Advanced backcross QTL analysis in tomato. I. Identification of QTLs for traits of agronomic importance from Lycopersicon hirsutum

 Advanced backcross QTL (AB-QTL) analysis is a new strategy for studying the effect of unadapted alleles on the agronomic performance of elite cultivated lines. In this paper we report results from the application of the AB-QTL strategy to cultivated tomato using the wild species Lycopersicon hirsutum LA1777 as the donor parent. RFLP genomic fingerprints were determined for 315 BC₂ plants and phenotypic data were collected for 19 agronomic traits from approximately 200 derived BC₃ lines which were grown in replicated field trials in three locations worldwide. Between 1 and 12 significant QTLs were identified for each of the 19 traits evaluated, with a total of 121 QTLs identified for all traits. For 25 of the QTLs (20%) corresponding to 12 traits (60%), the L. hirsutum allele was associated with an improvement of the trait from a horticultural perspective, despite the fact that L. hirsutum is overall phenotypically inferior to the elite parent. For example, L. hirsutum has fruit that remains green when ripe (lack of red pigment) yet alleles were found in this species that significantly increase red color when transferred into cultivated tomatoes. Wild alleles were also associated with increases in total yield and soluble solids (up to 15%) and brix×red yield (up to 41%). These results support the idea that one cannot predict the genetic potential of exotic germplasm based on phenotype alone and that marker-based methods, such as the AB-QTL strategy, should be applied to fully exploit exotic germplasm. Received: 27 October 1997 / Accepted: 25 November 1997     

Marker-assisted introgression of blackmold resistance QTL alleles from wild Lycopersicon cheesmanii to cultivated tomato (L. esculentum) and evaluation of QTL phenotypic effects

Blackmold, caused by the fungus Alternaria alternata, is a major ripe fruit disease of processing tomatoes. Previously, we found blackmold resistance in a wild tomato (Lycopersicon cheesmanii) and quantitative trait loci (QTL) for resistance were mapped in an interspecific population. Five QTLs were selected for introgression from L. cheesmanii into cultivated tomato using marker-assisted selection (MAS). Restriction fragment length polymorphism and PCR-based markers flanking, and within, the chromosomal regions containing QTLs were used for MAS during backcross and selfing generations. BC₁ plants heterozygous at the QTLs, and subsequent BC₁S₁ and BC₁S₂ lines possessing different homozygous combinations of alleles at the target QTLs, were identified using DNA markers. Field experiments were conducted in 1998 (with 80 marker-selected BC₁S₂ lines) and 1999 (with 151 marker-selected BC₁S₂ and BC₁S₃ lines) at three California locations. Blackmold resistance was assessed during both years, and horticultural traits were evaluated in 1999. The BC₁S₂ and BC₁S₃ lines containing L. cheesmanii alleles at the QTLs were associated with a large genetic variance for resistance to blackmold and moderate heritability, suggesting that significant genetic gain may be achieved by selection in this genetic material. L. cheesmanii alleles at three of the five introgressed QTLs showed a significant, positive effect on blackmold resistance. A QTL on chromosome 2 had the largest positive effect on blackmold resistance, alone and in combination with other QTLs, and was also associated with earliness, a positive horticultural trait. The other four QTLs were associated primarily with negative horticultural traits. Fine mapping QTLs using near isogenic lines could help determine if such trait associations are due to linkage drag or pleiotropy.     

Molecular marker-assisted introgression of the wild Solanum commersonii genome into the cultivated S. tuberosum gene pool

A breeding scheme involving ploidy and EBN manipulations was set up to overcome the interspecific barriers existing between the cultivated Solanum tuberosum and the wild species S. commersonii. Three backcross generations were obtained that were analyzed by means of molecular markers in order to verify the occurrence of recombination between homeologous chromosomes, the extent of the wild genome carried in each backcross, and the efficiency of introgressing useful genes. Twenty commersonii-specific RFLPs provided evidence for recombination on 5 out of 12 chromoso-mes; for the others no more than 1 commersonii-specific marker was found. Thirty-four commersonii-specific RAPDs and 61 commersonii-specific AFLPs were used to estimate the wild genome content in the BC₁, BC₂, and BC₃ generations. The mean value of commersonii-specific markers was 93% and 91% in the BC₁, 74% and 76% in the BC₂, and 31% and 26% in the BC₃ using RAPDs or AFLPs, respectively. Efficiency of the breeding scheme was evaluated by monitoring across these progenies the introgression of S. commersonii resistance to tuber soft rot caused by Erwinia carotovora. Eleven and five resistant genotypes were found among BC₂ and BC₃ hybrids, respectively. The same progenies were also evaluated for chromosome number and tuber traits. For all analyzed traits except stolon length, all BC₂ and BC₃ hybrids resembled the tuberosum type. In order to choose the best genotypes to obtain the following backcrosses, we performed, in each generation, a negative molecular-assisted selection against the wild genome combined with selection for resistance to Erwinia spp. and other traits. Received: 3 April 2000 / Accepted: 31 August 2000     

Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the<Emphasis Type="Italic"> Oryza sativa</Emphasis> variety IR64 and the wild relative<Emphasis Type="Italic"> O. rufipogon</Emphasis>

A BC₂F₂ population developed from an interspecific cross between Oryza sativa (cv IR64) and O. rufipogon (IRGC 105491) was used in an advanced backcross QTL analysis to identify and introduce agronomically useful genes from this wild relative into the cultivated gene pool. The objectives of this study were: (1) to identify putative yield and yield component QTLs that can be useful to improve the elite cultivar IR64; (2) to compare the QTLs within this study with previously reported QTLs in rice as the basis for identifying QTLs that are stable across different environments and genetic backgrounds; and (3) to compare the identified QTLs with previously reported QTLs from maize to examine the degree of QTL conservation across the grass family. Two hundred eighty-five families were evaluated in two field environments in Indonesia, with two replications each, for 12 agronomic traits. A total of 165 markers consisting of 131 SSRs and 34 RFLPs were used to construct the genetic linkage map. By employing interval mapping and composite interval mapping, 42 QTLs were identified. Despite its inferior performance, 33% of the QTL alleles originating from O. rufipogon had a beneficial effect for yield and yield components in the IR64 background. Twenty-two QTLs (53.4%) were located in similar regions as previously reported rice QTLs, suggesting the existence of stable QTLs across genetic backgrounds and environments. Twenty QTLs (47.6%) were exclusively detected in this study, uncovering potentially novel alleles from the wild, some of which might improve the performance of the tropical indica variety IR64. Additionally, several QTLs for plant height, grain weight, and flowering time detected in this study corresponded to homeologous regions in maize containing previously detected maize QTLs for these traits.     

AB-QTL analysis in winter wheat: I. Synthetic hexaploid wheat (<Emphasis Type="Italic">T. turgidum</Emphasis> ssp. <Emphasis Type="Italic">dicoccoides </Emphasis> × <Emphasis Type="Italic">T. tauschii</Emphasis>) as a source of favourable alleles for milling and baking quality traits

The advanced backcross QTL (AB-QTL) strategy was utilised to locate quantitative trait loci (QTLs) for baking quality traits in two BC₂F₃ populations of winter wheat. The backcrosses are derived from two German winter wheat cultivars, Batis and Zentos, and two synthetic, hexaploid wheat accessions, Syn022 and Syn086. The synthetics originate from hybridisations of wild emmer (T. turgidum spp. dicoccoides) and T. tauschii, rather than from durum wheat and T. tauschii and thus allowed for the first time to test for exotic QTL effects on wheat genomes A and B in addition to genome D. The investigated quality traits comprised hectolitre weight, grain hardness, flour yield Type 550, falling number, grain protein content, sedimentation volume and baking volume. One hundred and forty-nine SSR markers were applied to genotype a total of 400 BC₂F₃ lines. For QTL detection, a mixed-model ANOVA was conducted, including the effects DNA marker, BC₂F₃ line, environment and marker × environment interaction. Overall 38 QTLs significant for a marker main effect were detected. The exotic allele improved trait performance at 14 QTLs (36.8%), while the elite genotype contributed the favourable effect at 24 QTLs (63.2%). The favourable exotic alleles were mainly associated with grain protein content, though the greatest improvement of trait performance due to the exotic alleles was achieved for the traits falling number and sedimentation volume. At the QTL on chromosome 4B the exotic allele increased the falling number by 19.6% and at the QTL on chromosome 6D the exotic allele led to an increase of the sedimentation volume by 21.7%. The results indicate that synthetic wheat derived from wild emmer × T. tauschii carries favourable QTL alleles for baking quality traits, which might be useful for breeding improved wheat varieties by marker-assisted selection.     

