Nuclear and chloroplast genome variability in leek (Allium porrum L.)

Abstract

The genus Allium L. (Amaryllidaceae), the most numerous among monocotyledonous plants, includes such economically important vegetable crops as onion (A. cepa), garlic (A. sativum) and leek (A. porrum). Leek has a high taste and proven valuable dietary properties and is one of the most popular vegetable crops in Western Europe. Despite a high importance of leek as a vegetable, this species is rarely the subject of molecular genetic studies. The genetic diversity of leeks has never been studied before. Therefore, in this work, we studied the nuclear variability (AFLP) and the chloroplast (nucleotide sequence analysis) genomes using a broad sample. For this work, 65 leek accessions were selected from the collection of the Scientific Center of Vegetable Crops, which included varieties of domestic and foreign breeding. As a result of an AFLP analysis and processing of the DNA spectra obtained, 760 fragments were identified, of which 716 were polymorphic for the leek accessions being analyzed. The calculated genetic distances between the leek samples varied from 0.4 to 0.76, which is comparable to the intraspecific polymorphism of related Allium species (onions, garlic). Analysis of the genomic structure with STRUCTURE 2.3.4 divided the leek samples into seven groups, which generally coincides with the clustering of these samples. To assess the variability of the chloroplast genome, nine sites of the chloroplast genome were sequenced in the leek samples, both non-coding (intergenic spacers rpl32-trnL, ndhJ-trnL, and intron rps16 gene), and protein coding genes (psaA, psaB, psbA, psbB, psbE, petB). The analysis of the sites of the leek chloroplast genome revealed an extremely low level of their polymorphism, only six SNPs were detected in the studied sequences with a total length of about 10,500 bp. Thus, as a result of this work, a high level of polymorphism of the leek nuclear genome was revealed, while the polymorphism of the chloroplast genome was extremely low.

Primer Binding Site (PBS) Profiling of Genetic Diversity of Natural Populations of Endemic Species Allium ledebourianum Schult.

“…Studies of genetic polymorphism using genome in situ hybridization (GISH) and phylogenetic analysis have been carried out on this species of Allium [ 75 , 76 , 77 ]. Moreover, a significant part of the genetic diversity studies of Allium species have been carried out on cultivated species ( A. sativum , A. sepa ), or on species of breeding value [ 78 , 79 , 80 , 81 , 82 ]. In this work, we first tested the analysis of the molecular genetic diversity of natural populations of endemic A. ledebourianum using the DNA profiling method.…”

Yield of different onion varieties depending on the level of mineral nutrition and growth regulators in the conditions of the Southern Forest-steppe of the Republic of Bashkortostan

“…The soil was leached chernozem (humus), heavy loamy. The reaction of the soil medium was slightly acidic pH(kCl) 6,10 -6,21, thickness of humus horizon -57-65 cm, volume mass of arable layer soil 1,02-1,08 g/cm 3 . Humus in arable layer is 9,3-9,5%.…”

“…The genus Allium cepa (family Amaryllidaceae) is the most many among monocotyledonous plants, uniting about 1200 species. These include such important agricultural crops as onions (A. cepa L.), garlic (A. sativum), leeks (A. porrum L.), currently cultivated worldwide [3]. Onions (Allium cepa L.) Onions (Allium cepa L.) are cultivated everywhere in Russia, from the southern regions to the Far North.…”

DNA profiling and assessment of genetic diversity of relict speciesAllium altaicumPall. on the territory of Altai

“…Molecular genetic methods based on polymorphisms of certain genome sequences or proteins are applied to research the genetic polymorphisms of rare plant species. Various Allium species were already studied using various molecular genetic PCR markers such as RAPD, ISSR and AFLP ( Buso et al, 2008 ; Chen et al, 2014 ; Dyachenko, Seredin & Filyushin, 2019 ; Mitrová, Svoboda & Ovesná, 2016 ; Sudha et al, 2019 ; Villano et al, 2018 ). However, these PCR techniques are not efficient enough to determine genetic diversity or have problems with reproducibility or cost ( Nybom, 2004 ).…”