Interval mapping of quantitative trait loci affecting NESTUR, a stem growth efficiency index of radiata pine seedlings

 NESTUR (needle-to-stem unit rate) is a stem growth index of conifer seedlings that measures the efficiency of stemwood production per unit of needle growth, and is related to other seedling traits such as height, stem diameter, stem volume and needle volume. Quantitative trait loci (QTLs) affecting the expression of stem growth efficiency in radiata pine seedlings were investigated using a RAPD linkage map constructed from markers scored on haploid, megagametophytic DNA. Four putative QTLs were detected which accounted for 8.5–36.4% of the population variance. A search for evidence of epistasis, using both complete pairwise and conditional interactions, did not yield any statistically significant result. Over a 3-year period, seedlings with high-NESTUR marker alleles showed a superior growth performance of 17–40% for height, diameter and volume over those with low-NESTUR marker alleles. Received: 10 July 1997 / Accepted: 31 March 1998     

Identification of RAPD markers linked to genetic factors controlling the milling energy requirement of barley

Doubled haploid (DH) populations of barley have been used in combination with PCR-based polymorphic-assay procedures to identify molecular markers linked to genes controlling the milling energy requirement of the grain. Milling energy (ME) is a quantitative trait and locating individual quantitative trait loci (QTLs) involved the construction of bulks by combining DNA from DH families representing the extreme members of the distribution for ME. In addition, the individuals had alternative alleles at theRrn2 locus that has previously been shown to be linked to an ME QTL. The DNA bulks were screened with Randomly Amplified Polymorphic DNA (RAPD) markers and polymorphic amplification products tested for linkage to genes influencing the expression of ME in a DH population. Several markers were identified which are linked to a QTL controlling ME and the recombination fraction determined by maximum likelihood procedures. The results indicate that DHs in combination with RAPDs and bulked segregant analysis provide an efficient method for locating QTLs in barely. Furthermore, this approach is applicable to mapping other QTLs in a range of organisms from which DH or recombinant inbred lines can be extracted.     

Use of Random Amplified Polymorphic DNA Markers for Mapping the Chickpea Genome

Three interspecific crosses were developed using Cicer arietinum (ICC 4918) as the female parent and wild Cicer species [C. reticulatum - JM 2100, JM 2106 and C. echinospermum - ICCW 44] as the male parent. Cicer arietinum (ICC 4918) × C. reticulatum (JM 2100) cross produced the largest number of F₂ plants and was chosen for linkage mapping using Random Amplified Polymorphic DNA (RAPD) primers. A partial linkage map was constructed based upon the segregation of 36 RAPD markers obtained by amplification using 35 primers. The linkage map consists of two linkage groups with 17 linked markers covering a total of 464.9 cM. Analyses also revealed association of three morphological traits with linked RAPD markers. Out of seven morphological traits tested for association with linked markers in the segregating plants, four Quantitative trait loci (QTL) were detected for the trait leaf length and three QTLs each for the traits leaf width and erect plant habit.     

Identification of RAPD markers linked to the gene PM 1 for resistance to powdery mildew in wheat

 Powdery mildew caused by Blumeria graminis DC. f. sp. triticiém. Marchal is an important disease of wheat (Triticum aestivum L. em Thell). We report here the identification of three random amplified polymorphic DNA (RAPD) markers closely linked to a gene for resistance to B. graminis in wheat. RAPD-PCR (polymerase chain reaction) analysis was conducted using bulked segregant analysis of closely related lines developed from a segregating F₅ family. The F₅ family was derived from a cross between the susceptible cultivar Clark and the resistant line Zhengzhou 871124. Genetic analysis indicated that resistance of Zhengzhou 871124 to powdery mildew is conferred by the gene Pm1. After performing RAPD-PCR analysis with 1300 arbitrary 10-mer primers and agarose-gel electrophoresis, two RAPD markers, UBC320₄₂₀ and UBC638₅₅₀, were identified to be co-segregating with the disease resistance. No recombinants were observed between either of the RAPD markers and the gene for resistance to powdery mildew after analysis of 244 F₂ plants. The third RAPD marker, OPF12₆₅₀, was identified with denaturing gradient-gel electrophoresis (DGGE), and was determined to be 5.4±1.9 cM from the resistance gene. UBC320₄₂₀ and UBC638₅₅₀ were present in wheat powdery mildew differential lines carrying the gene Pm1, suggesting linkage between these markers and the Pm1 resistance gene. Co-segregation between Pm1 and the two markers UBC320₄₂₀ and UBC638₅₅₀ was confirmed in a segregating population derived from a cross with CI14114, the wheat differential line carrying Pm1. The method of deriving closely related lines from inbred families that are segregating for a trait of interest should find wide application in the identification of DNA markers linked to important plant genes. The RAPD marker UBC638₅₅₀ was converted to a sequence tagged site (STS). RAPD markers tightly linked to target genes may facilitate selection and enable gene pyramiding for powdery mildew resistance in wheat breeding programs. Received: 10 December 1995 / Accepted: 13 September 1996     

