Genomic Dissection of Leaf Angle in Maize (Zea mays L.) Using a Four-Way Cross Mapping Population

Increasing grain yield by the selection for optimal plant architecture has been the key focus in modern maize breeding. As a result, leaf angle, an important determinant of plant architecture, has been significantly improved to adapt to the ever-increasing plant density in maize production over the past several decades. To extend our understanding on the genetic mechanisms of leaf angle in maize, we developed the first four-way cross mapping population, consisting of 277 lines derived from four maize inbred lines with varied leaf angles. The four-way cross mapping population together with the four parental lines were evaluated for leaf angle in two environments. In this study, we reported linkage maps built in the population and quantitative trait loci (QTL) on leaf angle detected by inclusive composite interval mapping (ICIM). ICIM applies a two-step strategy to effectively separate the cofactor selection from the interval mapping, which controls the background additive and dominant effects at the same time. A total of 14 leaf angle QTL were identified, four of which were further validated in near-isogenic lines (NILs). Seven of the 14 leaf angle QTL were found to overlap with the published leaf angle QTL or genes, and the remaining QTL were unique to the four-way population. This study represents the first example of QTL mapping using a four-way cross population in maize, and demonstrates that the use of specially designed four-way cross is effective in uncovering the basis of complex and polygenetic trait like leaf angle in maize.     

The Genetic Basis of Natural Variation in Oenological Traits in Saccharomyces cerevisiae

Saccharomyces cerevisiae is the main microorganism responsible for wine alcoholic fermentation. The oenological phenotypes resulting from fermentation, such as the production of acetic acid, glycerol, and residual sugar concentration are regulated by multiple genes and vary quantitatively between different strain backgrounds. With the aim of identifying the quantitative trait loci (QTLs) that regulate oenological phenotypes, we performed linkage analysis using three crosses between highly diverged S. cerevisiae strains. Segregants from each cross were used as starter cultures for 20-day fermentations, in synthetic wine must, to simulate actual winemaking conditions. Linkage analysis on phenotypes of primary industrial importance resulted in the mapping of 18 QTLs. We tested 18 candidate genes, by reciprocal hemizygosity, for their contribution to the observed phenotypic variation, and validated five genes and the chromosome II right subtelomeric region. We observed that genes involved in mitochondrial metabolism, sugar transport, nitrogen metabolism, and the uncharacterized ORF YJR030W explained most of the phenotypic variation in oenological traits. Furthermore, we experimentally validated an exceptionally strong epistatic interaction resulting in high level of succinic acid between the Sake FLX1 allele and the Wine/European MDH2 allele. Overall, our work demonstrates the complex genetic basis underlying wine traits, including natural allelic variation, antagonistic linked QTLs and complex epistatic interactions between alleles from strains with different evolutionary histories.     

Genetic Dissection of Wheat Kernel Hardness Using Conditional QTL Mapping of Kernel Size and Protein-Related Traits

Kernel hardness (KH) is one of the primary quality parameters for common wheat (Triticum aestivum L.) and has a major impact on milling, flour quality, and end-product properties. In addition to Puroindoline (Pin) mutations and differences in Pin expression, other factors, such as kernel size and protein-related traits, play noticeable roles in determining hardness, but at the quantitative trait locus (QTL) level, the influence of these factors remains unclear. In this study, genetic relationships between KH and kernel size traits and between KH and protein-related traits were demonstrated by unconditional and conditional mapping using a wheat 90K genotyping assay with a segregating population of 173 recombinant inbred lines in four environments. Eight additive QTL for KH were detected using unconditional QTL mapping analysis; these QTL were primarily distributed on chromosomes 4B, 5A, 5B, and 6D, with phenotypic variation that ranged from 0.2 to 17.7%. In addition, one pair of epistatic QTL (QKH3B.4-65/QKH4B.6-2) was identified by unconditional mapping, and this pair accounted for 1.6% of the phenotypic variation. Through conditional mapping, after excluding the influences of kernel size and protein-related traits, 14 QTL were discovered and accounted for 0.6–18.5% of the phenotypic variation. Of them, the stable QTL QKH4B.4-17 made the largest contribution, which was partially contributed by the kernel length (KL), kernel thickness (KT), and dry gluten content (DGC). Furthermore, QKH4B.4-17 was crucially contributed by the kernel width (KW), kernel diameter (KD), kernel protein content (KPC), and wet gluten content (WGC) and was independent of the sedimentation volume (SV) and gluten index (GI). Another major QTL, QKH5B.10-63, was independent of the KW and KT; partly due to the variations in KL, KD, DGC, and WGC; and conclusively contributed by the KPC, SV, and GI. Seven additional QTL were only detected in the conditional analysis and were crucially contributed by kernel size or protein-related traits. These results demonstrated that kernel size and protein-related traits play significant roles in determining KH. The present study increases the understanding of the relationships between KH and kernel size and between KH and protein-related traits at the QTL level.     

