Gene 1-FEH-A was associated with grain yield, and 1-FEH-B was associated with thousand kernel weight and test weight [10]. In sunflower, HaCOI1-1 and HaCOI1-2 were found to be strongly associated with Sclerotinia stalk rot resistance [11]. In waxy rice, Xu et al. [12] associated starch synthase IIa (SSIIa or SSII-3) and SSI with starch properties. As these examples illustrate, AM is useful for dissecting

Epacadostat solubility dmso candidate genes underlying complex traits. In cotton, some AM studies have been reported [5], [13], [14], [15] and [16], but these were all genome wide association studies (GWAS) rather than candidate gene association studies. Expansin refers to a family of closely related non-enzymatic proteins found in the plant cell wall, with important roles in

plant cell growth, emergence of root hairs, meristem function, and other developmental processes in which cell wall loosening occurs. The elongation of cotton fiber is associated with the expression of many genes, among which Expansin is one of the most highly expressed [17], [18] and [19]. That Expansin may control Thiazovivin chemical structure fiber development is of interest in strategies aimed at improving fiber quality, because final fiber length and strength largely determine the quality of commercial cotton thread. Given that Expansins play a pivotal role in cell wall extension, they are attractive targets for strategies designed to alter cell shape and size, and this consideration led us to characterize some of the genes that encode Expansins in Gossypium. Six cDNAs encoding α-expansins were identified in a previous study of cotton fiber development [18]. RT-PCR expression

analysis showed that the mRNA from GhExp2 was specific to cotton fibers, where it was the second most abundant transcript (at a low level) during the elongation phase of fiber development [18]. Intron and exon sizes of GhExp2 were all different from those of the other five genes. In GhExp2, a Cys → Arg substitution at the first Cys [a residue conserved in most α-expansins previously described [20]] was found, and the Phe [which commonly is contained in a His-Phe-Asp (HFD) domain] residue had been replaced by Lys. But, the amino acid sequence Elongation factor 2 kinase derived from GhExp2 was most closely related (with 97% sequence identity) to that from GhExp1, which may play an important role in cell wall extension during fiber development [18]. It is still unclear whether the nucleotide diversity of GhExp2 is associated with phenotypic variation. After sequence alignment of six genes (GhExp1–GhExp6) and AY189969 (expansin mRNA), gene-specific primers were designed to amplify only Exp2. The objectives of this study were to investigate the nucleotide and haplotype diversity and the extent and pattern of linkage disequilibrium (LD) in the Exp2 gene, and then to validate the association between Exp2 and fiber quality by AM, and identify the most favorable allele of Exp2, with the aim of providing knowledge for future fiber quality breeding efforts in cotton.