Polymorphism profile of nine short tandem repeat Loci in the Han chinese

Nine short tandem repeat (STR) markers (D3S1358, VWA, FGA, THO1, TPOX, CSFIPO, D5S818, D13S317, and D7S820) and a sex-identification marker (Amel-ogenin locus) were amplified with multiplex PCR and were genotyped with a four-color fluorescence method in samples from 174 unrelated Han individuals in North China. The allele frequencies, genotype frequencies, heterozygosity, probability of discrimination powers, probability of paternity exclusion and Hardy-Weinberg equilibrium expectations were determined. The results demonstrated that the genotypes at all these STR loci in Han population conform to Hardy-Weinberg equilibrium expectations. The combined discrimination power (DP) was 1.05×10-10 within nine STR loci analyzed and the probability of paternity exclusion (EPP) was 0.9998. The results indicate that these nine STR loci and the Amelo-genin locus are useful markers for human identification, paternity and maternity testing and sex determination in forensic sciences.     

The Genetic Architecture of Flowering Time and Photoperiod Sensitivity in Maize as Revealed by QTL Review and Meta Analysis

The control of flowering is not only important for reproduction,but also plays a key role in the processes of domestication and adaptation.To reveal the genetic architecture for flowering time and photoperiod sensitivity,a comprehensive evaluation of the relevant literature was performed and followed by meta analysis.A total of 25 synthetic consensus quantitative trait loci(QTL)and four hot-spot genomic regions were identified for photoperiod sensitivity including 11 genes related to photoperiod response or flower morphogenesis and development.Besides,a comparative analysis of the QTL for flowering time and photoperiod sensitivity highlighted the regions containing shared and unique QTL for the two traits.Candidate genes associated with maize flowering were identified through integrated analysis of the homologous genes for flowering time in plants and the consensus QTL regions for photoperiod sensitivity in maize(Zea mays L.).Our results suggest that the combination of literature review,meta-analysis and homologous blast is an efficient approach to identify new candidate genes and create a global view of the genetic architecture for maize photoperiodic flowering.Sequences of candidate genes can be used to develop molecular markers for various models of marker-assisted selection,such as marker-assisted recurrent selection and genomic selection that can contribute significantly to crop environmental adaptation.     

单核苷酸多态性及其在鸡QTL定位上的应用

单核苷酸多态性是指DNA序列上的单个碱基变异,它具有分布广、多态信息含量大、易于检测和统计分析等优点,能较好用于基因图谱构建和数量性状QTL定位研究,被称为继RFLP和微卫星标记之后的第3代基因遗传标记。本文综述了单核苷酸多态性的性质及检测技术、利用候选基因SNP进行鸡QTL定位研究的现状,并对未来SNP的应用前景进行了展望。Abstract:Single nucleotide polymorphism (SNP) refers to the change of single nucleotide in DNA sequence.Because of its high density in genomes and easy in detection and analysis statistically,SNP can be used in genetic linkage map construction and QTL mapping.Here,the characters and detecting technology of SNP,as well as the status and foreground of the use of candidate gene SNP in chicken QTL mapping are introduced.     

我国主要地方绵羊品种随机扩增多态DNA研究

对蒙古羊、湖羊、滩羊、小尾寒羊、乌珠穆沁羊、藏绵羊、阿勒泰羊7个地方绵羊品种和无角陶赛特羊、德国美利奴羊、萨福克羊3个引入品种基因组DNA进行了RAPD分析。结果表明：（1）RAPD可作为一种有效的标记用于绵羊品种之间遗传亲缘关系的分析。（2）在所使用的43种随机引物中,有35种引物扩增出多态谱带,多态频率为66.24%,说明RAPD技术用于研究绵羊核DNA的遗传变异具有较高的检出率和灵敏度。（3）总群体平均遗传多样性指数（HSP）为0.9139,说明绵羊群体具有较为丰富的遗传多样性。（4）我国地方绵羊品种间的分子聚类关系与其所处的地理位置、考古学结果,以及细胞遗传学研究结果基本一致,引入品种间的分子聚类关系也与其育成史基本一致。 Abstract:The genetic polymorphism and relationship of 7 indigenous sheep breeds of China and 3 imported sheep breeds were studied using random amplified polymorphic DNA (RAPD).The results indicated that the RAPD was an effective marker for the analysis of genetic relationship among sheep breeds.Among 43 arbitrary primers,35 were polymorphic.The percentage of polymorphic markers was 66.24%,which indicated that the RAPD had higher efficiency of polymorphism detection and sensitivity in studying the genetic variation among sheep breeds.The average index of genetic polymorphism for whole population (Hsp) was 0.9139,which showed that the genetic polymorphism was abundant between sheep populations.The genetic relationship between different indigenous sheep breeds in China was in accord with their localities,the results from archeology and cytogenetics and the genetic relationship between imported sheep breeds was in accord with their breeding history.     

