COURSES SYLLABUS

Paolo AJMONE MARSAN – (GLOBALDIV Summer Schoool  Coordinator) & Johannes Arjen LENSTRA

 TILE OF THE COURSE: MODERN AND UPCOMING TECHNOLOGIES FOR GENOME ANALYSIS

SYLLABUS 

1)     From DNA diversity to phenotype: an overview

- Types of variation

      -  Variation and animal phenotypes

2)    New omic technologies for gene and protein expression, SNP typing, sequencing

     - Overview of omics

     - New sequencing technologies.

     - New SNP typing technologies

- Gene expression

3)    Omic technology aspects applied to genetic diversity

4)   Omic technologies for dissecting the phenotype

5)    Perspectives

 

Milan ZJALIC

TITLE OF THE COURSE: FARM ANIMAL PRODUCTION SYSTEM AND THREATS TO BIODIVERSITY IN EUROPE

 Farm animal production systems in Europe are generally classified as landless industrialized systems, grassland-based systems, and mixed crop-livestock systems. During the last ten years, EU has drawn a specific policy frame aiming at the conservation of farm animal genetic resources. According to the results of an EAAP inquiry, the impact of EU policies on farm animal biodiversity conservation seems generally positive for EU countries. The impact of the 2003 CAP reform on conservation programmes and biodiversity is variable among EU countries but, in general, no negative effects have been reported. Despite the effect of EU and global policies, genetic diversity of farm animals is under constant threat of erosion. While in some regions man-made disasters and disorders and policy issues represent specific threats for local AnGR, in other regions the main issue is protection from epizootic diseases and prevention of indiscriminate crossing with exotic breeds.

 

Jose’ FERNANDO GARCIA

 TITLE OF THE COURSE: FARM ANIMAL PRODUCTION SYSTEMS IN LATIN AMERICA AND THREATS TO BIODIVERSITY

 SYLLABUS:

1) Challenges for livestock sustainalble production and food production

2) Challenges to conserve livestock biodiversity in a high input and high output systems

3) Case studies of livestock biodiversity conservation (Brazilian animal genetics resources programme and the Peruvian project for alpaca selection and breeding).

Suggested readings:

 Dekkers JC. Commercial application of marker- and gene-assisted selection in livestock: strategies and lessons. J Anim Sci. 2004, 82 E-Suppl:E313-328.

 Dekkers JC. Prediction of response to marker-assisted and genomic selection using selection index theory. J Anim Breed Genet. 2007, 124(6):331-41.

Charlier C, Coppieters W, Rollin F, Desmecht D, Agerholm JS, Cambisano N, Carta E, Dardano S, Dive M, Fasquelle C, Frennet JC, Hanset R, Hubin X, Jorgensen C, Karim L, Kent M, Harvey K, Pearce BR, Simon P, Tama N, Nie H, Vandeputte S, Lien S, Longeri M, Fredholm M, Harvey RJ, Georges M. Highly effective SNP-based association mapping and management of recessive defects in livestock. Nat Genet. 2008 40(4):449-54.

K . Betteridge. Farm animal embryo technologies: Achievements and perspectives. Theriogenology 2006, 65 , 5 , 905 – 913

Van Eenennaam AL, Li J, Thallman RM, Quaas RL, Dikeman ME, Gill CA, Franke DE, Thomas MG. Validation of commercial DNA tests for quantitative beef quality traits. J Anim Sci. 2007, 85(4):891-900.

 

Linn FENNA GROENEVELD

TILE OF THE COURSE: APPLICATION TO PHYLOGEOGRAPHY TO WILD ANIMALS

 SYLLABUS

Madagascar is one of the top global biodiversity hotspots with extremely high endemism rates for both flora and fauna. Surprisingly, the diversity of the endemic primates is still not completely known. Especially within small and nocturnal taxa a number of new species have lately been described. In this project I wanted to characterize the genetic diversity of the genus Cheirogaleus, small (130-600g), nocturnal lemurs distributed throughout the dry and moist forests of Madagascar. Multiple genetic markers (mitochondrial and nuclear) and morphological data were used to obtain information about phylogenetic relationships of the sampled populations and their taxonomic status. In conjunction with geographical data I hoped to be able to uncover biogeographic patterns that I compared to existing bio- and phylogeographic hypotheses for Madgascar. Since the last revision of this genus is based solely on museum specimens, I included museum samples in my analyses, in order to match my results with the species described up to date.

