Development of SNP parentage assignment techniques in the yellowfin seabream Acanthopagrus latus

Acanthopagrus latus is an essential aquaculture species on the south coast of China.However,there is a lack of systematic breeding of A.latus,which considerably limits the sustainable development of A.latus.As a result,genetic improvements are urgently needed to breed new strains of A.latus with rapid growth and strong resistance to disease.During selective breeding,it is necessary to estimate the genetic parameters of the target trait,which in turn depends on an accurate disentangled pedigree for the selective population.Therefore,it is necessary to establish the parentage assignment technique for A.latus.In this study,95 individuals selected from their parents and their 14 families were used as experimental material.SNPs were developed by genome resequencing,and highly polymorphic SNPs were screened on the basis of optimized filtering parameters.A total of 14392738 SNPs were discovered and 205 SNPs were selected for parentage assignment using the CERVUS software.In the model where the gender of the parents is known,the assignment success rate is 98.61%for the male parent,97.22%for the female parent,and 95.83%for the parent pair.In the model where the gender of the parents is unknown,the assignment success rate is 100%for a single parent and 90.28%for the parent pair.The results of this study were expected to serve as a reference for the breeding of new varieties of A.latus.

Multiplex PCR Sets of Novel Microsatellite Loci for Iwagaki Oyster Crassostrea nippona and Their Application in Parentage Assignment

Iwagaki oyster,Crassostrea nippona,widely distributes along the seashore of Eastern Asia,and has been considered to be a potential breeding species due to its delicious taste and high commercial value.In order to study its genetic background and population structure,we developed 46 novel polymorphic microsatellite markers using next-generation sequencing technique and characterized them in 30 individuals.The number of alleles ranged from 3 to 22,while the observed and expected heterozygosities varied from 0.133 to 1.000 and 0.455 to 0.949,respectively.Fifteen microsatellite markers were selected and grouped into five highly informative multiplex PCRs for C.nippona.We evaluated and validated these multiplex PCRs in a cultured population including 173 candidate parents and 486 offspring.In actual parentage analysis,80%of the offspring were correctly assigned to their parental pairs using three multiplex PCRs.Furthermore,the success rate of parentage assignment reached 96%when the other two multiplex PCRs were added.These 46 microsatellite loci with high variability and the five multiplex PCRs described here provide a powerful tool for pedigree reconstruction,resource conservation and selective breeding program of C.nippona.

An inter-laboratory study of DNA-based identity,parentage and species testing in animal forensic genetics

The probative value of animal forensic genetic evidence relies on laboratory accuracy and reliability.Inter-laboratory comparisons allow laboratories to evaluate their performance on specific tests and analyses and to continue to monitor their output.The International Society for Animal Genetics(ISAG)administered animal forensic comparison tests(AFCTs)in 2016 and 2018 to assess the limitations and capabilities of laboratories offering forensic identification,parentage and species determination services.The AFCTs revealed that analyses of low DNA template concentrations(≤300 pg/μL)constitute a significant challenge that has prevented many laboratories from reporting correct identification and parentage results.Moreover,a lack of familiarity with species testing protocols,interpretation guidelines and representative databases prevented over a quarter of the participating laboratories from submitting correct species determination results.Several laboratories showed improvement in their genotyping accuracy over time.However,the use of forensically validated standards,such as a standard forensic short tandem repeat(STR)kit,preferably with an allelic ladder,and stricter guidelines for STR typing,may have prevented some common issues from occurring,such as genotyping inaccuracies,missing data,elevated stutter products and loading errors.The AFCTs underscore the importance of conducting routine forensic comparison tests to allow laboratories to compare results from each other.Laboratories should keep improving their scientific and technical capabilities and continuously evaluate their personnel’s proficiency in critical techniques such as low copy number(LCN)analysis and species testing.Although this is the first time that the ISAG has conducted comparison tests for forensic testing,findings from these AFCTs may serve as the foundation for continuous improvements of the overall quality of animal forensic genetic testing.

Using SSR Marker to Trace Chinese Shrimp Fenneropenaeus chinensis Released in Natural Sea-A Feasible Strategy for Assessment of Release Effect in Natural Resources Recovery Program

