DNA Polymorphisms of Genes Involved in Fiber Development in a Selected Set of Cultivated Tetraploid Cotton

The lack of genetic diversity within cultivated upland cotton (Gossypium hirsutum L.) has hindered the construction of genomewide linkage maps and their applications in genetics and breeding. The objective of this investigation was to develop candidate gene markers for fi ber quality and yield on the basis of approximately 90 genes implicated in fi ber development. Polymorphisms using sequence-tagged site (STS) and single nucleotide polymorphism (SNP) markers based on single strand conformation polymorphism (SSCP) and cleaved amplifi ed polymorphism (CAP) were evaluated among three upland and fi ve Pima cotton (G. barbadense L.) genotypes. Of the 90 primer pairs, 75 resulted in polymerase chain reaction amplifi cations, including 11 that yielded polymorphic STS markers. Of the 48 primer pairs that produced polymorphic SSCP markers, 27 yielded interspecifi c polymorphism, while 15 yielded both interand intraspecifi c polymorphisms. Six pairs yielded only intraspecifi c polymorphisms. A total of 18 SNPs, including four indels, were identifi ed in seven of the 15 fi ber gene fragments on the basis of direct DNA sequencing, and the average length was 350 bp, with a mean of 1.3 SNPs per fragment. The average rate of SNPs per nucleotide was 0.34%, and 0.31% and 0.41% in coding and noncoding regions, respectively. Eight of the 15 SNPs were interspecifi c and 78% were nucleotide substitutions, with the four indels contributing to interspecifi c polymorphism. Six selected SNPs were confi rmed by restriction enzyme digestion. The high level of SSCP polymorphism observed within a selected set of agronomically improved lines of upland cotton suggests that the use of SSCP will greatly facilitate genomewide mapping in upland cotton. Y. Lu, J. Curtiss, and J. Zhang, Dep. of Plant and Environmental Sci., Box 30003, MSC 3Q, New Mexico State Univ., Las Cruces, NM 88003. R.G. Percy, Southern Plains Agricultural Research Center, USDAARS, College Station, TX 77845. S.E. Hughs, Southwestern Cotton Ginning Research Lab., USDA-ARS, Mesilla Park, NM 88003. S. Yu, China Cotton Research Institute, Anyang, Henan 455112, China. Received 8 Dec. 2008. *Corresponding author ( [email protected]). Abbreviations: AFLP, amplifi ed fragment length polymorphism; bp, base pairs; CAP, cleaved amplifi ed polymorphism; EST, expressed sequence tag; GD, genetic distance; PCR, polymerase chain reaction QTL, quantitative trait loci; RFLP, restriction fragment length polymorphism; RIL, recombinant inbred line; RT-PCR, reverse transcription-polymerase chain reaction; SNP, single nucleotide polymorphism; SSCP, single strand conformation polymorphism; SSR, simple sequence repeat; STS, sequence-tagged site. Published in Crop Sci. 49:1695–1704 (2009). doi: 10.2135/cropsci2008.12.0693 © Crop Science Society of America 677 S. Segoe Rd., Madison, WI 53711 USA All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher.