R. Negrini

History or ecology? Substrate type as a major driver of spatial genetic structure in Alpine plants.

Climatic history and ecology are considered the most important factors moulding the spatial pattern of genetic diversity. With the advent of molecular markers, species historical fates have been widely explored. However, it has remained speculative what role ecological factors have played in shaping spatial genetic structures within species. With an unprecedented, dense large-scale sampling and genome-screening, we tested how ecological factors have influenced the spatial genetic structures in Alpine plants. Here, we show that species growing on similar substrate types, largely determined by the nature of bedrock, displayed highly congruent spatial genetic structures. As the heterogeneous and disjunctive distribution of bedrock types in the Alps, decisive for refugial survival during the ice ages, is temporally stable, concerted post-glacial migration routes emerged. Our multispecies study demonstrates the relevance of particular ecological factors in shaping genetic patterns, which should be considered when modelling species projective distributions under climate change scenarios.

Fine-scale genetic structure, phylogeny and systematics of threatened crayfish species complex

Systematic uncertainties in the crayfish Austropotamobius pallipes are well grounded by the number of species and subspecies described using different approaches, causing scientists to define this taxon as complex. However, a key task that conservation programmes are facing regarding the recent and drastic decline of European populations, is the coherent systematic classification of this threatened species. Here we present results obtained by coupling mtDNA and genome analysis suggestive of a novel evolutionary framework to explain the relationships among phylogenetic lineages of A. pallipes. The direct sequencing of mtDNA COI gene fragment revealed a strong geographic structure with four distinct haplogroups separated by a range of 5-25 mutations. However, mitochondrial data were not supported by genomic fingerprinting based on 535 AFLP polymorphisms. Nuclear markers showed an unexpected moderate level of genetic differentiation and the absence of any geographic structure. Consequently, this study proposes that the taxonomic hypothesis of a single species of A. pallipes settling the Italian continental waters, is affected by complex evolutionary events. To solve the paradox, we hypothesized an evolutive scenario in which the separation of ancient mtDNA lineages likely occurred before the latest glacial periods. However, the speciation process remained incomplete due to secondary intensive postglacial contacts that forced the mingling of the genomes, and confounds the phylogeographic signature still detectable within mtDNA. Postglacial dispersion and the following demographic events, such as founder effects, drift and bottlenecks, abruptly depleted the local mtDNA variation, and shaped the current genetic population structure of white-clawed crayfish.

Application of AFLP technology to radiation hybrid mapping.

We have investigated the use of AFLP® technology as a tool for the high throughput enrichment of Radiation Hybrid (RH) maps. The 3000 rad TM112 bovine RH panel was assayed with 37 EcoRI/TaqI AFLP primer combinations. The number of selective nucleotides used during PCR was increased to seven, to reduce the complexity of the AFLP profile and minimise the overlap between hamster and bovine bands co-amplified from hybrid cell clones. Seven-hundred-forty-seven bovine AFLP bands were amplified that could be distinguished following electrophoresis. Repeatability was tested within and between laboratories on independent template preparations and an error rate of 1.3% found. Two-point linkage analysis clustered 428 AFLP fragments in 39 linkage groups of at least 4 markers. Multi-point maps were constructed for 5 sample linkage groups. The study demonstrated that the AFLP approach could be used to rapidly screen for the most informative clones during panel construction and to increase the number of markers on RH maps, which could be useful for joining linkage groups formed by other markers. The use of AFLP markers as anchor points between existing RH maps and other physical maps, such as BAC contigs, is also discussed.

Beef characteristics predicted by NIRS

AIM Identify signals of fat deposition and adaptation through genome-wide scan of the Barbaresca fat-tail sheep. ANIMALS Barbaresca in an ancient Sicilian fat-tail sheep, highly endangered at present. Of the 35 000 heads of 1980, abour 1 300 are left nowadays in 20 flocks. The breed originated from crosses between Barbary sheep from North Africa and the Pinzirita breed at times of the Arab settling in Sicily (9th century). The breed is reared in a very restricted area in central Sicily on smalland medium-sized farms under a semi-extensive farming system. It is a dual-purpose breed: milk for cheese and meat. Barbaresca is one of the only two fat-tail sheep of Italy. METHODS Genotypic data were obtained with the OvineSNP50K array. Fst values of differentiation for 43072 markers were calculated in pairwise comparisons of Barbaresca with each of 13 Italian thin tail breeds. Fat-tail sheep still represent twenty-five percent of the world sheep population; they are predominant in pastoral, transhumant and low input systems. In Western countries and in high input systems they are generally endangered. Fat-tail sheep preserved genetic variability for functional adaptation. The identification of the genes with a role in the fat-tail phenotype contributes to the understanding of the physiology of fat deposition as well as the mechanisms of adaptation and is essential for maintaining future breeding options.uf071 Heritability estimates for the 1st litter size, pregnancy rate and whelping success were low (0.05-0.14) uf071 Grading size and quality had moderate heritability estimates 0.27 and 0.21, respectively uf071 Genetic correlations between animal grading size and fertility traits were unfavourable (from -0.15 to -0.53) uf071 Grading quality and guard hair coverage had antagonistic relationships with all the studied fertility traits (from -0.21 to -0.54) Genetic parameters of fertility and grading traits in Finnish blue foxTrabajo presentado al: 68th Annual Meeting of the European Federation of Animal Science (EAAP). (Tallin, Estonia. 28 agosto - 2 septiembre).As genomic selection has been used already for several years, it has become evident that the validation of genomic evaluations relying on traditional animal models is becoming unsuitable. The GEBV validation test recommended by Interbull is cross-validation based on the forward prediction. It was designed at the time when the multi-step genomic evaluation was the standard method.xa0 The aim of this study was to take a closer look on accuracy and stability of (G)EBVs. Validations for GEBVs were done using yield deviations (YD) or daughter yield deviations (DYD) calculated with single-step GBLUP instead of EBV model. Moreover, we studied the stability of (G)EBV estimations in consecutive evaluations. We used Nordic Holstein 305 days production data containing ca. 7.3 million cows with 15.6 million observations.xa0 Genotypes were available for 30056 animals which had either records or offspring in the full 305d data. The test setup consisted of four data sets: the full data, called data 0 , included calvings up to March 2016. Three reduced data sets were data -1 , data -2 , and data -3 , from which one year of calvings was deleted at a time.xa0 This allowed studying the accuracy of predictions by production years, and also the stability of (G)EBV estimates across lactations. The bull validation was a regression of DYD EBV on PA data-3 or, for GEBV data-3 , regression of DYD GEBV on GEBV data-3 .xa0 The results suggested that after use of genomic selection the DYD from EBV model become biased and that GEBVs validated using DYDs from the BLUP model might receive too low reliability. The validation reliability for protein GEBV (r 2 ) was 0.34 using DYD from EBV model and 0.36 using DYD from ssGBLUP. Similarly, when making cow validations, it might be advisable to use YDs calculated from ssGBLUP for the validation.xa0 The r 2 in GEBV validations using YD from ssGBLUP were on average 5 % units higher compared to validations using YDs from the EBV model.Trabajo presentado al: 68th Annual Meeting of the European Federation of Animal Science (EAAP). (Tallin, Estonia. 28 agosto - 2 septiembre).

Identification of milk protein percentage QTLs in Italian Friesian cattle by selective genotyping two GDD families with AFLP and SSR markers

Abstract In this work we evaluated the combined use of AFLP markers and selective genotyping in a Grand Daughter experimental design (GDD), to identify chromosomal regions candidate to contain QTL for milk protein percentage (PP) in Italian Friesian cattle. We verified the approach by microsatellite analysis of 4 candidate chromosomal regions. Twenty-five AFLP primer combinations, assayed on the extreme minus and plus-variant half-sibs and on the grandsires of 2 GDD families, produced 180 polymorphic bands of paternal origin. Association analysis resulted in 16 AFLPs significantly associated to PP-EBVs (P≤0.05), that mapped on 8 chromosomes, in regions where PP-QTLs were identified in previous studies. Microsatellite analysis confirmed association for 2 regions of BTA10 and BTA28.