The relative importance of meiotic gene conversion,selection and mutation pressure,in population genetics and evolution

Disparity in the direction of meiotic gene conversion can change allele frequencies, favouring one allele of a pair in heterozygotes. Equilibrium allele frequencies for large diploid populations are examined by means of equations relating them to meiotic gene conversion, selection and mutation for deleterious recessives, deleterious dominants, and deleterious alleles with no dominance. Using observed conversion parameters from various fungi,Zea mays andDrosophila, it is shown that conversion is generally much more important than mutation pressure and may be of greater or lesser importance than selection, depending on dominance and the strength of selection and conversion forces for the alleles involved.     

Comparison of targeted-gene replacement frequencies in Drosophila melanogaster at the forked and white loci.

P element-induced gene conversion has been previously used to modify the white gene of Drosophila melanogaster in a directed fashion. The applicability of this approach of gene targeting in Drosophila melanogaster, however, has not been analyzed quantitatively for other genes. We took advantage of the P element-induced forked allele, f(hd), which was used as a target, and we constructed a vector containing a modified forked fragment for converting f(hd). Conversion frequencies were analyzed for this locus as well as for an alternative white allele, w(eh812). Combination of both P element-induced mutant genes allowed the simultaneous analysis of conversion frequencies under identical genetic, developmental, and environmental conditions. This paper demonstrates that gene conversion through P element-induced gap repair can be applied with similar success rates at the forked locus and in the white gene. The average conversion frequency at forked was 0.29%, and that at white was 0.17%. These frequencies indicate that in vivo gene targeting in Drosophila melanogaster should be applicable for other genes in this species at manageable rates. We also confirmed the homolog dependence of reversions at the forked locus, indicating that P elements transpose via a cut-and-paste mechanism. In a different experiment, we attempted conversion with a modified forked allele containing the su(Hw) binding site. Despite an increased sample size, there were no conversion events with this template. One interpretation (under investigation) is that the binding of the su(Hw) product prevents double-strand break repair.     

The meiotic recombination hot spot ura4A in Schizosaccharomyces pombe

The meiotic recombination hot spot ura4A (formerly ura4-aim) of Schizosaccharomyces pombe was observed at the insertion of the ura4+ gene 15 kb centromere-proximal to ade6 on chromosome III. Crosses heterozygous for the insertion showed frequent conversion at the heterology with preferential loss of the insertion. This report concerns the characterization of 12 spontaneous ura4A mutants. A gradient of conversion ranging from 18% at the 5' end to 6% at the 3' end was detected. A novel phenomenon also was discovered: a mating-type-related bias of conversion. The allele entering with the h+ parent acts preferentially as the acceptor for conversion (ratio of 3:2). Tetrad analysis of two-factor crosses showed that heteroduplex DNA is predominantly asymmetrical, enters from the 5' end, and more often than not covers the entire gene. Restoration repair of markers at the 5' end was inferred. Random spore analyses of two-factor crosses and normalization of prototroph-recombinant frequencies to physical distance led to the demonstration of map expansion: Crosses involving distant markers yielded recombinant frequencies higher than the sum of the frequencies measured in the subintervals. Finally, marker effects on recombination were defined for two of the ura4A mutations.     

Associations of Alleles of the Esterase-1 Locus with Gene Arrangements of the Left Arm of the Second Chromosome in DROSOPHILA ROBUSTA

Evidence of strong associations of Est-1 alleles with the 2L, 2L1 and 2L3 gene arrangements of the left arm of the second chromosome in D. robusta is presented. Each gene arrangement is polymorphic for three to four Est-1 alleles. The allele frequencies differ in the 2L3 and 2L arrangements; the allele Est-1^.92 is 8% in the 2L3 arrangement (n=203)—this allele is 82% in the 2L arrangement (n=203); the allele Est-1^1.0 is 66% and 14.8% in the 2L3 and 2L arrangements, respectively. There are no differences in allele frequencies in 2L3 arrangements from any of the widely separated seven different populations; similarly the allele frequencies in the 2L arrangement are alike in all five widely separated populations studied. The allele frequencies in the 2L1 arrangement are intermediate to those observed in the 2L3 and the 2L arrangements and show north-south clinal change. These associations between Est-1 alleles and gene arrangements of the left arm of the second chromosome are due to natural selection favoring different allele frequencies in different gene arrangements, as a result of epistatic interactions between the Est-1 locus and the loci on the gene arrangements. As expected, we observe that the proportion of heterozygotes is greater in the inversion heterokaryotypes than in the homokaryotypes.     

