A intervarietal genetic map and QTL analysis for yield traits in wheat

A new genetic linkage map was constructed based on recombinant inbred lines (RILs) derived from the cross between the Chinese winter wheat (Triticum aestivum L.) varieties, Chuang 35050 and Shannong 483 (ChSh). The map included 381 loci on all the wheat chromosomes, which were composed of 167 SSR, 94 EST-SSR, 76 ISSR, 26 SRAP, 15 TRAP, and 3 Glu loci. This map covered 3636.7 cM with 1327.7 cM (36.5%), 1485.5 cM (40.9%), and 823.5 cM (22.6%) for A, B, and D genome, respectively, and contained 13 linkage gaps. Using the RILs and the map, we detected 46 putative QTLs on 12 chromosomes for grain yield (GY) per m², thousand-kernel weight (TKW), spike number (SN) per m², kernel number per spike (KNS), sterile spikelet number per spike (SSS), fertile spikelet number per spike (FSS), and total spikelet number per spike (TSS) in four environments. Each QTL explained 4.42–70.25% phenotypic variation. Four QTL cluster regions were detected on chromosomes 1D, 2A, 6B, and 7D. The most important QTL cluster was located on chromosome 7D near the markers of Xwmc31, Xgdm67, and Xgwm428, in which 8 QTLs for TKW, SN, SSS and FSS were observed with very high contributions (27.53–67.63%).     

Efficient construction of high-density linkage map and its application to QTL analysis in barley

Using a High Efficiency Genome Scanning (HEGS) system and recombinant inbred (RI) lines derived from the cross of Russia 6 and H.E.S. 4, a high-density genetic map was constructed in barley. The resulting 1,595.7-cM map encompassed 1,172 loci distributed on the seven linkage groups comprising 1,134 AFLP, 34 SSR, three STS and vrs1 (kernel row type) loci. Including PCR reactions, gel electrophoresis and data processing, 6 months of work by a single person was sufficient for the whole mapping procedure under a reasonable cost. To make an appraisal of the resolution of genetic analysis for the 95 RI lines based on the constructed linkage map, we measured three agronomic traits: plant height, spike exsertion length and 1,000-kernel weight, and the analyzed quantitative trait loci (QTLs) associated with these traits. The results were compared on the number of detected QTLs and their effects between a high-density map and a skeleton map constructed by selected AFLP and anchor markers. The composite interval mapping on the high-density map detected more QTLs than the other analyses. Closely linked markers with QTLs on the high-density map could be powerful tools for marker-assisted selection in barley breeding programs and further genetic analyses including an advanced backcross analysis or a map-based cloning of QTL. Electronic Supplementary Material Supplementary material is available in the online version of this article at Communicated by J.S. Heslop-Harrison     

基于F2群体的香菇遗传图谱构建及其在QTL定位中的应用

以171个F2双核体菌株为作图群体,通过相互配对的2个单核体的基因型推断双核体基因型,构建了第一张基于双核体群体的香菇遗传图谱。该图谱包含分布于15个连锁群的459个标记,覆盖长度为989.7cM,平均标记间隔为2.2cM。此外,以此双核体群体作为表型分离群体,定位了6个与香菇双核体菌丝生长速度相关的QTLs,位于5个连锁群上。采用全同胞单核体随机交配策略,易于构建相对大的双核体群体,用于连锁图构建和QTL定位。研究表明,在食用菌连锁图谱构建及QTL定位研究中,利用F2群体,可能为提高遗传作图效率,解决作图群体与表型分离群体间不一致问题提供新的途径。     

The components of life-history traits variation in Daphnia magna population

The variation of six growth and reproduction traits in the parthenogenetic clones of Daphnia magna and its relationships with the genotypes at 5 isozyme loci were studied under controlled conditions at three food concentrations. A significant genetic component of age at maturity, growth rate and fecundity variation was detected. Nested ANOVA revealed the influences of the genotypes of the isozyme loci, that are more pronounced at the high food concentration. In some cases the genotype-environment interactions were found.The variation of body length at 6 days and total number of offspring includes a significant heterozygosity — environment interaction. The most heterozygous clones show the least differences in life history traits between food conditions.Life-history traits heritability, genotype-environment interactions and different reproductive strategies of the clones are discussed.     

