Analysis of Genetic Diversity and Population Structure of Orobanche foetida Populations From Tunisia Using RADseq

Abstract

Orobanche foetida Poiret is a holoparasitic plant that lacks chlorophyll and totally depending on its host for its growth. Orobanche foetida parasitizes host plant roots and extract nutrient and water via a haustorium. Although O. foetida distributes in the Mediterranean region as a wild plant parasite, it parasitizes faba bean causing serious damages which may reach 90% yield losses in Tunisia. Analysis of genetic diversity of the parasite is important to better understand its evolution and spread, remained largely unknown. In this work, we present the first study on genetic diversity and population structure using the robust technique Restriction-site-Associated DNA sequencing (RADseq) for Orobanche spp. We collected 244 samples of O. foetida from 18 faba bean fields in the north of Tunisia including 17 populations from the north-west and one population form the north-east. To overcome the difficulty of SNP discovery in O. foetida genome as a non-model and tetraploid plant, we utilized three different informatics pipelines, namely UNEAK, pyRAD and Stacks. This study showed that genetic differentiation occurred in the Tunisian O. foetida emphasizing the isolation by distance effect. However, no strong population clustering was detected in this work basing on the three data sets and clustering methods used. The present study shed the light on the current distribution and the genetic variation situation of the fetid broomrape in Tunisia, highlighting the importance of understanding the evolution of this parasite and its genetic background. This will aid in developing efficient strategies to control this parasite and its expansion in Tunisia and worldwide.

Genomic Data Reveals Population Genetic and Demographic History of Magnolia fistulosa (Magnoliaceae), a Plant Species With Extremely Small Populations in Yunnan Province, China

“…The use of different analysis tools can verify the reliability of results ( Qi et al, 2015 ; Boukteb et al, 2021 ), and the adoption of a reference genome is known to greatly improve the performance of RAD-seq technologies ( Torkamaneh et al, 2016 ). Given that several genomes in the Magnoliaceae were available (BioProject ID PRJNA774088 , Dong et al, 2021 ; Yin et al, 2021 ), we adopted a reference guided approach to process the population genetics of Magnolia fistulosa using both the Stacks and ipyrad pipelines.…”

“…Compared with traditional RAD-seq, double digest RAD sequencing (ddRAD-seq) further improves efficiency and robustness while minimizing cost ( Peterson et al, 2012 ). However, several studies have shown that the choice of pipeline used for the analysis may have a significant impact on the accuracy of the results ( Qi et al, 2015 ; Torkamaneh et al, 2016 ; Boukteb et al, 2021 ). To improve the reliability of the results, multi-method analyses can be adopted to process data using different technical routes ( Qi et al, 2015 ; Boukteb et al, 2021 ).…”

Genotyping‐by‐sequencing analysis of Orobanche crenata populations in Algeria reveals genetic differentiation

“…Conversely, evidence of host differentiation has been found in other parasitic weeds, such as O . foetida (Román, Satovic, et al, 2007 ; Román, Hernández, et al, 2007 ; Vaz Patto et al, 2008 , Thorogood et al, 2008 ; but not Boukteb et al, 2021 ), Striga hermonthica (Unachukwu et al, 2017 ), and Phelipanche ramosa (Stojanova et al, 2019 ). These differences may be due to specific methods/sampling design or may arise from the type of genetic marker selected as single locus co‐dominant markers are more efficacious for population biology insights (Sunnucks, 2000 ).…”

Genomic Data Reveals Profound Genetic Structure and Multiple Glacial Refugia in Lonicera oblata (Caprifoliaceae), a Threatened Montane Shrub Endemic to North China

“…Restriction site-associated DNA (RAD) is one of the most effective genotyping-by-sequencing (GBS) methods that allow for extensive SNP discovery on the genome level ( Davey et al, 2011 ; Sonah et al, 2013 ; Puritz et al, 2014 ). It has been widely applied in population genetics for numerous model and non-model species (e.g., Wang et al, 2013 ; Luo et al, 2019 ; Feng et al, 2020 ; Xiong et al, 2020 ; Boukteb et al, 2021 ; Qiao et al, 2021 ). In particular, the UGbS-Flex (also denoted as SuperGBS) is a powerful tool for population genetic research with the ability to generate long reads (300–700 bp) and maximize SNP callings irrespective of the species ploidy level, breeding system, and reference genome availability ( Qi et al, 2018 ; Cheng et al, 2020 ).…”