Start codon targeted (SCoT) polymorphism reveals genetic diversity in wild and domesticated populations of ramie (Boehmeria nivea L. Gaudich.), a premium textile fiber producing species

Abstract

Twenty-four start codon targeted (SCoT) markers were used to assess genetic diversity and population structure of indigenous, introduced and domesticated ramie (Boehmeria nivea L. Gaudich.). A total of 155 genotypes from five populations were investigated for SCoT polymorphism, which produced 136 amplicons with 87.5% polymorphism. Polymorphism information content and resolving power of the SCoT markers were 0.69 and 3.22, respectively. The Indian ramie populations exhibited high SCoT polymorphism (> 50%), high genetic differentiation (GST = 0.27) and moderate gene flow (Nm = 1.34). Analysis of molecular variance identified significant differences for genetic polymorphism among the populations explaining 13.1% of the total variation. The domesticated population exhibited higher genetic polymorphism and heterozygosity compared to natural populations. Cluster analysis supported population genetic analysis and suggested close association between introduced and domesticated genotypes. The present study shows effectiveness of employing SCoT markers in a cross pollinated heterozygous species like Boehmeria, and would be useful for further studies in population genetics, conservation genetics and cultivar improvement.

Geographical diversity pattern in Iranian landrace durum wheat (Triticum turgidum) accessions using start codon targeted polymorphism and conserved DNA-derived polymorphism markers

“…The SCoT primers are based on conserved regions flanking the initiation codon sequences of genes and CDDPs are short primers to generate useful genetic markers across functional domains of well-characterised plant genes (Collard, Mackill 2009a;Collard, Mackill 2009b). These marker techniques has been successfully employed in genetic diversity analysis of several plants, such as chickpea (Pakseresht et al 2013), wheat (Hamidi et al 2014), ramie (Satya et al 2015) and jojoba (Heikrujam et al 2015). The aim of the present study was to investigate the gentic diversity in Iranian landrace durum wheat accessions and examine the relationships of geographical sources of these accessions with their genetic diversity pattern.…”

Micropropagation and Assessment of Genetic Stability of In Vitro Raised Jojoba (Simmondsia chinensis Link.) Plants Using SCoT and ISSR Markers

“…In this context, random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) markers were screened to test the genetic integrity of jojoba (Kumar et al 2011). Start codon targeted (SCoT) polymorphism, the novel marker system based on the short conserved region in plant genes surrounding the ATG translation start codon (Collard and Mackill 2009) has been successfully employed indetermining the genetic diversity analysis and finger printing the population (Mulpuri et al 2013, Guo et al 2014, Satya et al 2015. A better analysis of genetic stability of in vitro raised plantlets can be made by using a combination of two types of markers that amplify different regions of the genome (Martins et al 2004).…”

Genetic structure and relationships of an associated population in ramie (Boehmeria niveaL. Gaud) evaluated by SSR markers

“…Genetic variability in natural populations is crucial for their evolutionary fitness and ecological adaptation [4], whereas, in cultivated populations, the diversity is crucial for their genetic improvement [5]. According to Vavilov [6], the domestication of ramie took place in central and western China.…”