Genetic architecture of traits associated with serpentine adaptation of Silene vulgaris

Serpentine soils provide a difficult substrate for plant colonization and growth and therefore represent an ideal system for studying the genetics of habitat adaptation and the evolution of plant-ecotypes. Using an F2 mapping population derived from an intraspecific cross between a serpentine and a nonserpentine ecotype of Silene vulgaris, the genetic architecture of seven morphological, physiological and life-history traits was explored. A quantitative trait locus (QTL) analysis identified 23 QTLs, 15 of which were classified as major QTLs. The observed genetic architecture suggests that traits potentially involved in habitat adaptation are controlled by few genes of major effect and have evolved under consistent directional selection. Several linkage groups harboured overlapping QTLs for different traits, which can be due to either pleiotropy or linkage. The potential roles of these factors and of the time available for habitat adaptation and ecological speciation on serpentine are discussed.     

Mapping quantitative trait loci for a common bean (Phaseolus vulgaris L.) ideotype.

Breeding a model plant that encompasses individual traits thought to enhance yield potential, known as ideotype breeding, has traditionally focused on phenotypic selection of plants with desirable morphological traits. Broadening this breeding method to the molecular level through the use of molecular markers would avoid the environmental interactions associated with phenotypic selection. A population of 110 F5 recombinant inbred lines (RILs), derived from the cross between WO3391 and 'OAC Speedvale', was used to develop a genetic linkage map consisting of 105 random amplified polymorphic DNA (RAPD), simple sequence repeat (SSR), and sequence-tagged site (STS) markers. The map has a total length of 641 cM distributed across 8 linkage groups (LGs). Five of them were aligned on the core linkage map of bean. Twenty-one quantitative trait loci (QTLs) were identified over three environments for eight agronomic and architectural traits previously defined for a bean (Phaseolus vulgaris L.) ideotype. The QTLs were mapped to seven LGs with several regions containing QTLs for multiple traits. At least one QTL was located for each trait and a maximum of four were associated with lodging. Total explained phenotypic variance ranged from 10.6% for hypocotyl diameter to 45.4% for maturity. Some of the QTLs identified will be useful for early generation selection of tall, upright, high-yielding lines in a breeding program.     

Identification of quantitative trait loci for agronomically important traits and their association with genic-microsatellite markers in sorghum

The identification of quantitative trait loci (QTLs) affecting agronomically important traits enable to understand their underlying genetic mechanisms and genetic basis of their complex interactions. The aim of the present study was to detect QTLs for 12 agronomic traits related to staygreen, plant early development, grain yield and its components, and some growth characters by analyzing replicated phenotypic datasets from three crop seasons, using the population of 168 F₇ RILs of the cross 296B × IS18551. In addition, we report mapping of a subset of genic-microsatellite markers. A linkage map was constructed with 152 marker loci comprising 149 microsatellites (100 genomic- and 49 genic-microsatellites) and three morphological markers. QTL analysis was performed by using MQM approach. Forty-nine QTLs were detected, across environments or in individual environments, with 1–9 QTLs for each trait. Individual QTL accounted for 5.2–50.4% of phenotypic variance. Several genomic regions affected multiple traits, suggesting the phenomenon of pleiotropy or tight linkage. Stable QTLs were identified for studied traits across different environments, and genetic backgrounds by comparing the QTLs in the study with previously reported QTLs in sorghum. Of the 49 mapped genic-markers, 18 were detected associating either closely or exactly as the QTL positions of agronomic traits. EST marker Dsenhsbm19, coding for a key regulator (EIL-1) of ethylene biosynthesis, was identified co-located with the QTLs for plant early development and staygreen trait, a probable candidate gene for these traits. Similarly, such exact co-locations between EST markers and QTLs were observed in four other instances. Collectively, the QTLs/markers identified in the study are likely candidates for improving the sorghum performance through MAS and map-based gene isolations.     

