Unexpected LD with NAM 2.7 RIL SNP

[Mark Gee]

I'm getting unusual LD results when using TASSEL 5.2.87 on a subset of the NAM RIL (~1300 lines) with the NAM marker data from Panzea. Markers that are very close often have low levels of linkage, even when they are very close.

I started with "ZeaGBSv27_publicSamples_imputedV5_AGPv4-181023.h5" and observe a similar pattern with the unfiltered SNP, filtered SNP, and filtered+imputed SNP.

I have created a reproducible example with the genotypic data files and a taxa list for my subset of RIL. I used TASSEL5 GUI to filter the SNP dataset, calculate the LD (sliding window of 50 for NAM2.7), export the LD data, then use the R script to create the LD plot. The zip file and plots can't be attached to this message, please let me know if you would like me to send it to you.

The same analysis in Plink produces similar results.

I plotted the LD results by family and by chromosome. I also included histograms of the distance between markers and the R^2. The results [I can send them directly] are from family Z002 which is representative of the other families. There is a grouping of markers in high LD and low LD, even at very close distances. 

Any thoughts on why such an unusual LD pattern is observed?

[Muyu Gu]

Hi Mark,

Did you get the reason for this? I an encounter exactly the same problem here where LD are extreme high for large distance SNPs marker. I looked at your description and found that your steps are exactly like what I did in my analysis. I have attached a screenshot of one of the NAM subpopulation I analyzed. Thanks!

Best

Muyu

[Mark Gee]

Hi Muyu,

I did not find an explanation. After reaching out to Peter Bradbury, he said that he had not done this type of analysis before on the dataset. I repeated the study using PLINK and obtained the exact same results so I know that it is not an error in the TASSEL program.

I'm still trying to understand why this occurred. Please let me know if you find the answer.

Mark

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[Amir FARTASH]

Hi Muyu

Try to manipulate the site min count (increase it) and redo your analysis

Good luck

Ph.D. Student of Functional Ecology and Environment

École Nationale Supérieure Agronomique de Toulouse (INP- ENSAT)

Toulouse,France

phone  number : +33-(0)6 58 88 2930

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