Components of reproductive isolation between the monkeyflowers Mimulus lewisii and M. cardinalis (Phrymaceae)

Evolutionists have long recognized the role of reproductive isolation in speciation, but the relative contributions of different reproductive barriers are poorly understood. We examined the nature of isolation between Mimulus lewisii and M. cardinalis, sister species of monkeyflowers. Studied reproductive barriers include: ecogeographic isolation; pollinator isolation (pollinator fidelity in a natural mixed population); pollen competition (seed set and hybrid production from experimental interspecific, intraspecific, and mixed pollinations in the greenhouse); and relative hybrid fitness (germination, survivorship, percent flowering, biomass, pollen viability, and seed mass in the greenhouse). Additionally, the rate of hybridization in nature was estimated from seed collections in a sympatric population. We found substantial reproductive barriers at multiple stages in the life history of M. lewisii and M. cardinalis. Using range maps constructed from herbarium collections, we estimated that the different ecogeographic distributions of the species result in 58.7% reproductive isolation. Mimulus lewisii and M. cardinalis are visited by different pollinators, and in a region of sympatry 97.6% of pollinator foraging bouts were specific to one species or the other. In the greenhouse, interspecific pollinations generated nearly 50% fewer seeds than intraspecific controls. Mixed pollinations of M. cardinalis flowers yielded >75% parentals even when only one-quarter of the pollen treatment consisted of M. cardinalis pollen. In contrast, both species had similar siring success on M. lewisii flowers. The observed 99.915% occurrence of parental M. lewisii and M. cardinalis in seeds collected from a sympatric population is nearly identical to that expected, based upon our field observations of pollinator behavior and our laboratory experiments of pollen competition. F1 hybrids exhibited reduced germination rates, high survivorship and reproduction, and low pollen and ovule fertility. In aggregate, the studied reproductive barriers prevent, on average, 99.87% of gene flow, with most reproductive isolation occurring prior to hybrid formation. Our results suggest that ecological factors resulting from adaptive divergence are the primary isolating barriers in this system. Additional studies of taxa at varying degrees of evolutionary divergence are needed to identify the relative importance of pre- and postzygotic isolating mechanisms in speciation.     

Genetics of Cryptic Speciation within an Arctic Mustard,Draba nivalis

Crossing experiments indicate that hybrid sterility barriers frequently have developed within diploid, circumpolar plant species of the genus Draba. To gain insight into the rapid evolution of postzygotic reproductive isolation in this system, we augmented the linkage map of one of these species, D. nivalis, and searched for quantitative trait loci (QTLs) associated with reproductive isolation. The map adds 63 new dominant markers to a previously published dataset of 31 co-dominant microsatellites. These markers include 52 amplified fragment length polymorphisms (AFLPs) and 11 sequence-specific amplified polymorphisms (SSAPs) based on retrotransposon sequence. 22 markers displaying transmission ratio distortion were further included in the map. We resolved eight linkage groups with a total map length of 894 cM. Significant genotype-trait associations, or quantitative trait loci (QTL), were detected for reproductive phenotypes including pollen fertility (4 QTLs), seed set (3 QTLs), flowering time (3 QTLs) and number of flowers (4 QTLs). Observed patterns of inheritance were consistent with the influence of both nuclear-nuclear interactions and chromosomal changes on these traits. All seed set QTLs and one pollen fertility QTL displayed underdominant effects suggestive of the involvement of chromosomal rearrangements in hybrid sterility. Interestingly, D. nivalis is predominantly self-fertilizing, which may facilitate the establishment of underdominant loci and contribute to reproductive isolation.     

