Genetic diversity and population structure of advanced clones selected over forty years by a potato breeding program in the USA

Jeewan Pandey,Joseph Coombs,David G Holm,Richard G Novy,Jeffrey W Koym,M Isabel Vales,David S Douches,Asunta L Thompson,Douglas C Scheuring,J Creighton Miller

doi:10.1038/s41598-021-87284-x

Abstract

Knowledge regarding genetic diversity and population structure of breeding materials is essential for crop improvement. The Texas A&M University Potato Breeding Program has a collection of advanced clones selected and maintained in-vitro over a 40-year period. Little is known about its genetic makeup and usefulness for the current breeding program. In this study, 214 potato clones were genotyped with the Infinium Illumina 22 K V3 Potato Array. After filtering, a total of 10,106 single nucleotide polymorphic (SNP) markers were used for analysis. Heterozygosity varied by SNP, with an overall average of 0.59. Three groups of tetraploid clones primarily based on potato market classes, were detected using STRUCTURE software and confirmed by discriminant analysis of principal components. The highest coefficient of differentiation observed between the groups was 0.14. Signatures of selection were uncovered in genes controlling potato flesh and skin color, length of plant cycle and tuberization, and carbohydrate metabolism. A core set of 43 clones was obtained using Core Hunter 3 to develop a sub-collection that retains similar genetic diversity as the whole population, minimize redundancies, and facilitates long-term conservation of genetic resources. The comprehensive molecular characterization of our breeding clone bank collection contributes to understanding the genetic diversity of existing potato resources. This analysis could be applied to other breeding programs and assist in the selection of parents, fingerprinting, protection, and management of the breeding collections.

Highlights

Potato (Solanum tuberosum L.) is the world’s fourth most important crop after maize, rice, and wheat[1]
The single nucleotide polymorphic (SNP) were distributed across the 12 chromosomes. 10,106 SNP markers were mapped to 12 chromosomes represented as the 12 pseudomolecules of the potato genome DMv4.0323 (Supplementary Information Table S3)
The average distance between SNPs was 71 kb, but the SNP to SNP distribution was skewed: 39% of the marker to marker distances were less than 1 kb, and 18% were less than 10 kb

Summary

Introduction

Potato (Solanum tuberosum L.) is the world’s fourth most important crop after maize, rice, and wheat[1]. Of all the cultivars released over the past 15 years by the 12 US potato breeding programs, those developed by the Texas program have ranked in the top four to five nationally in the total area approved for seed certification over the past several y ears[3]. This has been due, in large measure, to the popularity of the four Texas Russet Norkotah strains (Russet Norkotah 112, Russet Norkotah 223, Russet Norkotah 278, and Russet Norkotah 296) with improved plant type to withstand environmental stresses. The Potato SNP array has been very useful for performing a robust and direct comparison of genetic diversity among different gene pools but has never been applied to the advanced clones selected over multiple years

Objectives

Methods

Results

Conclusion