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United States Department of Agriculture

Agricultural Research Service


Location: Coastal Plain Soil, Water and Plant Conservation Research

2012 Annual Report

1a. Objectives (from AD-416):
1) Develop genetic resources and cropping practices that increase cotton water-use efficiency. 2) Develop new cotton genetic resources with improved fiber quality, lint yield stability, and adaptation. 3) Develop management techniques for cotton grown with conservation tillage after a winter biofuel crop.

1b. Approach (from AD-416):
Basic genomic and applied research will be conducted on improving cotton water use efficiency. In this research, molecular techniques will be used to search for genes that may provide more tolerance to water-deficit stress. Field studies will be conducted to screen cotton germplasm for water-deficit stress tolerance and to determine how agronomic practices affect plant water status. Contemporary plant breeding methods will be used to develop and release high yielding germplasm lines with improved fiber quality. Germplasm combining ability studies as well as studies determining genetic mechanisms for improved fiber quality will be conducted to accelerate the germplasm development program. We will evaluate cotton production potential when double cropped with winter crops harvested for biofuels. Winter crop biomass and energy content, cotton seedling establishment, and cotton fertility needs will be assessed.

3. Progress Report:
Objective 1: We conducted two experiments to identify genes in cotton that are involved in plant water use. The first experiment focused on identifying the aquaporin genes. Aquaporin gene products are proteins in cell membranes that facilitate water movement in and out of cells. Our research identified 71 cotton aquaporin genes. The expression of some aquaporin genes depends on plant tissue types and/or soil water availability. The second experiment focused on identifying a broad set of genes that show expression patterns sensitive to soil water availability. Our research identified greater than 500 water sensitive genes. We anticipate that both research experiments will provide useful targets for the genetic improvement of water use efficiency in cotton. In research to address cropping practices under this objective, data were analyzed from a two-year study investigating how nitrogen fertilizer rate influences root hydraulic conductivity of four cotton genotypes. Experiments were conducted in Florence, South Carolina, and Stoneville, Mississippi. This preliminary analysis suggests that nitrogen does not play a large role in regulating whole root hydraulic conductance under field conditions. Objective 2: We are currently conducting two experiments with the ultimate goal of developing new cotton genetic resources with improved fiber quality, lint yield stability, and adaptation. The first experiment is evaluating the breeding combining ability of the high fiber quality and genetically diverse Pee Dee germplasm with cotton germplasm developed in numerous other U.S. cotton production areas. Analysis of two years of field data identifies specific Pee Dee germplasm lines that combine well with other U.S. cotton germplasm. This finding allows for the development of breeding offspring with high fiber quality and excellent lint yield potential. The second experiment is determining the genetic relationships between several germplasm sources of high fiber quality. A preliminary analysis of two years of field data suggests that these germplasm sources contain and transmit different genetic factors for high fiber quality that can be combined to further improve fiber quality. We anticipate that both research experiments will provide information and breeding populations to develop new cotton genetic resources with improved fiber quality, lint yield stability, and adaptation. Objective 3: Four cotton genotypes were evaluated in a field experiment to determine cotton productivity when grown following harvested winter biomass crops. Data are now being collected in the second year of that study. Data were also summarized from a two-year field study evaluating the fertilizer effectiveness of phosphorus recovered from swine wastewater when used in cotton following a rye winter biomass crop. The results suggest that recovered calcium phosphate can be an effective fertilizer for cotton.

4. Accomplishments
1. Changing the negative relationship between yield and fiber quality following 70 years of cotton breeding. After 70 years of cotton breeding activities, the Pee Dee cotton germplasm program has developed a unique and diverse collection of high fiber quality germplasm resources that continue to contribute to the development of current commercial cultivars. Using extensive field performance data collected over three years across four U.S. states, ARS researchers from Florence, South Carolina, estimated the changes in yield and fiber quality trait correlations within the Pee Dee cotton germplasm program over these 70 years. The research has two important implications for cotton breeders and producers. First, the research shows that the breeding methods used have substantially lessened the negative relationship between yield and fiber quality. Second, the research provides cotton breeders unique germplasm resources where the negative linkage between high yield and high fiber quality has been eliminated. The research is expected to help commercial companies develop high yield and high quality cultivars for farmers to grow and will facilitate a broadening of the genetic base for the development of new cultivars long into the future.

