A first linkage map and downy mildew resistance QTL discovery for sweet basil (Ocimum basilicum) facilitated by double digestion restriction site associated DNA sequencing (ddRADseq)

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.

CRISPR/Cas9-mediated mutagenesis of sweet basil candidate susceptibility gene ObDMR6 enhances downy mildew resistance

“…Resistance has been found in an exotic sweet basil variety Mrihani and other Ocimum species that differ vastly from popular sweet basil cultivars in ploidy, appearance, aroma and taste [ 12 – 14 ]. Transferring disease resistance to popular sweet basil varieties through traditional breeding is very time-consuming and faced with significant challenges, such as sexual incompatibility, hybrid F1 sterility, and linkage drag [ 7 , 13 , 15 ]. After eight years of breeding work, several BDM-resistant varieties were recently commercialized for sweet basil production [ 14 ].…”

CRISPR-Editing of Sweet Basil (Ocimum basilicum L.) Homoserine Kinase Gene for Improved Downy Mildew Disease Resistance

“…The pathogen produces chlorotic lesions on basil leaves with dark brown sporangia on the abaxial side of the leaf surfaces, greatly reducing basil quality and market value (Cohen et al, 2017 ). A substantial breeding effort has been made to identify and introgress DM resistance into commercial cultivars while simultaneously maintaining other key traits, such as aroma and taste (Wyenandt et al, 2015 ; Pyne et al, 2017 , 2018 ). To-date, almost all sweet basil cultivars are DM susceptible, whereas resistant lines that incorporate genetic resistance from other Ocimum species exhibit sexual incompatibility with sweet basil (Cohen et al, 2017 ).…”

Optimizing ddRADseq in Non-Model Species: A Case Study in Eucalyptus dunnii Maiden

“…The original ddRADseq protocol was built and trained based on animal data, and it has been widely applied in SNP marker development and genotyping for several species in this kingdom. Applications of this technology to plants have been reported [10][11][12][13][14], especially in forest and fruit trees (reviewed in [15]), and were specifically improved [16,17]. However, most researchers still use universal default protocols that carry some limitations.…”