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PubMed2006

Power of QTL mapping experiments in commercial Atlantic salmon populations, exploiting linkage and linkage disequilibrium and effect of limited recombination in males.

Whereas detection and positioning of genes that affect quantitative traits (quantitative trait loci (QTL)) using linkage mapping uses only information from recombinants in the genotyped generations, linkage disequilibrium (LD) mapping uses historical recombinants. Thus, whereas linkage mapping requires large family sizes to detect and accurately position QTL, LD mapping is more dependent on the number of families sampled from the population. In commercial Atlantic salmon breeding programmes, only a small number of individuals per family are routinely phenotyped for traits such as disease resistance and meat colour. In this paper, we assess the power and accuracy of combined linkage disequilibrium linkage analysis (LDLA) to detect QTL in the commercial population using simulation. When 15 half-sib sire families (each sire mated to 30 dams, each dam with 10 progeny) were sampled from the population for genotyping, we were able to detect a QTL explaining 10% of the phenotypic variance in 85% of replicates and position this QTL within 3 cM of the true position in 70% of replicates. When recombination was absent in males, a feature of the salmon genome, power to detect QTL increased; however, the accuracy of positioning the QTL was decreased. By increasing the number of sire families sampled from the population to be genotyped to 30, we were able to increase both the proportion of QTL detected and correctly positioned (even with no recombination in males). QTL with much smaller effect could also be detected. The results suggest that even with the existing recording structure in commercial salmon breeding programmes, there is considerable power to detect and accurately position QTL using LDLA.

Animals↗

PubMed1996

Comparative genetic and QTL mapping in sorghum and maize.

DNA markers and genetic maps will be important tools for direct investigations of several facets of crop improvement and will provide vital links between plant breeding and basic plant biology. The markers and maps will become more important for increased crop production because plant genetics will be required to extend or replace extant management practices such as chemical fertilizers, pesticides, and irrigation (Lee, 1995). Despite the importance of the sorghum crop, comprehensive genetic characterization has been limited. Therefore, the primary goal of this research program was to develop basic genetic tools to facilitate research in the genetics and breeding of sorghum. The first phase of this project consisted of constructing a genetic map based on restriction fragment length polymorphisms (RFLPs). The ISU sorghum map was created through linkage analysis of 78 F2 plants of an intraspecific cross between inbred CK60 and accession P1229828 (Pereira et al., 1994). The map consists of 201 loci distributed among 10 linkage groups covering 1,299 cM. Comparison of sorghum and maize RFLP maps on the basis of common sets of DNA probes revealed a high degree of conservation as reflected by homology, copy number, and collinearity. Examples of conserved and rearranged locus orders were observed. The same sorghum population was used to map genetic factors (mutants and QTL) for several traits including vegetative and reproductive morphology, maturity, insect, and disease resistance. This presentation will emphasize analysis of genetic factors affecting plant height, an important character for sorghum adaptation in temperate latitudes for grain production. Four QTL for plant height were identified in a sample of 152 F2 plants (Pereira and Lee, 1995) whereas 6 QTL were detected among their F3 progeny. These observations and assessments of other traits at 4 QTL common to F2 plants and their F3 progeny indicate some of these regions correspond to loci (dw) previously identified on the basis of alleles with highly qualitative effects. Four of the six sorghum plant height QTL seem to be orthologous to plant height QTL in maize. Other possible instances of orthologous QTL included regions for maturity and tillering. These observations suggest that the conservation of the maize and sorghum genomes encompasses sequence homology, collinearity, and function. The genetic information and technology developed on the basis of DNA markers could be used in several facets of breeding, genetics, and other basic biological investigations. In addition, DNA markers have been used to survey large collections of elite sorghum germ plasm to determine the degree of genetic relationships and genetic diversity (Ahnert et al., 1996). RFLP data seem to portray genetic relationships more accurately than the methods based exclusively on the coancestry coefficient. This information provides the basis for more accurate perceptions of genetic relationships and diversity.

