Rapid Identification of Major-Effect Genes Using the Collaborative Cross

The Collaborative Cross (CC) was designed to facilitate rapid gene mapping and consists of hundreds of recombinant inbred lines descended from eight diverse inbred founder strains. A decade in production, it can now be applied to mapping projects. Here, we provide a proof of principle for rapid identification of major-effect genes using the CC. To do so, we chose coat color traits since the location and identity of many relevant genes are known. We ascertained in 110 CC lines six different coat phenotypes: albino, agouti, black, cinnamon, and chocolate coat colors and the white-belly trait. We developed a pipeline employing modifications of existing mapping tools suitable for analyzing the complex genetic architecture of the CC. Together with analysis of the founders’ genome sequences, mapping was successfully achieved with sufficient resolution to identify the causative genes for five traits. Anticipating the application of the CC to complex traits, we also developed strategies to detect interacting genes, testing joint effects of three loci. Our results illustrate the power of the CC and provide confidence that this resource can be applied to complex traits for detection of both qualitative and quantitative trait loci.     

Analogues of virus resistance genes map to QTLs for resistance to sharka disease in <Emphasis Type="Italic">Prunus davidiana</Emphasis>

Plum pox virus (PPV), the causative agent of sharka disease in Prunoideae, is one of the most serious problems affecting stone fruit production in Europe and America. Resistance to PPV was previously described in a Prunus davidiana clone, P1908, and introduced into peach (Prunus persica) genotypes. Genetic resistance to PPV displays a complex pattern of quantitative inheritance. An analysis of quantitative trait loci (QTLs) for resistance was performed on an F1 interspecific peach population obtained from a cross between the susceptible nectarine cultivar Summergrand and P. davidiana. The hybrids were graft-inoculated with PPV in duplicate following a classical procedure. The incidence of infection was evaluated four times, over two vegetative cycles, by symptom observation and enzyme-linked immunoadsorbent assays (ELISA). Restriction of systemic downward movement of the PPV virus was also evaluated by testing the susceptible rootstocks. Using both analysis of variance and non-parametric tests, six genomic regions involved in PPV resistance were detected. Depending on the scoring data considered, between 22 and 51% of the phenotypic variance could be explained by the quantitative model. One QTL, located in the distal region of linkage group 1, maps in a genomic region that is syntenic to the location of a resistance gene previously identified in the apricot cv. Goldrich. Some QTLs appeared to be temporally specific, reflecting the environmental dependence of PPV-resistance scoring. Candidate gene fragments were amplified by PCR, isolated and mapped on the peach interspecific linkage map. We report here the co-localization of three analogues of virus resistance genes with two distinct genomic regions linked to PPV resistance in P. davidiana.Electronic Supplementary Material Supplementary material is available for this article at     

Evidence for quantitative trait loci affecting twinning rate in North American Holstein cattle

Twinning in dairy cattle has been associated with many negative health and reproductive events that cause economic loss to the producer. Reports have suggested that twinning rates are increasing and that there may be a positive relationship between milk production and twinning frequency. Putative quantitative trait loci (QTL) for twinning and ovulation rate on bovine chromosomes 5, 7, 19 and 23 have been previously identified in other populations. The objective of this study was to detect and possibly confirm the existence and effects of these QTL in the North American Holstein population. Half-sib families of 20 North American Holstein sires with above average twinning rate predicted transmitting abilities (PTA) comprised the sample population under investigation. Twinning rate PTA values had been estimated from calving data. DNA extracted from semen samples was analysed using 45-61 microsatellite markers across the four chromosomes. Marker heterozygosity of the patriarchs averaged 62%. Evidence of twinning QTL was found in multiple families on chromosomes 5, 7 and 23 and in one family on chromosome 19. Four of the sires formed one three-generation family: one sire and three half-sib sons with sons of their own. This extended family was analysed with additional markers confirming a twinning QTL of significant size on chromosome 5.     

