Genetic dissection of vegetative propagation traits in Eucalyptus tereticornis and E. globulus

We have detected quantitative trait loci (QTLs) affecting vegetative propagation traits in Eucalyptus tereticornis and Eucalyptus globulus. Using amplified fragment length polymorphism (AFLP) genetic linkage maps, the inheritance of 199 markers was assessed in 94 F₁ individuals with extreme adventitious rooting response, and in 221 randomly chosen F₁ individuals. Phenotypes were scored in 1995 and 1996. QTL analyses were performed using chi-square tests (χ²), single-marker analysis (SMA), interval mapping (IM) and composite interval mapping (CIM). All approaches yielded similar QTL detection results. Three QTLs are hypothesized for mortality (MORT=% dead cuttings), nine for adventitious rooting (ROOT, RCT=% rooted cuttings relative to the surviving or total cuttings, respectively), four for petrification (PETR=% surviving unrooted cuttings), one for sprouting ability (SPR=number of stump sprout cuttings harvested in 1995) and four for the stability of adventitious rooting (STAB=absolute value of the difference ROOT95-ROOT96). All putative QTLs for MORT and PETR were located on the E. tereticornis map, and for SPR and STAB on the E. globulus map. We found different QTLs for MORT, ROOT, RCT, SPR and STAB. Putative QTLs accounted for 2.6–17.0% of the phenotypic variance of a trait (R²). Estimated standardized gene substitution effects varied between 0.13 and 0.49 phenotypic standard deviations (σ_p). These results indicate that the phenotypic variation in these traits has a meaningful genetic component and that stable QTLs can be found in a family of reasonable size where no previous knowledge of the trait was available. Received: 1 September 1998 / Accepted: 24 February 1999     

Identification of quantitative trait loci for resistance to Verticillium wilt and yield parameters in hop (Humulus lupulus L.)

Verticillium wilt (VW) can cause substantial yield loss in hop particularly with the outbreaks of the lethal strain of Verticillium albo-atrum. To elucidate genetic control of VW resistance in hop, an F₁ mapping population derived from a cross of cultivar Wye Target, with the predicted genetic basis of resistance, and susceptible male breeding line BL2/1 was developed to assess wilting symptoms and to perform QTL mapping. The genetic linkage map, constructed with 203 markers of various types using a pseudo-testcross strategy, formed ten major linkage groups (LG) of the maternal and paternal maps, covering 552.98 and 441.1 cM, respectively. A significant QTL for VW resistance was detected at LOD 7 on a single chromosomal region on LG03 of both parental maps, accounting for 24.2–26.0 % of the phenotypic variance. QTL analysis for alpha-acid content and yield parameters was also performed on this map. QTLs for these traits were also detected and confirmed our previously detected QTLs in a different pedigree and environment. The work provides the basis for exploration of QTL flanking markers for possible use in marker-assisted selection.     

Molecular-marker analysis of quantitative traits for growth and development in juvenile apple trees

Random amplified polymorphic DNAs (RAPDs) were used in combination with a double pseudo-testcross mapping strategy to estimate the position and effects of quantitative trait loci (QTLs) for traits influencing juvenile tree growth and development in two apple cultivars. The mapping population consisted of 172 F₁ trees from a cross between the columnar mutant ‘Wijcik McIntosh’ and a standard form disease-resistant selection NY 75441-58. Significant associations were found between markers and height increment, internode number, internode length, base diameter increment, base diameter after 9 years of growth, branch number, and leaf break. The number of genomic regions associated with each trait varied from one to eight. The amount of variation explained by linear regression on individual marker loci (R²) ranged from 3.9 to 24.3%, with an average of 7%. Multiple regression using markers for each putative QTL explained from 6.6 to 41.6% of the phenotypic variation, with an average value of 24.3%. A large number of traits had significant variation associated with the map position of the dominant columnar gene, Co. QTL stability over years was estimated by comparing the locations of putative QTLs for traits measured in multiple years. The majority of genomic regions were associated with a trait in only a single year, although regions associated with a trait in more than 1 year were also detected. The limitations of dominant markers and an outbred mapping pedigree for QTL analysis are discussed. Received: 27 August 1997 / Accepted: 10 February 1998     