Adaptation, Physiological↗

PubMed2004

Inheritance and QTL mapping of low temperature germinability in rice (Oryza sativa L.).

Quantitative trait loci (QTL) controlling low temperature germinability (LTG) in rice were identified using 81 recombinant inbreed lines (RILs) derived from a cross between a japonica variety Kinmaze and an indica variety DV85. The accurate condition of LTG evaluation was assumed at 15 degrees C for 10 d after removing the effect of dormancy and the second dormancy. By setting check, the scores of LTG in this study were evaluated. The germination rate at 15 degrees C for 10 d was scored to represent the LTG. The LTG of the RILs ranged from 0 to 99%. By single point analysis, simple interval mapping, and composite interval mapping, 5 putative QTL, qLTG-2, qLTG-6, qLTG-7, qLTG-LTG-11 and qLTG-12 were detected on chromosomes 2, 6, 7, 11 and 12 respectively. At the regions of qLTG-2, qLTG-6 and qLTG-11, DV85 alleles increased the LTG, while Kinmaze alleles increased it at the regions of qLTG-7 and qLTG-12. Among the five QTLs reported here, qLTG-2, qLTG-7 and qLTG-12 were newly detected, while the other two QTL-containing regions were close to those previously reported. Epistatic QTL were also detected in this paper.

Cold Temperature↗

PubMed2005

QTL mapping for teat number in an Iberian-by-Meishan pig intercross.

The aim of this study was to investigate chromosomal regions affecting the number of teats in pigs and possible epistatic interactions between the identified quantitative trait loci (QTL). An experimental F2 cross between Iberian and Chinese Meishan lines was used for this purpose. A genomic scan was conducted with 117 markers covering the 18 porcine autosomes. Linkage analyses were performed by interval mapping using an animal model to estimate QTL and additive polygenic effects. Complementary analyses with models fitting two QTL were also carried out. The results showed three genomewide significant QTL mapping on chromosomes 5, 10 and 12, whose joint action control up to 30% of the phenotypic variance of the trait. Meishan alleles had a positive additive effect on teat number, and a positive-additive x additive-epistatic interaction was detected between QTL on chromosomes 10 and 12.

Animals↗

PubMed2003

Mapping QTL for traits associated with resistance to ferrous iron toxicity in rice (Oryza sativa L.), using japonica chromosome segment substitution lines.

A mapping population of 66 japonica chromosome segment substitution lines (CSSLs) in indica genetic background, derived from a cross between a japonica variety Asominori and an indica variety IR24 by the single-seed descent, backcrossing and marker-assisted selection, was used to detect quantitative trait loci (QTLs) for leaf bronzing index (LBI), stem dry weight (SDW), plant height (PH), root length (RL) and root dry weight (RDW) under Fe2+ stress condition in rice. Two parents and 66 japonica CSSLs were phenotyped for the traits by growing them in Fe2+ toxicity nutrient solution. A total of fourteen QTLs were detected on chromosome 3, 6, 7, 9, 11 and 12, respectively, with LOD of QTLs ranging from 2.72 to 6.63. Three QTLs controlling LBI were located at the region of C515-XNpb279, R2638-C1263 and G1465-C950 on chromosome 3, 9 and 11, their contributions to whole variation were 16.45%, 11.16% and 28.02%, respectively. Comparing with the other mapping results, the QTL for LBI located at the region of C515-XNpb279 on chromosome 3 was identical with the QTL for chlorophyll content on a rice function map. The results indicated that ferrous iron toxicity of rice is characterized by bronzing spots on the lower leaves, which spread over the whole leaves, causing the lower leaves to turn dark gray and to product chlorophyll catabolites or derivatives which reduce cytotoxicity of some heavy metals, such as ferrous iron. Furthermore, the QTL for LBI, SDW and RDW located at the region of G1465-C950 on chromosome 11 is a major QTL. Whether the QTL for SDW, PH, RL and RDW at the region of XNpb386-XNpb342 on chromosome 6 is associated with resistance to ferrous iron toxicity need further studies. Our goal is to identify breeding materials for resistance to Fe2+ toxicity through marker-assisted selection based on the detected markers.