Molecular mapping and location of QTLs for drought-resistance traits in <Emphasis Type="Italic">indica</Emphasis> rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) lines adapted to target environments

Drought is a major limitation for rice production in rainfed ecosystems. Identifying quantitative trait loci (QTLs) linked to drought resistance provides opportunity to breed high yielding rice varieties suitable for drought-prone areas. Although considerable efforts were made in mapping QTLs associated with drought-resistance traits in rice, most of the studies involved indica × japonica crosses and hence, the drought-resistance alleles were contributed mostly by japonica ecotypes. It is desirable to look for genetic variation within indica ecotypes adapted to target environment (TE) as the alleles from japonica ecotype may not be expressed under lowland conditions. A subset of 250 recombinant inbred lines (RILs) of F₈ generation derived from two indica rice lines (IR20 and Nootripathu) with contrasting drought-resistance traits were used to map the QTLs for morpho-physiological and plant production traits under drought stress in the field in TE. A genetic linkage map was constructed using 101 polymorphic PCR-based markers distributed over the 12 chromosomes covering a total length of 1,529 cM in 17 linkage groups with an average distance of 15.1 cM. Composite interval mapping analysis identified 22 QTLs, which individually explained 4.8–32.2% of the phenotypic variation. Consistent QTLs for drought-resistance traits were detected using locally adapted indica ecotypes, which may be useful for rainfed rice improvement.     

亚麻主要农艺与品质相关性状的QTL定位

为了全面了解亚麻产量和品质相关性状的遗传基础,为亚麻基因克隆和分子标记辅助育种提供理论依据,在已构建SNP连锁遗传图谱的基础上,以LH-89为父本,R43为母本构建F2:3家系QTL定位群体,用R/QTL软件采用复合区间作图法对13个农艺和品质性状进行QTL定位。结果表明:(1)该研究共检测出35个QTL位点,与粗脂肪及其组成成分相关的QTL有20个,与农艺性状相关的QTL有15个;其中:亚油酸和粗脂肪各5个,亚麻酸、千粒重各4个,棕榈酸、株高、工艺长度各3个,硬脂酸、分枝数各2个,单株果数、果粒数、单株粒重、油酸各1个。(2)共有18个QTL的表型贡献率超10%(主效基因),其中农艺性状定位8个主效基因,品质性状定位10个主效基因。     

Quantitative Genetic Analysis Indicates Natural Selection on Leaf Phenotypes Across Wild Tomato Species (Solanum sect. Lycopersicon; Solanaceae)

Adaptive evolution requires both raw genetic material and an accessible path of high fitness from one fitness peak to another. In this study, we used an introgression line (IL) population to map quantitative trait loci (QTL) for leaf traits thought to be associated with adaptation to precipitation in wild tomatoes (Solanum sect. Lycopersicon; Solanaceae). A QTL sign test showed that several traits likely evolved under directional natural selection. Leaf traits correlated across species do not share a common genetic basis, consistent with a scenario in which selection maintains trait covariation unconstrained by pleiotropy or linkage disequilibrium. Two large effect QTL for stomatal distribution colocalized with key genes in the stomatal development pathway, suggesting promising candidates for the molecular bases of adaptation in these species. Furthermore, macroevolutionary transitions between vastly different stomatal distributions may not be constrained when such large-effect mutations are available. Finally, genetic correlations between stomatal traits measured in this study and data on carbon isotope discrimination from the same ILs support a functional hypothesis that the distribution of stomata affects the resistance to CO₂ diffusion inside the leaf, a trait implicated in climatic adaptation in wild tomatoes. Along with evidence from previous comparative and experimental studies, this analysis indicates that leaf traits are an important component of climatic niche adaptation in wild tomatoes and demonstrates that some trait transitions between species could have involved few, large-effect genetic changes, allowing rapid responses to new environmental conditions.     

