High genetic diversity in population of <Emphasis Type="Italic">Lepturichthys fimbriata</Emphasis> from the Yangtze River revealed by microsatellite DNA analysis

Lepturichthys fimbriata (Günther) is one of the benthic and rock-attached fish species that is typically found in torrential flows of the upper reaches of the Yangtze River in China. Several dams in the Yangtze River (the Ertan Dam, the Three Gorges Dam, the Gezhouba Dam, the Xiluodu Dam and the Xiangjiaba Dam (the latter two dams are under construction)) may have significant effects on the habitat and spawning behaviors of L. fimbriata, and could ultimately threaten the survival of this fish. We studied the population genetic diversity of L. fimbriata samples collected at three sites within the Yangtze River and one of its tributaries, the Yalong River. Genetic diversity patterns were determined by analyzing genetic data from 14 polymorphic microsatellite loci isolated in Jinshaia sinensis (Sauvage et Dabry). A high genetic diversity among these L. fimbriata local populations was indicat- ed by the number of microsatellite alleles (A) and the expected heterozygosity. No reductions of genetic diversity in any L. fimbriata population were observed. However, significant population differentiations were observed among three local populations by pairwise comparisons (P<0.001). We deduced that L. fimbriata local populations were not small ones. In addition, the habitat behaviors of rock-attachment and possible residence of L. fimbriata could account for the genetic differences found in local populations.     

Isolation and characterization of class I MHC genes in the giant panda (Ailuropoda melanoleuca)

Artificial breeding is an important project to protect,recover and reintroduce endangered species.Knowledge of the population’s genetic diversity at functional loci is important for the establishment of effective captive breeding programs.The major histocompatibility complex(MHC) genes are ideal candidate genetic markers to inform planned breeding,due to their high levels of polymorphism and importance in the main immune coding region of the vertebrate genome.In this study,we constructed BAC-based contigs and isolated six functional MHC class Ⅰ genes from the giant panda(Ailuropoda melanoleuca),which we designated Aime-C,Aime-F,Aime-I,Aime-K,Aime-L and Aime-1906.Analyses of the tissue expression patterns and full-length cDNA sequences of these class I genes revealed that Aime-C,-F,-I and-L could be considered classical class Ⅰ loci,due to their extensive expression patterns and normal exonic structures.In contrast,Aime-K and-1906 appeared to be nonclassical genes based on their tissue-specific expression patterns and the presence of an abnormal exon 7 in both genes.We established techniques for genotyping exons 2 and 3 of the classical loci using locus-specific single strand conformation polymorphism(SSCP) and sequence analysis.In the Chengdu captive population,we identified one monomorphic locus(Aime-F) and three polymorphic loci with different numbers of alleles(4/4/4 exon 2 alleles at Aime-C/I/L and 6/5/5 exon 3 alleles at Aime-C/I/L).The distributions of the Aime-C,-I and-L alleles among members of different families were in good agreement with the known pedigree relationships,suggesting that the genotyping results are reliable.Therefore,the MHC-I genotyping techniques established in this study may provide a powerful tool for the future design of scientific breeding or release/reintroduction programs.     

Genetic diversity of Chinese summer soybean germplasm revealed by SSR markers

There are abundant soybean germplasm in China. In order to assess genetic diversity of Chinese summer soybean germplasm, 158 Chinese summer soybean accessions from the primary core collection of G max were used to analyze genetic variation at 67 SSR loci. A total of 460 alleles were detected, in which 414 and 419 alleles occurred in the 80 Huanghuai and the 78 Southern summer accessions, respectively. The average number of alleles per locus was 6.9 for all the summer accessions, and 6.2 for both Huanghuai and Southern summer accessions. Marker diversity (D) per locus ranged from 0.414 to 0.905 with an average of 0.735 for all the summer accessions, from 0.387 to 0.886 with an average of 0.708 for the Huanghuai summer accessions, and from 0.189 to 0.884 with an average of 0.687 for the Southern summer accessions. The Huanghuai and Southern summer germplasm were different in the specific alleles, allelic-frequencies and pairwise genetic similarities. UPGMA cluster analysis based on the similarity data clearly separated the Huanghuai from Southern summer soybean accessions, suggesting that they were different gene pools. The results indicate that Chinese Huanghuai and Southern summer soybean germplasm can be used to enlarge genetic basis for developing elite summer soybean cultivars by exchanging their germplasm.     

