Effect of selection and selective genotyping for creation of reference on bias and accuracy of genomic prediction

Reference populations for genomic selection usually involve selected individuals, which may result in biased prediction of estimated genomic breeding values (GEBV). In a simulation study, bias and accuracy of GEBV were explored for various genetic models with individuals selectively genotyped in a typical nucleus breeding program. We compared the performance of three existing methods, that is, Best Linear Unbiased Prediction of breeding values using pedigree‐based relationships (PBLUP), genomic relationships for genotyped animals only (GBLUP) and a Single‐Step approach (SSGBLUP) using both. For a scenario with no‐selection and random mating (RR), prediction was unbiased. However, lower accuracy and bias were observed for scenarios with selection and random mating (SR) or selection and positive assortative mating (SA). As expected, bias disappeared when all individuals were genotyped and used in GBLUP. SSGBLUP showed higher accuracy compared to GBLUP, and bias of prediction was negligible with SR. However, PBLUP and SSGBLUP still showed bias in SA due to high inbreeding. SSGBLUP and PBLUP were unbiased provided that inbreeding was accounted for in the relationship matrices. Selective genotyping based on extreme phenotypic contrasts increased the prediction accuracy, but prediction was biased when using GBLUP. SSGBLUP could correct the biasedness while gaining higher accuracy than GBLUP. In a typical animal breeding program, where it is too expensive to genotype all animals, it would be appropriate to genotype phenotypically contrasting selection candidates and use a Single‐Step approach to obtain accurate and unbiased prediction of GEBV.     

Introduction of bovine tuberculosis to north-east England by bought-in cattle

The source of bovine tuberculosis was investigated in 31 herds in north-east England that experienced confirmed breakdowns between January 2002 and June 2004; nine of the herds had been restocked after the UK outbreak of foot-and-mouth disease in 2001. In all but one of the breakdowns the most likely source of infection was identified as one or more purchased animals. In 17 of the breakdowns, reactor animals were traced to herds from which the same combination of spoligotype and variable number tandem repeats was isolated, and in five breakdowns a different spoligotype was isolated. The most likely sources were located in Wales and the west and north of England, and included a Cheshire herd that was the most likely source of nine of the breakdowns. Three breakdowns were traced to Irish imports. Reactors in five of the breakdowns included homebred as well as purchased animals, providing evidence for the likely spread of the disease within the herds. The lack of geographical clustering of molecular types pointed to the overwhelming source of infection being cattle that had been bought-in.     

Nitrogen deficiency effects on plant growth, leaf photosynthesis, and hyperspectral reflectance properties of sorghum

An experiment was conducted under outdoor pot-culture conditions to determine effects of nitrogen (N) deficiency on sorghum growth, physiology, and leaf hyperspectral reflectance properties. Sorghum (cv. DK 44C) was seeded in 360 twelve-litre pots filled with fine sand. All pots were irrigated with half-strength Hoagland's nutrient solution from emergence to 25 days after sowing (DAS). Thereafter, pots were separated into three identical groups and the following treatments were initiated: (1) the control (100% N) continued receiving the half-strength nutrient solution; (2) reduced N to 20% of the control (20% N); and (3) withheld N from the solution (0% N). Photosynthetic rate (Pn), chlorophyll (Chl) and N concentrations, and hyperspectral reflectance of the uppermost, fully expanded leaves were determined at 3- to 4-day-interval from 21 to 58 DAS during the N treatments. Plants were harvested 58 DAS to determine effects of N deficiency on leaf area (LA), biomass accumulation, and partitioning. Nitrogen deficiency significantly reduced LA, leaf Chl content and Pn, resulting in lower biomass production. Decreased leaf Pn due to N deficiency was mainly associated with lower stomatal conductance rather than carboxylation capacity of leaf chemistry. Among plant components of dry weights, leaf dry weight had the greatest and root dry weight had the smallest decrease under N deficiency. Nitrogen-deficit stress mainly increased leaf reflectance at 555 (R₅₅₅) and 715 nm (R₇₁₅) and caused a red-edge shift to shorter wavelength. Leaf N and Chl concentrations were linearly correlated with not only the reflectance ratios of R₄₀₅/R₇₁₅ (r² = 0.68^***) and R₁₀₇₅/R₇₃₅ (r² = 0.64^***), respectively, but also the first derivatives of the reflectance (dR/dλ) in red edge centered 730 or 740 nm (r² = 0.73–0.82^***). These specific reflectance ratios or dR/dλ may be used for rapid and non-destructive estimation of sorghum leaf Chl and plant N status.     

Morphological diversity in sorghum germplasm from India

Summary Of the 5000 sorghum (Sorghum bicolor L. Monench) germplasm accessions assembled at ICRISAT Asia Center (IAC), over 4000 accessions from 11 major sorghum growing states in India were evaluated for morphological and agronomical characters at IAC during rainy and postrainy seasons.Considerable diversity was observed for all the characters studied. Diversity was more among states than within states. Variation among the seasons was also considerable. Days to flowering ranged from 42 to 129 days during postrainy and 33 to 180 days during the rainy season indicating their day length sensitivity. Plant height ranged from 65 to 330 cm during postrainy and 75 to 655 cm during rainy season. Panicle length ranged from 5 cm to 52 cm and panicle width from 1 to 51 cm. Erect and compact panicles are more frequent although all possible panicle shapes and compactness were found. In general, sorghums from India produce medium to large, lustrous grains in which the subcoat (testa) is absent. All the 5 basic and 10 intermediate sorghum races were found in India though durra or half-durra predominate. Racial diversity is maximal in the state of Andhra Pradesh followed by Maharashatra state. In the world collection a majority of the sources of resistance to shoot fly, stem borer, and striga are from India. Based on diversity for morphological and agronomical characters, India could be considered as the secondary center of diversity. Sorghum germplasm from India is useful for good quality large grain.     

