A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig

Most traits and disorders have a multifactorial background indicating that they are controlled by environmental factors as well as an unknown number of quantitative trait loci (QTLs). The identification of mutations underlying QTLs is a challenge because each locus explains only a fraction of the phenotypic variation. A paternally expressed QTL affecting muscle growth, fat deposition and size of the heart in pigs maps to the IGF2 (insulin-like growth factor 2) region. Here we show that this QTL is caused by a nucleotide substitution in intron 3 of IGF2. The mutation occurs in an evolutionarily conserved CpG island that is hypomethylated in skeletal muscle. The mutation abrogates in vitro interaction with a nuclear factor, probably a repressor, and pigs inheriting the mutation from their sire have a threefold increase in IGF2 messenger RNA expression in postnatal muscle. Our study establishes a causal relationship between a single-base-pair substitution in a non-coding region and a QTL effect. The result supports the long-held view that regulatory mutations are important for controlling phenotypic variation.     

Pleiotropy as a mechanism to stabilize cooperation

Most genes affect many traits. This phenomenon, known as pleiotropy, is a major constraint on evolution because adaptive change in one trait may be prevented because it would compromise other traits affected by the same genes. Here we show that pleiotropy can have an unexpected effect and benefit one of the most enigmatic of adaptations--cooperation. A spectacular act of cooperation occurs in the social amoeba Dictyostelium discoideum, in which some cells die to form a stalk that holds the other cells aloft as reproductive spores. We have identified a gene, dimA, in D. discoideum that has two contrasting effects. It is required to receive the signalling molecule DIF-1 that causes differentiation into prestalk cells. Ignoring DIF-1 and not becoming prestalk should allow cells to cheat by avoiding the stalk. However, we find that in aggregations containing the wild-type cells, lack of the dimA gene results in exclusion from spores. This pleiotropic linkage of stalk and spore formation limits the potential for cheating in D. discoideum because defecting on prestalk cell production results in an even greater reduction in spores. We propose that the evolution of pleiotropic links between cheating and personal costs can stabilize cooperative adaptations.     

Genetic mechanisms of floral trait correlations in a natural population

Genetic correlations among traits are important in evolution, as they can constrain evolutionary change or reflect past selection for combinations of traits. Constraints and integration depend on whether the correlations are caused by pleiotropy or linkage disequilibrium, but these genetic mechanisms underlying correlations remain largely unknown in natural populations. Quantitative trait locus (QTL) mapping studies do not adequately address the mechanisms of within-population genetic correlations because they rely on crosses between distinct species, inbred lines or selected lines (see ref. 5), and they cannot distinguish moderate linkage disequilibrium from pleiotropy because they commonly rely on only one or two episodes of recombination. Here I report that after nine generations of enforced random mating (nine episodes of recombination), correlations between six floral traits in wild radish plants are unchanged, showing that pleiotropy generates the correlations. There is no evidence for linkage disequilibrium despite previous correlational selection acting on one functionally integrated pair of traits. This study provides direct evidence of the genetic mechanisms underlying correlations between quantitative traits in a natural population and suggests that there may be constraints on the independent evolution of pairs of highly correlated traits.     

Genetic linkage of ecological specialization and reproductive isolation in pea aphids

The evolution of ecological specialization generates biological diversity and may lead to speciation. Genetic architecture can either speed or retard this process. If resource use and mate choice have a common genetic basis through pleiotropy or close linkage, the resulting genetic correlations can promote the joint evolution of specialization and reproductive isolation, facilitating speciation. Here we present a model of the role of genetic correlations in specialization and speciation, and test it by analysing the genetic architecture of key traits in two highly specialized host races of the pea aphid (Acyrthosiphon pisum pisum; Hemiptera : Aphididae). We found several complexes of pleiotropic or closely linked quantitative trait loci (QTL) that affect key traits in ways that would promote speciation: QTL with antagonistic effects on performance on the two hosts are linked to QTL that produce asortative mating (through habitat choice). This type of genetic architecture may be common in taxa that have speciated under divergent natural selection.     

