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.     

Guava decline: effect of root exudates from Meloidogyne enterolobii-parasitized plants on Fusarium solani in vitro and on growth and development of guava seedlings under controlled conditions

In guava decline, Fusarium solani-immune guava trees become susceptible to extensive root rot caused by this fungus after parasitism by Meloidogyne enterolobii. To understand the mechanisms involved in this disease, root exudates were collected from nematode-inoculated (NI) or uninoculated (UN) guava plants cultivated in sand. After filtration through a Millipore® membrane, NI and UN exudates were used: i) to prepare media to assess their effect on mycelial growth and production of propagules of F. solani isolate UENF/CF 163, and ii) to incubate macro- and microconidia to assess their effect on germination. NI exudates promoted (P?<?0.05) more mycelial growth and production of propagules than UN exudates or water. NI and UN exudates were used to water guava seedlings laid over seed germination paper inside plastic boxes. Half of the seedlings had an agar plug colonized by the fungus positioned in the collar region. Upon watering with NI exudates the fungus caused (P?<?0.05) extensive rotting of the seedlings’ rootlets. NI and UN exudates, either unlyophilized or lyophilized and re-suspended to the original concentration, were used to water guava seedlings grown in sterile sand before being inoculated (or left uninoculated) as described before. Solely upon watering with NI exudates, in its unlyophilized form or after lyophilization, the fungus caused a reduction (P?<?0.05) of shoot and root biomass associated with rotting of roots. These results suggest that M. enterolobii induces chemical changes in the root exudates of guava trees, which are necessary for root invasion causing root rotting by F. solani.     

Comparison Between a γ-IFN Assay and Intradermal Tuberculin Test for the Diagnosis of Bovine Tuberculosis in Field Trials in Brazil

Bovine tuberculosis is a major problem in Brazil. The intradermal tuberculin test is the standard test for detection of bovine tuberculosis in Brazil but can lack both sensitivity and specificity. The purpose of this study was to compare a bovine γ-IFN assay with the tuberculin test under field conditions in Brazil. A total of 1632 animals from 13 dairy farms were tested using the single cervical tuberculin test (SCTT). Among those animals, about 15% of each herd, 220 in total, represented a high-risk group and were selected to be tested using the γ-IFN test. Of the 1632 animals tested, 207 presented significant reactions representing 12.7% of the cattle studied. In the selected group the number of animals positive by the γ-IFN assay was 126/220 (57.3%) and the total number of reactive cows on SCTT was 106/220 (48.2%). The real number of infected cattle, following standards, was 120/220 (54.5%). From these results the relative sensitivity rate of γ-IFN test was 100% including the false-positive results and 88.3% for the SCTT — a significant (P < 0.01) difference in favour of the γ-IFN test of 11.7%. The γ-IFN assay also identified some positive animals 60–120 days earlier than the SCTT. In conclusion, we believe that the γ-IFN assay can be used alone or in combination with the SCTT, as a valuable tool for the control of bovine tuberculosis in the Brazilian national herd.     

Leishmania spp. in Didelphis albiventris and Micoureus paraguayanus (Didelphimorphia: Didelphidae) of Brazil

Leishmaniasis is kept in nature by the participation of several animal species. This study evaluated the presence of Leishmania spp. in skin samples of free-ranging marsupials Micoureus paraguayanus (n=95) and Didelphis albiventris (n=191), captured in Morro do Diabo State Park and in sections of its surrounding forest, in the region of Pontal do Paranapanema, S?o Paulo State, Brazil. The samples were tested for the presence of kDNA of Leishmania spp. by polymerase chain reaction (PCR) and by real time PCR (qPCR). All samples from D. albiventris tested by PCR were negative for the presence of kDNA of Leishmania spp. However, when tested by qPCR, the positivity was 1.6%. A positivity of 7.4% by PCR and 11.6% by qPCR was observed for M. paraguayanus. Sixty-four per cent (9/14) of positive animals were limited to the same forest fragment. Presence of Leishmania (Leishmania) amazonensis and Leishmania (Viannia) braziliensis was detected in M. paraguayanus samples. While D. albiventris is the most studied marsupial species due to its urban habits, other marsupial species such as M. paraguayanus can be potential reservoirs of Leishmania spp. and should also be studied.     

Mapping genomic regions for reproductive traits in beef cattle: Inclusion of the X chromosome

Although the second largest chromosome of the genome, the X chromosome is usually excluded from genome-wide association studies (GWAS). Considering the presence and importance of genes on this chromosome that are involved in reproduction, the aim of this study was to evaluate the effect of its inclusion in GWAS on reproductive traits (scrotal circumference [SC], early pregnancy [P16] and age at first calving [AFC]) in a Nelore herd. Genotype data from 3,263 animals with the above-mentioned phenotypes were used. The results showed an increase in the variances explained by the autosomal markers for all traits when the X chromosome was not included. For SC, there was an increase of more than 10% for the windows on chromosomes 2 and 6. For P16, the effect was increased by almost 20% for windows on chromosome 5. The same pattern was found for AFC, with an increase of more than 10% for the most important windows. The results indicate that the noninclusion of the X chromosome can overestimate the effects of autosomes on SC, P16 and AFC not only because of the additive effect of the X chromosome itself but also because of its epistatic effect on autosomal genes.