RAPD markers associated with salt tolerance in an interspecific cross of tomato (Lycopersicon esculentum×L. pennellii)

This study was conducted to identify randomly amplified polymorphic DNA (RAPD) markers associated with quantitative trait loci (QTLs) conferring salt tolerance during germination in tomato. Germination response of an F₂ population (2000 individuals) of a cross between UCT5 (Lycopersicon esculentum, salt-sensitive) and LA716 (L. pennellii, salt-tolerant) was evaluated at a salt-stress level of 175 mM NaCl+17.5 mM CaCl₂ (water potential ca. –9.5 bars). Germination was scored visually as radicle protrusion at 6-h intervals for 30 consecutive days. Individuals at both extremes of the response distribution (i.e., salt-tolerants and salt-sensitives) were selected. The selected individuals were genotyped for 53 RAPD markers and allele frequencies at each marker locus were determined. The linkage association among the markers was determined using a “Mapmaker” program. Trait-based marker analysis (TBA) identified 13 RAPD markers at eight genomic regions that were associated with QTLs affecting salt tolerance during germination in tomato. Of these genomic regions, five included favorable QTL alleles from LA716, and three included favorable alleles from UCT5. The approximate effects of individual QTLs ranged from 0.46 to 0.82 phenotypic standard deviation. The results support our previous suggestion that salt tolerance during germination in tomato is polygenically controlled. The identification of favorable QTLs in both parents suggests the likelihood of recovering transgressive segregants in progeny derived from these genotypes. Results from this study are discussed in relation to using marker-assisted selection in breeding for salt tolerance. Received: 16 June 1997 / Revision received: 11 August 1997 / Accepted: 2 September 1997     

Identification of a RAPD marker associated with somatic embryogenesis in alfalfa

The current study was conducted to identify random amplified polymorphic DNA (RAPD) markers linked to genes controlling somatic embryogenesis in alfalfa. Segregation analyses of the somatic embryogenesis trait and the RAPD markers in an F₁ population of 83 plants, derived from a cross between embryogenic A70-34 and non-embryogenic Arrow36 alfalfa plants, identified a polymorphic band that is associated with somatic embryogenesis. Based on the assumptions that somatic embryogenesis in alfalfa is controlled by two dominant genes with complementary effects and that the genotypes of A70-34 and Arrow36 are AAaaBbbb and aaaabbbb, respectively, the segregation data for the marker and the somatic embryogenesis trait in the F₁s indicate that the marker is linked to the A locus. The maximum recombination fraction estimated for the linkage between the marker and the gene is 36.3%.     

Development of SCAR markers linked to male sterility and very high linoleic acid content in safflower

Practically no molecular tools have been developed so far for safflower (Carthamus tinctorius L.) breeding. The objective of the present research was to develop molecular markers for the closely linked genes Li, controlling very high linoleic acid content, and Ms, controlling nuclear male sterility (NMS). A mapping population of 162 individuals was developed from the NMS line CL1 (64–79% linoleic acid) and the line CR-142 (84–90%), and phenotyped in the F₂ and F₃ generations. Bulked segregant analysis with random amplified polymorphic (RAPD) markers revealed linkage of five RAPD bands to the Li and Ms genes. RAPD fragments were converted into sequence-characterized amplified region (SCAR) markers. A linkage map including the five SCAR markers and the Li and Ms genes was constructed. SCAR markers flanked both loci at minimum distances of 15.7 cM from the Li locus and 3.7 cM from the Ms locus. These are the first molecular markers developed for trait selection in safflower.     

