Reference genome and the number of SNPs

[Sigal Popovsky]

In my GBS project we seek to find SNPs on F2 segregate population.

This population was generated from an intra-specific cross between two species of pepper: Capsicum annuum X Capsicum chinense.

So-far, our pipline in Tassel resulted with 37,000 SNPs when we used the C.Annuum as a reference genome, while 55,000 SNPs were produced when we used the C.chinense genome as a reference.

Does the reference genome we are using should has an effect on the amount of SNPs we receiving?

[Edward S. Buckler]

Yes.  The quality of the reference could have a large effect like you are seeing here.  I would recommend using the better quality genome as the reference.

We are building pan genome haplotypes graph that deal with this, and allow both genomes to be used as reference, but it is not ready for the public consumption yet.  Sorry.

Cheers-

Ed

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[Sigal Popovsky]

OK, Thank you.

Indeed it will be great to mapp with two genomes reference.

Following my question I would also like to ask:

1.Is it possible that the genotype of the plants in the same SNP in the same location, can be different in different genome reference?

2. .Is it possible that the genotype of the plants in the same SNP in different location will be different in different genome reference?

Thanks a bunch

Sigal

On 10 September 2017 at 21:57, Edward S. Buckler <es...@cornell.edu> wrote:

Yes.  The quality of the reference could have a large effect like you are seeing here.  I would recommend using the better quality genome as the reference.

We are building pan genome haplotypes graph that deal with this, and allow both genomes to be used as reference, but it is not ready for the public consumption yet.  Sorry.

Cheers-

Ed

On Sep 9, 2017, at 6:09 PM, Sigal Popovsky <sigal...@gmail.com> wrote:

In my GBS project we seek to find SNPs on F2 segregate population.

This population was generated from an intra-specific cross between two species of pepper: Capsicum annuum X Capsicum chinense.

So-far, our pipline in Tassel resulted with 37,000 SNPs when we used the C.Annuum as a reference genome, while 55,000 SNPs were produced when we used the C.chinense genome as a reference.

Does the reference genome we are using should has an effect on the amount of SNPs we receiving?

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Sigal Popovsky-Sarid, PhD

Dr. Paran Lab

Institute of Plant Sciences

ARO, the Volcani Center, Israel 

cell: +972-(0)50-722-6768

Email: sigal...@gmail.com                                                   

[Marlee Labroo]

Hi Sigal,

I think you're asking whether the chosen reference genome will influence whether a site is called as a SNP in your test individuals. The answer is yes; if an individual is more related to the reference genome, fewer SNPs will of course be present and called. In contrast, if an individual is less related to the reference genome, more SNPs will be present and called.

To me it seems like a SNP should always be in approximately the same location, and I don't understand that aspect of your question. Hope this helps, sorry if I misunderstood!

Marlee

On Monday, September 11, 2017 at 3:21:53 PM UTC+8, Sigal Popovsky wrote:

OK, Thank you.

Indeed it will be great to mapp with two genomes reference.

Following my question I would also like to ask:

1.Is it possible that the genotype of the plants in the same SNP in the same location, can be different in different genome reference?

2. .Is it possible that the genotype of the plants in the same SNP in different location will be different in different genome reference?

Thanks a bunch

Sigal

On 10 September 2017 at 21:57, Edward S. Buckler <es...@cornell.edu> wrote:

Yes.  The quality of the reference could have a large effect like you are seeing here.  I would recommend using the better quality genome as the reference.

We are building pan genome haplotypes graph that deal with this, and allow both genomes to be used as reference, but it is not ready for the public consumption yet.  Sorry.

Cheers-

Ed

On Sep 9, 2017, at 6:09 PM, Sigal Popovsky <sigal...@gmail.com> wrote:

In my GBS project we seek to find SNPs on F2 segregate population.

This population was generated from an intra-specific cross between two species of pepper: Capsicum annuum X Capsicum chinense.

So-far, our pipline in Tassel resulted with 37,000 SNPs when we used the C.Annuum as a reference genome, while 55,000 SNPs were produced when we used the C.chinense genome as a reference.

Does the reference genome we are using should has an effect on the amount of SNPs we receiving?

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[Sigal Popovsky]

As I understand, the SNP's location is determain according to its allighment to the ref. genome, not necessarilly with full identity.

If that correct. I'll expect different numbers of SNPs in different ref.genome. (I think it match Ed's answer).

At the other hand, as I understand, the SNP's genotype (for each plant) is set only according to the comparison between the TAGs that "sticked" to the same location in the ref.genome. 

Meaning:  without considering the sequence of the ref.genome at that point of the analysis.

Is that  is the case?

Sigal

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