Establishing core collection for different crops:
- chickpea,
- fieldpea,
- lupin
- lentils
Objective: core collection will be based on two objectives.
Distance based measures
Average entry-to-nearest-entry distance (diversity)
Average accession-to-nearest-entry distance (representativeness)
steps:
SNP calling and data Filtering
Multi-dimensional scaling all lines
selection of core collection using core hunter
The package corehunter is available on CRAN and can be installed with
install.packages("corehunter") library(corehunter)
overlaying Multi-dimensional scaling with the core selection to visualise the genetic diversity and representativeness