The population genetics of ecological specialization in evolving Escherichia coli populations

When organisms adapt genetically to one environment, they may lose fitness in other environments. Two distinct population genetic processes can produce ecological specialization-mutation accumulation and antagonistic pleiotropy. In mutation accumulation, mutations become fixed by genetic drift in genes that are not maintained by selection; adaptation to one environment and loss of adaptation to another are caused by different mutations. Antagonistic pleiotropy arises from trade-offs, such that the same mutations that are beneficial in one environment are detrimental in another. In general, it is difficult to distinguish between these processes. We analysed the decay of unused catabolic functions in 12 lines of Escherichia coli propagated on glucose for 20,000 generations. During that time, several lines evolved high mutation rates. If mutation accumulation is important, their unused functions should decay more than the other lines, but no significant difference was observed. Moreover, most catabolic losses occurred early in the experiment when beneficial mutations were being rapidly fixed, a pattern predicted by antagonistic pleiotropy. Thus, antagonistic pleiotropy appears more important than mutation accumulation for the decay of unused catabolic functions in these populations.     

Molecular mapping of QTLs for root response to phosphorus deficiency at seedling stage in wheat (Triticum aestivum L.)

Phosphorus (P) deficiency in the soil is one of the major abiotic stresses that limit plant growth and crop productivity throughout the world. Development of cultivars with improved P-deficiency tolerance is an efficient strategy for sustainable agriculture. Plant roots play an important role in crop growth and development, especially in nutrient uptake and improvement of P-efficiency. Mapping quantitative trait loci (QTLs) for root traits and their response to low P stress at seedling stage will facilitate the development of P-efficient wheat cultivars. In this study, 30 QTLs (LOD>2.0) were mapped for the three root traits, such as root length, root number and root dry matter under different P supply conditions and their response to P-stress. These QTLs were distributed on 14 chromosomes, with each of the 5 QTLs explaining more than 10% phenotype variance. Analyses showed that root traits and their response to P-deficiency were controlled by different QTLs. In addition, alleles with positive effects were separated on both parents, and wheat cultivars with improved P-efficiency could be developed by accumulating these positive effect alleles together.     

Molecular mapping of QTLs for root response to phosphorus deficiency at seedling stage in wheat (Triticum aestivum L.)

Phosphorus (P) deficiency in the soil is one of the major abiotic stresses that limit plant growth and crop productivity throughout the world. Development of cultivars with improved P-deficiency tolerance is an efficient strategy for sustainable agriculture. Plant roots play an important role in crop growth and development, especially in nutrient uptake and improvement of P-efficiency. Mapping quantitative trait loci (QTLs) for root traits and their response to low P stress at seedling stage will facilitate the development of P-efficient wheat cultivars. In this study, 30 QTLs (LOD>2.0) were mapped for the three root traits, such as root length, root number and root dry matter under different P supply conditions and their response to P-stress. These QTLs were distributed on 14 chromosomes, with each of the 5 QTLs explaining more than 10% phenotype variance. Analyses showed that root traits and their response to P-deficiency were controlled by different QTLs. In addition, alleles with positive effects were separated on both parents, and wheat cultivars with improved P-efficiency could be developed by accumulating these positive effect alleles together.     

A new statistical method for mapping QTLs underlying endosperm traits

Genetic expression for an endosperm trait in seeds of cereal crops may be controlled simultaneously by the triploid endosperm genotypes and the diploid maternal genotypes. However, current statistical methods for mapping quantitative trait loci （QTLs） underlying endosperm traits have not been effective in dealing with the putative maternal genetic effects. Combining the quantitative genetic model for diploid maternal traits with triploid endosperm traits, here we propose a new statistical method for mapping QTLs controlling endosperm traits with maternal genetic effects. This method applies the data set of both DNA molecular marker genotypes of each plant in segregation population and the quantitative observations of single endosperms in each plant to map QTL. The maximum likelihood method implemented via the expectation-maximization algorithm was used to the estimate parameters of a putative QTL. Since this method involves the maternal effect that may contribute to endosperm traits, it might be more congruent with the genetics of endosperm traits and more helpful to increasing the precision of QTL mapping. The simulation results show the proposed method provides accurate estimates of the QTL effects and locations with high statistical power.     

Quantitative trait loci （QTLs） for quality traits related to protein and starch in wheat