Chromosome Mapping↗

PubMed2006

Quantitative trait loci (QTL) mapping of resistance to strongyles and coccidia in the free-living Soay sheep (Ovis aries).

A genome-wide scan was performed to detect quantitative trait loci (QTL) for resistance to gastrointestinal parasites and ectoparasitic keds segregating in the free-living Soay sheep population on St. Kilda (UK). The mapping panel consisted of a single pedigree of 882 individuals of which 588 were genotyped. The Soay linkage map used for the scans comprised 251 markers covering the whole genome at average spacing of 15cM. The traits here investigated were the strongyle faecal egg count (FEC), the coccidia faecal oocyst count (FOC) and a count of keds (Melophagus ovinus). QTL mapping was performed by means of variance component analysis so that the genetic parameters of the study traits were also estimated and compared with previous studies in Soay and domestic sheep. Strongyle FEC and coccidia FOC showed moderate heritability (h(2)=0.26 and 0.22, respectively) in lambs but low heritability in adults (h(2)<0.10). Ked count appeared to have very low h(2) in both lambs and adults. Genome scans were performed for the traits with moderate heritability and two genomic regions reached the level of suggestive linkage for coccidia FOC in lambs (logarithm of the odds=2.68 and 2.21 on chromosomes 3 and X, respectively). We believe this is the first study to report a QTL search for parasite resistance in a free-living animal population and therefore may represent a useful reference for similar studies aimed at understanding the genetics of host-parasite co-evolution in the wild.

Animals↗

PubMed2006

Gene by environment QTL mapping through multiple trait analyses in blood pressure salt-sensitivity: identification of a novel QTL in rat chromosome 5.

BACKGROUND: The genetic mechanisms underlying interindividual blood pressure variation reflect the complex interplay of both genetic and environmental variables. The current standard statistical methods for detecting genes involved in the regulation mechanisms of complex traits are based on univariate analysis. Few studies have focused on the search for and understanding of quantitative trait loci responsible for gene x environmental interactions or multiple trait analysis. Composite interval mapping has been extended to multiple traits and may be an interesting approach to such a problem. METHODS: We used multiple-trait analysis for quantitative trait locus mapping of loci having different effects on systolic blood pressure with NaCl exposure. Animals studied were 188 rats, the progenies of an F2 rat intercross between the hypertensive and normotensive strain, genotyped in 179 polymorphic markers across the rat genome. To accommodate the correlational structure from measurements taken in the same animals, we applied univariate and multivariate strategies for analyzing the data. RESULTS: We detected a new quantitative train locus on a region close to marker R589 in chromosome 5 of the rat genome, not previously identified through serial analysis of individual traits. In addition, we were able to justify analytically the parametric restrictions in terms of regression coefficients responsible for the gain in precision with the adopted analytical approach. CONCLUSION: Future work should focus on fine mapping and the identification of the causative variant responsible for this quantitative trait locus signal. The multivariable strategy might be valuable in the study of genetic determinants of interindividual variation of antihypertensive drug effectiveness.

Animals↗

PubMed2004

QTL mapping of Sclerotinia midstalk-rot resistance in sunflower.

In many sunflower-growing regions of the world, Sclerotinia sclerotiorum (Lib.) de Bary is the major disease of sunflower (Helianthus annuus L.). In this study, we mapped and characterized quantitative trait loci (QTL) involved in resistance to S. sclerotiorum midstalk rot and two morphological traits. A total of 351 F3 families developed from a cross between a resistant inbred line from the germplasm pool NDBLOS and the susceptible line CM625 were assayed for their parental F2 genotype at 117 codominant simple sequence repeat markers. Disease resistance of the F3 families was screened under artificial infection in field experiments across two sowing times in 1999. For the three resistance traits (leaf lesion, stem lesion, and speed of fungal growth) and the two morphological traits, genotypic variances were highly significant. Heritabilities were moderate to high (h2=0.55-0.89). Genotypic correlations between resistance traits were highly significant (P<0.01) but moderate. QTL were detected for all three resistance traits, but estimated effects at most QTL were small. Simultaneously, they explained between 24.4% and 33.7% of the genotypic variance for resistance against S. sclerotiorum. Five of the 15 genomic regions carrying a QTL for either of the three resistance traits also carried a QTL for one of the two morphological traits. The prospects of marker-assisted selection (MAS) for resistance to S. sclerotiorum are limited due to the complex genetic architecture of the trait. MAS can be superior to classical phenotypic selection only with low marker costs and fast selection cycles.

