Imputation accuracy of cattle in ultra lowpass whole genome sequencing

AGBT Ag 2023, San Antonio, Texas.

Imputation Accuracy of Cattle in Ultra Lowpass Whole Genome Sequencing

Element: Ben Krajacich, Junhua Zhao, Kelly Blease, Semyon Kruglyak
Gencove: Andy Liu, Jahan Parsa, Jesse Hoff
seqWell: Ariele Hanek, Calude Hamby, Kenneth Tenan, Michelle Rahardja

The use of genomic prediction in agriculture has been shown to be an effective way to accelerate breeding by affordably providing accurate predictions of genetic merit. Genome wide genotypes of sufficient density and accuracy can substitute for phenotypic data collection in far less time. Several sequencing methods have been adopted to provide genotypes for these applications. Here we demonstrate an approach to ultra low-pass (ULP) sequence that will optimize cost, turnaround time flexibility and accuracy in a benchtop format. With a few dollars of sequence data it is possible to drive genomic improvement.

We aimed to evaluate the effectiveness of using a high throughput, ultra low coverage genotyping strategy using efficient library preparation, benchtop sequencers and low-pass sequencing combined with imputation. In total, libraries from 1,536 cattle samples were prepared using seqWell’s plexWellTM Low Pass 384 kit and sequenced using the AVITI sequencer on two flow cells in a single run. We targeted average output of less than .2x coverage of the cattle genome. Data was demultiplexed and run on the Gencove analysis platform, resulting in imputation of over 60 million SNPs and indels. The genotype accuracy was calculated. We estimated the genomic relationship matrix of the ULP samples and compared to higher coverage data. We also evaluated the impact of further reductions in coverage, representing higher index counts.

The relative loss in genotyping accuracy from ULP would be low when compared to cost and throughput savings. A small lab with plant or animal samples can process up to 6,000 samples a week using this method, or more with additional indices. Our study demonstrates that the use of the Element AVITI system for genotyping in cows is a reliable and efficient method.

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