Targeted and Untargeted Approaches Unravel Novel Candidate Genes and Diagnostic SNPs for Quantitative Resistance of the Potato (Solanum tuberosum L.) to Phytophthora infestans Causing the Late Blight Disease.
The oomycete Phytophthora infestans causes late blight of potato, which can completely destroy the crop. Therefore, for the past 160 years, late blight has been the most important potato disease worldwide. The identification of cultivars with high and durable field resistance to P. infestans is an objective of most potato breeding programs. This type of resistance is polygenic and therefore quantitative. Its evaluation requires multi-year and location trials. Furthermore, quantitative resistance to late blight correlates with late plant maturity, a negative agricultural trait. Knowledge of the molecular genetic basis of quantitative resistance to late blight not compromised by late maturity is very limited. It is however essential for developing diagnostic DNA markers that facilitate the efficient combination of superior resistance alleles in improved cultivars. We used association genetics in a population of 184 tetraploid potato cultivars in order to identify single nucleotide polymorphisms (SNPs) that are associated with maturity corrected resistance (MCR) to late blight. The population was genotyped for almost 9000 SNPs from three different sources. The first source was candidate genes specifically selected for their function in the jasmonate pathway. The second source was novel candidate genes selected based on comparative transcript profiling (RNA-Seq) of groups of genotypes with contrasting levels of quantitative resistance to P. infestans. The third source was the first generation 8.3k SolCAP SNP genotyping array available in potato for genome wide association studies (GWAS). Twenty seven SNPs from all three sources showed robust association with MCR. Some of those were located in genes that are strong candidates for directly controlling quantitative resistance, based on functional annotation. Most important were: a lipoxygenase (jasmonate pathway), a 3-hydroxy-3-methylglutaryl coenzyme A reductase (mevalonate pathway), a P450 protein (terpene biosynthesis), a transcription factor and a homolog of a major gene for resistance to P. infestans from the wild potato species Solanum venturii. The candidate gene approach and GWAS complemented each other as they identified different genes. The results of this study provide new insight in the molecular genetic basis of quantitative resistance in potato and a toolbox of diagnostic SNP markers for breeding applications.
Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Cologne, Germany.|Faculty of Agricultural Sciences, Universidad Nacional de Colombia, Bogotá, Colombia.
Teresa
http://orcid.org/0000-0003-4854-1079
T
Mosquera
Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Cologne, Germany.|Faculty of Agricultural Sciences, Universidad Nacional de Colombia, Bogotá, Colombia.
Maria Fernanda
MF
Alvarez
Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Cologne, Germany.|Institute Jean-Pierre Bourgin, INRA, AgroParis Tech, CNRS, Université Paris-Saclay, Versailles, France.
José M
JM
Jiménez-Gómez
Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Cologne, Germany.
Meki Shehabu
MS
Muktar
Biometris, Wageningen University, Wageningen, The Netherlands.
Maria João
MJ
Paulo
Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Cologne, Germany.
Sebastian
S
Steinemann
Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Cologne, Germany.
Jinquan
J
Li
Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Cologne, Germany.
Astrid
A
Draffehn
Department of Genomics, Life & Brain Center, Institute of Human Genetics, University of Bonn, Bonn, Germany.
Andrea
A
Hofmann
SaKa-Pflanzenzucht GmbH & Co. KG, 24340, Windeby, Germany.
Jens
J
Lübeck
SaKa-Pflanzenzucht GmbH & Co. KG, 24340, Windeby, Germany.
Josef
J
Strahwald
Bioplant GmbH, Ebstorf, Germany.
Eckhard
E
Tacke
Böhm-Nordkartoffel Agrarproduktion GbR, Ebstorf, Germany.
Hans-Reinhardt
HR
Hofferbert
Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Cologne, Germany.
Birgit
B
Walkemeier
Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Cologne, Germany.
Christiane
C
Gebhardt
D002874:Chromosome Mapping; D008040:Genetic Linkage; D005838:Genotype; D007113:Immunity, Innate / Q000235:genetics; D009868:Oomycetes / Q000472:pathogenicity*; D010641:Phenotype; D055750:Phytophthora infestans / Q000235:genetics* / Q000469:parasitology; D010935:Plant Diseases / Q000235:genetics / Q000469:parasitology*; D010940:Plant Proteins / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D040641:Quantitative Trait Loci; D011198:Solanum tuberosum / Q000235:genetics* / Q000469:parasitology*
D010940:Plant Proteins