Evaluation of SSR and SNP Markers for Molecular Breeding in Rice

Abstract

This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.Plant Breed. Biotech. 2015 (June) 3(2):139~152 http://dx.ABSTRACT Simple sequence repeats (SSRs) have been the marker of choice for rice molecular breeding due to the high level of polymorphism, technical simplicity and low cost. Recent advances in rice genomics have led to the discovery of abundant single nucleotide polymorphism (SNPs) which have enormous potential for rice molecular breeding. To assess both marker systems for molecular breeding in rice, SSR and SNP markers were evaluated on a set of 23 genotypes representing indica germplasm for their usefulness in molecular research and breeding program. Seven hundred SSR and sequence tagged sites (STS) markers and 384 SNPs were screened for polymorphism. Highly polymorphic markers based on polymorphic information content (PIC) values were identified, which will be useful for molecular breeding. Data was used to identify an "indica genotyping set" based on high level of polymorphism, chromosome position and marker quality which will provide kits of markers for marker assisted selection (MAS). Genetic diversity analysis using SSR data was more consistent with pedigrees compared to analysis with SNP data indicating that more than 384 SNPs are required when elite indica breeding material is used. The results also indicated that there were polymorphic "blind spots" for the fixed SNP set suggesting that SSRs could still be used to complement fixed-SNP genotyping platforms for some molecular breeding applications.

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Role of Reactive Oxygen Species and Contribution of New Players in Defense Mechanism under Drought Stress in Rice

“…Overexpression of OsOAT in rice also increases the activities of certain enzymes involved in ROS quenching and antioxidants such as GSH content and protect cells from oxidative damage (You et al, 2012). Access to these genes is due to molecular breeding which upgraded many varieties with enhanced tolerance against abiotic stress in rice (Gonzaga et al, 2015).…”

Genomic Tools for the Enhancement of Vegetable Crops: A Case in Eggplant

“…SNPs, like SSRs, are codominant, robust and easy to identify by NGS platform through sequencing (Davey et al, 2011;Scheben et al, 2016), and in addition have the advantage that are more abundant, ubiquitous and easy to automate than SSRs (Thomson et al, 2014;Kim et al, 2016), although are less informative (Filippi et al, 2015;Gonzaga, 2015). SSRs are generally considered as dispersed markers, even though in some species tend to concentrate more frequently in heterochromatic regions and it is unlikely to cover all the genomic regions assessing just SSRs (Hong et al, 2007;Shirasawa et al, 2010).…”