 

Licia COLLI and Anna OLIVIERI

 TITLE OF THE COURSE: METHODS FOR THE ANALYSIS OF MITOCHONDRIAL DNA DATA

SYLLABUS

 L. Colli

•                    The mitochondrial genome

•                    Sequence format and alignment

•                    Input file formats most frequently used in mtDNA analyses

•                    Molecular diversity indices

•                    Analysis of Molecular VAriance (AMOVA)

•                    Mismatch distribution and estimates of population expansion

•                    Admixture analysis

•                    Trees:

                   -generalities;

                  -models of DNA sequence evolution and choice of the best-fitting model

                  -tree reconstruction strategies

                  -distance-based methods (NJ)

                  -character-based methods (MP, ML, Bayesian)

                  -molecular clock and calculations of divergence times

                  -Bootstrap and Jacknife

•                    Software list

•                    Rereferences

 

A. Olivieri

 ·         introduction (mtDNA, advantages and limits of uniparental markers)

·         overview of different approaches on mtDNA studies
1. Phylogenetic study of a single haplogroup
2. Study of a whole phylogeny
3. Population study

·         Phylogenetic study of a single haplogroup

o        introduction to M1 and U6 analysis

o        methods for phylogenetic studies: how to get preliminary data, sample selection, sequencing (sequencher), tree design (parsimony, an example), network, age estimate.

o       results of the work

·         2. Study of a whole phylogeny

o        introduction to the bovine phylogeny

o        methods of sample selection

o         mutation rate estimate

o        results of the work

·         3. Population study

o         methods of classification into haplogroups and sub-haplogroups (an example)

o        advantages of a good level of classification

·         Final remarks and conclusions

 

Miika TAPIO & Juha TAPIO KANTANEN

TITLE OF THE COURSE: METHODS FOR THE ANALYSIS OF NUCLEAR DNA DATA

SYLLABUS:

 A) Introduction to molecular markers and molecular livestock diversity  studies (Kantanen, 1.5h)

  B) Diversity analysis (2h)

    1)Within-population diversity (Tapio)

    2)Between-population diversity (Tapio)  3)Phylogenetic patterns (Tapio)  4)Bayesian clustering (Kantanen/Tapio)

  C) Wrap-up discussion (0.5h) (Kantanen/Tapio)

 

Paul BOETTCHER

TITLE OF THE COURSE: SOFTWARE FOR THE ANALYSIS OF MOLECULAR DATA

SYLLABUS

1. Overview of software available for genetic analyes (1 hour)  40 minutes for nuclear DNA and 20 for mitochondrial

2. Overview and demonstration of the Genalex software (1/2 hour)

3. Overview and demonstration of the Structure software (1/2 hour)

4. Practical exercises by students using Genalex and Structure software (2 hours)

  

Ercole ZERBINI

TITLE OF THE COURSE: DYNAMICS OF LIVESTOCK PRODUCTION SYSTEMS, DRIVERS OF CHANGE AND PROSPECTS FOR ANIMAL GENETIC RESOURCES. From a paper by sere et al. 2008

Global dynamics in agriculture: growth of human populations and increasing demand in animal products; competition between uses of agricultural land among food, feed and energy production; animal breeding and climate change; intensification vs. extensification  and organic animal farming; need for increasing the efficiency of animal production.

Husbandry system in Asia and Africa and challenges to biodiversity. Dramatic impact of diseases on human and livestock. Danger of non controlled crossbreeding. Strategy for conservations in developing Countries.

 

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