Genome-wide association mapping in a wild avian population identifies a link between genetic and phenotypic variation in a life-history trait

Understanding the genetic basis of traits involved in adaptation is a major challenge in evolutionary biology but remains poorly understood. Here, we use genome-wide association mapping using a custom 50 k single nucleotide polymorphism (SNP) array in a natural population of collared flycatchers to examine the genetic basis of clutch size, an important life-history trait in many animal species. We found evidence for an association on chromosome 18 where one SNP significant at the genome-wide level explained 3.9% of the phenotypic variance. We also detected two suggestive quantitative trait loci (QTLs) on chromosomes 9 and 26. Fitness differences among genotypes were generally weak and not significant, although there was some indication of a sex-by-genotype interaction for lifetime reproductive success at the suggestive QTL on chromosome 26. This implies that sexual antagonism may play a role in maintaining genetic variation at this QTL. Our findings provide candidate regions for a classic avian life-history trait that will be useful for future studies examining the molecular and cellular function of, as well as evolutionary mechanisms operating at, these loci.     

Mapping of QTL for Body Conformation and Behavior in Cattle

Genome scans for quantitative trait loci (QTL) in farm animals have concentrated on primary production and health traits, and information on QTL for other important traits is rare. We performed a whole genome scan in a granddaughter design to detect QTL affecting body conformation and behavior in dairy cattle. The analysis included 16 paternal half-sib families of the Holstein breed with 872 sons and 264 genetic markers. The markers were distributed across all 29 autosomes and the pseudoautosomal region of the sex chromosomes with average intervals of 13.9 cM and covering an estimated 3155.5 cM. All families were analyzed jointly for 22 traits using multimarker regression and significance thresholds determined empirically by permutation. QTL that exceeded the experiment-wise significance threshold (5% level) were detected on chromosome 6 for foot angle, teat placement, and udder depth, and on chromosome 29 for temperament. QTL approaching experiment-wise significance (10% level) were located on chromosome 6 for general quality of feet and legs and general quality of udder, on chromosome 13 for teat length, on chromosome 23 for general quality of feet and legs, and on chromosome 29 for milking speed. An additional 51 QTL significant at the 5% chromosome-wise level were distributed over 21 chromosomes. This study provides the first evidence for QTL involved in behavior of dairy cattle and identifies QTL for udder conformation on chromosome 6 that could form the basis of recently reported QTL for clinical mastitis.     

THE VARIABILITY IS IN THE SEX CHROMOSOMES

Sex differences in the mean trait expression are well documented, not only for traits that are directly associated with reproduction. Less is known about how the variability of traits differs between males and females. In species with sex chromosomes and dosage compensation, the heterogametic sex is expected to show larger trait variability (“sex‐chromosome hypothesis”), yet this central prediction, based on fundamental genetic principles, has never been evaluated in detail. Here we show that in species with heterogametic males, male variability in body size is significantly larger than in females, whereas the opposite can be shown for species with heterogametic females. These results support the prediction of the sex‐chromosome hypothesis that individuals of the heterogametic sex should be more variable. We argue that the pattern demonstrated here for sex‐specific body size variability is likely to apply to any trait and needs to be considered when testing predictions about sex‐specific variability and sexual selection.     

Mapping quantitative trait Loci underlying fitness-related traits in a free-living sheep population

We searched for quantitative trait loci (QTL) underlying fitness-related traits in a free-living pedigree of 588 Soay sheep in which a genetic map using 251 markers with an average spacing of 15 cM had been established previously. Traits examined included birth date and weight, considered both as maternal and offspring traits, foreleg length, hindleg length, and body weight measured on animals in August and jaw length and metacarpal length measured on cleaned skeletal material. In some cases the data were split to consider different age classes separately, yielding a total of 15 traits studied. Genetic and environmental components of phenotypic variance were estimated for each trait and, for those traits showing nonzero heritability (N= 12), a QTL search was conducted by comparing a polygenic model with a model including a putative QTL. Support for a QTL at genome-wide significance was found on chromosome 11 for jaw length; suggestive QTL were found on chromosomes 2 and 5 (for birth date as a trait of the lamb), 8 (birth weight as a trait of the lamb), and 15 (adult hindleg length). We discuss the prospects for refining estimates of QTL position and effect size in the study population, and for QTL searches in free-living pedigrees in general.     