The control of gene conversion properties and corresponding-site interference: the effects of conversion control factor 5 on conversion at locus w9 in Ascobolus immersus

The controls of various aspects and parameters of gene conversion at locus w-9 in the fungus Ascobolus immersus were investigated, along with positive and negative corresponding-site interference in meiotic chromatid pairing. When conversion control factor 5 alleles A and B were heterozygous, conversion frequencies at the closely linked target locus w9 were reduced to 3%, compared with 10.7% when A or B was homozygous, through effects on hybrid-DNA (h-DNA) formation parameters gamma1 and gamma2. In different ways, not related to whether ccf-5 alleles were homozygous or heterozygous, ccf-5 also affected parameters relating to the relative frequencies of asymmetric and symmetric h-DNA, the frequency with which the chromatid bearing the wild-type allele was the invading chromatid in asymmetric h-DNA, and h-DNA correction parameters for the frequency and direction of correction of mispairs. Corresponding-site interference is interference between the two pairs of non-sister chromatids of a bivalent in h-DNA formation at exactly corresponding sites. This interference was positive in the high conversion frequency crosses homozygous for ccf-5 alleles but was strongly negative in the low conversion frequency crosses heterozygous for ccf-5 alleles, through differential effects on parameters gamma1 and gamma2. Models of chromatid pairing are discussed.     

Heterozygosity, Heteromorphy, and Phylogenetic Trees in Asexual Eukaryotes

Little attention has been paid to the consequences of long-term asexual reproduction for sequence evolution in diploid or polyploid eukaryotic organisms. Some elementary theory shows that the amount of neutral sequence divergence between two alleles of a protein-coding gene in an asexual individual will be greater than that in a sexual species by a factor of 2tu, where t is the number of generations since sexual reproduction was lost and u is the mutation rate per generation in the asexual lineage. Phylogenetic trees based on only one allele from each of two or more species will show incorrect divergence times and, more often than not, incorrect topologies. This allele sequence divergence can be stopped temporarily by mitotic gene conversion, mitotic crossing-over, or ploidy reduction. If these convergence events are rare, ancient asexual lineages can be recognized by their high allele sequence divergence. At intermediate frequencies of convergence events, it will be impossible to reconstruct the correct phylogeny of an asexual clade from the sequences of protein coding genes. Convergence may be limited by allele sequence divergence and heterozygous chromosomal rearrangements which reduce the homology needed for recombination and result in aneuploidy after crossing-over or ploidy cycles.     

红鳍东方鲀(Takifugu rubripes)MC4R基因的多态性分析

采用PCR-SSCP(single strand conformation polymorphism)技术和DNA测序方法分析红鳍东方鲀MC4R(Melanocortin-4receptor)基因编码区多态性。在MC4R基因编码区48 nt和264 nt均发生了碱基的转换突变(G→A),两个突变位点分别位于M1和M2引物扩增产物中。引物M1扩增产物SSCP分析得到两种基因型:AA基因型和AB基因型,并且AA基因型和A等位基因频率明显高于AB基因型和B等位基因。引物M2扩增产物也得到两种基因型:CC基因型和CD基因型,CC基因型和C等位基因频率明显高于CD基因型和D等位基因。遗传变异结果分析表明,两个突变位点均属于低度多态性,而且群体遗传杂合度较低,反映了该群体的遗传一致性较高。     

Gene Conversion at the Gray Locus of SORDARIA FIMICOLA: Fit of the Experimental Data to a Hybrid DNA Model of Recombination

