Abstract
Limited understanding of sweet basil (Ocimum basilicum L.) genetics and genome structure has reduced efficiency of breeding strategies. This is evidenced by the rapid, worldwide dissemination of basil downy mildew (Peronospora belbahrii) in the absence of resistant cultivars. In an effort to improve available genetic resources, expressed sequence tag simple sequence repeat (EST-SSR) and single nucleotide polymorphism (SNP) markers were developed and used to genotype the MRI x SB22 F2 mapping population, which segregates for response to downy mildew. SNP markers were generated from genomic sequences derived from double digestion restriction site associated DNA sequencing (ddRADseq). Disomic segregation was observed in both SNP and EST-SSR markers providing evidence of an O. basilicum allotetraploid genome structure and allowing for subsequent analysis of the mapping population as a diploid intercross. A dense linkage map was constructed using 42 EST-SSR and 1,847 SNP markers spanning 3,030.9 cM. Multiple quantitative trait loci (QTL) model (MQM) analysis identified three QTL that explained 37–55% of phenotypic variance associated with downy mildew response across three environments. A single major QTL, dm11.1 explained 21–28% of phenotypic variance and demonstrated dominant gene action. Two minor QTL dm9.1 and dm14.1 explained 5–16% and 4–18% of phenotypic variance, respectively. Evidence is provided for an additive effect between the two minor QTL and the major QTL dm11.1 increasing downy mildew susceptibility. Results indicate that ddRADseq-facilitated SNP and SSR marker genotyping is an effective approach for mapping the sweet basil genome.
Highlights
Sweet basil (Ocimum basilicum L.) is the most widely cultivated and economically salient Ocimum species in the United States and Europe [1]
Six expressed sequence tag simple sequence repeat (EST-simple sequence repeats (SSRs)) markers fit scenario (i) (Fig 1A) in which a single homozygous, polymorphic locus is amplified within a single sub-genome and segregated in 1:2:1
Two additional scenarios were observed for markers OBNJR2sg21 and OBNJR2cn92, in which two independently segregating loci represented putative homeologs
Summary
Sweet basil (Ocimum basilicum L.) is the most widely cultivated and economically salient Ocimum species in the United States and Europe [1]. Hybridization of commercial O. basilicum varieties with resistant genotypes is largely met with F1 sterility or sexual incompatibility [17,18] Despite these challenges, an initial characterization of downy mildew resistance was provided by a multi-site field trial that evaluated F2 and backcross generations derived from a cross between downy mildew resistant inbred cultivar Mrihani (MRI) and susceptible inbred Rutgers University breeding line SB22 [19]. An initial characterization of downy mildew resistance was provided by a multi-site field trial that evaluated F2 and backcross generations derived from a cross between downy mildew resistant inbred cultivar Mrihani (MRI) and susceptible inbred Rutgers University breeding line SB22 [19] These efforts generated important results that have helped to inform an effective breeding program targeting genetic resistance. A resistant commercial sweet basil variety remains to be seen 15 years after the first report of P. belbahrii, reflecting the difficulties currently associated with genetic improvement of this poorly characterized plant species
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