Characterization of QTL for oil content in maize kernel

Kernel oil content in maize is a complex quantitative trait. Phenotypic variation in kernel oil content can be dissected into its component traits such as oil metabolism and physical characteristics of the kernel, including embryo size and embryo-to-endosperm weight ratio (EEWR). To characterize quantitative trait loci (QTL) for kernel oil content, a recombinant inbred population derived from a cross between normal line B73 and high-oil line By804 was genotyped using 228 molecular markers and phenotyped for kernel oil content and its component traits [embryo oil content, embryo oil concentration, EEWR, embryo volume, embryo width, embryo length, and embryo width-to-length ratio (EWLR)]. A total of 58 QTL were identified for kernel oil content and its component traits in 26 genomic regions across all chromosomes. Eight main-effect QTL were identified for kernel oil content, embryo oil content, embryo oil concentration, EEWR, embryo weight, and EWLR, each accounting for over 10?% of the phenotypic variation in six genomic regions. Over 90?% of QTL identified for kernel oil content co-localized with QTL for component traits, validating their molecular contribution to kernel oil content. On chromosome 1, the QTL that had the largest effect on kernel oil content (qKO1-1) was associated with embryo width; on chromosome 9, the QTL for kernel oil content (qKO9) was related to EEWR (qEEWR9). Embryo oil concentration and embryo width were identified as the most important component traits controlling the second largest QTL for kernel oil content on chromosome 6 (qKO6) and a minor QTL for kernel oil content on chromosome 5 (qKO5-2), respectively. The dissection of kernel oil QTL will facilitate future cloning and/or functional validation of kernel oil content, and help to elucidate the genetic basis of kernel oil content in maize.     

Contrasting results from GWAS and QTL mapping on wing length in great reed warblers

A major goal in evolutionary biology is to understand the genetic basis of adaptive traits. In migratory birds, wing morphology is such a trait. Our previous work on the great reed warbler (Acrocephalus arundinaceus) shows that wing length is highly heritable and under sexually antagonistic selection. Moreover, a quantitative trait locus (QTL) mapping analysis detected a pronounced QTL for wing length on chromosome 2, suggesting that wing morphology is partly controlled by genes with large effects. Here, we re‐evaluate the genetic basis of wing length in great reed warblers using a genomewide association study (GWAS) approach based on restriction site‐associated DNA sequencing (RADseq) data. We use GWAS models that account for relatedness between individuals and include covariates (sex, age and tarsus length). The resulting association landscape was flat with no peaks on chromosome 2 or elsewhere, which is in line with expectations for polygenic traits. Analysis of the distribution of p‐values did not reveal biases, and the inflation factor was low. Effect sizes were however not uniformly distributed on some chromosomes, and the Z chromosome had weaker associations than autosomes. The level of linkage disequilibrium (LD) in the population decayed to background levels within c. 1 kbp. There could be several reasons to why our QTL study and GWAS gave contrasting results including differences in how associations are modelled (cosegregation in pedigree vs. LD associations), how covariates are accounted for in the models, type of marker used (multi‐ vs. biallelic), difference in power or a combination of these. Our study highlights that the genetic architecture even of highly heritable traits is difficult to characterize in wild populations.     

