A comparison of interval mapping procedures including the QTL-cluster mapping

Using the deterministic sampling, patterns of the log-likelihood surfaces expected in some interval mapping procedures for estimating the position of, and the effect for, QTL(s) were investigated for the situations where a single QTL or closely linked QTLs are contained in a chromosome segment bracketed with two markers. The mapping procedures compared were the conventional, likelihood-based interval mapping (IM), the regression interval mapping (RIM), and the QTL-cluster mapping (CM) in which the conditional probabilities of transmission of the whole segment marked by the flanking markers were taken into consideration. The half-sib design was used here, and several cases of the true genetic model were considered, differing in the number of QTLs contained in the marker interval, the linkage phase for the sire, and the magnitude of the QTL(s) effect. For the true genetic models where a single QTL or closely linked QTLs being in coupling phase are contained in the interval, with (R)IM, clear global maxima of the log-likelihood were observed within the range of the marker interval. It was shown that the estimates of the QTL(s) effect at the marked segment level are expected to be unbiased. On the other hand, in a setting where the linkage phase for the linked QTLs located in the interval was different from coupling and repulsion, there was found a ridge along the interval for the log-likelihood surface with (R)IM, indicating the dependency between the estimates of the position of, and the effect for, the putative QTL. For this case, it was found that the position of the putative QTL could be estimated as that of one of the flanking markers, and the estimate of the QTL effect be biased. In contrast, it was revealed that CM is expected to provide the unbiased estimate of the QTL(s)-effect at the segment level for any case of the true genetic models considered here. If the aim is for marker-assisted selection rather than mapping closely linked QTLs individually, then the CM approach is considered to be useful.     

Volume measures for linkage disequilibrium

Background

A major QTL for fatness and growth, denoted FAT1, has previously been detected on pig chromosome 4q (SSC4q) using a Large White – wild boar intercross. Progeny that carried the wild boar allele at this locus had higher fat deposition, shorter length of carcass, and reduced growth. The position and the estimated effects of the FAT1 QTL for growth and fatness have been confirmed in a previous study. In order to narrow down the QTL interval we have traced the inheritance of the wild boar allele associated with high fat deposition through six additional backcross generations.

Results

Progeny-testing was used to determine the QTL genotype for 10 backcross sires being heterozygous for different parts of the broad FAT1 region. The statistical analysis revealed that five of the sires were segregating at the QTL, two were negative while the data for three sires were inconclusive. We could confirm the QTL effects on fatness/meat content traits but not for the growth traits implying that growth and fatness are controlled by distinct QTLs on chromosome 4. Two of the segregating sires showed highly significant QTL effects that were as large as previously observed in the F₂ generation. The estimates for the remaining three sires, which were all heterozygous for smaller fragments of the actual region, were markedly smaller. With the sample sizes used in the present study we cannot with great confidence determine whether these smaller effects in some sires are due to chance deviations, epistatic interactions or whether FAT1 is composed of two or more QTLs, each one with a smaller phenotypic effect. Under the assumption of a single locus, the critical region for FAT1 has been reduced to a 3.3 cM interval between the RXRG and SDHC loci.

Conclusion

We have further characterized the FAT1 QTL on pig chromosome 4 and refined its map position considerably, from a QTL interval of 70 cM to a maximum region of 20 cM and a probable region as small as 3.3 cM. The flanking markers for the small region are RXRG and SDHC and the orthologous region of FAT1 in the human genome is located on HSA1q23.3 and harbors approximately 20 genes. Our strategy to further refine the map position of this major QTL will be i) to type new markers in our pigs that are recombinant in the QTL interval and ii) to perform Identity-By-Descent (IBD) mapping across breeds that have been strongly selected for lean growth.     

