Pollen viability restoration in a <Emphasis Type="Italic">Coffea canephora</Emphasis> P. and <Emphasis Type="Italic">C. heterocalyx</Emphasis> Stoffelen backcross. QTL identification for marker-assisted selection

Male fertility of interspecific hybrids was analysed in one F1 and two backcrossed progenies originating from a cross between Coffea canephora and Coffea heterocalyx. Male fertility was tested using pollen stainability with acetic carmine. The results showed a marked decline in fertility at the F1 level, and fertility was almost fully restored after two backcrosses. The computed broad-sense heritability represented 47% of the variance. Quantitative trait loci (QTLs) locations and effects on pollen viability were estimated using an amplified fragment length polymorphism (AFLP) genetic linkage map constructed in the segregating BC1 population. Three significant QTLs (LOD>3 and p < 0.001 by ANOVA) were detected for pollen viability, two of which were responsible for the bimodal distribution of pollen viability in the segregating population. One QTL was involved in fertility variations among fertile BC1 plants. Fertility inheritance is discussed in relation with previously demonstrated chromosomal sterility in Coffea hybrids and the effect of detected QTLs. The potential use of genetic markers to overcome sterility in interspecific hybrids is also discussed.     

Genetics of intrinsic postzygotic isolation in a circumpolar plant species, Draba nivalis (Brassicaceae)

Sterility barriers, ranging from incomplete to fully developed, were recently demonstrated within taxonomic species of the genus Draba, suggesting the existence of numerous, cryptic biological species. Because these taxa are predominately selfers and of Pleistocene origin, it was concluded that hybrid sterility evolved quickly and possibly by genetic drift. Here we used genetic mapping and QTL analyses to determine the genetic basis of hybrid sterility between geographically distant populations of one of these taxonomic species, Draba nivalis. Fifty microsatellite loci were mapped, and QTL analyses identified five loci underlying seed fertility and two underlying pollen fertility. Four of five seed fertility QTLs reduced fertility in heterozygotes, an observation most consistent with drift-based fixation of underdominant sterility loci. However, several nuclear-nuclear interactions were also found, including two that acted like reciprocal translocations with lowest fitness in double heterozygotes, and two that had a pattern of fitness consistent with Bateson-Dobzhansky-Muller incompatibilities. In contrast, pollen fertility QTLs exhibited additive inheritance, with lowest fertility associated with the paternal allele, a pattern of inheritance suggestive of cytonuclear incompatibilities. The results imply that multiple genetic mechanisms underlie the rapid evolution of reproductive barriers in Draba.     

水稻籼粳杂种生殖障碍的基因定位分析

籼稻(Oryza sativa L.ssp.indica)与粳稻(O.sativa ssp.japonica)杂交优势明显但存在生殖隔离。生殖障碍主要表现为胚囊败育、花粉败育、开花时花药不开裂和雌雄异熟。应用具有137个标记位点的籼、粳杂交(“窄叶青8号”/“京系17”)F_1花药培养获得的127个双单倍体(DH)群体构建的RFLP图谱,对控制籼、粳杂种小穗败育的基因座位进行了定位研究。结果在第1、3、4、5、6、7、8、12染色体上检测到10个基因座位,其中第3、12染色体上的2个不育基因位点stj-3和stj-12与同一杂交组合F_2分离群体中发现的异常分离热点处于相同的染色体区段。Ssj-6的基因加性效应为负值,有增加籼、粳亲和性的作用;其余的不育基因座位皆有增加籼、粳杂种不育性的作用。     

Chromosomal rearrangements directly cause underdominant F1 pollen sterility in Mimulus lewisii–Mimulus cardinalis hybrids

