Is single-step genomic REML with the algorithm for proven and young more computationally efficient when less generations of data are present?

Efficient computing techniques allow the estimation of variance components for virtually any traditional dataset. When genomic information is available, variance components can be estimated using genomic REML (GREML). If only a portion of the animals have genotypes, single-step GREML (ssGREML) is the method of choice. The genomic relationship matrix (G) used in both cases is dense, limiting computations depending on the number of genotyped animals. The algorithm for proven and young (APY) can be used to create a sparse inverse of G (GAPY~-1) with close to linear memory and computing requirements. In ssGREML, the inverse of the realized relationship matrix (H⁻¹) also includes the inverse of the pedigree relationship matrix, which can be dense with a long pedigree, but sparser with short. The main purpose of this study was to investigate whether costs of ssGREML can be reduced using APY with truncated pedigree and phenotypes. We also investigated the impact of truncation on variance components estimation when different numbers of core animals are used in APY. Simulations included 150K animals from 10 generations, with selection. Phenotypes (h² = 0.3) were available for all animals in generations 1–9. A total of 30K animals in generations 8 and 9, and 15K validation animals in generation 10 were genotyped for 52,890 SNP. Average information REML and ssGREML with G⁻¹ and GAPY~-1 using 1K, 5K, 9K, and 14K core animals were compared. Variance components are impacted when the core group in APY represents the number of eigenvalues explaining a small fraction of the total variation in G. The most time-consuming operation was the inversion of G, with more than 50% of the total time. Next, numerical factorization consumed nearly 30% of the total computing time. On average, a 7% decrease in the computing time for ordering was observed by removing each generation of data. APY can be successfully applied to create the inverse of the genomic relationship matrix used in ssGREML for estimating variance components. To ensure reliable variance component estimation, it is important to use a core size that corresponds to the number of largest eigenvalues explaining around 98% of total variation in G. When APY is used, pedigrees can be truncated to increase the sparsity of H and slightly reduce computing time for ordering and symbolic factorization, with no impact on the estimates.     

Effect of distribution and concentration of topically applied neonicotinoid insecticides in buffalograss,Buchloe dactyloides,leaf tissues on the differential mortality of Blissus occiduus under field conditions

BACKGROUND: Neonicotinoid insecticides are generally efficacious against many turfgrass pests, including several important phloem‐feeding insects. However, inconsistencies in control of western chinch bugs, Blissus occiduus, have been documented in field efficacy studies. This research investigated the efficacy of three neonicotinoid insecticides (clothianidin, imidacloprid and thiamethoxam) against B. occiduus in buffalograss under field conditions and detected statistically significant differences in B. occiduus numbers among treatments. A subsequent study documented the relative quantity and degradation rate of these insecticides in buffalograss systemic leaf tissues, using HPLC. RESULTS: Neonicotinoid insecticides initially provided significant reductions in B. occiduus numbers, but mortality diminished over the course of the field studies. Furthermore, while all three neonicotinoids were present in the assayed buffalograss leaf tissues, imidacloprid concentrations were significantly higher than those of clothianidin and thiamethoxam. Over the course of the 28 day study, thiamethoxam concentrations declined 700‐fold, whereas imidacloprid and clothianidin declined only 70‐fold and 60‐fold respectively. CONCLUSIONS: Field studies continued to verify inconsistencies in B. occiduus control with neonicotinoid insecticides. This is the first study to document the relative concentrations of topically applied neonicotinoid insecticides in buffalograss systemic leaf tissues. Copyright © 2012 Society of Chemical Industry     

Allelopathy and the active metabolites of the endophytic fungus,Alternaria J46, from Platycladus orientalis

The endophytic fungus, Alternaria J46, was isolated from the stem of the medicinal plant, Platycladus orientalis. A suspension of Alternaria J46 mycelial segments and the culture filtrates of the fungi exhibited marked seed germination inhibition against the monocot wheat, large crabgrass, bromegrass, rice and barnyardgrass and weak inhibition against the dicot redroot pigweed and morning glory, but it was safe for use on soybean, rape, cucumber, tomato, lettuce and radish crops. It is possible to use J46 culture filtrates in order to prevent monocot weeds in dicot cropland. Three active metabolites were isolated from an extract of the fungus cultures and elucidated as 3‐acetyl‐5‐sec‐butyltetramic acid (1, tenuazonic acid), 3‐acetyl‐5‐iso‐butyltetramic acid (2, vivotoxin II) and cyclo‐(L‐leucyl‐L‐proline) (3). Among these three compounds, compounds 1 and 2 showed significant phytotoxic effects on the seed germination of large crabgrass, while compound 3 exhibited weak activity, and all were safe for lettuce at 100 μg mL^?1. Accordingly, compounds 1 and 2 were the main active metabolites that were responsible for endophytic fungus Alternaria J46's strong seed germination inhibition against monocotyledons.