Salt tolerance in Lycopersicon species VI. Genotype-by-salinity interaction in quantitative trait loci detection: constitutive and response QTLs

 A study of genotype-by-salinity interaction was carried out to compare the behavior of quantitative trait loci (QTLs) in two F₂ populations derived from crosses between the cherry tomato, Lycopersicon esculentum Mill. var. cerasiforme, and two wild relatives Lycopersicon pimpinellifolium (Jusl.) Mill. and Lycopersicon chesmannii f. minor (Hook. f.) Mull., grown at two environmental conditions (optimum and high salinity). QTLs for earliness and fruit yield could be classified into four groups: “response-sensitive”, those detected only under control conditions or whose contribution significantly decreased in salinity; “response-tolerant”, detected only in salinity or in which the direction of their additive effects changed; “constitutive”, detected in both growing conditions; and “altered” QTLs, those where the degree of dominance changed according to the presence or absence of salt. Epistatic interactions were also influenced by the salt treatment. This differential allele effect at some (non-constitutive) QTLs induced by salt stress will make selection under an “optimum environment” unfruitful for the “response-tolerant” QTLs. Similarly, selection under salinity will ignore “response-sensitive” QTLs. Given that salinity is highly variable in the field, marker-assisted selection should take into account not only the “response-tolerant” but also the “response-sensitive” QTLs although there might be cases where selection in some QTLs for both conditions is not feasible. Comparing both populations, very few QTLs showed the same behavior. Received: 5 August 1996 / Accepted: 25 October 1996     

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     

Study of tree architecture of apple (<Emphasis Type="Italic">Malus</Emphasis> × <Emphasis Type="Italic">domestica</Emphasis> Borkh.) by QTL analysis of growth traits

Apple tree architecture is naturally very diverse, but for fruit production, certain tree habits are more desirable than others. Here we describe the results of a QTL analysis performed to study the genetic control of growth traits in apple. This was carried out on the progeny of a cross between two apple cultivars of contrasting tree architectures. “Telamon” has a columnar tree form and “Braeburn” has a more standard, “normal” growth habit. The growth traits were measured on the F ₁ seedlings of the Telamon × Braeburn population for two consecutive years of growth on own roots and for the first year of growth on M9 rootstock. QTL analysis was carried out using either the Kruskal–Wallis method or the Multiple QTL Method. For all but one growth characteristic, significant QTLs were detected. A major cluster of QTLs was located in the Co gene region of “Telamon”, confirming the major influence of the Co gene on tree architecture, although this influence changed as the plant material aged and was generally more pronounced for rootstock-grown plants. Additional QTL results suggest the occurrence of genes with pleiotropic effects on tree architecture. The observed QTL instability over different years and for different root systems indicates that the genetic control of tree architecture is largely influenced by environmental factors and probably changes as the tree matures. Finally, a major influence of the root system on all the traits determining tree architecture was clearly demonstrated.     

The QTL analysis on maternal and endosperm genome and their environmental interactions for characters of cooking quality in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L<Emphasis Type="Italic">.</Emphasis>)

Investigations to identify quantitative trait loci (QTLs) governing cooking quality traits including amylose content, gel consistency and gelatinization temperature (expressed by the alkali spread value) were conducted using a set of 241 RIL populations derived from an elite hybrid cross of “Zhenshan 97” × “Minghui 63” and their reciprocal backcrosses BC₁F₁ and BC₂F₁ populations in two environments. QTLs and QTL × environment interactions were analyzed by using the genetic model with endosperm and maternal effects and environmental interaction effects on quantitative traits of seed in cereal crops. The results suggested that a total of seven QTLs were associated with cooking quality of rice, which were subsequently mapped to chromosomes 1, 4 and 6. Six of these QTLs were also found to have environmental interaction effects.     

Quantitative trait loci controlling vernalisation requirement, heading time and number of panicles in meadow fescue (Festuca pratensis Huds.)