The Genetic Basis of Natural Variation in Seed Size and Seed Number and Their Trade-Off Using Arabidopsis thaliana MAGIC Lines

Offspring number and size are key traits determining an individual’s fitness and a crop’s yield. Yet, extensive natural variation within species is observed for these traits. Such variation is typically explained by trade-offs between fecundity and quality, for which an optimal solution is environmentally dependent. Understanding the genetic basis of seed size and number, as well as any possible genetic constraints preventing the maximization of both, is crucial from both an evolutionary and applied perspective. We investigated the genetic basis of natural variation in seed size and number using a set of Arabidopsis thaliana multiparent advanced generation intercross (MAGIC) lines. We also tested whether life history affects seed size, number, and their trade-off. We found that both seed size and seed number are affected by a large number of mostly nonoverlapping QTL, suggesting that seed size and seed number can evolve independently. The allele that increases seed size at most identified QTL is from the same natural accession, indicating past occurrence of directional selection for seed size. Although a significant trade-off between seed size and number is observed, its expression depends on life-history characteristics, and generally explains little variance. We conclude that the trade-off between seed size and number might have a minor role in explaining the maintenance of variation in seed size and number, and that seed size could be a valid target for selection.     

Genetic Variation for Sex Ratio Traits within a Natural Population of a Parasitic Wasp, Nasonia Vitripennis

By analyzing isofemale strains extracted from a natural population of Nasonia vitripennis, we detected variation for the sex ratios produced in fresh hosts (first sex ratios) and in previously parasitized hosts (second sex ratios). Under simple assumptions of population structure, this between-strain heterogeneity of first sex ratios results in heterogeneity of fitnesses. There is approximately ten percent difference in average fitnesses between the strains. (The fitnesses of second sex ratios are analyzed in the accompanying paper.) Average first and average second sex ratios are uncorrelated. There is significant between-female heterogeneity within some strains for first sex ratios but not for second sex ratios. In addition, the average direct-developing and diapause first sex ratios (but not second sex ratios) are significantly correlated. There are significant correlations between the direct-developing and diapause sex ratios produced by the same female. The strains differ in their effects on the sex ratio and size of another female's brood in the same host. Data on these types of variation for sex ratio traits are essential for further progress in the study of sex ratio evolution.     

The Genetic Basis of Natural Variation in Caenorhabditis elegans Telomere Length

Telomeres are involved in the maintenance of chromosomes and the prevention of genome instability. Despite this central importance, significant variation in telomere length has been observed in a variety of organisms. The genetic determinants of telomere-length variation and their effects on organismal fitness are largely unexplored. Here, we describe natural variation in telomere length across the Caenorhabditis elegans species. We identify a large-effect variant that contributes to differences in telomere length. The variant alters the conserved oligonucleotide/oligosaccharide-binding fold of protection of telomeres 2 (POT-2), a homolog of a human telomere-capping shelterin complex subunit. Mutations within this domain likely reduce the ability of POT-2 to bind telomeric DNA, thereby increasing telomere length. We find that telomere-length variation does not correlate with offspring production or longevity in C. elegans wild isolates, suggesting that naturally long telomeres play a limited role in modifying fitness phenotypes in C. elegans.     