Enhancement release has been proven effective in natural resources recovery of Chinese shrimp Fenneropenaeus chinensis in the last several decades in China, however, to assess the effectiveness of enhancement release, we still need to develop a high-efficient and easy-operational method to replace those physical-tagging release method with labor intensive, size-and number-limited. In the present study, single(with maternal known) parentage identification using eight simple sequence repeat(SSR) markers genotype fingerprint was used to trace Chinese shrimp released in Bohai Bay in 2013. A total of 884 shrimp spawners were collected from two hatcheries in Tianjin City respectively after enhancement release of shrimp larvae in May 2013. A total of 844 shrimp samples were recaptured around the release location approximately 4 months after the shrimp larvae were released into the natural sea. Genotype data of 8 SSR loci of the 1,726 samples were used for maternal-offspring parentage identification using CEervus 3.0 software. The allele number in each locus ranged from 8 to 68 with an average value of 33.25, which produced the cumulative exclusion probability with one parent known of all these sight loci up to 99%. Among the 844 recaptured shrimp samples, 448(♂:♀=212:232, gender information was lost for 4 samples) were successfully traced to their 337 maternal parents using a logarithm of odds(LOD) > 3.0 threshold. Among these 337 maternal parents, 253 had a single offspring, 62 had two offspring, 18 had three offspring, 3 had four offspring, and 1 had five offspring. For the first time, a large number of released shrimp were identified from recapture samples, and this study showed that it is possible to trace all released Chinese shrimp without using any type of physical tag in enhancement release activities. This not only means more precise recapture ratio assessment than ever expected, but also this method demonstrates an effective method for large-scale hatchery release as well as for organisms used in hatchery enhancement which are not suitable for physical tagging.

Characterization of 12 polymorphic microsatellite markers in the Chinese tree shrew(Tupaia belangeri chinensis)

The Chinese tree shrew(Tupaia belangeri chinensis)is a small experimental animal with a close affinity to primates.This species has long been proposed to be an alternative experimental animal to primates in biomedical research.Despite decades of study,there is no pure breed for this animal,and the overall genetic diversity of wild tree shrews remains largely unknown.In order to obtain a set of genetic markers for evaluating the genetic diversity of tree shrew wild populations and tracing the lineages in inbreeding populations,we developed 12 polymorphic microsatellite markers from the genomic DNA of the tree shrew.An analysis of a wild population of 117 individuals collected from the suburb of Kunming,China,showed that these loci exhibited a highly expected heterozygosity(0.616).These 12 microsatellites were sufficient for individual identification and parentage analysis.The microsatellite markers developed in this study will be of use in evaluating genetic diversity and lineage tracing for the tree shrew.

WAVEFUNCTIONS OF L-S COUPLING FERMION SYSTEM(Ⅰ): SINGLE-l

In this paper. it is discussed how to constrnct wavefunctions of L-S couplingfermion system, which are classified by group chain A recurrent formula of fractional parentage coefficients with fixedseniority is also given.

WAVEFUNCTIONS OF L-S COUPLING FERMION SYSTEM (Ⅱ):DOUBLE■-l

The wavefunctions of L-S coupling fermion system, which are classified by group chain U(4ι1 + 4ι2 + 4) Us(2)×(U L(2ι+ 2ι2 + 2) O(2ι1 + 2ι2 + 2) O(2ι+1) ×O(2ι2 + 1) O1 (3)×O2 (3) O(3)), are constructed through introducing generalized pairs coupled by fermions with different ι. With the help of the fractional parentage coefficients of single-ιfermion system, the author obtains the corresponding fractional parentage coefficients of double-ιfermion system.

Reducing the Common Environmental Effect on Litopenaeus vannamei Body Weight by Rearing Communally at Early Developmental Stages and Using a Reconstructed Pedigree

Heritability estimates may be severely biased when a large common environmental effect on a family arises from a longlasting separate rearing at early stages(SRES)in traditional selective breeding programs,especially when bred populations have weak genetic ties.Communal rearing at early stages(CRES)may reduce common environmental effect since all families are reared in the same environment immediately after hatching.Here,we compared the effects of CRES and SRES strategies on genetic parameter estimation for harvest body weight in a selective breeding population of Litopenaeus vannamei with a small number of half-sib families.Genetic parameters of each strategy were estimated by using animal models excluding and including the common environmental effect(Model 1 and Model 2,respectively).Heritability estimates for body weight were 0.21±0.06(P<0.05)and 0.69±0.09(P<0.05)for CRES and SRES,respectively,in Model 1,and 0.21±0.06(P<0.05)and 0.52±0.27(P>0.05)in Model 2.The ratio of common environmental variance to phenotypic variance was 0.002±0.000 and 0.071±0.112 for CRES and SRES,respectively.Neither strategy precisely partitioned the common environmental variance according to likelihood ratio test.Lower heritability for body weight in CRES than in SRES implied that a large common environmental variance was confounded with additive genetic variance and was not effectively partitioned in SRES.Moreover,genetic correlation of body weight between the two strategies was 0.75±0.15,indicating that family rankings truly changed.The CRES should be followed in the selective breeding program of shrimp,especially in a population with a shallow pedigree and weak genetic ties between families.

