Establishing Genetic Relationship Using Snp Data

Question

[Thakurdas Saha]

Greetings! I work on rubber (Hevea brasiliensis), I would like to know the way you input SNP data set for "Darwin" to draw a dendrogram for establishing genetic relationship, as there may be some heterozygous SNPs. If it is only homozygous SNPs then it is easy to deal with. We use "Kimura two parameters model" or Tajima and Nei, where the nucleotide changes among individuals are homozygous. For example,

Individual 1: ...AATTCCTTGGA-G....
Individual 2: ...AAGTCCATGGATG....
Individual 3: ...AATTCCATGGA-G....

But with heterozygous SNPs/indels (as in individual 2 in the following example) how do we make the data for distance analysis among the individuals using Kimura model?

Individual 1: ...AATTCCTTGGA-G...
Individual 2: ...AA(T/G)TCCATGGA(T/-)G...
Individual 3: ...AATTCCATGGA-G...

I understand that only DNASP can recognize diploid heterozygous SNPs. but how the same data could be useded in Darwin? Please let me know how to do that? If you know any other software which can handle efficiently the heterozygous SNPs data, please let me know. Waiting for your reply.

Regards, Thakurdas saha

Answer 1

[Carlos Villacorta]

Hi Thakurdas,

if you don't want to use DnaSP, one approach would be inferring the haplotypes (for example with HaploBlock) and then using this non-ambiguous data as input for DARwin.

Cheers,