Assigning alleles to different loci in amplifications of duplicated loci

Duplicated loci, for example those associated with major histocompatibility complex (MHC) genes, often have similar DNA sequences that can be coamplified with a pair of primers. This results in genotyping difficulties and inaccurate analyses. Here, we present a method to assign alleles to different loci in amplifications of duplicated loci. This method simultaneously considers several factors that may each affect correct allele assignment. These are the sharing of identical alleles among loci, null alleles, copy number variation, negative amplification, heterozygote excess or heterozygote deficiency, and linkage disequilibrium. The possible multilocus genotypes are extracted from the alleles for each individual and weighted to estimate the allele frequencies. The likelihood of an allele configuration is calculated and is optimized with a heuristic algorithm. Monte‐Carlo simulations and three empirical MHC data sets are used as examples to evaluate the efficacy of our method under different conditions. Our new software, mhc‐typer V1.1, is freely available at https://github.com/huangkang1987/mhc-typer .     

Comparative analysis of metabolome of rice seeds at three developmental stages using a recombinant inbred line population

Plants are considered an important food and nutrition source for humans. Despite advances in plant seed metabolomics, knowledge about the genetic and molecular bases of rice seed metabolomes at different developmental stages is still limited. Here, using Zhenshan 97 (ZS97) and Minghui 63 (MH63), we performed a widely targeted metabolic profiling in seeds during grain filling, mature seeds and germinating seeds. The diversity between MH63 and ZS97 was characterized in terms of the content of metabolites and the metabolic shifting across developmental stages. Taking advantage of the ultra‐high‐density genetic map of a population of 210 recombinant inbred lines (RILs) derived from a cross between ZS97 and MH63, we identified 4681 putative metabolic quantitative trait loci (mQTLs) in seeds across the three stages. Further analysis of the mQTLs for the codetected metabolites across the three stages revealed that the genetic regulation of metabolite accumulation was closely related to developmental stage. Using in silico analyses, we characterized 35 candidate genes responsible for 30 structurally identified or annotated compounds, among which LOC_Os07g04970 and LOC_Os06g03990 were identified to be responsible for feruloylserotonin and l ‐asparagine content variation across populations, respectively. Metabolite?agronomic trait association and colocation between mQTLs and phenotypic quantitative trait loci (pQTLs) revealed the complexity of the metabolite?agronomic trait relationship and the corresponding genetic basis.     

德州汉族人群37个Y⁃STR基因座遗传多态性分析

调查德州汉族人群598名男性无关个体37个Y-STR基因座的遗传多态性,分析其在法医学和群体遗传学方面的应用价值,用AGCU Y37荧光检测试剂盒对德州汉族群体的37个Y-STR基因座进行扩增,用3500xL基因分析仪对其进行检测。用MEGA 7.0软件,通过邻接法（neighbor-joining, NJ）构建德州汉族群体和其他15个参考群体的系统发生树,探索群体间的遗传关系。结果共检出593种单倍型,基因多样性（genetic diversity, GD）值为0.113 9（DYS645）～0.971 4（DYS385a/b）,单倍型多样性（haplotype diversity, HD）和识别能力（discriminative capacity, DC）分别为0.999 971 989和0.991 6。结果表明,这37个Y-STR基因座在德州汉族人群中有较高的多态性分布。群体遗传分析中,遗传距离、多维尺度分析( multi-dimensional scaling,MDS) 和系统发生树分析结果表明,德州汉族与其他地区的汉族群体遗传距离更近。不同群体的遗传特征与语系划分、历史形成、地理分布等方面具有一致性。研究结果可为德州汉族人群的法庭科学和群体遗传学研究提供基础数据支持。     

Low Inbreeding and High Pollen Dispersal Distances in Populations of Two Amazonian Forest Tree Species

Recent studies suggest that tropical tree species exhibit low inbreeding and high gene dispersal levels despite the typically low density of conspecifics in tropical forests. To examine this, we undertook a study of pollen gene dispersal and mating system of two Amazonian tree species. We analyzed 341 seeds from 33 trees at four microsatellite loci in a Carapa guianensis population from Brazil, and 212 seeds from 22 trees at four microsatellite loci in a Sextonia rubra population from French Guiana. Differentiation of allele frequencies among the pollen pool of individual trees was Φ_FT= 0.053 (95% CI: 0.027–0.074) for C. guianensis and Φ_FT= 0.064 (95% CI: 0.017–0.088) for S. rubra. The mean pollen dispersal distances were estimated at 69–355 m for C. guianensis , and 86–303 m for S. rubra , depending on the pollen dispersal model and the estimate of reproductive tree density used. The multi-locus outcrossing rate was estimated at 0.918 and 0.945, and the correlation of paternity at 0.089 and 0.096, for C. guianensis and S. rubra , respectively, while no significant levels of biparental inbreeding were detected. Comparing trees with high and low local density of conspecifics, we found no evidence for differences in inbreeding levels. The results are discussed within the framework of the emerging picture of the reproductive biology of tropical forest trees.     

