QTL analysis of plant development and fruit traits in pepper and performance of selective phenotyping

A QTL analysis was performed to determine the genetic basis of 13 horticultural traits conditioning yield in pepper (Capsicum annuum). The mapping population was a large population of 297 recombinant inbred lines (RIL) originating from a cross between the large-fruited bell pepper cultivar ‘Yolo Wonder’ and the small-fruited chilli pepper ‘Criollo de Morelos 334’. A total of 76 QTLs were detected for 13 fruit and plant traits, grouped in 28 chromosome regions. These QTLs explained together between 7% (internode growth time) and 91% (fruit diameter) of the phenotypic variation. The QTL analysis was also performed on two subsets of 141 and 93 RILs sampled using the MapPop software. The smaller populations allowed for the detection of a reduced set of QTLs and reduced the overall percentage of trait variation explained by QTLs. The frequency of false positives as well as the individual effect of QTLs increased in reduced population sets as a result of reduced sampling. The results from the QTL analysis permitted an overall glance over the genetic architecture of traits considered by breeders for selection. Colinearities between clusters of QTLs controlling fruit traits and/or plant development in distinct pepper species and in related solanaceous crop species (tomato and eggplant) suggests that shared mechanisms control the shape and growth of different organs throughout these species.     

QTL analysis of horticultural traits differentiating the cultivated tomato from the closely related species Lycopersicon pimpinellifolium

Molecular markers were used to map and characterize quantitative trait loci (QTLs) for several characters of agronomic and biological importance in an interspecific backcross of tomato. The parents of the cross were an elite processing inbred Lycopersicon esculentum cv M82-1-7 and the closely related red-fruited wild species L. pimpinellifolium (LA1589). A total of 257 BC₁ plants were grown under field conditions in Ithaca, New York and scored for 19 quantitative traits. A genetic linkage map was constructed for the same population using 115 RFLP, 3 RAPD and 2 morphological markers that spanned 1,279 cM of the tomato genome with an average interval length of 10.7 cM. A minimum of 54 putatively significant QTLs (P<0.001; LOD> 2.4) were detected for all characters with a range of 1–7 QTLs detected per character. Of the total 54 QTLs 11% had alleles with effects opposite to those predicted by the parental phenotypes. The percentage of phenotypic variation associated with single QTLs ranged from 4% to 47%. Multilocus analysis showed that the cumulative action of all QTLs detected for each trait accounted for 12–59% of the phenotypic variation. The difference in fruit weight was controlled largely by a single major QTL (fw2.2). Digenic epistasis was not evident. Several regions of the genome (including the region near sp on chromosome 6) showed effects on more than one trait. Implications for variety improvement and inferences about the domestication of the cultivated tomato are discussed.     

Mapping quantitative trait loci controlling seed dormancy and heading date in rice, Oryza sativa L., using backcross inbred lines

 To detect quantitative trait loci (QTLs) controlling seed dormancy, 98 BC₁F₅ lines (backcross inbred lines) derived from a backcross of Nipponbare (japonica)/Kasalath (indica)//Nipponbare were analyzed genetically. We used 245 RFLP markers to construct a framework linkage map. Five putative QTLs affecting seed dormancy were detected on chromosomes 3, 5, 7 (two regions) and 8, respectively. Phenotypic variations explained by each QTL ranged from 6.7% to 22.5% and the five putative QTLs explained about 48% of the total phenotypic variation in the BC₁F₅ lines. Except for those of the QTLs on chromosome 8, the Nipponbare alleles increased the germination rate. Five putative QTLs controlling heading date were detected on chromosomes 2, 3, 4, 6 and 7, respectively. The phenotypic variation explained by each QTL for heading date ranged from 5.7% to 23.4% and the five putative QTLs explained about 52% of the total phenotypic variation. The Nipponbare alleles increased the number of days to heading, except for those of two QTLs on chromosomes 2 and 3. The map location of a putative QTL for heading date coincided with that of a major QTL for seed dormancy on chromosome 3, although two major heading-date QTLs did not coincide with any seed dormancy QTLs detected in this study. Received: 10 October 1997 / Accepted: 12 January 1998     

Salt tolerance in Lycopersicon species. V. Does genetic variability at quantitative trait loci affect their analysis?

