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PubMed2005

Mapping of interactions and mouse congenic strains identified novel epistatic QTLs controlling the persistence of Salmonella Enteritidis in mice.

The host response to infection in humans is multifactorial and involves the complex interaction between two genomes (the host and the pathogen) and the environment. Using an experimental mouse model of chronic infection, we have previously identified the individual effect of three significant and one suggestive quantitative trait loci (QTLs) (Ses1, Ses2, Ses3 and Ses1.1) on Salmonella Enteritidis persistence in target organs of 129S6/SvEvTac mice. Congenic strain construction was performed by transferring each of these QTLs from C57BL/6J onto the 129S6/SvEvTac background, and phenotypic analysis confirmed that Ses1 and Ses1.1 contribute to bacterial clearance. Additional QTLs regulating Salmonella carriage in 129S6/SvEvTac mice were identified using a two-locus epistasis QTL linkage mapping approach conducted separately in females and males. The epistatic model for females included the individual effect of Ses3 and two significant interactions (Ses1-D7Mit267 and Ses1-DXMit48) accounting for 47% of the total phenotypic variance. The model for males included the individual effect of Ses1.1, three interactions (Ses1-D9Mit218, D2Mit197-D4Mit2 and D3Mit256-D13Mit36) and explained 47% of the phenotypic variance. Our results suggest that the oligogenic nature of Salmonella persistence and epistasis are important constituents of the genetic architecture of the host response to chronic Salmonella infection.

Animals↗
PubMed2006

Isolation of three dormancy QTLs as Mendelian factors in rice.

Seed dormancy is a key adaptive trait under polygenic control in many plants. We introduced the chromosomal regions containing the dormancy QTLs qSD1, qSD7-1, and qSD12 from an accession of weedy rice into a nondormant genetic background to examine component genetic effects and their interactions with time of afterripening (DAR). A BC4F2 plant, which was heterozygous for the three loci, was selected to develop the BC4F3 population. Single point analysis detected only qSD7-1 and qSD12 (R2 = 38-72%) at 10, 30, and 50 DAR in the population. However, multiple linear regression analysis detected genetic effects of the three QTLs and their trigenic epistasis, an environmental effect of DAR (E), and interactions of E with qSD12 and with the qSD1 x qSD7-1 and qSD7-1 x qSD12 epistases. The linear model demonstrates that QTL main effects varied with DAR, and that some epistasis or epistasis-by-DAR interactions partially counteract the main effects. The three QTLs were isolated as single Mendelian factors from the BC4F3 population and estimated for component genic effects based on the BC4F4 populations. Isolation improved estimation of the qSD1 effect and confirmed the major effect of qSD12. The qSD1 and qSD12 loci displayed a gene-additive effect. The qSD7-1, which was further narrowed to a chromosomal region encompassing the red pericarp color gene Rc, displayed gene additive and dominant effects.

Adaptation, Physiological↗
PubMed2006

Individual QTLs controlling quantitative variation in blood pressure inherited in a Mendelian mode.

We studied three possible genotypes at 10 well-defined blood pressure (BP) QTLs using congenic rat lines. The central question was whether the hypertensive or normotensive allele is dominant, or whether there is partial dominance. The congenic strains were employed to investigate the BP effects of alleles originating from normotensive rats in the background of hypertensive Dahl salt-sensitive (DSS) rats. The normotensive alleles at eight QTLs were fully dominant over DSS alleles, which we tentatively interpreted as indicating that DSS rats incurred a loss of function at these loci and that the QTLs produced BP-reducing agents. In contrast, the normotensive allele of only one QTL was recessive over its DSS counterpart, implying a gain of function at this QTL or a null allele involved in generating a BP-elevating agent. Only one locus, C17QTL, had alleles exhibiting partial dominance. These estimates of dominance differ considerably from those obtained by QTL analysis in a F2 cross. This disagreement demonstrates the importance of establishing a cause-effect relationship between a QTL and its phenotypic effect via congenic strains. The dominance relationships suggest pertinent strategies for gene identification and pharmaceutical intervention.

Alleles↗
PubMed2003

The twofold difference in adult size between the red junglefowl and White Leghorn chickens is largely explained by a limited number of QTLs.

