery mildew-resistance and closely linked genetic markers will support efforts to develop wheat varieties with powdery mildew resistance.

     

Conservation genetics of the threatened catfish <Emphasis Type="Italic">Conorhynchos conirostris</Emphasis> (Siluriformes: <Emphasis Type="Italic">incertae sedis</Emphasis>), an evolutionary relict endemic to the São Francisco River Basin,Brazil

Analysis of genetic datasets can be particularly useful in providing guidelines for conservation management of understudied species targeted by commercial activities. Here we used population genetic approaches to inform on the conservation status of the Neotropical long-nose pirá catfish, Conorhynchos conirostris. Pirá is a large migratory fish endemic to the São Francisco River Basin (SFRB). It is an evolutionarily divergent and relict species, being the sole representative of an incertae sedis family. The species is considered locally extinct in the upper and lower SFRB, listed as vulnerable on the IUCN Red List and as endangered on the Brazilian Red List (ICMBIO). Fishing prohibition has received severe criticism from middle SFRB fisheries that claim that this understudied species is relatively abundant in that region. We used information from 13 microsatellite markers and COI mitochondrial sequences to clarify the genetic diversity of this enigmatic species in the middle SFRB, to estimate contemporary effective population size (N_e), and to assess its conservation status. Results from bottleneck analyses indicated that the species has experienced recent reductions in population size, which is consistent with small estimates of contemporary N_e. The predicted amount of heterozygosity loss (H_t) in t generations ranged from 0.1152 (for an estimated N_e of 26.4; t?=?100) to 0.7573 (for an estimated N_e of 169.9; t?=?10). Our study supports the conservation status proposed by the ICMBIO to the remaining pirá population. Moreover, we highlight the need for demographic data and the re-assessment of the current IUCN classification for this evolutionary relict lineage.     

A mountain range is a strong genetic barrier between populations of <Emphasis Type="Italic">Afzelia quanzensis</Emphasis> (pod mahogany) with low genetic diversity

Understanding patterns of genetic diversity of plants is important in guiding conservation programs. The aim of our study was to characterize genetic diversity in Afzelia quanzensis, an economically important African tree species. We genotyped 192 individuals at 10 nuclear microsatellite loci. Samples were collected from nine sites in Zimbabwe, five in the north and four in the south, separated by a mountain range, the Kalahari-Zimbabwe axis. Overall, genetic diversity was relatively low across all sites (expected heterozygosity (H _E)?=?0.452, mean number of alleles (A)?=?4.367, allelic richness (A _R)?=?2.917, effective number of alleles (A _E)?=?2.208, and private allelic richness (PA_R)?=?0.197). Genetic diversity estimates, H _E, A, A _R, and PA_R, were not significantly different between northern and southern sites. Allelic richness was significantly higher in southern sites. Significant population differentiation was observed among all sites (F _ST ?=?0.0936, G′ _ST ?=?0.1982, G _ST ?=?0.1001, D _JOST?=?0.0598). STRUCTURE analysis and principal components analysis identified two gene pools, one predominantly made up of southern individuals, and the other of northern individuals. A Monmonier’s function detected a genetic barrier that coincided with the Kalahari-Zimbabwe axis. The relatively low level of genetic diversity in A. quanzensis may reduce adaptability and limit future evolutionary responses. All sites should be monitored for deleterious effects of low genetic diversity, and genetic resource management should take into consideration the existence of the distinct gene pools to capture the entire extant genetic variation.     

Genome-wide association study of body weight in Wenshang Barred chicken based on the SLAF-seq technology

Chicken body weight (BW) is an economically important trait, and many studies have been conducted on genetic selection for BW. However, previous studies have detected functional chromosome mutations or regions using gene chips. The present study used the specific-locus amplified fragment sequencing (SLAF-seq) technology to perform a genome-wide association study (GWAS) on purebred Wengshang Barred chicken. A total of 1,286,715 single-nucleotide polymorphisms (SNPs) were detected, and 175,211 SNPs were selected as candidate SNPs for genome-wide association analysis using TASSEL general linear models. Six SNP markers reached genome-wide significance. Of these, rs732048524, rs735522839, rs738991545, and rs15837818 were significantly associated with body weight at 28 days (BW28), while rs314086457 and rs315694878 were significantly associated with BW120. These SNPs are close to seven genes (PRSS23, ME3, FAM181B, NABP1, SDPR, TSSK6L2, and RBBP8). Moreover, 24 BW-associated SNPs reached “suggestive” genome-wide significance. Of these, 6, 13, 1, and 4 SNPs were associated with BW28, BW56, BW80, and BW120, respectively. These results would enrich the studies on BW and promote the use of Chinese chicken, especially the Wenshang Barred chicken.