The WRKY proteins constitute a large family of transcription factors in plants containing highly conserved WRKYGQK sequences and zinc-finger-like motifs. To comprehensively study WRKY III genes in cotton, we analyzed the genome sequences of Gossypium hirsutum, G. raimondii and G. arboreum. According to the three genome sequences, 18 group III GhWRKY genes were identified in G. hirsutum, 12 both in G. raimondii and G. arboreum. Phylogenetic and motif analysis showed that proteins with high similarities could be clustered together and had the same motif components. The ratios of non-synonymous (Ka) to synonymous (Ks) of the GhWRKY to GrWRKY or GaWRKY were lower than 1, which indicated that group III WRKY genes in Gossypium species are under purifying selection. Expression analysis revealed that group III GhWRKY genes expressed during fiber development and leaf senescence, and most of them could be induced by salicylic acid (SA), jasmonic acid (JA), ethylene, abscisic acid (ABA), mannitol, and NaCl both in roots and cotyledons. Our study gives a briefly introduction on cotton group III WRKY genes and implicates their potential function in cotton fiber development, leaf senescence and abiotic stresses.

Plant calcium-dependent protein kinases (CDPKs) play important roles in diverse physiological processes by regulating the downstream components of calcium signaling. To date, only a few species of the plant CDPK gene family have been functionally identified. In addition, there has been no systematic analysis of the CDPK family in cotton. Here, 41 putative cotton CDPK (GrCDPK) genes were identified via bioinformatics analysis of the entire genome of Gossypium raimondii and were classified into four groups based on evolutionary relatedness. Gene structure analysis indicated that most of these GrCDPK genes share a similar intron-exon structure (7 or 8 exons), strongly supporting their close evolutionary relationships. Chromosomal distributions and phylogenetics analysis showed that 13 pairs of GrCDPK genes arose via segmental duplication events. Furthermore, using microarray data of upland cotton (G. hirsutum L.), comparative profiles analysis of these GhCDPKs indicated that some of the encoding genes might be involved in the responses to multiple abiotic stresses and play important regulatory roles during cotton fiber development. This study is the first genome-wide analysis of the CDPK family in cotton, and it will provide valuable information for the further functional characterization of cotton CDPK genes.

MIKCC-type MADS-box genes encode transcription factors that are involved in plant developmental control and signal transduction. Few Gossypium hirsutum MADS-box genes have been reported thus far. Recently, the genome of Gossypium raimondii, considering the contributor of the D subgenome to G. hirsutum, was sequenced and provided a valuable resource to identify and analyze multiple MADS-box genes in G. hirsutum. Here we comprehensively analyzed 53 MIKCC-type MADSbox genes, including 34 newly cloned genes. Phylogenetic analysis of these genes with those from Arabidopsis and grapevine showed that the FLC and AGL12 subfamilies were absent in G. hirsutum. Proteins within a gene subfamily tended to share conserved motifs, and large differences occurred among subfamilies. Expression analysis in multiple tissues and floral organs implied differing roles for the subfamilies in G. hirsutum. At nine loci, two or three genes co-occurred, indicating that they came from different subgenomes; these groups had similar expression patterns. The identification of MIKCC-type MADSbox genes in G. hirsutum provides a valuable resource for further research into flowering time, flower development and ovule development in this important crop plant.

Inheritance and interrelationship of phenotype and genotype of earliness traits were evaluated in a diallel analysis involving six early-maturing parents. Date of first square (DFS), date of first flower (DFF), date of first open boll (DFOB), number of node first sympodial branch (NNFSB), and harvested rate before frost (HRBF) as earliness traits of six parents, 15 F1 hybrids and 15 F2 progenies were investigated from 2005 to 2008. The experiment design was a randomized complete block design with three replications. Additive, dominance and epistasis effects were analyzed with ADAA (additivedominance- epistasis) model. HRBF, DFF, and DFOB showed significant additive genetic variances. Heritability estimates ranged from 0.088 (HN, narrow sense) and 0.416 (HNE, environment interaction) for HRBF, to 0.103 (HN) and 0.524 (HNE) for DFF, and to 0.187 (HN) and 0.519 (HNE) for DFOB. Dominance genetic effects for DFS, DFF, DFOB, and NNSFB were stronger than additive effects. Additive-by-additive epistatic effects for DFS, DFOB, and NNSFB were detected and affected by environment. Correlation analysis showed generally that HRBF had a significant negative genetic and phenotypic correlation with DFS, DFOB, and NNFSB; DFS had significant positive genetic and phenotypic correlations with DFF, DFOB, and NNFSB; significant positive genetic and phenotypic correlations were also detected between DFF and DFOB, DFF and NNFSB, DFOB and NNFSB. The results showed that the lower the node to the first fruiting branch and the shorter the plant, the earlier was the onset of squaring, flowering, and boll opening, the higher was the harvest rate before frost. Heredity of earliness traits among parents and their hybrids were also detected and parents A1, A2, B1, B2, and B3 could be used to improve earliness traits of short season cotton cultivars.