A large intercross between the domestic White Leghorn chicken and the wild ancestor, the red junglefowl, has been used in a Quantitative Trait Loci (QTL) study of growth and egg production. The linkage map based on 105 marker loci was in good agreement with the chicken consensus map. The growth of the 851 F2 individuals was lower than both parental lines prior to 46 days of age and intermediate to the two parental lines thereafter. The QTL analysis of growth traits revealed 13 loci that showed genome-wide significance. The four major growth QTLs explained 50 and 80% of the difference in adult body weight between the founder populations for females and males, respectively. A major QTL for growth, located on chromosome 1 appears to have pleiotropic effects on feed consumption, egg production and behaviour. There was a strong positive correlation between adult body weight and average egg weight. However, three QTLs affecting average egg weight but not body weight were identified. An interesting observation was that the estimated effects for the four major growth QTLs all indicated a codominant inheritance.

Alleles↗
PubMed2002

Sex specificity, life-span QTLs, and statistical power.

Most of the quantitative trait loci (QTLs) that have been found to influence life span in Drosophila and Mus organisms are reported to have genetic effects limited to one sex. Here I study the statistical properties of sex-limited QTLs by randomly sampling data from an exceptionally large Drosophila experiment, and then asking how sample size influences outcomes. The sampling study suggests that, for the particular data analyzed here, even moderately large experiments, of the order of 10(4) individuals, can have a high probability of detecting sex-limited effects when they are not actually present. If a particular QTL is present in both sexes, and if the probability of detecting it in each sex is moderately high, say 80%, then there is a 32% chance of erroneously concluding that there is sex specificity. A comparison of interval mapping and composite interval mapping methods of data analysis suggests that the latter can inflate the appearance of sex specificity and sexual antagonism, depending on the choice of number of background covariates in the analysis. Conclusive evidence for sex-limited QTLs will require demonstration that results are robust to methods of statistical analysis, and experimental replication.

Animals↗
PubMed2004

A genetic map of candidate genes and QTLs involved in tomato fruit size and composition.

In order to screen for putative candidate genes linked to tomato fruit weight and to sugar or acid content, genes and QTLs involved in fruit size and composition were mapped. Genes were selected among EST clones in the TIGR tomato EST database (http://www.tigr.org/tdb/tgi/lgi/) or corresponded to genes preferentially expressed in the early stages of fruit development. These clones were located on the tomato map using a population of introgression lines (ILs) having one segment of Lycopersicon pennellii (LA716) in a L. esculentum (M82) background. The 75 ILs allowed the genome to be segmented into 107 bins. Sixty-three genes involved in carbon metabolism revealed 79 loci. They represented enzymes involved in the Calvin cycle, glycolysis, the TCA cycle, sugar and starch metabolism, transport, and a few other functions. In addition, seven cell-cycle-specific genes mapped into nine loci. Fourteen genes, primarily expressed during the cell division stage, and 23 genes primarily expressed during the cell expansion stage, revealed 24 and 26 loci, respectively. The fruit weight, sugars, and organic acids content of each IL was measured and several QTLs controlling these traits were mapped. Comparison between map location of QTLs and candidate gene loci indicated a few candidate genes that may influence the variation of sugar or acid contents. Furthermore, the gene/QTL locations could be compared with the loci mapped in other tomato populations.

Chromosome Mapping↗
PubMed2005

Mapping of QTLs for androgenetic response based on a molecular genetic map of x Triticosecale Wittmack.

Quantitative trait loci (QTLs) for androgenetic response were mapped in a doubled haploid (DH) population derived from the F1 hybrid of 2 unrelated varieties of triticale, 'Torote' and 'Presto'. A molecular marker linkage map of this cross was previously constructed using 73 DH lines. This map contains 356 markers (18 random amplified 5 polymorphic DNA, 40 random amplified microsatellite polymorphics, 276 amplified fragment length polymorphisms, and 22 simple sequence repeats) and was used for QTL analysis. The genome was well covered, and of the markers analysed, 336 were located in 21 linkage groups (81.9%) identified using SSR markers. The map covered a total length of 2465.4 cM with an average of 1 marker for each 6.9 cM. The distribution of the markers was not homogeneous across the 3 genomes, with 50.7% detected in the R genome. Several QTLs were found for the following variables related to the androgenetic response: number of embryos/100 anthers; plants regenerated from 100 embryos; number of green plants/total number of plants; and number of green plants/1000 anthers. Two were detected on chromosome 6B and 4R, which together had a 30% total influence on the induction of embryos. Another was found on 6B and on the unidentified LG1; these influenced the production of total plants from haploid embryo cultures. One QTL on chromosome 3R determined the photosynthetic viability of the haploid plantlets regenerated from microspores. Other QTLs were found on chromosomes 1B, 1R, 4R, and 7R, which helped the control of the final androgenetic response (the number of plantlets obtained for every 1000 anthers cultured).