Development of RAPD and SCAR markers linked to the Russian wheat aphid resistance gene Dn2 in wheat

 RAPD (random amplified polymorphic DNA) analysis was used to identify molecular markers linked to the Dn2 gene conferring resistance to the Russian wheat aphid (Diuraphis noxia Mordvilko). A set of near-isogenic lines (NILs) was screened with 300 RAPD primers for polymorphisms linked to the Dn2 gene. A total of 2700 RAPD loci were screened for linkage to the resistance locus. Four polymorphic RAPD fragments, two in coupling phase and two in repulsion phase, were identified as putative RAPD markers for the Dn2 gene. Segregation analysis of these markers in an F₂ population segregating for the resistance gene revealed that all four markers were closely linked to the Dn2 locus. Linkage distances ranged from 3.3 cM to 4.4 cM. Southern analysis of the RAPD products using the cloned RAPD markers as probes confirmed the homology of the RAPD amplification products. The coupling-phase marker OPB10_880c and the repulsion-phase marker OPN1_400r were converted to sequence characterized amplified region (SCAR) markers. SCAR analysis of the F₂ population and other resistant and susceptible South African wheat cultivars corroborated the observed linkage of the RAPD markers to the Dn2 resistance locus. These markers will be useful for marker-assisted selection of the Dn2 gene for resistance breeding and gene pyramiding. Received: 1 July 1997 / Accepted: 20 October 1997     

RAPD linkage mapping of the shell thickness locus in oil palm (Elaeis guineensis Jacq.)

Shell thickness is an important trait in oil palm breeding programs and is the basis for the classification of the varieties of oil palm into the types dura, tenera and pisifera. This trait seems to be controlled by a single locus, with two alleles (sh ⁺ and sh ⁻) showing codominant expression. Two single-tree linkage maps were constructed for a maternal tenera (sh ⁺ sh ⁻) palm and for a paternal pisifera (sh ⁻ sh ⁻) palm using the pseudo-testcross mapping strategy in combination with RAPD markers through the analysis of an F₁ tenera×pisifera progeny. A total of 308 arbitrary primers were screened in a sample of eight F₁ plants and 121 markers were detected in a testcross configuration. An average of 1.66 polymorphic marker per selected primer were identified in this cross. At LOD 5.0 (with some few exceptions) and θ=0.25 the maternal tenera map included a total of 48 markers distributed in 12 linkage groups or pairs of markers (449.3 cM) while the paternal pisifera map included 42 markers distributed in 15 linkage groups or pairs of markers (399.7 cM). We used RAPD and bulked segregant analysis (BSA) to identify markers more tightly linked to the sh ⁺ locus. A total of 174 new primers not previously used in the linkage analysis were screened using bulks of DNA extracted from plants selected for the contrasting shell-thickness phenotypes. Two RAPD markers (R11–1282 and T19–1046) were identified to be linked on both sides of the sh ⁺ locus on linkage group 4. The estimated map distances from sh ⁺ to R11–1282 and to T19–1046 were 17.5 cM and 23.9 cM, respectively. The results demonstrate the usefulness of RAPD markers and the pseudo-testcross mapping strategy for developing genetic linkage information, and constitute an important step towards early marker-assisted selection for shell thickness in oil palm. Received: 21 February 1999 / Accepted: 29 April 1999     

Detection of quantitative trait loci for juvenile growth, flower bearing and rooting ability based on a linkage map of sugi (Cryptomeria japonica D. Don)

 Quantitative traits, including juvenile growth, flower bearing and rooting ability, of a woody plant species, Cryptomeria japonica D. Don, were analyzed in a three-generation pedigree with 73 F₂ progenies using a linkage map with 85 genetic markers (72 RFLP, 11 RAPD, one isozyme and one morphological loci). A cluster of quantitative trait loci (QTLs) related to juvenile growth and female flower bearing was detected on linkage group 2. Some of the influence of this cluster could be attributed to pleiotropic effects of a dwarf locus located in its vicinity. QTLs related to male and female flower bearing were detected at different locations and showed different effects from each other, suggesting that the genetic systems controlling male and female flowering are different. No large QTL affecting rooting ability was detected in the material analyzed in this study. Received: 15 December 1997 / Accepted: 4 February 1998     

Identification of molecular markers linked to quantitative trait loci for soybean resistance to corn earworm

