One important advantage in plant&animal genetic studies is the availability of experimental populations. A Recombinant Inbred Line (RIL) population can be maintained and used over and over again to map all kinds of different traits. Now, RIL population is not confined to bi-parental RIL population. It can be nested association mapping (NAM) population or multiparent advanced generation intercross (MAGIC) population of arbitrary number of founders. I present a method BCFR for constructing bin-map for RILs of arbitrary number of founders. BCFR use identity by state between RILs and their founders in sliding windows, and a pedigree relationship can be optionally used to refine the bin-map, that is, individuals derived from single F1 hybrid can only have two types of alleles.

• Python (>=3.5.5)

• Click (>=7.0)

• Numpy (>=1.13.1)

• Pandas (>=0.21.0)

• Matplotlib (>=1.5.0)

Unzip the bcfr code and install

unzip bcfr-master.zip
cd bcfr-master
python setup.py install

List all the options and commands:

bcfr --help

Convert the VCF file to bcfr format:

bcfr converter --v my_genotypes.vcf --d output_dir --n number_of_founder 

Construct bin map without pedigree:

bcfr birds --n number_of_founder --d output_dir

Construct bin map with pedigree:

bcfr birds --n number_of_founder --d output_dir --p pedigree.txt

Plot individual haplotype map:

bcfr plot-hap --r ril_individual_name --d output_dir

Note: the output_dir should be the same directory in all these steps.

​ pedigree template was offered as foder.txt

bimDic.pkl is the pickled bin map object created by birds command which can be loaded in python:

with open('bimDic.pkl','rb') as f:
	bin_size,bin_map=pickle.load(f)

bin_size and bin_map are dictionary with chromosome names as key. bin_size stores the start position and end position of each bin; bin_map stores the genotypes.

The individual-wise haplotype map data was hpfDic.pkl.

The whole genome bin map chart was output as whole_genome_bin_map.jpg:

The plot-hap command output individual haplotype map chart haplotype_ril_individual_name.jpg:

Zhongmin Han - National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University

Bin-based genome-wide association analyses improve power and resolution in QTL mapping and identify favorable alleles from multiple parents in a 4-way MAGIC rice population. Theoretical and Applied Genetics by Zhongmin Han, Gang Hu, Hua Liu, Famao Liang, Lin Yang, Hu Zhao, Qinghua Zhang, Zhixin Li, Qifa Zhang, Yongzhong Xing

• Lots of memory and fast disk for large projects