Chromosome Mapping↗
PubMed2006

Multiple QTLs influence variation in paraoxonase 1 activity in Mexican Americans.

Paraoxonase 1 (PON1), a high-density-lipoprotein-associated enzyme known to protect against cellular damage from toxic agents, may also have antioxidant properties. Although the importance of the influence of the PON1 structural locus on chromosome 7q21-22 for variation in the concentration and activity of the enzyme is well-documented, the contribution of other loci is poorly understood. Based on the recent observations of at least one additional quantitative trait locus (QTL) for PON1 activity in pedigreed baboons, we conducted a whole-genome linkage screen for QTLs other than the PON1 structural locus that may influence PON1 activity in humans. We measured PON1 activity in frozen serum for 1,406 individuals in more than 40 extended pedigrees from the San Antonio Family Heart Study (SAFHS). We used a maximum-likelihood-based variance decomposition approach implemented in SOLAR to test for QTLs that may influence PON1 activity. In addition to a QTL for which we detected the strongest, significant evidence (LOD = 31.41) at or near the PON1 structural locus on chromosome 7q21-22, we also localized at least one additional significant QTL on chromosome 12 (LOD = 3.56). Furthermore, we detected suggestive evidence for two more PON-related QTLs on chromosomes 17 and 19. We have provided evidence that other genes, in addition to the well-known ones on chromosome 7, play a role in influencing normal variation in PON1 activity.

Adult↗
PubMed2005

Genome-wide scan identified QTLs underlying femoral neck cross-sectional geometry that are novel studied risk factors of osteoporosis.

UNLABELLED: A genome-wide screen was conducted using a large white sample to identify QTLs for FNCS geometry. We found significant linkage of FNCS parameters to 20q12 and Xq25, plus significant epistatic interactions and sex-specific QTLs influencing FNCS geometry variation. INTRODUCTION: Bone geometry, a highly heritable trait, is a critical component of bone strength that significantly determines osteoporotic fracture risk. Specifically, femoral neck cross-sectional (FNCS) geometry is significantly associated with hip fracture risk as well as genetic factors. However, genetic research in this respect is still in its infancy. MATERIALS AND METHODS: To identify the underlying genomic regions influencing FNCS variables, we performed a remarkably large-scale whole genome linkage scan involving 3998 individuals from 434 pedigrees for four FNCS geometry parameters, namely buckling ratio (BR), cross-sectional area (CSA), cortical thickness (CT), and section modulus (Z). The major statistical approach adopted is the variance component method implemented in SOLAR. RESULTS: Significant linkage evidence (threshold LOD = 3.72 after correction for tests of multiple phenotypes) was found in the regions of 20q12 and Xq25 for CT (LOD = 4.28 and 3.90, respectively). We also identified eight suggestive linkage signals (threshold LOD = 2.31 after correction for multiple tests) for the respective geometry traits. The above findings were supported by principal component linkage analysis. Of them, 20q12 was of particular interest because it was linked to multiple FNCS geometry traits and significantly interacted with five other genomic loci to influence CSA variation. The effects of 20q12 on FNCS geometry were present in both male and female subgroups. Subgroup analysis also revealed the presence of sex-specific quantitative trait loci (QTLs) for FNCS traits in the regions such as 2p14, 3q26, 7q21 and 15q21. CONCLUSIONS: Our findings laid a foundation for further replication and fine-mapping studies as well as for positional and functional candidate gene studies, aiming at eventually finding the causal genetic variants and hidden mechanisms concerning FNCS geometry variation and the associated hip fractures.