The genetic architecture of Drosophila sensory bristle number

We have mapped quantitative trait loci (QTL) for Drosophila mechanosensory bristle number in six recombinant isogenic line (RIL) mapping populations, each of which was derived from an isogenic chromosome extracted from a line selected for high or low, sternopleural or abdominal bristle number and an isogenic wild-type chromosome. All RILs were evaluated as male and female F(1) progeny of crosses to both the selected and the wild-type parental chromosomes at three developmental temperatures (18 degrees, 25 degrees, and 28 degrees ). QTL for bristle number were mapped separately for each chromosome, trait, and environment by linkage to roo transposable element marker loci, using composite interval mapping. A total of 53 QTL were detected, of which 33 affected sternopleural bristle number, 31 affected abdominal bristle number, and 11 affected both traits. The effects of most QTL were conditional on sex (27%), temperature (14%), or both sex and temperature (30%). Epistatic interactions between QTL were also common. While many QTL mapped to the same location as candidate bristle development loci, several QTL regions did not encompass obvious candidate genes. These features are germane to evolutionary models for the maintenance of genetic variation for quantitative traits, but complicate efforts to understand the molecular genetic basis of variation for complex traits.     

QTLs for days to silking in a recombinant inbred line maize population subjected to high and low nitrogen regimes

Days to silking (DTS) is one of the most important traits in maize (Zea mays). To investigate its genetic basis, a recombinant inbred line population was subjected to high and low nitrogen (N) regimes to detect quantitative trait loci (QTLs) associated with DTS. Three QTLs were identified under the high N regime; these explained 25.4% of the phenotypic variance. Due to additive effects, the QTL on chromosome 6 increased DTS up to 0.66 days; while the other two QTLs mapped on chromosome 9 (one linked with Phi061 and the other linked with Nc134) decreased DTS 0.89 and 0.91 days, respectively. Under low N regime, two QTLs were mapped on chromosomes 6 and 9, which accounted for 25.9% of the phenotypic variance. Owing to additive effects, the QTL on chromosome 6 increased DTS 0.67 days, while the other QTL on chromosome 9 decreased it 1.48 days. The QTL on chromosome 6, flanked by microsatellite markers Bnlg1600 and Phi077, was detected under both N regimes. In conclusion, we identified four QTLs, one on chromosome 6 and three on chromosome 9. These results contribute to our understanding of the genetic basis of DTS and will be useful for developing marker-assisted selection in maize breeding programs.     

A genome scan for loci affecting adipocyte size and number in abdominal fat in a White Duroc × Erhualian F2 resource population

Adipocyte size and number are correlated with fat deposition, which is of major concern to human health and pork producers. To identify quantitative trait loci (QTL) for adipocyte size and number in pigs, a total of 341 F2 animals at 240 days in a White Duroc × Erhualian cross were measured for the area, perimeters, volume and number of adipocyte in abdominal fat. A genome scan was performed on these animals and their parents and grandparents with 183 microsatellite markers spanning the pig genome. Five chromosomal regions showed effects on the traits measured, predominantly on adipocyte size, on pig chromosome (SSC) 1, 4, 7 and 9. Neither of these QTL has been reported before this study. The QTL for adipocyte size detected in this study perfectly correspond to the previously reported QTL for fatness traits on SSC1, 4 and 7. The most significant association was evidenced at 58 cM on SSC7. At the locus, the favorable allele decreasing adipocyte size was unusually originated from the obese Erhualian breed. Only a suggestive QTL was detected for adipocyte number on SSC9. The results shed new lights on the understanding of the genetic basis of fatness traits in pigs.     