Mapping candidate QTLs related to plant persistency in red clover

Red clover (Trifolium pratense L.) is a diploid (2n = 14), self-incompatible legume that is widely cultivated as a forage legume in cold geographical regions. Because it is a short-lived perennial species, improvement of plant persistency is the most important objective for red clover breeding. To develop a marker-assisted selection (MAS) approach for red clover, we identified candidate QTLs related to plant persistency. Two full-sib mapping populations, 272 × WF1680 and HR × R130, were used for QTL identification. Resistance to Sclerotinia trifoliorum and Fusarium species, as well as to winter hardiness, was investigated in the laboratory and in field experiments in Moscow region (Russia), and Sapporo (Japan). With the genotype data derived from microsatellite and other DNA markers, candidate QTLs were identified by simple interval mapping (SIM), Kruskal–Wallis analysis (KW analysis) and genotype matrix mapping (GMM). A total of 10 and 23 candidate QTL regions for plant persistency were identified in the 272 × WF1680 and the HR × R130 mapping populations, respectively. The QTLs identified by multiple mapping approaches were mapped on linkage group (LG) 3 and LG6. The significant QTL interactions identified by GMM explained the higher phenotypic variation than single effect QTLs. Identification of haplotypes having positive effect QTLs in each parent were first demonstrated in this study for pseudo-testcross mapping populations in plant species using experimental data.     

Quantitative trait loci controlling vegetative propagation traits mapped in European pear (<Emphasis Type="Italic">Pyrus communis</Emphasis> L.)

The ease of vegetative propagation by hardwood cuttings is a critical trait for consideration by breeders of woody perennial rootstocks. This is especially so for Pyrus, because most Pyrus rootstock are known to be difficult to propagate. This report presents progress on the identification of loci controlling rooting of hardwood cuttings in European pear (Pyrus communis L.). Quantitative trait loci (QTLs) controlling the development of adventitious roots on hardwood cuttings were identified in both parents of a mapping population developed by crossing “Old Home” and “Louise Bonne de Jersey,” with the goal of investigating the genetic control of several rootstock related traits, which would be useful for rootstock breeding. A QTL for root development was identified on chromosome 7, co-located in both parents and exhibiting male and female additive and dominance effects. These results will assist in developing genetic markers that can be utilized by rootstock breeders for marker-assisted selection for this complex trait.     

QTL mapping for downy mildew resistance in cucumber via bulked segregant analysis using next-generation sequencing and conventional methods

Key message

QTL mapping using NGS-assisted BSA was successfully applied to an F ₂ population for downy mildew resistance in cucumber. QTLs detected by NGS-assisted BSA were confirmed by conventional QTL analysis.

Abstract

Downy mildew (DM), caused by Pseudoperonospora cubensis, is one of the most destructive foliar diseases in cucumber. QTL mapping is a fundamental approach for understanding the genetic inheritance of DM resistance in cucumber. Recently, many studies have reported that a combination of bulked segregant analysis (BSA) and next-generation sequencing (NGS) can be a rapid and cost-effective way of mapping QTLs. In this study, we applied NGS-assisted BSA to QTL mapping of DM resistance in cucumber and confirmed the results by conventional QTL analysis. By sequencing two DNA pools each consisting of ten individuals showing high resistance and susceptibility to DM from a F₂ population, we identified single nucleotide polymorphisms (SNPs) between the two pools. We employed a statistical method for QTL mapping based on these SNPs. Five QTLs, dm2.2, dm4.1, dm5.1, dm5.2, and dm6.1, were detected and dm2.2 showed the largest effect on DM resistance. Conventional QTL analysis using the F₂ confirmed dm2.2 (R ² = 10.8–24 %) and dm5.2 (R ² = 14–27.2 %) as major QTLs and dm4.1 (R ² = 8 %) as two minor QTLs, but could not detect dm5.1 and dm6.1. A new QTL on chromosome 2, dm2.1 (R ² = 28.2 %) was detected by the conventional QTL method using an F₃ population. This study demonstrated the effectiveness of NGS-assisted BSA for mapping QTLs conferring DM resistance in cucumber and revealed the unique genetic inheritance of DM resistance in this population through two distinct major QTLs on chromosome 2 that mainly harbor DM resistance.