 One hundred and thirty nine restriction fragment length polymorphisms (RFLPs) were used to construct a soybean (Glycine max L. Merr.) genetic linkage map and to identify quantitative trait loci (QTLs) associated with resistance to corn earworm (Helicoverpa zea Boddie) in a population of 103 F₂-derived lines from a cross of ‘Cobb’ (susceptible) and PI229358 (resistant). The genetic linkage map consisted of 128 markers which converged onto 30 linkage groups covering approximately 1325 cM. There were 11 unlinked markers. The F₂-derived lines and the two parents were grown in the field under a plastic mesh cage near Athens, Ga., in 1995. The plants were artificially infested with corn earworm and evaluated for the amount of defoliation. Using interval-mapping analysis for linked markers and single-factor analysis of variance (ANOVA), markers were tested for an association with resistance. One major and two minor QTLs for resistance were identified in this population. The PI229358 allele contributed insect resistance at all three QTLs. The major QTL is linked to the RFLP marker A584 on linkage group (LG) ‘M’ of the USDA/Iowa State University public soybean genetic map. It accounts for 37% of the total variation for resistance in this cross. The minor QTLs are linked to the RFLP markers R249 (LG ‘H’) and Bng047 (LG ‘D1’). These markers explain 16% and 10% of variation, respectively. The heritability (h²) for resistance was estimated as 64% in this population. Received: 15 October 1997 / Accepted: 4 November 1997     

Identification of RAPD markers linked to a locus involved in quantitative resistance to TYLCV in tomato by bulked segregant analysis

 In tomato, Bulked Segregant Analysis was used to identify random amplified polymorphic DNA (RAPD) markers linked to a quantitative trait locus (QTL) involved in the resistance to the Tomato Yellow Leaf Curl Virus. F₄ lines were distributed into two pools, each consisting of the most resistant and of the most susceptible individuals, respectively. Both pools were screened using 600 random primers. Four RAPD markers were found to be linked to a QTL responsible for up to 27.7% of the resistance. These markers, localized in the same linkage group within a distance of 17.3 cM, were mapped to chromosome 6 on the tomato RFLP map. Received: 21 August 1996 / Accepted: 4 April 1997     

Inheritance of inter-simple-sequence-repeat polymorphisms and linkage with a fusarium wilt resistance gene in chickpea

 The inheritance of an inter-simple-sequence-repeat (ISSR) polymorphism was studied in a cross of cultivated chickpea (Cicer arietinum L.) and a closely related wild species (C. reticulatum Lad.) using primers that anneal to a simple repeat of various lengths, sequences and non-repetitive motifs. Dinucleotides were the majority of those tested, and provided all of the useful banding patterns. The ISSR loci showed virtually complete agreement with expected Mendelian ratios. Twenty two primers were used for analysis and yielded a total of 31 segregating loci. Primers based on (GA)_n repeats were the most abundant while primers with a (TG)_n repeat gave the largest number of polymorphic loci. Nucleotides at the 5′ and 3′ end of the primers played an important role in detecting polymorphism. All the markers showed dominance. We found an ISSR marker linked to the gene for resistance to fusarium wilt race 4. The marker concerned, UBC-855₅₀₀, was found to be linked in repulsion with the fusarium wilt resistance gene at a distance of 5.2 cM. It co-segregated with CS-27₇₀₀, a RAPD marker previously shown to be linked to the gene for resistance to fusarium wilt race 1, and was mapped to linkage group 6 of the Cicer genome. This indicated that genes for resistance to fusarium wilt races 1 and 4 are closely linked. The marker UBC-855₅₀₀ is located 0.6 cM from CS-27₇₀₀ and is present on the same side of the wilt resistance gene. To our knowledge this is the first report of the utility of an ISSR marker in gene tagging. These markers may provide valuable information for the development of sequence-tagged microsatellite sites (STMS) at a desired locus. Received: 10 August 1997 / Accepted: 6 October 1997     

Molecular-marker-facilitated studies of morphological traits in maize. II: Determination of QTLs for grain yield and yield components

Genetic factors controlling quantitative inheritance of grain yield and its components have not previously been investigated by using replicated lines of an elite maize (Zea mays L.) population. The present study was conducted to identify quantitative trait loci (QTLs) associated with grain yield and grain-yield components by using restriction fragment length polymorphism (RFLP) markers. A population of 150 random F₂₃ lines was derived from the single cross of inbreds Mo17 and H99, which are considered to belong to the Lancaster heterotic group. Trait values were measured in a replicated trial near Ames, Iowa, in 1989. QTLs were located on a linkage map constructed with one morphological and 103 RFLP loci. QTLs were found for grain yield and all yield components. Partial dominance to overdominance was the primary mode of gene action. Only one QTL, accounting for 35% of the phenotypic variation, was identified for grain yield. Two to six QTLs were identified for the other traits. Several regions with pleiotropic or linked effects on several of the yield components were detected.     

