Genetic mapping of EST-derived microsatellites from the diploid Gossypium arboreum in allotetraploid cotton

Abstract

To increase the numbers of microsatellites available for use in constructing a genetic map, and facilitate the use of functional genomics to elucidate fiber development and breeding in cotton, we sampled microsatellite sequences from expressed sequence tags (ESTs) transcribed during fiber elongation in the A-genome species Gossypium arboreum to evaluate their frequency of occurrence, level of polymorphism and distribution in the At and Dt subgenomes of tetraploid cotton. From among ESTs derived from G. arboreum fibers at 7-10 days post anthesis (dpa), 931 ESTs were found to contain simple sequence repeats (SSRs); 544 (58.4%) EST-SSR primer pairs were developed, and 468 (86%) amplified PCR products from allotetraploid cotton (G. hirsutumcv. TM-1 and G. barbadense cv. Hai7124). However, only 99 (18.2%) of these were found to be polymorphic and segregating in our interspecific BC1 mapping population [(TM-1xHai7124)xTM-1]. In these amplified and informative EST-SSRs, hexa- and tri-nucleotide repeat motifs were the most frequent, representing 40.1 and 30%, respectively, of the total. A total of 111 loci detected with these 99 EST-SSRs were integrated into our backbone map including 511 SSR loci. The distribution of the EST-SSRs appeared to be non-random, since 72 loci were anchored to the At and 37 to the Dt subgenome of allotetraploid cotton based on linkage tests. Interestingly, out of the 10 pairs of duplicate loci amplified, seven were mapped to the corresponding homologous linkage groups and/or chromosomes. BLASTX analysis revealed that 69 of the 99 ESTs showed significant similarities to known genes. Some genes important for fiber development, such as sucrose synthase, were mapped to corresponding chromosomes. These EST-SSRs provide structural and functional genomic information that will be useful for understanding cotton fiber development.

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

“…Hai7124. Among them, 744 of the primer pairs amplified polymorphisms and yielded a 47.9% polymorphic rate, which is more than twice as high as the 18.2% rate from G. hirsutum and the 23.3% rate from G. arboreumderived eSSRs reported previously (Han et al 2004. The highly polymorphic G. raimondii-derived primers can supply the more portable PCR markers needed for saturated genetic map construction and markerassisted improvement of the world's leading fiber crop.…”

“…All linkage groups were determined at log-of-odds (LOD) scores $6. Linkage groups were assigned to chromosomes on the basis of our backbone linkage maps (Han et al 2004 and BAC-FISH [fluorescence in situ hybridization (FISH) using bacterial artificial chromosome (BAC) clones as probes] results (K. ). So we used our published chromosome naming system (K. in which the A-subgenome chromosomes are identified as A1 through A13, and the homeologous D-subgenome chromosomes are designated D1 through D13 since chromosome homeology has been established following Cotton Genetic Nomenclature in the United States (Kohel 1973).…”

“…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.…”

“…In our laboratory, a polymerase chain reaction (PCR)-based linkage map was constructed and enhanced using a [(TM-1 3 Hai7124) 3 TM-1] interspecific BC 1 mapping population in allotetraploid cotton (Han et al 2004Song et al 2005). In this study, 2218 new eSSR markers from EST sequences in G. raimondii (C. B. and G. hirsutum were developed and used to screen polymorphisms between the mapping parents TM-1 and Hai7124.…”