A hybrid DNA (hDNA) model of recombination has been algebraically formulated, which allows the prediction of frequencies of postmeiotic segregation and conversion of a given allele and their probability of being associated with a crossing over. The model considered is essentially the "Aviemore model." In contrast to some other interpretations of recombination, it states that gene conversion can only result from the repair of heteroduplex hDNA, with postmeiotic segregation resulting from unrepaired heteroduplexes. The model also postulates that crossing over always occurs distally to the initiation site of the hDNA. Eleven types of conversion and postmeiotic segregation with or without associated crossover were considered. Their theoretical frequencies are given by 11 linear equations with ten variables, four describing heteroduplex repair, four giving the probability of hDNA formation and its topological properties and two giving the probability that crossing over occurs at the left or right of the converting allele. Using the experimental data of Kitani and coworkers on conversion at the six best studied gray alleles of Sordaria fimicola, we found that the model considered fit the data at a P level above or very close (allele h4) to the 5% level of sampling error provided that the hDNA is partly asymmetric. The best fitting solutions are such that the hDNA has an equal probability of being formed on either chromatid or, alternatively, that both DNA strands have the same probability of acting as the invading strand during hDNA formation. The two mismatches corresponding to a given allele are repaired with different efficiencies. Optimal solutions are found if one allows for repair to be more efficient on the asymmetric hDNA than on the symmetric one. In the case of allele g1, our data imply that the direction of repair is nonrandom with respect to the strand on which it occurs.     

Interchromosomal Biased Gene Conversion, Mutation and Selection in a Multigene Family

A mathematical model of the effects of interchromosomal biased gene conversion, mutation and natural selection on a multigene family is developed and analyzed. The model assumes two allelic states at each of n loci. The effects of genetic drift are ignored. The model is developed under the assumption of no recombination, but the analysis shows that, at equilibrium, there is no linkage disequilibrium, which implies that the conclusions are valid for arbitrary recombination among loci. At equilibrium, the balance between mutation, gene conversion and selection depends on the ratio of the mutation rates to the quantity [s + g(2α - 1)/ n], where s is the increment or decrement in relative fitness with each additional copy of one of the alleles, g is the conversion rate, and α is a measure of the bias in favor of one of the alleles. When this quantity is large relative to the mutation rates, the allele that has the net advantage, combining the effects of selection and conversion, will be nearly fixed in the multigene family. A comparison of these results with those from a comparable model of intrachromosomal biased conversion shows that biased interchromosomal conversion leads to approximately the same equilibrium copy number as does intrachromosomal conversion of the same strength. Interchromosomal conversion is much more effective in causing the substitution of one allele by another. The relative frequencies of interchromosomal and intrachromosomal conversion is indicated by the extent of the linkage disequilibrium among the loci in a multigene family.     

P-element-induced interallelic gene conversion of insertions and deletions in Drosophila melanogaster.

We studied the process by which whd, a P-element insertion allele of the Drosophila melanogaster white locus, is replaced by its homolog in the presence of transposase. These events are interpreted as the result of double-strand gap repair following excision of the P transposon in whd. We used a series of alleles derived from whd through P-element mobility as templates for this repair. One group of alleles, referred to collectively as whd-F, carried fragments of the P element that had lost some of the sequences needed in cis for mobility. The other group, whd-D, had lost all of the P insert and had some of the flanking DNA from white deleted. The average replacement frequencies were 43% for whd-F alleles and 7% for the whd-D alleles. Some of the former were converted at frequencies exceeding 50%. Our data suggest that the high conversion frequencies for the whd-F templates can be attributed at least in part to an elevated efficiency of repair of unexpanded gaps that is possibly caused by the closer match between whd-F sequences and the unexpanded gap endpoints. In addition, we found that the gene substitutions were almost exclusively in the direction of whd being replaced by the whd-F or whd-D allele rather than the reverse. The template alleles were usually unaltered in the process. This asymmetry implies that the conversion process is unidirectional and that the P fragments are not good substrates for P-element transposase. Our results help elucidate a highly efficient double-strand gap repair mechanism in D. melanogaster that can also be used for gene replacement procedures involving insertions and deletions. They also help explain the rapid spread of P elements in populations.     