Chromosomal rearrangements can contribute to the evolution of postzygotic reproductive isolation directly, by disrupting meiosis in F₁ hybrids, or indirectly, by suppressing recombination among genic incompatibilities. Because direct effects of rearrangements on fertility imply fitness costs during their spread, understanding the mechanism of F₁ hybrid sterility is integral to reconstructing the role(s) of rearrangements in speciation. In hybrids between monkeyflowers Mimulus cardinalis and Mimulus lewisii, rearrangements contain all quantitative trait loci (QTLs) for both premating barriers and pollen sterility, suggesting that they may have facilitated speciation in this model system. We used artificial chromosome doubling and comparative mapping to test whether heterozygous rearrangements directly cause underdominant male sterility in M. lewisii–M. cardinalis hybrids. Consistent with a direct chromosomal basis for hybrid sterility, synthetic tetraploid F₁s showed highly restored fertility (83.4% pollen fertility) relative to diploids F₁s (36.0%). Additional mapping with Mimulus parishii–M. cardinalis and M. parishii–M. lewisii hybrids demonstrated that underdominant male sterility is caused by one M. lewisii specific and one M. cardinalis specific reciprocal translocation, but that inversions had no direct effects on fertility. We discuss the importance of translocations as causes of reproductive isolation, and consider models for how underdominant rearrangements spread and fix despite intrinsic fitness costs.     

CHROMOSOMAL REARRANGEMENTS AND THE GENETICS OF REPRODUCTIVE BARRIERS IN MIMULUS (MONKEY FLOWERS)

Chromosomal rearrangements may directly cause hybrid sterility and can facilitate speciation by preserving local adaptation in the face of gene flow. We used comparative linkage mapping with shared gene‐based markers to identify potential chromosomal rearrangements between the sister monkeyflowers Mimulus lewisii and Mimulus cardinalis, which are textbook examples of ecological speciation. We then remapped quantitative trait loci (QTLs) for floral traits and flowering time (premating isolation) and hybrid sterility (postzygotic isolation). We identified three major regions of recombination suppression in the M. lewisii × M. cardinalis hybrid map compared to a relatively collinear Mimulus parishii × M. lewisii map, consistent with a reciprocal translocation and two inversions specific to M. cardinalis. These inferences were supported by targeted intraspecific mapping, which also implied a M. lewisii‐specific reciprocal translocation causing chromosomal pseudo‐linkage in both hybrid mapping populations. Floral QTLs mapped in this study, along with previously mapped adaptive QTLs, were clustered in putatively rearranged regions. All QTLs for male sterility, including two underdominant loci, mapped to regions of recombination suppression. We argue that chromosomal rearrangements may have played an important role in generating and consolidating barriers to gene flow as natural selection drove the dramatic ecological and morphological divergence of these species.     

Genetic mapping of two components of reproductive isolation between two sibling species of moths,Ostrinia nubilalis and O. scapulalis

We report the quantitative trait loci (QTL) mapping of reproductive isolation traits between Ostrinia nubilalis (the European corn borer) and its sibling species O. scapulalis (the Adzuki bean borer), focusing on two traits: mating isolation (mi) and pheromone production (Pher). Four genetic maps were generated from two backcross families, with two maps (one chromosomal map and one linkage map) per backcross. We located 165–323 AFLP markers on these four maps, resulting in the identification of 27–31 linkage groups, depending on the map considered. No-choice mating experiments with the offspring of each backcross led to the detection of at least two QTLs for mi in different linkage groups. QTLs underlying Pher were located in a third linkage group. The Z heterochromosome was identified by a specific marker (Tpi) and did not carry any of these QTLs. Finally, we considered the global divergence between the two sibling species, distortions of segregation throughout the genome, and the location and effect of mi and Pher QTLs in light of the known candidate genes for reproductive isolation within the genus Ostrinia and, more broadly, in phytophagous insects.     