Genetic Variance for Body Size in a Natural Population of Drosophila Buzzatii

Previous work has shown thorax length to be under directional selection in the Drosophila buzzatii population of Carboneras. In order to predict the genetic consequences of natural selection, genetic variation for this trait was investigated in two ways. First, narrow sense heritability was estimated in the laboratory F2 generation of a sample of wild flies by means of the offspring-parent regression. A relatively high value, 0.59, was obtained. Because the phenotypic variance of wild flies was 7-9 times that of the flies raised in the laboratory, "natural" heritability may be estimated as one-seventh to one-ninth that value. Second, the contribution of the second and fourth chromosomes, which are polymorphic for paracentric inversions, to the genetic variance of thorax length was estimated in the field and in the laboratory. This was done with the assistance of a simple genetic model which shows that the variance among chromosome arrangements and the variance among karyotypes provide minimum estimates of the chromosome's contribution to the additive and genetic variances of the trait, respectively. In males raised under optimal conditions in the laboratory, the variance among second-chromosome karyotypes accounted for 11.43% of the total phenotypic variance and most of this variance was additive; by contrast, the contribution of the fourth chromosome was nonsignificant. The variance among second-chromosome karyotypes accounted for 1.56-1.78% of the total phenotypic variance in wild males and was nonsignificant in wild females. The variance among fourth chromosome karyotypes accounted for 0.14-3.48% of the total phenotypic variance in wild flies. At both chromosomes, the proportion of additive variance was higher in mating flies than in nonmating flies.     

Genetic Variation and Population Differentiation in Natural Populations of Cryptomeria japonica

Abstract Sugi (Cryptomeria japonica D. Don) is a valuable tree species in Japan. The present natural distribution is limited to small scattered areas in temperate moist regions, and most of these areas are surrounded by vast artificial plantations. We studied natural populations of C. japonica in an effort to determine the amount and distribution of genetic diversity using 12 allozyme markers. The amount of genetic variation within the species is high (H_T=0.196) but most is found within populations with little among populations (G_ST=0.034) despite their isolated distribution. This pattern of genetic diversity is inferred to be the consequence of the following: (1) the distribution of this species in the past was wider and more continuous than it is now; (2) a high rate of gene flow occurs, perhaps including gene flow between natural populations and plantations; and (3) the long lifespan. However, the distribution of allele frequencies at the 6Pg-1 in northern populations on the side near the Sea of Japan is clearly different from those in other populations. This observation is inferred to result from founding events.     

普通玉米籽粒性状的遗传效应分析

采用二倍体种子遗传模型及其分析方法,研究了５个玉米籽粒性状的直接效应、母体效应和细胞质效应．分析结果表明,各性状的遗传同时受种子直接效应和母体效应的影响,细胞质基因对百粒重和粒宽具有极显著影响．除粒长、粒厚的直接显性效应与母体显性效应间的协方差外,直接效应与母体效应间的协方差均不显著．因此,通过母体植株的表现可对这些性状进行有效的选择．Ｓ_２２和 ８７－１是改良粒重的优良亲本．选择粒较宽的自交系作母本有利于提高后代选系及Ｆ_１的百粒重．     

Quantitative Genetic Variation of Odor-Guided Behavior in a Natural Population of Drosophila Melanogaster

Quantitative genetic variation in behavioral response to the odorant, benzaldehyde, was assessed among a sample of 43 X and 35 third chromosomes extracted from a natural population and substituted into a common inbred background. Significant genetic variation among chromosome lines was detected. Heritability estimates for olfactory response, however, were low, as is typical for traits under natural selection. Furthermore, the loci affecting naturally occurring variation in olfactory response to benzaldehyde were not the same in males and females, since the genetic correlation between the sexes was low and not significantly different from zero for the chromosome 3 lines. Competitive fitness, viability and fertility of the chromosome 3 lines were estimated using the balancer equilibrium technique. Genetic correlations between fitness and odor-guided behavior were not significantly different from zero, suggesting the number of loci causing variation in olfactory response is small relative to the number of loci causing variation in fitness. Since different genes affect variation in olfactory response in males and females, genetic variation for olfactory response could be maintained by genotype X sex environment interaction. This unusual genetic architecture implies that divergent evolutionary trajectories for olfactory behavior may occur in males and females.     

