Development of a core set of SSR markers for the characterization of Gossypium germplasm

Abstract

Molecular markers such as simple sequence repeats (SSR) are a useful tool for characterizing genetic diversity of Gossypium germplasm. Genetic profiles by DNA fingerprinting of cotton accessions can only be compared among different collections if a common set of molecular markers are used by different laboratories and/or research projects. Herein, we propose and report a core set of 105 SSR markers with wide genome coverage of at least four evenly distributed markers per chromosome for the 26 tetraploid cotton chromosomes. The core marker set represents the efforts of ten research groups involved in marker development, and have been systematically evaluated for DNA polymorphism on the 12 genotypes belonging to six Gossypium species [known collectively as the cotton marker database (CMD) panel]. A total of 35 marker bins in triplex sets were arranged from the 105 markers that were each labeled with one of the three fluorescent dyes (FAM, HEX, and NED). Results from this study indicated that the core marker set was robust in revealing DNA polymorphism either between and within species. Average value of polymorphism information content (PIC) among the CMD panel was 0.65, and that within the cultivated cotton Electronic supplementary material The online version of this article

Genetic diversity of Turkish commercial cotton varieties revealed by molecular markers and fiber quality traits

“…PIC values provide an estimation of marker power by considering both the number of alleles at a locus and the relative frequencies of those alleles in the population under study (Pei et al, 2010). Our observed Table 1. average PIC value was 0.23, whereas the average PIC value of a core set of SSR markers for Gossypium species ranged from 0.0 to 0.82 (Yu et al, 2012). One of the findings of the present study is that the most informative markers are CIR246 with 0.749 PIC value among fiber quality linked SSR markers and DPL513 with 0.724 PIC value among tested DPL series primers.…”

Research Article Genetic diversity of arboreal cotton populations of the Brazilian semiarid: a remnant primary gene pool for cotton cultivars.

“…The PIC values were also more elevated than those found for cultivars (Yu et al, 2012;Hinze et al, 2015;Moiana et al, 2015) showing discriminative potential conferred by 12 loci. The large genetic basis of mocó cotton is due to multiple contributions during domestication and selection (Moreira et al, 1995), including introgressions (Freire and Moreira, 1991;Lacape et al, 2007) and selection by local farmers (Freire et al, 1990;Menezes et al, 2010).…”

Screening of highly informative and representative microsatellite markers for genotyping of major cultivated cotton varieties

“…A core set of SSR markers was evaluated for DNA polymorphisms in 12 genotypes of 6 Gossypium species, collectively known as the cotton marker database panel. The results indicated that the core marker set was robust for characterization of Gossypium germplasm (Yu et al, 2012a). Although polymorphism levels for these primers are high in different Gossypium germplasms, levels are low in cultivated varieties such as upland cotton.…”

“…Cultivated cotton is the world's leading fiber crop and the second most important oilseed crop (Yu et al, 2012a). The authorization and release of high-quality cultivars is important in agricultural production.…”

“…Over the last decade, thousands of SSRs have been identified (Blenda et al, 2006;Guo et al, 2007;Lacape et al, 2009;Yu et al, 2011Yu et al, , 2012a. These cotton SSR markers were developed either from random-enriched small genomic clones, large insert bacterial artificial chromosome clones, or expressed sequence tags (ESTs) of Gossypium species.…”