基于元分析的抗玉米丝黑穗病QTL比较定位

以玉米遗传连锁图谱IBM2 2005 Neighbors为参考图谱,通过映射整合不同试验中的抗玉米丝黑穗病QTL,构建QTL综合图谱。在国内外种质中,共发现22个抗病QTL,分布在除第7染色体外的9条玉米染色体上。采用元分析技术,获得2个“一致性”抗病QTL,图距分别为8.79 cM和18.92cM。从MaizeGDB网站下载“一致性”QTL区间内基因和标记的原始序列;采用NCBI网站在线软件BLASTx通过同源比对在2个“一致性”QTL区间内初步获得4个抗病位置候选基因。借助比较基因电子定位策略,将69个水稻和玉米抗性基因定位于玉米IBM2图谱上,在2个“一致性”QTL区间内分别发现1个水稻抗性基因,初步推断为抗病位置候选基因。本文结果为抗玉米丝黑穗病QTL精细定位和分子育种提供了基础。     

玉米抗甘蔗花叶病毒基因的比较定位

收集了玉米抗甘蔗花叶病毒基因/QTL定位信息, 借助玉米遗传图谱IBM2 2005 Neighbors进行了整合。在国内外研究中, 累计报道81个抗病毒基因位点, 分布在玉米7条染色体上, 比较定位发现这些位点集中分布于第3和6染色体。采用元分析技术, 确定3个“一致性”抗病毒QTL, 其中1个位于第3染色体, 在遗传图谱IBM2 2005 Neighbors上覆盖的范围为6.44 cM; 2个位于第6染色体, 覆盖范围分别为6.16 cM和27.48 cM。借助比较基因组学策略, 在第3染色体“一致性”QTL区间内筛选出4个抗病位置候选基因。该研究结果为确定和克隆抗病主效基因提供了基础。     

Genetic Regulation of Bone Metabolism in the Chicken: Similarities and Differences to Mammalian Systems

Birds have a unique bone physiology, due to the demands placed on them through egg production. In particular their medullary bone serves as a source of calcium for eggshell production during lay and undergoes continuous and rapid remodelling. We take advantage of the fact that bone traits have diverged massively during chicken domestication to map the genetic basis of bone metabolism in the chicken. We performed a quantitative trait locus (QTL) and expression QTL (eQTL) mapping study in an advanced intercross based on Red Junglefowl (the wild progenitor of the modern domestic chicken) and White Leghorn chickens. We measured femoral bone traits in 456 chickens by peripheral computerised tomography and femoral gene expression in a subset of 125 females from the cross with microarrays. This resulted in 25 loci for female bone traits, 26 loci for male bone traits and 6318 local eQTL loci. We then overlapped bone and gene expression loci, before checking for an association between gene expression and trait values to identify candidate quantitative trait genes for bone traits. A handful of our candidates have been previously associated with bone traits in mice, but our results also implicate unexpected and largely unknown genes in bone metabolism. In summary, by utilising the unique bone metabolism of an avian species, we have identified a number of candidate genes affecting bone allocation and metabolism. These findings can have ramifications not only for the understanding of bone metabolism genetics in general, but could also be used as a potential model for osteoporosis as well as revealing new aspects of vertebrate bone regulation or features that distinguish avian and mammalian bone.     

Quantitative trait locus mapping of pyrethroid resistance in Colorado potato beetle, Leptinotarsa decemlineata (Say) (Coleoptera: Chrysomelidae)