A genetic linkage map of lentil (Lens sp.) based on RAPD and AFLP markers using recombinant inbred lines

 A genetic linkage map of Lens sp. was constructed with 177 markers (89 RAPD, 79 AFLP, six RFLP and three morphological markers) using 86 recombinant inbred lines (F_6:8) obtained from a partially interspecific cross. The map covered 1073 cM of the lentil genome with an average distance of 6.0 cM between adjacent markers. Previously mapped RFLP markers were used as anchor probes. The morphological markers, pod indehiscence, seed-coat pattern and flower-color loci were mapped. Out of the total linked loci, 8.4% showed segregation distortion. More than one-fourth of the distorted loci were clustered in one linkage group. AFLP markers showed more segregation distortion than the RAPD markers. The AFLP and RAPD markers were intermingled and clustering of AFLPs was seldom observed. This is the most extensive genetic linkage map of lentil to-date. The marker density of this map could be used for the identification of markers linked to quantitative trait loci in this population. Received: 6 November 1997 / Accepted: 10 February 1998     

RAPD linkage map of the genomic region encompassing the root-knot nematode (Meloidogyne javanica) resistance locus in carrot

Inheritance studies have indicated that resistance to the root-knot nematode (Meloidogyne javanica) in carrot inbred line ’Brasilia-1252’ is controlled by the action of one or two (duplicated) dominant gene(s) located at a single genomic region (designated the Mj-1 locus). A systematic search for randomly amplified polymorphic DNA (RAPD) markers linked to Mj-1 was carried out using bulked segregant analysis (BSA). Altogether 1000 ten-mer primers were screened with 69.1% displaying scorable amplicons. A total of approximately 2400 RAPD bands were examined. Four reproducible markers (OP-C2₁₇₀₀, OP-Q6₅₀₀, OP-U12₇₀₀, and OP-AL15₅₀₀) were identified, in coupling-phase linkage, flanking the Mj-1 region. The genetic distances between RAPD markers and the Mj-1 locus, estimated using an F₂ progeny of 412 individuals from ’Brasilia 1252’×’B6274’, ranged from 0.8 to 5.7 cM . The two closest flanking markers (OP-Q6₅₀₀ and OP-AL15₅₀₀) encompassed a region of 2.7 cM . The frequency of these RAPD loci was evaluated in 121 accessions of a broad-based carrot germplasm collection. Only five entries (all resistant to M. javanica and genetically related to ’Brasilia 1252’) exhibited the simultaneous presence of all four markers. An advanced line derived from the same cross, susceptible to M. javanica but relatively resistant to another root-knot nematode species (M. incognita), did not share three of the closest markers. These results suggest that at least some genes controlling resistance to M. incognita and M. javanica in ’Brasilia 1252’ reside at distinct loci. The low number of markers suggests a reduced amount of genetic divergence between the parental lines at the region surrounding the target locus. Nevertheless, the low rate of recombination indicated these markers could be useful landmarks for positional cloning of the resistance gene(s). These RAPD markers could also be used to increase the Mj-1 frequency during recurrent selection cycles and in backcrossing programs to minimize ’linkage drag’ in elite lines employed for the development of resistant F₁ hybrids. Received: 22 June 1999 / Accepted: 6 July 1999     

Identification and molecular mapping of loci controlling fruit ripening time in tomato

Using RAPD marker analysis, two quantitative trait loci (QTLs) associated with earliness due to reduced fruit-ripening time (days from anthesis to ripening = DTR) were identified and mapped in an F₂ population derived from a cross between Lycopersicon esculentum’E6203’ (normal ripening) and Lycopersicon esculentum’Early Cherry’ (early ripening). One QTL, on chromosome 5, was associated with a reduction in both ripening time (5 days) and fruit weight (29.3%) and explained 15.8 and 13% of the total phenotypic variation for DTR and fruit weight, respectively. The other QTL, on chromosome 12, was primarily associated with a reduction only in ripening time (7 days) and explained 12.3% of the total phenotypic variation for DTR. The gene action at this QTL was found to be partially dominant (d/a=0.41). Together, these two QTLs explained 25.1% of the total phenotypic variation for DTR. Additionally, two QTLs associated with fruit weight were identified in the same F₂ population and mapped to chromosomes 4 and 6, respectively. Together, these two QTLs explained 30.9% of the total phenotypc variation for fruit weight. For all QTLs, the ’Early Cherry’ alleles caused reductions in both ripening time and fruit weight. The polymorphic band for the most significant RAPD marker (OPAB-06), linked to the reduced ripening time QTL on chromosome 12, was converted to a cleaved amplified polymorphism (CAP) assay for marker-aided selection and further introgression of early ripening time (DTR) into cultivated tomato. Received: 15 March 1999 / Accepted: 29 April 1999     