湖羊、同羊12个同工酶座位的检测

Gene frequencies of Hu sheep and Tong sheep were obtained with “Random sampling in typical colonies of a central area“.of the 12 loci tested in Hu shpee.11 loci were polymorphic.Reliability of the estimated frequencies of 27 alleles reached 0.95 except for Po^F,Tf^A,Tfd,Hb-β^A and CAF which had reliabilities of 0.5222,0.7478,0.5222,0.6212 and 0.899,respectively,Of the 12 loci tested in Tong sheep,11 loci were polymorphic.Reliability of the estimated frequency of 25 alleles reached 0.95 except for Tf^A,Tf^E and CAF which had reliabilities of 0.931,0.6922 and 0.7924,respectively.The average heterozygosity(H) and average homozygosity(J) was computed and the J of the two sheep colonies was 0.6619 and 0.6448,respectively.Consistent with our conclusions based on genetic data,previous research divided the native sheep populations of East and South Central Asia into three group:the “mongolian group“ “south-Asian group“and “European group“ .Consequently,the degree of genetic similarity between populations and known groups would seem to provide a reliable means of determining the genetic relationships between populations and may reflect the true genetic origin of Hu sheep and Tong sheep in China.     

Mapping QTLs with epistatic effects and QTL×environment interactions for plant height using a doubled haploid population in cultivated wheat

Quantitative trait loci (QTLs) for plant height in wheat (Triticum aestivum L.) were studied using a set of 168 doubled haploid (DH) lines, which were derived from the cross Huapei 3/Yumai 57. A genetic linkage map was constructed using 283 SSR and 22 EST-SSR markers. The DH population and the parents were evaluated for wheat plant height in 2005 and 2006 in Tai’an and 2006 in Suzhou. QTL analyses were performed using the software of QTLNetwork version 2.0 based on the mixed linear model. Four additive QTLs and five pairs of epistatic effects were detected, which were distributed on chromosomes 3A, 4B, 4D, 5A, 6A, 7B, and 7D. Among them, three additive QTLs and three pairs of epistatic QTLs showed QTL×environment interactions (QEs). Two major QTLs, Qph4B and Qph4D, which accounted for 14.51% and 20.22% of the phenotypic variation, were located similar to the reported locations of the dwarfing genes Rht1 and Rht2, respectively. The Qph3A-2 with additive effect was not reported in previous linkage mapping studies. The total QTL effects detected for the plant height explained 85.04% of the phenotypic variation, with additive effects 46.07%, epistatic effects 19.89%, and QEs 19.09%. The results showed that both additive effects and epistatic effects were important genetic bases of wheat plant height, which were subjected to environmental modifications, and caused dramatic changes in phenotypic effects. The information obtained in this study will be useful for manipulating the QTLs for wheat plant height by molecular marker-assisted selection (MAS).     

Quantitative genetic analysis of chlorophyll a fluorescence parameters in maize in the field environments

Chlorophyll fluorescence transient from initial to maximum fluorescence("P" step) throughout two intermediate steps("J" and "I")(JIP‐test) is considered a reliable early quantitative indicator of stress in plants. The JIP‐test is particularly useful for crop plants when applied in variable field environments. The aim of the present study was to conduct a quantitative trait loci(QTL) analysis for nine JIP‐test parameters in maize during flowering in four field environments differing in weather conditions. QTL analysis and identification of putative candidate genes might help to explain the genetic relationship between photosynthesis and different field scenarios in maize plants. The JIP‐test parameters were analyzed in the intermated B73 Mo17(IBM) maize population of 205 recombinant inbred lines. A set of 2,178 molecular markers across the whole maize genome was used for QTL analysis revealing 10 significant QTLs for seven JIP‐test parameters, of which five were co‐localized when combinedover the four environments indicating polygenic inheritance and pleiotropy. Our results demonstrate that QTL analysis of chlorophyll fluorescence parameters was capable of detecting one pleiotropic locus on chromosome 7, coinciding with the gene gst23 that may be associated with efficient photosynthesis under different field scenarios.     