     

A haplotype inference algorithm for trios based on deterministic sampling

Background

The three-dimensional shape of grain, measured as grain length, width, and thickness (GL, GW, and GT), is one of the most important components of grain appearance in rice. Determining the genetic basis of variations in grain shape could facilitate efficient improvements in grain appearance. In this study, an F_7:8 recombinant inbred line population (RIL) derived from a cross between indica and japonica cultivars (Nanyangzhan and Chuan7) contrasting in grain size was used for quantitative trait locus (QTL) mapping. A genetic linkage map was constructed with 164 simple sequence repeat (SSR) markers. The major aim of this study was to detect a QTL for grain shape and to fine map a minor QTL, qGL7.

Results

Four QTLs for GL were detected on chromosomes 3 and 7, and 10 QTLs for GW and 9 QTLs for GT were identified on chromosomes 2, 3, 5, 7, 9 and 10, respectively. A total of 28 QTLs were identified, of which several are reported for the first time; four major QTLs and six minor QTLs for grain shape were also commonly detected in both years. The minor QTL, qGL7, exhibited pleiotropic effects on GL, GW, GT, 1000-grain weight (TGW), and spikelets per panicle (SPP) and was further validated in a near isogenic F₂ population (NIL-F₂). Finally, qGL7 was narrowed down to an interval between InDel marker RID711 and SSR marker RM6389, covering a 258-kb region in the Nipponbare genome, and cosegregated with InDel markers RID710 and RID76.

Conclusion

Materials with very different phenotypes were used to develop mapping populations to detect QTLs because of their complex genetic background. Progeny tests proved that the minor QTL, qGL7, could display a single mendelian characteristic. Therefore, we suggested that minor QTLs for traits with high heritability could be isolated using a map-based cloning strategy in a large NIL-F₂ population. In addition, combinations of different QTLs produced diverse grain shapes, which provide the ability to breed more varieties of rice to satisfy consumer preferences.     

QTL Analysis of Popping Fold and the Consistency of QTLs Under Two Environments in Popcorn

Popping fold (PF) is the most important quality trait in popcorn. In this study, a total of 259 F_2:3 families, derived from the cross between a dent corn inbred Dan232 and a popcorn inbred N04, were evaluated for their popping folds in replicated experiments under two environments. Of 613 simple sequence repeat (SSR) primer pairs screened, 183 pairs were selected to construct a genetic linkage map with the genetic distance of 1 762.2 cM (centimorgan) and on average 9.63 cM every marker. Quantative trait loci (QTL) were identified, and their genetic effects were estimated using CIM (composite interval mapping) method. The interactions among QTLs detected were calculated using MIM (multiple interval mapping) method. In all, 22 QTLs were detected, and only 5 of them were common under two environments. Contribution to phenotypic variation of a single QTL varied from 3.07% to 12.84%, and total contributions of all QTLs under two environments were 66.46% and 51.90%, respectively. Three QTLs (qPF-6-1, qPF-8-1 and qPF-1-3) with more than 10% contributions were observed. The additive effects were larger than dominant effects for most QTLs. The amount of QTLs showing additive, partially dominant, dominant and over-dominant effects were 4, 5, 0, 2 in spring sowing and 2, 5, 2, 2 in summer sowing, respectively. There were only 2.60% pairs of QTLs or maker intervals expressing AA, DA or DD interactions.     

