# Strategy to imputation of large genomic deletions and utilizing them in mapping and genomic prediction in cattle

Md Mesbah-Uddin, Bernt Guldbrandtsen, Aurélien Capitan, Mogens Sandø

Lund, Didier Boichard, Goutam Sahana

<figure><img src="image_1.png" /></figure>

## ► To cite this version:

Md Mesbah-Uddin, Bernt Guldbrandtsen, Aurélien Capitan, Mogens Sandø Lund, Didier Boichard, et al.. Strategy to imputation of large genomic deletions and utilizing them in mapping and genomic prediction in cattle. 6th International Conference on Quantitative Genetics, Nov 2020, Melbourne (en virtuel), Australia. . [hal-04728931](https://hal.inrae.fr/hal-04728931v1)

HAL Id: hal-04728931

https://hal.inrae.fr/hal-04728931v1

Submitted on 9 Oct 2024

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

<figure><img src="image_2.png" /></figure>

Distributed under a Creative Commons Attribution 4.0 International License
<figure><img src="image_3.png" /></figure>

# Strategy to imputation of large genomic deletions and utilizing them in mapping and genomic prediction in cattle

Md Mesbah-Uddin<fnref n="1" />,<fnref n="2" />, Bernt Guldbrandtsen<fnref n="1" />, Aurélien Capitan<fnref n="2" />, Mogens Sandø Lund<fnref n="1" />, Didier Boichard<fnref n="2" />, Goutam Sahana<fnref n="1" />*

- Large genomic deletions can be detected from whole-genome sequencing (WGS), and imputed to SNP array-typed cattle population with high accuracy

- Use of deletions, beside SNPs and indels, provide better mapping signal, and gains in genomic prediction accuracy

## Hypothesis

* Large deletions can be identified from WGS and imputed with high accuracy

* Addition of deletions will improve mapping and genomic prediction

## Objectives

* To identify large deletions, and impute to existing SNP-array genotyped animals

* To use large deletions in GWAS and genomic prediction

## Methods

* Large deletions were identified from WGS using GenomeSTRIP-2 software

* Genotype phasing was performed using Beagle-4 and SHAPIT-2, and imputation was done using Minimac-3 software

* Single-marker GWAS and conditional association, and genomic prediction was performed using GCTA software

<figure><img src="image_4.png" /><figcaption>Fig1. A 525-KB deletion on chromosome 23 in Nordic Red Dairy Cattle.</figcaption></figure>

<figure><img src="image_5.png" /><figcaption>Fig2. Scatter plot of imputation accuracy of 5,739 large deletions.</figcaption></figure>

<figure><img src="image_6.png" /><figcaption>Fig3. Manhattan plot of single-marker GWAS for Fertility Index in (a) Holstein, (b) Jersey, and (c) Nordic Red Dairy Cattle.</figcaption></figure>

<figure><img src="image_7.png" /><figcaption>Fig4. Reliability of genomic prediction (Fertility) in Jersey cattle.</figcaption></figure>

## Results

* Provided a high-resolution map of large deletions (Fig 1, Ref 1)

* Deletions can be imputed with high accuracy (Fig 2, Ref 2)

* Besides SNPs and indels, some deletions showed strong association with female fertility in dairy cattle (Fig 3, Ref 3)

* Addition of GWAS markers provided higher gains in prediction accuracy (Fig 4, Ref 3)

## Reference

1. Mesbah-Uddin, M., et al., Genome-wide mapping of large deletions and their population-genetic properties in dairy cattle. DNA Res., 2018, 25(1): p. 49-59.

2. Mesbah-Uddin, M., et al., Joint imputation of whole-genome sequence variants and large chromosomal deletions in cattle. J Dairy Sci., 2019, 102(12): p. 1193-1126.

3. Mesbah-Uddin, M. (2019), Identification of causal factors for recessive effects in dairy cattle with a single focus on large chromosomal deletions. Retrieved from http://www.theseas.org/2019MVF0018 document Available from http://www.theseas.org/2019MVF0018

<figure><img src="image_8.png" /></figure>

<figure><img src="image_9.png" /></figure>

<figure><img src="image_10.png" /></figure>

<figure><img src="image_11.png" /></figure>

<figure><img src="image_12.png" /></figure>

<figure><img src="image_13.png" /></figure>

<figure><img src="image_14.png" /></figure>

<footnote n="1">¹Centre for Quantitative Genetics and Genomics, Aarhus University, Denmark</footnote>

<footnote n="2">²Animal Genetics and Integrative Biology, UMR 1313 GABI, INRAE, AgroParisTech, Université Paris-Saclay, France</footnote>

<footnote>*Contact: goutam.sahana@qcg.au.dk</footnote>