Identification of an ovulation rate QTL in cattle on BTA14 using selective DNA pooling and interval mapping

Increased twinning incidence in beef cattle has the potential to improve production efficiency. However, phenotypic selection for twinning rate is difficult because of the trait's low heritability and the long time interval necessary to collect phenotypic records. Therefore, this trait and the correlated trait of ovulation rate are ideal candidates for marker-assisted selection. The objective of this study was to complete a genome-wide search for ovulation rate quantitative trait loci (QTL) in two related sire families. The families (paternal halfsib sires 839802 and 839803) were from a population of cattle selected for ovulation rate at the USDA Meat Animal Research Center, Clay Center, Nebraska. Putative ovulation rate QTL have previously been identified in the 839802 family on chromosomes 7 and 19; however, marker coverage in the original scan was not complete. This study fills the gaps in marker coverage of the earlier study by adding approximately 60 informative microsatellites to each sire family. Each family was genotyped using selective DNA pooling. Sons and daughters were included in either the high or low pool based on their estimated breeding value deviations from the mid-parent average (EBVMD) for ovulation rate. Approximately 40% (839802) and 26% (839803) of available progeny comprised the high and low pools combined. Pooled typing revealed possible associations (nominal P < 0.05) between ovulation rate and marker genotype for 11 and 15 microsatellites in the 839802 and 839803 families, respectively. Subsequent interval mapping strengthened support for the presence of an ovulation rate QTL on BTA14 (chromosome-wise P < 0.02).     

Genetic mapping of quantitative trait loci affecting body weight, egg character and egg production in F2 intercross chickens

Phenotypic measurements of chicken egg character and production traits are restricted to mature females only. Marker assisted selection of immature chickens using quantitative trait loci (QTL) has the potential to accelerate the genetic improvement of these traits in the chicken population. The QTL for 12 traits (i.e. body weight (BW), six for egg character, three for egg shell colour and two for egg production) of chickens were identified. An F2 population comprising 265 female chickens obtained by crossing White Leghorn and Rhode Island Red breeds and genotyped for 123 microsatellite markers was used for detecting QTL. Ninety-six markers were mapped on 25 autosomal linkage groups, and 13 markers were mapped on one Z chromosomal linkage group. Eight previous unmapped markers were assigned to their respective chromosomes in this study. Significant QTL were detected for BW on chromosomes 4 and 27, egg weight on chromosome 4, the short length of egg on chromosome 4, and redness of egg shell colour (using the L*a*b* colour system) on chromosome 11. A significant QTL on the Z chromosome was linked with age at first egg. Significant QTL could account for 6-19% of the phenotypic variance in the F2 population.     

Ontogenetics of QTL: the genetic architecture of trichome density over time in Arabidopsis thaliana

Although much is known about the molecular genetic basis of trichome development in Arabidopsis thaliana, less is known about the underlying genetic basis of continuous variation in a trait known to be of adaptive importance: trichome density. The density of leaf trichomes is known to be a major determinant of herbivore damage in natural populations of A. thaliana and herbivores are a significant selective force on genetic variation for trichome density. A number of developmental changes occur during ontogeny in A. thaliana, including changes in trichome density. I used multiple interval mapping (MIM) analysis to identify QTL responsible for trichome density on both juvenile leaves and adult leaves in replicate, independent trials and asked whether those QTL changed with ontogeny. In both juvenile and adult leaves, I detected a single major QTL on chromosome 2 that explained much of the genetic variance. Although additional QTL were detected, there were no consistent differences in the genetic architecture of trichome density measured on juvenile and adult leaves. The finding of a single QTL of major effect for a trait of known adaptive importance suggests that genes of major effect may play an important role in adaptation.     

Developing prolamine protein bodies are associated with the cortical cytoskeleton in rice endosperm cells

 The mRNAs that encode the prolamine storage proteins in rice (Oryza sativa L.) endosperm cells are enriched on the surface of the prolamine protein bodies (PBs), a subcellular structure consisting of a prolamine intracisternal granule surrounded by rough endoplasmic reticulum membrane. Previous biochemical studies (D.G. Muench et al., 1998, Plant Physiol. 116: 559–569) have shown that prolamine mRNAs may be anchored to the PB surface via the cytoskeleton. To better understand the mechanism and role of mRNA localization in rice endosperm cells, we studied the subcellular development of prolamine PBs and their relationship with the cytoskeleton in rice endosperm cells. Confocal microscopy of endosperm cells showed that, unlike the glutelin PBs, the developing prolamine PBs are not randomly distributed within the cell, but instead are often enriched in the cortical region of the cell only a few micrometers beneath the plasma membrane. In addition, the peripheral prolamine PBs are closely associated with the cortical microtubule and actin filament networks. The cortical enrichment of rice prolamine protein bodies represents a unique example of endoplasmic reticulum subdomain localization in plant cells. The interaction of this endoplasmic reticulum subdomain with the cytoskeleton provides new insights on the possible mechanism and role of mRNA localization in plants. Received: 30 September 1999 / Accepted: 12 November 1999     