Adult↗
PubMed2001

[Molecular tagging and mapping of QTLs for super quality fiber properties in upland cotton].

A G. anomalum introgression line, 7235, characterized as super quality fiber properties, was used to identify molecular markers linked to fiber property QTLs. By use of (7235 x TM-1)F2 in Nanjing and College Station, USA, and (7235 x TM-1)F3 in Nanjing and Hainan. Bulked segregation analysis was employed to produce 3 pairs of mixed DNA pools for fiber strength, micronaire and fiber length according to individual value of (7235 x TM-1)F2 and F2:3. A total of 221 pairs of SSR primers, 1,840 arbitrary 10-mer oligonucleotide primers and 77 ISSR primers were used to screen polymorphism between two parents, and 3 pairs of bulked DNA pools. Fifteen markers amplified by thirteen primers were identified to be linked with fiber quality QTLs through DNA polymorphism surveying between the parents, and then paired bulked DNAs, and screening the individual plant of (7235 x TM1)F2. Linkage test indicated 15 markers could be mapped to three linkage groups. In the first linkage group, eight markers (two SSR and six RAPD markers) associated with fiber strength were tightly linked with 2.2 cM interval genetic distance on average, and located on chromosome 10 in cotton. Two major QTLs for fiber quality characters were identified. One for fiber strength could explain 35% of the phenotypic variation in F2, and 53.8% in F2:3 at Hainan, which has the greatest single QTL effect of fiber strength and could be identified in all four environments, and tightly linked to 6 RAPD markers and 2 SSR markers with genetic distance no more than 16 cM in chromosome 10, in which FSRl933 is the nearest with the distance no more than 0.6 cM. One QTL linked to FMR1(603) for Micronaire could explain 7.8% of the phenotypic variation in F2, and 25.4% in F2:3 at Hainan, and expressed in all four environments. One QTL linked to FLR1(1550) for fiber length could explain 9.5% of the phenotypic variation in F2:3 at Hainan, very little in other environments. So they can be used in marker-assisted selection in increasing fiber quality of commercial cultivars.

Chromosome Mapping↗
PubMed2002

[Mapping QTLs for horizontal resistance to sheath blight in an elite rice restorer line, Minghui 63].

This study was conducted with a recombinant inbred line (RILs) population consisting of 240 recombination lines, derived from an elite combination, Zhenshan 97B x Minghui 63. The RILs and their parents were grown in a randomized complete design with two replications in the years of 1999 and 2000. Sheath blight response ratings for the population and their parents were identified by an improved method of inoculation, which was carried out with short woody toothpicks incubated with a Rhizoctonia solani strain, RH-9, and inserted the third sheath in the late tillering/green ring stage of growth. A linkage map was constructed from the RILs. The QTL mapping of sheath blight resistance was carried out by the method of interval QTL mapping. Two QTLs for sheath blight resistance were detected in each year, and were located on chromosome 5 and chromosome 9, respectively. The QTL for sheath blight resistance on chromosome 5 was flanked by markers C624 and C246 on the basis of 1999 data, and by markers C246 and RM26 using 2000 data. The 1-LOD-confidence intervals of QTLs for sheath blight resistance on chromosome 5 detected in two years greatly overlapped with each other, and the peak of the 1-LOD-confidence intervals were approximately the same site. This suggested that the QTL for resistance on chromosome 5 detected in 1999 was probably the same as the QTL detected in 2000. The QTL for sheath blight resistance on chromosome 9 was located on the marker interval of C472-R2638 in term of 1999 data, and on the interval of RM257-RM242 based on 2000 data, and the two intervals were 9.7 cM away from each other. Based on the effect analysis of QTLs for resistance, the genotype of MH63 had negative additive effects or reduced sheath blight rating.

Chromosome Mapping↗
PubMed2002

Interval mapping of QTLs controlling some morphological traits in pea.

A linkage map of pea was constructed based on a 104 RIL population derived from the cross combination Wt10245 x Wt11238. The map, which consisted of 204 morphological, isozyme, AFLP, ISSR, STS, CAPS and RAPD markers, was used for interval mapping of the QTLs controlling the stem length and internode number of pea. In the characterization of a given QTL, we included an identification of its position with reference to the flanking markers, an estimation of the part of variance explained by it, and a determination of gene action. Six QTLs per trait were identified as demonstrating linkage to ten intervals on five linkage groups. As many as seven QTLs influencing the analysed traits were mapped on linkage group II, indicating the important role of this region of the pea genome in plant height control.

