Multivariate meta-analysis of QTL mapping studies

A large number of quantitative trait loci (QTLs) for milk production and quality traits in dairy cattle has been reported in literature. The large amount of information available could be exploited by meta-analyses to draw more general conclusions from results obtained in different experimental conditions (animals, statistical methodologies). QTL meta-analyses have been carried out to estimate the distribution of QTL effects in livestock and to find consensus on QTL position. In this study, multivariate dimension reduction techniques are used to analyse a database of dairy cattle QTL published results, in order to extract latent variables able to characterise the research. A total of 92 papers by 72 authors were found on 25 scientific Journals for the period January 1995-February 2008. More than thirty parameters were picked up from the articles. To overcome the problem of different map location, the flanking markers were mapped on release 4.1 of the Bos taurus genome sequence (www.ensembl. org). Their position was retrieved from public databases and, when absent, was calculated in silico by blasting (http://blast.wustl.edu/) the markers’ nucleotide sequence against the genomic sequence. Records were discarded if flanking markers or P-values were not available. After these edits, the final archive consisted of 1,162 records. Seven selected variables were analysed both with the Factor Analysis (FA), combined with the varimax rotation technique, and Principal Component Analysis (PCA). FA was able to explain 68% of the original variability with 3 latent factors: the first factor extracted was highly associated (factor loading of 0.98) to marker location along the chromosome and could be considered as a marker map index; the second factor showed factor loadings of 0.74 and 0.84 related to the variable number of animals involved and year of the experiment, respectively, and it can be regarded as an indicator of the dimension of the study; the third factor was correlated to the significance level of the statistical test (0.78), number of families (0.63), and, negatively, to the marker density (-0.43). It can be named as index of power of the experiment. Same patterns can be observed in the eigenvectors of PCA. Four PCs were able to explain about 80% of the original variance. The first two PCs basically underlined accurately the same structure found with the first two factors in FA, whereas PC3 and PC4 summarized the structure of F3. The score that each QTL gets on each Factor or PC could be useful to classify the original QTL records and make them more comparable once that the redundancy of information has been removed

Analysis of MC1R polymorphism in Sardo-Modicana cattle

Coat colour has been a topic of interest for both breeders and geneticists. Currently most cattle breeds are identified by their coat colour. In mammals, red/yellow and black/brown colours are determined by the distribution of two pigments: pheomelanin and eumelanin. The relative amounts of these pigments are primarily controlled by two loci, namely Extension (E) and Agouti (A). Extension gene encodes a seven trans-membrane domain receptor called Melanocortin 1 Receptor (MC1R). Activation of MC1R causes the production of eumelanin, whereas its inhibition leads to the production of pheomelanin. In cattle, three main alleles are known for MC1R gene: i) E+ (wild type), ii) ED (dominant black), and iii) e (recessive red). Mutations in coat colour genes have already been utilized for breed traceability of livestock products. Sardo-Modicana is an old local breed that experienced a gradual decrease in numbers as a result of the mechanization of agriculture. Following the recent tendency of market for typical products, there is a renewed interest for cheese and meet produced by this breed. Traceability protocols for this breed will be useful to guarantee the consumers and protect Sardo-Modicana breeders. The aim of this investigation was to analyse MC1R polymorphism in Sardo-Modicana cattle breed and evaluate if these DNA markers can be useful for product traceability in this breed. A total of 60 genomic DNA samples from Sardo-Modicana cattle collected in seven farms in the Monti Ferru area of western Sardinia were analysed by PCR-RFLP method. DNA was amplified using specific primers designed on the base of the bovine sequence from GenBank Acc. no. U39469. The obtained 402 bp amplicons were separately digested with restriction endonucleases MspA1l to score allele ED and Msp1 for allele e respectively. The fragments were run on 2.5% agarose gel stained with Ethidium Bromide. Results on Sardo-Modicana breed highlighted an almost exclusive occurrence of wild type allele except in one animal that resulted heterozygous E+/e. A larger number of animals of the same or other breeds farmed in Sardinia is needed to clarify if the locus polymorphism for MC1R is a valid DNA marker for the identification of Sardo-Modicana products

Cloning and expression analysis of a Petunia hybrida flower specific mitotic-like cyclin

AbstractA cyclin cDNA clone (Pethy;CycB1;1) was isolated from a Petunia hybrida ovary specific cDNA library. Sequence comparison revealed that Pethy;CYCB1;1 protein is highly homologous to mitotic B1 cyclins. Northern analysis and in situ hybridisation experiments showed that its expression is developmentally regulated and restricted to flower organs. We have attempted to define some of the cell division patterns which contribute to shaping each floral organ by analysing Pethy;CycB1;1 expression on Petunia flower sections. While in sepals, epidermis and parenchyma cell division patterns were comparable, there were two distinct cell division patterns in petals. In the epidermis, Pethy;CYCB1;1 expression was found both at the petal tip and along epidermis, whereas in the parenchyma only at the petal tips. In reproductive organs cell divisions were detected only in sporophytic tissues. No signals were detected inside meiotic cells

Mode of reproduction is detected by Parth1 and Sex1 SCAR markers in a wide range of facultative

Abstract Gametophytic apomixis in Kentucky bluegrass (Poa pratensis L.) involves the parthenogenetic development of unreduced eggs from aposporic embryo sacs. Marker-assisted selection for the mode of reproduction in P. pratensis would avoid costly and time-consuming phenotypic progeny tests. We developed and tested two SCAR primer pairs that are associated with the mode of reproduction in P. pratensis. The SCAR primers identified the apomictic and sexual genotypes among progenies of sexual x apomictic crosses with very low bias. Furthermore, when tested on a wide range of Italian and exotic P. pratensis germplasm, they were able to unequivocally distinguish sexual from apomictic genotypes. This system should, therefore, allow new selection models to be set up in this species

Mode of reproduction is detected by Parth1 and Sex1 SCAR markers in a wide range of facultative apomictic Kentucky bluegrass varieties

Gametophytic apomixis in Kentucky bluegrass (Poa pratensis L.) involves the parthenogenetic development of unreduced eggs from aposporic embryo sacs. Marker-assisted selection for the mode of reproduction in P. pratensis would avoid costly and time-consuming phenotypic progeny tests. We developed and tested two SCAR primer pairs that are associated with the mode of reproduction in P. pratensis. The SCAR primers identified the apomictic and sexual genotypes among progenies of sexual x apomictic crosses with very low bias. Furthermore, when tested on a wide range of Italian and exotic P. pratensis germplasm, they were able to unequivocally distinguish sexual from apomictic genotypes. This system should, therefore, allow new selection models to be set up in this species

Molecular characterization and expression of a divergent α-tubulin in planarian <i>Schmidtea polychroa</i>

We report the cloning and sequencing of a cDNA from planarian Schmidtea polychroa (Platyhelminthes, Turbellaria, Tricladida) encoding for an unusual tubulin isoform (SpTub-1) which is specifically expressed in testis. Sequence comparison of SpTub-1 with other known tubulins reveals that it has the highest homology with &#x3b1;-tubulins, even though the analysis of the molecular features shows that this isoform is significantly divergent. Hybridization of SpTub-1 to restriction-digested genomic DNA to Southern blotting produced a multiple banding pattern indicating that in planarian, a tubulin multigene family exists. Using in situ hybridization, we showed that the transcript is specifically detectable in planarian testis, suggesting that it may play a role in spermatogenesis