Identification of QTLs affecting traits of agronomic importance in a recombinant inbred population derived from a subspecific rice cross

To detect QTLs controlling traits of agronomic importance in rice, two elite homozygous lines 9024 and LH422, which represent the indica and japonica subspecies of rice (Oryza sativa), were crossed. Subsequently a modified single-seed-descent procedure was employed to produce 194 recombinant inbred lines (F₈). The 194 lines were genotyped at 141 RFLP marker loci and evaluated in a field trial for 13 quantitative traits including grain yield. Transgressive segregants were observed for all traits examined. The number of significant QTLs (LOD 2.0) detected affecting each trait ranged from one to six. The percentage of phenotypic variance explained by each QTL ranged from 5.1% to 73.7%. For those traits for which two or more QTLs were detected, increases in the traits were conditioned by indica alleles at some QTLs Japonica alleles at others. No significant evidence was found for epistasis between markers associated with QTLs and all the other markers. Pleitropic effects of single QTLs on different traits are suggested by the observation of clustering of QTLs. No QTL for traits was found to map to the vicinity of major gene loci governing the same traits qualitatively. Evidence for putative orthologous QTLs across rice, maize, oat, and barley is discussed.     

Identification and Validation of Quantitative Trait Loci for Agronomic Traits in Advanced Backcross Breeding Lines Derived from Oryza rufipogon × Oryza sativa Cultivar MR219

A backcross breeding strategy was used to identify quantitative trait loci (QTLs) associated with 14 traits in a BC₂F₂ population derived from a cross between MR219, an indica rice cultivar and an accession of Oryza rufipogon (IRGC 105491). A total of 261 lines were genotyped with 96 microsatellite markers and evaluated for plant morphology, yield components and growth period. The genetic linkage map generated for this population with an average interval size of 16.2?cM, spanning 1,553.4?cM (Kosambi) of the rice genome. Thirty-eight QTLs were identified with composite interval mapping (CIM), whereas simple interval mapping (SIM) resulted in 47 QTLs (LOD >3.0). The O. rufipogon allele was favourable for 59% of QTLs detected through CIM. Of 261 BC₂F₂ families, 26 advanced backcross breeding lines (BC₂F₅) were used for QTL validation. These lines were selected on the basis of the yield traits potentiality in BC₂F₃ and BC₂F₄ generations. The field trial was conducted at three different locations in Malaysia using randomized complete block design with three replications. Trait based marker analysis was done for QTL determination. Twenty-five QTLs were detected in BC₂F₅ generation whereas 29 QTLs were detected in BC₂F₂ generation of the same population. Two QTLs (qPL-1 and qSPL-7) were not considered for validation due to their low R ² values and two QTLs (qPSS-3-2 and qGW-3-2) were not detected in the BC₂F₅ population. Fifteen QTLs showed the beneficial effect to enhance the trait value of the breeding lines. QTL validation aided to select the promising lines for further utilization.     

Advanced back-cross QTL analysis of tomato. II. Evaluation of near-isogenic lines carrying single-donor introgressions for desirable wild QTL-alleles derived from Lycopersicon hirsutum and L. pimpinellifolium

 Improved-processing tomato lines were produced by the molecular breeding strategy of advanced backcross QTL (AB-QTL) analysis. These near-isogenic lines (NILs) contained unique introgressions of wild alleles originating from two donor wild species, Lycopersicon hirsutum (LA1777) and L. pimpinellifolium (LA1589). Wild alleles targeted for trait improvement were selected on the basis of previously published replicated QTL data obtained from advanced backcross populations for a battery of important agronomic traits. Twenty three NILs were developed for 15 genomic regions which were predicted to contain 25 quantitative trait factors for the improvement of seven agronomic traits: total yield, red yield, soluble solids, brix×red yield, viscosity, fruit color, and fruit firmness. An evaluation of the agronomic performance of the NILs in five locations worldwide revealed that 22 out of the 25 (88%) quantitative factors showed the phenotypic improvement predicted by QTL analysis of the BC₃ populations, as NILs in at least one location. Per-location gains over the elite control ranged from 9% to 59% for brix×red yield; 14% to 33% for fruit color; 17% to 34% for fruit firmness; 6% to 22% for soluble-solids content; 7% to 22% for viscosity; 15% to 48% for red yield, and 20% to 28% for total yield. The inheritance of QTLs, the implementation of the AB-QTL methodology for characterizing unadapted germplasm and the applicability of this method to other crops are discussed. Theor Appl Genet (1998) 97 : 170–180 Received: 27 October 1997 / Accepted: 25 November 1997     

Quantitative trait loci for yield and yield components in an Oryza sativa×Oryza rufipogon BC2F2 population evaluated in an upland environment