Quantitative trait loci for lodging resistance in a segregating wheat×spelt population

 Lodging can strongly affect both the grain yield and the quality of wheat. Lodging represents a quantitative trait and is difficult to assess on a phenotypic basis. Marker-assisted selection (MAS) could therefore become an important tool in breeding for lodging resistance. In this study, we mapped and characterised quantitative trait loci (QTLs) for lodging resistance, as well as morphological traits correlated with lodging, in a segregating population of 226 recombinant inbred lines derived from the cross of the lodging-resistant wheat variety Forno with the susceptible spelt variety Oberkulmer. Lodging, plant height, leaf width, leaf-growth habit, culm stiffness, culm swinging, culm thickness, days to ear emergence and days to flowering were assessed in field trials at two locations in 1996 and at one location in 1997. Additionally, at one location weight and length parameters were also assessed. Plant height and culm stiffness explained 77% of the phenotypic variance of lodging in a multiple regression model over all three environments. QTL analysis of lodging and morphological parameters was based on a genetic map containing 230 loci with 23 linkage groups (2469 cM). With the method of composite interval mapping nine QTLs for lodging resistance were detected, explaining 63% of the phenotypic variance in a simultaneous fit. Seven of these QTLs coincided with QTLs for morphological traits, reflecting the correlations between these traits and lodging. In our population the most efficient way to improve lodging resistance would be by a combination of indirect selection on plant height and culm stiffness together with MAS on the two QTLs for lodging resistance which did not coincide with QTLs for morphological traits. Received: 3 August 1998 / Accepted: 28 November 1998     

Collinsia sparsiflora in serpentine and nonserpentine habitats: using F2 hybrids to detect the potential role of selection in ecotypic differentiation

Here we document phenotypic differences between serpentine and nonserpentine ecotypes of Collinsia sparsiflora, as well as patterns of selection in these contrasting soil habitats. We transplanted the two parental ecotypes and experimental F2 hybrids into six field sites, and collected morphological, phenological and fitness data on emergent plants. To focus on edaphically mediated selection, rather than on pollinator-mediated selection, we used pollinator-exclusion cages. Transplanted parentals of the two ecotypes showed genetic differentiation for floral traits, but not for phenological traits or cotyledon size. For the F2 hybrids growing on serpentine soils, there was significant directional selection on cotyledon size, flower size and flower shape. However, the pattern of selection did not differ significantly between serpentine and nonserpentine sites. Overall, we did not see evidence for divergent selection on the two soil types. We conclude that differences in floral traits between the ecotypes do not reflect adaptation to physical conditions associated with soil type, and that there are unmeasured traits that must be contributing to ecotypic differentiation.     

Yield-enhancing quantitative trait loci (QTLs) from wild species

Wild species of crop plants are increasingly being used to improve various agronomic traits including yield in cultivars. Dense molecular maps have enabled mapping of quantitative trait loci (QTLs) for complex traits such as yield. QTLs for increased yield have been identified from wild relatives of several crop plants. Advanced backcross QTL analysis has been used to identify naturally occurring favorable QTL alleles for yield and minimize the effect of unwanted alleles from wild species. Yield QTLs from wild species are distributed on almost all chromosomes but more often in some regions. Many QTLs for yield and related traits derived from different wild accessions or species map to identical chromosomal regions. QTLs for highly correlated yield associated traits are also often co-located implying linkage or pleiotropic effects. Many QTLs have been detected in more than one environment and in more than one genetic background. The overall direction of effect of some QTLs however, may vary with genetic context. Thus, there is evidence of stable and consistent major effect yield-enhancing QTLs derived from wild species in several crops. Such QTLs are good targets for use in marker assisted selection though their context-dependency is a major constraint. Literature on yield QTLs mapped from wild species is summarized with special reference to rice and tomato.     