Leishmania (Viannia) braziliensis: epidemiology of canine cutaneous leishmaniasis in the State of Paraná (Brazil)

The present study examines the role that dogs play in the maintenance of the Leishmania cycle in the State of Paraná, Southern Brazil. Dogs were examined in three regions where cutaneous leishmaniasis is endemic or epidemic (R1-Vale da Ribeira; R2-Central region of Paraná State and R3-Northern region). To determine serum prevalence rates ELISA was used. In regions endemic for Trypanosoma cruzi (R1 and R3), serum from dogs seroreactive towards Leishmania antigen was subjected to T. cruzi adsorption in order to eliminate cross-reaction with common antigen epitopes. Concomitantly, dogs with cutaneous lesions were biopsied to isolate and identify parasites using RAPD. Leishmania were classified by the phenetic method using the Jaccard coefficient of similarity, and grouped by Unweighted Pair-Group Method using an Arithmetic Average (UPGMA). A total of 410 dogs were studied. In R1 (Vale da Ribeira) 159 dogs were evaluated of which 10 had anti-Leishmania antibody. In R2 (Central Paraná), 39 animals were examined of which 8 were seropositive. In R3 (the North) 212 dogs were evaluated of which 39 animals were seropositive. Thirteen dogs had cutaneous lesions and the parasites were isolated from a dog with mucocutaneous lesion in R1, two animals with simple skin lesions in R2 and 10 dogs with multiple lesions in R3. The identification of the parasite by molecular methods showed it to be L. (Viannia) braziliensis. Based on this information, the role of domestic dogs in Leishmania infection of cutaneous leishmaniasis in Paraná is discussed.     

The significance of multiple mating in the social wasp Vespula maculifrons

The evolution of the complex societies displayed by social insects depended partly on high relatedness among interacting group members. Therefore, behaviors that depress group relatedness, such as multiple mating by reproductive females (polyandry), are unexpected in social insects. Nevertheless, the queens of several social insect species mate multiply, suggesting that polyandry provides some benefits that counteract the costs. However, few studies have obtained evidence for links between rates of polyandry and fitness in naturally occurring social insect populations. We investigated if polyandry was beneficial in the social wasp Vespula maculifrons. We used genetic markers to estimate queen mate number in V. maculifrons colonies and assessed colony fitness by counting the number of cells that colonies produced. Our results indicated that queen mate number was directly, strongly, and significantly correlated with the number of queen cells produced by colonies. Because V. maculifrons queens are necessarily reared in queen cells, our results demonstrate that high levels of polyandry are associated with colonies capable of producing many new queens. These data are consistent with the explanation that polyandry is adaptive in V. maculifrons because it provides a fitness advantage to queens. Our research may provide a rare example of an association between polyandry and fitness in a natural social insect population and help explain why queens in this taxon mate multiply.     

Resolving the genetic basis of invasiveness and predicting invasions

Considerable effort has been invested in determining traits underlying invasiveness. Yet, identifying a set of traits that commonly confers invasiveness in a range of species has proven elusive, and almost nothing is known about genetic loci affecting invasive success. Incorporating genetic model organisms into ecologically relevant studies is one promising avenue to begin dissecting the genetic underpinnings of invasiveness. Molecular biologists are rapidly characterizing genes mediating developmental responses to diverse environmental cues, i.e., genes for plasticity, as well as to environmental factors likely to impose strong selection on invading species, e.g., resistance to herbivores and competitors, coordination of life-history events with seasonal changes, and physiological tolerance of heat, drought, or cold. Here, we give an overview of molecular genetic tools increasingly used to characterize the genetic basis of adaptation and that may be used to begin identifying genetic mechanisms of invasiveness. Given the divergent traits that affect invasiveness, “invasiveness genes” common to many clades are unlikely, but the combination of developmental genetic advances with further evolutionary studies and modeling may provide a framework for identifying genes that account for invasiveness in related species.     

Characterization of novel microsatellite markers from the Yesso scallop Mizuhopecten yessoensis

Twelve polymorphic and informative microsatellite markers were isolated and characterized for the Yesso scallop, Mizuhopecten yessoensis. We characterized these loci by genotyping 48 individuals; the number of alleles ranged from two to eight, and the values of observed heterozygosity and expected heterozygosity varied from 0 to 0.8333 and from 0.2546 to 0.8231, respectively. No significant linkage disequilibrium between pairs of loci was found and three loci showed significant heterozygote deficiency from the Hardy–Weinberg equilibrium. These markers are potential for studies of the population structure, individual or hybrid identification of the species.     

Isolation and characterization of microsatellite loci in the flat‐headed bat (Tylonycteris pachypus)

Microsatellite loci were developed in the flat‐headed bat (Tylonycteris pachypus) from genomic DNA using an enriched library method. Nine loci were tested on 48 individuals sampled from Guangxi Province, China. The mean number of observed alleles per locus was 6.4 (range 4–12). Observed and expected heterozygosity values ranged from 0.24 to 0.83 and from 0.30 to 0.89, respectively. One locus revealed significant departure from Hardy–Weinberg equilibrium and no significant linkage disequilibrium was detected between loci pairs. These markers will be used to examine genetic structure and parentage analysis in this species.