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A Bioinformatics Pipeline to Identify a Subset of SNPs for Genomics-Assisted Potato Breeding

Selga, Catja and Koc, Alexander and Chawade, Aakash and Ortiz, Rodomiro (2021). A Bioinformatics Pipeline to Identify a Subset of SNPs for Genomics-Assisted Potato Breeding. Plants. 10 , 30
[Research article]

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Abstract

Modern potato breeding methods following a genomic-led approach provide means for shortening breeding cycles and increasing breeding efficiency across selection cycles. Acquiring genetic data for large breeding populations remains expensive. We present a pipeline to reduce the number of single nucleotide polymorphisms (SNPs) to lower the cost of genotyping. First, we reduced the number of individuals to be genotyped with a high-throughput method according to the multi-trait variation as defined by principal component analysis of phenotypic characteristics. Next, we reduced the number of SNPs by pruning for linkage disequilibrium. By adjusting the square of the correlation coefficient between two adjacent loci, we obtained reduced subsets of SNPs. We subsequently tested these SNP subsets by two methods; (1) a genome-wide association study (GWAS) for marker identification, and (2) genomic selection (GS) to predict genomic estimated breeding values. The results indicate that both GWAS and GS can be done without loss of information after SNP reduction. The pipeline allows for creating custom SNP subsets to cover all variation found in any particular breeding population. Low-throughput genotyping will reduce the genotyping cost associated with large populations, thereby making genomic breeding methods applicable to large potato breeding populations by reducing genotyping costs.

Authors/Creators:Selga, Catja and Koc, Alexander and Chawade, Aakash and Ortiz, Rodomiro
Title:A Bioinformatics Pipeline to Identify a Subset of SNPs for Genomics-Assisted Potato Breeding
Series Name/Journal:Plants
Year of publishing :2021
Volume:10
Article number:30
Number of Pages:12
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 404 Agricultural Biotechnology > Genetics and Breeding
(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 404 Agricultural Biotechnology > Plant Biotechnology
Keywords:linkage disequilibrium pruning, genomic selection, genotyping, GWAS, potato breeding
URN:NBN:urn:nbn:se:slu:epsilon-p-109402
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-109402
Additional ID:
Type of IDID
DOI10.3390/plants10010030
ID Code:21234
Faculty:LTV - Fakulteten för landskapsarkitektur, trädgårds- och växtproduktionsvetenskap
Department:(LTJ, LTV) > Department of Plant Breeding (from 130101)
Deposited By: SLUpub Connector
Deposited On:14 Jan 2021 16:23
Metadata Last Modified:14 Jan 2021 16:31

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