Genome-wide association mapping of agronomic traits in relevant barley germplasm in Uruguay

The genetic basis of agronomic traits determining adaptation to specific production conditions is a key factor for the improvement of crops, including malting barley (Hordeum vulgare L.). The aim of this study was to determine the genome-wide genetic components associated with agronomic phenotypes of local and global significance in a population of 76 barley genotypes that have been introduced into Uruguay in different chronological periods. The phenotypic database was obtained from five field experiments, planted in 2 years and in two locations, where a total of 13 agronomic traits were determined. The population was genotyped with 1,033 single nucleotide polymorphisms. We found a total of 41 quantitative trait loci (QTL) in a combined analysis using all datasets and 79 QTL if we considered all the trait/experiment combinations analyzed. The highest concentration of QTL was detected on chromosomes 2H and 4H. Most QTL were detected for grain plumpness and weight. Two linkage disequilibrium (LD) blocks associated with a large number of traits were detected on 2HS. The largest LD block was composed of three haplotypes, possibly derived from three ancestors of different geographical origin. We also detected three genomic regions in different chromosomes (2H, 5H and 7H) in LD between them, associated with agronomic traits. This study provides a contribution to the understanding of the genetics of barley adaptation in the southern cone of South America. Our results showed that elite varieties have favorable alleles at different QTL, indicating that gains can be made through plant breeding.     

Genetic architecture of sexual dimorphism in a subdioecious plant with a proto-sex chromosome

The rise of sexual dimorphism is thought to coincide with the evolution of sex chromosomes. Yet because sex chromosomes in many species are ancient, we lack empirical evidence of the earliest stages of this transition. We use QTL analysis to examine the genetic architecture of sexual dimorphism in subdioecious octoploid Fragaria virginiana. We demonstrate that the region housing the male-function locus controls the majority of quantitative variation in proportion fruit set, confirming the existence of a proto-sex chromosome, and houses major QTL for eight additional sexually dimorphic traits, consistent with theory and data from animals and plants with more advanced sex chromosomes. We also detected autosomal QTL, demonstrating contributions to phenotypic variation in sexually dimorphic traits outside the sex-determining region. Moreover, for proportion seed set we found significant epistatic interactions between autosomal QTL and the male-function locus, indicating sex-limited QTL. We identified linked QTL reflecting trade-offs between male and female traits expected from theory and positive integration of male traits. These findings indicate the potential for the evolution of greater sexual dimorphism. Involvement of linkage groups homeologous to the proto-sex chromosome in these correlations reflects the polyploid origin of F. virginiana and raises the possibility that chromosomes in this homeologous group were predisposed to become the sex chromosome.     

Linkage disequilibrium on the bovine X chromosome: characterization and use in quantitative trait locus mapping

We herein demonstrate that in the Holstein-Friesian dairy cattle population, microsatellites are as polymorphic on the X chromosome as on the autosomes but that the level of linkage disequilibrium between these markers is higher on the X chromosome than on the autosomes. The latter observation is not compatible with the small male-to-female ratio that prevails in this population and results in a higher gonosomal than autosomal effective population size. It suggests that the X chromosome undergoes distinct selective or mutational forces. We describe and characterize a novel Markovian approach to exploit this linkage disequilibrium to compute the probability that two chromosomes are identical-by-descent conditional on flanking marker data. We use the ensuing probabilities in a restricted maximum-likelihood approach to search for quantitative trait loci (QTL) affecting 48 traits of importance to the dairy industry and provide evidence for the presence of QTL affecting 5 of these traits on the bovine X chromosome.     

Genetic mapping of quantitative trait loci for aseasonal reproduction in sheep

The productivity and economic prosperity of sheep farming could benefit greatly from more effective methods of selection for year-round lambing. Identification of QTL for aseasonal reproduction in sheep could lead to more accurate selection and faster genetic improvement. One hundred and twenty microsatellite markers were genotyped on 159 backcross ewes from a Dorset × East Friesian crossbred pedigree. Interval mapping was undertaken to map the QTL underlying several traits describing aseasonal reproduction including the number of oestrous cycles, maximum level of progesterone prior to breeding, pregnancy status determined by progesterone level, pregnancy status determined by ultrasound, lambing status and number of lambs born. Seven chromosomes (1, 3, 12, 17, 19, 20 and 24) were identified to harbour putative QTL for one or more component traits used to describe aseasonal reproduction. Ovine chromosomes 12, 17, 19 and 24 harbour QTL significant at the 5% chromosome-wide level, chromosomes 3 and 20 harbour QTL that exceeded the threshold at the 1% chromosome-wide level, while the QTL identified on chromosome 1 exceeded the 1% experiment-wide significance level. These results are a first step towards understanding the genetic mechanism of this complex trait and show that variation in aseasonal reproduction is associated with multiple chromosomal regions.     