Genetic mapping of grapevine ( Vitis vinifera L.) applied to the detection of QTLs for seedlessness and berry weight

Parental and consensus genetic maps of Vitis vinifera L. (2n = 38) were constructed using a F₁ progeny of 139 individuals from a cross between two partially seedless genotypes. The consensus map contained 301 markers [250 amplification fragment length polymorphisms (AFLPs), 44 simple sequence repeats (SSRs), three isozymes, two random amplified polymorphic DNAs (RAPDs), one sequence-characterized amplified region (SCAR), and one phenotypic marker, berry color] mapped onto 20 linkage groups, and covered 1,002 cM. The maternal map consisted of 157 markers covering 767 cM (22 groups). The paternal map consisted of 144 markers covering 816 cM (23 groups). Differences in recombination rates between these maps and another unpublished map are discussed. The major gene for berry color was mapped on both the paternal and consensus maps. Quantitative trait loci (QTLs) for several quantitative subtraits of seedlessness in 3 successive years were searched for, based on parental maps: berry weight, seed number, seed total fresh and dry weights, seed percent dry matter, and seed mean fresh and dry weights. QTLs with large effects (R² up to 51%) were detected for all traits and years at the same location on one linkage group, with some evidence for the existence of a second linked major QTL for some of them. For these major QTLs, differences in relative parental effects were observed between traits. Three QTLs with small effects (R² from 6% to 11%) were also found on three other linkage groups, for berry weight and seed number in a single year, and for seed dry matter in 2 different years.     

Exploring the genetic characteristics of 93-11 and Nipponbare recombination inbred lines based on the GoldenGate SNP assay

Understanding genetic characteristics in rice populations will facilitate exploring evolutionary mechanisms and gene cloning. Numerous molecular markers have been utilized in linkage map construction and quantitative trait locus (QTL) mappings. However, segregation-distorted markers were rarely considered, which prevented understanding genetic characteristics in many populations. In this study, we designed a 384-marker GoldenGate SNP array to genotype 283 recombination inbred lines (RILs) derived from 93-11 and Nipponbare Oryza sativa crosses. Using 294 markers that were highly polymorphic between parents, a linkage map with a total genetic distance of 1,583.2 cM was constructed, including 231 segregation-distorted markers. This linkage map was consistent with maps generated by other methods in previous studies. In total, 85 significant quantitative trait loci (QTLs) with phenotypic variation explained (PVE) values≥5% were identified. Among them, 34 QTLs were overlapped with reported genes/QTLs relevant to corresponding traits, and 17 QTLs were overlapped with reported sterility-related genes/QTLs. Our study provides evidence that segregation-distorted markers can be used in linkage map construction and QTL mapping. Moreover, genetic information resulting from this study will help us to understand recombination events and segregation distortion. Furthermore, this study will facilitate gene cloning and understanding mechanism of inter-subspecies hybrid sterility and correlations with important agronomic traits in rice.     

Extensive chromosomal repatterning and the evolution of sterility barriers in hybrid sunflower species

New species may arise via hybridization and without a change in ploidy. This process, termed homoploid hybrid speciation, is theoretically difficult because it requires the development of reproductive barriers in sympatry or parapatry. Theory suggests that isolation may arise through rapid karyotypic evolution and/or ecological divergence of hybrid neospecies. Here, we investigate the role of karyotypic change in homoploid hybrid speciation by generating detailed genetic linkage maps for three hybrid sunflower species, Helianthus anomalus, H. deserticola, and H. paradoxus, and comparing these maps to those previously generated for the parental species, H. annuus and H. petiolaris. We also conduct a quantitative trait locus (QTL) analysis of pollen fertility in a BC2 population between the parental species and assess levels of pollen and seed fertility in all cross-combinations of the hybrid and parental species. The three hybrid species are massively divergent from their parental species in karyotype; gene order differences were observed for between 9 and 11 linkage groups (of 17 total), depending on the comparison. About one-third of the karyoypic differences arose through the sorting of chromosomal rearrangements that differentiate the parental species, but the remainder appear to have arisen de novo (six breakages/six fusions in H. anomalus, four breakages/three fusions in H. deserticola, and five breakages/five fusions in H. paradoxus). QTL analyses indicate that the karyotypic differences contribute to reproductive isolation. Nine of 11 pollen viability QTL occur on rearranged chromosomes and all but one map close to a rearrangement breakpoint. Finally, pollen and seed fertility estimates for F1's between the hybrid and parental species fall below 11%, which is sufficient for evolutionary independence of the hybrid neospecies.     