Minor quantitative trait loci underlie floral traits associated with mating system divergence in Mimulus

The genetic basis of species differences provides insight into the mode and tempo of phenotypic divergence. We investigate the genetic basis of floral differences between two closely related plant taxa with highly divergent mating systems, Mimulus guttatus (large-flowered outcrosser) and M. nasutus (small-flowered selfer). We had previously constructed a framework genetic linkage map of the hybrid genome containing 174 markers spanning approximately 1800 cM on 14 linkage groups. In this study, we analyze the genetics of 16 floral, reproductive, and vegetative characters measured in a large segregating M. nasutus x M. guttatus F2 population (N = 526) and in replicates of the parental lines and F1 hybrids. Phenotypic analyses reveal strong genetic correlations among floral traits and epistatic breakdown of male and female fertility traits in the F2 hybrids. We use multitrait composite interval mapping to jointly locate and characterize quantitative trait loci (QTLs) underlying interspecific differences in seven floral traits. We identified 24 floral QTLs, most of which affected multiple traits. The large number of QTLs affecting each trait (mean = 13, range = 11-15) indicates a strikingly polygenic basis for floral divergence in this system. In general, QTL effects are small relative to both interspecific differences and environmental variation within genotypes, ruling out QTLs of major effect as contributors to floral divergence between M. guttatus and M. nasutus. QTLs show no pattern of directional dominance. Floral characters associated with pollinator attraction (corolla width) and self-pollen deposition (stigma-anther distance) share several pleiotropic or linked QTLs, but unshared QTLs may have allowed selfing to evolve independently from flower size. We discuss the polygenic nature of divergence between M. nasutus and M. guttatus in light of theoretical work on the evolution of selfing, genetics of adaptation, and maintenance of variation within populations.     

Floral volatile alleles can contribute to pollinator‐mediated reproductive isolation in monkeyflowers (Mimulus)

Pollinator‐mediated reproductive isolation is a major factor in driving the diversification of flowering plants. Studies of floral traits involved in reproductive isolation have focused nearly exclusively on visual signals, such as flower color. The role of less obvious signals, such as floral scent, has been studied only recently. In particular, the genetics of floral volatiles involved in mediating differential pollinator visitation remains unknown. The bumblebee‐pollinated Mimulus lewisii and hummingbird‐pollinated Mimulus cardinalis are a model system for studying reproductive isolation via pollinator preference. We have shown that these two species differ in three floral terpenoid volatiles – d ‐limonene, β‐myrcene, and E‐β‐ocimene – that are attractive to bumblebee pollinators. By genetic mapping and in vitro analysis of enzyme activity we demonstrate that these interspecific differences are consistent with allelic variation at two loci, LIMONENE‐MYRCENE SYNTHASE (LMS) and OCIMENE SYNTHASE (OS). Mimulus lewisii LMS (MlLMS) and OS (MlOS) are expressed most strongly in floral tissue in the last stages of floral development. Mimulus cardinalis LMS (McLMS) is weakly expressed and has a nonsense mutation in exon 3. Mimulus cardinalis OS (McOS) is expressed similarly to MlOS, but the encoded McOS enzyme produces no E‐β‐ocimene. Recapitulating the M. cardinalis phenotype by reducing the expression of MlLMS by RNA interference in transgenic M. lewisii produces no behavioral difference in pollinating bumblebees; however, reducing MlOS expression produces a 6% decrease in visitation. Allelic variation at the OCIMENE SYNTHASE locus is likely to contribute to differential pollinator visitation, and thus promote reproductive isolation between M. lewisii and M. cardinalis. OCIMENE SYNTHASE joins a growing list of ‘speciation genes’ (‘barrier genes’) in flowering plants.     