 Salt tolerance was studied comparatively in three families derived from crosses between Lycopersicon esculentum Mill. and two related wild species [two accessions of Lycopersicon pimpinellifolium (Jusl.) Mill. and one accession of Lycopersicon chesmannii f.minor (Hook.f.) Mull.] by means of QTL analysis of fruit yield and earliness under conditions of salinity. From six polymorphic genomic regions involved in salt tolerance, three contained segregant salt-tolerant QTLs for the three families; two were found only in both families derived from L.pimpinellifolium; and one, involved in fruit number, was detected only in one of the L.pimpinellifolium families. Some differences regarding the effects of the wild alleles at orthologous QTLs were found. These effects were always negative in the L. chesmannii family. Comparing both L. pimpinellifolium families, the “wild” alleles at two out of nine common QTLs for fruit number and weight had effects with opposite directions, and the mode of gene action was clearly different at five of them. QTL analysis of earliness revealed the largest genotypic differences among families. Most drastic differences were found for the epistatic interactions in which all genomic regions containing QTLs were involved. These interactions between unlinked genes increased the range of variation of means, mainly upwards, as compared with genotypes at individual QTLs. Only one (affecting fruit weight) out of 27 interactions was detected in both L.pimpinellifolium families. Heterotic effects found for salt tolerance in one of the families can be explained by the presence of overdominant (or pseudo-overdominant) and dominant gene effects at QTLs controlling final fruit yield under conditions of salinity. Allelic variation at salt-tolerant QTLs exists, changing the additive and, mainly, the non-additive components of the genotypic value. Consequently, it may negatively affect the general applicability (or efficiency) of marker-assisted selection to improve salt tolerance in other segregant populations where QTLs were not studied. The use of more informative co-dominant markers, like microsatelites, might overcome these problems. Received: 5 August 1996/Accepted: 25 October 1996     

Genetic analysis of organoleptic quality in fresh market tomato. 1. Mapping QTLs for physical and chemical traits

Improving organoleptic quality is an important but complex goal for fresh market tomato breeders. A total of 26 traits involved in organoleptic quality variation were evaluated, in order to understand the genetic control of this characteristic. A recombinant inbred line (RIL) population was developed from an intraspecific cross between a cherry tomato line with a good overall aroma intensity and an inbred line with a common taste but with bigger fruits. Physical traits included fruit weight, diameter, color (L,a,b), firmness and elasticity. Chemical traits were dry matter weight, titratable acidity, pH, and the contents of soluble solids, sugars, lycopene, carotene and 12 aroma volatiles. RILs showed a large range of variation for most of the traits and many of them were transgressive. Some correlations between aroma volatiles were in accordance with the metabolic pathway they originated from. A total of 81 significant QTLs were detected for the 26 traits by simple and composite interval mapping. They were mainly distributed in a few regions on chromosomes 2, 3, 4, 8, 9, 11 and 12. Major QTLs (R²>30%) were detected for fruit weight, diameter, and color, and for six aroma volatiles. Co-localization of QTLs controlling correlated traits was mainly found on chromosome 2. QTLs for fruit weight and sugar content or dry matter weight were often co-localized. However, a QTL for soluble-solids content and dry matter weight have been detected on chromosome 9 in a region without fruit weight QTLs. QTLs for seven aroma volatiles, lycopene content and fruit color were also co-localized. The QTL localizations were compared with those detected in crosses between Lycopersicon esculentum and wild tomato species. Received: 19 January 2000 / Accepted: 26 May 2000     

Quantitative trait loci for resistance to spot blotch caused by Bipolarissorokiniana in wheat (T.aestivum L.) lines ‘Ning 8201’ and ‘Chirya 3’