Mapping quantitative trait loci for principal components of bone measurements and osteochondrosis scores in a wild boar x large white intercross

Data on osteochondrosis and femur dimensions from 195 F2 pigs from a wild boar x Large White intercross were analysed with the aim of detecting quantitative trait loci (QTLs) for normal and disturbed bone formation. The information from numerous recorded traits was summarized by principal component analysis and analysed by least-squares interval mapping. An increase in the proportion of wild boar alleles across the genome increased length versus width of femur and reduced the prevalence of osteochondrosis. The presence of QTLs with an impact on femur dimensions was indicated on chromosomes 2, 4, 16 and 17 and on osteochondrosis on chromosomes 5, 13 and 15. A substantial effect of the chromosome 5 QTL calls for further studies within commercial populations to evaluate whether marker-assisted selection could be used to reduce the prevalence of osteochondrosis.     

Limitations of a two-step moment method for mapping linked multiple QTL

As an alternative to multiple-interval mapping a two-step moment method was recently proposed to map linked multiple quantitative trait loci (QTLs). The advantage of this moment method was supposed to be its simplicity and computational efficiency, especially in detecting closely linked QTLs within a marker bracket, but also in mapping QTLs in different marker intervals. Using simulations it is shown that the two-step moment method may give poor results compared with multiple-interval mapping, irrespective of whether the QTLs are in the same or in different marker intervals, especially if linked QTLs are in repulsion. The criteria of comparison are number of identified QTLs, likelihood ratio test statistics, means and empirical standard errors of the QTL position and QTL effects estimates, and the accuracy of the residual variance estimates. Further, the joint conditional probabilities of QTL genotypes for two putative QTLs within a marker interval were derived and compared with the unmodified approach ignoring the non-independence of the conditional probabilities.     

Detection of quantitative trait loci for body weight at 10 weeks from Philippine wild mice

A genome-wide scan for quantitative trait loci (QTLs) controlling body weight at 10 weeks after birth was carried out in a population of 387 intersubspecific backcross mice derived from a cross between C57BL/6J inbred mice (Mus musculus domesticus) and wild mice (M. m. castaneus) captured in the Philippines, in order to discover novel QTLs from the wild mice that have about 60% lower body weight than C57BL/6J. By interval mapping, we detected four QTLs: a highly significant QTL on Chromosome (Chr) 2, which was common in both sexes; two significant QTLs on Chr 13, one male-specific and the other female-specific; and a suggestive male-specific QTL on X Chr. By composite interval mapping, we confirmed the presence of the three QTLs on Chrs 2 and 13, but not of the male-specific X-linked QTL. The composite interval mapping analysis newly identified three QTLs: a significant male-specific QTL on Chr 11 and two highly significant female-specific QTLs on Chrs 9 and X. Individual QTLs explained 3.8–11.6% of the phenotypic variance, and all the QTL alleles derived from the wild mice decreased body weight. A two-way analysis of variance revealed a significant epistatic interaction between the Chr 2 QTL and the background marker locus D12Mit4 on Chr 12 only in males. The interaction effect unexpectedly increased body weight. The chromosomal region containing the Chr 2 QTL did not coincide with those of growth or fatness QTLs mapped in previous studies. These results suggest that a population of wild mice may play an important role as new sources of valuable QTLs. Received: 14 January 2000 / Accepted: 14 April 2000     

不同生长环境下水稻最上节间长度QTL定位研究

利用由98 个家系组成的 Nipponbare/Kasalath//Nipponbare 回交重组自交系(backcross inbred lines, BIL)作图群体(BC1F12和BC1F13)和复合区间作图方法(CIM), 在3种不同的生长环境下对水稻最上节间长度进行了 QTL 分析。结果表明, 3种不同的生长环境共检测到 13 个 QTL , 分布于第 1, 2, 3, 5, 6, 8, 10, 11 染色体上, 解释性状变异的 3.97%～15.21%。其中qUIL-6在3种不同生长环境中均检测到, qUIL-1a, qUIL-3a, qUIL-3b和 qUIL-10a 等4个位点在两种不同生长环境中均被检测到, 说明这些 QTL 位点受环境影响较小, 表达较为稳定。     