Analysis of Variance↗

PubMed2003

R/qtl: QTL mapping in experimental crosses.

SUMMARY: R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTLs) in experimental populations derived from inbred lines. It is implemented as an add-on package for the freely-available statistical software, R, and includes functions for estimating genetic maps, identifying genotyping errors, and performing single-QTL and two-dimensional, two-QTL genome scans by multiple methods, with the possible inclusion of covariates. AVAILABILITY: The package is freely available at http://www.biostat.jhsph.edu/~kbroman/qtl.

Algorithms↗

PubMed1998

On the use of linear regression and maximum likelihood for QTL mapping in half-sib designs.

Methods of identification of quantitative trait loci (QTL) using a half-sib design are generally based on least-squares or maximum likelihood approaches. These methods differ in the genetical model considered and in the information used. Despite these differences, the power of the two methods in a daughter design in very similar. Using an analogy with a one-way analysis of variance, we propose an equation connecting the two test-statistics (F ratio for regression and likelihood ratio test in the case of the maximum likelihood). The robustness of this relationship is tested by simulation for different single QTL models. In general, the correspondence between the two statistics is good under both the null hypothesis and the alternative hypothesis of a single QTL segregating. Practical implications are discussed with particular emphasis on the theoretical distribution of the likelihood ratio test.

Chromosome Mapping↗

PubMed2005

QTL mapping of resistance to gray leaf spot in ryegrass.

Gray leaf spot (GLS) is a serious fungal disease caused by Magnaporthe grisea, recently reported on perennial ryegrass (Lolium perenne L.), an important turf grass and forage species. This fungus also causes rice blast and many other grass diseases. Rice blast is usually controlled by host resistance, but durability of resistance is a problem. Little GLS resistance has been reported in perennial ryegrass. However, greenhouse inoculations in our lab using one ryegrass isolate and one rice-infecting lab strain suggest presence of partial resistance. A high density linkage map of a three generation Italian x perennial ryegrass mapping population was used to identify quantitative trait loci (QTL) for GLS resistance. Potential QTL of varying effect were detected on four linkage groups, and resistance to the ryegrass isolate and the lab strain appeared to be controlled by different QTL. Of three potential QTL detected using the ryegrass isolate, the one with strongest effect for resistance was located on linkage group 3 of the MFB parent, explaining between 20% and 37% of the phenotypic variance depending on experiment. Another QTL was detected on linkage group 6 of the MFA parent, explaining between 5% and 10% of the phenotypic variance. The two QTL with strongest effect for resistance to the lab strain were located on linkage groups MFA 2 and MFB 4, each explaining about 10% of the phenotypic variance. Further, the QTL on linkage groups 3 and 4 appear syntenic to blast resistance loci in rice. This work will likely benefit users and growers of perennial ryegrass, by setting the stage for improvement of GLS resistance in perennial ryegrass through marker-assisted selection.

Chromosome Mapping↗

PubMed2003

QTL mapping reveals a two-step model for the evolutionary reduction of inner microsporangia within the asteracean genus Microseris.