QTL mapping reveals a striking coincidence in the positions of genomic regions associated with adaptive variation in body size in parallel clines of Drosophila melanogaster on different continents

Latitudinal genetic clines in body size are common in many ectotherm species and are attributed to climatic adaptation. Here, we use Quantitative Trait Loci (QTL) mapping to identify genomic regions associated with adaptive variation in body size in natural populations of Drosophila melanogaster from extreme ends of a cline in South America. Our results show that there is a significant association between the positions of QTL with strong effects on wing area in South America and those previously reported in a QTL mapping study of Australian cline end populations (P < 0.05). In both continents, the right arm of the third chromosome is associated with QTL with the strongest effect on wing area. We also show that QTL peaks for wing area and thorax length are associated with the same genomic regions, indicating that the clinal variation in the body size traits may have a similar genetic basis. The consistency of the results found for the South American and Australian cline end populations indicate that the genetic basis of the two clines may be similar and future efforts to identify the genes producing the response to selection should be focused on the genomic regions highlighted by the present work.     

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.     

直播水稻茎鞘非结构碳水化合物积累与转运的遗传剖析

为了揭示水稻(Oryza sativa)茎鞘非结构碳水化合物(nonstructural carbohydrate, NSC)积累与转运的遗传基础, 在大田直播条件下, 利用来源于Lemont/特青的重组自交系群体, 对5个相关性状进行了QTL定位。始穗期和成熟期共检测到3个茎鞘NSC含量QTL, 分别位于第1、9和12染色体上, 贡献率分别为13%、7%和7%, 增效等位基因均来自特青。检测到的2个NSC转运率QTL均位于第12染色体上, 贡献率分别为8%和14%。检测到的结实率和千粒重QTL分别为3个和4个, 3个结实率QTL的贡献率分别为9%、24%和6%, 4个千粒重QTL的贡献率分别为14%、11%、12%和13%。进一步的分析表明,来自Lemont的等位基因降低成熟期茎鞘NSC含量的同时却能提高NSC转运率、结实率和千粒重, 而来自特青的等位基因对NSC转运率和结实率均有增效作用, 这为性状间表型相关提供了重要的遗传解释。     

Identification of QTLs associated with agronomic performance under nitrogen-deficient conditions using chromosome segment substitution lines of a wild rice relative, <Emphasis Type="Italic">Oryza rufipogon</Emphasis>

Improved root system architecture can enhance agronomic performance by increasing water and nitrogen (N) acquisition efficiency. However, little is known about interaction between root system architecture and agronomic performance under field environments. To gain a better understanding about the genetic basis of these relationships, we evaluated a set of chromosome segment substitution lines (CSSLs) derived from crosses between a tropical japonica rice cultivar ‘Curinga’ and a wild species Oryza rufipogon accession IRGC105491. Root system architectural traits were investigated using the CSSLs at 40 days old seedlings using the root basket method under hydroponic conditions, and agronomic performances were also tested under field conditions with different N treatments. Agronomic performances were computed as the ratio of a trait value under low to high N treatments, including grain yield and biomass yield as nitrogen-deficiency tolerance (NDT) traits. Root architecture and NDT trait QTLs were mapped using 238 SNP marker loci. A total of 13 QTLs for root system architectural, NDT and morpho-physiological traits were identified on chromosomes 1, 3, 4, 5, 7, 8, 9, 10 and 12. Interestingly, a QTL for deeper root number was identified the region of SNP markers between id1012330 and id1021697 on chromosome 1 under hydroponic conditions overlapped with a QTL for NDT trait of relative grain yield (qRGY1). These results suggest that deeper root trait is helpful to maintain grain yield under nitrogen-deficient conditions. The QTL associated root architecture could potentially be used in future rice-breeding efforts to increase agronomic performance under nitrogen-deficient conditions.     