普通野生稻中增产相关QTL的发掘

普通野生稻(Oryza Rufipogon)是重要的遗传资源,发掘其优良等位基因将对水稻遗传改良产生重要影响。文章从以珍汕97为轮回亲本,普通野生稻为供体的BC2F1群体中选择一个与珍汕97表型明显不同的单株BC2F1-15,经过连续自交获得回交重组自交系BC2F5群体。均匀分布于12条染色体的126个多态性SSR(Simplesequence repeats)标记基因型分析,发现BC2F1-15单株在30%的标记位点为杂合基因型;利用该群体共检测到4个抽穗期、3个株高、4个每穗颖花数、2个千粒重和1个单株产量QTL。在第7染色体RM481-RM2区间,检测到抽穗期、每穗颖花数和产量QTL,野生稻等位基因表现增效作用;其他3个每穗颖花数QTL位点,野生稻等位基因也均具有增效作用。结果表明野生稻携带有增产相关的等位基因,这些有利等位基因无疑是水稻遗传改良可资利用的新资源。     

Quantitative trait loci affecting knockdown resistance to high temperature in Drosophila melanogaster

Knockdown resistance to high temperature is an ecologically important trait in small insects. A composite interval mapping was performed on the two major autosomes of Drosophila melanogaster to search for quantitative trait loci (QTL) affecting knockdown resistance to high temperature (KRHT). Two dramatically divergent lines from geographically different thermal environments were artificially selected on KRHT. These lines were crossed to produce two backcross (BC) populations. Each BC was analysed for 200 males with 18 marker loci on chromosomes 2 and 3. Three X-linked markers were used to test for X-linked QTL in an exploratory way. The largest estimate of autosome additive effects was found in the pericentromeric region of chromosome 2, accounting for 19.26% (BC to the low line) and 29.15% (BC to the high line) of the phenotypic variance in BC populations, but it could represent multiple closely linked QTL. Complete dominance was apparent for three QTL on chromosome 3, where heat-shock genes are concentrated. Exploratory analysis of chromosome X indicated a substantial contribution of this chromosome to KRHT. The results show that a large-effect QTL with dominant gene action maps on the right arm of chromosome 3. Further, the results confirm that QTL for heat resistance are not limited to chromosome 3.     

Detection of QTLs for flowering date in three mapping populations of the model legume species Medicago truncatula

Adaptation to the environment and reproduction are dependent on the date of flowering in the season. The objectives of this paper were to evaluate the effect of photoperiod on flowering date of the model species for legume crops, Medicago truncatula and to describe genetic architecture of this trait in multiple mapping populations. The effect of photoperiod (12 and 18 h) was analysed on eight lines. Quantitative variation in three recombinant inbred lines (RILs) populations involving four parental lines was evaluated, and QTL detection was carried out. Flowering occurred earlier in long than in short photoperiods. Modelling the rate of progression to flowering with temperature and photoperiod gave high R(2), with line-specific parameters that indicated differential responses of the lines to both photoperiod and temperature. QTL detection showed a QTL on chromosome 7 that was common to all populations and seasons. Taking advantage of the multiple mapping populations, it was condensed into a single QTL with a support interval of only 0.9 cM. In a bioanalysis, six candidate genes were identified in this interval. This design also indicated other genomic regions that were involved in flowering date variation more specifically in one population or one season. The analysis on three different mapping populations detected more QTLs than on a single population, revealed more alleles and gave a more precise position of the QTLs that were common to several populations and/or seasons. Identification of candidate genes was a result of integration of QTL analysis and genomics in M. truncatula.     

Marker-assisted selection to introgress rice QTLs controlling root traits into an Indian upland rice variety

A marker-assisted back-crossing (MABC) breeding programme was conducted to improve the root morphological traits, and thereby drought tolerance, of the Indian upland rice variety, Kalinga III. This variety, the recurrent parent in the MABC, had not previously been used for quantitative trait locus (QTL) mapping. The donor parent was Azucena, an upland japonica variety from Philippines. Five segments on different chromosomes were targeted for introgression; four segments carried QTLs for improved root morphological traits (root length and thickness) and the fifth carried a recessive QTL for aroma. Some selection was made at non-target regions for recurrent parent alleles. We describe the selection made in three backcross (BC) generations and two further crosses between BC₃ lines to pyramid (stack) all five target segments. Pyramids with four root QTLs were obtained in eight generations, completed in 6 years using 3,000 marker assays in a total of 323 lines. Twenty-two near-isogenic lines (NILs) were evaluated for root traits in five field experiments in Bangalore, India. The target segment on chromosome 9 (RM242-RM201) significantly increased root length under both irrigated and drought stress treatments, confirming that this root length QTL from Azucena functions in a novel genetic background. No significant effects on root length were found at the other four targets. Azucena alleles at the locus RM248 (below the target root QTL on chromosome 7) delayed flowering. Selection for the recurrent parent allele at this locus produced early-flowering NILs that were suited for upland environments in eastern India.     