The reduction of inner (adaxial) pollen sacs (microsporangia, MS) as a diagnostic character for the three asteracean species, Microseris bigelovii, Microseris elegans and Microseris pygmaea, was analysed in an interspecific cross between Microseris douglasii and Microseris bigelovii with 4 MS and 2 MS, respectively, using the average number of MS per plant as a quantitative character. A previous QTL (Quantitative Trait Locus) analysis had revealed one major QTL (3B) and three modifier QTLs (3A, 4A, 7A) with epistatic effects only on the homozygous recessive 2 MS genotype of QTL 3B. Here we performed a bulked segregant analysis on four 2 MS and four 4 MS DNA-bulks with 407 EcoRI/ MseI AFLP-primer combinations each. In this way additional AFLP markers were mapped close to QTL 3B and QTL 3A. Three of them were converted to SCAR (Sequence Characterized Amplified region) markers. All markers were tested in natural populations of the disporangiate (2 MS) species M. bigelovii, M. elegans and M. pygmaea, and in different populations of tetrasporangiate (4 MS) M. douglasii. The marker distribution suggests that locus 3B mutated in a progenitor of the disporangiate species. QTL 3A has evolved in the 2 MS background of the major gene in the disporangiate species. Since M. pygmaea and M. bigelovii are the sister group to M. elegans, the 4 MS genotype for (markers of) QTL 3A in M. pygmaea populations is most likely due to a back mutation to the 4 MS state and could explain the slight instability of the 2 MS phenotype in this species.

Base Sequence↗

PubMed2006

QTL mapping for plant architecture traits in upland cotton using RILs and SSR markers.

Xiangzamian 2 (XZM2) is the most widely cultivated cotton hybrid in China. By crossing two parents Zhongmiansuo12 and 8891 and upon subsequent selfings, we got F8 and F9 populations having 180 recombinant inbred lines. Ten plant architecture traits were investigated in two years with this population. A genetic map was constructed mainly with SSR markers. Quantitative trait loci (QTL) conditioning plant architecture traits were determined at the single-locus and double-locus levels. The results showed that epistastic effects as well as additive effects of QTL played an important role as the genetic basis of cotton plant architecture. The QTL detected in our research might provide new information on improving plant architecture traits. The polymorphism of molecular markers between ZMS12 and 8891 were quite limited, while significant differences between their phenotypes were found and the hybrid XZM2 expressed high heterosis in yield. All these could be partly explained by the effect of epistatic QTL.

Breeding↗

PubMed2005

[QTL mapping of five agronomic traits in maize].

Agronomic traits have significant influence on stability and adaptability in maize production. In this investigation, using a population with 266 F2:3 families from Yuyu22 (Zong3 x 87-1), two-location field tests were conducted in Wuhan and Xiangfan in 2001, with a randomized complete block design, to characterize five agronomic traits: ear height, tassel branch number, stalk diameter, days to pollen, and days to silk. Correlation analysis of field performance indicated that ear height, tassel branch number and stalk diameter were significantly positive correlative with single-plant yield, days to pollen and days to silk were highly positive correlative with each other, and tassel branch number was significantly positive correlative with stalk diameter too. Utilizing data of field tests and molecular markers, Composite Interval Mapping (CIM) method was used to localize the quantitative trait loci of these traits and 500 times permutation test was conducted to have proper LOD threshold value. As the results, total seven QTL of ear height, nine QTL of tassel branch number, eight QTL of stalk diameter, nine QTL of days to pollen, and seven QTL of days to silk were mapped on 10 chromosomes of maize; all of these QTL distributed unevenly on chromosomes and trended to cluster together. According to analysis of this investigation, the phenotype correlations of quantitative traits may result from the correlations of QTL controlling those traits. Those will be helpful to further understand genetic basis of agronomic traits in maize.

Chromosome Mapping↗

PubMed2003

Haplotypic QTL mapping in an outbred pedigree.