Chromosome Mapping↗
PubMed2004

[Mapping QTLs of soybean root weight with RIL population NJRIKY].

The recombinant inbred line (RIL) population, NJRIKY with 184 families derived from a cross Kefeng No.1 x Nannong1138-2 was used in mapping QTLs of root weight of soybean. Based on the linkage map constructed by Wang, with the software Cartographer V. 1.21 of the composite interval mapping procedure, three QTLs of root weight were mapped on N3-B1 and N6-C2 linkage group. The left telomere distance of rw1 was 66.31cM on N3-B1 linkage group, and those of rw2 and rw3 were 169.91cM and 179.71 cM, respectively, on N6-C2 linkage group. The former was located in A520T approximately ACCCAGO5 and the latter were overlapped with OPW13 and ACGCATO6, respectively. Their LOD values were 10.34,4.01 and 3.15, respectively. The QTLs of the root weight explained 26.3%,9.2% and 6.8% of the total variation, and their additive effects were -0.514,-0.303 and -0.260, respectively.

Chromosome Mapping↗
PubMed2005

Molecular marker assisted selection and pyramiding of two QTLs for fiber strength in upland cotton.

Based on two major QTLs that control high fiber strength which originated from an elite fiber germ-plasm line 7235 (Gossypium hiusutum L.), the efficiency of molecular marker-assisted selection (MAS) was investigated using two populations from pedigree selection and modified backcrossing pyramiding developed for the breeding purpose. Simian 3 (SM3), a widely planted variety in the Yangtze River Valley, and 7235 were used as parents to develop the two populations. In the two major QTLs for fiber strength from 7235, QTLfs-1 could explain more than 30% of the phenotypic variation (PV) in the (7235 x TM-1) F2 population. QTLfs-2 was at first identified in another super quality fiber line HS427-10 from (HS427-10 x TM-1) F2 population with 12.5% of PV explanation,which was further also identified in 7235 line but was non-allelic with QTLfs-1. The result of molecular marker-assisted selection for fiber strength showed that the genetic effect of the QTLfs-1 was stable under different environmental conditions, and its molecular marker-assisted selection showed significant selective efficiency among breeding populations with different genetic backgrounds. QTLfs-2 also showed high selective efficiency in advanced generation populations though its effect was a little lower than the former. When QTLfs-1 was selected simultaneously with 2 molecular markers with known genetic distance, the selection efficiency for the fiber strength was greatly increased. The pyramiding for two QTLs that control high fiber strength by MAS greatly improved the selection efficiency for cotton fiber strength. This report provides a successful example of MAS pyramiding for QTL for favorable traits in breeding programs.

Cotton Fiber↗
PubMed1994

Quantitative trait loci (QTLs) for pollen thermotolerance detected in maize.

Pollen thermotolerance is an important component of the adaptability of crops to high temperature stress. The tolerance level of the different genotypes in a population of 45 maize recombinant inbred lines was determined as the degree of injury caused by high temperature to pollen germinability (IPGG) and pollen tube growth (IPTG) in an in vitro assay. Both traits revealed quantitative variability and high heritability. The traits were genetically dissected by the analysis of molecular markers using 184 mapped restriction fragment length polymorphisms (RFLPs). Significant genetic correlation between the markers and the trait allowed us to identify a minimum number of five qualitative trait loci (QTLs) for IPGG and six QTLs for IPTG. Their chromosomal localization indicated that the two characters are controlled by different sets of genes. In addition, IPGG and IPTG were shown to be basically independent of the pollen germination ability and pollen tube growth rate under non-stress conditions. These results are discussed in relation to their possible utilization in a breeding strategy for the improvement of thermotolerance in maize.

Adaptation, Biological↗
PubMed2002

Comparative analysis of QTLs affecting domestication traits between two domesticated x wild pearl millet ( Pennisetum glaucum L., Poaceae) crosses.

