The recombination landscape and multiple QTL mapping in a Solanum tuberosum cv. ‘Atlantic’-derived F1 population

• Published in: Heredity Vol. 126; no. 5; pp. 817 - 830
• Main Authors: da Silva Pereira, Guilherme, Mollinari, Marcelo, Schumann, Mitchell J., Clough, Mark E., Zeng, Zhao-Bang, Yencho, G. Craig
• Format: Journal Article
• Language: English
• Published: Cardiff Springer Nature B.V 01-05-2021; Springer International Publishing
• Subjects: Chipping; Chromosome 5; Chromosomes; Computer programs; Configurations; Density; Dry matter; Gene mapping; Genetic analysis; Mapping; Maturity; Necrosis; Nucleotides; Phenotypes; Plant breeding; Potatoes; Quantitative trait loci; Recombination; Single-nucleotide polymorphism; Software; Solanum tuberosum; Specific gravity
• ISSN: 0018-067X; 1365-2540
• DOI: 10.1038/s41437-021-00416-x

There are many challenges involved with the genetic analyses of autopolyploid species, such as the tetraploid potato, Solanum tuberosum (2 n = 4 x = 48). The development of new analytical methods has made it valuable to re-analyze an F 1 population ( n = 156) derived from a cross involving ‘Atlantic’, a widely grown chipping variety in the USA. A fully integrated genetic map with 4285 single nucleotide polymorphisms, spanning 1630 cM, was constructed with MAPpoly software. We observed that bivalent configurations were the most abundant ones (51.0~72.4% depending on parent and linkage group), though multivalent configurations were also observed (2.2~39.2%). Seven traits were evaluated over four years (2006–8 and 2014) and quantitative trait loci (QTL) mapping was carried out using QTLpoly software. Based on a multiple-QTL model approach, we detected 21 QTL for 15 out of 27 trait-year combination phenotypes. A hotspot on linkage group 5 was identified with co-located QTL for maturity, plant yield, specific gravity, and internal heat necrosis resistance evaluated over different years. Additional QTL for specific gravity and dry matter were detected with maturity-corrected phenotypes. Among the genes around QTL peaks, we found those on chromosome 5 that have been previously implicated in maturity ( StCDF1 ) and tuber formation ( POTH1 ). These analyses have the potential to provide insights into the biology and breeding of tetraploid potato and other autopolyploid species.