Population structure, genetic diversity and downy mildew resistance among Ocimum species germplasm

Abstract

BackgroundThe basil (Ocimum spp.) genus maintains a rich diversity of phenotypes and aromatic volatiles through natural and artificial outcrossing. Characterization of population structure and genetic diversity among a representative sample of this genus is severely lacking. Absence of such information has slowed breeding efforts and the development of sweet basil (Ocimum basilicum L.) with resistance to the worldwide downy mildew epidemic, caused by the obligate oomycete Peronospora belbahrii. In an effort to improve classification of relationships 20 EST-SSR markers with species-level transferability were developed and used to resolve relationships among a diverse panel of 180 Ocimum spp. accessions with varying response to downy mildew.ResultsResults obtained from nested Bayesian model-based clustering, analysis of molecular variance and unweighted pair group method using arithmetic average (UPGMA) analyses were synergized to provide an updated phylogeny of the Ocimum genus. Three (major) and seven (sub) population (cluster) models were identified and well-supported (P < 0.001) by PhiPT (ΦPT) values of 0.433 and 0.344, respectively. Allelic frequency among clusters supported previously developed hypotheses of allopolyploid genome structure. Evidence of cryptic population structure was demonstrated for the k1 O. basilicum cluster suggesting prevalence of gene flow. UPGMA analysis provided best resolution for the 36-accession, DM resistant k3 cluster with consistently strong bootstrap support. Although the k3 cluster is a rich source of DM resistance introgression of resistance into the commercially important k1 accessions is impeded by reproductive barriers as demonstrated by multiple sterile F1 hybrids. The k2 cluster located between k1 and k3, represents a source of transferrable tolerance evidenced by fertile backcross progeny. The 90-accession k1 cluster was largely susceptible to downy mildew with accession ‘MRI’ representing the only source of DM resistance.ConclusionsHigh levels of genetic diversity support the observed phenotypic diversity among Ocimum spp. accessions. EST-SSRs provided a robust evaluation of molecular diversity and can be used for additional studies to increase resolution of genetic relationships in the Ocimum genus. Elucidation of population structure and genetic relationships among Ocimum spp. germplasm provide the foundation for improved DM resistance breeding strategies and more rapid response to future disease outbreaks.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1284-7) contains supplementary material, which is available to authorized users.

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

“…Considering this fragment is only a small portion of the ObDMR6 gDNA and polymorphisms exist in sequences outside of this region ( S2 Appendix ), the number of ObDMR6 unique sequences could be much higher. Even taking into account that sweet basil is allotetraploid [ 4 ], the high number of ObDMR6 unique sequences with high homology suggests that there have been massive duplication events in the genome.…”

“…O . basilicum is considered to be an allotetraploid (2n = 4x = 48), while different ploidy levels were identified in other species within the Ocimum genus [ 4 ]. Basil downy mildew (BDM) caused by the obligate biotrophic oomycete Peronospora belbahrii threatens the global production of sweet basil [ 5 ].…”

Detection of the Downy Mildew Pathogen on Seed of Basil Following Field Infection in Southern New Jersey

“…Importantly, the lack of genetic resistance to the pathogen in widely grown sweet basil cultivars continues to make control difficult (Homa et al, 2014;Pyne et al, 2015Pyne et al, , 2017Wyenandt et al, 2015). Efforts have been made in recent years at breeding downy mildew resistance into commercially acceptable sweet basil lines (Ben-Naim et al, 2018;Pyne et al, 2015Pyne et al, , 2017Pyne et al, , 2018, but this has focused on using a few strains of the pathogen and, as with all disease-resistant plants, growers still need to use the improved germplasm within an integrated pest management program that still requires fungicide applications. Should additional strains (e.g., races) of basil downy mildew develop, such as for other downy mildews on other hosts, continued breeding efforts will be required.…”

Analysis of the genetic diversity and population structure of Salix psammophila based on phenotypic traits and simple sequence repeat markers

“…All tetraploid genotypes were read twice according to marker motifs. Although reading peaks is a little complicated, estimating polyploid genotypes using SSRs can clearly differentiate within genus by high throughput genotyping with multiplexed PCR (Guo et al, 2006; Pyne et al, 2018), and is also an auxiliary tool for determining ploidy (Wu et al, 2018). Representative two-microsatellite loci are shown in Fig.…”