Quality traits in wheat （Triticum aestirum L.） were studied by quantitative trait locus （QTL） analysis in a recombinant inbred line （RIL） population, a set of 131 lines derived from Chuan 35050 × Shannong 483 cross （ChSh）. Grains from RILs were assayed for 21 quality traits related to protein and starch. A total of 35 putative QTLs for 19 traits with a single QTL explaining 7.99-40.52% of phenotypic variations were detected on 10 chromosomes, 1D, 2A, 2D, 3B, 3D, 5A, 6A, 6B, 6D, and 7B. The additive effects of 30 QTLs were positive, contributed by Chuan 35050, the remaining 5 QTLs were negative with the additive effect contributed by Shannong 483. For protein traits, 15 QTLs were obtained and most of them were located on chromosomes 1 D, 3B and 6D, while 20 QTLs for starch traits were detected and most of them were located on chromosomes 3D, 6B and 7B. Only 7 QTLs for protein and starch traits were co-located in three regions on chromosomes 1D, 2A and 2D. These protein and starch trait QTLs showed a distinct distribution pattern in certain regions and chromosomes. Twenty-two QTLs were clustered in 6 regions of 5 chromosomes. Two QTL clusters for protein traits were located on chromosomes 1D and 3B, respectively, three clusters for starch traits on chromosomes 3D, 6B and 7B, and one cluster including protein and starch traits on chromosome 1D.     

Methods for mapping QTLs underlying endosperm traits based on random hybridization design

Cereal grains are mainly composed of endosperms, which are humans’ staple food containing rich nutri- tious substances such as starch, protein and lipid. Many endosperm traits are related to grain yield and quality. Therefore, studying the genetic basis …     

Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms

The conflict between the Mendelian theory of particulate inheritance and the observation of continuous variation for most traits in nature was resolved in the early 1900s by the concept that quantitative traits can result from segregation of multiple genes, modified by environmental effects. Although pioneering experiments showed that linkage could occasionally be detected to such quantitative trait loci (QTLs), accurate and systematic mapping of QTLs has not been possible because the inheritance of an entire genome could not be studied with genetic markers. The use of restriction fragment length polymorphisms (RFLPs) has made such investigations possible, at least in principle. Here, we report the first use of a complete RFLP linkage map to resolve quantitative traits into discrete Mendelian factors, in an interspecific back-cross of tomato. Applying new analytical methods, we mapped at least six QTLs controlling fruit mass, four QTLs for the concentration of soluble solids and five QTLs for fruit pH. This approach is broadly applicable to the genetic dissection of quantitative inheritance of physiological, morphological and behavioural traits in any higher plant or animal.     

The comparative analysis based on maize integrated QTL map and meta-analysis of plant height QTLs

Since the first publication of quantitative trait locus (QTL) localization using molecular markers[1], a large number of QTLs have been identified in different ge- netic backgrounds and environments. Affected by many factors, such as marker sets, experime…     

小麦品质性状的QTL定位研究进展

本文系统地总结了国内外小麦品质性状QTL定位研究的主要性状、所用群体、标记类型、QTL定位所在的染色体位置及贡献率的大小,提出了小麦品质性状QTL定位中存在的问题,展望了小麦品质性状QTL定位的发展方向。     

玉米穗部性状的QTL定位

以玉米自交系L26和095组配的Fz世代为定位群体,采用SSR分子标记技术构建了包括98个位点的连锁图谱,结合F2穗部性状的鉴定结果,利用复合区间作图法对秃尖长等8个穗部性状进行基因定位,共检出21个QTL.其中穗长检测到3个QTL;穗粗、穗行数分别检测到2个QTL;行粒数检测到3个QTL;轴粗检测到2个QTL;200粒质量检测到3个QTL;穗粒质量检测到6个QTL;秃尖长没有检测到QTL.检出的21个QTL中,有10个QTL的解释变异率超过了20%,表现为主效QTL效应.研究还发现,穗部性状QTL在玉米10条染色体上分布不均匀,且成簇分布.该试验中检测到的21个QTL中,有10个影响不同性状的QTL位于3个染色体区域.各个QTL位点上起增、减效作用的等位基因在亲本间分布不均匀.     

皖西民歌的文化属性研究

皖西民歌在艺术形式、形态上表现出鲜明的地域性文化特色,这些都是其内在文化属性的具体表现。通过对皖西民歌地域特质、社会功能和发展手法上的剖析,探析出它蕴含于内的文化品格和本质精髓。此研究不仅对深入认识独具韵律的皖西民歌文化属性有所裨益,还将在传统民歌的音乐特性研究与非物质文化遗产保护上提供参照。     

Evolutionary diversification of TTX-resistant sodium channels in a predator-prey interaction

Understanding the molecular genetic basis of adaptations provides incomparable insight into the genetic mechanisms by which evolutionary diversification takes place. Whether the evolution of common traits in different lineages proceeds by similar or unique mutations, and the degree to which phenotypic evolution is controlled by changes in gene regulation as opposed to gene function, are fundamental questions in evolutionary biology that require such an understanding of genetic mechanisms. Here we identify novel changes in the molecular structure of a sodium channel expressed in snake skeletal muscle, tsNa(V)1.4, that are responsible for differences in tetrodotoxin (TTX) resistance among garter snake populations coevolving with toxic newts. By the functional expression of tsNa(V)1.4, we show how differences in the amino-acid sequence of the channel affect TTX binding and impart different levels of resistance in four snake populations. These results indicate that the evolution of a physiological trait has occurred through a series of unique functional changes in a gene that is otherwise highly conserved among vertebrates.     

