Fine mapping and candidate gene screening of the downy mildew resistance gene RPF1 in Spinach

• Published in: Theoretical and applied genetics Vol. 131; no. 12; pp. 2529 - 2541
• Main Authors: She, Hongbing, Qian, Wei, Zhang, Helong, Liu, Zhiyuan, Wang, Xiaowu, Wu, Jian, Feng, Chunda, Correll, James C., Xu, Zhaosheng
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01-12-2018; Springer Nature B.V
• Subjects: Agriculture; Alleles; Amino acid sequence; Association analysis; Biochemistry; Biomedical and Life Sciences; Biotechnology; Chromosome 3; Chromosome Mapping; Cloning; Conserved sequence; Disease Resistance - genetics; Downy mildew; Gene mapping; Genes; Genes, Plant; Inbreeding; Leucine; Life Sciences; Marker-assisted selection; Original Article; Peronospora - pathogenicity; Peronospora farinosa; Phenotype; Plant Biochemistry; Plant Breeding/Biotechnology; Plant Diseases - genetics; Plant Diseases - microbiology; Plant Genetics and Genomics; Recombinants; Spinacia oleracea - genetics; Spinacia oleracea - microbiology
• ISSN: 0040-5752; 1432-2242
• DOI: 10.1007/s00122-018-3169-4

Key message
A SLAF-BSA approach was used to locate the
RPF1
locus. The three most likely candidate genes were identified which provide a basic for cloning the resistance gene at the
RPF1
locus.
Spinach downy mildew is a globally devastating oomycete disease. The use of downy mildew resistance genes constitutes the most effective approach for disease management. Hence, the objective of the present study was to fine map the first-reported resistance locus
RPF1
. The resistance allele at this resistance locus was effective against races 1–7, 9, 11, 13, and 15 of
Peronospora farinosa
f. sp.
spinaciae
(
P. effusa
). The approach fine mapped
RPF1
using specific-locus amplified fragment sequencing (SLAF-Seq) technology combined with bulked segregant analysis. A 1.72 Mb region localized on chromosome 3 was found to contain
RPF1
based on association analysis. After screening recombinants with the SLAF markers within the region, the region was narrowed down to 0.89 Mb. Within this region, 14
R
genes were identified based on the annotation information. To identify the genes involved in resistance, resequencing of two resistant inbred lines (12S2 and 12S3) and three susceptible inbred lines (12S1, 12S4, and 10S2) was performed. The three most likely candidate genes were identified via amino acid sequence analysis and conserved domain analysis between resistant and susceptible inbred lines. These included
Spo12729
, encoding a receptor-like protein, and
Spo12784
and
Spo12903
, encoding a nucleotide-binding site and leucine-rich repeat domains. Additionally, based on the sequence variation in the three genes between the resistant and susceptible lines, molecular markers were developed for marker-assisted selection. The results could be valuable in cloning the
RPF1
alleles and improving our understanding of the interaction between the host and pathogen.