A Set of Lotus japonicus Gifu x Lotus burttii Recombinant Inbred Lines Facilitates Map-based Cloning and QTL Mapping

Model legumes such as Lotus japonicus have contributed significantly to the understanding of symbiotic nitrogen fixation. This insight is mainly a result of forward genetic screens followed by map-based cloning to identify causal alleles. The L. japonicus ecotype 'Gifu' was used as a common parent for inter-accession crosses to produce F2 mapping populations either with other L. japonicus ecotypes, MG-20 and Funakura, or with the related species L. filicaulis. These populations have all been used for genetic studies but segregation distortion, suppression of recombination, low polymorphism levels, and poor viability have also been observed. More recently, the diploid species L. burttii has been identified as a fertile crossing partner of L. japonicus. To assess its qualities in genetic linkage analysis and to enable quantitative trait locus (QTL) mapping for a wider range of traits in Lotus species, we have generated and genotyped a set of 163 Gifu × L. burttii recombinant inbred lines (RILs). By direct comparisons of RIL and F2 population data, we show that L. burttii is a valid alternative to MG-20 as a Gifu mapping partner. In addition, we demonstrate the utility of the Gifu × L. burttii RILs in QTL mapping by identifying an Nfr1-linked QTL for Sinorhizobium fredii nodulation.     

Similarity of QTLs detected for in vitro and greenhouse development of potato plants

A relationship between quantitative trait loci (QTLs) detected for in vitro and greenhouse growing conditions was studied in a backcross population of 155 genotypes derived from a haploid potato (Solanum tuberosum) and a diploid wild species (S. berthaultii). Both plant height and tuberization earliness were characterized under two growing conditions. Main-effect QTLs and QTLs identified only through interaction were detected for each of the traits. For traits associated with plant height as well as for traits associated with early tuberization, the most significant QTL detected for greenhouse cultivated plants was also found when the population was grown in vitro. The most significant QTL for earliness of tuberization in vitro, which was located on chromosome 8, coincides with that detected for sucrose concentration in leaf exudate. The absence of a S. berthaultii allele was associated both with a higher amount of sucrose in the exudate and with earlier in vitro tuber formation. Epistasis was found to have a significant effect on all traits investigated. The QTL model that included main-effect QTLs and all significant interactions explained 83–88% of the total genetic variance for each of the developmental traits. The possibility of using an in vitro system combined with marker-assisted selection for preliminary selection of early tuberizing clones is discussed.     

The genetics of domestication of rice bean, Vigna umbellata

Background and Aims

The Asian genus Vigna, to which four cultivated species (rice bean, azuki bean, mung bean and black gram) belong, is suitable for comparative genomics. The aims were to construct a genetic linkage map of rice bean, to identify the genomic regions associated with domestication in rice bean, and to compare these regions with those in azuki bean.

Methods

A genetic linkage map was constructed by using simple sequence repeat and amplified fragment length polymorphism markers in the BC₁F₁ population derived from a cross between cultivated and wild rice bean. Using this map, 31 domestication-related traits were dissected into quantitative trait loci (QTLs). The genetic linkage map and QTLs of rice bean were compared with those of azuki bean.

Key Results

A total of 326 markers converged into 11 linkage groups (LGs), corresponding to the haploid number of rice bean chromosomes. The domestication-related traits in rice bean associated with a few major QTLs distributed as clusters on LGs 2, 4 and 7. A high level of co-linearity in marker order between the rice bean and azuki bean linkage maps was observed. Major QTLs in rice bean were found on LG4, whereas major QTLs in azuki bean were found on LG9.

Conclusions

This is the first report of a genetic linkage map and QTLs for domestication-related traits in rice bean. The inheritance of domestication-related traits was so simple that a few major QTLs explained the phenotypic variation between cultivated and wild rice bean. The high level of genomic synteny between rice bean and azuki bean facilitates QTL comparison between species. These results provide a genetic foundation for improvement of rice bean; interchange of major QTLs between rice bean and azuki bean might be useful for broadening the genetic variation of both species.     