TOTAL SYNTHESIS OF CRYSTALLINE BOVINE INSULIN

<正>We should like to communicate,as a result of our combined efforts for the past five years,this preliminary report on the total synthesis of crystalline bovine insulin,the structure of which was first elucidated by Sanger and coworkers[1]ten years ago.A number of papers on the synthetic work concerning insulin has been published during the past two years.Katsoyannis and coworkers[2,3].synthesized both the A and B chains of sheep insulin and,by combining them together according to the procedure of Dixon and Wardlow[4],observed only traces of insulin activity.Zahn,Meienhofer and co-     

Paternal inheritance of mitochondrial DNA in the sheep (Ovine aries)

Paternal inheritance of mitochondria DNA in sheep was discovered by examination of 152 sheep from 38 hybrid families for mtDNA D-loop polymorphisms using PCR-RFLP, amplification of repeated sequence somain, and PCR-SSCP of the D-loop 5' end region of a 253 bp fragment. Our findings have provided the first evidence of paternal inheritance of mtDNA in sheep and possible mechanisms of paternal inheritance were discussed.     

Molecular mapping of Verticillium wilt resistance QTL clustered on chromosomes D7 and D9 in upland cotton

Verticillium wilt is a destructive disease with international consequences for cotton production. Breeding broad-spectrum resistant cultivars is considered to be one of the most effective means for reducing crop losses. A resistant cotton cultivar, 60182, was crossed with a susceptible cultivar, Jun-mian 1, to identify markers for Verticillium resistance genes and validate the mode of its inheritance. Genetic segregation analysis for Verticillium wilt resistance was evaluated based upon infected leaf percentage in the seedling stage using major gene-polygene mixed inheritance models and joint analysis of P₁, P₂, F₁, B₁, B₂ and F₂ populations obtained from the cultivar cross. We found that resis-tance of upland cotton cultivar 60182 to isolates BP2, VD8 and T9, and their isoconcentration mixture was controlled by two major genes with additive-dominance-epistatic effects, and the inheritance of the major gene was dominant. Furthermore, a genetic linkage map was constructed using F₂ segregating population and resistance phenotypic data were obtained using F_2︰3 families inoculated with different isolates and detected in different developmental stages. The genetic linkage map with 139 loci was comprised of 31 linkage groups covering 1165 cM, with an average distance of 8.38 cM between two markers, or 25.89% of the cotton genome length. From 60182, we found 4 QTL on chromosome D7 and 4 QTL on D9 for BP2, 5 QTL on D7 and 9 QTL on D9 for VD8, 4 QTL on D7 and 5 QTL on D9 for T9 and 3 QTL on D7 and 7 QTL on D7 for mixed pathogens. The QTL mapping results revealed that QTL clusters with high contribution rates were screened simultaneously on chromosomes D9 and D7 by multiple interval mapping (CIM), whether from resistance phenotypic data from different developmental stages or for different isolates. The result is consistent with the genetic model of two major genes in 60182 and suggests broad-spectrum resistance to both defoliating isolates of V. dahliae and nondefoliating iso-lates. The markers associated with resistance QTL may facilitate the use of Verticillium wilt resistance genes in improving breeding programs for cotton.     

Parentage assignment of the mud crab (Scylla paramamosain) based on microsatellite markers

In this study, microsatellite markers were employed to identify the parentage relationship in Scylla paramamosain. The exclusion probability of loci was found to be related with the level of their heterozygosity. When no parent information or only one parent information was available, the exclusion probability ranged from 22.0% to 56.6% and from 41.2% to 73.1%, with the combined exclusion probability for ten loci being 97.0% and 99.8%, respectively. The cumulative assignment success rate was 100% when no parent information was available using seven most informative microsatellite markers. Moreover, the power of the seven microsatellite markers for parentage assignment was tested by a double-blind test, which indicated that 95% of the progeny can be correctly assigned to their parents. This study provided a microsatellite-based approach for parentage assignment in S. paramamosain that will be useful for investigation of genetic background and molecular marker-assisted selective breeding in this important crab species.     

A standardized microsatellite marker panel for parentage and kinship analyses in channel catfish,Ictalurus punctatus

This research was designed to produce a standardized set of microsatellite loci for parentage and kinship analyses in channel catfish, the leading species of US aquaculture. Three panels of five to six markers each were developed that contained a total of two dinucleotide‐, eight trinucleotide‐ and seven tetranucleotide‐microsatellite loci respectively. The loci had a range of nine to 31 alleles per locus in an outbred population. Based on the allele frequencies measured in commercial randomly bred broodstock, the combined probability of non‐exclusion of an unrelated candidate parent pair was 5.36e‐18. The combined probability of non‐exclusion of unrelated identical genotypes was 2.58e‐08. The microsatellite panels were validated by parentage and kinship evaluation in three populations. A total of 697 spawns were collected from matings of outbred broodstock over three spawning seasons, and parents were determined unambiguously for all but three spawns. Genotype analysis also enabled the identification of half‐sibling and full‐sibling families produced by pond spawning. In a second experiment, parentage was unambiguously determined in nine spawns from a population consisting of broodstock derived from only four families. A third experiment demonstrated that all but one of 374 individuals from 10 full‐sibling families could be assigned to a family after coculture in an earthen pond for 1 year. The standardized microsatellite panels enable the development of pedigreed catfish populations and large‐scale performance evaluations in common environments to support the genetic improvement of cultured catfish through selective breeding.     

