2021
DOI: 10.3390/agronomy11071342
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De Novo SNP Discovery and Genotyping of Iranian Pimpinella Species Using ddRAD Sequencing

Abstract: The species of Pimpinella, one of the largest genera of the family Apiaceae, are traditionally cultivated for medicinal purposes. In this study, high-throughput double digest restriction-site associated DNA sequencing technology (ddRAD-seq) was used to identify single nucleotide polymorphisms (SNPs) in eight Pimpinella species from Iran. After double-digestion with the enzymes HpyCH4IV and HinfI, a total of 334,702,966 paired-end reads were de novo assembled into 1,270,791 loci with an average of 28.8 reads pe… Show more

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Cited by 7 publications
(3 citation statements)
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“…As a reduced-representation sequencing technique, RAD-seq allows the identification of thousands of SNPs across the genome [ 30 ] and has been proven to be an applicable tool for investigating population structure and diversity in non-model organisms [ 31 , 32 ], including crop species. This approach has been applied to crops that are not widely cultivated but are important to the economies and communities of developing regions e.g., [ 33 , 34 , 35 , 36 , 37 ], as in the case of locoto chile in the Central Andes. Therefore, through the intended study, the following four questions have been addressed: (1) How much genetic diversity is present in C. pubescens ?…”
Section: Introductionmentioning
confidence: 99%
“…As a reduced-representation sequencing technique, RAD-seq allows the identification of thousands of SNPs across the genome [ 30 ] and has been proven to be an applicable tool for investigating population structure and diversity in non-model organisms [ 31 , 32 ], including crop species. This approach has been applied to crops that are not widely cultivated but are important to the economies and communities of developing regions e.g., [ 33 , 34 , 35 , 36 , 37 ], as in the case of locoto chile in the Central Andes. Therefore, through the intended study, the following four questions have been addressed: (1) How much genetic diversity is present in C. pubescens ?…”
Section: Introductionmentioning
confidence: 99%
“…This study aimed to evaluate the impact of using different Gleditsia rootstocks on the scion growth and development of Gleditsia plants, including (i) graft compatibility and the extent of compatibility among different Gleditsia species, (ii) the effects of different rootstocks on the morphology, physiology, and hormone levels of Gleditsia plants, and (iii) the differences between homograft and heterograft combinations. GBS is a cost-effective method for developing SNP markers without the need to consider the genome size, ploidy level, or the presence of background genomic sequences; this method allows for the genotyping of all markers derived from a population [40,41]. ISSR markers have the advantages of having rich polymorphism, a low cost, simple operation, high stability, and co-dominance, and they have been widely used in studies of plant germplasm selection, interspecific differentiation, and population diversity.…”
Section: Discussionmentioning
confidence: 99%
“…The experiment was implemented at the research field of Tarbiat Modares University in Tehran, Iran (51 • 09 E; 35 • 44 N, at an altitude of 1265 m above sea level). Before sowing, the seeds were disinfected in sodium hypochlorite solution (10%) (Sigma-Aldrich, Saint Louis, MI, USA) for 5 min and then fixed in ethanol (96%) for 1 min and rinsed in distilled water thereafter [31]. The 9 parents, 12 single crosses, and 6 three-way crosses were evaluated with different levels of water deficit (C, MWD, SWD) with a randomized complete block design with 3 replications.…”
Section: Experimental Site and Growth Conditionsmentioning
confidence: 99%