Identifying profiles of SSR and SNP markers in cultivars of tetraploid wheat: physical and chemical analysis

This is the accepted manuscript of the paper

Javana Iman Yousefi, Pagnotta Mario Augusto, D΄Ovidio Renato. 2019. Identifying profiles of SSR and SNP markers in cultivars of tetraploid wheat: physical and chemical analysis. Eurasian Chemical Communications, 2(4), 516-535. http://www.echemcom.com/article_99343.html Doi: 10.33945/SAMI/ECC.2020.4.9

Abstract
In this work, we studied the distribution of molecular markers in the chromosomes of tetraploid wheat. This distribution was drawn through the 192 line came from based on a cross between two durum wheat genotypes. The first parental line was a Triticum turgidum ssp. durum (Desf.). The second parental line was a durum wheat genotype derived from a cross between the Triticum turgidum ssp. Durum, (Omrabi 5). One hundred ninety-two F8 recombinant inbred lines (RILs) derived from the above mentioned cross by single-seed descent. A total of 254 markers were analyzed, including 216 microsatellites and 38 SNPs markers. Linkage analysis defined 14 linkage groups. Most markers (57.2%) were found to be located to the A genome, with an average of 12 markers per chromosome. The remaining (42.7%) were located to the B genome. To construct a stabilized (skeleton) map, markers interfering with map stability were removed. Efficient user-friendly methods for mapping plant genomes were highly desirable for the studies marker-assisted selection. SSR (microsatellite) markers are user-friendly and efficient in detecting polymorphism, but they detect few loci. The skeleton map consisted of 100 markers with a total length of 3170.29 cM and an average distance of 31.7 cM between adjacent markers. Majority of the markers showed a statistical significantly Mendelian segregation with 1:1 ratio (α=0.01). The highest percentage of markers was similar with the first parental. This SSR and SNP markers revealed a high proportion of clustering, which may be indicative of gene-rich regions. Some of the SSR, SNP markers were distributed for the first time on the current work. This project provided a useful groundwork for further genetic map, genetic analysis of important quantitative traits, positional cloning, and marker-assisted selection, as well as for genome comparative genomics and genome organization studies in wheat and other cereals.