QTL Mapping of Downy Mildew Resistance in an Introgression Line Derived from Interspecific Hybridization Between Cucumber and Cucumis hystrix

Downy mildew (DM), caused by Pseudoperonospora cubensis (Berk. & M.A. Curtis) Rostovzev, is a worldwide major disease of cucumbers (Cucumis sativus L.). By screening 10 introgression lines (ILs) derived from interspecific hybridization between cucumber and the wild Cucumis, C. hystrix, through a whole plant assay, one introgression line (IL52) was identified with high DM‐resistance. IL52 was further used as a resistant parent to make an F₂ population with ‘changchunmici’ (susceptible parent). The F₂ population (300 plants) was investigated for DM‐yellowing, DM‐necrosis and DM‐resistance in the adult stage. A genetic map spanning 642.5 cM with 104 markers was constructed and used for QTL analysis from the population. Three QTL regions were identified on chromosome 5 and chromosome 6. By interval mapping analysis, two QTLs for DM‐resistance were determined on chromosome 5 (DM_5.1 and DM_5.2), which explained 17.9% and 14.2% of the variation, respectively. QTLs for DM‐yellowing were in the same regions as DM‐resistance. For DM‐necrosis, by interval mapping analysis, one QTL was determined on chromosome 5 (Necr_5.1) that explained 18.3% of the variation and one on chromosome 6 (Necr_6.1) that explained 13.9% of the variation. Our results indicated that the identification of molecular markers linked to the QTLs could be further applied for marker‐assisted selection (MAS) of downy mildew resistance in cucumber.     

江西东乡野生稻苗期抗旱基因定位

普通野生稻是栽培稻的祖先种,其遗传多样性远远大于栽培稻,蕴涵着栽培品种中难以找到的重要性状.以江西东乡普通野生稻为供体、以桂朝2号为遗传背景的野生稻基因渗入系（BC4F5、BC4F6）为材料,利用30%的PEG人工模拟干旱环境,对渗入系二叶一心苗期进行抗旱鉴定,共定位了12个与抗旱有关的QTL,其中在第2、6和12染色体上发现了4个QTL的加性效应值为正,来自东乡野生稻的等位基因能使渗入系的抗旱性增强,特别是位于第12染色体RM17附近的qSDT12-2在多次重复中均被检测到,在PEG处理后1-8 d能稳定表达.通过对抗旱性QTL的动态分析,发现不同QTL表达时间不同.     

Analysis of QTLs for yield-related traits in Yuanjiang common wild rice （Oryza rufipogon Griff.）

Using an accession of common wild rice(Oryza rufipogon Griff.)collected from Yunnjiang County,Yunnan Province,China,as the donor and an elite cnltivar 93-11,widely used in two-line indica hybrid rice production in China,as the recurrent parent,an advanced backcross populations were developed.Through genotyping of 187 SSR markers and investigation of six yield-related traits of two generations(BC4F2 and BC4F4),a total of 26 QTLs were detected by employing single point analysis and interval mapping in both generations.Of the 26 QTLs,the alleles of 10(38.5%)QTLs originating from O.rufipogon had shown a beneficial effect for yield-related traits in the 93-11 genetic background.In addition,five QTLs controlling yield and its components were newly identified,indicating that there arc potentially novel alleles in Yuanjiang common wild rice.Three regions underling significant QTLs for several yield-related traits were detected on chromosome 1,7 and 12.The QTL clusters were founded and corresponding agronomic traits of those QTLs showed highly significant correlation,suggesting the pleiotropism or tight linkage.Fine-mapping and cloning of these yield-related QTLs from wild rice would be helpful to elucidating molecular mechanism of rice domestication and rice breeding in the future.     

