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Projecte llegit

Títol: Understanding emmer wheat population structure using genomics


Estudiant que ha llegit aquest projecte:


Tutor/Cotutor: CASALS MISSIO, JOAN

Departament: DEAB

Títol: Understanding emmer wheat population structure using genomics

Data inici oferta: 30-01-2023      Data finalització oferta: 30-04-2023


Estudis d'assignació del projecte:
    GR ENG SIS BIOLÒGICS

Lloc de realització:


En empresa (cal signar un conveni de cooperació)

        Tutor Extern: Laura Rodríguez Botigue
        Institució/Empresa: CRAG

Paraules clau:
Triticum durum, emmer wheat, landraces, plant evolution

Descripció del contingut i pla d'activitats:
1. Generation of the dataset
At the Botigué group, we have processed whole genome sequencing
data for a number of wild and domestic emmer wheat accessions. At
the moment another undergraduate student in the group is
processing data from other landraces that have been recently
published. Student will merge this data with exome data generated
in Avni et al. (2017) to have a dataset with all the polymorphic
sites that are shared in the two datasets, having the largest
emmer dataset studied so far. The reason why we want to merge the
two datasets is that in Avni et al. (20117) exome dataset there
are emmer landraces from the Mediterranean, a region that is
under-represented in the whole genome sequencing dataset.
2. Principle Component Analysis
With the merged dataset (a Variant Calling File or VCF), the
student will carry out a Principle Component Analysis to explore
how the different accessions are distributed in a two-dimensional
space, and how there are related to each other.
3. Admixture plot
With the merged dataset, he will also perform an unsupervised
clustering algorithm (ADMIXTURE) to explore the ancestral
relationships between accessions.
4. MSMC
Alice Iob, Ph.D. candidate in our group, has set up the code to
run MSMC. This algorithm uses polymorphic sites in an individual
genome to infer changes in size through time. We want to perform
these analyses to see whether landraces in Africa have a reduced
size compared to landraces in Europe and whether the wild emmer
accessions from the northeast Fertile Crescent experienced a
reduction in population size during the domestication event.

Overview (resum en anglès): I have carried out a project that deals with the investigation of the population structure and dispersal routes experienced by emmer wheat throughout history using genomics with the assistance of bioinformatic and biostatistical tools.


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