The “BF14/16×HF2/7” mapping population of meadow fescue (Festuca pratensis Huds.) was characterised for number of panicles produced by non-vernalised plants in the field, vernalisation requirement (number of weeks at 6°C and 8 h photoperiod), as well as days to heading, number of panicles and proportion of shoots heading after a 12 weeks vernalisation treatment. Quantitative trait loci (QTLs) were identified and compared to QTLs and genes related to the induction of flowering in cereals and grasses. A region on chromosome 1F affected days to heading and the proportion of shoots heading. Chromosome 4F appeared to have several genes with a strong effect on vernalisation requirement. The strongest effects were located in the proximal end of 4F and may correspond to the earliness per se (eps) QTL eps6L.2 in barley and a heading time QTL in perennial ryegrass. A part of the meadow fescue orthologue of VRN1 was sequenced and mapped to another region of 4F that also had a strong effect on vernalisation requirement. The proximal end of chromosome 5F had QTLs for days to heading and proportion of heading shoots. Syntenic regions in wheat and barley contain eps-loci. A QTL for number of panicles in the field and a QTL for proportion of heading shoots were present on chromosome 6. A region on 7F affected the variation in number of panicles among plants without a vernalisation requirement, and is syntenic to regions in perennial ryegrass, barley and rice containing orthologues of Arabidopsis thaliana CO.     

QTL Mapping for Frond Length and Width in Laminaria japonica Aresch (Laminarales, Phaeophyta) Using AFLP and SSR Markers

In Laminaria japonica Aresch breeding practice, two quantitative traits, frond length (FL) and frond width (FW), are the most important phenotypic selection index. In order to increase the breeding efficiency by integrating phenotypic selection and marker-assisted selection, the first set of QTL controlling the two traits were determined in F₂ family using amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers. Two prominent L. japonicas inbred lines, one with “broad and thin blade” characteristics and another with “long and narrow blade” characteristics, were applied in the hybridization to yield the F₂ mapping population with 92 individuals. A total of 287 AFLP markers and 11 SSR markers were used to construct a L. japonica genetic map. The yielded map was consisted of 28 linkage groups (LG) named LG1 to LG28, spanning 1,811.1 cM with an average interval of 6.7 cM and covering the 82.8% of the estimated genome 2,186.7 cM. While three genome-wide significant QTL were detected on LG1 (two QTL) and LG4 for “FL,” explaining in total 42.36% of the phenotypic variance, two QTL were identified on LG3 and LG5 for the trait “FW,” accounting for the total of 36.39% of the phenotypic variance. The gene action of these QTL was additive and partially dominant. The yielded linkage map and the detected QTL can provide a tool for further genetic analysis of two traits and be potential for maker-assisted selection in L. japonica breeding.     

Fruit size QTL analysis of an F<Subscript>1</Subscript> population derived from a cross between a domesticated sweet cherry cultivar and a wild forest sweet cherry

Maximizing fruit size is critical for profitable sweet cherry (Prunus avium L.) production. Yet, despite its importance, little is known about the genetic control of fruit size. The objective of this study was to identify quantitative trait loci (QTLs) for fruit size and two essential components of fruit size, mesocarp cell number and size. This study utilized a double pseudo-testcross population derived from reciprocal crosses between a sweet cherry cultivar with ~8 g fruit, “Emperor Francis” (EF), and a wild forest sweet cherry selection with ~2 g fruit, “New York 54” (NY). A total of 190 F₁ progeny previously utilized for the construction of the linkage maps were evaluated in 2006 and 2007 for fruit weight, length, and diameter; mesocarp cell number and length; and pit length and diameter. In 2008, a subset of this population was again evaluated for fruit weight. Correlation analysis revealed that the three fruit size traits were highly correlated with each other, and mesocarp cell number, not cell length, was correlated with fruit size. Three QTLs were identified for each fruit size trait, and one QTL was identified for mesocarp cell number. Fruit size QTLs were found on linkage group 2 on the EF map (EF 2) and linkage groups 2 and 6 on the NY map (NY 2 and NY 6). On EF 2, the cell number QTL clustered with the fruit size QTL, suggesting that the underlying basis of the fruit size increase associated with this QTL was an increase in mesocarp cell number. On NY 6, pit length and diameter QTLs clustered with those for fruit size, suggesting that the underlying morphological basis of this fruit size QTL is the difference in pit size.     