The evolution of species' distributions: reciprocal transplants across the elevation ranges of Mimulus cardinalis and M. lewisii

Every species occupies a limited geographic area, but it remains unclear why traits that limit distribution do not evolve to allow range expansion. Hypotheses for the evolutionary stability of geographic ranges assume that species are maladapted at the range boundary and unfit beyond the current range, but this assumption has rarely been tested. To examine how fitness varies across species' ranges, we reciprocally transplanted two species of monkeyflowers, Mimulus cardinalis and M. lewisii, within and beyond their present elevation ranges. We used individuals of known parentage from populations collected across the elevation ranges of both species to examine whether populations are adapted to position within the range. For both species we found the greatest average fitness at elevations central within the range, reduced fitness at the range margin, and zero or near-zero fitness when transplanted beyond their present elevation range limits. However, the underlying causes of fitness variation differed between the species. At high elevations beyond its range, M. cardinalis displayed reduced growth and fecundity, whereas at low elevations M. lewisii experienced high mortality. Weak differences in performance were observed among populations within each species and these were not related to elevation of origin. Low fitness of both species at their range margin and weak differentiation among populations within each species suggest that adaptation to the environment at and beyond the range margin is hindered, illustrating that range margins provide an interesting system in which to study limits to adaptation.     

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.     

Genomic collinearity and the genetic architecture of floral differences between the homoploid hybrid species Iris nelsonii and one of its progenitors,Iris hexagona

Hybrid speciation represents a relatively rapid form of diversification. Early models of homoploid hybrid speciation suggested that reproductive isolation between the hybrid species and progenitors primarily resulted from karyotypic differences between the species. However, genic incompatibilities and ecological divergence may also be responsible for isolation. Iris nelsonii is an example of a homoploid hybrid species that is likely isolated from its progenitors primarily by strong prezygotic isolation, including habitat divergence, floral isolation and post-pollination prezygotic barriers. Here, we used linkage mapping and quantitative trait locus (QTL) mapping approaches to investigate genomic collinearity and the genetic architecture of floral differences between I. nelsonii and one of its progenitor species I. hexagona. The linkage map produced from this cross is highly collinear with another linkage map produced between I. fulva and I. brevicaulis (the two other species shown to have contributed to the genomic makeup of I. nelsonii), suggesting that karyotypic differences do not contribute substantially to isolation in this homoploid hybrid species. Similar to other studies of the genetic architecture of floral characteristics, at least one QTL was found that explained >20% variance in each color trait, while minor QTLs were detected for each morphological trait. These QTLs will serve as hypotheses for regions under selection by pollinators.     

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.     

The relationship between loci for mating system and fitness-related traits in Mimulus (Scrophulariaceae): a test for deleterious pleiotropy of QTLs with large effects.

Loci with large phenotypic effects are generally not thought to be important in the evolution of quantitative traits because of their deleterious pleiotropic effects, yet empirical studies of such pleiotropic effects are lacking. Here I use molecular markers to test the extent of deleterious pleiotropy of quantitative trait loci (QTLs) that have large effects on mating system differences between the wild plants Mimulus guttatus and M. platycalyx (Scrophulariaceae). Six fitness-related traits, namely germination rate (GR), number of nodes (NN), number of flowers (NF), plant height (HT), above-ground biomass (WT), and flowering time (FT) were examined in a growth chamber for a backcross population between M. guttatus and M. platycalyx (with M. platycalyx as recurrent parent). Interval mapping based upon a linkage map consisting of isozyme and random amplified polymorphic DNA (RAPD) markers detected no QTL for fitness-related traits near the mating system QTLs. Single-marker analysis based upon 13 markers flanking the mating system QTLs detected three significant marker-fitness trait associations, and these associations indicate beneficial effects of mating system loci. This suggests that QTLs with large effects on mating system traits do not have significant deleterious pleiotropic effects, and that they could be important factors in adaptive evolution of Mimulus.     

