GENE EXPRESSION ANALYSIS IN A COTTON NAKED SEED MUTANT USING COTTON OLIGO-GENE MICROARRAYS DESIGNED FROM ARABIDOPSIS ORTHOLOGOUS GENES

Authors: LEE, JINSUK - TEXAS A&M UNIVER.; HASSAN, OSAMA - TEXAS A&M UNIVER.; GAO, WENXIANG - TEXAS A&M UNIVER.; WANG, JIYUAN - TEXAS A&M UNIVER.; WEI, NING - TEXAS A&M UNIVER.; Kohel, Russell; CHEN, XIAO-YA - CHINESE ACAD. OF SCIENCE; Payton, Paxton; STELLY, DAVID - TEXAS A&M UNIVER.; CHEN, Z JEFFREY - TEXAS A&M UNIVER.

Submitted to: Planta
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/25/2005
Publication Date: 11/3/2006
Citation: Lee, J.J., Hassan, O.S., Gao, W., Wang, J.J., Wei, N.E., Kohel, R.J., Chen, X., Payton, P.R., Stelly, D.M., Chen, Z. 2006. Gene expression analysis in a cotton naked seed mutant using cotton oligo-gene microarrays designed from Arabidopsis orthologous genes. Planta. 223(3):418-432.

Interpretive Summary: Cotton fibers undergo four overlapping developmental stages: fiber cell initiation, elongation, secondary wall biosynthesis, and maturation. The most extensively studied processes of fiber development are fiber elongation and cell wall biosynthesis, partly because fiber tissues are readily available in the later stages of development. During fiber elongation and secondary wall metabolism, the fiber cells elongate rapidly, synthesize secondary wall proteins, and show dramatic changes in cellular, physiological, and molecular features. Fiber elongation is coupled with rapid cell growth and expansion and constant synthesis of a large amount of cell metabolites and cell wall components such as cellulose. Conversely, fiber initiation is poorly understood. Approximately half a million fibers are produced per cotton boll, some forming 'fuzz' and some forming lint. although most epidermal cells do not become fiber initials. Initiation of an epidermal cell into fiber requires a change in cell fate, which is a fundamental biological process involving genetic, physiological, and developmental "switches". Fiber cell initiation and development is amazingly synchronized. Genetic mutations, genotypes, pollination, fertilization, and hormone regulation can affect the number of cells developing into fibers or alter fiber cell properties ('fuzz' vs. lint). However, it is unclear how these factors control gene expression changes that orchestrate the pattern and timing of fiber development. Genetic mutations, such as the naked seed N1N1 mutant, not only delay the onset of fiber cell initiation by ~12 hours, but also reduce the number of epidermal cells that develop into fibers. Furthermore, the fiber cell initials in the mutant are loosely attached to the surface of epidermal cells. The data suggest that the N1N1 mutation has wide-ranging effects in the early stages of fiber development. To gain a better understanding of the genetic regulation of the early stages of fiber development, we developed a pilot cotton oligo-microarray using ~1,400 cotton genes. The genes were selected using Arabidopsis orthologous gene families. Using microarray analysis, we compared gene expression profiles in young ovules 3 days after flowering in the naked seed dominant mutant (N1N1) and its isogenic wild type (Gossypium hirsutum L. cv. Texas Maker-1 or TM-1). Our data indicate that (1) using Arabidopsis orthologous genes is a valid approach to select cotton ESTs and full-length cDNAs for oligo design; (2) the N1N1 mutation affects an unknown 'master'-control gene or a set of target genes; and (3) fiber cell initiation may be controlled by homoeologous genes in several biological pathways involving chromatin structure, cell differentiation, cellular growth, and development. We are gaining insight into fiber initiation with the ultimate goal of determining the molecular switch that determines a cell's fate (fiber vs. non-fiber; lint vs. fuzz). Potential genetic modification of this master control would have significant impacts on fiber production.

Technical Abstract: Fiber development is a fundamental biological phenomenon, and cotton fiber is pivotal to the textile industry. However, the molecular basis of fiber cell initiation and elongation is poorly understood. Fibers are essentially maternally derived seed trichomes. Fiber initiation is a quasi-synchronous process in developing ovules that commences shortly after anthesis. We examined developmental processes of fiber cell initiation in the naked seed N1N1 mutant and the isogenic Texas Maker-1 (TM-1) line. The dominant mutation not only delayed the process of fiber cell initiation and cell elongation but also reduced the total number of fiber cells, resulting in short and sparsely distributed lint or "fuzz'. Changes of gene expression in the N1N1 mutant were analyzed using spotted cotton oligo-gene microarrays. Using the Arabidopsis orthologous genes, we selected and designed ~1,384 70-mer oligos from a subset of fiber genes encoding putative chromatin and transcription factors, cell cycle regulation, cell wall biosynthesis, signal transduction and stress-related pathways. The microarray data collected from four dye-swap experiments were analyzed using a linear model and by adjusting multiple comparisons. More than 110 candidate genes were up- or down-regulated in the young ovules of the fiberless mutant. The expression of a few candidate genes was examined in allotetraploid cotton (Gossypium hirsutum L.). Some homoeologous genes were equally affected in the mutant, whereas others were expressed differently between the mutant and wild type, suggesting that homoeologous genes in allopolyploids play an important role in the early stages of fiber development.