Identification of QTL regions and SSR markers associated with resistance to reniform nematode in <Emphasis Type="Italic">Gossypium barbadense</Emphasis> L. accession GB713

The identification of molecular markers that are closely linked to gene(s) in Gossypium barbadense L. accession GB713 that confer a high level of resistance to reniform nematode (RN), Rotylenchulus reniformis Linford & Oliveira, would be very useful in cotton breeding programs. Our objectives were to determine the inheritance of RN resistance in the accession GB713, to identify SSR markers linked with RN resistance QTLs, and to map these linked markers to specific chromosomes. We grew and scored plants for RN reproduction in the P₁, P₂, F₁, F₂, BC₁P₁, and BC₁P₂ generations from the cross of GB713 × Acala Nem-X. The generation means analysis using the six generations indicated that one or more genes were involved in the RN resistance of GB713. The interspecific F₂ population of 300 plants was genotyped with SSR molecular markers that covered most of the chromosomes of Upland cotton (G. hirsutum L.). Results showed two QTLs on chromosome 21 and one QTL on chromosome 18. One QTL on chromosome 21 was at map position 168.6 (LOD 28.0) flanked by SSR markers, BNL 1551_162 and GH 132_199 at positions 154.2 and 177.3, respectively. A second QTL on chromosome 21 was at map position 182.7 (LOD 24.6) flanked by SSR markers BNL 4011_155 and BNL 3279_106 at positions 180.6 and 184.5, respectively. Our chromosome 21 map had 61 SSR markers covering 219 cM. One QTL with smaller genetic effects was localized to chromosome 18 at map position 39.6 (LOD 4.0) and flanked by SSR markers BNL 1721_178 and BNL 569_131 at positions 27.6 and 42.9, respectively. The two QTLs on chromosome 21 had significant additive and dominance effects, which were about equal for each QTL. The QTL on chromosome 18 showed larger additive than dominance effects. Following the precedent set by the naming of the G. longicalyx Hutchinson & Lee and G. aridum [(Rose & Standley) Skovsted] sources of resistance, we suggest the usage of Ren ^barb1 and Ren ^barb2 to designate these QTLs on chromosome 21 and Ren ^barb3 on chromosome 18.     

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     

Analyzing quantitative trait loci for yield using a vegetatively replicated F2 population from a cross between the parents of an elite rice hybrid

Although F₂s are the most informative populations for genetic analysis, it has been difficult to use F₂ populations directly for QTL analysis because it is usually difficult to assess the reliability of the data, due to an inability to estimate the experimental errors. In this study, we performed a QTL analysis for yield and yield-component traits of an F₂ population based on data from replicated field trials over 2 years using vegetative shoots of ratooned plants, making use of the ratooning habit of rice. The objective of this study was to explore the possibility of conducting QTL analyses directly based on an F₂ population by means of ratooning plants. The experimental population was from a cross between ’Zhenshan 97’ and ’Minghui 63’, the parents of ’Shanyou 63’, an elite rice hybrid widely grown in China. A genetic linkage map containing 151 molecular markers was constructed for QTL mapping. A total of 20 distinct QTLs were detected; eight of these were detected in both years and remaining 12 in only 1 year. Compared with the results of our previous analysis of the F_2:3 families from the same cross, it was shown that most of the QTLs detected in the ratooned F₂ population were also detected in the F_2:3 population. However, the estimates of both additive and dominant types of genetic effects for many of the QTLs based on F₂ ratoons were substantially larger than those based on F_2:3 families. The results indicate that vegetatively ratooned F₂ populations may have considerable utility in the mapping of QTLs, especially if dominant types of gene actions are of concern, although there were certain technical limitations in making use of such populations in the experiments. Received: 11 November 1999 / Accepted: 24 November 1999     

Salt tolerance in Lycopersicon species. IV. Efficiency of marker-assisted selection for salt tolerance improvement