The genetic architecture of reproductive isolation in Louisiana irises: pollination syndromes and pollinator preferences

In animal-pollinated plants, pollinator preferences for divergent floral forms can lead to partial reproductive isolation. We describe regions of plant genomes that affect pollinator preferences for two species of Louisiana Irises, Iris brevicaulis and Iris fulva, and their artificial hybrids. Iris brevicaulis and I. fulva possess bee and bird-pollination syndromes, respectively. Hummingbirds preferred I. fulva and under-visited both I. brevicaulis and backcrosses toward this species. Lepidopterans preferred I. fulva and backcrosses toward I. fulva, but also under-visited I. brevicaulis and I. brevicaulis backcrosses. Bumblebees preferred I. brevicaulis and F1 hybrids and rarely visited I. fulva. Although all three pollen vectors preferred one or the other species, these preferences did not prevent visitation to other hybrid/parental classes. Quantitative trait locus (QTL) mapping, in reciprocal BC1 mapping populations, defined the genetic architecture of loci that affected pollinator behavior. We detected six and nine QTLs that affected pollinator visitation rates in the BCIb and BCIf mapping populations, respectively, with as many as three QTLs detected for each trait. Overall, this study reflects the possible role of quantitative genetic factors in determining (1) reproductive isolation, (2) the pattern of pollinator-mediated genetic exchange, and thus (3) hybrid zone evolution.     

Close clustering of anthers and stigma in Ipomoea hederacea enhances prezygotic isolation from Ipomoea purpurea

Theory predicts that, for taxa that are already substantially postzygotically isolated but for which hybrid mating is still costly, enhanced prezygotic isolation will be favored. Here, we tested this hypothesis by examining the potential contribution of one particular floral trait, herkogamy, to prezygotic isolation between two species of morning glory, Ipomoea hederacea and Ipomoea purpurea. This trait was experimentally manipulated to determine whether it is a likely prezygotic isolating barrier in naturally pollinated arrays in the field. Emasculated I. hederacea flowers set significantly fewer seeds than did control flowers, indicating that clustering of anthers and stigma in I. hederacea enhances prezygotic isolation from I. purpurea. We hypothesize that this occurs through some combination of mechanical protection and increased self-pollination, with the effect of mechanical protection estimated to be 30% greater than the effect of increased selfing. Our results identify stigma-anther proximity as a likely prezygotic isolating barrier and target of selection in the presence of heterospecific pollen flow, and provide motivation for further study of the role of floral morphology in reproductive isolation in this system.     

Reinforcement and divergence under assortative mating

Traits that cause assortative mating such as the flowering time in plants and body size in animals can produce reproductive isolation between hybridizing populations. Can selection against unfit hybrids cause two populations to diverge in their mean values for these kinds of traits? Here I present a haploid analytical model of one population that receives gene flow from another. The partial pre-zygotic isolation between the two populations is caused by assortative mating for a trait that is influenced by any number of genes with additive effects. The post-zygotic isolation is caused by selection against genetic incompatibilities that can involve any form of selection on individual genes and gene combinations (epistasis). The analysis assumes that the introgression rate and selection coefficients are small. The results show that the assortment trait mean will not diverge from the immigrants unless there is direct selection on the trait favouring it to do so or there are genes of very large effect. The amount of divergence at equilibrium is determined by a balance between direct selection on the assortment trait and introgression from the other population. Additional selection against hybrid genetic incompatibilities reduces the effective migration rate and allows greater divergence. The role of assortment in speciation is discussed in the light of these results.     

Mapping quantitative trait loci for heat tolerance of reproductive traits in tomato (<Emphasis Type="Italic">Solanum lycopersicum</Emphasis>)

Global warming has become a worldwide concern due to its adverse effects on agricultural output. In particular, long-term mildly high temperatures interfere with sexual reproduction and thus fruit and seed set. To uncover the genetic basis of observed variation in tolerance against heat, a bi-parental F₂ mapping population from two contrasting cultivars, i.e. Nagcarlang and NCHS-1, was generated and phenotyped under continuous mild heat conditions for a number of traits underlying reproductive success, i.e. pollen viability, pollen number, style length, anther length, style protrusion, female fertility and flowering characteristics, i.e. inflorescence number and flowers per inflorescence. Quantitative trait loci (QTLs) were identified for most of these traits, including a single, highly significant one for pollen viability, which accounted for 36% of phenotypic variation in the population and modified pollen viability under high temperature with around 20%. QTLs for some traits colocalised, indicating trait dependency or pleiotropic-effect loci. We conclude that a limited set of major genes determines differences in performance of reproductive traits under continuous mild heat in tomato. The results contribute to our fundamental understanding of pollen thermotolerance and may support development of more heat-tolerant tomato varieties.     