Comparative mapping of rice root traits in seedlings grown in nutrient or non-nutrient solution

The component and amount of nutrient in the growth medium are the major factors affecting root growth.For the systematic dissection of root gene expression,evaluation of nutrient and non-nutrient solutions was conducted for their effect on root traits and quantitative trait loci(QTL)mapping.Three rice root parameters,maximum root length(MRL),root dry weight(RDW),and root/ shoot ratio of dry weight(RSR),were characterized within a double haploid(DH)population from a cross of ZYQ8(indica)and JX17(japonica).The value of the three root traits in two parents all decreased under the nutrient condition compared to those under the nonnutrient condition,of which RSR decreased up to 2.6-fold on average.In the DH population,more than 70 % lines in MRL,94 % lines in RDW,and all the lines in RSR were scored lower.In total,eight QTLs were identified in nutrient system(5 from JX17 alleles and 3 from ZYQ8 alleles)while five QTLs were detected in non-nutrient system(4 from JX17 alleles and 1 from ZYQ8 alleles).Of them,one QTL for RSR was shared by both culturing systems,seven QTLs were specific in nutrient system and the other four QTLs were specific in non-nutrient system.All 13 QTLs were distributed over 7 rice chromosomes-2,3,4,5,6,9 and 10,respectively.     

Polymorphisms of chemokine receptors and its ligand alleles influencing genetic susceptibity to HIV-1 infection in eight ethnic groups in Chinese mainland

Limited genetic information is available concerning the polymorphisms of HIV-1 resistant genes in indigenous Chinese populations. The aim of this study is to identify the allelic frequencies of the chemokine and chemokine receptor genes in the Chinese mainland. Genomic DNA samples extracted from whole blood of 2318 subjects were analyzed by using PCR or PCR/restriction fragment length polymorphism (RFLP) assays, and further confirmed by direct DNA sequencing. Higher frequencies of mutant CCR2-64I (19.15%—28.79%) and SDF1-3’A (19.10%—29.86%) alleles were found in subjects of 8 ethnic groups in the Chinese mainland. In contrast, the △32 mutation in CCR5 gene occurs at a very low frequency (0.0016, n=1287) in Han population. A relatively high frequency of CCR5- wt/D32 heterozygotes was observed in Uygurian and Mongolian populations. No △32 mutation allele was detected in Tibetan and other 4 ethnic groups in Yunnan Province. There was no CCR5-m303 mutation in subjects of any ethnic group in the Chinese mainland. Our results suggest that the CCR5-△32 mutation is not a major resistant factor against HIV-1 infection and disease progression in Han, Tibetan and other ethnic groups in Yunnan Province. Whether higher frequencies of CCR2-64I and SDF1-3′A alleles constitute major genetic resistant factors or not remains to be clarified.     

Microsatellite and mitochondrial DNA assessment of the genetic diversity of captive Saiga antelopes (Saiga tatarica) in China

To estimate the genetic diversity of the only captive Saiga antelope(Saiga tatarica) population in China,40 umbilical cord samples were collected and mitochondrial(control region) and nuclear(microsatellite) variabilities were assessed.Both of the markers revealed low genetic variability(or high genetic homogeneity) within the population.The microsatellites yielded monitoring ranges of 2-6 alleles.The observed heterozygosities ranged from 0.28 to 0.83,and the expected heterozygosities were between 0.27 and 0.71.The Shannon information index(Shannon I) and Polymorphic Information Content(PIC) presented overall means of 0.87 and 0.43,respectively.The gene diversity was 0.49.We found only two haplotypes in the population,and the haplotype and nucleotide diversities were 39.1% and 1.13%,respectively.Founder events,bottlenecks and inbreeding have contributed to the low genetic variation observed in this population.Our findings revealed the extent of genetic diversity maintained in the present population and the urgency of implementing a protection plan,introducing animals from other populations to enhance saiga’s genetic variation.     