Interval mapping of QTLs controlling yield-related traits and seed protein content in Pisum sativum

A linkage map of garden pea was constructed on the basis of 114 plants (F2 generation) derived from a cross combination Wt10245 x Wt11238. The map, consisting of 204 morphological, isozyme, AFLP, ISSR, STS, CAPS and RAPD markers, was used for interval mapping of quantitative trait loci (QTLs) controlling seed number, pod number, 1000-seed weight, 1000-yield, and seed protein content. Characterization of each QTL included identification of QTL position with reference to the flanking markers, estimation of the part of variance explained by this QTL, and determination of its gene action. The yield-related traits were measured in F2 plants and in F4 recombinant inbred lines (RILs). The interval mapping revealed two to six QTLs per trait, demonstrating linkage to seven pea chromosomes. A total of 37 detected QTLs accounted for 9.1-55.9% of the trait's phenotypic variation and showed different types of gene action. As many as eight and ten QTLs influencing the analysed traits were mapped in linkage groups III and V, respectively, indicating an important role of these regions of the pea genome in the control of yield and seed protein content.     

Mapping of quantitative trait loci (QTLs) for oil yield using SSRs and gene-based markers in African oil palm (<Emphasis Type="Italic">Elaeis guineensis</Emphasis> Jacq.)

The identification of quantitative trait loci (QTLs) based on anchor markers, especially candidate genes that control a trait of interest, has been noted to increase the power of QTL detection. Since these markers can be scored as co-dominant data, they are also valuable for comparing and integrating the QTL linkage maps from diverse mapping populations. To estimate the position and effects of QTLs linked to oil yield traits in African oil palm, co-dominant microsatellites (SSR) and candidate gene-based sequence polymorphisms were applied to construct a linkage map for a progeny showing large differences in oil yield components. The progeny was genotyped for 97 SSR markers, 93 gene-linked markers, and 12 non-gene-linked SNP markers. From these, 190 segregating loci could be arranged into 31 linkage groups while 12 markers remained unmapped. Using the single marker linkage, interval mapping and multiple QTL methods, 16 putative QTLs on seven linkage groups affecting important oil yield related traits such as fresh fruit bunch yield (FFB), ratio of oil per fruit (OF), oil per bunch (OB), fruit per bunch (FB) and wet mesocarp per fruit (WMF) could be identified in the segregating population with estimated values for explained variance ranging from 12.4 % to 54.5 %. Markers designed from some candidate genes involved in lipid biosynthesis were found to be mapped near significant QTLs for various economic yield traits. Associations between QTLs and potential candidate genes are discussed.     

Seed and agronomic QTL in low linolenic acid, lipoxygenase-free soybean (Glycine max (L.) Merrill) germplasm.

Linolenic acid and seed lipoxygenases are associated with off flavours in soybean products. F5 recombinant inbred lines (RILs) from a cross between a low linolenic acid line (RG10) and a seed lipoxygenase-free line (OX948) were genotyped for simple sequence repeats (SSR), random amplified polymorphic DNA (RAPD), sequence-tagged sites (STS), and cleaved amplified polymorphic sequence (CAPS) markers and evaluated for seed and agronomic traits at 3 Ontario locations in 2 years. One hundred twenty markers covering 1247.5 cM were mapped to 18 linkage groups (LGs) in the soybean composite genetic map. Seed lipoxygenases L-1 and L-2 mapped as single major genes to the same location on LG G13-F. L-3 mapped to LG G11-E. This is the first report of a map position for L-3. A major quantitative trait locus (QTL) associated with reduced linolenic acid content was identified on LG G3-B2. QTLs for 12 additional seed and agronomic traits were detected. Linolenic acid content, linoleic acid content, yield, seed mass, protein content, and plant height QTL were present in at least 4 of 6 environments. Three to 8 QTLs per trait were detected that accounted for up to 78% of total variation. Linolenic acid and lipoxygenase loci did not overlap yield QTL, suggesting that it should be possible to develop high-yielding lines resistant to oxidative degradation by marker-assisted selection (MAS).     