Mapping soybean aphid resistance genes in PI 567598B

The soybean aphid (Aphis glycines Matsumura) has been a major pest of soybean [Glycine max (L.) Merr.] in North America since it was first reported in 2000. Our previous study revealed that the strong aphid resistance of plant introduction (PI) 567598B was controlled by two recessive genes. The objective of this study was to locate these two genes on the soybean genetic linkage map using molecular markers. A mapping population of 282 F_4:5 lines derived from IA2070 × E06902 was evaluated for aphid resistance in a field trial in 2009 and a greenhouse trial in 2010. Two quantitative trait loci (QTLs) were identified using the composite and multiple interval mapping methods, and were mapped on chromosomes 7 (linkage group M) and 16 (linkage group J), respectively. E06902, a parent derived from PI 567598B, conferred resistance at both loci. In the 2010 greenhouse trial, each of the two QTLs explained over 30 % of the phenotypic variation. Significant epistatic interaction was also found between these two QTLs. However, in the 2009 field trial, only the QTL on chromosome 16 was found and it explained 56.1 % of the phenotypic variation. These two QTLs and their interaction were confirmed with another population consisting of 94 F_2:5 lines in the 2008 and 2009 greenhouse trials. For both trials in the alternative population, these two loci explained about 50 and 80.4 % of the total phenotypic variation, respectively. Our study shows that soybean aphid isolate used in the 2009 field trial defeated the QTL found on chromosome 7. Presence of the QTL on chromosome 16 conferred soybean aphid resistance in all trials. The markers linked to the aphid-resistant QTLs in PI 567598B or its derived lines can be used in marker-assisted breeding for aphid resistance.     

Genetic Architecture of Palm Oil Fatty Acid Composition in Cultivated Oil Palm (Elaeis guineensis Jacq.) Compared to Its Wild Relative E. oleifera (H.B.K) Cortés

We searched for quantitative trait loci (QTL) associated with the palm oil fatty acid composition of mature fruits of the oil palm E. guineensis Jacq. in comparison with its wild relative E. oleifera (H.B.K) Cortés. The oil palm cross LM2T x DA10D between two heterozygous parents was considered in our experiment as an intraspecific representative of E. guineensis. Its QTLs were compared to QTLs published for the same traits in an interspecific Elaeis pseudo-backcross used as an indirect representative of E. oleifera. Few correlations were found in E. guineensis between pulp fatty acid proportions and yield traits, allowing for the rather independent selection of both types of traits. Sixteen QTLs affecting palm oil fatty acid proportions and iodine value were identified in oil palm. The phenotypic variation explained by the detected QTLs was low to medium in E. guineensis, ranging between 10% and 36%. The explained cumulative variation was 29% for palmitic acid C16:0 (one QTL), 68% for stearic acid C18:0 (two QTLs), 50% for oleic acid C18:1 (three QTLs), 25% for linoleic acid C18:2 (one QTL), and 40% (two QTLs) for the iodine value. Good marker co-linearity was observed between the intraspecific and interspecific Simple Sequence Repeat (SSR) linkage maps. Specific QTL regions for several traits were found in each mapping population. Our comparative QTL results in both E. guineensis and interspecific materials strongly suggest that, apart from two common QTL zones, there are two specific QTL regions with major effects, which might be one in E. guineensis, the other in E. oleifera, which are independent of each other and harbor QTLs for several traits, indicating either pleiotropic effects or linkage. Using QTL maps connected by highly transferable SSR markers, our study established a good basis to decipher in the future such hypothesis at the Elaeis genus level.     

Mapping species differences for adventitious rooting in a <Emphasis Type="Italic">Corymbia torelliana</Emphasis> × <Emphasis Type="Italic">Corymbia citriodora</Emphasis> subspecies <Emphasis Type="Italic">variegata</Emphasis> hybrid

