Impact of QTL properties on the accuracy of multi-breed genomic prediction

Background

Although simulation studies show that combining multiple breeds in one reference population increases accuracy of genomic prediction, this is not always confirmed in empirical studies. This discrepancy might be due to the assumptions on quantitative trait loci (QTL) properties applied in simulation studies, including number of QTL, spectrum of QTL allele frequencies across breeds, and distribution of allele substitution effects. We investigated the effects of QTL properties and of including a random across- and within-breed animal effect in a genomic best linear unbiased prediction (GBLUP) model on accuracy of multi-breed genomic prediction using genotypes of Holstein-Friesian and Jersey cows.

Methods

Genotypes of three classes of variants obtained from whole-genome sequence data, with moderately low, very low or extremely low average minor allele frequencies (MAF), were imputed in 3000 Holstein-Friesian and 3000 Jersey cows that had real high-density genotypes. Phenotypes of traits controlled by QTL with different properties were simulated by sampling 100 or 1000 QTL from one class of variants and their allele substitution effects either randomly from a gamma distribution, or computed such that each QTL explained the same variance, i.e. rare alleles had a large effect. Genomic breeding values for 1000 selection candidates per breed were estimated using GBLUP modelsincluding a random across- and a within-breed animal effect.

Results

For all three classes of QTL allele frequency spectra, accuracies of genomic prediction were not affected by the addition of 2000 individuals of the other breed to a reference population of the same breed as the selection candidates. Accuracies of both single- and multi-breed genomic prediction decreased as MAF of QTL decreased, especially when rare alleles had a large effect. Accuracies of genomic prediction were similar for the models with and without a random within-breed animal effect, probably because of insufficient power to separate across- and within-breed animal effects.

Conclusions

Accuracy of both single- and multi-breed genomic prediction depends on the properties of the QTL that underlie the trait. As QTL MAF decreased, accuracy decreased, especially when rare alleles had a large effect. This demonstrates that QTL properties are key parameters that determine the accuracy of genomic prediction.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0124-6) contains supplementary material, which is available to authorized users.     

Cloning of a coconut endosperm cDNA encoding a 1-acyl-sn-glycerol-3-phosphate acyltransferase that accepts medium-chain-length substrates.

Immature coconut (Cocos nucifera) endosperm contains a 1-acyl-sn-glycerol-3-phosphate acyltransferase (LPAAT) activity that shows a preference for medium-chain-length fatty acyl-coenzyme A substrates (H.M. Davies, D.J. Hawkins, J.S. Nelsen [1995] Phytochemistry 39:989-996). Beginning with solubilized membrane preparations, we have used chromatographic separations to identify a polypeptide with an apparent molecular mass of 29 kD, whose presence in various column fractions correlates with the acyltransferase activity detected in those same fractions. Amino acid sequence data obtained from several peptides generated from this protein were used to isolate a full-length clone from a coconut endosperm cDNA library. Clone pCGN5503 contains a 1325-bp cDNA insert with an open reading frame encoding a 308-amino acid protein with a calculated molecular mass of 34.8 kD. Comparison of the deduced amino acid sequence of pCGN5503 to sequences in the data banks revealed significant homology to other putative LPAAT sequences. Expression of the coconut cDNA in Escherichia coli conferred upon those cells a novel LPAAT activity whose substrate activity profile matched that of the coconut enzyme.     

No support for the emergence of lichens prior to the evolution of vascular plants

The early‐successional status of lichens in modern terrestrial ecosystems, together with the role lichen‐mediated weathering plays in the carbon cycle, have contributed to the long and widely held assumption that lichens occupied early terrestrial ecosystems prior to the evolution of vascular plants and drove global change during this time. Their poor preservation potential and the classification of ambiguous fossils as lichens or other fungal–algal associations have further reinforced this view. As unambiguous fossil data are lacking to demonstrate the presence of lichens prior to vascular plants, we utilize an alternate approach to assess their historic presence in early terrestrial ecosystems. Here, we analyze new time‐calibrated phylogenies of ascomycete fungi and chlorophytan algae, that intensively sample lineages with lichen symbionts. Age estimates for several interacting clades show broad congruence and demonstrate that fungal origins of lichenization postdate the earliest tracheophytes. Coupled with the absence of unambiguous fossil data, our work finds no support for lichens having mediated global change during the Neoproterozoic‐early Paleozoic prior to vascular plants. We conclude by discussing our findings in the context of Neoproterozoic‐Paleozoic terrestrial ecosystem evolution and the paleoecological context in which vascular plants evolved.     