Genetic polymorphism in sheep plasma detected using antibodies to human plasminogen

Protein variation was identified in sheep when Western blots of polyacrylamide gels (routinely used to resolve transferrin polymorphism) were stained using antibodies to human plasminogen. The affinity of the antibodies to ovine plasma was less than 7% that of a human standard but they bound specifically to a single polymorphic protein. In 146 lambs and their parents the inheritance of the ovine plasminogen antigen polymorphism was consistent with four autosomal alleles segregating codominantly. However, an additional two lambs had types which were incompatible with their putative parents. The pedigrees of these lambs were tested by DNA fingerprinting and shown to have been incorrectly recorded. The genetic polymorphism detected by human plasminogen antiserum provided a probability of sire exclusion (PE) ranging from 0.04 to 0.32 and a polymorphic information content (PIC) of 0.08 to 0.50 in flocks of five sheep breeds: Perendale, Romney, Merino, Texel and Coopworth (in order of increasing genetic variation in this locus). Significant differences in allele frequency were observed between breeds but sampling did not assess the variation among flocks within a breed.     

微卫星DNA在吉戎兔亲子鉴定中的应用研究

选用Sat2、Sat3、Sat4、Sat5、Sat7、Sat8、Sat12、Sat13、Sat16、Sol08、Sol28、Sol30、Sol03 等13个微卫星位点PCR扩增30只吉戎兔的基因组DNA,然后在8%聚丙烯酰胺凝胶上电泳分型,检测结果为平均等位基因数为3.46个,平均杂合度（H）为0.578,平均多态信息含量（PIC）为0.531,双亲资料未知时13个位点的累计非父排除率（PE1）为0.935226,置信度低于80%,一亲本资料已知时13个位点的累计非父排除率（PE2）为0.999329,置信度为95%。由于所鉴定兔群的母本资料已知,因此基因型的分型结果能有效确认18只仔兔子的真父。     

Power of exclusion of 19 microsatellite markers for parentage testing in river buffalo (Bubalus bubalis)

In the present study, 19 microsatellite markers were assessed for their power of exclusion to test parentage in river buffalo. Microsatellite genotypes of 216 unrelated buffaloes belonging to five different breeds were utilized for the study. The probabilities of exclusion were calculated for three hypothetical situations viz. paternity testing (PE1), one parental genotype unavailable (PE2) and exclusion of both parents i.e. substituted offspring (PE3). The mean probability of exclusion across 19 investigated markers in buffalo was 0.578 (PE1), 0.405 (PE2) and 0.764 (PE3) respectively. The probability of exclusion for paternity (PE1) ranged between 0.297 and 0.814 across different markers. The exclusion probability for the cases one parent unavailable (PE2) and substituted offspring (PE3) varied from 0.143 to 0.688 and 0.465 to 0.946 respectively. Polymorphism information content and expected heterozygosity were found to have significantly high correlation with probability of exclusion of microsatellite markers. The cumulative PE1 of nine marker loci was estimated to be 0.9999 while in case of absence of one of the parental genotypes, a minimum of 11 markers were required to achieve a cumulative PE2 of 0.999. In conclusion, the present study proposes two multiplex sets with four and five markers respectively for routine parentage testing in buffalo and an additional set of four markers for doubtful cases of paternity.     

The aunt and uncle effect: an empirical evaluation of the confounding influence of full sibs of parents on pedigree reconstruction.

This study used simulations and a known two-generation pedigree of chinook salmon (Oncorhynchus tshawytscha) to evaluate the effect of full sibs of parents on pedigree reconstruction. Parentage analysis was conducted on 100 parent pair-offspring relationships from pedigrees with unrelated (simulation) and related (chinook salmon) candidate parents. Parentage assignment success for the chinook salmon was lower than in the simulated populations. For example, the six most variable loci (mean H(E) = 0.87) provided a mean of 97% unambiguous assignments in the simulated population and 67% unambiguous assignments for the chinook salmon. Estimates of the pairwise relatedness coefficient ((xy)) for most nonexcluded false parents and true parents of chinook salmon offspring exceeded 0.50. These results support the conclusion that closely related candidate parents decrease the power of genetic markers for pedigree reconstruction based on exclusion. Ambiguous parentage may be resolved using single parent- and parent pair-offspring likelihood analysis, however, these methods should be used with caution and they are not replacements for using more loci when many candidate parents are full sibs.     