Quantitative trait loci (QTL) detection was carried out for adventitious rooting and associated propagation traits in a second-generation outbred Corymbia torelliana × Corymbia citriodora subspecies variegata hybrid family (n = 186). The parental species of this cross are divergent in their capacity to develop roots adventitiously on stem cuttings and their propensity to form lignotubers. For the ten traits studied, there was one or two QTL detected, with some QTL explaining large amounts of phenotypic variation (e.g. 66% for one QTL for percentage rooting), suggesting that major effects influence rooting in this cross. Collocation of QTL for many strongly genetically correlated rooting traits to a single region on linkage group 12 suggested pleiotropy. A three locus model was most parsimonious for linkage group 12, however, as differences in QTL position and lower genetic correlations suggested separate loci for each of the traits of shoot production and root initiation. Species differences were thought to be the major source of phenotypic variation for some rooting rate and root quality traits because of the major QTL effects and up to 59-fold larger homospecific deviations (attributed to species differences) relative to heterospecific deviations (attributed to standing variation within species) evident at some QTL for these traits. A large homospecific/heterospecific ratio at major QTL suggested that the gene action evident in one cross may be indicative of gene action more broadly in hybrids between these species for some traits.     

Lz-0 × Berkeley: a new Arabidopsis recombinant inbred line population for the mapping of complex traits

This study describes the generation and test of a genetic resource suited to identify determinants of cell biological traits in plants. The use of quantitative trait loci (QTL) mapping for a better genetic understanding of cell biological traits is still at an early stage, even for biotechnologically important cell properties, such as the dimensions of fiber cells. A common strategy, the mapping of QTLs in recombinant inbred line (RIL) populations, is limited by the fact that the existing RIL populations exploit only a small fraction of the existing natural variation. Here, we report the mapping of QTLs impacting on the length of fiber cells in Arabidopsis inflorescence stems in a newly generated RIL population derived from a cross between the accessions Berkeley and the little known Lz-0. Through inbreeding of individual F₂ plants, a total of 159 new F₈ lines were produced and genotyped with a set of 49 single nucleotide polymorphism markers. The population was successfully used not only for the mapping of three QTLs controlling fiber length, but also to map five QTL controlling flowering time under short and long-day conditions. Our study demonstrates the usefulness of this new genetic resource by mapping in it QTLs underlying a poorly explored cellular trait as well as an already better explored regulatory pathway. The new RIL population and an online platform for the continuous supplementation of genetic markers will be generally available to substantially broaden the genetic diversity through which loci with impact on plant quantitative traits can be identified.     

The lose of juvenility elicits adventitious rooting recalcitrance in apple rootstocks

For perennial woody plants, softwood cutting is an efficient technique for larger scale propagation and adventitious rooting of cuttings is one of the most crucial steps. To evaluate the significance of juvenility on adventitious rooting, rooting rates was compared between softwood cuttings collected from apomictic seedlings (juvenile), in vitro cultured plants (rejuvenated), suckers (juvenile like) and canopy shoots (adult) of reproductively mature trees in Malus xiaojinensis. After pre-treatment with indole-3-butytric acid (IBA) (3,000 mg L^?1) + H₂O₂ (50 mM), rooting rates in cutting from juvenile, juvenile like and rejuvenated donor plants were significantly higher (>90 %) than that from adult trees. The effects of IBA on adventitious rooting were enhanced significantly by exogenous H₂O₂. After 15 passages of in vitro subculture, the micro-shoots from adult phase explants were rejuvenated successfully, marked by the elevated expression of miR156 in the leaflets of the micro-shoots. But the rooting ability of rejuvenated micro-shoots was recovered delayed at the 18th or 21st passage of subculture. During the process of rejuvenation, the leaf indole-3-acetic acid contents and the expressions of rooting related genes CKI1, ARRO-1, ARF7 and ARF19 increased significantly. In contrary, the leaf abscisic acid contents decreased. A lack of juvenility is the most important limiting factor governing adventitious rooting of softwood cuttings in apple rootstocks.     

Application of an Effective Statistical Technique for an Accurate and Powerful Mining of Quantitative Trait Loci for Rice Aroma Trait