Quantitative genetic analysis of natural variation in body size in Drosophila melanogaster

Latitudinal, genetic variation in body size is a commonly observed phenomenon in many invertebrate species and is shaped by natural selection. In this study, we use a chromosome substitution and a quantitative trait locus (QTL) mapping approach to identify chromosomes and genomic regions associated with adaptive variation in body size in natural populations of Drosophila melanogaster from the extreme ends of clines in South America and Australia. Chromosome substitution revealed the largest effects on chromosome three in both continents, and minor effects on the X and second chromosome. Similarly, QTL analysis of the Australian cline identified QTL with largest effects on the third chromosome, with smaller effects on the second. However, no QTL were found on the X chromosome. We also compared the coincidence of locations of QTL with the locations of five microsatellite loci previously shown to vary clinally in Australia. Permutation tests using both the sum of the LOD scores and the sum distance to nearest QTL peak revealed there were no significant associations between locations of clinal markers and QTL's. The lack of significance may, in part, be due to broad QTL peaks identified in this study. Future studies using higher resolution QTL maps should reveal whether the degree of clinality in microsatellite allele frequencies can be used to identify QTL in traits that vary along an environmental gradient.     

Quantitative trait locus mapping reveals complex genetic architecture of quantitative virulence in the wheat pathogen Zymoseptoria tritici

We conducted a comprehensive analysis of virulence in the fungal wheat pathogen Zymoseptoria tritici using quantitative trait locus (QTL) mapping. High‐throughput phenotyping based on automated image analysis allowed the measurement of pathogen virulence on a scale and with a precision that was not previously possible. Across two mapping populations encompassing more than 520 progeny, 540 710 pycnidia were counted and their sizes and grey values were measured. A significant correlation was found between pycnidia size and both spore size and number. Precise measurements of percentage leaf area covered by lesions provided a quantitative measure of host damage. Combining these large and accurate phenotypic datasets with a dense panel of restriction site‐associated DNA sequencing (RADseq) genetic markers enabled us to genetically dissect pathogen virulence into components related to host damage and those related to pathogen reproduction. We showed that different components of virulence can be under separate genetic control. Large‐ and small‐effect QTLs were identified for all traits, with some QTLs specific to mapping populations, cultivars and traits and other QTLs shared among traits within the same mapping population. We associated the presence of four accessory chromosomes with small, but significant, increases in several virulence traits, providing the first evidence for a meaningful function associated with accessory chromosomes in this organism. A large‐effect QTL involved in host specialization was identified on chromosome 7, leading to the identification of candidate genes having a large effect on virulence.     

QTL modulating ear size and erectness in pigs

Ear size and erectness are important conformation measurements in pigs. An F(2) population established by crossing European Large White (small, erect ears) with Chinese Meishan (large, flop ears) was used to study the genetic influence of the two ear traits for the first time. A linkage map incorporating 152 markers on 18 autosomal chromosomes was utilised in a genome scan for QTL. Significant QTL were found on SSC1, 5, 7, 9 and 12 for the two traits. The QTL on SSC5 and SSC7 had major effects and were significant at the genome-wide level (P < 0.01). The QTL on SSC1 for ear erectness also had a major effect and was genome-wide significant (P < 0.01). The 95% confidence interval (CI) of the ear size QTL on SSC5 spanned only 4 cM. The QTL on SSC7 for the two ear traits each had a CI of <20 cM, and their positions overlapped with those of the major QTL affecting subcutaneous fat depths on the same chromosome. This study provides insights on the complex genetic influences underlying pig ear traits and will facilitate positional candidate gene analysis to identify causative DNA variants.