Empirical comparison between different methods for genomic prediction of number of piglets born alive in moderate sized breeding populations.

Currently used multi-step methods to incorporate genomic information in the prediction of breeding values (BV) implicitly involve many assumptions which, if violated, may result in loss of information, inaccuracies and bias. To overcome this, single-step genomic best linear unbiased prediction (ssGBLUP) was proposed combining pedigree, phenotype and genotype of all individuals for genetic evaluation. Our objective was to implement ssGBLUP for genomic predictions in pigs and to compare the accuracy of ssGBLUP with that of multi-step methods with empirical data of moderately sized pig breeding populations. Different predictions were performed: conventional parent average (PA), direct genomic value (DGV) calculated with genomic BLUP (GBLUP), a GEBV obtained by blending the DGV with PA, and ssGBLUP. Data comprised individuals from a German Landrace (LR) and Large White (LW) population. The trait 'number of piglets born alive' (NBA) was available for 182,054 litters of 41,090 LR sows and 15,750 litters from 4534 LW sows. The pedigree contained 174,021 animals, of which 147,461 (26,560) animals were LR (LW) animals. In total, 526 LR and 455 LW animals were genotyped with the Illumina PorcineSNP60 BeadChip. After quality control and imputation, 495 LR (424 LW) animals with 44,368 (43,678) SNP on 18 autosomes remained for the analysis. Predictive abilities, i.e., correlations between de-regressed proofs and genomic BV, were calculated with a five-fold cross validation and with a forward prediction for young genotyped validation animals born after 2011. Generally, predictive abilities for LR were rather small (0.08 for GBLUP, 0.19 for GEBV and 0.18 for ssGBLUP). For LW, ssGBLUP had the greatest predictive ability (0.45). For both breeds, assessment of reliabilities for young genotyped animals indicated that genomic prediction outperforms PA with ssGBLUP providing greater reliabilities (0.40 for LR and 0.32 for LW) than GEBV (0.35 for LR and 0.29 for LW). Grouping of animals according to information sources revealed that genomic prediction had the highest potential benefit for genotyped animals without their own phenotype. Although, ssGBLUP did not generally outperform GBLUP or GEBV, the results suggest that ssGBLUP can be a useful and conceptually convincing approach for practical genomic prediction of NBA in moderately sized LR and LW populations.

Single-step elongation of oligodeoxynucleotides using terminal deoxynucleotidyl transferase.

Procedures for the stepwise addition of one or more deoxyribonucleotide residues to the 3' end of an oligodeoxyribonucleoside phosphate acceptor using commercially available terminal deoxynucleotidyl transferase is described. 2-80 nmol of acceptors with a chain length of four, five or nine monomer units were elongated with a single 2'-deoxyribonucleoside 5'-triphosphate in yields of 20-30%. The monomers carried no protecting groups and were used both radioactively labelled and unlabelled. The elongated oligodeoxynucleoside phosphates were isolated by reverse-phase (Nucleosil C18) high-performance liquid chromatography or paper chromatography. The isolated products were sequenced by the fingerprint method. Advantages and disadvantages of this new methodology for the enzymatic synthesis of defined oligodeoxynucleotides are discussed.

[Isolation of oligonucleotides from partial hydrolysates of DNA using template chromatography]. / Isolierung von Oligonucleotiden aus DNA-partialhydrolysaten mit Hilfe der Template-Chromatographie.

Purine oligonucleotides are adsorbed at 0 degree C on poly(vinyl alcohol)-p(dC)n-DEAE-cellulose, and pyrimidine oligonucleotides on oligo(guanylic acid) gel according to the base-pairing mechanism, if their sequences contain at least three or more homologous, consecutive guanylic or cytidylic moieties. By increasing the temperature all base-paired oligonucleotides are desorbed. With this template chromatography mixtures of defined purine- or pyrimidine oligonucleotides could be isolated from fractionated partial hydrolyzates of herring sperm DNA. Afterwards these mixtures are rechromatographed on QAE-Sephadex and/or Nucleosil C18. Using this approach oligonucleotides up to nine monomer units can be isolated either as single substances or as mixtures with defined composition on a preparative scale, which would be not possible with the already existing separation procedures when partial hydrolyzates of herring sperm DNA as starting material are used. Purity and sequence of the isolated oligonucleotides are determined by the "fingerprint" method.

[Preparative isolation of tetra-, penta- and hexapurine oligonucleotides from partial hydrolysates of depyrimidinated herring sperm DNA]. / Präparative Isolierung von Tetra-, Penta- und Hexapurinoligonucleotiden aus Partialhydrolysaten depyrimidinierter Heringsspermen-DNA.

Herring sperm DNA is chemically degraded to a complex mixture of purine nucleotides. The oligonucleotides are separated from the partial hydrolysates by column chromatography. The resulting mixture of trimer to hexamer purine oligonucleotides is subsequently fractionated on QAE-Sephadex into different mixtures of sequence-isomeric purine oligonucleotides. In a final separation, which uses reversed-phase (Nucleosil C18) high-performance liquid chromatography, these mixtures are separated under isocratic conditions into 35 pure defined purine oligonucleotides with four to six monomer units, 14 defined mixtures of sequence-isomeric purine oligonucleotides and several unidentified products. Purity and sequence of the isolated oligonucleotides are determined by the "fingerprint" method. The results of the high-performance liquid chromatographic and the "fingerprint" methods of the isolated oligonucleotides are discussed.

[Preparative isolation of mono-, di- and tripurine nucleotides from hydrolysates of depyrimidinated herring sperm DNA]. / Präparative Isolierung von Mono-, Di- und Tripurinnucleotiden aus Hydrolysaten depyrimidinierter Heringsspermen-DNA.

The purine nucleotides pdAp, pdGp, (dA)2, (dA-dG), (dG-dA), (dG)2, (dA)3, (dA-dG-dA), (dA-dA-dG), (dG-dA-dA), (dG-dA-dG) and known mixtures of purine nucleotide sequence isomers were separated by preparative scale chromatography of partial hydrolysates of depyrimidinated herring sperm DNA. Herring sperm DNA is first partially hydrolysed to a mixture of purine nucleotides. The low-molecular-weight oligonucleotides are then separated by column chromatography on DEAE-cellulose at pH 7.5, and fractionated by chromatography on QAE-Sephadex. Impurities which are not fully removed by column chromatography are separated by paper chromatography. The sequence of the isolated DNA fragments and the composition of the mixtures of sequence isomers were determined from the chromatographic data, absorption characteristics and by enzymatic degradation.