Spot blotch caused by Bipolaris sorokiniana is a destructive disease of wheat in warm and humid wheat growing regions of the world. To identify quantitative trait loci (QTLs) for spot blotch resistance, two mapping populations were developed by making the crosses between common susceptible cultivar ‘Sonalika’ with the resistant breeding lines ‘Ning 8201’ and ‘Chirya 3’. Single seed descent derived F₆, F₇, F₈ lines of the first cross ‘Ning 8201’ × ‘Sonalika’ were evaluated for resistance to spot blotch in three blocks in each of the 3 years. After screening of 388 pairs of simple sequence repeat primers between the two parents, 119 polymorphic markers were used to genotype the mapping population. Four QTLs were identified on the chromosomes 2AS, 2BS, 5BL and 7DS and explained 62.9% of phenotypic variation in a simultaneous fit. The QTL on chromosome 2A was detected only in 1 year and explained 22.7% of phenotypic variation. In the second cross (‘Chirya 3’ × ‘Sonalika’), F₇ and F₈ population were evaluated in three blocks in each of the 2 years. In this population, five QTLs were identified on chromosomes 2BS, 2DS, 3BS, 7BS and 7DS. The QTLs identified in the ‘Chirya 3’ × ‘Sonalika’ population explained 43.4% of phenotypic variation in a simultaneous fit. The alleles for reduced disease severity in both the populations were derived from the respective resistant parent. The QTLs QSb.bhu-2B and QSb.bhu-7D from both populations were placed in the same deletion bins, 2BS1-0.53-0.75 and 7DS5-0.36-0.61, respectively. The closely linked markers Xgwm148 to the QTL on chromosome 2B and Xgwm111 to the QTL on chromosome 7D are potentially diagnostic markers for spot blotch resistance.     

Quantitative trait locus analysis of a recombinant inbred line population derived from a Lycopersicon esculentum x Lycopersicon cheesmanii cross

Quantitative trait loci influencing fruit traits were identified by restriction fragment length polymorphism (RFLP) analysis in a population of recombinant inbred lines (RIL) derived from a cross of the cultivated tomato, Lycopersicon esculentum with a related wild species Lycopersicon cheesmanii. One hundred thirty-two polymorphic RFLP loci spaced throughout the tomato genome were scored for 97 F₈ RIL families. Fruit weight and soluble solids were measured in replicated trials during 1991 and 1992. Seed weight was measured in 1992. Significant (P<0.01 level) quantitative trait locus (QTL) associations of marker loci were identified for each trait. A total of 73 significant marker locus-trait associations were detected for the three traits measured. Fifty-three of these associations were for fruit weight and soluble solids, many of which involved marker loci signficantly associated with both traits. QTL with large effects on all three traits were detected on chromosome 6. Greater homozygosity at many loci in the RIL population as compared to F₂ populations and greater genomic coverage resulted in increased precision in the estimation of QTL effects, and large proportions of the total phenotypic variance were explained by marker class variation at significant marker loci for many traits. The RIL population was effective in detecting and discriminating among QTL for these traits previously identified in other investigations despite skewed segregation ratios at many marker loci. Large additive effects were measured at significant marker loci. Lower fruit weight, higher soluble solids, and lower seed weight were generally associated with RFLP alleles from theL. cheesmanii parent.     

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

 Most cultivars of tomato (Lycopersicon esculentum) are sensitive to salinity during seed germination and at later stages. Genetic resources for salt tolerance have been identified within the related wild species of tomato. The purpose of the present study was to identify quantitative trait loci (QTLs) for salt tolerance during germination in an inbred backcross (BC₁S₁) population of an interspecific cross between a salt-sensitive tomato breeding line (NC84173, maternal and recurrent parent) and a salt-tolerant Lycopersicon pimpinellifolium accession (LA722). Onehundred and nineteen 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 119 BC₁ individuals) were evaluated for germination at an intermediate salt-stress level (150 mM NaCl+15 mM CaCl₂, water potential approximately −850 kPa). Germination was scored visually as radicle protrusion at 8-h intervals for 28 consecutive days. Germination response was analyzed by survival analysis and the time to 25, 50, and 75% germination was determined. In addition, a germination index (GI) was calculated as the weighted mean of the time from imbibition to germination for each family/line. Interval mapping, single-marker analysis and distributional extreme analysis, were used to identify QTLs and the results of all three mapping methods were generally similar. Seven chromosomal locations with significant effects on salt tolerance were identified. The L. pimpinellifolium accession had favorable QTL alleles at six locations. The percentage of phenotypic variation explained (PVE) by individual QTLs ranged from 6.5 to 15.6%. Multilocus analysis indicated that the cumulative action of all significant QTLs accounted for 44.5% of the total phenotypic variance. A total of 12 pairwise epistatic interactions were identified, including four between QTL-linked and QTL-unlinked regions and eight between QTL-unlinked regions. Transgressive phenotypes were observed in the direction of salt sensitivity. The graphical genotyping indicated a high correspondence between the phenotypes of the extreme families and their QTL genotypes. The results indicate that tomato salt tolerance during germination can be improved by marker-assisted selection using interspecific variation. Received: 29 January 1998 / Accepted: 4 June 1998     

