Mining, characterization, and exploitation of EST-derived microsatellites in Gossypium barbadense

Quantitative Trait Locus Mapping and Candidate Gene Analysis for Verticillium Wilt Resistance Using Gossypium barbadense Chromosomal Segment Introgressed Line

Verticillium wilt (VW) is a soil-borne fungal disease that is caused by Verticillium dahliae Kleb and seriously damages cotton production annually in China. To date, many efforts have been made to improve the resistance of upland cotton against VW, but little progress has been achieved because of a lack of resistant upland cotton to VW. G. barbadense is known to carry high resistance to VW; however, it is difficult to transfer the resistance trait from G. barbadense to upland cotton because of linkage drag and distortion in the interspecific hybrid. In this study, a chromosomal segment introgression line (CSIL), SuVR043, containing a single and homozygous chromosome segment of G. barbadense cv. H7124 D04 (Chr 22), was created and used to construct an F₂ population for mapping of VW resistance quantitative trait loci (QTLs) in the greenhouse. Two major resistance QTLs against nondefoliating V. dahliae isolate Bp2, called qVW-Bp2-1 and qVW-Bp2-2, which were flanked by the markers cgr6409-ZHX37 and ZHX57-ZHX70 and explained an average of 16.38 and 22.36% of the observed phenotypic variation, respectively, were detected in three independent replicate experiments. The genetic distances from cgr6409 to ZHX37 and from ZHX57 to ZHX70 were 2.4 and 0.8 cM, respectively. By analyzing the genome sequence of the qVW-Bp2-1 and qVW-Bp2-2 regions, we determined that the accurate physical distances from cgr6409 to ZHX37 and from ZHX57 to ZHX70 in the G. barbadense genome are 254 and 140 kb, and that those spans 36 and 20 putative genes, respectively. The results of the expression analysis showed significant differences in the expression profiles of GbCYP450, GbTMEM214, and GbRLK among G. barbadense cv. H7124, CSIL SuVR043 and G. hirsutum acc. Sumian 8 at different times after inoculation with V. dahliae isolate Bp2. Virus-induced gene silencing (VIGS) analysis showed that silencing of GbCYP450 and GbTMEM214 decreased H7124 and CSIL SuVR043 resistance to VW. These results form a solid foundation for fine mapping and cloning of resistance genes in the substituted segment and will provide valuable assistance in future efforts to breed for VW resistance.

Characterization of expressed sequence tags from developing fibers of Gossypium barbadense and evaluation of insertion-deletion variation in tetraploid cultivated cotton species

Background

Cotton is the leading fiber crop worldwide. Gossypium barbadense is an important species of cotton because of its extra-long staple fibers with superior luster and silkiness. However, a systematic analysis and utilization of cDNA sequences from G. barbadense fiber development remains understudied.

Results

A total of 21,079 high quality sequences were generated from two non-normalized cDNA libraries prepared by using a mixture of G. barbadense Hai7124 fibers and ovules. After assembly processing, a set of 8,653 unigenes were obtained. Of those, 7,786 were matched to known proteins and 7,316 were assigned to functional categories. The molecular functions of these unigenes were mostly related to binding and catalytic activity, and carbohydrate, amino acid, and energy metabolisms were major contributors among the subsets of metabolism. Sequences comparison between G. barbadense and G. hirsutum revealed that 8,245 unigenes from G. barbadense were detected the similarity with those released publicly in G. hirsutum, however, the remaining 408 sequences had no hits against G. hirsutum unigenes database. Furthermore, 13,275 putative ESTs InDels loci involved in the orthologous and/or homoeologous differences between/within G. barbadense and G. hirsutum were discovered by in silico analyses, and 2,160 InDel markers were developed by ESTs with more than five insertions or deletions. By gel electrophoresis combined with sequencing verification, 71.11% candidate InDel loci were reconfirmed orthologous and/or homoeologous loci polymorphisms using G. hirsutum acc TM-1 and G. barbadense cv Hai7124. Blastx result showed among 2,160 InDel loci, 81 with significant function similarity with known genes associated with secondary wall synthesis process, indicating the important roles in fiber quality in tetraploid cultivated cotton species.

Conclusion

Sequence comparisons and InDel markers development will lay the groundwork for promoting the identification of genes related to superior agronomic traits, genetic differentiation and comparative genomic studies between G. hirsutum and G. barbadense.

Development and characterization of genomic and expressed SSRs for levant cotton (Gossypium herbaceum L.)

Four microsatellite-enriched genomic libraries for CA(15), GA(15), AAG(8) and ATG(8) repeats and transcriptome sequences of five cDNA libraries of Gossypium herbaceum were explored to develop simple sequence repeat (SSR) markers. A total of 428 unique clones from repeat enriched genomic libraries were mined for 584 genomic SSRs (gSSRs). In addition, 99,780 unigenes from transcriptome sequencing were explored for 8,900 SSR containing sequences with 12,471 expressed SSRs. The present study adds 1,970 expressed SSRs and 263 gSSRs to the public domain for the use of genetic studies of cotton. When 150 gSSRs and 50 expressed SSRs were tested on a panel of four species of cotton, 68 gSSRs and 12 expressed SSRs revealed polymorphism. These 200 SSRs were further deployed on 15 genotypes of levant cotton for the genetic diversity assessment. This is the first report on the successful use of repeat enriched genomic library and expressed sequence database for microsatellite markers development in G. herbaceum.