测序水稻品种SSR遗传连锁图谱的构建及其农艺性状基因座分析

利用测序水稻品种"Nipponbare（粳）/广陆矮4号（籼）"杂交F2群体90个单株为作图群体,构建含148个SSR标记的水稻遗传连锁图谱,覆盖基因组全长1737.81cM,标记间平均距11.90cM。利用该图谱及Excel2000和Mapmaker/QTL1.1b软件对分蘖数、穗数、穗长、主穗长、株高、剑叶长等六个农艺性状间的相互关系和基因位点进行分析,结果在LOD>2.2和P<0.005的条件下共检测到28个QTLs,它们分布在水稻所有染色体上,单个QTL对性状的分子贡献率11.1%-42.9%,其中大于20%有10个,并对选用已测序材料为亲本构建图谱来探讨水稻农艺性状的分子基础及其育种意义进行了讨论。     

An AFLP and RFLP linkage map and quantitative trait locus (QTL) analysis of growth traits in Salix

A genetic linkage map of Salix (2n = 38), composed of 325 AFLP and 38 RFLP markers has been constructed. The map was based on a population ( n = 87) derived from a cross between the male hybrid clone "Bj?rn" ( Salix viminalis x Salix schwerinii) and the female clone "78183" ( S. viminalis). Three hundred fifty seven AFLPs corresponding to DNA polymorphisms heterozygous in one parent and null in the other were scored. A total of 87 RFLP probes, most (83) derived from the Populus genome, yielded 39 and 11 polymorphic loci segregating in a 1:1 and 1:2:1 ratio respectively. Two maps, one for each parent, were constructed according to the "two-way pseudo-testcross" mapping strategy. The S. viminalis x S. schwerinii map (2,404 cM) included 217 markers and formed 26 major linkage groups while S. viminalis (1,844 cM) consisted of 146 markers placed on 18 major groups. In addition, eight and 14 additional minor linkage groups composed of less than four markers (doubles and triplets) were obtained in the S. viminalis x S. schwerinii and the S. viminalis maps, respectively. Both maps provided 70-80% genome coverage with an average density of markers of 14 cM. To investigate possible homologies between the parental maps, 20 AFLPs and 11 RFLPs segregating in 3:1 or 1:2:1 ratios were included in the linkage analysis. Eight linkage groups homologous between the two maps were detected. The present genetic map was used to identify quantitative trait loci (QTLs) affecting growth-related traits. Eleven QTLs were identified; seven QTLs for height growth, one QTL for stem diameter, one QTL for the height: diameter ratio, one QTL for the number of vegetative buds during flowering time and one QTL for the number of shoots. The estimated magnitude of the QTL effect ranged from 14 to 22% of the total phenotypic variance. One QTL associated with height growth and one affecting the height: diameter ratio were overlapping in the same marker interval with the QTL affecting stem diameter. QTL stability over years was estimated for traits measured in multiple years. Generally, QTLs were only significant in a single year although two QTLs for height growth were close to reaching the significance level in 2 consecutive years.     

An intervarietal genetic linkage map of Indian bread wheat (Triticum aestivum L.) and QTL maps for some metric traits

Bread wheat (Triticum aestivum L.) exhibits very narrow genetic diversity and hence there is high relatedness among cultivated varieties. However, a population generated from an intervarietal cross, with the parents differing in a large number of traits, could lead to the generation of QTL maps which will be useful in practice. In this report a genetic linkage map of wheat is constructed using a cross between two Indian bread wheat varieties: Sonalika and Kalyansona. The linkage map consisted of 236 markers and spanned a distance of 3639 cM, with 1211.2 cM for the A genome, 1669.2 cM for the B genome, 192.4 cM for the D genome and 566.2 cM for unassigned groups. Linkage analysis defined 37 linkage groups of which 24 were assigned to 17 chromosomes. The genetic map was used to identify QTLs by composite internal mapping (CIM) for three metric traits, viz. culm length (CL), flag leaf length (FLL) and flag leaf breadth (FLB). Of 25 QTLs identified in this study, 15 have not been reported previously. Multitrait CIM (MCIM) analysis was carried out for traits that were significantly correlated such as FLB-FLL and CL-FLB-FLL. Detection of a large number of QTLs for the three traits analysed suggests that in parent cultivars that are not too diverse, the differences at genetic level detected as polymorphisms may be mostly associated with QTLs for the observed differences.     