fw 2.2:a major QTL controlling fruit weight is common to both red- and green-fruited tomato species

We have shown that a major QTL for fruit weight (fw2.2) maps to the same position on chromosome 2 in the green-fruited wild tomato species, Lycopersicon pennellii and in the red-fruited wild tomato species, L. pimpinellifolium. An introgression line F₂ derived from L. esculentum (tomato) x L. pennellii and a backcross 1 (BC₁) population derived from L. esculentum x L. pimpinellifolium both place fw2.2 near TG91 and TG167 on chromosome 2 of the tomato highdensity linkage map. fw2.2 accounts for 30% and 47% of the total phenotypic variance in the L. pimpinellifolium and L. pennellii populations, respectively, indicating that this is a major QTL controlling fruit weight in both species. Partial dominance (d/a of 0.44) was observed for the L. pennellii allele of fw 2.2 as compared with the L. esculentum allele. A QTL with very similar phenotypic affects and gene action has also been identified and mapped to the same chromosomal region in other wild tomato accessions: L. cheesmanii and L. pimpinellifolium. Together, these data suggest that fw2.2 represents an orthologous QTL (i.e., derived by speciation as opposed to duplication) common to most, if not all, wild tomato species. High-resolution mapping may ultimately lead to the cloning of this key locus controlling fruit development in tomato.     

Three QTLs from Lycopersicon peruvianum confer a high level of resistance to Clavibactermichiganensis ssp. michiganensis

Lycopersicon peruvianum LA2157 originates from 1650 m above sea level and harbours several beneficial traits for cultivated tomatoes such as cold tolerance, nematode resistance and resistance to bacterial canker (Clavibacter michiganensis ssp. michiganensis). In order to identify quantitative trait loci (QTLs) for bacterial canker resistance, a QTL mapping approach was carried out in an F₂ population derived from the interspecific F₁ between Lycopersicon esculentum cv Solentos and L. peruvianum LA2157. Three QTLs for resistance mapped to chromosomes 5, 7 and 9 respectively. The resistance loci were additive and co-dominant with the QTL on chromosome 7 explaining the largest part of the variation for resistance in the F₂ population. The combination of this QTL with either of the other two QTLs conferred a resistance similar to the level in the resistant parent L. peruvianum. Some RFLP markers flanking this QTL on chromosome 7 were converted into SCAR markers allowing efficient marker-assisted selection of plants with high resistance to bacterial canker. Received: 26 February 1999 / Accepted: 12 March 1999     

RFLP mapping of QTLs conferring salt tolerance during the vegetative stage in tomato

 Quantitative trait loci (QTLs) contributing to salt tolerance during the vegetative stage in tomato were investigated using an interspecific backcross between a salt-sensitive Lycopersicon esculentum breeding line (NC84173, maternal and recurrent parent) and a salt-tolerant Lycopersicon pimpinellifolium accession (LA722). One hundred and nineteen BC₁ individuals were genotyped for 151 RFLP markers and a linkage map was constructed. The parental lines and 119 BC₁S₁ families (self-pollinated progeny of the BC₁ individuals) were evaluated for salt tolerance in aerated saline-solution cultures with the salt concentration gradually raised to 700 mM NaCl+70 mM CaCl₂ (equivalent to an electrical conductivity of approximately 64 dS/m and a water potential of approximately −35.2 bars). The two parental lines were distinctly different in salt tolerance: 80% of the LA722 plants versus 25% of the NC84173 plants survived for at least 2 weeks after the final salt concentration was reached. The BC₁S₁ population exhibited a continuous variation, typical of quantitative traits, with the survival rate of the BC₁S₁ families ranging from 9% to 94% with a mean of 51%. Two QTL mapping techniques, interval mapping (using MAPMAKER/QTL) and single-marker analysis (using QGENE), were used to identify QTLs. The results of both methods were similar and five QTLs were identified on chromosomes 1 (two QTLs), 3, 5 and 9. Each QTL accounted for between 5.7% and 17.7%, with the combined effects (of all five QTLs) exceeding 46%, of the total phenotypic variation. All QTLs had the positive QTL alleles from the salt-tolerant parent. Across QTLs, the effects were mainly additive in nature. Digenic epistatic interactions were evident among several QTL-linked and QTL-unlinked markers. The overall results indicate that tomato salt tolerance during the vegetative stage could be improved by marker-assisted selection using interspecific variation. Received: 4 January 1999 / Accepted: 4 January 1999     