An advanced backcross breeding strategy was used to identify quantitative trait loci (QTLs) associated with eight agronomic traits in a BC₂F₂ population derived from an interspecific cross between Caiapo, an upland Oryza sativa subsp. japonica rice variety from Brazil, and an accession of Oryza rufipogon from Malaysia. Caiapo is one of the most-widely grown dryland cultivars in Latin America and may be planted as a monoculture or in a multicropping system with pastures. The objectives of this study were: (1) to determine whether trait-enhancing QTLs from O. rufipogon would be detected in 274 BC₂F₂ families grown under the drought-prone, acid soil conditions to which Caiapo was adapted, (2) to compare the performance with and without pasture competition, and (3) to compare putative QTL-containing regions identified in this study with those previously reported for populations adapted to irrigated, low-land conditions. Based on analyses of 125 SSLP and RFLP markers distributed throughout the genome and using single-point, interval, and composite interval mapping, two putative O. rufipogon derived QTLs were detected for yield, 13 for yield components, four for maturity and six for plant height.We conclude that advanced backcross QTL analysis offers a useful germplasm enhancement strategy for the genetic improvement of cultivars adapted to stress-prone environments. Although the phenotypic performance of the wild germplasm would not suggest its value as a breeding parent, it is noteworthy that 56% of the trait-enhancing QTLs identified in this study were derived from O. rufipogon. This figure is similar to the 51% of favorable QTLs derived from the same parent in crosses with a high-yielding hybrid rice cultivar evaluated under irrigated conditions in a previous study. In conclusion, parallel studies in rice using AB-QTL analysis provide increasing evidence that certain regions of the rice genome are likely to harbor genes of interest for plant improvement in multiple environments. Received: 3 September 1999 / Accepted: 16 May 2000     

Identification and verification of QTLs for agronomic traits using wild barley introgression lines

A set of 39 wild barley introgression lines (hereafter abbreviated with S42ILs) was subjected to a QTL study to verify genetic effects for agronomic traits, previously detected in the BC₂DH population S42 (von Korff et al. 2006 in Theor Appl Genet 112:1221–1231) and, in addition, to identify new QTLs and favorable wild barley alleles. Each line within the S42IL set contains a single marker-defined chromosomal introgression from wild barley (Hordeum vulgare ssp. spontaneum), whereas the remaining part of the genome is exclusively derived from elite spring barley (H. vulgare ssp. vulgare). Agronomic field data of the S42ILs were collected for seven traits from three different environments during the 2007 growing season. For detection of putative QTLs, a two-factorial mixed model ANOVA and, subsequently, a Dunnett test with the recurrent parent as a control were conducted. The presence of a QTL effect on a wild barley introgression was accepted, if the trait value of a particular S42IL was significantly (P < 0.05) different from the control, either across all environments and/or in a particular environment. A total of 47 QTLs were localized in the S42IL set, among which 39 QTLs were significant across all tested environments. For 19 QTLs (40.4%), the wild barley introgression was associated with a favorable effect on trait performance. Von Korff et al. (2006 in Theor Appl Genet 112:1221–1231) mapped altogether 44 QTLs for six agronomic traits to genomic regions, which are represented by wild barley introgressions of the S42IL set. Here, 18 QTLs (40.9%) revealed a favorable wild barley effect on the trait performance. By means of the S42ILs, 20 out of the 44 QTLs (45.5%) and ten out of the 18 favorable effects (55.6%) were verified. Most QTL effects were confirmed for the traits days until heading and plant height. For the six corresponding traits, a total of 17 new QTLs were identified, where at six QTLs (35.3%) the exotic introgression caused an improved trait performance. In addition, eight QTLs for the newly studied trait grains per ear were detected. Here, no QTL from wild barley exhibited a favorable effect. The introgression line S42IL-107, which carries an introgression on chromosome 2H, 17–42 cM is an example for S42ILs carrying several QTL effects simultaneously. This line exhibited improved performance across all tested environments for the traits days until heading, plant height and thousand grain weight. The line can be directly used to transfer valuable Hsp alleles into modern elite cultivars, and, thus, for breeding of improved varieties.     