Quantitative trait locus (QTL) mapping is a valuable new tool for locating genomic regions that underlie variation in important traits such as insecticide resistance. Because QTL mapping complements a candidate gene strategy for understanding the genetic architecture of important traits, it may also facilitate the identification of genes causing important variation. After mapping the QTL locations, markers closely linked to QTL can be used for genetic analysis of population structure and to measure the spread and increase of resistance-causing QTL alleles. In this study, QTL influencing resistance to the pyrethroid insecticide esfenvalerate were mapped in the Colorado potato beetle Leptinotarsa decemlineata (Say) (CPB). Three QTL contributing to esfenvalerate resistance were identified from a mapping population of 79 individuals analyzed at 90 marker loci. One QTL had a large effect and two QTL had smaller effects. The major QTL occurs on the X chromosome, overlapping the position of a candidate gene (Leptinotarsa decemlineata Voltage sensitive sodium channel [LdVssc1]) previously implicated in pyrethroid resistance. Resistance-increasing alleles at the two minor-effect QTL originated with the susceptible parent, suggesting that alleles of small effect may be segregating in susceptible populations. Comparison of the New York population from which the susceptible parent originated with a more-susceptible population from North Carolina suggests that the minor-effect loci identified here may explain some of the variation in tolerance observed among susceptible populations. DNA sequencing of a portion of LdVssc1 shows that the resistance-conferring allele from the resistant parent does not contain the kdr mutation previously found in CPB and typically observed in other insects that are resistant to pyrethroid insecticides because of changes in this gene.     

植物抗病遗传育种中的QTL定位和克隆(综述)

对植物抗病遗传育种中QTL定位与克隆研究进行综述。主要阐述了数量抗性的遗传学基础、作物抗病性QTL的定位作图、QTL作图的可靠性及应对措施、QTLs候选基因的证实和定位克隆等,并对植物抗病遗传育种未来的研究方向予以讨论。     

Novel quantitative trait loci for broad-based resistance to soybean cyst nematode (Heterodera glycines Ichinohe) in soybean PI 567516C

Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is the most destructive pest of soybean worldwide. Host plant resistance is an effective approach to control this pest. Plant introduction PI 567516C has been reported to be highly resistant to multiple-HG types of SCN. The objectives of this study were to identify and map novel quantitative trait loci (QTL) for SCN resistance to six HG types (also known as races 1, 2, 3, 5, 14, and LY1). Mapping was conducted using 250 F_2:3 progeny derived from a Magellan (susceptible) × PI 567516C (resistant) cross. F_6:7 recombinant inbred lines (RILs) developed from the F_2:3 progeny were employed to confirm the putative QTL identified. A total of 927 polymorphic simple sequence repeats (SSR) and single nucleotide polymorphism (SNP) markers were genotyped. Following the genetic linkage analysis, permutation tests and composite interval mapping were performed to identify and map QTL. Four QTL were associated with resistance to either multiple- or single-SCN HG types. Two QTL for resistance to multiple-SCN HG types were mapped to Chromosomes 10 and 18 and have not been reported in other SCN resistance sources. New QTL were confirmed by analysis of 250 F_6:7 RILs from the same population. SSR and SNP markers closely associated with these QTL can be useful for the development of near-isogenic lines for fine-mapping and positional cloning of candidate genes for SCN resistance.     

Complex traits analysis of chicken growth using targeted genetical genomics

Dissecting the genetic control of complex trait variation remains very challenging, despite many advances in technology. The aim of this study was to use a major growth quantitative trait locus (QTL) in chickens mapped to chromosome 4 as a model for a targeted approach to dissect the QTL. We applied a variant of the genetical genomics approach to investigate genome-wide gene expression differences between two contrasting genotypes of a marked QTL. This targeted approach allows the direct quantification of the link between the genotypes and the genetic responses, thus narrowing the QTL-phenotype gap using fewer samples (i.e. microarrays) compared with the genome-wide genetical genomics studies. Four differentially expressed genes were localized under the region of the QTL. One of these genes is a potential positional candidate gene (AADAT) that affects lysine and tryptophan metabolism and has alternative splicing variants between the two genotypes. In addition, the lysine and glycolysis metabolism pathways were significantly enriched for differentially expressed genes across the genome. The targeted approach provided a complementary route to fine mapping of QTL by characterizing the local and the global downstream effects of the QTL and thus generating further hypotheses about the action of that QTL.     

