Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton

Abstract

In order to construct a saturated genetic map and facilitate marker-assisted selection (MAS) breeding, it is necessary to enhance the current reservoir of known molecular markers in Gossypium. Microsatellites or simple sequence repeats (SSRs) occur in expressed sequence tags (EST) in plants. Many ESTs are publicly available now and represent a good tool in developing EST-SSRs. From 13,505 ESTs developed from our two cotton fiber/ovule cDNA libraries constructed for Upland cotton, 966 (7.15%) contained one or more SSRs and from them, 489 EST-SSR primer pairs were developed. Among the EST-SSRs, 59.1% are trinucleotides, followed by dinucleotides (30%), tetranucleotides (6.4%), pentanucleotides (1.8%), and hexanucleotides (2.7%). AT/TA (18.4%) is the most frequent repeat, followed by CTT/GAA (5.3%), AG/TC (5.1%), AGA/TCT (4.9%), AGT/TCA (4.5%), and AAG/TTC (4.5%). One hundred and thirty EST-SSR loci were produced from 114 informative EST-SSR primer pairs, which generated polymorphism between our two mapping parents. Of these, 123 were integrated on our allotetraploid cotton genetic map, based on the cross [(TM-1xHai7124)TM-1]. EST-SSR markers were distributed over 20 chromosomes and 6 linkage groups in the map. These EST-SSR markers can be used in genetic mapping, identification of quantitative trait loci (QTLs), and comparative genomics studies of cotton.

A Microsatellite-Based, Gene-Rich Linkage Map Reveals Genome Structure, Function and Evolution in Gossypium

“…In recent years, many ESTs from different cotton genomes or tissues, especially cotton fiber, have been released, and the allelic diversity of microsatellites in coding sequences has been exploited. Han et al (2004Han et al ( , 2006 mapped 109 G. arboreum-derived and 123 G. hirsutum-derived eSSR loci into our backbone map. Park et al (2005) also developed 1232 eSSR markers derived from G. arboreum and identified 193 polymorphic loci with 121 anchored in a tetraploid cotton map.…”

“…A roughly similar polymorphism rate was observed between G. hirsutum and G. barbadense for eSSR markers. Han et al (2004Han et al ( , 2006) identified a 23.3 and 18.2% polymorphic rate between TM-1 and Hai7124, respectively, from G. arboreum and G. hirsutum-derived eSSRs. Similarly, Park et al (2005) also detected a 19.8% polymorphic rate using G. arboreum-derived eSSRs.…”

“…In recent years, great efforts have been made to develop genome SSRs (Reddy et al 2001;Nguyen et al 2004;Frelichouski et al 2006) (http:/ /www.resgen. com) and EST-SSRs (Saha et al 2003;Qureshi et al 2004;Han et al 2004Han et al , 2006Taliercio et al 2006) for cotton, and a web page (http://www.genome.clemson. edu/projects/cotton) for cotton microsatellite database (CMD) involving all of the available cotton SSR information has been constructed (Blenda et al 2006).…”

“…edu/projects/cotton) for cotton microsatellite database (CMD) involving all of the available cotton SSR information has been constructed (Blenda et al 2006). These SSR markers have been widely used in cotton genetic mapping (Reddy et al 2001;Zhang et al 2002;Han et al 2004;Nguyen et al 2004;Abdurakhmonov et al 2005;Song et al 2005;Park et al 2005;Frelichouski et al 2006;Han et al 2006). Recently, more cotton ESTs, mostly from different fiber developmental stages, were publicly released in GenBank (http://www.ncbi.nlm.…”

Genetic Mapping in Cotton

“…Both "A" & "D" genomes have maintained some level of sequence similarity, resulting in a high transferability of markers among the Gossypium species [18,19]. F 1s of mostly cultivated cotton species (G. hirsutum L. and G. barbadense L.) can further be used in making the crosses with wild tetraploid species (G. darwinii G. Watt, G. mustelinum Miers ex G. Watt, G. tomentosum Nutt.…”