An offspring genome can be viewed as a mosaic of chromosomal segments or haplotypes contributed by multiple founders in any quantitative trait locus (QTL) detection study but tracing these is especially complex to achieve for outbred pedigrees. QTL haplotypes can be traced from offspring back to individual founders in outbred pedigrees by combining founder-origin probabilities with fully informative flanking markers. This haplotypic method was illustrated for QTL detection using a three-generation pedigree for a woody perennial plant, Pinus taeda L. Growth rate was estimated using height measurements from ages 2 to 10 years. Using simulated and actual datasets, power of the experimental design was shown to be efficient for detecting QTLs of large effect. Using interval mapping and fully informative markers, a large QTL accounting for 11.3% of the phenotypic variance in the growth rate was detected. This same QTL was expressed at all ages for height, accounting for 7.9-12.2% of the phenotypic variance. A mixed-model inheritance was more appropriate for describing genetic architecture of growth curves in P. taeda than a strictly polygenic model. The positive QTL haplotype was traced from the offspring to its contributing founder, GP3, then the haplotypic phase for GP3 was determined by assaying haploid megagametophytes. The positive QTL haplotype was a recombinant haplotype contributed by GP3. This study illustrates the combined power of fully informative flanking markers and founder origin probabilities for (1) estimating QTL haplotype magnitude, (2) tracing founder origin and (3) determining haplotypic transmission frequency.

Haplotypes↗

PubMed2004

QTL mapping of chromosomal regions conferring reproductive frost tolerance in barley ( Hordeum vulgare L.).

Spring radiation frost is a major abiotic stress in southern Australia, reducing yield potential and grain quality of barley by damaging sensitive reproductive organs in the latter stages of development. Field-based screening methods were developed, and genetic variation for reproductive frost tolerance was identified. Mapping populations that were segregating for reproductive frost tolerance were screened and significant QTL identified. QTL on chromosome 2HL were identified for frost-induced floret sterility in two different populations at the same genomic location. This QTL was not associated with previously reported developmental or stress-response loci. QTL on chromosome 5HL were identified for frost-induced floret sterility and frost-induced grain damage in all three of the populations studied. The locations of QTL were coincident with previously reported vegetative frost tolerance loci close to the vrn- H1 locus. This locus on chromosome 5HL has now been associated with response to cold stress at both vegetative and reproductive developmental stages in barley. This study will allow reproductive frost tolerance to be seriously pursued as a breeding objective by facilitating a change from difficult phenotypic selection to high-throughput genotypic selection.

Acclimatization↗

PubMed2005

[One major QTL mapping and physical map construction for rolled leaf in rice].

A clonally propagated F2 population (F2CP), derived from the rice cross of Qimiaoxiang/91SP068, was used to map rolled leaf QTLs. As the parent Qimiaoxiang is an unrolling leaf variety, while 91SP068 is a medium rolling variety with about 34% rolling index. One major QTL, rl8, which came from 91SP068, was mapped between two flanking SSR markers, RM6954 and RM6841, on chromosome 5, with genetic distance 3.8 cM, and was 1.0 cM away from RM6954. Its additive effect estimated by composite interval mapping (CIM) was 9.61 in 2002 and 6.23 in 2003, and the dominance effect was also different between two years, -1.19 in 2002 and -4.44 in 2003, respectively. It explained about 20% - 33% of the total phenotypic variation between two years. Furthermore, an integrated physical and genetic map encompassing rl8 region was constructed, and the physical distance of the interval was 542 kb, and the ratio of physical to genetic distance was 144 kb/cM. Based on this research, fine mapping of rolled leaf QTLs will not only facilitate the map-based cloning of the gene itself, but also improve the efficiency of marker-assisted selection in plant breeding.

Chromosomes, Plant↗

PubMed2004

QTL mapping and molecular marker analysis for the resistance of rice to ozone.

The resistance of rice to ozone (O3) is a quantitative trait controlled by nuclear genes. The identification of quantitative trait loci (QTL) and analysis of molecular markers of O3 resistance is important for increasing the resistance of rice to O3 stress. QTL associated with the O3 resistance of rice were mapped on chromosomes 1, 7 and 11 using 164 recombinant inbred (RI) lines from a cross between 'Milyang 23' and 'Gihobyeo'. The quantitative trait loci were tightly linked to the markers RG109, C507 and RG1094 and were detected in each of three replications. The association between these markers and O3 resistance in 26 rice cultivars and doubled haploid (DH) populations was analysed. The markers permit the screening of rice germplasm for O3 resistance and the introduction of resistance into elite lines in breeding programs.

Biomarkers↗