Analysis of Genetic Variation in Natural Populations of Medicago truncatula of Southern Tunisian Ecological Areas, Using Morphological Traits and SSR Markers

We used 19 quantitative traits and 14 microsatellite markers (SSRs) to analyze the genetic variation in four natural populations of the model legume Medicago truncatula sampled in southern Tunisia. The greatest genetic variation of quantitative traits and molecular markers occurred within populations (>71%). In contrast to quantitative population differentiation (Q _ST ?=?0.09), a high level of molecular differentiation (F _ST ?=?0.23) was found among populations. The majority of quantitative traits exhibited Q _ST values significantly less than F _ST values, suggesting that selection may be acting to suppress differentiation for these traits. There was no significant correlation between genetic variation of quantitative traits and molecular markers within populations. On the other hand, significant correlations were found between measured quantitative characters and the site-of-origin environmental factors. The eco-geographical factors with the greatest influence on the variation of measured traits among populations were altitude, followed by soil texture, assimilated phosphorus (P₂O₅) and organic matter. Nevertheless, there were no consistent patterns of associations between gene diversity (He) and eco-geographical factors.     

The Genetic Basis of Transgressive Ovary Size in Honeybee Workers

Ovarioles are the functional unit of the female insect reproductive organs and the number of ovarioles per ovary strongly influences egg-laying rate and fecundity. Social evolution in the honeybee (Apis mellifera) has resulted in queens with 200–360 total ovarioles and workers with usually 20 or less. In addition, variation in ovariole number among workers relates to worker sensory tuning, foraging behavior, and the ability to lay unfertilized male-destined eggs. To study the genetic architecture of worker ovariole number, we performed a series of crosses between Africanized and European bees that differ in worker ovariole number. Unexpectedly, these crosses produced transgressive worker phenotypes with extreme ovariole numbers that were sensitive to the social environment. We used a new selective pooled DNA interval mapping approach with two Africanized backcrosses to identify quantitative trait loci (QTL) underlying the transgressive ovary phenotype. We identified one QTL on chromosome 11 and found some evidence for another QTL on chromosome 2. Both QTL regions contain plausible functional candidate genes. The ovariole number of foragers was correlated with the sugar concentration of collected nectar, supporting previous studies showing a link between worker physiology and foraging behavior. We discuss how the phenotype of extreme worker ovariole numbers and the underlying genetic factors we identified could be linked to the development of queen traits.THE number of ovariole filaments per ovary is an important female reproductive character that affects fecundity across insect taxa (Richard et al. 2005; Makert et al. 2006). Social insect lineages have evolved a strong dimorphism in ovariole number between reproductive and nonreproductive castes. For example, while most families of bees consistently have 6 total ovarioles, and most species in the family Apidae have 8, the highly social species in the genus Apis (the honeybees) have queens that can have >360 total ovarioles and workers that often have <10 (Winston 1987; Michener 2003). This queen–worker dimorphism is of primary importance because it translates into differential reproductive potential that defines the social roles of these female castes (Winston 1987) and classifies social species in general (Sherman et al. 1995). Furthermore, ovary size (i.e., ovariole number) is the most sensitive indicator of caste-specific development in honeybees (Dedej et al. 1998). The extreme increase in ovariole number for queen honeybees enables high egg-laying rates (>1500 per day) and is apparently a result of selection for increased colony reproduction (growth and fission by swarming) (Seeley 1997). Honeybee queens are thus highly specialized for egg laying, similar to queens of several other social insect taxa, such as army ants or higher termites (Hölldobler and Wilson 1990). Honeybee workers in contrast, do not normally reproduce but perform all other essential activities including foraging for nectar, pollen, and water; caring for brood; and building, maintaining, and defending the colony (Winston 1987; Seeley 1997).While worker honeybees have drastically reduced ovariole numbers relative to queens, they have retained functional ovaries and can produce unfertilized (haploid) male-destined eggs in the absence of queen pheromonal inhibition (Velthuis 1970; Page and Robinson 1994). In the absence of a queen, variation in worker ovariole number translates into differential reproductive success (Makert et al. 2006), but in the presence of a queen this variation is correlated with several other worker attributes. Variation in worker ovariole number may underlie the pollen hoarding syndrome of honeybees, a set of correlated behavioral and