Proline Accumulation in Water-stressed Barley Leaves in Relation to Translocation and the Nitrogen Budget

Mobilization of N from leaves of barley (Hordeum vulgare L.) during water stress, and the role of proline as a mobilized species, were examined in plants at the three-leaf stage. The plants responded to water stress by withdrawing about 25% of the total reduced N from the leaf blades via phloem translocation. Most of this N loss was during the first 2 days while translocation of ¹⁴C-photosynthate out of the stressed blade still remained active. Free proline accumulation in the blade was initially slow, and became more rapid during the 2nd day of stress. Although a major free amino acid, proline accounted for only about 5% of the total N (soluble + insoluble) retained in severely stressed blades. When the translocation pathway in water-stressed leaves was interrupted just below the blade by a heat girdle, a cold jacket, or by blade excision, N loss from the blade was prevented and proline began to accumulate rapidly on 1st day of stress. Little free proline accumulated in the blades until after the ability to translocate was lost. Proline was, however, probably not a major species of N translocated during stress, because proline N accumulation in heat-girdled stressed leaves was five times slower than the rate of total N export from intact blades.     

Measuring respiratory symptoms of COPD: performance of the EXACT- Respiratory Symptoms Tool (E-RS) in three clinical trials

Background

Symptomatic relief is an important treatment goal for patients with COPD. To date, no diary for evaluating respiratory symptoms in clinical trials has been developed and scientifically-validated according to FDA and EMA guidelines. The EXACT – Respiratory Symptoms (E-RS) scale is a patient-reported outcome (PRO) measure designed to address this need. The E-RS utilizes 11 respiratory symptom items from the existing and validated 14-item EXACT, which measures symptoms of exacerbation. The E-RS total score quantifies respiratory symptom severity, and 3 domains assess breathlessness, cough and sputum, and chest symptoms.

Methods

This study examined the performance of the E-RS in each of 3 controlled trials with common and unique validation variables: one 6-month (N = 235, US) and two 3-month (N = 749; N = 597; international). Subjects completed the E-RS as part of a daily eDiary. Tests of reliability, validity, and responsiveness were conducted in each dataset.

Results

In each study, RS-Total score was internally consistent (Cronbach α) (0.88, 0.92, 0.92) and reproducible (intra-class correlation) in stable patients (2 days apart: 0.91; 7 days apart: 0.71, 0.74). RS-Total scores correlated significantly with the following criterion variables (Spearman’s rho; p < 0.01, all comparisons listed here): FEV₁% predicted (−0.19, −0.14, −0.15); St. George’s Respiratory Questionnaire (SGRQ) (0.65, 0.52, 0.51); Breathlessness, Cough, and Sputum Scale (BCSS) (0.89, 0.89); modified Medical Research Council dyspnoea scale (mMRC) (0.40); rescue medication use (0.43, 0.42); Functional Performance Inventory Short-Form (FPI-SF) (0.43); 6-minute walk distance (6-MWT) (−0.30, −0.14) and incremental shuttle walk (ISWT) (−0.18) tests. Correlations between these variables and RS-Breathlessness, RS-Cough and Sputum, RS-Chest Symptoms scores supported subscale validity. RS-Total, RS-Breathlessness, and RS-Chest Symptoms differentiated mMRC levels of breathlessness severity (p < 0.0001). RS-Total and domain scores differentiated subjects with no rescue medication use and 3 or more puffs (p < 0.0001). Sensitivity to changes in health status (SGRQ), symptoms (BCSS), and exercise capacity (6MWT, ISWT) were also shown and responder definitions using criterion- and distribution-based methods are proposed.

