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United States Department of Agriculture

Agricultural Research Service

Title: EST-SSR: A NEW CLASS OF GENETIC MARKERS IN COTTON

Authors
item Qureshi, Samina - MISS STATE UNIVERSITY
item Saha, Sukumar
item Kantety, R - CORNELL UNIVERSITY
item Jenkins, Johnie

Submitted to: Journal of Heredity
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 30, 2004
Publication Date: August 1, 2004
Citation: Qureshi, S.N., Saha, S., Kantety, R.V., Jenkins, J.N. 2004. EST-SSR: A new class of genetic markers in cotton. Journal of Cotton Science. 8:112-123.

Interpretive Summary: One of the challenges in the application of marker assisted selection in a cotton breeding program is the limited information about suitable molecular markers. Microsatelites or simple sequence repeats (SSRs) are considered the DNA marker of choice in many crop species. In the past, SSRs have been developed in cotton based on isolating and sequencing clones containing putative SSR region, together with designing and testing flanking primers. These methods are typically costly, time-consuming, and labor-intensive. Here we report a cost-effective, rapid, and efficient strategy of developing EST (express sequence tag) derived SSRs (EST-SSR) by exploiting EST databases of GeneBank. One hundred and thirty-three SSR-containing ESTs (SSR-ESTs) were identified by analyzing 9,948 EST sequences belonging to Gossypium hirsutum. Primers were designed for 84 of these SSR-ESTs and were tested for their ability to detect diversity among four cotton lines of G. hirsutum and G. barbadense. The intraspecies polymorphism rate among the G. hirsutum cotton cultivars was 26% and interspecific polymorphism between G. hirsutum and G. barbadense was 52%. Blast results showed that about seventy four percent of the SSR-ESTs were from fiber related tissues in G. hirsutum. Fifty-five percent of these SSR-EST sequences matched with G. arboreum and about 19% of the sequences showed considerable sequence similarity with sequences in the Arabidopsis thaliana genome, thus these markers are very useful for comparative mapping. These markers will provide for the first time DNA markers that may give a more direct estimate of diversity in functional genome of cotton.

Technical Abstract: Expressed sequence tags (ESTs) containing simple sequence repeats (SSRs) represent a new class of genetic markers for cotton (Gossypium spp.). One hundred and thirty-three SSR-containing ESTs (SSR-ESTs) were identified by analyzing 9,948 sequences belonging to Gossypium hirsutum. Primers were designed for 84 of these SSR-ESTs and were tested for their ability to detect diversity among four cotton lines belonging to G. hirsutum and G. barbadense. Selected primers were also tested against one line from G. arboreum and G. raimondi, respectively. An average of 3 amplicons was obtained per primer pair. The intraspecies polymorphism rate among the G. hirsutum cotton cultivars was 26%, and interspecific polymorphism between G. hirsutum and G. barbadense was 52%. The presence of SSRs in the SSR-EST sequences was confirmed by cloning and sequencing of the selected amplified products from four different lines. To explore the potential utility of the SSR-EST loci for comparative mapping, these sequences were compared using BLAST search against different plant species assuming an e-value <1E-10 as a significant homology. BLAST results showed that about seventy-four percent of the SSR-ESTs were from fiber related tissues in G. hirsutum, whereas, 26% were from other tissues such as cotton boll abscission, cotton seed, etc. Fifty-five percent of these SSR-EST sequences matched with G. arboreum and about 19% of the sequences showed considerable sequence similarity with sequences in the Arabidopsis thaliana genome. We reported in this paper information about the primer sequence, repeat motif, and the degree of polymorphism of these EST-SSR markers against a panel of four lines. We demonstrated for the first time, in cotton, a cost-effective strategy to develop EST-SSR markers exploiting the recently increased EST databases. EST-SSRs enhanced their importance in marker assisted selection because they are expression dependent and may provide an estimate of functional diversity in the genome.

Last Modified: 10/31/2014
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