PCR技术在法医生物学中的应用

遗传学认为,DNA是人体性状及遗传变异的物质基础,它是遗传信息的携带者.DNA决定着我们的肤色、性别、身高、健康状况等个体特征.每个人的DNA都是不完全一样的.在法医学上,往往需要鉴别现场留下的物证是否属于犯罪嫌疑人.传统的方法主要是通过指纹、脚印、唇纹、化学物质等物证进行核对,这在一些情况下能起到作用.然而,有时候犯罪分子相当狡猾,或者现场被破坏的很严重,根本找不到上述痕迹.但是在理论上,只要犯罪分子在现场留下血渍、精斑、头发、阴毛、唾液等,通过分析其中的DNA,仍可查获真凶.另外,也可通过分析在现场找到的死者的残留物(如毛发、牙齿、骨骼等)中所含的DNA,来验明他们的真实身份.以前由于这些物证中DNA的含量甚微,再加上无法排除在分析时受到的干扰,DNA分析还或多或少是一种幻想.直到1985年,诺贝尔奖获得者Kary mullis发明了聚合酶链反应(polymerasechain reaction,PCR).再加上1988年Saiki对PCR的重大改进,才使DNA分析在法医学领域的应用取得了惊人的突破.所谓PCR,就是通过特定的DNA序列作为引物,在酶的作用下,经过几十次循环,使目的DNA得以快速复制、扩增,从而得到足以进行检测和分析的目的DNA片段.目的DNA(或称模板DNA)就好象是“轮子”,引物好象有汽车的“方向”,酶好象是“(?)

Local Altruism as an Environmental Ethic in CO₂Emissions Control

When considering emissions control problems associated with carbon dioxide (CO2), social planning over quite a long-term horizon is usually considered to be necessary because it takes much time for the full absorption of CO2 by oceans and forests. Sometimes the required time horizon even becomes infinite. Such a fact seems to impose patience beyond the limits of human cognition. However, this study proves that the first-best emissions scenario can be achieved only by local altruism, which is dubbed parentage. Parentage is defined as the action of applying zero social discount rate to its subsequent generation, and discounting the utility of generations thereafter infinitely. In this sense, the nearly first-best emissions scenario is feasible within the ordinal cognition and benevolence of human beings. This paper also examines the definition of egalitarian sustainability, in which the utility of every generation must be kept constant, and reveals that such a definition of sustainability possibly provokes the inefficient intergenerational allocation of CO2. This is because the vested interest of the predecessors is put much importance in the process of the planning. It is required more rigid sustainability concept, in which the utility of each generation is no less decreasing through time and at least strictly increasing locally, to achieve the efficient allocation of CO2. One will find that the intergenerational allocation by the local altruism satisfies this property.

Cluster-Cluster Potentials for the Carbon Nucleus

Two types of potentials are given in the present paper. The two potentials have Gaussian radial dependences. Such shapes of radial functions are suitable for using in the unitary scheme model. The first potential is given in the form of an attractive force and the second is given in the form of a superposition of repulsive and attractive forces. The two potentials are used to calculate the binding energy of the carbon nucleus 12C. For this purpose, we expand the ground-state wave function of carbon in a series of the bases of the unitary scheme model and apply the variational method. To calculate the necessary matrix elements required to obtain the binding energy of carbon, we factorized the unitary scheme model bases in the form of products of two wave functions: the first function represents the set of the A-4 nucleons and the second function represents the set of the last four nucleons by using the well-known four-body fractional parentage coefficients. Good results are obtained for the binding energy of 12C by using the two potentials.

Integrated tool for microsatellite isolation and validation from the reference genome and their application in the study of breeding turnover in an endangered avian population

Accurate individual identification is required to estimate survival rates in avian populations.For endangered species,non-invasive methods of obtaining individual identification,such as using molted feathers as a source of DNA for microsatellite markers,are preferred because of less disturbance,easy sample preparation and high efficiency.With the availability of many avian genomes,a few pipelines isolating genome-wide microsatellites have been published,but it is still a challenge to isolate microsatellites from the reference genome efficiently.Here,we have developed an integrated tool comprising a bioinformatic pipeline and experimental procedures for microsatellite isolation and validation based on the reference genome.We have identified over 95000 microsatellite loci and established a system comprising 10 highly polymorphic markers(PIC value:0.49–0.93,mean:0.79)for an endangered species,saker falcon(Falco cherrug).These markers(except 1)were successfully amplified in 126 molted feathers,exhibiting high amplification success rates(83.9–99.7%),high quality index(0.90–0.97)and low allelic dropout rates(1–9.5%).To further assess the efficiency of this marker system in a population study,we identified individual sakers using these molted feathers(adult)and 146 plucked feathers(offspring).The use of parent and offspring samples enabled us to infer the genotype of missing samples(N=28),and all adult genotypes were used to ascertain that breeding turnover is a useful proxy for survival estimation in sakers.Our study presents a cost-effective tool for microsatellite isolation based on publicly available reference genomes and demonstrates the power of this tool in estimating key parameters of avian population dynamics.