Construction of the First High-Density Genetic Linkage Map and Analysis of Quantitative Trait Loci for Growth-Related Traits in <Emphasis Type="Italic">Sinonovacula constricta</Emphasis>

The razor clam (Sinonovacula constricta) is an important aquaculture species, for which a high-density genetic linkage map would play an important role in marker-assisted selection (MAS). In this study, we constructed a high-density genetic map and detected quantitative trait loci (QTLs) for Sinonovacula constricta with an F₁ cross population by using the specific locus amplified fragment sequencing (SLAF-seq) method. A total of 315,553 SLAF markers out of 467.71 Mreads were developed. The final linkage map was composed of 7516 SLAFs (156.60-fold in the parents and 20.80-fold in each F₁ population on average). The total distance of the linkage map was 2383.85 cM, covering 19 linkage groups with an average inter-marker distance of 0.32 cM. The proportion of gaps less than 5.0 cM was on average 96.90%. A total of 16 suggestive QTLs for five growth-related traits (five QTLs for shell height, six QTLs for shell length, three QTLs for shell width, one QTL for total body weight, and one QTL for soft body weight) were identified. These QTLs were distributed on five linkage groups, and the regions showed overlapping on LG9 and LG13. In conclusion, the high-density genetic map and QTLs for S. constricta provide a valuable genetic resource and a basis for MAS.     

Mapping of QTLs for morpho-agronomic and seed quality traits in a RIL population of common bean (Phaseolus vulgaris L.)

The objective of this research was to determine the quantitative trait loci (QTLs) controlling phenological traits (days to flowering, days to end of flowering, days to harvest as green pod, and days to maturity), seed size traits (seed length, seed height, seed width, and seed weight), and seed quality traits (water absorption, and coat proportion), in common bean. A population of 104 F₇ recombinant inbred lines (RILs) derived from an inter-gene pool cross between Xana, and Cornell 49242, was used to develop a genetic linkage map including 175 AFLPs, 27 microsatellites, 30 SCARs, 33 ISSRs, 12 RAPDs, 13 loci codifying for seed proteins, and the four genes Fin,fin (growth habit); Asp,asp (seed coat shininess); P,p (seed color); and I,i (resistance to bean common mosaic virus). The map has a total length of 1,042 cM distributed across 11 linkage groups aligned to those of the core linkage map of bean using common molecular markers as anchor points. The QTL analyses were carried out over three environments using the mean environment data with composite interval mapping. Thirty-one QTLs for ten traits were found to be significant in at least one environment and in the mean environment data, the number of significant QTLs identified per trait ranging from two to five. Twenty-seven of these QTLs mapped forming clusters in eight different chromosomal regions. The rationale for this clustered mapping and the possible relationship between some QTLs for phenological traits and the genes Fin and I are discussed.     

