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United States Department of Agriculture

Agricultural Research Service


Location: Cotton Fiber Bioscience Research

2012 Annual Report

1a. Objectives (from AD-416):
Objective 1: To characterize spatial, temporal, and/or genotypic variation in cotton fiber gene expression and the mechanisms leading to this variation to identify strategies for producing cotton fiber with enhanced or novel properties. Objective 2: Determine the consequences of environmental factors on cotton fiber development and develop tools to mitigate these effects.

1b. Approach (from AD-416):
Determine global patterns of genetic differences and gene expression in genotypes that differ in fiber properties. Determine global patterns of gene expression in cotton ovule cultures that are induced to express secondary cell wall CesA genes prematurely. Validate transcription factor candidates by functional genomic approaches in model systems and cotton. Compare the gene expression profiles from controls and cotton plants undergoing heat and/or drought stresses. Determine the effects of heat units on fiber strength and expression of genes specifically involved in the transition period. Evaluate the effects of drought on the fiber quality in a group of varieties (germplasm lines).

3. Progress Report:
Recombinant inbred lines (RILs) are made to increase the cotton germplasm gene base so that cotton breeders will have the maximum available genes and traits to work with in cotton germplasm improvement for any trait of interest. The 550 RILs derived from random mating of 11 cotton varieties demonstrated a wide range of variations in fiber quality and yield. ARS scientists at New Orleans, LA, analyzed 275 RILs with 798 DNA molecular markers. The RILs were planted in Mississippi in 2009-2012 to collect yield and fiber data. We are analyzing the associations between molecular markers and fiber quality traits. Future work will be to validate the marker-fiber trait associations using the remaining 275 RILs, and utilize the markers in breeding. Cotton hybrids were developed by a series of crosses and chromosome doubling using upland cotton cultivar SG747 and three diploid (double set of chromosomes)cotton species. Although Gossypium amourianum is fiberless, it is a major contributor to fiber strength when introgressed into upland cotton resulting in an 80 to 146% increase in strength. Pollens from synthetic tetraploid (four sets of chromosomes) hybrid plants were crossed with cotton varieties SG747 plants in a greenhouse. In FY 12, ARS scientists at Stoneville, MS and New Orleans, LA, planted F2 progeny in Stoneville, MS, to evaluate the segregation of fiber strength. In FY 11, ARS scientists at New Orleans, LA, identified one DNA marker NAU3991 that was completely co-segregated with the Li2 gene. In FY 12, we screened a bacterial artificial chromosome (BAC) library using the NAU3991 gene as a probe, and identified 9 clones. One largest clone was sequenced. The clone of 160 kilo base pairs (kb) was from the chromosome 13, while the 130 kb clone was from chromosome 18 that harbors the Li2 gene. Many single nucleotide polymorphisms (SNPs) which can be used as DNA markers were identified. Currently, we are analyzing 50 SNPs in a 400 progeny of F2 population to confirm the linkage between the markers and the Li2 gene. The overall goal is to clone the Li2 gene and understand the mechanism that will enable us to manipulate the fiber length. Gene expressions between two cotton lines, TM-1 and its near isogenic (almost identical) immature mutant were compared using ribonucleic acid (RNA) sequencing techniques. Genes related to fiber fineness and maturity were differentially expressed between these two lines. Next step will be to verify the identified genes using a technique called real-time quantitative polymerase chain reaction (RT-qPCR).

4. Accomplishments

Review Publications
Fang, D.D., Stetina, S.R. 2011. Improving Cotton (Gossypium hirsutum L.) Plant Resistance to Reniform Nematodes by Pyramiding Ren1 and Ren2. Plant Breeding. 130:673-678.

Hinchliffe, D.J., Turley, R.B., Naoumkina, M.A., Kim, H.J., Tang, Y., Yeater, K.M., Li, P., Fang, D.D. 2011. A combined functional and structural genomics approach identified an EST-SSR marker with complete linkage to the Ligon lintless-2 genetic locus in cotton (Gossypium hirsutum L.). Biomed Central (BMC) Genomics. 12:445.

Han,, X.Y., Xu, X.Y., Fang, D.D., Zhang, T.Z., Guo, W.Z. 2012. Cloning and expression analysis of novel Aux/IAA family genes in Gossypium hirsutum. Gene. 503:83-91.

Kim, H.J., Triplett, B.A., Zhang, H., Lee, M., Hinchliffe, D.J., Li, P., Fang, D.D. 2012. Cloning and characterization of homeologous cellulose synthase catalytic subunit 2 genes from allotetraploid cotton (Gossypium hirsutum L.). Gene. 494(2):181-189.

Last Modified: 10/18/2017
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