When a phenotype of interest is associated with an external/internal covariate, covariate inclusion in quantitative trait loci (QTL) analyses can diminish residual variation and subsequently enhance the ability of QTL detection. In the in vitro synthesis of 2-acetyl-1-pyrroline (2AP), the main fragrance compound in rice, the thermal processing during the Maillard-type reaction between proline and carbohydrate reduction produces a roasted, popcorn-like aroma. Hence, for the first time, we included the proline amino acid, an important precursor of 2AP, as a covariate in our QTL mapping analyses to precisely explore the genetic factors affecting natural variation for rice scent. Consequently, two QTLs were traced on chromosomes 4 and 8. They explained from 20% to 49% of the total aroma phenotypic variance. Additionally, by saturating the interval harboring the major QTL using gene-based primers, a putative allele of fgr (major genetic determinant of fragrance) was mapped in the QTL on the 8th chromosome in the interval RM223-SCU015RM (1.63 cM). These loci supported previous studies of different accessions. Such QTLs can be widely used by breeders in crop improvement programs and for further fine mapping. Moreover, no previous studies and findings were found on simultaneous assessment of the relationship among 2AP, proline and fragrance QTLs. Therefore, our findings can help further our understanding of the metabolomic and genetic basis of 2AP biosynthesis in aromatic rice.     

Molecular genetic analysis of grain protein content and flour whiteness degree using RILs in common wheat

Grain protein content (GPC) and flour whiteness degree (FWD) are important qualitative traits in common wheat. Quantitative trait locus (QTL) mapping for GPC and FWD was conducted using a set of 131 recombinant-inbred lines derived from the cross ‘Chuan 35050 × Shannong 483’ in six environmental conditions. A total of 22 putative QTLs (nine GPC and 13 FWD) were identified on 12 chromosomes with individual QTL explaining 4.5–34.0% phenotypic variation. Nine QTLs (40.9%) were detected in two or more environments. The colocated QTLs were on chromosomes 1B and 4B. Among the QTLs identified for GPC, QGpc.sdau-4A from the parent Shannong 483 represented some important favourable QTL alleles. QGpc.sdau-2A.1 and QFwd.sdau-2A.1 had a significant association with both GPC and FWD. The markers detected on top of QTL regions could be potential targets for marker-assisted selection.     

QTL Analysis of Na+ and K+ Concentrations in Roots and Shoots under Different Levels of NaCl Stress in Rice (Oryza sativa L.)

The key to plant survival under NaCl salt stress is maintaining a low Na⁺ level or Na⁺/K⁺ ratio in the cells. A population of recombinant inbred lines (RILs, F_2∶9) derived from a cross between the salt-tolerant japonica rice variety Jiucaiqing and the salt-sensitive indica variety IR26, was used to determine Na⁺ and K⁺ concentrations in the roots and shoots under three different NaCl stress conditions (0, 100 and 120 mM NaCl). A total of nine additive QTLs were identified by QTL Cartographer program using single-environment phenotypic values, whereas eight additive QTLs were identified by QTL IciMapping program. Among these additive QTLs, five were identified by both programs. Epistatic QTLs and QTL-by-environment interactions were detected by QTLNetwork program in the joint analyses of multi-environment phenotypic values, and one additive QTL and nine epistatic QTLs were identified. There were three epistatic QTLs identified for Na⁺ in roots (RNC), three additive QTLs and two epistatic QTLs identified for Na⁺ in shoots (SNC), four additive QTLs identified for K⁺ in roots (RKC), four additive QTLs and three epistatic QTLs identified for K⁺ in shoots (SKC) and one additive QTL and one epistatic QTL for salt tolerance rating (STR). The phenotypic variation explained by each additive, epistatic QTL and QTL×environment interaction ranged from 8.5 to 18.9%, 0.5 to 5.3% and 0.7 to 7.5%, respectively. By comparing the chromosomal positions of these additive QTLs with those previously identified, five additive QTLs, qSNC9, qSKC1, qSKC9, qRKC4 and qSTR7, might represent novel salt tolerance loci. The identification of salt tolerance in selected RILs showed that a major QTL qSNC11 played a significant role in rice salt tolerance, and could be used to improve salt tolerance of commercial rice varieties with marker-assisted selection (MAS) approach.     