QTL mapping for sexually dimorphic fitness-related traits in wild bighorn sheep

Dissecting the genetic architecture of fitness-related traits in wild populations is key to understanding evolution and the mechanisms maintaining adaptive genetic variation. We took advantage of a recently developed genetic linkage map and phenotypic information from wild pedigreed individuals from Ram Mountain, Alberta, Canada, to study the genetic architecture of ecologically important traits (horn volume, length, base circumference and body mass) in bighorn sheep. In addition to estimating sex-specific and cross-sex quantitative genetic parameters, we tested for the presence of quantitative trait loci (QTLs), colocalization of QTLs between bighorn sheep and domestic sheep, and sex × QTL interactions. All traits showed significant additive genetic variance and genetic correlations tended to be positive. Linkage analysis based on 241 microsatellite loci typed in 310 pedigreed animals resulted in no significant and five suggestive QTLs (four for horn dimension on chromosomes 1, 18 and 23, and one for body mass on chromosome 26) using genome-wide significance thresholds (Logarithm of odds (LOD) >3.31 and >1.88, respectively). We also confirmed the presence of a horn dimension QTL in bighorn sheep at the only position known to contain a similar QTL in domestic sheep (on chromosome 10 near the horns locus; nominal P<0.01) and highlighted a number of regions potentially containing weight-related QTLs in both species. As expected for sexually dimorphic traits involved in male-male combat, loci with sex-specific effects were detected. This study lays the foundation for future work on adaptive genetic variation and the evolutionary dynamics of sexually dimorphic traits in bighorn sheep.     

MULTIVARIATE ANALYSIS OF SELECTION IN EXPERIMENTAL POPULATIONS DERIVED FROM HYBRIDIZATION OF TWO ECOTYPES OF THE ANNUAL PLANT DIODIA TERES W. (RUBIACEAE)

Morphologically variable F₂ genotypes derived from hybridization of coastal and inland ecotypes of the annual plant Diodia teres were used to identify selection on morphological traits in the natural habitat of each ecotype. These ecotypes occur in very different habitats, and have evolved pronounced morphological differentiation. Selection analysis can suggest whether present patterns of selection can explain morphological differences between ecotypes. F₂ genotypes were characterized morphologically, clonally replicated, and transplanted into the habitat of each ecotype. Selection was measured on six morphological traits. Directional and stabilizing selection occurred on many traits; direction and strength of selection varied sharply at different stages of growth, as revealed by a path-analysis approach that divided selection into a set of independent components. Directional selection favored traits of the native population at the coastal habitat, but less so at the inland habitat. Selection was of sufficient strength to create the observed morphological differences between ecotypes in 25–100 generations, given constant selection and sufficient genetic variation. In effects on fitness, most traits were neither independent nor consistently interactive with other traits. Rather, many traits entered into strong but evanescent interactions affecting particular components of fitness. Observed interactions did not support the hypothesis that the morphology of each ecotype was functionally integrated to a high degree.     

QTL analysis of root traits as related to phosphorus efficiency in soybean

Background and Aims

Low phosphorus (P) availability is a major constraint to soybean growth and production, especially in tropical and subtropical areas. Root traits have been shown to play critical roles in P efficiency in crops. Identification of the quantitative trait loci (QTLs) conferring superior root systems could significantly enhance genetic improvement in soybean P efficiency.

Methods

A population of 106 F₉ recombinant inbred lines (RILs) derived from a cross between BD2 and BX10, which contrast in both P efficiency and root architecture, was used for mapping and QTL analysis. Twelve traits were examined in acid soils. A linkage map was constructed using 296 simple sequence repeat (SSR) markers with the Kosambi function, and the QTLs associated with these traits were detected by composite interval mapping and multiple-QTL mapping.