The usefulness of marker-assisted selection (MAS) to develop salt-tolerant breeding lines from a F₂ derived from L. esculentum x L. pimpinellifolium has been studied. Interval mapping methodology of quantitative trait locus (QTL) analysis was used to locate more precisely previously detected salt tolerance QTLs. A new QTL for total fruit weight under salinity (TW) near TG24 was detected. Most of the detected QTLs [3 for TW, 5 for fruit number, (FN) and 4 for fruit weight (FW)] had low R ² values, except the FW QTL in the TG180-TG48 interval, which explains 36.6% of the total variance. Dominant and overdominant effects were detected at the QTLs for TW, whereas gene effects at the QTLs for FJV and FW ranged from additive to partial dominance. Phenotypic selection of F₂ familes and marker-assisted selection of F₃ families were carried out. Yield under salinity decreased in the F₂ generation. F₃ means were similar to those of the F₁ as a consequence of phentoypic selection. The most important selection response for every trait was obtained from the F₃ to F₄ where MAS was applied. While F₃ variation was mainly due to the within-family component, in the F₄ the FN and FW between-family component was larger than the within-family one, indicating an efficient compartmentalization and fixation of QTLs into the F₄ families. Comparison of the yield of these families under control versus saline conditions showed that fruit weight is a key trait to success in tomato salt-tolerance improvement using wild Lycopersicon germplasm. The QTLs we have detected under salinity seem to be also working under control conditions, although the interaction family x treatment was significant for TW, thereby explaining the fact that the selected families responded differently to salinity.     

Restriction fragment length polymorphism analysis of loci associated with disease resistance genes and developmental traits in Pisum sativum L.

An F₂ population of pea (Pisum sativum L.) consisting of 174 plants was analysed by restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD) techniques. Ascochyta pisi race C resistance, plant height, flowering earliness and number of nodes were measured in order to map the genes responsible for their variation. We have constructed a partial linkage map including 3 morphological character genes, 4 disease resistance genes, 56 RFLP loci, 4 microsatellite loci and 2 RAPD loci. Molecular markers linked to each resistance gene were found: Fusarium wilt (6 cM from Fw), powdery mildew (11 cM from er) and pea common Mosaic virus (15 cM from mo). QTLs (quantitative traits loci) for Ascochyta pisi race C resistance were mapped, with most of the variation explained by only three chromosomal regions. The QTL with the largest effect, on chromosome 4, was also mapped using a qualitative, Mendelian approach. Another QTL displayed a transgressive segregation, i.e. the parental line that was susceptible to Ascochyta blight had a resistance allele at this QTL. Analysis of correlations between developmental traits in terms of QTL effects and positions suggested a common genetic control of the number of nodes and earliness, and a loose relationship between these traits and height.     

Fine mapping of quantitative trait loci Hd-1, Hd-2 and Hd-3, controlling heading date of rice, as single Mendelian factors

 Fine mapping was carried out on three putative QTLs (tentatively designated as Hd-1 to Hd-3) of five such QTLs controlling heading date in rice that had been earlier identified using an F₂ population derived from a cross between a japonica variety, ‘Nipponbare’, and an indica variety, ‘Kasalath’, using progeny backcrossed with ‘Nipponbare’ as the recurrent parent. One BC₃F₂ and two BC₃F₁ plants, in which the target QTL regions were heterozygous and most other chromosomal regions were homozygous for the ‘Nipponbare’ allele, were selected as the experimental material. Self-pollinated progeny (BC₃F₂ and BC₃F₃) of the BC₃F₁ or BC₃F₂ showed continuous variation in days to heading. By means of progeny testing based on BC₃F₃ or BC₃F₄ lines, we determined the genotypes of each BC₃F₂ or BC₃F₃ individual at target QTLs. Their segregation patterns fitted Mendelian inheritance ratios. When the results obtained by RFLP analysis and progeny tests were combined, Hd-1, Hd-2 and Hd-3 were mapped precisely on chromosomes 6, 7 and 6, respectively, of a rice RFLP linkage map. The results demonstrated that QTLs can be treated as Mendelian factors. Moreover, these precise locations were in good agreement with the regions estimated by QTL analysis of the initial F₂ population, demonstrating the high reliability of QTL mapping using a high-density linkage map. Received: 5 November 1997 / Accepted: 10 February 1998     

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     

Accumulation of additive effects generates a strong photoperiod sensitivity in the extremely late-heading rice cultivar ‘Nona Bokra’

