DNA fingerprinting and genetic diversity analysis of world quinoa germplasm using iPBS-retrotransposon marker system

Abstract

Quinoa is an important staple food crop for millions of impoverished rural inhabitants of the Andean region. Quinoa is considered a good source of protein,vitamins, minerals, and antioxidants. This study aimed to investigate the genetic diversity and population structure of world quinoa germplasm originating from 8 countries through the iPBS-retrotransposon marker system. Molecular characterization was performed using the 11 most polymorphic primers. A total of 235 bands were recorded, of which 66.8% were polymorphic. Mean polymorphism information content (PIC) was 0.410. Various diversity indices including mean effective number of alleles (1.269), mean Shannon's information index (0.160) and gene diversity (0.247) revealed the existence of sufficient amount of genetic diversity in studied germplasm. Bolivia-17 and Mexico-1 were found to be genetically distinct accessions and can be suggested as candidate parents for future breeding activities. Various diversity indices were also calculated among germplasm collection counries and the results clearly showed the existence of higher genetic diversity in Bolivian and Peruvian accessions. The model-based structure, neighbor-joining, and principal coordinate analysis (PCoA) grouped quinoa germplasm according to their collection country. Analysis of molecular variance (AMOVA) revealed that most of the variations (69%) in world quinoa germplasm are due to differences within populations. Findings of this study can be used for deeper understanding of the genetic relationship and in the determination of appropriate breeding and conservation strategies for quinoa.

Basic concepts and methodologies of DNA marker systems in plant molecular breeding

“…IPBS marker is a useful tool for analyzing variations in primer binding site (PBS) intervals in LTR retrotransposons between or among individuals using PCR. PBS occurs universally in all LTR-based retrotransposon sequences ( Barut et al., 2020 ; Kalendar et al., 2010 ). PBS are conserved regions that are found in the LTRs of retrotransposons and are usually located next to the 5′ LTR sequences.…”

“…Inter-Primer Binding Site (IPBS) basically relies on the primer binding site. The function of the PBS primers is to bind LTRs and effect the amplification of diverse sequences ( Barut et al., 2020 ).…”

Genetic Diversity, Population Structure and Marker-Trait Association for 100-Seed Weight in International Safflower Panel Using SilicoDArT Marker Information

“…Moreover, various genetic diversity indices also confirmed the existence of higher polymorphism in the evaluated germplasm. Characterization of germplasm provides us with an opportunity to unlock the novel genetic variations that can be utilized for breeding purposes [55][56][57]. This is a pioneer study concerning the investigation of marker-trait association for 100-seed weight for safflower using GBS analysis.…”

Molecular characterisation of the oldest domesticated Turkish einkorn wheat landraces with simple sequence repeat (SSR) markers

“…Germplasm characterization is considered a prerequisite for breeding by providing novel information that can be used for future breeding activities [35,36]. Molecular markers can provide opuurtunities to detect precise genetic diversity among different cultivated and wild wheat species with different ploidy levels [37][38][39].…”