Comparative mapping of Quantitative trait loci (QTLs) involved in domestication of adaptative syndrome traits of pearl millet was realized at the intra-specific level using two F(2) populations derived from domesticated ( Pennisetum glaucum ssp. glaucum) x wild ( Pennisetum glaucum ssp. monodii) crosses. The two domesticated parents analyzed differ in their geographical origins, agronomic characteristics and life cycles. In both populations, two regions of the genome were identified on linkage groups 6 and 7, that controlled most of the key morphological differences. The importance of these two linkage groups reveals their central role both in the developmental control of spikelet structure and in the domestication process of this crop. In contrast, QTLs involved in traits that are components of yield and measure differences in resource allocation (such as the shape of the spike, the number of spikes per plant and plant height) show a low level of correspondence among our two crosses. The results of the comparative mapping between cereals, although preliminary, reveal that genes involved in seed-shattering could correspond in maize, rice and sorghum. The evolutionary significance of our results, and especially the relationships between genome organization and cereal domestication, are discussed. The potential use of these results in pearl millet genetic-resources enhancement are presented.

Journal Article↗
PubMed2002

Genetic mapping of QTLs associated with greenbug resistance and tolerance in Sorghum bicolor.

Ninety three recombinant inbreds of Sorghum bicolor (L. Moench) were derived from a cross between two sorghum lines GBIK and Redlan. This population was used to identify quantitative trait loci (QTLs) for resistance and tolerance to greenbug ( Schizaphids graminum Rondani) Biotypes I and K. One hundred and thirteen loci (38 SSRs and 75 RAPDs) were mapped in 12 linkage groups covering 1,530 cM. In general, nine QTLs were detected affecting both resistance and tolerance to greenbug (GB) Biotypes I and K. The phenotypic variance explained by each QTL ranged from 5.6% to 38.4%. Four SSRs and one RAPD marker were associated with the expression of all resistance and tolerance traits. These markers appear to be linked to biotype non-specific resistance and tolerance genes. Four additional markers were associated with biotype-specific resistance or tolerance traits. The detection of more than one locus for each biotype supports the hypothesis that several regions, which represent different genes, control the expression of resistance and tolerance to greenbug in sorghum. The results can be used for marker-assisted selection and the breeding of greenbug-tolerant sorghum cultivars.

Journal Article↗
PubMed2002

Mapping QTLs for grain hardness and puroindoline content in wheat ( Triticum aestivum L.).

Genes for puroindoline-a (Pin-a), puroindoline-b (Pin-b) and grain-softness proteins (GSP) have been shown to be linked to the dominant Ha locus responsible for the soft texture of the grain. Though linkage has been demonstrated of the puroindoline genes to the Ha locus, there is no clear evidence that puroindoline content is the product of the gene Ha. A segregating population of 115 recombinant inbred lines (RILs) originating from a cross between the hexaploid Synthetic wheat ( Triticum durum x Aegilops tauschii, W 7984) and the cultivar 'Opata' (M 85) was studied in two different experimental years to detect Quantitative Trait Loci (QTLs) for three traits: grain hardness (Hard), puroindoline-a (Pin-a) and puroindoline-b (Pin-b) contents. The detection of QTLs was performed using marker linear regression. Negative correlation coefficients (-0.86 and -0.80) were identified between grain hardness and puroindoline content (a and b, respectively) on data obtained in 1996. Results obtained in 1999 confirmed the negative correlation between Hard and Pin-a (-0.73); however a positive correlation coefficient was found with Pin-b content (0.41). Total phenotypic variation explained by each QTL was calculated (R2). For each of the Hard, Pin-a and Pin-b traits one major QTL was detected on the short arm of chromosome 5D, located close to the mta9 allele (puroindoline-a). For the first year (1996) the QTL in this region explained around 63% of the phenotypic variability in grain hardness, 77% in Pin-a and 45% in Pin-b contents. These values were confirmed in trials carried out in 1999 with a R2 value of 0.71, 0.72 and 0.25 for Hard, Pin-a and Pin-b, respectively. In 1996 and 1999 a second major QTL was detected for grain hardness on the long arm of the same chromosome. Present results indicate that it cannot be definitely concluded that puroindoline content represents a linear explanation for variations in grain hardness.

Chromosome Mapping↗