Many rice cultivars that originated from lower-latitude regions exhibit a strong photoperiod sensitivity (PS) and show extremely late heading under long-day conditions. Under natural day-length conditions during the cropping season in Japan, the indica rice cultivar ‘Nona Bokra’ from India showed extremely late heading (202 days to heading) compared to the japonica cultivar ‘Koshihikari’ (105 days), from Japan. To elucidate the genetic factors associated with such extremely late heading, we performed quantitative trait locus (QTL) analyses of heading date using an F₂ population and seven advanced backcross progeny (one BC₁F₂ and six BC₂F₂) derived from a cross between ‘Nona Bokra’ and ‘Koshihikari’. The analyses revealed 12 QTLs on seven chromosomes. The ‘Nona Bokra’ alleles of all QTLs contributed to an increase in heading date. Digenic interactions were rarely observed between QTLs. Based on the genetic parameters of the QTLs, such as additive effects and percentage of phenotypic variance explained, these 12 QTLs are likely generate a large proportion of the phenotypic variation observed in the heading dates between ‘Nona Bokra’ and ‘Koshihikari’. Comparison of chromosomal locations between heading date QTLs detected in this study and QTLs previously identified in ‘Nipponbare’ × ‘Kasalath’ populations revealed that eight of the heading date QTLs were recognized nearby the Hd1, Hd2, Hd3a, Hd4, Hd5, Hd6, Hd9, and Hd13. These results suggest that the strong PS in ‘Nona Bokra’ was generated mainly by the accumulation of additive effects of particular alleles at previously identified QTLs.     

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.     

Quantitative trait locus analysis of abnormal circadian period in CS mice

CS mice show a free-running period (κ) longer than 24 h and rhythm splitting in constant darkness (DD). These features in behavioral circadian rhythms are distinctive as compared with other inbred strains of mice, which exhibit robust free-running rhythms with κ shorter than 24 h. To identify the genes affecting κ, quantitative trait locus (QTL) analysis was initially conducted by using 289 F₂ mice derived from a cross between CS and C57BL/6J strain. A suggestive QTL (LOD = 3.71) with CS allele increasing κ was detected on the distal region of Chromosome (Chr) 19. Next, using 192 F₂ mice from a cross between CS and MSM strain, the presence of the QTL on Chr 19 was examined, and we confirmed the QTL at the genome-wide significant level (LOD = 4.61 with 10.4% of the total variance explained). This QTL was named long free-running period (Lfp). Three other suggestive QTLs (LOD = 3.24–4.28) were mapped to the midportion of Chr 12 in (CS×C57BL/6J)F₂ mice, and to the proximal and middle region of Chr 19 in (CS×MSM)F₂ mice, respectively, of which, CS alleles for two QTLs on Chr 19 have the effect of lengthening κ. None of these QTLs were mapped to the chromosomal regions of previously described QTLs for κ and known clock genes (Clock, mPer1, Bmal1, mCry1, mCry2, mTim, and Csnk1e). Received: 5 July 2000 / Accepted: 5 December 2000     

Advanced backcross-QTL analysis in spring barley (H. vulgare ssp. spontaneum) comparing a REML versus a Bayesian model in multi-environmental field trials

A common difficulty in mapping quantitative trait loci (QTLs) is that QTL effects may show environment specificity and thus differ across environments. Furthermore, quantitative traits are likely to be influenced by multiple QTLs or genes having different effect sizes. There is currently a need for efficient mapping strategies to account for both multiple QTLs and marker-by-environment interactions. Thus, the objective of our study was to develop a Bayesian multi-locus multi-environmental method of QTL analysis. This strategy is compared to (1) Bayesian multi-locus mapping, where each environment is analysed separately, (2) Restricted Maximum Likelihood (REML) single-locus method using a mixed hierarchical model, and (3) REML forward selection applying a mixed hierarchical model. For this study, we used data on multi-environmental field trials of 301 BC₂DH lines derived from a cross between the spring barley elite cultivar Scarlett and the wild donor ISR42-8 from Israel. The lines were genotyped by 98 SSR markers and measured for the agronomic traits “ears per m2,” “days until heading,” “plant height,” “thousand grain weight,” and “grain yield”. Additionally, a simulation study was performed to verify the QTL results obtained in the spring barley population. In general, the results of Bayesian QTL mapping are in accordance with REML methods. In this study, Bayesian multi-locus multi-environmental analysis is a valuable method that is particularly suitable if lines are cultivated in multi-environmental field trials. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Molecular detection of QTLs for agronomic and quality traits in a doubled haploid population derived from two Canadian wheats (Triticum aestivum L.)