Comparative mapping of bovine chromosome 27 with human chromosome 8 near a dairy form QTL in cattle

In the absence of a complete and annotated bovine genome sequence, detailed human-bovine comparative maps are one of the most effective tools for identification of positional candidate genes contributing to quantitative trait loci (QTL) in cattle. In the present study, eight genes from human chromosome 8 were selected for mapping in cattle to improve breakpoint resolution and confirm gene order on the comparative map near the 40 cM region of the BTA27 linkage map where a QTL affecting dairy form had previously been identified. The resulting map identified ADRB3 as a positional candidate gene for the QTL contributing to the dairy form trait based on its estimated position between 40 and 45 cM on the linkage map. It is also a functional candidate gene due to its role in fat metabolism, and polymorphisms in the ADRB3 gene associated with obesity and metabolic disease in humans, as well as, carcass fat in sheep. Further studies are underway to investigate the existence of polymorphisms in the bovine ADRB3 gene and their association with traits related to fat deposition in cattle.     

Genetic mapping of quantitative trait loci affecting susceptibility to Marek's disease virus induced tumors in F2 intercross chickens.

Marek''s disease (MD) is a lymphoproliferative disease caused by the MD virus (MDV), which costs the poultry industry nearly $1 billion annually. To identify quantitative trait loci (QTL) affecting MD susceptibility, the inbred lines 6(3) (MD resistant) and 7(2) (MD susceptible) were mated to create more than 300 F2 chickens. The F2 chickens were challenged with MDV JM strain, moderately virulent) at 1 wk of age and assessed for MD susceptibility. The QTL analysis was divided into three stages. In stage 1, 65 DNA markers selected from the chicken genetic maps were typed on the 40 most MD-susceptible and the 40 most MD-resistant F2 chickens, and 21 markers residing near suggestive QTL were revealed by analysis of variance (ANOVA). In stage 2, the suggestive markers plus available flanking markers were typed on 272 F2 chickens, and three suggestive QTL were identified by ANOVA. In stage 3, using the interval mapping program Map Manager and permutation tests, two significant and two suggestive MD QTL were identified on four chromosomal subregions. Three to five loci collected explained between 11 and 23% of the phenotypic MD variation, or 32-68% of the genetic variance. This study constitutes the first report in the domestic chicken on the mapping of non-major histocompatibility complex QTL affecting MD susceptibility.     

Development, genetic mapping of candidate gene-based markers and their significant association with the shoot fly resistance quantitative trait loci in sorghum [Sorghum bicolor (L.) Moench]

The associations of candidate genes with quantitative trait loci (QTL) for insect resistance provide primary insight into the molecular mechanisms of resistance. The objectives of the present study were to genetically map the candidate genes and identify their association with shoot fly resistance, and update the genetic map with new markers to locate additional QTL. In this study, 80 candidate gene (CG)-based markers were developed, targeting the seven most important shoot fly resistance genomic regions reported in our previous study. Of the 17 polymorphic CGs, the allelic polymorphisms of seven genes were significantly associated with 18 major QTL for component traits of resistance in multiple QTL mapping (MQM), and two genes in the single-marker analysis. MQM with an updated map revealed 20 new QTL with LOD and R ² (%) values ranging from 2.6 to 15.6 and 5.5 to 34.5?%, respectively. The susceptible parent 296B contributed resistance at 10 QTL. Interestingly, an orthologous insect resistance gene Cysteine protease-Mir1 (XnhsbmSFC34/SBI-10), previously presumed to be a CG based on synteny with maize, was significantly associated with major QTL for all traits (except seedling vigor) explaining 22.1?% of the phenotypic variation for deadhearts%, a direct measure of shoot fly resistance. Similarly, a NBS?CLRR gene (XnhsbmSFCILP2/SBI-10), involved in rice brown planthopper resistance, was associated with deadhearts% and number of eggs per plant. Beta-1,3-glucanase (XnhsbmSFC4/SBI-10), involved in aphid and brown planthopper resistance, was associated with deadhearts% and leaf glossiness. Comparative QTL analysis revealed the existence of common QTL for shoot fly and other important sorghum insect pests such as greenbug, head bug, and midge. Finally, the associated CGs should aid in elucidating the molecular basis of resistance, high-resolution mapping, and map-based cloning of major QTL, besides providing powerful gene tags for marker-assisted selection of shoot fly resistance.     