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 new QTL for <Emphasis Type="Italic">Fusarium</Emphasis> head blight resistance in the wheat genotype “Wang shui-bai”

Fusarium head blight (FHB) is one of the most devastating wheat diseases, causing both yield loss and quality reduction. To detect quantitative trait loci (QTL) responsible for FHB resistance, plants of the F _2:3 population derived from a ‘Wangshui-bai’ × ‘Sy95-7’ cross were artificially inoculated. Of 396 simple sequence repeats (SSRs), 125 amplified fragment length polymorphisms were used for FHB resistance QTL analysis. Five QTLs for FHB resistance were detected on chromosomes 3B, 6B, 7A, 1B and 2D. The effect of the QTL located on chromosome 3B on phenotypic variation was 31.69%, while that of the QTL found on 2D was the smallest and only accounted for 4.98% of the variation. The resistance alleles originated from ‘Wangshibai’ and association of the QTLs using these SSR markers may facilitate marker-assisted selection to improve FHB resistance in the wheat breeding programs of southwest China.     

Fine mapping of the region on wheat chromosome 7D controlling grain weight

We report the fine mapping of the previously described quantitative trait loci (QTL) for grain weight QTgw.ipk-7D associated with microsatellite marker Xgwm1002-7D by using introgression lines (ILs) carrying introgressions of the synthetic wheat W-7984 in the genetic background of the German winter wheat variety ‘Prinz’. The BC₄F₃ ILs had a 10% increased thousand grain weight compared to the control group and the recurrent parent ‘Prinz’, and 84.7% of the phenotypic variance could be explained by the segregation of marker Xgwm1002-7D, suggesting the presence of a gene modulating grain weight, which was preliminarily designated gw1. It was possible to delimit the QTL QTgw.ipk-7D to the interval Xgwm295–Xgwm1002, which is located in the most telomeric bin 7DS4-0.61-1.00 in the physical map of wheat chromosome arm 7DS. Furthermore, our data suggest the presence of a novel plant height-reducing locus Rht on chromosome arm 7DS of ‘Prinz’. Larger grain and increased plant height may reflect the pleiotropic action of one gene or may be caused by two linked genes. In general, our data support the concept of using nearly isogenic ILs for validating and dissecting QTLs into single Mendelian genes and open the gateway for map-based cloning of a grain-weight QTL in wheat.     

Genetic basis and mapping of the resistance to rice yellow mottle virus. II. Evidence of a complementary epistasis between two QTLs

 The genetic basis of resistance to rice yellow mottle virus (RYMV) was studied in a doubled-haploid (DH) population derived from a cross between the very susceptible indica variety ‘IR64’ and the resistant upland japonica variety Azucena. As a quantitative trait locus (QTL) involved in virus content estimated with an ELISA test has been previously identified on chromosome 12, we performed a wide search for interactions between this QTL and the rest of the genome, and between this QTL and morphological traits segregating in the population. Multiple regression with all identified genetic factors was used to validate the interactions. Significant epistasis accounting for a major part of the total genetic variation was observed. A complementary epistasis between the QTL located on chromosome 12 and a QTL located on chromosome 7 could be the major genetic factor controlling the virus content. Resistance was also affected by a morphology-dependent mechanism since tillering was interfering with the resistance mechanism conditioned by the epistasis between the two QTLs. Marker-assisted backcross breeding was developed to introgress the QTLs of chromosome 7 and chromosome 12 in the susceptible ‘IR64’ genetic background. First results confirmed that if both QTLs do not segregate in a backcross-derived F₂ population, then the QTL of chromosome 12 cannot explain differences in virus content. A near-isogenic line (NIL) approach is currently being developed to confirm the proposed genetic model of resistance to RYMV. Received: 20 April 1990 / Accepted: 30 April 1998     