Conclusions

Results suggest the E-RS is a reliable, valid, and responsive measure of respiratory symptoms of COPD suitable for use in natural history studies and clinical trials.

Trial registration

MPEX: {"type":"clinical-trial","attrs":{"text":"NCT00739648","term_id":"NCT00739648"}}NCT00739648; AZ1: {"type":"clinical-trial","attrs":{"text":"NCT00949975","term_id":"NCT00949975"}}NCT00949975; AZ 2: {"type":"clinical-trial","attrs":{"text":"NCT01023516","term_id":"NCT01023516"}}NCT01023516

Electronic supplementary material

The online version of this article (doi:10.1186/s12931-014-0124-z) contains supplementary material, which is available to authorized users.     

Microorganisms for degrading simmondsin and related cyanogenic toxins in jojoba

Summary Four microorganisms that metabolize simmondsin (S) and related cyanogenic toxins from jojoba (Simmondsia chinensis) were isolated by enrichment: Pseudallescheria boydii, a fungus which specifically degrades simmondsin ferulate but not S; Fusarium moniliforme; Flavobacterium aurantiacum; and Pseudomonas maltophilia. The latter three organisms grow on S as a sole carbon and nitrogen source in culture media, but only F. moniliforme attacks S in the complete jojoba meal. Combinations of the four microorganisms at two temperatures, and with free air or limited air exchange for up to 20 days, were tested on jojoba meal to determine an optimum detoxification method. Degradation of toxins was most rapid and complete when Pseudallescheria boydii and Fusarium moniliforme together were incubated on jojoba meal at 25°C with free air exchange for 20 days. Mice were fed fermented meals at 0, 5, 10 and 20% substitution levels to determine detoxification and nutritional quality. Average daily gains during rapid growth of weanling (1–3 weeks) and mature (4–8 weeks) mice did not differ significantly from controls for mice on all diets containing fermented meal. Diets containing fungally detoxified jojoba meal were more efficient for maintaenance of mature weight than jojoba meal detoxified with enzymes naturally present in the meal. Meal can be detoxified by ensilage for 20 days at 80% water content. Detoxification is attributed to as yet unidentified enzymes inherent in the jojoba seed.The mention of firm names or trade products does not imply that they are endorsed or recommended by the U. S. Department of Agriculture over other firms or similar products not mentionedOffprint requests to: Thomas P. Abbott     

How the mirror-image pattern specified by a janus mutation of Tetrahymena thermophila comes to expression

The initial changes of cell-surface organization that occurred as the recessive janAl (janus) mutation of Tetrahymena thermophila first became expressed were elucidated in a special mating scheme in which old macronuclei homozygous for janA⁺ were synchronously replaced by new macronuclei homozygous for janAl. During this period of onset of expression, the number, regularity, and asymmetry of the ciliary rows remained unchanged. New normal (primary) oral apparatuses (OAs) continued to be formed posterior to old OAs, as in normal cells. At about four fissions after conjugation, abnormal (secondary) OAs with a partial reversal of asymmetry began to appear nearly opposite to the primary OAs, close to but not at the eventual circumferential position of janAl secondary OAs. The array of contractile vacuole pores (CVPs), normally located adjacent to two ciliary rows centered near 22% of the cell circumference to the righ of the primary oral meridian, underwent a two-step transformation: first, the number of adjacent ciliary rows bearing CVPs increased to 3, 4, and sometimes 5, then “skipped” rows appeared within this broadened CVP-arc to split the single set of CVPs into two separated subsets. The CVP transformations occurred gradually and progressively. They began prior to the expression of secondary OAs but accelerated as secondary OAs appeared. As the CVP are became broader, its midpoint shifted somewhat to the right, away from the primary oral meridian, but ended up close to halfway between the primary and secondary oral meridians. The data provide a better fit to an intercalation model than to an alternative double gradient model, suggesting that the janAl mutation alters the large-scale organization of positional values by preventing the expression of a subset of these values and thus provoking reverse-intercalation of the remainder.