Plastid genome characterisation in Brassica and Brassicaceae using a new set of nine SSRs

The objective of the present study was to identify favourable exotic Quantitative Trait Locus (QTL) alleles for the improvement of agronomic traits in the BC₂DH population S42 derived from a cross between the spring barley cultivar Scarlett and the wild barley accession ISR42-8 (Hordeum vulgare ssp. spontaneum). QTLs were detected as a marker main effect and/or a marker × environment interaction effect (M × E) in a three-factorial ANOVA. Using field data of up to eight environments and genotype data of 98 SSR loci, we detected 86 QTLs for nine agronomic traits. At 60 QTLs the marker main effect, at five QTLs the M × E interaction effect, and at 21 QTLs both the effects were significant. The majority of the M × E interaction effects were due to changes in magnitude and are, therefore, still valuable for marker assisted selection across environments. The exotic alleles improved performance in 31 (36.0%) of 86 QTLs detected for agronomic traits. The exotic alleles had favourable effects on all analysed quantitative traits. These favourable exotic alleles were detected, in particular on the short arm of chromosome 2H and the long arm of chromosome 4H. The exotic allele on 4HL, for example, improved yield by 7.1%. Furthermore, the presence of the exotic allele on 2HS increased the yield component traits ears per m² and thousand grain weight by 16.4% and 3.2%, respectively. The present study, hence, demonstrated that wild barley does harbour valuable alleles, which can enrich the genetic basis of cultivated barley and improve quantitative agronomic traits.     

Advanced backcross QTL analysis of tomato. II. Evaluation of near-isogenic lines carrying single-donor introgressions for desirable wild QTL-alleles derived from Lycopersicon hirsutum and L. pimpinellifolium

 Improved-processing tomato lines were produced by the molecular breeding strategy of advanced backcross QTL (AB-QTL) analysis. These near-isogenic lines (NILs) contained unique introgressions of wild alleles originating from two donor wild species, Lycopersicon hirsutum (LA1777) and L. pimpinellifolium (LA1589). Wild alleles targeted for trait improvement were selected on the basis of previously published replicated QTL data obtained from advanced backcross populations for a battery of important agronomic traits. Twenty three NILs were developed for 15 genomic regions which were predicted to contain 25 quantitative trait factors for the improvement of seven agronomic traits: total yield, red yield, soluble solids, brix×red yield, viscosity, fruit color, and fruit firmness. An evaluation of the agronomic performance of the NILs in five locations worldwide revealed that 22 out of the 25 (88%) quantitative factors showed the phenotypic improvement predicted by QTL analysis of the BC₃ populations, as NILs in at least one location. Per-location gains over the elite control ranged from 9% to 59% for brix×red yield; 14% to 33% for fruit color; 17% to 34% for fruit firmness; 6% to 22% for soluble-solids content; 7% to 22% for viscosity; 15% to 48% for red yield, and 20% to 28% for total yield. The inheritance of QTLs, the implementation of the AB-QTL methodology for characterizing unadapted germplasm and the applicability of this method to other crops are discussed. Received: 27 October 1997 / Accepted: 25 November 1997     

Genetic analysis of vertical root pulling resistance (VRPR) in maize using two genetic populations

Root traits are important in improving nutrient and water use efficiency. Vertical root pulling resistance (VRPR) has been shown to be closely related to root system characteristics in maize (Zea mays L.). In the present study, two genetic populations derived from the same parents, one containing 218 recombinant inbred lines (RILs) and the other containing 187 advanced backcross BC₄F₃ lines, were genotyped using 184 SSR markers and evaluated for VRPR, grain yield (GY), stover yield (SY), and nitrogen uptake (N_up) under field conditions over 2 years. Our aims were (1) to locate QTLs associated with VRPR, SY, GY, and N_up, (2) to determine whether QTL detection is consistent between the BC₄F₃ and RIL populations, and (3) to identify backcross lines harboring favorable VRPR QTLs for use in future breeding programs. Using composite interval mapping (CIM), 12 and 17 QTLs were detected in BC₄F₃ and RIL populations, respectively. An important QTL region in bin 6.02 within the interval umc1006-umc1257 was found to control VRPR, SY, and N_up in both populations. These favorable alleles were contributed by the large-rooted parent Ye478. A significant positive correlation was detected between VRPR, SY, and N_up, but not between VRPR and GY. Backcross lines harboring VRPR QTLs could be useful germplasm for developing near isogenic lines (NILs) and for map-based cloning of genes controlling root growth.     