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

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

Genetic mapping of local adaptation along the altitudinal gradient in <Emphasis Type="Italic">Abies sachalinensis</Emphasis>

Understanding the genetic bases of local adaptation in dominant conifer species is critical in predicting the impacts of rapid climate change on forest ecosystems. However, the genetic basis of adaptation is not yet fully understood due to the huge and complex genomes of conifers and the unavailability to date of suitable crossing material. In this study, we constructed a linkage map for Abies sachalinensis (2n = 24) and investigated quantitative trait loci (QTLs) associated with local adaptation along an altitudinal gradient. A segregating population of 239 seedlings was produced from a cross between two F₁ hybrids (high-altitude × low-altitude genotypes). QTL mapping of phenological and growth traits was performed using a pseudo-testcross strategy with linkage maps based on 1251 single-nucleotide polymorphism (SNP) and three simple sequence repeat (SSR) markers. Two maps consisting of 12 linkage groups with an average marker interval of ca. 3 cM were constructed for each parent. The total lengths of the maps were 1861 and 1949 cM. A permutation test identified four significant QTLs and 11 additional suggestive QTLs, with high logarithm of odds (LOD) scores (> 3.0). This is the first highly saturated linkage map produced for Abies taxa. Our results suggest that spring bud phenology is controlled by several QTLs with moderate effects. The use of the mapping population created by crossing two hybrids (high × low altitude genotypes) and numerous SNP markers enabled us to investigate the genetic basis of adaptive traits in conifer species.     

QTL analysis of flower and fruit traits in sour cherry

The map locations and effects of quantitative trait loci (QTLs) were estimated for eight flower and fruit traits in sour cherry (Prunus cerasus L.) using a restriction fragment length polymorphism (RFLP) genetic linkage map constructed from a double pseudo-testcross. The mapping population consisted of 86 progeny from the cross between two sour cherry cultivars, Rheinische Schattenmorelle (RS)×Erdi Botermo (EB). The genetic linkage maps for RS and EB were 398.2 cM and 222.2 cM, respectively, with an average interval length of 9.8 cM. The RS/EB linkage map that was generated with shared segregating markers consisted of 17 linkage groups covering 272.9 cM with an average interval length of 4.8 cM. Eleven putatively significant QTLs (LOD >2.4) were detected for six characters (bloom time, ripening time, % pistil death, % pollen germination, fruit weight, and soluble solids concentration). The percentage of phenotypic variation explained by a single QTL ranged from 12.9% to 25.9%. Of the QTLs identified for the traits in which the two parents differed significantly, 50% had allelic effects opposite to those predicted from the parental phenotype. Three QTLs affecting flower traits (bloom time, % pistil death, and % pollen germination) mapped to a single linkage group, EB 1. The RFLP closest to the bloom time QTL on EB 1 was detected by a sweet cherry cDNA clone pS141 whose partial amino acid sequence was 81% identical to that of a Japanese pear stylar RNase. Received: 4 March 1999 / Accepted: 27 August 1999     

Somatic embryogenesis and vegetative cutting capacity are under distinct genetic control in Coffea canephora Pierre

The purpose of the study was to evaluate the possible genetic effect on vegetative propagation of Coffea canephora. Diversity for somatic embryogenesis (SE) ability was observed not only among two groups of C. canephora Pierre (Congolese and Guinean), but also within these different genetic groups. The results therefore showed that, under given experimental conditions, SE ability is depending on genotype. Furthermore the detection of quantitative trait loci (QTLs) controlling the SE and cutting abilities of C. canephora was performed on a large number of clones including accessions from a core collection, three parental clones and their segregating progenies. On the one hand we detected eight QTLs determining SE. Six positive QTLs for SE ability, whatever the criteria used to quantify this ability, were localized on one single chromosome region of the consensus genetic map. Two negative QTLs for SE ability (frequency of micro calli without somatic embryo) were detected on another linkage group. Deep analysis of the six QTLs detected for SE ability came to the conclusion that they can be assimilated to one single QTL explaining 8.6–12.2% of the observed variation. On the other hand, two QTLs for average length of roots and length of the longest sprouts of cuttings were detected in two linkage groups. These QTLs detected for cutting ability are explaining 12–27% of the observed variation. These observations led to conclude that SE and cutting abilities of C. canephora Pierre appeared to be genetic dependent but through independent mechanisms.