Detecting quantitative trait loci for water use efficiency in rice using a recombinant inbred line population

Breeding rice with high water use efficiency (WUE) can ameliorate water shortage through water-saving irrigation.However,WUE is a complex quantitative trait and very few studies have been conducted to measure WUE directly.In this study,a recombined inbred line population derived from a cross between an indica lowland rice and upland japonica rice was used to dissect the genetic control of WUE by fine-monitored water supply experiments.Quantitative trait loci (QTL) were scanned for 10 traits including heading date (HD),water-consumption per day (water/d),shoot weight gain per day (shootw/d),root weight gain per day (rootw/d),kernel weight gain per day (kernelw/d),average WUE at whole plant level (WUEwhole/d),average WUE for up-ground biomass (WUEup/d),average WUE for grain yield (WUEyield/d),average economic index (econindex/d),and average root/shoot ratio per day (ratio/d).The results show that most of the traits were significantly correlated to each other.Twenty-four QTL (LOD ≥ 2.0) were detected for econindex,econindex/d,WUEyield,WUEyield/d,WUEup,WUEup/d,WUEwhole,WUEwhole/d,kernelw,kernelw/d,rootw,and water/d by composite interval mapping.These QTLs are located on chromosomes 1,2,4,6,7,8,and 12.Individual QTLs accounted for 4.97%-10.78% of the phenotypic variation explained.Some of these QTLs overlapped with previously reported drought resistance QTLs detected in this population.These results provide useful information for further dissection of the genetic basis and marker-assisted selection of WUE in rice.     

Molecular dissection of genetic basis of significant correlation among five morphological traits in rice (Oryza sativa L.)

To enhance understanding of the genetic basis of trait correlation in rice, a recombinant inbred line (RIL) population (F₆ and F₇) from a cross between Zhenshan97 and HR5 was employed to identify main quantitative trait loci (QTLs) and epistatic QTL (E-QTL). Highly significant positive correlations were detected among five traits of heading date (HD), plant height (PH), panicle length (PL), flag leaf length (FLL) and flag leaf width (FLW) in 2 environments. Four to 8 main QTLs were detected for an individual trait. No E-QTL was detected for PH. One, 4, 4 and 5 E-QTLs were detected for FLL, HD, FLW and PL, respectively. Each E-QTL individually explained less than 3% of trait variation except E-QFll1. Comparison of QTL results was made in order to dissect the genetic basis of trait correlation. We found that main QTLs with pleiotropic effects and QTL clusters were the main genetic basis of trait correlation. No E-QTL had pleiotropic effects. E-QTL played an important role in the genetic basis of individual trait, but it made a little contribution to trait correlation.     

Germ-line transmission of a mutated p53 gene in a cancer-prone family with Li-Fraumeni syndrome

Tumour suppressor genes, whose usual function seems to be controlling normal cell proliferation, have been implicated in many inherited and sporadic forms of malignancies Much evidence supports the concept of tumour formation by loss-of-function mutations in suppressor genes, as predicted by the two-hit model of Knudson and DeMars. The suppressor gene, p53, is affected in such a manner by numerous mutations, which occur in a variety of human tumours. These mutations usually represent the loss of one allele and the substitution of a single base in the other. We have now analysed the p53 gene in a family affected by Li-Fraumeni syndrome, a rare autosomal dominant syndrome characterized by the occurrence of diverse mesenchymal and epithelial neoplasms at multiple sites. In some instances the neoplasms seem to be related to exposure to carcinogens, including ionizing radiation. The Li-Fraumeni family that we studied had noncancerous skin fibroblasts (NSF) with an unusual radiation-resistant phenotype. DNA derived from the NSF cells of four family members, spanning two generations, had the same point mutation in codon 245 (GGC----GAC) of the p53 gene. This mutation leads to substitution of aspartic acid for glycine in one of the regions identified as a frequent target of point mutations in p53. The NSF cell lines with the mutation also retained the normal p53 allele. This inherited p53 mutation may predispose the members of this family to increased susceptibility to cancer.