Combined genetic and physiological analysis of a locus contributing to quantitative variation

The natural variation of many traits is controlled by multiple genes, individually referred to as quantitative trait loci (QTL), that interact with the environment to determine the ultimate phenotype of any individual. A QTL has yet to be described molecularly, in part because strategies to systematically identify them are underdeveloped and because the subtle nature of QTLs prevents the application of standard methods of gene identification. Therefore, it will be necessary to develop a systematic approach(es) for the identification of QTLs based upon the numerous positional data now being accumulated through molecular marker analyses. We have characterized a QTL by the following three-step approach: (1) identification of a QTL in complex populations, (2) isolation and genetic mapping of this QTL in near-isogenic lines, and (3) identification of a candidate gene using map position and physiological criteria. Using this approach we have characterized a plant height QTL in maize that maps to chromosome 9 near the centromere. Both map position and physiological criteria suggest the gibberillin biosynthesis gene dwarf3 as a candidate gene for this QTL.     

Vanaso is a candidate quantitative trait gene for Drosophila olfactory behavior

Most animals depend on olfaction for survival and procreation. Odor-guided behavior is a quantitative trait, with phenotypic variation due to multiple segregating quantitative trait loci (QTL). Despite its profound biological importance, the genetic basis of naturally occurring variation in olfactory behavior remains unexplored. Here, we mapped a single Drosophila QTL affecting variation in avoidance response to benzaldehyde, using a population of recombinant inbred lines. Deficiency complementation mapping resolved this region into one female- and one male-specific QTL. Subsequent quantitative complementation tests to all available mutations of positional candidate genes showed that the female-specific QTL failed to complement a P-element insertional mutation, l(3)04276. The P-element insertion was in the intron of a novel gene, Vanaso, which contains a putative guanylate binding protein domain, is highly polymorphic, and is expressed in the third antennal segment, the major olfactory organ of Drosophila. No expression was detected in the fly brain, suggesting that Vanaso plays a role in peripheral chemosensory processes rather than in central integration of olfactory information. QTL mapping followed by quantitative complementation tests to deficiencies and mutations is an effective strategy for gene discovery that allows characterization of effects of recessive lethal genes on adult phenotypes and here enabled identification of a candidate gene that contributes to sex-specific quantitative variation in olfactory behavior.     

Quantitative trait loci for floral morphology in Arabidopsis thaliana

A central question in biology is how genes control the expression of quantitative variation. We used statistical methods to estimate genetic variation in eight Arabidopsis thaliana floral characters (fresh flower mass, petal length, petal width, sepal length, sepal width, long stamen length, short stamen length, and pistil length) in a cosmopolitan sample of 15 ecotypes. In addition, we used genome-wide quantitative trait locus (QTL) mapping to evaluate the genetic basis of variation in these same traits in the Landsberg erecta x Columbia recombinant inbred line population. There was significant genetic variation for all traits in both the sample of naturally occurring ecotypes and in the Ler x Col recombinant inbred line population. In addition, broad-sense genetic correlations among the traits were positive and high. A composite interval mapping (CIM) analysis detected 18 significant QTL affecting at least one floral character. Eleven QTL were associated with several floral traits, supporting either pleiotropy or tight linkage as major determinants of flower morphological integration. We propose several candidate genes that may underlie these QTL on the basis of positional information and functional arguments. Genome-wide QTL mapping is a promising tool for the discovery of candidate genes controlling morphological development, the detection of novel phenotypic effects for known genes, and in generating a more complete understanding of the genetic basis of floral development.     

