Use of the multivariate discriminant analysis for genome-wide association studies in cattle

Genome-wide association studies (GWAS) are traditionally carried out by using the single marker regression model that, if a small number of individuals is involved, often lead to very few associations. The Bayesian methods, such as BayesR, have obtained encouraging results when they are applied to the GWAS. However, these approaches, require that an a priori posterior inclusion probability threshold be fixed, thus arbitrarily affecting the obtained associations. To partially overcome these problems, a multivariate statistical algorithm was proposed. The basic idea was that animals with different phenotypic values of a specific trait share different allelic combinations for genes involved in its determinism. Three multivariate techniques were used to highlight the differences between the individuals assembled in high and low phenotype groups: the canonical discriminant analysis, the discriminant analysis and the stepwise discriminant analysis. The multivariate method was tested both on simulated and on real data. The results from the simulation study highlighted that the multivariate GWAS detected a greater number of true associated single nucleotide polymorphisms (SNPs) and Quantitative trait loci (QTLs) than the single marker model and the Bayesian approach. For example, with 3000 animals, the traditional GWAS highlighted only 29 significantly associated markers and 13 QTLs, whereas the multivariate method found 127 associated SNPs and 65 QTLs. The gap between the two approaches slowly decreased as the number of animals increased. The Bayesian method gave worse results than the other two. On average, with the real data, the multivariate GWAS found 108 associated markers for each trait under study and among them, around 63% SNPs were also found in the single marker approach. Among the top 118 associated markers, 76 SNPs harbored putative candidate genes

GENOME BANK OF CHIANINA IN UMBRIA

Banka DNA genoma Chianine mora se dobiti od 5100/4500 krava i 600 bikova/grla u četiri godine. Testirana su tri različita paketa prema trošku, dobivenoj količini DNA i vremenu potrebnom za ekstrakciju. 1.paket paket niskog troška ali manje dobivenog DNA (15 - 20 µg) ako se upotrijebi 200 µl čitave krvi. Dobra količina DNA dobivena je samo ako se upotrijebe kuglice/pelete leukocita ali zbog zasićenja stupca mogućnost ponavljanja bila je vrlo niska. Kako bi se riješio ovaj problem obavljena je dvostruka ekstrakcija s dva različita stupca. Trošak je još uvijek bio manji nego onaj iz drugih paketa koji su mogli obraditi velike količine krvi ali je za postupak ekstrakcije trebalo previše vremena. 2. paket bio je velikog opsega. Ovom metodom dobivena je ista količina DNA kao i kod dvostruke ekstrakcije u paketu 1. Rezultati su bili dosljedniji ali je još uvijek došlo do zasićenja stupca. 3. paket: bio je to paket bez stupca; paket je omogućio dobivanje 30-40 µg DNA iz 1.5 ml krvi, s mogućim dobrim ponavljanjem i uz relativno nizak trošak. Ova je metoda, stoga, izabrana za stvaranje banke genoma Chianine

Characterization of endophytic and symbiotic bacteria within plants of the endemic association Centaureetum horridae Mol.

We investigated the internal association of bacteria with Astragalus terraccianoi and Centaurea horrida, two endemic plants of the Mediterranean islands, forming the phytosociological association Centaureetum horridae, typical of windswept cliffs on the rocky shores of Asinara (Sardinia, Italy) and other limited locations. Sampling occurred in the protected natural park of the Asinara island. Roots and stems of the two plants and the root nodules of A. terraccianoi were surface sterilized in order to remove external and rhizospheric microbiota and to subsequently isolate the culturable bacterial communities. Plate counts revealed densities of endophytes between 3.7 7 102 and 2.8 7 104 colony forming units per gram of fresh weight. 16S rDNA sequencing revealed the occurrence of bacteria displaying high similarity with Actinobacterium sp., Paenibacillus sp., Rhizobium sp., Methylobacterium sp., Pedobacter panaciterrae, Aerococcus viridans, Stenotrophomonas rhizophila, Bacillus sporothermodurans, Bacillus pumilus, Bacillus simplex, Bacillus flexus, Streptomyces ciscaucasicus and Dyella sp. The putative nitrogen-fixing rhizobium symbiont of A. terraccianoi was identified for the first time. It turned out to belong to the slow-growing Bradyrhizobium genus and to share a 97% similarity with Bradyrhizobium canariense. It was found to be nonculturable and to coexist in nodules with a number of different endophytes

Mode of reproduction is detected by Parth1 e 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