An analysis of the phototactic behaviour of Daphnia magna clones and their sexual descendants

Daphnia magna clones, isolated from different natural populations, were inbred and crossbred. Some aspects of the heredity of the phototactic behaviour, quantified by an index, were analysed. Heritability in the broad sense was determined for several assemblages of clones through calculation of the clonal repeatability. Heritability sensu strictu was determined by offspring-parent regressions. Frequency distributions of a phototactic index of several inbred and crossbred families are given.The results indicate a significant contribution of additive genetic variance to the total phenotypic variance. Comparison of heritability estimates suggests an important genetic interaction component.Some implications of these results on the variability of vertical migration patterns in natural populations are discussed.     

Plasticity of Daphnia magna life history traits in response to temperature and information about a predator

1. Exudates from predators often elicit early maturation in Daphnia, which may protect them from predation. Diel vertical migration (DVM) is also a predator-avoidance device and affects life history traits because of the variable temperature experienced during migration. This study asks, therefore, how do these two effects interact and what are the net costs and benefits of the two defences combined? 2. Key life history features were studied in a two factorial life table experiment in a monoclonal cohort of Daphnia magna to quantify the costs of predator-induced defences. 3. The costs of DVM, associated with low temperature, yielded a 30% decrease in the intrinsic rate of population increase. This was caused by later maturation and longer egg development time, despite a higher fecundity. 4. Chemical information that predators were present resulted in smaller, more numerous offspring, but had no significant effect on size and age at first reproduction. The costs of induction were therefore associated with smaller, and thus presumably lower quality, offspring. 5. Changes in life history induced by fish exudates were independent of the shifts caused by low temperature. 6. The measure of fitness chosen to assess the costs of induced defences is important because the costs often depend on the environment.     

Negative effects of UVB-irradiated phytoplankton on life history traits and fitness of Daphnia magna

SUMMARY 1. We tested the effect of ultraviolet-B (UVB)-irradiated phytoplankton on life history characteristics of Daphnia magna . Two phytoplankton species were used, Chlamydomonas reinhardtii and Cryptomonas pyrenoidifera . The phytoplankton species were cultured under photosynthetically active radiation (PAR) conditions, and under PAR supplemented with ultraviolet-A and ultraviolet-B radiation, and fed to Daphnia .
2. Life history traits of Daphnia were negatively affected when fed on UVB-irradiated Cryptomonas . Size at maturity was depressed and fewer juveniles with lower fitness were produced in the UVB treatments. In the Chlamydomonas experiment, no significant effects were found.
3. The cause of the observed UVB effects is likely to be constraints in food quality. Ultraviolet-B radiation thus has the potential of inhibiting energy transfer from the first to the second trophic level.     

Constructing a dense genetic linkage map and mapping QTL for the traits of flower development in Brassica carinata

Key message

An integrated dense genetic linkage map was constructed in a B. carinata population and used for comparative genome analysis and QTL identification for flowering time.

Abstract

An integrated dense linkage map of Brassica carinata (BBCC) was constructed in a doubled haploid population based on DArT-Seq^TM markers. A total of 4,031 markers corresponding to 1,366 unique loci were mapped including 639 bins, covering a genetic distance of 2,048 cM. We identified 136 blocks and islands conserved in Brassicaceae, which showed a feature of hexaploidisation representing the suggested ancestral crucifer karyotype. The B and C genome of B. carinata shared 85 % of commonly conserved blocks with the B genome of B. nigra/B. juncea and 80 % of commonly conserved blocks with the C genome of B. napus, and shown frequent structural rearrangements such as insertions and inversions. Up to 24 quantitative trait loci (QTL) for flowering and budding time were identified in the DH population. Of these QTL, one consistent QTL (qFT.B4-2) for flowering time was identified in all of the environments in the J block of the B4 linkage group, where a group of genes for flowering time were aligned in A. thaliana. Another major QTL for flowering time under a winter-cropped environment was detected in the E block of C6, where the BnFT-C6 gene was previously localised in B. napus. This high-density map would be useful not only to reveal the genetic variation in the species with QTL analysis and genome sequencing, but also for other applications such as marker-assisted selection and genomic selection, for the African mustard improvement.     

The effect of diapause on the genetic structure of Daphnia magna populations

For intermittent Daphnia magna populations embryonic diapause following bisexual reproduction is the means of surviving in harsh environmental conditions. Another advantage of bisexuality is genetic recombination which produces a variety of genotypes. Crowding and short-day photo-periods promote bisexual reproduction, but photoperiod, at least, can not be an obligatory factor in D. magna since some bisexual females have been found also during the periods of long daylength. Because the catastrophe dates vary considerably, the most advantageous reproductive strategy must be one with some flexibility in reacting to irregular catastrophes by producing ephippial resting eggs whenever the probability of a catastrophe exceeds a certain threshold value. Extensive genetic changes occurring during diapause suggest that there are considerable genetic differences in ephippial egg production and egg survival. Genetic drift alone can not account for the great genetic changes observed, although in populations reacting slowly to changing conditions the number of diapausing ephippia can be relatively low. If the ephippia hatch over a long period of time, they can act as a stabilizing mechanism for genotype frequencies.     