Variation in Galr1 expression determines susceptibility to exocitotoxin-induced cell death in mice

Inbred strains of mice differ in their susceptibility to excitotoxin-induced cell death, but the genetic basis of individual variation in differential susceptibility is unknown. Previously, we identified a highly significant quantitative trait locus (QTL) on chromosome 18 that influenced susceptibility to kainic acid-induced cell death ( Sicd1 ). Comparison of susceptibility to seizure-induced cell death between reciprocal congenic lines for Sicd1 and parental background mice indicates that genes influencing this trait were captured in both strains. Two positional gene candidates, Galr1 and Mbp , map to 55 cM, where the Sicd1 QTL had been previously mapped. Thus, this study was undertaken to determine if Galr1 and/or Mbp could be considered as candidate genes. Genomic sequence comparison of these two functional candidate genes from the C57BL/6J (resistant at Sicd1 ) and the FVB/NJ (susceptible at Sicd1 ) strains showed no single-nucleotide polymorphisms. However, expression studies confirmed that Galr1 shows significant differential expression in the congenic and parental inbred strains. Galr1 expression was downregulated in the hippocampus of C57BL/6J mice and FVB.B6- Sicd1 congenic mice when compared with FVB/NJ or B6.FVB- Sicd1 congenic mice. A survey of Galr1 expression among other inbred strains showed a significant effect such that 'susceptible' strains showed a reduction in Galr1 expression as compared with 'resistant' strains. In contrast, no differences in Mbp expression were observed. In summary, these results suggest that differential expression of Galr1 may contribute to the differences in susceptibility to seizure-induced cell death between cell death-resistant and cell death-susceptible strains.     

Genetic mapping revealed two loci for soybean aphid resistance in PI 567301B

The soybean aphid (Aphis glycines Matsumura) is the most damaging insect pest of soybean [Glycine max (L.) Merr.] in North America. New soybean aphid biotypes have been evolving quickly and at least three confirmed biotypes have been reported in USA. These biotypes are capable of defeating most known aphid resistant soybean genes indicating the need for identification of new genes. Plant Introduction (PI) 567301B was earlier identified to have antixenosis resistance against biotype 1 and 2 of the soybean aphid. Two hundred and three F_7:9 recombinant inbred lines (RILs) developed from a cross of soybean aphid susceptible cultivar Wyandot and resistant PI 567301B were used for mapping aphid resistance genes using the quantitative trait loci (QTL) mapping approach. A subset of 94 RILs and 516 polymorphic SNP makers were used to construct a genome-wide molecular linkage map. Two candidate QTL regions for aphid resistance were identified on this linkage map. Fine mapping of the QTL regions was conducted with SSR markers using all 203 RILs. A major gene on chromosome 13 was mapped near the previously identified Rag2 gene. However, an earlier study revealed that the detached leaves of PI 567301B had no resistance against the soybean aphids while the detached leaves of PI 243540 (source of Rag2) maintained aphid resistance. These results and the earlier finding that PI 243540 showed antibiosis resistance and PI 567301B showed antixenosis type resistance, indicating that the aphid resistances in the two PIs are not controlled by the same gene. Thus, we have mapped a new gene near the Rag2 locus for soybean aphid resistance that should be useful in breeding for new aphid-resistant soybean cultivars. Molecular markers closely linked to this gene are available for marker-assisted breeding. Also, the minor locus found on chromosome 8 represents the first reported soybean aphid-resistant locus on this chromosome.     

