iPBS-Retrotransposon Markers in the Analysis of Genetic Diversity among Common Bean (Phaseolus vulgaris L.) Germplasm from Türkiye

Abstract

Beans are legumes that play extremely important roles in human nutrition, serving as good sources of protein, vitamins, minerals, and antioxidants. In this study, we tried to elucidate the genetic diversity and population structure of 40 Turkish bean (Phaseolus vulgaris L.) local varieties and 5 commercial cultivars collected from 8 different locations in Erzurum-Ispir by using inter-primary binding site (iPBS) retrotransposon markers. For molecular characterization, the 26 most polymorphic iPBS primers were used; 52 bands per primer and 1350 bands in total were recorded. The mean polymorphism information content was 0.331. Various diversity indices, such as the mean effective allele number (0.706), mean Shannon’s information index (0.546), and gene diversity (0.361) revealed the presence of sufficient genetic diversity in the germplasm examined. Molecular analysis of variance (AMOVA) revealed that 67% of variation in bean germplasm was due to differences within populations. In addition, population structure analysis exposed all local and commercial bean varieties from five sub-populations. Expected heterozygosity values ranged between 0.1567 (the fourth sub-population) and 0.3210 (first sub-population), with an average value of 0.2103. In contrary, population differentiation measurement (Fst) was identified as 0.0062 for the first sub-population, 0.6372 for the fourth subpopulations. This is the first study to investigate the genetic diversity and population structure of bean germplasm in Erzurum-Ispir region using the iPBS-retrotransposon marker system. Overall, the current results showed that iPBS markers could be used consistently to elucidate the genetic diversity of local and commercial bean varieties and potentially be included in future studies examining diversity in a larger collection of local and commercial bean varieties from different regions.

Determining Genetic Diversity and Population Structure of Common Bean (Phaseolus vulgaris L.) Landraces from Türkiye Using SSR Markers

“…However, Öztürk et al [ 2 ], who investigated genetic diversity by using 27 iPBS markers in 71 bean genotypes and 4 commercial varieties collected from Erzincan, determined that the genotypes clustered into two groups and both groups were further divided into two subgroups. In a study by [ 58 ], they conducted a genetic diversity study in beans using 26 iPBS primers. At the end of the research, it was determined that the bean inclusions were divided into three main clusters.…”

Current State of Natural Populations of Paeonia anomala (Paeoniaceae) in East Kazakhstan

“…However, when selecting the optimal marker type, their prevalence in the genome and the possibility of identification via PCR methods play an important role. Retrotransposons, as a constantly changing composition of the genome of any eukaryotic species, have an advantage in the assessment of genetic polymorphism compared with other markers because they do not require prior data of the DNA sequence and give more reproducible results, which is especially important in studies of rare or little-studied plant species [78,[80][81][82].…”

Ефективність Різних Методів Екстракції Днк, Придатної Для Плр Із Гербарних Зразків Водоростей Роду Cladophora Kütz.

“…Для оцінки придатності виділеної ДНК для молекулярно-генетичного аналізу була проведена ПЛР із використанням праймера iPBS 2080, який розроблений до послідовності довгих термінальних повторів ретротранспозонів, що присутні у всіх еукаріот [10]. Тому цей праймер є універсальним для різних видів та успішно застосовувався як для вищих рослин, так і для тварин та грибів [2,6,10]. У якості контрольних зразків використовували рослинну та тваринну ДНК видів Triticum spelta L. та Atherina boyeri.…”