Key Results

The first soybean genetic map based on field data from parental genotypes contrasting both in P efficiency and root architecture was constructed. Thirty-one putative QTLs were detected on five linkage groups, with corresponding contribution ratios of 9·1–31·1 %. Thirteen putative QTLs were found for root traits, five for P content, five for biomass and five for yield traits. Three clusters of QTLs associated with the traits for root and P efficiency at low P were located on the B1 linkage group close to SSR markers Satt519 and Satt519-Sat_128, and on the D2 group close to Satt458; and one cluster was on the B1 linkage group close to Satt519 at high P.

Conclusions

Most root traits in soybean were conditioned by more than two minor QTLs. The region closer to Satt519 on the B1 linkage group might have great potential for future genetic improvement for soybean P efficiency through root selection.     

Detection of Quantitative Trait Loci for Yield and Drought Tolerance Traits in Soybean Using a Recombinant Inbred Line Population

To investigate the genetic basis of drought tolerance in soybean ( Glycine max L. Merr.) a recombinant inbred population with 184 F_2:7:11 lines developed from a cross between Kefeng1 (drought tolerant) and Nannong1138-2 (drought sensitive) were tested under water-stressed and well-watered conditions in field and greenhouse trials. Traits measured included leaf wilting coefficient, excised leaf water loss and relative water content as indicators of plant water status and seed yield. A total of 40 quantitative trait loci (QTLs) were identified: 17 for leaf water status traits under drought stress and 23 for seed yield under well-watered and drought-stressed conditions in both field and greenhouse trials. Two seed yield QTLs were detected under both well-watered and drought-stressed conditions in the field on molecular linkage group H and D1b, while two seed yield QTLs on molecular linkage group C2 were found under greenhouse conditions. Several QTLs for traits associated with plant water status were identified in both field and greenhouse trials, including two leaf wilting coefficient QTLs on molecular linkage group A2 and one excised leaf water loss QTL on molecular linkage group H. Phenotypic correlations of traits suggested several QTLs had pleiotropic or location-linked associations. These results will help to elucidate the genetic basis of drought tolerance in soybean, and could be incorporated into a marker-assisted selection breeding program to develop high-yielding soybean cultivars with improved tolerance to drought stress.     

Serpentine and non-serpentine ecotypes of Collinsia sparsiflora associate with distinct arbuscular mycorrhizal fungal assemblages

Although plant adaptation to serpentine soils has been studied for several decades, the mechanisms of plant adaptation to edaphic extremes are still poorly understood. Arbuscular mycorrhizal fungi (AMF) are common root symbionts that can increase the plant hosts' establishment and growth in stressful environments. However, little is known about the role plant-AMF interactions play in plant adaptation to serpentine. As a first step towards understanding this role, we examined the AMF assemblages associated with field populations of serpentine and non-serpentine ecotypes of California native plant Collinsia sparsiflora. We sampled roots of C. sparsiflora from three serpentine and three non-serpentine sites in close proximity (110 m to 1.94 km between sites) and analysed the small subunit ribosomal DNA gene amplified from root DNA extracts using AMF-specific primers. A total of 1952 clones from 24 root samples (four from each site) were sequenced. We used sequence similarity and phylogenetic analysis to determine operational taxonomic units (OTU) resulting in 19 OTUs representing taxa from six AMF genera, including one serpentine-specific OTU. We used Bray-Curtis similarity, multidimensional scaling and analysis of similarity to compare root sample AMF assemblages. These analyses clearly showed that plant ecotypes associated with distinct AMF assemblages; an Acaulospora OTU-dominated serpentine, and a Glomus OTU-dominated non-serpentine assemblages. Species diversity and evenness were significantly higher in serpentine assemblages. Finally, relate analysis showed a relationship between ecotype AMF assemblages and soil nutrients. This study reveals a strong relationship between AMF associates and plant adaptation to edaphic extremes.     