Development of high-yielding wheat varieties with good end-use quality has always been a major concern for wheat breeders. To genetically dissect quantitative trait loci (QTLs) for yield-related traits such as grain yield, plant height, maturity, lodging, test weight and thousand-grain weight, and for quality traits such as grain and flour protein content, gluten strength as evaluated by mixograph and SDS sedimentation volume, an F₁-derived doubled haploid (DH) population of 185 individuals was developed from a cross between a Canadian wheat variety “AC Karma” and a breeding line 87E03-S2B1. A genetic map was constructed based on 167 marker loci, consisting of 160 microsatellite loci, three HMW glutenin subunit loci: Glu-A1, Glu-B1 and Glu-D1, and four STS-PCR markers. Data for investigated traits were collected from three to four environments in Manitoba, Canada. QTL analyses were performed using composite interval mapping. A total of 50 QTLs were detected, 24 for agronomic traits and 26 for quality-related traits. Many QTLs for correlated traits were mapped in the same genomic regions forming QTL clusters. The largest QTL clusters, consisting of up to nine QTLs, were found on chromosomes 1D and 4D. HMW glutenin subunits at Glu-1 loci had the largest effect on breadmaking quality; however, other genomic regions also contributed genetically to breadmaking quality. QTLs detected in the present study are compared with other QTL analyses in wheat.     

Development of a fertile genetic bridge between Trifolium ambiguum M. Bieb. and T. repens L.

  Trifolium ambiguum M. Bieb and T. repens L. are taxonomically related but very difficult to cross. The rare hybrids so far reported between these two species were obtained only by embryo culture. This difficulty has been overcome in the present research by the creation of a “fertile bridge” between T. ambiguum and T. repens. Characters of interest can now be transferred from T. ambiguum to T. repens by using this “fertile bridge” without the use of sophisticated techniques. An array of backcross progenies was generated from crosses between a T. ambiguum×T. repens F₁ hybrid (8x H-435) and its parental species. The 8x hybrid was cross-fertile only with T. repens and resulted in 145 seeds from 1578 reciprocal crosses. Eleven of nineteen initially grown BC₁F₁ plants were all hexaploid with an average pollen stainability of 41.6%. A high frequency of multivalents at metaphase-I indicated that both autosyndetic and allosyndetic pairing occurred. Backcrosses of 6x BC₁F₁ plants to T. repens resulted in 5x BC₂F₁ plants with an average pollen stainability of 59.3%. On the other hand, 6x BC₁F₁×6x T. ambiguum crosses did not produce any seed and only two pentaploid plants were obtained from 6x BC₁F₁×4x T. ambiguum crosses. The difficulty encountered in generating 6x backcross progeny with 6x T. ambiguum was overcome by intercrossing the 6x BC₁F₁ plants and producing 6x BC₁F₂ plants with an average pollen stainability of 65.8%. One of these 6x BC₁F₂ plants was cross-compatible as a female with 6x T. ambiguum and resulted in CBC₂ plants that were all cross-compatible with 6x T. ambiguum. The 6x BC₁F₂ plants are likely to be superior to 6x BC₁F₁ progeny, as they have exhibited better expression of the combined rhizomatous and stoloniferous growth habit, improved fertility, more frequent nodal rooting and heavier nodulation. Consequently, the 6x BC₁F₂ plants can either be used directly in the selection programme or as a “fertile bridge” between the two parental species. The present work has resulted in the development of a series of fertile hybrids by the manipulation of chromosome numbers, combining the agronomic characteristics of the parent species in varying genome balances and at a range of ploidy levels. It is concluded that the initial sterility of the primary interspecific hybrids need not be a barrier to successful inter-breeding. Received: 2 August 1996 / Accepted: 4 April 1997