Mapping genome-wide QTL of ratio traits with Bayesian shrinkage analysis for its component traits

The ratio trait is defined as a ratio of two regular quantitative traits with normal distribution, which is distinguished from regular quantitative traits in the genetic analysis because it does not follow the normal distribution. On the basis of maximum likelihood method that uses a special linear combination of the two component traits, we develop a Bayesian mapping strategy for ratio traits, which firstly analyzes the two component traits by Bayesian shrinkage method, and then generates a new posterior sample of genetic effects for a ratio trait from ones of population means and genetic effects for the two component traits, finally, infers QTL for the ratio trait via post MCMC analysis for the new posterior sample. A simulation study demonstrates that the new method has higher detecting power of the QTL than maximum likelihood method. An application is illustrated to map genome-wide QTL for relative growth rate of height on soybean.     

Habitat size and the genetic structure of a cyclical parthenogen, Daphnia magna

In populations of a cyclical parthenogen, the diversity of clonal lineages, derived from sexually produced eggs, declines during the parthenogenetic phase. Even though Daphnia magna populations from small ponds may harbour millions of individuals, we show that observed clonal and allelic diversity in populations from such small water bodies are lower than in populations from larger water bodies. Populations from small water bodies also show significant fluctuations in allele frequencies among years and a stronger among-population genetic differentiation than populations inhabiting larger water bodies. Persistent founder effects can only explain part of these results. Our data link the population genetic structure of cyclical parthenogens to the size of the habitat and suggest that genetic drift is a more prominent feature of populations inhabiting small water bodies than previously thought.     

A comprehensive SNP-based genetic analysis of inbred mouse strains

Dense genetic maps of mammalian genomes facilitate a variety of biological studies including the mapping of polygenic traits, positional cloning of monogenic traits, mapping of quantitative or qualitative trait loci, marker association, allelic imbalance, speed congenic construction, and evolutionary or phylogenetic comparison. In particular, single nucleotide polymorphisms (SNPs) have proved useful because of their abundance and compatibility with multiple high-throughput technology platforms. SNP genotyping is especially suited for the genetic analysis of model organisms such as the mouse because biallelic markers remain fully informative when used to characterize crosses between inbred strains. Here we report the mapping and genotyping of 673 SNPs (including 519 novel SNPs) in 55 of the most commonly used mouse strains. These data have allowed us to construct a phylogenetic tree that correlates and expands known genealogical relationships and clarifies the origin of strains previously having an uncertain ancestry. All 55 inbred strains are distinguishable genetically using this SNP panel. Our data reveal an uneven SNP distribution consistent with a mosaic pattern of inheritance and provide some insight into the changing dynamics of the physical architecture of the genome. Furthermore, these data represent a valuable resource for the selection of markers and the design of experiments that require the genetic distinction of any pair of mouse inbred strains such as the generation of congenic mice, positional cloning, and the mapping of quantitative or qualitative trait loci.The content of this publication does not necessarily reflect the view or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsement by the U.S. Government.     

SNP-based analysis of genetic substructure in the German population

OBJECTIVE: To evaluate the relevance and necessity to account for the effects of population substructure on association studies under a case-control design in central Europe, we analysed three samples drawn from different geographic areas of Germany. Two of the three samples, POPGEN (n = 720) and SHIP (n = 709), are from north and north-east Germany, respectively, and one sample, KORA (n = 730), is from southern Germany. METHODS: Population genetic differentiation was measured by classical F-statistics for different marker sets, either consisting of genome-wide selected coding SNPs located in functional genes, or consisting of selectively neutral SNPs from 'genomic deserts'. Quantitative estimates of the degree of stratification were performed comparing the genomic control approach [Devlin B, Roeder K: Biometrics 1999;55:997-1004], structured association [Pritchard JK, Stephens M, Donnelly P: Genetics 2000;155:945-959] and sophisticated methods like random forests [Breiman L: Machine Learning 2001;45:5-32]. RESULTS: F-statistics showed that there exists a low genetic differentiation between the samples along a north-south gradient within Germany (F(ST)(KORA/POPGEN): 1.7 . 10(-4); F(ST)(KORA/SHIP): 5.4 . 10(-4); F(ST)(POPGEN/SHIP): -1.3 . 10(-5)). CONCLUSION: Although the F(ST )-values are very small, indicating a minor degree of population structure, and are too low to be detectable from methods without using prior information of subpopulation membership, such as STRUCTURE [Pritchard JK, Stephens M, Donnelly P: Genetics 2000;155:945-959], they may be a possible source for confounding due to population stratification.     