Integrating QTL and high-density SNP analyses in mice to identify Insig2 as a susceptibility gene for plasma cholesterol levels

The use of inbred strains of mice to dissect the genetic complexity of common diseases offers a viable alternative to human studies, given the control over experimental parameters that can be exercised. Central to efforts to map susceptibility loci for common diseases in mice is a comprehensive map of DNA variation among the common inbred strains of mice. Here we present one of the most comprehensive high-density, single nucleotide polymorphism (SNP) maps of mice constructed to date. This map consists of 10,350 SNPs genotyped in 62 strains of inbred mice. We demonstrate the utility of these data via a novel integrative genomics approach to mapping susceptibility loci for complex traits. By integrating in silico quantitative trait locus (QTL) mapping with progressive QTL mapping strategies in segregating mouse populations that leverage large-scale mapping of the genetic determinants of gene expression traits, we not only facilitate identification of candidate quantitative trait genes, but also protect against spurious associations that can arise in genetic association studies due to allelic association among unlinked markers. Application of this approach to our high-density SNP map and two previously described F2 crosses between strains C57BL/6J (B6) and DBA/2J and between B6 ApoE(-/-) and C3H/HeJ ApoE(-/-) results in the identification of Insig2 as a strong candidate susceptibility gene for total plasma cholesterol levels.     

Lactuca saligna,a non-host for lettuce downy mildew ( Bremia lactucae), harbors a new race-specific Dm gene and three QTLs for resistance

Lactuca sativa (lettuce) is susceptible to Bremia lactucae (downy mildew). In cultivated and wild Lactuca species, Dm genes have been identified that confer race-specific resistance. However, these genes were soon rendered ineffective by adaptation of the pathogen. Lactuca saligna (wild lettuce) is resistant to all downy mildew races and can be considered as a non-host. Therefore, L. saligna might be an alternative source for a more-durable resistance to downy mildew in lettuce. In order to analyze this resistance, we have developed an F(2) population based on a resistant L. saligna x susceptible L. sativa cross. This F(2) population was fingerprinted with AFLP markers and tested for resistance to two Bremia races NL14 and NL16. The F(2) population showed a wide and continuous range of resistance levels from completely resistant to completely susceptible. By comparison of disease tests, we observed a quantitative resistance against both Bremia races as well as a race-specific resistance to Bremia race NL16 and not to NL14. QTL mapping revealed a qualitative gene ( R39) involved in the race-specific resistance and three QTLs ( RBQ1, RBQ2 and RBQ3) involved in the quantitative resistance. The qualitative gene R39 is a dominant gene that gives nearly complete resistance to race NL16 in L. saligna CGN 5271 and therefore it showed features similar to Dm genes. The three QTLs explained 51% of the quantitative resistance against NL14, which indicated that probably only the major QTLs have been detected in this F(2) population. The perspectives for breeding for durable resistance are discussed.     

Linkage mapping of genes controlling resistance to white rust (Albugo candida) in Brassica rapa (syn. campestris) and comparative mapping to Brassica napus and Arabidopsis thaliana.

Genes for resistance to white rust (Albugo candida) in oilseed Brassica rapa were mapped using a recombinant inbred (RI) population and a genetic linkage map consisting of 144 restriction fragment length polymorphism (RFLP) markers and 3 phenotypic markers. Young seedlings were evaluated by inoculating cotyledons with A. candida race 2 (AC2) and race 7 (AC7) and scoring the interaction phenotype (IP) on a 0-9 scale. The IP of each line was nearly identical for the two races and the population showed bimodal distributions, suggesting that a single major gene (or tightly linked genes) controlled resistance to the two races. The IP scores were converted to categorical resistant and susceptible scores, and these data were used to map a single Mendelian gene controlling resistance to both races on linkage group 4 where resistance to race 2 had been mapped previously. A quantitative trait loci (QTL) mapping approach using the IP scores detected the same major resistance locus for both races, plus a second minor QTL effect for AC2 on linkage group 2. These results indicate that either a dominant allele at a single locus (Acal) or two tightly linked loci control seedling resistance to both races of white rust in the biennial turnip rape cultivar Per. The map positions of white rust resistance genes in B. rapa and Brassica napus were compared and the results indicate where additional loci that have not been mapped may be located. Alignment of these maps to the physical map of the Arabidopsis genome identified regions to target for comparative fine mapping using this model organism.