Salt tolerance in Lycopersicon spp. VII. Pleiotropic action of genes controlling earliness on fruit yield

 The change from vegetative to reproductive development (earliness) in Lycopersicon chesmannii line L2 was delayed for 20 weeks when compared to other Lycopersicon species under greenhouse conditions. The interspecific hybrid of L. chesmannii L2 and L. esculentum E9, a cherry tomato cultivar, also showed this delay in reproductive development. The distribution of this character in the F₂-derived population showed a bimodal shape, plants could be scored easily as “early” or “late” in two nutrient conditions (optimum and high salinity). A QTL with major effects on earliness was detected in salinity, which explained 35.6% of the phenotypic variation. The effect of this QTL greatly diminished under control conditions, indicating differences in the genetic control of earliness between treatments. ACC synthase or phytochrome B2 are the products of candidate genes for such a major QTL. Other QTLs with minor effects, and epistatic interactions, are also involved in earliness under both conditions. A “late” F₂ subpopulation yielded twice as much as an “early” F₂; conversely, “early” plants were taller than “late” plants, regardless of the treatment. QTL analysis, carried out in both subpopulations, showed that yield differences may be explained by chesmannii alleles showing negative additive effects at some QTLs only in the “early” subpopulation. The effect of population subdivision on QTL analysis was investigated by computer simulations to show sample-size or random effects; thus, important pleiotropic or regulatory effects of genes controlling earliness on yield that affect QTL analysis, have been reveiled. Therefore alleles controlling earliness in L. chesmannii have to be taken into account for a more efficient utilization of the genetic resources of this species. Received: 30 June 1998 / Accepted: 31 August 1998     

QTL analysis for capsaicinoid content in Capsicum

Pungency or “heat” found in Capsicum fruit results from the biosynthesis and accumulation of alkaloid compounds known as capsaicinoids in the dissepiment, placental tissue adjacent to the seeds. Pepper cultivars differ with respect to their level of pungency because of quantitative and qualitative variation in capsaicinoid content. We analyzed the segregation of three capsaicinoids: capsaicin, dihydrocapsaicin and nordihydrocapsaicin in an inter-specific cross between a mildly pungent Capsicum annuum ‘NuMex RNaky’ and the wild, highly pungent C. frutescens accession BG2814-6. F₃ families were analyzed in three trials in California and in Israel and a dense molecular map was constructed comprised mostly of loci defined by simple sequence repeat (SSR) markers. Six QTL controlling capsaicinoid content were detected on three chromosomes. One gene from the capsaicinoid biosynthetic pathway, BCAT, and one random fruit EST, 3A2, co-localized with QTL detected in this study on chromosomes 3 and 4. Because one confounding factor in quantitative determination of capsaicinoid is fruit size, fruit weight measurements were taken in two trials. Two QTL controlling fruit weight were detected, however, they did not co-localize with QTL detected for capsaicinoid content. The major contribution to the phenotypic variation of capsaicinoid content (24–42% of the total variation) was attributed to a digenic interaction between a main-effect QTL, cap7.1, and a marker located on chromosome 2 that did not have a main effect on the trait. A second QTL, cap7.2 is likely to correspond to the QTL, cap, identified in a previous study as having pronounced influence on capsaicinoid content.     