physiological traits associated with biases in pollen vs. nectar foraging within honeybee colonies (Amdam et al. 2004, 2006). Ovariole number is thus an important phenotype associated with queen–worker dimorphism but also worker reproduction and division of labor.In honeybees, adult ovariole number is determined during larval development by nutrition. Nurse workers feed queen-destined larvae an overabundance of food while the diet of worker-destined larvae is restricted in the fourth and fifth larval instar (Beetsma 1985). Nurse feeding behavior and thus indirect genetic effects of the colony environment can strongly influence larval developmental trajectory (Beekman et al. 2000; Allsopp et al. 2003; Linksvayer et al. 2009). The differential feeding affects larval gene networks sensitive to nutritional status (the target of rapamycin (TOR) pathway; Patel et al. 2007) to change DNA methylation (Kucharski et al. 2008) and juvenile hormone (JH) titers, with titers higher in queen- than in worker-destined larvae (Hartfelder and Engels 1998). Until the fourth instar, queen- and worker-destined larvae have the same number of ovariole primordia (Reginato and Cruz-Landim 2001). Lower JH titer in workers coincides with disintegration of parts of the cytoskeleton in the germ cells and apoptosis, which decreases ovariole number by the fifth instar (Capella and Hartfelder 1998, 2002). In accord, worker ovarioles can be rescued by JH application during the fourth and early fifth instar (Capella and Hartfelder 1998, 2002).Worker ovariole number and the extent of queen–worker dimorphism for ovariole number vary between species of Apis and between recognized races and strains of Apis mellifera. Both A. cerana and A. mellifera workers typically have <20 total ovarioles (Kapil 1962; Michener and Brothers 1974), but A. cerana queens have only ∼140 ovarioles (Velthuis et al. 1971) while A. mellifera have 200–360 (Michener 1974). In contrast, A. dorsata queens have 248–274 ovarioles and workers have 22–106 (Velthuis et al. 1971). Ruttner and Hesse (1981) studied seven races of A. mellifera and found mean total worker ovariole numbers ranging from 6.4 in A. mellifera mellifera to 18.8 in A. mellifera capensis. Several studies provide evidence that variation in worker ovariole number within populations and between strains has a strong genetic component (Diniz et al. 1993; Thuller et al. 1996, 1998; Jordan et al. 2008).Here, we compared the distribution of worker ovariole number in colonies from a population of feral Africanized bees in Arizona with commercial European bees. Africanized and European bees are derived from lineages separated for ∼1 million years (Whitfield et al. 2006a) and differ in a variety of traits including body size, development time, defensiveness, and behavioral traits associated with the pollen hoarding syndrome (Winston et al. 1983, 1987; Pankiw 2003). Genome scans have identified a number of loci that differ between Africanized and European lineages, and at least some of these genetic differences seem to be the result of divergent selection (Pankiw 2003; Whitfield et al. 2006a; Zayed and Whitfield 2008). In addition, QTL mapping studies for body size and defensive behavior (Hunt et al. 1998, 2007) have suggested few genes with major effect underlying some of these lineage differences.We first describe crosses between Africanized and European bees that revealed segregating variation for extreme ovariole number in workers that were sensitive to the social environment. Next, we describe the results of selective pooled DNA QTL mapping of worker ovariole number in two Africanized backcrosses with transgressive worker ovariole phenotypes, and we list potential candidate genes in the regions of the detected QTL. Finally, we demonstrate that variation in ovariole number, albeit unusual, correlates with differences in worker foraging behavior that have previously been shown to be linked to normal variation in ovariole number.     

Genetic Basis of Metabolome Variation in Yeast

Metabolism, the conversion of nutrients into usable energy and biochemical building blocks, is an essential feature of all cells. The genetic factors responsible for inter-individual metabolic variability remain poorly understood. To investigate genetic causes of metabolome variation, we measured the concentrations of 74 metabolites across 100 segregants from a Saccharomyces cerevisiae cross by liquid chromatography-tandem mass spectrometry. We found 52 quantitative trait loci for 34 metabolites. These included linkages due to overt changes in metabolic genes, e.g., linking pyrimidine intermediates to the deletion of ura3. They also included linkages not directly related to metabolic enzymes, such as those for five central carbon metabolites to ira2, a Ras/PKA pathway regulator, and for the metabolites, S-adenosyl-methionine and S-adenosyl-homocysteine to slt2, a MAP kinase involved in cell wall integrity. The variant of ira2 that elevates metabolite levels also increases glucose uptake and ethanol secretion. These results highlight specific examples of genetic variability, including in genes without prior known metabolic regulatory function, that impact yeast metabolism.