De Novo SNP Discovery and Genotyping of Iranian Pimpinella Species Using ddRAD Sequencing

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 per locus. After stringent filtering, 2440 high-quality SNPs were identified for downstream analysis. Analysis of genetic relationships and population structure, based on these retained SNPs, indicated the presence of three major groups. Gene ontology and pathway analysis were determined by using comparison SNP-associated flanking sequences with a public non-redundant database. Due to the lack of genomic resources in this genus, our present study is the first report to provide high-quality SNPs in Pimpinella based on a de novo analysis pipeline using ddRAD-seq. This data will enhance the molecular knowledge of the genus Pimpinella and will provide an important source of information for breeders and the research community to enhance breeding programs and support the management of Pimpinella genomic resources

Detection of Epistasis for Seed and Some Phytochemical Traits in Coriander under Different Irrigation Regimes

Coriander (Coriander sativum L.) is an annual herb mainly cultivated for its seed characteristics. Drought stress is a major problem which affects coriander behaviour through biochemical responses. This study aimed to determine the nature and magnitude of epistasis in inheritance of seed yield (SY), percent of dehulled seed (PODS), percent of seed hulls (POSH), essential oil content (EOC), essential oil yield (EOY), dehulled seed fatty acid content (DSFAC), hull fatty acid content (HFAC), fatty acid content (FAC), and fatty acid yield (FAY), and to estimate additive and dominance variance for the traits not influenced by epistasic effects. Three testers, TN-59-158 (highly drought-susceptible), TN-58-230 (highly drought-tolerant, but low-yielding), and their F1 hybrid were each crossed for six genotypes. The experiment was performed under different levels of water deficit: control (C), moderate water deficit (MWD), and severe water deficit (SWD) conditions. Epistasis affected the expression of SY, EOC, EOY, FAC, and FAY in all water conditions, PODS in C, POSH in SWD, HFAC in MWD, and DSFAC in both C and MWD conditions. Total epistasic effects were partitioned, showing that both [i] and [j + l] type interactions were significant, with a prevalent influence of [i] type interactions on these traits except for POSH and FAC in the SWD condition, which exhibited a higher value of the [j + l] type. Both additive and non-additive gene actions were significant for those traits not significantly affected by epistasis in C, MWD, or SWD conditions. An additive type of gene action was preponderant for PODS in MWD and SWD, POSH in MWD, DSFAC in SWD, and HFAC in C and SWD conditions