Construction of Chromosome Segment Substitution Lines in Peanut (Arachis hypogaea L.) Using a Wild Synthetic and QTL Mapping for Plant Morphology

Chromosome segment substitution lines (CSSLs) are powerful QTL mapping populations that have been used to elucidate the molecular basis of interesting traits of wild species. Cultivated peanut is an allotetraploid with limited genetic diversity. Capturing the genetic diversity from peanut wild relatives is an important objective in many peanut breeding programs. In this study, we used a marker-assisted backcrossing strategy to produce a population of 122 CSSLs from the cross between the wild synthetic allotetraploid (A. ipaënsis×A. duranensis)^4x and the cultivated Fleur11 variety. The 122 CSSLs offered a broad coverage of the peanut genome, with target wild chromosome segments averaging 39.2 cM in length. As a demonstration of the utility of these lines, four traits were evaluated in a subset of 80 CSSLs. A total of 28 lines showed significant differences from Fleur11. The line×trait significant associations were assigned to 42 QTLs: 14 for plant growth habit, 15 for height of the main stem, 12 for plant spread and one for flower color. Among the 42 QTLs, 37 were assigned to genomic regions and three QTL positions were considered putative. One important finding arising from this QTL analysis is that peanut growth habit is a complex trait that is governed by several QTLs with different effects. The CSSL population developed in this study has proved efficient for deciphering the molecular basis of trait variations and will be useful to the peanut scientific community for future QTL mapping studies.     

Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data.

A novel fine structure mapping method for quantitative traits is presented. It is based on Bayesian modeling and inference, treating the number of quantitative trait loci (QTLs) as an unobserved random variable and using ideas similar to composite interval mapping to account for the effects of QTLs in other chromosomes. The method is introduced for inbred lines and it can be applied also in situations involving frequent missing genotypes. We propose that two new probabilistic measures be used to summarize the results from the statistical analysis: (1) the (posterior) QTL intensity, for estimating the number of QTLs in a chromosome and for localizing them into some particular chromosomal regions, and (2) the locationwise (posterior) distributions of the phenotypic effects of the QTLs. Both these measures will be viewed as functions of the putative QTL locus, over the marker range in the linkage group. The method is tested and compared with standard interval and composite interval mapping techniques by using simulated backcross progeny data. It is implemented as a software package. Its initial version is freely available for research purposes under the name Multimapper at URL http://www.rni.helsinki.fi/mjs.     

Identification of fruit yield loci controlling the salt tolerance conferred by solanum rootstocks

The rootstock effect on the fruit yield of a grafted tomato variety was genetically analyzed under salinity using as rootstock two populations of F(9) lines developed from a salt sensitive genotype of Solanum lycopersicum var. cerasiforme, as female parent, and two salt tolerant lines, as male parents, from S. pimpinellifolium, the P population (123 lines), and S. cheesmaniae, the C population (100 lines). There were rootstock lines from the two populations (up to 65% in the P population) that raised the fruit yield of the commercial hybrid under saline conditions. It is shown that this salt tolerance rootstock effect is a heritable trait (h (2) near 0.3), governed by at least eight QTLs. The most relevant component was the number of fruits. Thus most detected QTLs correspond to this component. In general, QTL gene effects are medium-sized, with contributions from 8.5 up to 15.9% at most, and the advantageous allele comes from the wild, salt tolerant species. Only two fruit yield QTLs on chromosomes P9 and C11 might correspond to fruit yield QTLs of the non-grafted lines indicating their root system dependence. A fruit yield QTL on chromosome 3 is acting epistatically in both populations. The epistatic interactions found were dominant and they were unveiled using the associated marker as cofactor in the composite interval mapping methodology. Therefore, an efficient and profitable utilization of wild germplasm can be carried out through the improvement of rootstocks that confer salt tolerance in terms of fruit yield to the grafted variety.     

