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

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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 (Kantety et al., Plant Mol Biol 48:501–510, 2002). 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-1×Hai7124)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.

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Abbreviations

EST:

Expression sequence tag

PCR:

Polymerase chain reaction

dpa:

Day post-anthesis

bp:

Base pair

SSR:

Simple sequence repeats

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Acknowledgments

This research was supported by grants from the National High-tech Program (2004AA211172, 2003AA222050), the State Key Basic Research and Development Plan of China (2002CB111301), Program for Changjiang Scholars and Innovative Research Team in University, the Key Project of Chinese Ministry of Education (10418) and Jiangsu High-tech Project (BG2002306).

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Correspondence to Tianzhen Zhang.

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Communicated by C. Möllers

Zhiguo Han and Changbiao Wang contributed equally to this work.

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Han, Z., Wang, C., Song, X. et al. Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton. Theor Appl Genet 112, 430–439 (2006). https://doi.org/10.1007/s00122-005-0142-9

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  • DOI: https://doi.org/10.1007/s00122-005-0142-9

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