Explaining the heritability of an ecologically significant trait in terms of individual quantitative trait loci

Most natural populations display substantial genetic variation in behaviour, morphology, physiology, life history and the susceptibility to disease. A major challenge is to determine the contributions of individual loci to variation in complex traits. Quantitative trait locus (QTL) mapping has identified genomic regions affecting ecologically significant traits of many species. In nearly all cases, however, the importance of these QTLs to population variation remains unclear. In this paper, we apply a novel experimental method to parse the genetic variance of floral traits of the annual plant Mimulus guttatus into contributions of individual QTLs. We first use QTL-mapping to identify nine loci and then conduct a population-based breeding experiment to estimate V(Q), the genetic variance attributable to each QTL. We find that three QTLs with moderate effects explain up to one-third of the genetic variance in the natural population. Variation at these loci is probably maintained by some form of balancing selection. Notably, the largest effect QTLs were relatively minor in their contribution to heritability.     

QTL clusters reflect character associations in wild and cultivated rice

The genetic basis of character association related to differentiation found in the primary gene pool of rice was investigated based on the genomic distribution of quantitative trait loci (QTLs). Major evolutionary trends in cultivated rice of Asiatic origin (Oryza sativa) and its wild progenitor (O. rufipogon) are: (1) differentiation from wild to domesticated types (domestication), (2) ecotype differentiation between the perennial and annual types in wild races, and (3) the Indica versus Japonica type differentiation in cultivated races. Using 125 recombinant inbred lines (RILs) derived from a cross between an Indica cultivar of O. sativa and a strain of O. rufipogon carrying some Japonica-like characteristics, we mapped 147 markers, mostly RFLPs, on 12 chromosomes. Thirty-seven morphological and physiological quantitative traits were evaluated, and QTLs for 24 traits were detected. The mapped loci showed a tendency to form clusters that are composed of QTLs of the domestication-related traits as well as Indica/Japonica diagnostic traits. QTLs for perennial/annual type differences did not cluster. This cluster phenomenon could be considered "multifactorial linkages" followed by natural selection favoring co-adapted traits. Further, it is possible that the clustering phenomenon is partly due to pleiotropy of some unknown key factor(s) controlling various traits through diverse metabolic pathways. Chromosomal regions where QTL clusters were found coincided with the regions harboring genes or gene blocks where the frequency of cultivar-derived alleles in RILs is higher than expected. This distortion may be partly due to unconscious selection favoring cultivated plant type during the establishment of RILs.     

Genomic architecture of habitat‐related divergence and signature of directional selection in the body shapes of Gnathopogon fishes

Evolution of ecomorphologically relevant traits such as body shapes is important to colonize and persist in a novel environment. Habitat‐related adaptive divergence of these traits is therefore common among animals. We studied the genomic architecture of habitat‐related divergence in the body shape of Gnathopogon fishes, a novel example of lake–stream ecomorphological divergence, and tested for the action of directional selection on body shape differentiation. Compared to stream‐dwelling Gnathopogon elongatus, the sister species Gnathopogon caerulescens, exclusively inhabiting a large ancient lake, had an elongated body, increased proportion of the caudal region and small head, which would be advantageous in the limnetic environment. Using an F₂ interspecific cross between the two Gnathopogon species (195 individuals), quantitative trait locus (QTL) analysis with geometric morphometric quantification of body shape and restriction‐site associated DNA sequencing‐derived markers (1622 loci) identified 26 significant QTLs associated with the interspecific differences of body shape‐related traits. These QTLs had small to moderate effects, supporting polygenic inheritance of the body shape‐related traits. Each QTL was mostly located on different genomic regions, while colocalized QTLs were detected for some ecomorphologically relevant traits that are proxy of body and caudal peduncle depths, suggesting different degree of modularity among traits. The directions of the body shape QTLs were mostly consistent with the interspecific difference, and QTL sign test suggested a genetic signature of directional selection in the body shape divergence. Thus, we successfully elucidated the genomic architecture underlying the adaptive changes of the quantitative and complex morphological trait in a novel system.