Large Heterologies Impose Their Gene Conversion Pattern onto Closely Linked Point Mutations

We have studied the meiotic non-Mendelian segregation (NMS) pattern of seven large heterologous combinations located in the b2 ascospore gene of Ascobolus. The NMS patterns of these aberration heterozygotes widely differ from each other and from those of point mutations located in the same genetic region. They give lower gene conversion frequencies than point mutations, no postmeiotic segregations (PMS), and either parity or disparity that favors the wild type allele. Two related deletions, G234 and G40, were studied for their effects on the conversion behavior of closely linked point mutations. We found that, when heterozygous, the deletions impose their own NMS pattern onto close mutations. These effects occur on both sides of the heterologies. The effects upon PMS and disparity of linked point mutations gradually disappear as point mutations become more distant. The effects on NMS frequencies and on aberrant 4:4 are polar. They persist for all mutations located downstream from the high conversion end of the gene. This last effect can reflect a blockage of symmetric hDNA formation by large heterologies, whereas the epistasis of the NMS pattern of large heterologies over that of closely linked point mutations suggests that large heterologies and point mutations undergo conversion by means of distinct pathways.     

诱导型一氧化氮合酶基因多态性与2型糖尿病关系研究

目的：观察诱导型一氧化氮合酶（iNOs）基因Ser608Leu位点基因多态性与2型糖尿病的相关性。方法：采用测序法测定261例2型糖尿病患者和128例正常对照者iNOS基因Ser608Leu位点基因多态性。结果：两组间iNOS基因Ser608Leu位点基因型及等位基因频率构成存在差异。结论：iNOS基因Ser608Leu位点多态性与2型糖尿病有关。     

诱导型一氧化氮合酶基因多态性与2型糖尿病关系研究

目的:观察诱导型一氧化氮合酶(iNOS)基因Ser608Leu位点基因多态性与2型糖尿病的相关性。方法:采用测序法测定261例2型糖尿病患者和128例正常对照者iNOS基因Ser608Leu位点基因多态性。结果:两组间iNOS基因Ser608Leu位点基因型及等位基因频率构成存在差异。结论:iNOS基因Ser608Leu位点多态性与2型糖尿病有关。     

Deep Genome-Wide Measurement of Meiotic Gene Conversion Using Tetrad Analysis in Arabidopsis thaliana

Gene conversion, the non-reciprocal exchange of genetic information, is one of the potential products of meiotic recombination. It can shape genome structure by acting on repetitive DNA elements, influence allele frequencies at the population level, and is known to be implicated in human disease. But gene conversion is hard to detect directly except in organisms, like fungi, that group their gametes following meiosis. We have developed a novel visual assay that enables us to detect gene conversion events directly in the gametes of the flowering plant Arabidopsis thaliana. Using this assay we measured gene conversion events across the genome of more than one million meioses and determined that the genome-wide average frequency is 3.5×10⁻⁴ conversions per locus per meiosis. We also detected significant locus-to-locus variation in conversion frequency but no intra-locus variation. Significantly, we found one locus on the short arm of chromosome 4 that experienced 3-fold to 6-fold more gene conversions than the other loci tested. Finally, we demonstrated that we could modulate conversion frequency by varying experimental conditions.     