Developing a genome-wide selection model for genetic improvement of residual feed intake and carcass merit in a beef cattle breeding program

Residual feed intake (RFI) and carcass merit (CM) are both complex traits emerging as critical targets for beef genetic improvement.RFI and CM traits are difficult and expensive to measure and genetic improvement for these traits through traditional selection methods is not very effective.Therefore,genome-wide selection using DNA markers may be a potential alternative for genetic improvement of these traits.In this study,the efficiency of a genome-wide selection model for genetic improvement of RFI and CM was assessed.The Illumina Bovine50K bead chip was used to genotype 922 beef cattle from the Kinsella Beef Research Ranch of the University of Alberta.A Bayes model and multiple marker regression using a stepwise method were used to conduct the association test.The number of significant SNP markers for carcass weight (CWT),carcass back fat (BF),carcass rib eye area (REA),carcass grade fat (GDF),lean meat yield (LMY),and residual feed intake (RFI) were 75,54,67,57,44 and 50,respectively.Bi-variate analysis of marker scores and phenotypes for all traits were made using DMU Software.The genetic parameter for each trait was estimated.The genetic correlations of marker score and phenotype for CWT,BF,REA,GDF,LMY and RFI were 0.75,0.69,0.87,0.77,0.78,and 0.85,respectively.The average prediction accuracies of phenotypic EBV for the six traits were increased by 0.05,0.16,0.24,0.23,0.17 and 0.19,respectively.The results of this study indicated that the two-trait marker-assisted evaluation model used was a suitable alternative of genetic evaluation for these traits in beef cattle.     

Genetic diversity, geographic differentiation and evolutionary relationship among ecotypes of Glycine max and G. soja in China

The knowledge of origin and evolution of cultivated soybeans is one of the basic issues in both biology and agronomy of the crop. In order to investigate the nuclear and cytoplasmic genetic diversity, geographic differentiation and genetic relationship among geographic ecotypes of cultivated （Glycine max） and wild （G. soja） soybeans, the allelic profiles at 60 nuclear simple-sequence repeat （nuSSR） loci and 11 chloroplastic SSR （cpSSR） loci evenly distributed on whole genome of 393 landraces and 196 wild accessions from nation-wide growing areas in China were analyzed. （i） The genetic diversity of the wild soybean was obviously larger than that of the cultivated soybean, with their nuSSR and cpSSR alleles as 1067 vs. 980 and 57 vs 44, respectively. Of the 980 nuclear alleles detected in the cultivated soybean, 377 new ones （38.5%） emerged, while of the 44 chloroplastic alleles in the cultivated soybean, seven new ones （15.9%） emerged after domestication. （ii） Among the cultivated geographic ecotypes, those from southern China, including South-Central China, Southwest China and South China possessed relatively great genetic diversity than those from northern China, while among the wild geographic ecotypes, the Middle and Lower Changjiang Valleys wild ecotype showed the highest genetic diversity. （iii） The analysis of molecular variance, association analysis between geographic grouping and molecular marker clustering and analysis of specific-present alleles of ecotypes demonstrated that the geographic differentiation of both cultivated and wild soybeans associated with their genetic differentiation, or in other words, had their relevant genetic bases. （iv） The cluster analysis of all accessions clearly showed that the wild accessions from Middle and Lower Changjiang Valleys and South-Central ＆ Southwest China had relatively small genetic distances with all cultivated accessions. The UPGMA dendrogram among geographic ecotypes further showed that the genetic distances between all cultivated ecotypes and the Middle and Lower Changjiang Valleys wild ecotype were smaller than those with other wild ones, including their local wild counterparts. Therefore, it is inferred that the wild ancestors in southern China, especially those from Middle and Lower Changjiang Valleys might be the common ancestor of all the cultivated soybeans.     

Genetic analysis and identification of a large leaf angles （lla） mutant in rice

Mutants are essential genetic muterials to elucidation of biological functions of genes involved.Characterization and isolation of genes in mutants is one of the research tasks in functional genomic era.T-DNA insertional mutagenesis has provided an efficient way to identify genes in plant species.in which the mutated genes could be rapidly isolated once the mutant was confirmed by T-DNA inscrtion.     

Generation of mutants with developmental defects in zebrafish by ENU mutagenesis

As a good model for studying early development of vertebrates, zebrafish (Danio rerio) is attracting more and more attention. Following ENU mutagenesis, 320 F2 families were established. Mutants, which showed defects in epiboly, axis, somite, head, and cardiac and blood systems, were identified by observing morphological changes in F3 embryos. So far, 35 mutant lines have been established, the majority of which showed anomalies in axis and somite formation. These mutant lines provide useful genetic resources for cloning of the mutant genes and for studying mechanisms of early development of vertebrate embryos.     

