Identification of differentially expressed genes associated with semigamy in Pima cotton (Gossypium barbadenseL.) through comparative microarray analysis

Abstract

BackgroundSemigamy in cotton is a type of facultative apomixis controlled by an incompletely dominant autosomal gene (Se). During semigamy, the sperm and egg cells undergo cellular fusion, but the sperm and egg nucleus fail to fuse in the embryo sac, giving rise to diploid, haploid, or chimeric embryos composed of sectors of paternal and maternal origin. In this study we sought to identify differentially expressed genes related to the semigamy genotype by implementing a comparative microarray analysis of anthers and ovules between a non-semigametic Pima S-1 cotton and its doubled haploid natural isogenic mutant semigametic 57-4. Selected differentially expressed genes identified by the microarray results were then confirmed using quantitative reverse transcription PCR (qRT-PCR).ResultsThe comparative analysis between isogenic 57-4 and Pima S-1 identified 284 genes in anthers and 1,864 genes in ovules as being differentially expressed in the semigametic genotype 57-4. Based on gene functions, 127 differentially expressed genes were common to both semigametic anthers and ovules, with 115 being consistently differentially expressed in both tissues. Nine of those genes were selected for qRT-PCR analysis, seven of which were confirmed. Furthermore, several well characterized metabolic pathways including glycolysis/gluconeogenesis, carbon fixation in photosynthetic organisms, sesquiterpenoid biosynthesis, and the biosynthesis of and response to plant hormones were shown to be affected by differentially expressed genes in the semigametic tissues.ConclusionAs the first report using microarray analysis, several important metabolic pathways affected by differentially expressed genes in the semigametic cotton genotype have been identified and described in detail. While these genes are unlikely to be the semigamy gene itself, the effects associated with expression changes in those genes do mimic phenotypic traits observed in semigametic plants. A more in-depth analysis of semigamy is necessary to understand its expression and regulation at the genetic and molecular level.

Transcriptome Analysis Reveals Crosstalk of Responsive Genes to Multiple Abiotic Stresses in Cotton (Gossypium hirsutum L.)

“…In this study, we aimed to identify components of the regulatory network of multiple abiotic stresses. The stress treatments were performed separately on seedlings 4-day after germination (DAG), and RNA was isolated from specimens of 10-day treatment before a 24K Affymetrix cotton genome array [31,37] was conducted to compare the transcription profiles of the plant's response to ABA, cold, drought, salinity and alkalinity (pH=11, hereinafter referred to pH in this paper). The expression level of transcripts was compared, so that genes with more than two-fold change and a p-value of ≤ 0.05 were defined as those with significant different expression.…”

Transcriptome Profiling Analysis Reveals That Flavonoid and Ascorbate-Glutathione Cycle Are Important during Anther Development in Upland Cotton

“…We also identified 1,165 anther stage-enriched genes and some important biological processes during anther development in Upland cotton. To our knowledge, Curtiss et al have recently used anthers and ovules of Pima cotton ( G. barbadense ) at 0 dpa to compare differentially expressed genes between Pima S-1 and isogenic 57-4 [36] . And this is the first study to construct an anther cDNA library of Upland cotton and investigate transcriptional changes during anther development in this species.…”

Prospects for Molecular Breeding in Cotton,Gossypiumspp

“…Many characters have been targeted to find the key responsible genes and pathways, especially fiber initiation, and elongation being highly focused up on [61][62][63][64][65][66][67][68]. Other characters like Green and Brown colored cotton [69-71], Cadmium tolerance [72], Cold stress [73], Drought stress [74], Nematode resistance [75], Semigamy in Pima cotton [76], Whitefly mediated cotton leaf curl infection transcriptome [77], the transcriptome of Mepiquat chloride-induced compact types using in cotton [78] have also been done in cotton. Many studies have been carried out to identify genes that are differentially expressed, however paucity of the causes of the differential expression, hints us towards epigenetic regulations and transcription factors as the probable cause.…”