Assessment of Functional EST-SSR Markers (Sugarcane) in Cross-Species Transferability, Genetic Diversity among Poaceae Plants, and Bulk Segregation Analysis

Abstract

Expressed sequence tags (ESTs) are important resource for gene discovery, gene expression and its regulation, molecular marker development, and comparative genomics. We procured 10000 ESTs and analyzed 267 EST-SSRs markers through computational approach. The average density was one SSR/10.45 kb or 6.4% frequency, wherein trinucleotide repeats (66.74%) were the most abundant followed by di- (26.10%), tetra- (4.67%), penta- (1.5%), and hexanucleotide (1.2%) repeats. Functional annotations were done and after-effect newly developed 63 EST-SSRs were used for cross transferability, genetic diversity, and bulk segregation analysis (BSA). Out of 63 EST-SSRs, 42 markers were identified owing to their expansion genetics across 20 different plants which amplified 519 alleles at 180 loci with an average of 2.88 alleles/locus and the polymorphic information content (PIC) ranged from 0.51 to 0.93 with an average of 0.83. The cross transferability ranged from 25% for wheat to 97.22% for Schlerostachya, with an average of 55.86%, and genetic relationships were established based on diversification among them. Moreover, 10 EST-SSRs were recognized as important markers between bulks of pooled DNA of sugarcane cultivars through BSA. This study highlights the employability of the markers in transferability, genetic diversity in grass species, and distinguished sugarcane bulks.

Development of EST-SSR markers for Pongamia pinnata by transcriptome database mining: cross-species amplification and genetic diversity

“…Recently, due to the accessibility of a significant amount of genomic information, a lot of EST datasets are available for many crop plants (Savadi et al 2012;Huang et al 2016;Zhu et al 2016). These databases have been successfully utilised to develop novel molecular markers linked to genes of agronomically important traits (Zhang et al 2016;Ul Haq et al 2016). Interestingly, very few EST-SSRs or genelinked markers were developed and tested in P. pinnata (Huang et al 2016).…”

“…Simple sequence repeats (SSRs) are distributed throughout the genome, including coding or genic region of the nuclear genome (Zhu et al 2016;Huang et al 2016). Hence, expressed sequence tags (ESTs) and transcriptome libraries are often used for SSR marker preparation (Huang et al 2016;Ul Haq et al 2016). Moreover, the marker derived from a transcribed portion of genes is involved in variety of metabolic functions and unveils the biological significance (Savadi et al 2012;Zhang et al 2016).…”

Development and Use of Simple Sequence Repeats (SSRs) Markers for Sugarcane Breeding and Genetic Studies

“…Their study found a high level of polymorphism (96.3%) among these samples, and cross-transferability of 98.0% and 88.27% within the Saccharum complex and across cereals, respectively. Ul haq et al [30] procured 10,000 ESTs across 20 plants, and used a computational method to evaluate 267 EST-SSRs and synthesize 63 EST-SSRs. Among those, expansion genetics allowed identification of 42 markers amplifying 519 alleles.…”

Phylogenetic relationships of some Egyptian soybean cultivars (Glycine max L.) using SCoT marker and protein pattern

“…After the advent of PCR, the improvement of different molecular markers such as amplified fragment length polymorphism (AFLP), single-nucleotide polymorphism (SNP), inter simple sequence repeats (ISSRs), simple sequence repeats (SSR), and several new concepts were used. Different markers were used for the determination of the relationships between plant species by many researchers in tomato cultivars (Nawaz et al, 2015), Poaceae plants (Haq et al, 2016), and Citrullus colocynthis (Verma et al, 2017).…”