2. Identifying candidate genes for improving cotton’s performance under water deficit stress conditions. Water deficit stress is known to be a major inhibitor of economically sustainable cotton production systems. In this study, a single cultivar reported to be tolerant to water deficit stress was grown in the field under well-watered and water-limited conditions. We compared gene expression changes in below ground (root) and above ground (leaf) plant tissue following exposure to water deficit stress. In total, approximately 500 genes were identified with differential expression in response to water deficit stress. For many of the identified genes, tissue specific expression patterns (root, leaf, or both tissues) were identified. The DNA sequences of these genes were deposited in the GenBank gene sequence database where they are being made available to the scientific community. The genes identified in this report provide a vast collection of candidate genes for improving cotton’s water use efficiency and/or performance under water-limited conditions.

3. Fertilizer value of recovered phosphorus from animal manures. Many fields around large animal feeding operations in the Southeast U.S. have excessive soil phosphorus from land-applied animal manures. Previously, a method to recover phosphorus from animal waste in a concentrated form was developed by ARS at this laboratory. ARS scientists in Florence, South Carolina, field-tested the recovered phosphorus for its value as a fertilizer product. We found that the material can be processed into commercial-sized fertilizer pellets with relative ease. We also found that when it is land-applied as small particles (between 0.5 and 1.0 mm diameter), recovered phosphorus is effective as a fertilizer source. Since recovered phosphorus can be transported in concentrated form and recycled as plant fertilizer, adoption of this technology by animal producers will reduce the environmental impact of excessive phosphorus in soils around these animal farms. In addition, recycling manure phosphorus will lengthen the duration of the world’s finite supply of minable phosphorus.

Review Publications
Baenziger, P.S., Dweikat, I., Gill, K., Eskridge, K., Berke, T., Shah, M., Campbell, B.T., Ali, M.L., Mengistu, N., Mahmood, A., Auvuchanon, A., Yen, Y., Rustgi, S., Moreno-Sevilla, B., Mujeeb-Kazi, A., Morris, M.R. 2011. Understanding grain yield: It is a journey, not a destination. Czech Journal of Genetics and Plant Breeding. 47:S77-S84.

Ali, M.L., Baenziger, P.S., Ajlouni, Z.A., Campbell, B.T., Gill, K.S., Eskridge, K.M., Mujeeb-Kazi, A., Dweikat, I. 2011. Mapping QTL for agronomic traits on wheat chromosome 3A and a comparison of recombinant inbred chromosome line populations. Crop Science. 51:553-566.

Campbell, B.T., Chee, P.W., Lubbers, E., Bowman, D.T., Meredith Jr, W.R., Johnson, J., Fraser, D.E. 2011. Genetic improvement of the Pee Dee cotton germplasm collection following seventy years of plant breeding. Crop Science. 51:955-968.

Horn, P.J., Neogi, P., Tombokan, X., Ghosh, S., Campbell, B.T., Chapman, K.D. 2011. Simultaneous quantification of oil and protein in cottonseed by low-field time-domain nuclear magnetic resonance. Journal of the American Oil Chemists' Society. 88:1521-1529.

Campbell, B.T., Chee, P.W., Lubbers, E., Bowman, D.T., Meredith Jr, W.R., Johnson, J., Fraser, D.E., Bridges, W., Jones, D.C. 2012. Dissecting genotype × environment interactions and trait correlations present in the Pee Dee cotton germplasm collection following seventy years of plant breeding. Crop Science. 52:690-699.

Bauer, P.J., Szogi, A.A., Novak, J.M., Vanotti, M.B. 2012. Phosphorus recovered from swine wastewater as a fertilizer for cotton grown with conservation tillage. Journal of Cotton Science. 16:97-104.

Zeng, L., Meredith Jr, W.R., Campbell, B.T. 2010. Registration of four exotic germplasm lines derived from an introgressed population of cotton. Journal of Plant Registrations. 4:240-243.

Saha, S., Stelly, D.M., Raska, D.A., Wu, J., Jenkins, J.N., McCarty, Jr., J.C., Makamov, A., Gotmare, V., Abudurakhmonov, I., Campbell, B.T. 2012. Chromosome substitution lines: Concept, development and utilization in the genetic improvement of upland cotton. In: Abdurakhmoov, I.Y., editor. Plant Breeding. InTech. p. 107-128.

Park, W., Scheffler, B.E., Bauer, P.J., Campbell, B.T. 2012. Genome-wide identification of differentially expressed genes under water deficit stress in Upland cotton (Gossypium hirsutum L.). Biomed Central (BMC) Plant Biology. Available:

Kumar, P., Singh, R., Lubbers, E.L., Shen, X., Paterson, A.H., Campbell, B.T., Jones, D.C., Chee, P.W. 2012. Mapping and validation of fiber strength quantitative trait loci on chromosome 24 in Upland cotton. Crop Science. 52:1115-1122.

Last Modified: 2/23/2016
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