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

Aakash Chawade,Rodomiro Ortiz,Catja Selga,Alexander Koc

doi:10.3390/plants10010030

Aakash Chawade, Rodomiro Ortiz + Show 2 more

Open Access

https://doi.org/10.3390/plants10010030

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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.

Highlights

Potato is the world’s third most important food crop, with an annual production of more than 300 million ton fresh-weight worldwide [1,2]
The results indicate that both genome-wide association study (GWAS) and genomic selection (GS) can be done without loss of information after single nucleotide polymorphisms (SNPs) reduction
The subset consisted of 11 individuals from each of the eight crosses, which were selected through a principal component analysis (PCA)

Summary

Introduction

Potato is the world’s third most important food crop, with an annual production of more than 300 million ton fresh-weight worldwide [1,2]. Potato is a staple crop for a large portion of the world’s population, and besides being one of the main sources of starch in our diets, it provides a high amount of protein, minerals, and vitamins [3]. The target traits for breeding are host plant resistance to pathogens and pests, tuber traits, such as weight and number, quality defined by starch content and reducing sugars, and other traits of importance to local producers [4]. A challenge in breeding tetraploid table potatoes (Solanum tuberosum L.) is the heterozygosity of the plants being used as parents, as it leads to difficulties in predicting the outcome of a cross [8]

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