RFLP mapping of QTLs conferring cold tolerance during seed germination in an interspecific cross of tomato

Most cultivars of tomato, Lycopersicon esculentum, are sensitive to low (chilling) temperatures (0–15 °C) during seed germination; however, genetic sources of cold (chilling) tolerance have been identified within the related wild species. The purpose of this study was to identify quantitative trait loci (QTLs) that contribute to cold tolerance during germination in tomato using a backcross population of an interspecific cross between a cold-sensitive tomato line (NC84173, recurrent parent) and a L. pimpinellifolium accession (LA722) that germinates rapidly under low temperatures. A total of 119 BC1 individuals were genotyped for 151 restriction fragment length polymorphism (RFLP) markers and a genetic linkage map was constructed. The parental lines and 119 BC1S1 families (self-pollinated progeny of the BC1 individuals) were evaluated for germination at a low temperature (11±0.5 °C). Germination was scored visually as radicle protrusion at 8 h intervals for 28 consecutive days. Germination response was analyzed by the survival analysis and the times to 25, 50 and 75% germination were calculated. In addition, a germination index (GI) was calculated as the weighted mean of the time from imbibition to germination for each family/line. Two QTL mapping techniques, interval mapping (using MAPMAKER/QTL) and single-point analysis (using QGENE), were used to identify QTLs. The results of both methods were similar and two chromosomal locations (3–5 putative QTLs) with significant effects on low temperature germination were identified. The L. pimpinellifolium accession had favorable QTL alleles on chromosomes 1 and NC84173 had favorable QTL alleles on chromosome 4. The percentage of phenotypic variation explained (PVE) by individual QTLs ranged from 11.9% to 33.4%. Multilocus analysis indicated that the cumulative action of all significant QTLs accounted for 43.8% of the total phenotypic variance. Digenic epistatic interactions were evident between two of the QTL-linked markers and two unlinked markers. Transgressive phenotypes were observed in the direction of cold sensitivity. The results indicate that low temperature germination of tomato seed can be improved by marker-assisted selection.     

Mapping and Isolation of Quantitative Trait Loci Controlling Plant Height and Heading Date in Rice

Quantitative trait loci (QTL) were identified for heading date and plant height in rice ( Oryza sativa L.) using a recombinant inbred line population consisting of 241 lines. Totally 4 QTLs for heading date and 4 QTLs for plant height were detected in three years. The QTL with large effects located in the interval C1023-R1440 on chromosome 7 was simultaneously detected in three years for both traits. In order to distinguished the interval whether contained one QTL with pleiotropy effect or two close linked QTLs, a recombinant line RIL50, whose genetic background was high similar to Zhenshan 97 except the regions covered the major QTL from Minghui 63, was selected to cross with Zhenshan 97. A BC1F2 population from the cross, which could be regarded as near isogenic lines (NIL) with the targeted QTL (QTL-NIL), was used to collect heading date and plant height data. The frequency distribution of the two traits in the BC1F2 population was bimodal, and their segregation ratios were in accordance with the expected Mendelian inheritance ratios. Normally, the short plants flowered early in the population, the high plants with late heading date, but the relationships between the plant height and the heading date of 6 plants conflicted with the case. The above results clearly demonstrated that QTL could be treated as single Mendelian factor. Moreover, there are two close linked genes controlling the heading date and the plant height on chromosome 7, respectively.     

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.     

Interval Mapping of Multiple Quantitative Trait Loci

The interval mapping method is widely used for the mapping of quantitative trait loci (QTLs) in segregating generations derived from crosses between inbred lines. The efficiency of detecting and the accuracy of mapping multiple QTLs by using genetic markers are much increased by employing multiple QTL models instead of the single QTL models (and no QTL models) used in interval mapping. However, the computational work involved with multiple QTL models is considerable when the number of QTLs is large. In this paper it is proposed to combine multiple linear regression methods with conventional interval mapping. This is achieved by fitting one QTL at a time in a given interval and simultaneously using (part of) the markers as cofactors to eliminate the effects of additional QTLs. It is shown that the proposed method combines the easy computation of the single QTL interval mapping method with much of the efficiency and accuracy of multiple QTL models.