Quantitative trait loci affecting a courtship signal in Drosophila melanogaster

Courtship plays a major role in the sexual isolation of species, yet the genetics underlying courtship behaviour are poorly understood. Here we analyse quantitative trait loci (QTL) for a major component of courtship song in recombinant inbred lines derived from two laboratory strains of Drosophila melanogaster. The total variance among lines exceeds that between parental strains, and is broadly similar to that seen among geographic strains of the Cosmopolitan form of this species. Previous studies of the quantitative genetics of fly song have implied a polygenic additive inheritance with numerous genes spread throughout the genome. We find evidence for only three significant QTLs explaining 54% of the genetic variance in total. Thus there is evidence for a few large effect genes contributing to the genetic variance among lines. Interestingly, almost all of the candidate song genes previously described for D. melanogaster do not coincide with our QTLs.     

Epistat : a computer program for identifying and testing interactions between pairs of quantitative trait loci

 We describe a computer program, Epistat, which combines statistical methods and color-graphic displays to facilitate the analysis of interactions between pairs of quantitative trait loci (QTLs). Epistat organizes genetic-mapping data and quantitative-trait values into graphic displays which illustrate the individual effects of single loci as well as the interactions between any two loci. Keyboard commands allow the user to search the data set for individual QTLs and to test for interactions between QTLs. For a given trait, the program displays the effects of the alleles at each of two loci on the quantitative-trait value, as well as the effects of the interactions between these alleles. Loglikelihood ratios are used to compare the likelihood of explaining the effects by null, additive, or epistatic models. Examples of interactions in soybean are presented for near-infrared transmittance (NIT), seed number, and reproductive period. Epistat has been used to find numerous interactions between QTLs in soybean in which trait variation at one locus is conditional upon a specific allele at another. Received: 16 January 1996 / Accepted: 27 September 1996     

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.     

Identification of genetic factors controlling domestication-related traits of rice using an F2 population of a cross between Oryza sativa and O. rufipogon

 Domesticated rice differs from the wild progenitor in large arrays of morphological and physiological traits. The present study was conducted to identify the genetic factors controlling the differences between cultivated rice and its wild progenitor, with the intention to assess the genetic basis of the changes associated with the processes of rice domestication. A total of 19 traits, including seven qualitative and 12 quantitative traits, that are related to domestication were scored in an F₂ population from a cross between a variety of the Asian cultivated rice (Oryza sativa) and an accession of the common wild rice (O. rufipogon). Loci controlling the inheritance of these traits were determined by making use of a molecular linkage map consisting of 348 molecular-marker loci (313 RFLPs, 12 SSRs and 23 AFLPs) based on this F₂ population. All seven qualitative traits were each controlled by a single Mendelian locus. Analysis of the 12 quantitative traits resolved a total of 44 putative QTLs with an average of 3.7 QTLs per trait. The amount of variation explained by individual QTLs ranged from a low of 6.9% to a high of 59.8%, and many of the QTLs accounted for more than 20% of the variation. Thus, genes of both major and minor effect were involved in the differences between wild and cultivated rice. The results also showed that most of the genetic factors (qualitative or QTLs) controlling the domestication-related traits were concentrated in a few chromosomal blocks. Such a clustered distribution of the genes may provide explanations for the genetic basis of the “domestication syndrome” observed in evolutionary studies and also for the “linkage drag” that occurs in many breeding programs. The information on the genetic basis of some desirable traits possessed by the wild parent may also be useful for facilitating the utilization of these traits in rice-breeding programs. Received: 1 June 1998 / Accepted: 28 July 1998     

