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

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.

Population structure analysis to explore genetic diversity and geographical distribution characteristics of cultivated-type tea plant in Guizhou Plateau

“…Previous studies showed population bottlenecks and/or balancing selection when positive Tajima’s D values were determined for a population [ 39 , 40 ]. The positive Tajima’s D values of all tea populations here suggest that they all underwent population bottlenecks and/or balancing selection (Table 2 ).…”

“…Previous studies demonstrated that positive Tajima’s D values indicated population bottlenecks and/or balancing selection [ 39 , 40 ]. Positive Tajima’s D values were observed in all populations in the present study.…”

Germplasm, Breeding, and Genomics in Potato Improvement of Biotic and Abiotic Stresses Tolerance

“…First, genotyping-by-Sequencing (GBS) is a now popular method of HTG in crops including potato (Uitdewilligen et al, 2013;Bastien et al, 2018). GBS has been applied effectively in genome-wide studies in potato on genetic diversity and population structure (Pandey et al, 2021), QTL mapping (Schönhals et al, 2017), and SNP discovery (Caruana et al, 2019). Secondly, the SNP array-based HTG system has already been developed and applied in potato for population structure and SNP discovery using 20K SNP array (Vos et al, 2015(Vos et al, , 2017, 22K SNP array for starch phosphorylation (Khlestkin et al, 2019), and 12K SNP array (Illumina) for genetic diversity in the genbank of the International Potato Centre, Peru (Ellis et al, 2018).…”

Diversity and population structure of Nordic potato cultivars and breeding clones grown under long daylength in Europe

“…Previous research found that market class was a good biological explanation to subpopulations in cultivated tetraploid potato (Hirsch et al 2013;Igarashi et al 2019;Pandey et al 2021). In this study, all potato accessions are classi ed as table potato with one exception, the cultivar 'Kuras' from the population of cultivars grown in Sweden today.…”