Directional non-cell autonomy and the transmission of polarity information by the frizzled gene of Drosophila

The function of the frizzled (fz) locus is required for the development of a parallel array of bristles and hairs on the adult cuticle of Drosophila melanogaster. Marked fz mitotic clones from five alleles were generated and examined in the wing. Three alleles have a non-cell-autonomous hair polarity phenotype; wild-type cells distal to fz clones produce hairs that have an abnormal polarity. In contrast, fz clones of the other two fz alleles examined do not disrupt the polarity of neighbouring cells. These data suggest that fz has two mutably separate functions in establishing hair polarity on the wing. One function involves the transmittance and/or generation of a polarity signal along the proximal-distal axis of the wing. The second function involves the cellular interpretation of a polarity signal.     

沙塘鳢不同组织同工酶生化表现型及遗传基础

采用垂直板聚丙烯酰胺凝胶电泳方法，对沙塘鳢（Odontobutis abscura）的消化道、心脏、肌肉、脾脏、肾脏、脑、肝脏、生殖腺和晶体9种组织的4种同工酶(EST、LDH、ADH、MDH)进行了研究，讨论了这几种同工酶在沙塘鳢不同组织中的分布以及遗传基础。EST有5个基因位点，单体酶；LDH只有1个基因位点，为四聚体酶；MDH为由3个基因位点控制的二聚体酶；ADH亦为二聚体酶，但仅在肝脏中得到表达。结果表明，同工酶的表达具有组织特异性。     

微卫星与生化位点法对BALB/c小鼠遗传检测比较分析

目的 应用微卫星DNA标记检测BALB/c小鼠的遗传质量,并与现行国家标准生化标记法进行比较,探讨其在近交系小鼠遗传监测中的应用,为建立微卫星DNA检测方法奠定基础。方法 采用20个微卫星基因位点和毛细管电泳技术对BALB/c小鼠进行遗传质量检测,同时采用现行国家标准生化标记法进行检测比较分析。结果 各样品20个微卫星基因位点DNA片段大小相同,没有新的等位基因出现;生化标记检测结果亦显示Akp1等14个生化标记基因均为纯合,个体间生化标记表型均一致,根据国家标准符合品系特征。微卫星DNA标记检测结果与生化标记检测结果一致。结论 微卫星DNA标记可准确可靠、方便快捷地检测近交系小鼠遗传质量,本研究所选的20个微卫星基因位点可用于BALB/c小鼠遗传质量监测。     

Detection of single base substitutions in total genomic DNA

Certain single base substitutions causing genetic diseases or resulting in polymorphisms linked to mutant alleles, alter a restriction enzyme cleavage site and can therefore be detected in total genomic DNA using DNA blots. Many base substitutions do not lead to an altered restriction site, but these can be detected using synthetic oligonucleotides as hybridization probes if the DNA sequence surrounding the base substitution is known. In the case of beta-thalassaemia, where 22 different single base mutations have been identified, a large number of probes would be required for diagnosis. An approach which was used to detect mutations in viral DNA involves the S1 nuclease treatment of heteroduplexes formed between wild-type and mutant DNA. Although certain single base mismatches are cleaved by S1 nuclease (ref. 11 and T. Shenk, personal communication), many other mismatches examined by this procedure are not cleaved (B. Seed, personal communication; R.M.M., unpublished data). Heteroduplexes between mutant and wild-type subgenomic fragments of double-stranded reovirus RNA migrate slower than the corresponding homoduplexes in polyacrylamide gels containing 7 M urea, but it is not known whether this method is applicable to DNA heteroduplexes containing single base mismatches. Here we describe a procedure that involves the electrophoretic separation of DNA heteroduplexes in a well-characterized gel system. We show that four different human beta-thalassaemia alleles with known single base mutations can be detected with as little as 5 micrograms of total genomic DNA. The method should be useful in the localization and diagnosis of mutations associated with genetic diseases.     