Development of conventional multiplex PCR method for discrimination between Dispharynx nasuta and Cheilospirura hamulosa (Nematoda: Acuariidae) parasitizing poultry

The poultry infections caused by Dispharynx nasuta and Cheilospirura hamulosa nematodes are difficult to be diagnosed by fecal examination because of their egg similarity. In this study, we analyzed DNA sequences of nuclear ribosomal 18S-ITS1-5.8S-ITS2-28S region of D. nasuta and C. hamulosa and developed conventional multiplex PCR method using species-specific primers for discriminating between the two species. The method amplified 455-bp and 319-bp fragments specific to D. nasuta and C. hamulosa, respectively, and did not produce them against the other chicken nematode species, Ascaridia galli, Oxyspirura mansoni, Heterakis gallinarum, Heterakis beramporia, and Heterakis indica, suggesting that the multiplex PCR is sensitive and available for species diagnosis.     

Identification and expression profiles of multiple genes in Nile tilapia in response to bacterial infections

To understand the molecular mechanisms involved in response of Nile tilapia (Oreochromis niloticus) to bacterial infection, suppression subtractive cDNA hybridization technique was used to identify upregulated genes in the posterior kidney of Nile tilapia at 6h post infection with Aeromonas hydrophila. A total of 31 unique expressed sequence tags (ESTs) were identified from 192 clones of the subtractive cDNA library. Quantitative PCR revealed that nine of the 31 ESTs were significantly (p<0.05) upregulated in Nile tilapia at 6h post infection with A. hydrophila at an injection dose of 10(5)CFU per fish (≈ 20% mortality). Of the nine upregulated genes, four were also significantly (p<0.05) induced in Nile tilapia at 6h post infection with A. hydrophila at an injection dose of 10(6)CFU per fish (≈ 60% mortality). Of the four genes induced by A. hydrophila at both injection doses, three were also significantly (p<0.05) upregulated in Nile tilapia at 6h post infection with Streptococcus iniae at doses of 10(6) and at 10(5)CFU per fish (≈ 70% and ≈ 30% mortality, respectively). The three genes induced by both bacteria included EST 2A05 (similar to adenylate kinase domain containing protein 1), EST 2G11 (unknown protein, shared similarity with Salmo salar IgH locus B genomic sequence with e value of 0.02), and EST 2H04 (unknown protein). Significant upregulation of these genes in Nile tilapia following bacterial infections suggested that they might play important roles in host response to infections of A. hydrophila and S. iniae.     

Estimates of (co)variance components and genetic parameters for growth traits in Sirohi goat

Data were collected over a period of 21 years (1988–2008) to estimate (co)variance components for birth weight (BWT), weaning weight (WWT), 6-month weight (6WT), 9-month weight (9WT), 12-month weight (12WT), average daily gain from birth to weaning (ADG1), weaning to 6WT (ADG2), and from 6WT to 12WT (ADG3) in Sirohi goats maintained at the Central Sheep and Wool Research Institute, Avikanagar, Rajasthan, India. Analyses were carried out by restricted maximum likelihood, fitting six animal models with various combinations of direct and maternal effects. The best model was chosen after testing the improvement of the log-likelihood values. Heritability estimates for BWT, WWT, 6WT, 9WT, 12WT, ADG1, ADG2, and ADG3 were 0.39 ± 0.05, 0.09 ± 0.03, 0.06 ± 0.02, 0.09 ± 0.03, 0.11 ± 0.03, 0.10 ± 0.3, 0.04 ± 0.02, and 0.01 ± 0.01, respectively. For BWT and ADG1, only direct effects were significant. Estimate of maternal permanent environmental effect were important for body weights from weaning to 12WT and also for ADG2 and ADG3. However, direct maternal effects were not significant throughout. Estimate of c ² were 0.06 ± 0.02, 0.03 ± 0.02, 0.06 ± 0.02, 0.05 ± 0.02, 0.02 ± 0.02, and 0.02 ± 0.02 for 3WT, 6WT, 9WT, 12WT, ADG2, and ADG3, respectively. The estimated repeatabilities across years of ewe effects on kid body weights were 0.10, 0.08, 0.05, 0.08, and 0.08 at birth, weaning, 6, 9, and 12 months of age, respectively. Results suggest possibility of modest rate of genetic progress for body weight traits and ADG1 through selection, whereas only slow progress will be possible for post-weaning gain. Genetic and phenotypic correlations between body weight traits were high and positive. High genetic correlation between 6WT and 9WT suggests that selection of animals at 6 months can be carried out instead of present practice of selection at 9 months.     

Genetic parameters for direct and maternal effects on post-weaning body measurements of Muzaffarnagari sheep in India

Variance components and genetic parameters were estimated for post-weaning (i.e., at 6, 9, and 12 months of age) body measurements in Muzaffarnagari sheep maintained at the Central Institute for Research on Goats, Makhdoom, Mathura, India over a period of 29 years (1976 through 2004). Records of 2,965 lambs descended from 162 rams and 1,213 ewes were used in the study. Analyses were carried out by REML fitting an animal model and ignoring or including maternal genetic or permanent environmental effects. Six different animal models were fitted for all traits. The best model was chosen after testing the improvement of the log-likelihood values. Direct heritability estimates were inflated substantially for all traits when maternal effects were ignored. Moderate estimates of direct heritability for body length (0.11–0.15), height at withers (0.14–0.19), and heart girth (0.14–0.24) of lambs were observed at post-weaning stages of growth. Results suggest that only direct additive genetic effects were important for body measurements at post-weaning stages of growth, and hence, modest rates of genetic progress were possible for post-weaning body measurements.