Development and Characterization of Simple Sequence Repeat Markers Providing Genome-Wide Coverage and High Resolution in Maize

Abstract

Simple sequence repeats (SSRs) have been widely used in maize genetics and breeding, because they are co-dominant, easy to score, and highly abundant. In this study, we used whole-genome sequences from 16 maize inbreds and 1 wild relative to determine SSR abundance and to develop a set of high-density polymorphic SSR markers. A total of 264 658 SSRs were identified across the 17 genomes, with an average of 135 693 SSRs per genome. Marker density was one SSR every of 15.48 kb. (C/G)n, (AT)n, (CAG/CTG)n, and (AAAT/ATTT)n were the most frequent motifs for mono, di-, tri-, and tetra-nucleotide SSRs, respectively. SSRs were most abundant in intergenic region and least frequent in untranslated regions, as revealed by comparing SSR distributions of three representative resequenced genomes. Comparing SSR sequences and e-polymerase chain reaction analysis among the 17 tested genomes created a new database, including 111 887 SSRs, that could be develop as polymorphic markers in silico. Among these markers, 58.00, 26.09, 7.20, 3.00, 3.93, and 1.78% of them had mono, di-, tri-, tetra-, penta-, and hexa-nucleotide motifs, respectively. Polymorphic information content for 35 573 polymorphic SSRs out of 111 887 loci varied from 0.05 to 0.83, with an average of 0.31 in the 17 tested genomes. Experimental validation of polymorphic SSR markers showed that over 70% of the primer pairs could generate the target bands with length polymorphism, and these markers would be very powerful when they are used for genetic populations derived from various types of maize germplasms that were sampled for this study.

Identification of molecular markers linked to Fusarium ear rot genes in maize plantsZea maysL

“…These may propose an advanced method for genetic differences existing among plant genomes at DNA level and also the differences involved in sequencing and procedures. [27] This observation was similar to Nikhou et al [28] indicating that SSR are efficient markers to classify closely related lines. SSR markers were able to detect the extent of genetic diversity and to detect considerable level of genetic diversity among maize hybrids.…”

Molecular characterization of red clover genotypes utilizing microsatellite markers

“…Simple Sequence Repeats (SSR) or microsatellite markers are the arrays of DNA sequences, consisting of tandemly repeating mono-, di-, tri-, tetra-, penta-, and hexanucleotide motifs, and they are flanked by unique sequences (Xu et al, 2013). These markers are based on PCRpolymerase chain reaction, there are many of them, they are codominant, highly reproducible (He et al, 2009) and also among the most preferred types of molecular markers for their ubiquitous distribution (Zhao et al, 2011).…”

Genetic analysis of microsatellite markers for salt stress in two contrasting maize parental lines and their RIL population

“…The development and mapping of DNA markers are essential for using QTL mapping of salt tolerance and marker-assisted selection of this trait in maize genotypes. Maize is one of the fi rst major crop species to have had maps of different molecular markers (Davis et al 1999, Sharopova et al 2002, Sibov et al 2003, Lima et al 2009, Xu et al 2013, Zhou et al 2011. Recently, research has focused on genetic dissection in maize using QTL mapping of recombinant inbred lines (RILs) derived from a cross between two maize inbred lines with contrasting salinity tolerance.…”

“…Many maize ESTs contained simple sequence repeats and could be readily converted to functional markers (Lee 2007). In recent years, a number of maize EST-SSRs have been developed (Xu et al 2013) and applied to construct linkage maps (Sharopova et al 2002, Zhou et al 2011, Orsini et al 2012, Sa et al 2012, QTL mapping and markerassisted breeding (Orsini et al 2012, Cui et al 2015. In addition, Banisetti et al (2012) identifi ed candidate genebased SSR markers for lysine, tryptophan pathway and opaque2 modifi ers.…”