Quantitative trait loci affecting amylose,amylopectin and starch content in maize recombinant inbred lines

The loci explaining the variability of quantitative traits related to starch content and composition (amylose, amylopectin and water soluble fraction) were searched for in maize kernels. Multifactorial genetic methods were used to detect and locate QTLs (quantitative trait loci) on a genetic map consisting mainly of RFLP markers for genes with known function. The genetic material was recombinant inbred lines originating from parents differing in starch structure (dent vs. flint). Kernels were harvested from field grown plants for two successive years and under two pollination systems. Main effect and epistasis QTLs were detected using two methods, composite interval mapping (MQTL) and ANOVA. Despite large year-to-year differences, physiologically meaningful co-locations were observed between trait QTLs. Moreover, the number of expressed sequences on our map allowed the search for co-locations between QTLs and genes involved in carbohydrate metabolism. The main co-location was between an amylose QTL and Shrunken 2 (SH2) locus, on chromosome 3 (SH2 encoding for the large subunit of ADPglucose pyrophosphorylase). The importance of this locus as a candidate gene for a starch QTL is in agreement with previous studies based either on QTL co-locations or on revertant analysis. Other co-locations were observed between amylose and amylopectin QTLs and the two loci of IVR1 invertase genes on chromosomes 2 and 10. Further comparison with previously detected QTLs for carbohydrate metabolism in maize leaves showed consistent co-location in map regions devoid of candidate genes, such as near chromosome 1S telomere. The possible contribution of regulatory genes in this region is discussed.     

QTL‐seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations

The majority of agronomically important crop traits are quantitative, meaning that they are controlled by multiple genes each with a small effect (quantitative trait loci, QTLs). Mapping and isolation of QTLs is important for efficient crop breeding by marker‐assisted selection (MAS) and for a better understanding of the molecular mechanisms underlying the traits. However, since it requires the development and selection of DNA markers for linkage analysis, QTL analysis has been time‐consuming and labor‐intensive. Here we report the rapid identification of plant QTLs by whole‐genome resequencing of DNAs from two populations each composed of 20–50 individuals showing extreme opposite trait values for a given phenotype in a segregating progeny. We propose to name this approach QTL‐seq as applied to plant species. We applied QTL‐seq to rice recombinant inbred lines and F₂ populations and successfully identified QTLs for important agronomic traits, such as partial resistance to the fungal rice blast disease and seedling vigor. Simulation study showed that QTL‐seq is able to detect QTLs over wide ranges of experimental variables, and the method can be generally applied in population genomics studies to rapidly identify genomic regions that underwent artificial or natural selective sweeps.     

Metabolite profiling and quantitative genetics of natural variation for flavonoids in Arabidopsis

Little is known about the range and the genetic bases of naturally occurring variation for flavonoids. Using Arabidopsis thaliana seed as a model, the flavonoid content of 41 accessions and two recombinant inbred line (RIL) sets derived from divergent accessions (Cvi-0×Col-0 and Bay-0×Shahdara) were analysed. These accessions and RILs showed mainly quantitative rather than qualitative changes. To dissect the genetic architecture underlying these differences, a quantitative trait locus (QTL) analysis was performed on the two segregating populations. Twenty-two flavonoid QTLs were detected that accounted for 11-64% of the observed trait variations, only one QTL being common to both RIL sets. Sixteen of these QTLs were confirmed and coarsely mapped using heterogeneous inbred families (HIFs). Three genes, namely TRANSPARENT TESTA (TT)7, TT15, and MYB12, were proposed to underlie their variations since the corresponding mutants and QTLs displayed similar specific flavonoid changes. Interestingly, most loci did not co-localize with any gene known to be involved in flavonoid metabolism. This latter result shows that novel functions have yet to be characterized and paves the way for their isolation.