Advanced backcross QTL analysis of a Lycopersicon esculentum ×Lycopersicon parviflorum cross

Lycopersicon parviflorum is a sexually compatible, wild tomato species which has been largely unutilized in tomato breeding. The Advanced Backcross QTL (AB-QTL) strategy was used to explore this genome for QTLs affecting traits of agronomic importance in an interspecific cross between a tomato elite processing inbred, Lycopersicon esculentum E6203, and the wild species L. parviflorum (LA2133). A total of 170 BC2 plants were genotyped by means of 133 genetic markers (131 RFLPs; one PCR-based marker, I-2, and one morphological marker, u, uniform ripening). Approximately 170 BC3 families were grown in replicated field trials, in California, Spain and Israel, and were scored for 30 horticultural traits. Significant putative QTLs were identified for all traits, for a total of 199 QTLs, ranging from 1 to 19 QTLs detected for each trait. For 19 (70%) traits (excluding traits for which effects of either direction are not necessarily favourable or unfavourable) at least one QTL was identified for which the L. parviflorum allele was associated with an agronomically favourable effect, despite the overall inferior phenotype of the wild species. Received: 14 September 1999 / Accepted: 7 October 1999     

Advanced backcross QTL analysis in progenies derived from a cross between a German elite winter wheat variety and a synthetic wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis>L.)

We report here the second advanced backcross quantitative trait locus (AB-QTL) analysis carried out in winter wheat. Seven agronomic traits were studied in a BC₂F₁population derived from a cross between the German winter wheat variety Flair and the synthetic wheat line XX86 developed in Japan. We selected 111 BC₂F₁ lines and genotyped these with 197 microsatellite markers. Field data for seven agronomic traits were collected from corresponding BC₂F₃ families that were grown at up to six locations in Germany. QTL analyses for yield and yield components were performed using single-marker regression and interval mapping. A total of 57 putative QTLs derived from XX86 were detected, of which 24 (42.1%) were found to have a positive effect from the synthetic wheat XX86. These favourable QTLs were mainly associated with thousand-grain weight and grain weight per ear. Many QTLs for correlated traits were mapped in similar chromosomal regions. The AB-QTL data obtained in the present study are discussed and compared with results from previous QTL analyses.     

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     

Identification of Quantitative Trait Loci Controlling Drought Tolerance at Seedling Stage in Chinese Dongxiang Common Wild Rice (Oryza rufipogon Griff.)

Common wild rice (Oryza rufipogon Griff.) is the ancestor of cultivated rice (O. sativa L.), which has a greater genetic diversity and important traits that remain to be employed in cultivated rice. In this study, a set of introgression lines (BC₄F₅ and/or BC₄F₆) carrying various introgressed segments from common wild rice, collected from Dongxiang county, Jiangxi Province, China, in the background of an Indica (O. sativa L. ssp. indica) cultivar, Guichao 2, was used. A total of 12 drought-related quantitative trait loci (QTL) were identified by investigating drought tolerance of introgression lines under 30% PEG treatment at the young seedlings stage. Of these QTLs, the alleles of 4 QTLs on chromosome 2, 6 and 12 from Dongxiang common wild rice were responsible for increased drought tolerance of the introgression lines. In particular, a QTL qSDT12-2, near RM17 on chromosome 12, was consistently detected in different replications, and expressed stably under PEG stress throughout the study. It was also found that the QTLs located on different chromosomes might express at different stages.     

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     

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.     

QTL-based analysis of leaf senescence in an indica/japonica hybrid in rice (Oryza sativa L.)

In order to identify quantitative trait loci (QTLs) for leaf senescence and related traits in rice (Oryza sativa L.), we developed two backcross populations, indica/japonica// japonica and indica/japonica//indica, using IR36 as the indica parent and Nekken-2 as the japonica parent. The QTLs were mapped using a set of simple sequence-repeat markers (SSRs) in the BC₁F₁ population. Senescence was characterized in these plants by measuring the leaf chlorophyll content 25 days after flowering (DAF), the reduction in chlorophyll content (the difference between the chlorophyll content at flowering and at 25 DAF), and the number of late-discoloring leaves per panicle at 25 DAF in five plants from each BC₁F₂ line. These plants were moved into a temperature-controlled growth cabinet at the time of flowering and allowed to mature under identical conditions. Eleven QTLs were detected in the two populations. The major of QTLs for senescence were found on the short arm of chromosome 6 and on the long arm of chromosome 9. Of these, one QTL on chromosome 6 and two on chromosome 9 were verified by confirming the effects of the genotypes on the phenotypes of the BC₁F₃ lines. The japonica parent was found to contribute to late senescence at all but one QTL. Based on a comparison of the effects of heterozygotes and homozygotes on the phenotypic values of each QTL genotype, we concluded that the differential senescence observed in the indica-japonica hybrid was not due to over-dominance; rather, it was the result of partial-dominance genes that were donated from either of the parents.