Effects of a change in the level of inbreeding on the genetic load

"The effects of inbreeding may not be as noticeable in the first generation as the invigoration immediately apparent after crossing". This statement, published in 1919, has received little attention, and has apparently never been tested empirically, although the reduction of the genetic load of populations by inbreeding is well known in theoretical terms. Because inbreeding increases homozygosity, and hence the effectiveness of selection against recessive or partially recessive detrimental alleles, changes in levels of inbreeding can lead to a reduction in the frequencies of such mutant alleles. This results in equilibration at higher population mean fitness and is referred to as 'purging' populations of their genetic load. Severe inbreeding can also reduce genetic load due to overdominant alleles, provided selection coefficients are not symmetrical at all loci, because alleles giving lower fitness will be reduced in frequency at equilibrium. With either fitness model, however, reduction in genetic load takes time, and the initial effect of an increase in inbreeding is reduced fitness due to homozygosity. There are few data relating to the extent to which fitness is reduced during inbreeding in a set of lines and to how long the reduction lasts before increasing again to the initial level, or higher. Inbreeding experiments involving sib mating in mice and Drosophila subobscura, and successive bottlenecks in house flies have yielded some evidence consistent with the purging hypothesis. Here, we report results of an experiment demonstrating a prolonged time-course of recovery of mean fitness under self-fertilization of a naturally outcrossing plant, and also compare our results with expectations derived by computer calculations. Our results show that the genetic load present in an outcrossing population can be explained only with a high mutation rate to partially recessive deleterious alleles, and that inbreeding purges the population of mutant alleles.     

Genome-wide non-mendelian inheritance of extra-genomic information in Arabidopsis

A fundamental tenet of classical mendelian genetics is that allelic information is stably inherited from one generation to the next, resulting in predictable segregation patterns of differing alleles. Although several exceptions to this principle are known, all represent specialized cases that are mechanistically restricted to either a limited set of specific genes (for example mating type conversion in yeast) or specific types of alleles (for example alleles containing transposons or repeated sequences). Here we show that Arabidopsis plants homozygous for recessive mutant alleles of the organ fusion gene HOTHEAD (HTH) can inherit allele-specific DNA sequence information that was not present in the chromosomal genome of their parents but was present in previous generations. This previously undescribed process is shown to occur at all DNA sequence polymorphisms examined and therefore seems to be a general mechanism for extra-genomic inheritance of DNA sequence information. We postulate that these genetic restoration events are the result of a template-directed process that makes use of an ancestral RNA-sequence cache.     

Neurogenic phenotypes and altered Notch processing in Drosophila Presenilin mutants

Presenilin proteins have been implicated both in developmental signalling by the cell-surface protein Notch and in the pathogenesis of Alzheimer's disease. Loss of presenilin function leads to Notch/lin-12-like mutant phenotypes in Caenorhabditis elegans and to reduced Notch1 expression in the mouse paraxial mesoderm. In humans, presenilins that are associated with Alzheimer's disease stimulate overproduction of the neurotoxic 42-amino-acid beta-amyloid derivative (Abeta42) of the amyloid-precursor protein APP. Here we describe loss-of-function mutations in the Drosophila Presenilin gene that cause lethal Notch-like phenotypes such as maternal neurogenic effects during embryogenesis, loss of lateral inhibition within proneural cell clusters, and absence of wing margin formation. We show that presenilin is required for the normal proteolytic production of carboxy-terminal Notch fragments that are needed for receptor maturation and signalling, and that genetically it acts upstream of both the membrane-bound form and the activated nuclear form of Notch. Our findings provide evidence for the existence of distinct processing sites or modifications in the extracellular domain of Notch. They also link the role of presenilin in Notch signalling to its effect on amyloid production in Alzheimer's disease.     

Interference among deleterious mutations favours sex and recombination in finite populations

Sex and recombination are widespread, but explaining these phenomena has been one of the most difficult problems in evolutionary biology. Recombination is advantageous when different individuals in a population carry different advantageous alleles. By bringing together advantageous alleles onto the same chromosome, recombination speeds up the process of adaptation and opposes the fixation of harmful mutations by means of Muller's ratchet. Nevertheless, adaptive substitutions favour sex and recombination only if the rate of adaptive mutation is high, and Muller's ratchet operates only in small or asexual populations. Here, by tracking the fate of modifier alleles that alter the frequency of sex and recombination, we show that background selection against deleterious mutant alleles provides a stochastic advantage to sex and recombination that increases with population size. The advantage arises because, with low levels of recombination, selection at other loci severely reduces the effective population size and genetic variance in fitness at a focal locus (the Hill-Robertson effect), making a population less able to respond to selection and to rid itself of deleterious mutations. Sex and recombination reveal the hidden genetic variance in fitness by combining chromosomes of intermediate fitness to create chromosomes that are relatively free of (or are loaded with) deleterious mutations. This increase in genetic variance within finite populations improves the response to selection and generates a substantial advantage to sex and recombination that is fairly insensitive to the form of epistatic interactions between deleterious alleles. The mechanism supported by our results offers a robust and broadly applicable explanation for the evolutionary advantage of recombination and can explain the spread of costly sex.