Genes active in developing wheat endosperm

This paper describes the construction and characterisation of a cDNA library from wheat endosperm tissue during the early stages of grain filling. Developing wheat endosperm tissue was characterised with respect to standard measures including dry weight, cytological appearance and timing of expression of major sources of mRNA such as the seed storage protein genes. In addition, the full complement of proteins present at mid-endosperm development was examined using 2D-electrophoretic techniques. Based on this characterisation, endosperm from the developing grain 8–12 days post-anthesis was chosen for isolating mRNA and preparing cDNA. At this stage in development the mRNA population is not yet dominated by the accumulation of mRNA from seed storage protein genes. A cDNA library, not normalised, containing a high percentage of full length cDNA clones was constructed and 4,319 clones sequenced ("single-pass"). Partitioning of the cDNA sequences into gene families and singletons provided the basis for quantifying the accumulation of sequence classes relative to the total number of sequences determined. The accumulation of gene families/singletons was not linear. However, mathematical modeling of the data suggested that the maximum number of different genes expressed is within the range of 4,500–8,000 (detailed in the Appendix). If an average is taken of these extremes, approximately 27% of the gene products were visible as proteins in the 2D-electrophoretic analysis. Analysis of a functional class of genes relevant to wheat grain end-use, namely the glutenin/gliadin seed storage protein class of genes, revealed a new category of gene characterised by a distinctive N-terminal domain and a reduced central repetitive domain. Electronic Publication     

Somatic embryogenesis by liquid culture of epidermal layers in sunflower: from genetic control to cell development

Embryos were obtained using liquid medium culture of sunflower hypocotyl epidermis layers according to the Pélissier etal. (1990) method. In the present work we identified genetic factors controlling somatic embryogenesis and we evidenced the role of ionic channels in embryogenic tissues. Two traits, the number of embryogenic explants (EE) and the number of embryos (EM) were scored in 74 recombinant inbred lines (RILs) from a cross between lines PAC-2 and RHA-266. Analysis of variance indicated the existence of highly significant differences among the parental genotypes and their RILs. Heritability for the somatic embryogenesis traits studied were high (0.64 for EE and 0.77 for EM). Four quantitative trait loci (QTLs) for EE and seven for EM were detected using composite interval mapping. The QTLs for EE explained 48% of the phenotypic variation while the QTLs for EM explained about 89% of the variation, thus revealing several genomic regions related to somatic embryogenesis control in sunflower. In order to study the distribution of ion channels in somatic embryos as compared to zygotic ones, we used a fluorescent-labelled phenylalkylamine, DM-Bodipy PAA, as a probe. Fluorescence labelling was determined by confocal microscopy. The probe intensively labelled the protoderm and epidermis cells in both zygotic and somatic embryos. Callus exhibited labelling on sites where somatic embryos developed. Considering that the location of phenylalkylamine (PAA) binding sites is related to the distribution of ion channels, the high intensity in the protoderm and epidermis of embryos, point to similar properties and functions and their key role in embryo development.     

Genome screen for twinning rate QTL in four North American Holstein families

The objective of this study was to identify twinning rate quantitative trait loci (QTL) by typing pooled samples in a preliminary screening followed by interval mapping to test QTL effects. Four elite North American Holstein half-sib sire families with high twinning rate predicted transmitting abilities (PTA) were used in this study. Chromosomes 5, 7, 19 and 23 were not genotyped as these chromosomes were scanned for QTL in these families in a previous study. DNA was extracted from phenotypically extreme sons in each sire family. Two pools were prepared from sons of sires in each phenotypic tail, two each for high and low PTA levels for twinning rates. Each pool contained DNA from 4 to 15% of all sons of the sire depending on family. A total of 268 fluorescently labelled microsatellite markers were tested for heterozygosity in sires. About 135--170 informative markers per family were genotyped using pooled DNA samples. Based on the preliminary evidence for potential twinning rate QTL from pooled typing, interval mapping was performed subsequently on 12 chromosomal regions by family combinations. Evidence of QTL for twinning rate was found in one family on BTA 21 and 29 at a chromosome-wide P<0.05 and on BTA 8, 10 and 14 with a chromosome-wide P<0.01.