An SSR genetic map of Sorghum bicolor (L.) Moench and its comparison to a published genetic map.

Sorghum bicolor (L.) Moench is an important grain and forage crop grown worldwide. We developed a simple sequence repeat (SSR) linkage map for sorghum using 352 publicly available SSR primer pairs and a population of 277 F2 individuals derived from a cross between the Westland A line and PI 550610. A total of 132 SSR loci appeared polymorphic in the mapping population, and 118 SSRs were mapped to 16 linkage groups. These mapped SSR loci were distributed throughout 10 chromosomes of sorghum, and spanned a distance of 997.5 cM. More important, 38 new SSR loci were added to the sorghum genetic map in this study. The mapping result also showed that chromosomes SBI-01, SBI-02, SBI-05, and SBI-06 each had 1 linkage group; the other 6 chromosomes were composed of 2 linkage groups each. Except for 5 closely linked marker flips and 1 locus (Sb6_34), the marker order of this map was collinear to a published sorghum map, and the genetic distances of common marker intervals were similar, with a difference ratio 相似文献   

Using genetic networks and homology to understand the evolution of phenotypic traits

Homology can have different meanings for different kinds of biologists. A phylogenetic view holds that homology, defined by common ancestry, is rigorously identified through phylogenetic analysis. Such homologies are taxic homologies (=synapomorphies). A second interpretation, "biological homology" emphasizes common ancestry through the continuity of genetic information underlying phenotypic traits, and is favored by some developmental geneticists. A third kind of homology, deep homology, was recently defined as "the sharing of the genetic regulatory apparatus used to build morphologically and phylogenetically disparate features." Here we explain the commonality among these three versions of homology. We argue that biological homology, as evidenced by a conserved gene regulatory network giving a trait its "essential identity" (a Character Identity Network or "ChIN") must also be a taxic homology. In cases where a phenotypic trait has been modified over the course of evolution such that homology (taxic) is obscured (e.g. jaws are modified gill arches), a shared underlying ChIN provides evidence of this transformation. Deep homologies, where molecular and cellular components of a phenotypic trait precede the trait itself (are phylogenetically deep relative to the trait), are also taxic homologies, undisguised. Deep homologies inspire particular interest for understanding the evolutionary assembly of phenotypic traits. Mapping these deeply homologous building blocks on a phylogeny reveals the sequential steps leading to the origin of phenotypic novelties. Finally, we discuss how new genomic technologies will revolutionize the comparative genomic study of non-model organisms in a phylogenetic context, necessary to understand the evolution of phenotypic traits.     

Combining QTL and candidate gene analysis with phenotypic model to unravel the relationship between lodging and related traits in soybean

Lodging is one of the major influencing factors of yield and quality in soybean [Glycine max (L.) Merr.] and other crops. To dissect the genetic basis of lodging in soybean, a recombinant inbred line population consisting of 165 lines was used to evaluate lodging percentage and eight related traits (branch number, internode length, number of nodes, plant height, stem diameter, stem strength, root length, and root weight) in three environments. Regression analysis indicated that plant height and root weight, which explain more than 55% of the variation in lodging percentage, might be the key factors influencing lodging in soybean. Nine consensus quantitative trait locus (QTLs) of lodging percentage were detected in one to three environments. Of which, eight consensus QTLs were colocated with 16 consensus QTLs of lodging-related traits by meta-analysis. In addition, seven candidate genes with the biological functions of shoot branching, root development, internode elongation, and lignin biosynthesis were identified on four pleiotropic QTL regions (oq.13-1, oq.13-2, oq.19-2, and oq.19-3) for lodging percentage and related traits. These findings showed that the consensus QTLs of lodging percentage might result from the pleiotropic QTLs affecting the lodging-related traits. Soybean lodging is determined by the cumulative effect of many traits/processes of growth and development. The combination of MAS, statistical model, and phenotypic selection will provide a powerful breeding strategy for lodging resistance in soybean.