QTL analysis of an advanced backcross of Lycopersicon peruvianum to the cultivated tomato and comparisons with QTLs found in other wild species

 A BC₃ population previously developed from a backcross of Lycopersicon peruvianum, a wild relative of tomato, into the cultivated variety L. esculentum was analyzed for QTLs. Approximately 200 BC₄ families were scored for 35 traits in four locations worldwide. One hundred and sixty-six QTLs were detected for 29 of those traits. For more than half of those 29 traits at least 1 QTL was detected for which the presence of the wild allele was associated with an agronomically beneficial effect despite the inferior phenotype of the wild parent. Eight QTLs for fruit weight could be followed through the BC₂, BC₃, and BC₄, generations, supporting the authenticity of these QTLs. Comparisons were made between the QTLs found in this study and those found in studies involving two other wild species; the results showed that while some of these QTLs can be presumed to be allelic, most of the QTLs detected in this study are ones not previously discovered. Received: 9 April 1997 / Accepted: 20 May 1997     

Mapping of QTLs for lycopene and other fruit traits in a Lycopersicon esculentum × L. pimpinellifolium cross and comparison of QTLs across tomato species

Quantitative trait loci (QTLs) for several fruit traits in tomato were mapped and characterized in a backcross population of an interspecific cross between Lycopersicon esculentum fresh-marker breeding line NC84173 and L. pimpinellifolium accession LA722. A molecular linkage map of this cross that was previously constructed based on 119 BC1 individuals and 151 RFLP markers was used for the QTL mapping. The parental lines and 119 BC1S1 families (self-pollinated progeny of BC1 individuals) were grown under field conditions at two locations, Rock Spring, PA, and Davis, CA, and fruits were scored for weight (FW), polar (PD) and equatorial diameters (ED), shape (FS), total soluble solids content (SSC), pH and lycopene content (LYC). For each trait, between 4 and 10 QTLs were identified with individual effects ranging between 4.4% and 32.9% and multilocus QTL effects ranging between 39% and 75% of the total phenotypic variation. Most QTL effects were predictable from the parental phenotypes, and several QTLs were identified that affected more than one trait. A few pairwise epistatic interactions were detected between QTL-linked and QTL-unlinked markers. Despite great differences between PA and CA growing conditions, the majority of FW QTLs (78%) and SSC QTLs (75%) in the two locations shared similar genomic positions. Almost all of the QTLs that were identified in the present study for FW and SSC were previously identified in six other studies that used different interspecific crosses of tomato; this indicates conservation of QTLs for fruit traits across tomato species. Altogether, the seven studies identified at least 28 QTLs for FW and 32 QTLs for SSC on the 12 tomato chromosomes. However, for each trait a few major QTLs were commonly identified in 4 or more studies; such ‘popular’ QTLs should be of considerable interest for breeding purposes as well as basic research towards cloning of QTLs. Notably, a majority of QTLs for increased SSC also contributed to decreased fruit size. Therefore, to significantly increase SSC of the cultivated tomato, some compromise in fruit size may be unavoidable. This revised version was published online in June 2006 with corrections to the Cover Date.     

Quantitative trait loci for yield components in oil palm (Elaeis guineensis Jacq.)

The development of an oil palm RFLP marker map has enabled marker-based QTL mapping studies to be undertaken. Information from 153 RFLP markers was used in combination with phenotypic data from an F₂ population to estimate the position and effects of quantitative trait loci (QTLs) for traits including yield of fruit and its components and measures of vegetative growth. The mapping population consisted of 84 palms segregating for the major gene influencing shell thickness. Marker data were analysed to produce a linkage map consisting of 22 linkage groups. The QTL mapping analysis was carried out by interval mapping and single-marker analysis for the unlinked markers; significance thresholds were generated by permutation. Using both single-marker and interval-mapping analysis significant marker associated QTL effects were found for 11 of the 13 traits analysed. The results of interval-mapping analysis of fruit weight, petiole cross section and rachis length, and ratios of shell:fruit, mesocarp:fruit and kernel:fruit indicated significant (P<0.05) QTLs at the genome-wide threshold. The putative QTLs were associated with between 8.2% and 44.0% of the phenotypic variation, with an average of 27% for the single-marker analysis and 19% for the interval-mapping analysis. The higher percentage of phenotypic variation explained in the single-marker analysis, when compared to the interval-mapping analysis, is likely to be due to the lower stringency associated with the single-marker analysis. Large dominance deviations were associated with a sizeable proportion of the putative QTLs. The ultimate objective of mapping QTLs in commercial populations is to utilise novel breeding strategies such as marker-assisted selection (MAS). The potential impact of MAS in oil palm breeding programmes is discussed. Received: 26 June 2000 / Accepted: 24 October 2000