Three representative inter and intra‐subspecific crosses reveal the genetic architecture of reproductive isolation in rice

Systematic characterization of genetic and molecular mechanisms in the formation of hybrid sterility is of fundamental importance in understanding reproductive isolation and speciation. Using ultra‐high‐density genetic maps, 43 single‐locus quantitative trait loci (QTLs) and 223 digenic interactions for embryo‐sac, pollen, and spikelet fertility are depicted from three crosses between representative varieties of japonica and two varietal groups of indica, which provide an extensive archive for investigating the genetic basis of reproductive isolation in rice. Ten newly detected single‐locus QTLs for inter‐ and intra‐subspecific fertility are identified. Three loci for embryo‐sac fertility are detected in both Nip × ZS97 and Nip × MH63 crosses, whereas QTLs for pollen fertility are not in common between the two crosses thus leading to fertility variation. Five loci responsible for fertility and segregation distortion are observed in the ZS97 × MH63 cross. The importance of two‐locus interactions on fertility are quantified in the whole genome, which identify that three types of interaction contribute to fertility reduction in the hybrid. These results construct the genetic architecture with respect to various forms of reproductive barriers in rice, which have significant implications in utilization of inter‐subspecific heterosis along with improvement in the fertility of indica–indica hybrids at single‐ and multi‐locus level.     

QTL analysis of heterostyly in Primula sieboldii and its application for morph identification in wild populations

Background and Aims

Primula sieboldii is a perennial clonal herb that is distributed around the Sea of Japan and is endangered in Japan. Its breeding system is characterized by heteromorphic self-incompatibility, and the morph ratio within a population is very important for reproductive success. The aims of this study were to construct a linkage map, map the S locus as a qualitative trait and quantitative trait loci (QTLs) for floral morphological traits related to heterostyly, and predict the morph type in wild populations by using molecular markers for devising a conservation strategy.

Methods

A linkage map was constructed with 126 markers. The QTLs for four floral traits and the S locus were mapped. Using the genotypes of loci that were located near both the S locus and the QTLs with large effects, morphs of 59 wild genets were predicted.

Key Results

The linkage map consisted of 14 linkage groups (LGs). The S locus was mapped to LG 7. Major QTLs for stigma and anther heights were detected in the same region as the S locus. These QTLs exhibited high logarithm of the odds scores and explained a high percentage of the phenotypic variance (>85 %). By analysing these two traits within each morph, additional QTLs for each trait were detected. Using the four loci linked to the S locus, the morphs of 43 genets in three wild populations could be predicted.

Conclusions

This is the first report of a linkage map and QTL analysis for floral morphology related to heterostyly in P. sieboldii. Floral morphologies related to heterostyly are controlled by the S locus in LG 7 and by several QTLs in other LGs. Additionally, this study showed that molecular markers are effective tools for investigating morph ratios in a population containing the non-flowering individuals or during the non-flowering seasons.     

Interspecific Tests of Allelism Reveal the Evolutionary Timing and Pattern of Accumulation of Reproductive Isolation Mutations

Despite extensive theory, little is known about the empirical accumulation and evolutionary timing of mutations that contribute to speciation. Here we combined QTL (Quantitative Trait Loci) analyses of reproductive isolation, with information on species evolutionary relationships, to reconstruct the order and timing of mutations contributing to reproductive isolation between three plant (Solanum) species. To evaluate whether reproductive isolation QTL that appear to coincide in more than one species pair are homologous, we used cross-specific tests of allelism and found evidence for both homologous and lineage-specific (non-homologous) alleles at these co-localized loci. These data, along with isolation QTL unique to single species pairs, indicate that >85% of isolation-causing mutations arose later in the history of divergence between species. Phylogenetically explicit analyses of these data support non-linear models of accumulation of hybrid incompatibility, although the specific best-fit model differs between seed (pairwise interactions) and pollen (multi-locus interactions) sterility traits. Our findings corroborate theory that predicts an acceleration (‘snowballing’) in the accumulation of isolation loci as lineages progressively diverge, and suggest different underlying genetic bases for pollen versus seed sterility. Pollen sterility in particular appears to be due to complex genetic interactions, and we show this is consistent with a snowball model where later arising mutations are more likely to be involved in pairwise or multi-locus interactions that specifically involve ancestral alleles, compared to earlier arising mutations.     