上海地区汉族人5-HT2a受体基因T102C多态性的基因频率分布

为了揭示中国汉族人5-HT2a受体基因T102C多态性基因频率的分布,我们随机抽取了226例汉族健康人作研究,用限制性片段长度多态性(RFLPs)技术测定研究对象的基因型和等位基因。结果发现汉族正常人5-HT2a受体基因T102C多态性基因型频率依次为:A1/A2=0.5044,A1/A1=0.2965,A2/A2 =0.1991,两种等位基因频率依次为:A1=0.5487,A2=0.4513,杂合度H=0.50 44、期望杂合度h=0.4953,多态信息量PIC=0.3726,表明T102C多态性具有合适信息,对疾病的关联研究,法医学鉴定有一定的价值。 Abstract:To investigate the distribution about genotype and allele frequencies of T102C polymorphism in the 5-HT2a receptor gene Chinese Han population,the genotypes and alleles of 226 healthy person were examined with Restriction Fragment Length Polymorphisms(RFLPs)technique.The genotype frequencies are as follows:A1/A2=0.5044,A1/A1=0.2965,A2/A2=0.1991,respectively,and the allele frequencies are as follows:A1=0.5487,A2=0.4513,respectively.The heterozygosity(H)is 0.5044,the expected heterozygosity(h)is 0.4953,and the Polymorphism Information Content(PIC)is 0.3726.Our findings suggest that the T102C polymorphism in 5-HT2a receptor gene may have suitable information to be used for association study or forensic identification.     

AGPAT6 polymorphism and its association with milk traits of dairy goats

As one of the eight members in the 1-acylglycerol-3-phosphate-O-acyltransferase (AGPATs) family, AGPAT6 is a crucial enzyme for the biosynthesis of glycerolipids and triacylglycerol in eukaryotes, as well as catalyzing the conversion from lysophosphatidic acid to phosphatidic acid. AGPAT6 can be considered as a candidate gene for regulating milk composition. DNA sequencing and PCR-RFLP methods were applied to detect genetic variation in the AGPAT6 gene in 549 Chinese dairy goats. Four polymorphisms (NC_007328.3:g.152G>C, 8124G>A, 9263C>G, 16436G>A) were detected in 5'UTR, intron 2, exon 4, and 3'UTR, respectively. For the KpnΙ locus, the frequencies of the AGPAT6-G allele were 0.955 and 0.936 for SN (Xinong Sannen) and GZ (Guanzhong) dairy goat breeds, respectively. In the PCR-RFLP analysis for KpnΙ, EcoRII, NcoΙ, and BglΙ, the frequencies of the G allele of AGPAT6 were 0.955 and 0.936, 0.694 and 0.819, 0.206 and 0.254, 0.729 and 0.623 for SN and GZ dairy goat breeds, respectively. The 9263C>G mutation revealed a synonymous genetic code of Thr (threonine). Associations between the four mutations and milk traits were analyzed in two dairy goat breeds. At the 9263C>G locus, genotype GG and CG individuals showed significantly better milk performance than genotype CC individuals (P < 0.05). Therefore, the G allele is suggested to be a molecular marker for milk production in dairy goats.     