Establishment of paternity testing system using microsatellite markers in Chinese Holstein

To estimate the efficiency of microsatellite markers in paternity testing among Chinese Holstein, 30 microsatellite loci were used to differentiate 330 Chinese Holstein genotypes, according to the calculation of the allele frequency, number of alleles, effective number of alleles, genetic heterozygosity, polymorphic information content (PIC), and the exclusion probability in this cattle population. The results demonstrated that the exclusion probability ranged from 0.620 in locus BM1818 to 0.265 in locus INRA005 with the average of 0.472 and 11 microsatellite markers exceeding 0.5. The combined exclusion probability of nine microsatellite markers was over 0.99. The result showed that paternity testing of Chinese Holstein was basically resolved using the nine microsatellite markers selected.     

Parentage in natural populations: novel methods to detect parent-offspring pairs in large data sets

Parentage analysis in natural populations presents a valuable yet unique challenge because of large numbers of pairwise comparisons, marker set limitations and few sampled true parent-offspring pairs. These limitations can result in the incorrect assignment of false parent-offspring pairs that share alleles across multi-locus genotypes by chance alone. I first define a probability, Pr(δ), to estimate the expected number of false parent-offspring pairs within a data set. This probability can be used to determine whether one can accept all putative parent-offspring pairs with strict exclusion. I next define the probability Pr(φ|λ), which employs Bayes' theorem to determine the probability of a putative parent-offspring pair being false given the frequencies of shared alleles. This probability can be used to separate true parent-offspring pairs from false pairs that occur by chance when a data set lacks sufficient numbers of loci to accept all putative parent-offspring pairs. Finally, I propose a method to quantitatively determine how many loci to let mismatch for study-specific error rates and demonstrate that few data sets should need to allow more than two loci to mismatch. I test all theoretical predictions with simulated data and find that, first, Pr(δ) and Pr(φ|λ) have very low bias, and second, that power increases with lower sample sizes, uniform allele frequency distributions, and higher numbers of loci and alleles per locus. Comparisons of Pr(φ|λ) to strict exclusion and CERVUS demonstrate that this method may be most appropriate for large natural populations when supplemental data (e.g. genealogies, candidate parents) are absent.     

An improved method for typing of plasma α1-protease inhibitor (PI1) variants in sheep

Summary
Sheep plasma α₁-protease inhibitor (PI1) variants were typed by analysing neuraminidase treated samples by isoelectric focusing in ultra-thin polyacrylamide gels followed by staining for trypsin inhibition. The 10 different PI1 pheno-types observed were shown to be controlled by four codominant alleles. The probability of sire exclusion provided by PI1 polymorphism was about 0.45 in both of the studied milk sheep breeds (Latxa and Karrantzar) of the Basque Country.     

Polymix breeding with paternity analysis in Populus: a test for differential reproductive success (DRS) among pollen donors

Polymix breeding with paternity analysis (PMX/WPA) has been proposed as an alternative to traditional full-sib breeding and testing schemes. To fully capture the benefits of PMX/WPA, differential reproductive success (DRS) of pollen parents used in the polymix must be modest. DRS was evaluated in an operational test of PMX/WPA for a hybrid poplar breeding program. A 16-parent pollen polymix (Populus nigra L.) was used to pollinate seven clones of Populus deltoides (Bartr. ex. Marshall) under greenhouse breeding conditions. Progeny were grown out briefly and randomly sampled (357) prior to out-planting in field trials. Twenty-eight simple sequence repeat (SSR) loci were evaluated and 15 were selected for genetic characterization in small populations of three Populus spp (P. nigra, P. deltoides, and P. balsamifera spp trichocarpa Torr. & Gray). Seven loci were ultimately selected for paternity analysis of progeny. The average exclusion probability of the seven loci in P. nigra was 0.604; combined, the theoretical exclusion probability was 0.9999. However, only 95% of sampled progeny were unambiguously assigned a single paternal parent. Missing data likely accounted for most of the ambiguity. DRS was statistically significant though not prohibitive for practical utility of PMX/WPA as a breeding system. Of the 112 potential crosses in this study, 92 were represented. Eight of the 16 pollen parents contributed 83% of the progeny. Good pollen vigor, as measured by germination percent, did not ensure paternal success, but poor vigor was associated with lack of paternal success. PMX/WPA appears to be logistically and economically attractive for hybrid poplar breeding and testing.