ARS | Publication request: SEQUENCE ANALYSIS OF SIX A-EXPANSIN GENES IN COTTON

Submitted to: National Cotton Council Beltwide Cotton Conference
Publication Type: Abstract Only
Publication Acceptance Date: January 3, 2006
Publication Date: March 6, 2006
Citation: An, C., Saha, S., Jenkins, J.N., Scheffler, B.E., Wilkins, T.A. 2006. Chromosomal assignment of six alpha-expansin genes using SNP markers in cotton (Gossypium spp.). Beltwide Cotton Conferences. p. 737.

Technical Abstract: A-Expansins are cell wall proteins that facilitate cell wall extension by disrupting noncovalent bonds between wall components. Some of the expansin genes play a very important role in cell wall extension during cotton fiber development. The objectives of this study were, (1) to discern the sequence variation of the Expansin genes in diploid and tetraploid cotton species; and (2) to find the chromosomal location of Expansin genes in the tetraploid cotton. Thirteen pairs of PCR primers were designed based on available sequence information of the six members of cotton a-expansin gene family for amplification. A total of 104 (13 pairs primer × 8 lines) fragments were successfully amplified from the eight lines, including two diploid species (Gossypium arboreum, G. raimondii), and four tetraploid species, TM-1, RIL-1 and RIL-2 (G. hirsutum), 3-79 (G. barbadense), G. tomentosum, and G. mustelinum. The PCR amplified fragments were cloned into pCR4-TOPO vector by the TA cloning method. Twelve colonies were selected from each of the 104 fragments for forward and reverse sequencing. The alignment of the 96 (12 colonies × 8 lines) amplified fragments, for each pair of PCR primer, was performed with the SeqMan program of DNASTAR software (DNASTAR, Inc., Madison, Wisconsin, USA). A phylogenetic tree was conducted based on the sequence similarity using the UPGMA method of PAUP software (Swofford et al., 1993). Comparative analysis of sequence similarity of a-Expansin genes revealed the presence of several SNP markers. Chromosomal locations of these genes were identified with SNP markers based on deletion method using the aneuploid F1 interspecific chromosome substitution stocks and backcrossed chromosome substitution lines. Expansin-1 to Expansin-6 gene was located to 20Lo, 10Lo, 10Lo, 9Lo, 1Lo and 3Lo chromosome, respectively. The chromosomal location may facilitate research on candidate gene mapping and possible association of these genes with important fiber QTLs.