猪L-FABP基因的克隆、表达特征及遗传多态性研究

FABPs属于脂结合蛋白超家族成员,是一类分子量较小而对脂肪酸有高亲和力的蛋白质,广泛存在于脊椎动物和非脊椎动物的细胞质中.FABPs担当细胞内脂肪酸的运输任务,它们与脂肪酸结合将其运输到脂肪酸氧化的位置、脂肪酸脂化成甘油三醋或磷脂的位置,或者进入细胞核内发挥其可能的调控功能.因此FABPs对脂类代谢具有重要的调控作用.本研究把L-FABP基因作为影响猪肌内脂肪含量的候选基因.为此,利用cDNA末端快速扩增(RACE)和PCR技术,克隆到猪肝脏型脂肪酸结合蛋白基因(L-FABP)的全长cDNA序列(GenBank登录号AY960623)和部分基因组序列(GenBank登录号DQ182323).猪L-FABP基因的cDNA序列全长518 bp,该序列包括起始密码子TGA和38 bp的5'末端非编码区(5'URT),终止密码子TAG和99 bp的3'末端非编码区(3'URT),在3'URT结构区域中包含polyA加尾信号序列AATAAA.猪L-FABP基因与其他FABPs基因一样,也由4个外显子(67 bp、173 bp、93 bp和51 bp)和3个内含子组成,内含子1和3的大小是1 679bp和565 bp,没有获得内含子2的序列,外显子和内含子剪接处符合GT/AG规律.应用Clustal W/X程序对猪L-FABP与其他物种的L-FABP进行多重序列比对,发现猪L-FABP与人、大鼠、鸡的L-FABP的相似性分别为89.8%、81.9%和72.4%.亲水性分析表明,猪L-FABP也是一个潜在的跨膜蛋白,在氨基酸残基57-65之间有一个明显的跨膜α螺旋.应用半定量RT-PCR分析发现,猪L-FABP在猪体组织中广泛存在,但在肝脏和小肠组织中表达量最为丰富.分析还发现,所克隆得到的编码区核苷酸序列与已知猪L-FABP基因的编码区核苷酸序列存在一定的变异,分别是外显子2中T→C(116位)、C→T(231位)、C→A(236位)和A→C(258位),演绎成氨基酸在Leu74Met存在差异.为进一步证实这些突变位点在猪群中真实存在,利用PCR-SSCP检测方法对4个猪种(藏猪、大河猪、雅南猪和约克夏)的157头个体的外显子2全序列进行SNP位点多态性片段的基因型分型,结果发现一个C→T的单核苷酸多态,等位基因频率在中国地方猪种(藏猪、大河猪、雅南猪)与国外约克夏猪种间存在极显著的差异(P＜0.01).连锁分析发现,基因型CC的肌内脂肪含量(4.86±0.22%)显著的高于基因型CT(4.16±0.23%)和TT(4.05±0.27%)的肌内脂肪含量(P＜0.05).因此,推测L-FABP基因可能是影响猪肌内脂肪含量的主效基因或与主效基因紧密连锁的标记基因,并且能够在分子标记辅助选择中用于对猪肌内脂肪含量的遗传改良.     

Polymorphisms of DNA repair genes ERCC2 and XRCC1 in populations of Russia

We have conducted a comparative study of allele frequencies of single nucleotide polymorphisms (SNPs) rs1799793 and rs13181 of the ERCC2 gene as well as rs1799782 and rs25487 of the XRCC1 gene in population samples from European regions of Russia as well as in populations of Izhemsk and Priluzsk Komi and Yakuts. Significant differences in the distribution of polymorphic variants of the ERCC2 gene were demonstrated between populations of Yakuts and populations of Russians and Komi. In case of XRCC1 gene Izhemsk Komi population exhibited dissimilar allele frequencies compared to other populations.     

The effects of gene conversion control factors on conversion-induced changes in allele frequencies in populations and on linkage disequilibrium

Conversion control factors (ccfs) are widespread. They control conversion properties at their target loci, affecting the conversion frequency and the amount and even the direction of gene conversion disparity. Three major types of ccf can be recognised. Experimental studies of the effects of ccfs have been combined with theoretical studies and modelling to examine the effects of ccfs on the evolutionary population genetics of alleles at the target locus. The ccf alleles present can greatly affect the rate and the direction of conversion-induced changes in target locus allele frequencies. Gene conversion can both cause and remedy linkage disequilibrium, with causation being related to polymorphismfor ccfs. Disparity in conversion direction does not by itself necessarily cause linkage disequilibrium.     

An entropy-based statistic for genomewide association studies

Efficient genotyping methods and the availability of a large collection of single-nucleotide polymorphisms provide valuable tools for genetic studies of human disease. The standard chi2 statistic for case-control studies, which uses a linear function of allele frequencies, has limited power when the number of marker loci is large. We introduce a novel test statistic for genetic association studies that uses Shannon entropy and a nonlinear function of allele frequencies to amplify the differences in allele and haplotype frequencies to maintain statistical power with large numbers of marker loci. We investigate the relationship between the entropy-based test statistic and the standard chi2 statistic and show that, in most cases, the power of the entropy-based statistic is greater than that of the standard chi2 statistic. The distribution of the entropy-based statistic and the type I error rates are validated using simulation studies. Finally, we apply the new entropy-based test statistic to two real data sets, one for the COMT gene and schizophrenia and one for the MMP-2 gene and esophageal carcinoma, to evaluate the performance of the new method for genetic association studies. The results show that the entropy-based statistic obtained smaller P values than did the standard chi2 statistic.