Development of new SSR markers for homoeologous WFZP gene loci based on the study of the structure and location of microsatellites in gene-rich regions of chromosomes 2AS, 2BS, and 2DS in bread wheat

A set of 44 bread wheat landraces was used to determine the efficacy of 16 amplifed fragment length polymorphism (AFLP) primers and 63 wheat simple sequence repeat (SSR) markers in identifying polymorphisms between accessions. The SSR markers detected approximately 10 alleles per locus with a mean gene diversity (Hz) of 0.63, whereas AFLP primers identified approximately 147 fragments per primer with a mean gene diversity of 0.25. A set of 54 SSR markers and 11 AFLP primers was identified as highly polymorphic (polymorphic information content (PIC) ≥ 0.5 and 0.3 for SSR and AFLP, respectively), and suitable for molecular characterisation of germplasm. Principle coordinate analysis suggested that the AFLP and SSR loci could be used to discriminate among accessions collected from North Africa and southern Europe from those collected from the Middle East. Both marker types indicate that accessions from North Africa and southern Europe, the Middle East, and southern and eastern Asia are genetically diverse. The results indicate the usefulness of the molecular markers to assess genetic diversity present within germplasm collections.

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Characterization of EST‑SSR markers in bread wheat EST related to drought tolerance and functional analysis of SSR‑containing unigenes

10.36462/h.biosci.20203 ◽

2020 ◽

pp. 1-12

Author(s):

Laila Dabab Nahas ◽

Alsamman M. Alsamman ◽

Aladdin Hamwieh ◽

Naim Al-Husein ◽

Ghinwa Lababidi

Keyword(s):

Drought Tolerance ◽

Bread Wheat ◽

Ssr Markers ◽

Web Sites ◽

Wheat Breeding ◽

Genic Ssr ◽

Drought Tolerant ◽

Ssr Loci ◽

Weather Changes

Bread wheat (Triticum aestivum) is an important staple food around the world. The enormous volume of the genome of wheat makes it quite slow to progress in traditional scientific research. On the other hand, incessant databases and suitable tools on web sites make progress in wheat research quicker and easier. Drought is a major abiotic stress in accordance with weather changes and accelerated increase in drylands. In this study, 9077 ESTs related to drought tolerance in hexaploid wheat were downloaded from NCBI and assembled into 12062 contigs and 4141 singletons. It was found that trinucleotide had the highest frequency 64.71%. Moreover, 53.80% of SSRs found in coding regions in respect of ORFs. The highest amino acids found for tri-and hexanucleotides were Arginine. In addition, 81% of SSR-containing unigenes had one chromosome location and the highest number of loci was found in chromosomes 1B (69). The distribution of genic SSR loci among the 21 wheat chromosomes, the three subgenomes, and the seven homoeologous groups of wheat chromosomes was significant, with P<0.01 indicating a non-random distribution. Functional annotation and characterization of SSR-containing unigenes have been performed. Eighty-six sequences were identified and sorted into 25 putative TF families and establish 166 pathways using KEGG. Primer-BLAST was used to predict the polymorphism, which was 39% of the 63 primer pairs of SSR markers. Our current study attempts to help farmers in wheat breeding programs to have drought-tolerant accessions, particularly in developing countries

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RELATION BETWEEN SSR MARKERS AND VARIATION IN STOMATAL FREQUENCY OF BREAD WHEAT

Fiziologia rastenij i genetika ◽

10.15407/frg2017.05.414 ◽

2017 ◽

Vol 49 (5) ◽

pp. 414-424

Author(s):

N.P. Lamari ◽

◽

M.V. Galayeva ◽

V.I. Fait ◽

O.O. Pogrebnuk ◽

...

Keyword(s):

Bread Wheat ◽

Ssr Markers ◽

Stomatal Frequency

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Targetting microsatellites (SSRs) in genetic linkage maps of bread wheat

Australian Journal of Agricultural Research ◽

10.1071/ar01026 ◽

2001 ◽

Vol 52 (12) ◽

pp. 1143 ◽

Cited By ~ 2

Author(s):

M. J. Hayden ◽

S. Khatkar ◽

P. J. Sharp

Keyword(s):

Bread Wheat ◽

Ssr Markers ◽

Genetic Linkage ◽

Linkage Maps ◽

Linkage Groups ◽

Intraspecific Polymorphism ◽

Chromosomal Origin ◽

Genetic Linkage Maps ◽

Genomic Regions ◽

Simple Sequence

The construction of genetic linkage maps from intraspecific crosses of bread wheat is slow and difficult due to very limited levels of polymorphism, which hinder the assignment of linkage groups to chromosomes and leave large genomic regions without markers. Simple sequence repeats (SSRs) reveal a higher incidence of polymorphism and are more informative than any other DNA marker, and are therefore considered a marker of choice for self-pollinating crops with little intraspecific polymorphism. However, the availability of SSRs in bread wheat is still limited. In this study, selectively amplified microsatellite (SAM) analysis was used to develop informative SSR markers to assist in the construction of an intraspecific wheat map. Three markers were developed for under-represented regions in the genetic map, and 7 for unassigned linkage groups. The latter SSRs permitted the chromosomal origin of 4 unassigned linkage groups to be determined. These results demonstrate the utility of SAM analysis for the targetted development of informative SSR markers to genomic regions of interest, and assignment of linkage groups to chromosomes. Furthermore, SAM analysis facilitates the development of markers for relatively short (<11) dinucleotide repeat sequences, a class of SSRs generally inaccessible to traditional hybridisation-based methods used to develop these markers.

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