Identification and mapping on chromosome 9 of RAPD markers linked to Sw-5 in tomato by bulked segregant analysis

Bulked segregant analysis was used to identify random amplified polymorphic DNA (RAPD) markers linked to the Sw-5 gene for resistance to tomato spotted wilt virus (TSWV) in tomato. Using two pools of phenotyped individuals from one segregating population, we identified four RAPD markers linked to the gene of interest. Two of these appeared tightly linked to Sw-5, whereas another, linked in repulsion phase, enabled the identification of heterozygous and susceptible plants. After linkage analysis of an F₂ population, the RAPD markers were shown to be linked to Sw-5 within a distance of 10.5 cM. One of the RAPD markers close to Sw-5 was used to develop a SCAR (sequence characterized amplified region) marker. Another RAPD marker was stabilized into a pseudo-SCAR marker by enhancing the specificity of its primer sequence without cloning and sequencing. RAPD markers were mapped to chromosome 9 on the RFLP tomato map developed by Tanksley et al. (1992). The analysis of 13 F₃ families and eight BC₂ populations segregating for resistance to TSWV confirmed the linkage of the RAPD markers found. These markers are presently being used in marker-assisted plant breeding.     

谭清苏铁性别连锁的RAPD和SCAR分子标记

利用RAPD(Random amplified polymorphic DNA)分子标记技术,寻找谭清苏铁（Cycas tanqingii）中与性别相关的分子标记,筛选了160个10bp的随机引物,产生了2500多个RAPD条带。只有引物S0465 (CCCCGGTAAC)产生了一条大约500bp的雌性特异RAPD标记,该分子标记出现在所有的供试雌性植株中,而所有的供试雄性植株都不具有该标记。对该特异片段进行了克隆和序列测定,并根据序列分析结果将RAPD标记转化为重复性和特异性更好的特异特征序列扩增区域（SCAR）分子标记,并命名为STQC-S465-483。分子标记的建立可用于谭清苏铁幼苗性别的早期鉴定,为谭清苏铁就地保护和迁地保护提供技术支持。     

Quantitative trait loci and underlying candidate genes controlling agronomical and fruit quality traits in octoploid strawberry <Emphasis Type="Italic">(Fragaria</Emphasis> × <Emphasis Type="Italic">ananassa</Emphasis>)

Breeding for fruit quality traits in strawberry (Fragaria × ananassa, 2n = 8x = 56) is complex due to the polygenic nature of these traits and the octoploid constitution of this species. In order to improve the efficiency of genotype selection, the identification of quantitative trait loci (QTL) and associated molecular markers will constitute a valuable tool for breeding programs. However, the implementation of these markers in breeding programs depends upon the complexity and stability of QTLs across different environments. In this work, the genetic control of 17 agronomical and fruit quality traits was investigated in strawberry using a F₁ population derived from an intraspecific cross between two contrasting selection lines, ‘232’ and ‘1392’. QTL analyses were performed over three successive years based on the separate parental linkage maps and a pseudo-testcross strategy. The integrated strawberry genetic map consists of 338 molecular markers covering 37 linkage groups, thus exceeding the 28 chromosomes. 33 QTLs were identified for 14 of the 17 studied traits and approximately 37% of them were stable over time. For each trait, 1–5 QTLs were identified with individual effects ranging between 9.2 and 30.5% of the phenotypic variation, indicating that all analysed traits are complex and quantitatively inherited. Many QTLs controlling correlated traits were co-located in homoeology group V, indicating linkage or pleiotropic effects of loci. Candidate genes for several QTLs controlling yield, anthocyanins, firmness and l-ascorbic acid are proposed based on both their co-localization and predicted function. We also report conserved QTLs among strawberry and other Rosaceae based on their syntenic location.