The genetic basis of floral traits associated with mating system evolution in Leptosiphon (Polemoniaceae): an analysis of quantitative trait loci

Mapping of quantitative trait loci (QTL) was used to investigate the genetic architecture of divergence in floral characters associated with the mating system, an important adaptive trait in angiosperms. Two species of Leptosiphon (Polemoniaceae), one strongly self-fertilizing (L. bicolor) and the other partially outcrossing (L. jepsonii), were crossed to produce F2 and both backcross progenies. For each crossing population, a linkage map was created using amplified fragment length polymorphism markers, and QTL were identified for several dimensions of floral size. For each of the five traits examined, three to seven QTL were detected, with independent datasets yielding congruent results in some but not all cases. The phenotypic effect of individual QTL was generally moderate. We estimated that many of the QTL were additive or showed dominance toward L. bicolor, whereas comparison of mean trait values for parental and cross progenies showed apparent overall dominance of L. jepsonii traits. Colocalization of QTL for different dimensions of floral size was consistent with high phenotypic correlations between floral traits. Substantial segregation distortion was observed in marker loci, the majority favoring alleles from the large-flowered parent. A low frequency of male sterility in the F2 population is consistent with the Dobzhansky-Muller model for the evolution of reproductive isolation.     

Identification of quantitative trait loci for wood quality and growth across eight full-sib coastal Douglas-fir families

Typical linkage and quantitative trait locus (QTL) analyses in forest trees have been conducted in single pedigrees with sex-averaged linkage maps. The results of a QTL analysis for wood quality and growth traits of coastal Douglas-fir using eight full-sib families, each consisting of 40 progeny, replicated on four sites are presented. The resulting map of segregating genetic markers consisted of 120 amplified fragment length polymorphism (AFLP) loci distributed across 19 linkage groups. The wood quality traits represent the widest suite of traits yet examined for QTL analysis in a tree species in a single study. Wood fiber traits showed the lowest number of QTLs (3) with relatively small effect (ca. 4%); wood density traits also showed just three QTLs but with slightly larger effect; wood chemistry traits showed more QTLs (7), while ring density traits showed many QTLs with large numbers of QTLs (78) and interesting patterns of temporal variation. Growth traits gave just five QTLs but of major effect (10–16%). Trees, with their long generation times, provide a rich resource for studies of temporal variation of QTL expression.     

Quantitative trait loci for spawning date and body weight in rainbow trout: testing for conserved effects across ancestrally duplicated chromosomes

We incorporated 69 microsatellite loci into an existing data set of 132 markers to test for quantitative trait loci (QTLs) affecting spawning date and body weight in a backcross between two outbred strains of rainbow trout (Oncorhynchus mykiss). Twenty-six linkage groups were identified and synteny of duplicated microsatellite markers was used to confirm 13 homeologous chromosome pairs. Gene-centromere data were used to localize the centromeres for 13 linkage groups whose orientations were previously unknown. We applied a combination of interval mapping and single marker analysis to the segregating maternal and paternal alleles at 201 microsatellite loci. Four spawning date QTLs with suggestive evidence for an additional two QTLs were detected in female trout spawning at 3 and 4 years of age. Similarly we detected three QTLs for body weight in females at 2 years of age plus four suggestive QTLs for this trait. We found marginal evidence that three pairs of ancestral homeologues contained detectable QTLs for the same trait. In one of the three pairs of homeologues, the duplicated QTL regions mapped to the same relative chromosomal location, while the exact localization of the QTL position in one of the other pairs was difficult to infer since it was based on data from a male-derived map. The existing data were unable to refute a hypothesis that duplicated functional genes will be maintained within the telomeric regions of salmonids due to preferential male-mediated crossing over in this region. Two of the four spawning date QTLs were detected on linkage groups with unknown homeologous relationships. QTLs with possible pleiotropic effects on both spawning date and body size were localized to two linkage groups.