Location: Cotton Fiber Bioscience Research
2021 Annual Report
Objectives
1. Use genome-wide association analysis to identify genes and molecular markers that are positively associated with cotton fiber quality and yield traits, and work with breeders to evaluate their effectiveness for simultaneous improvement of fiber quality and yield in diverse genetic backgrounds.
1.A. Use genome-wide association analysis to identify genes and molecular markers that are associated with cotton fiber quality and yield trait QTL.
1.B. Validate the stability and transferability of fiber QTL in diverse genetic backgrounds and work with breeders to evaluate their effectiveness for simultaneous improvement of fiber quality and yield.
2. Use short fiber mutants to evaluate cotton fiber elongation to discover and characterize biochemical pathways and genes controlling fiber elongation.
3. Use cotton mutants to determine impacts of genes and environment on cotton fiber maturity and fineness.
Approach
Fiber quality and yield are controlled by multiple genes that physically reside on chromosomes. Re-sequencing the genomes of a population of recombinant inbred lines (RILs) that differ in fiber quality and yield will identify genes or genomic regions controlling these traits.
Fiber quality is controlled by genes that physically reside on chromosomes. Selection of DNA markers physically adjacent to the superior alleles of these genes will enable breeders to more efficiently and effectively breed a cotton genotype with improved fiber quality.
Genes, by way of their products such as transcripts or proteins, affect fiber development and physical properties. Therefore, manipulation of these genes or their products will alter fiber development.
Biological processes affecting fiber maturity and fineness are regulated by genes, and are significantly affected by environmental factors. Manipulation of these genes will alter fiber maturity and fineness and may reduce the influence of environmental factors.
Progress Report
This is the third annual progress report of the Project 6054-21000-018-00D that started on May 29, 2018. Progress was made by ARS scientists at New Orleans, Louisiana on all three objectives and their sub-objectives, which fall under National Program 301, Component 1: Crop Genetic Improvement; Problem Statement 1A: Trait discovery, analysis and superior breeding methods; and Component 3: Crop Biological and Molecular Processes; Problem Statement 3A: Fundamental knowledge of plant biological and molecular processes.
Objective 1, ARS scientists at New Orleans, Louisiana analyzed the functions of two genes that are likely responsible for controlling fiber strength. In addition, ARS scientists at New Orleans, Louisiana used previously identified DNA markers to select cotton plants with stronger fiber in field breeding. Objective 2, ARS scientists at New Orleans, Louisiana identified the chromosomal location of a chemically-induced mutation that causes fuzzless seeds. Fuzz is short cotton fiber that strongly adheres to the seed surface. Objective 3, ARS scientists at New Orleans, Louisiana developed a method to measure cotton fiber maturity using a new instrument called CottonScope. Overall, ARS scientists at New Orleans, Louisiana research progress is in line with the Project Plan. Detailed progress for each objective is described below.
Objective 1, Functional analysis of genes responsible for the improved cotton fiber strength. Previously (as part of Objective 1), ARS Researchers in New Orleans, Louisiana identified one chromosome location (also called “locus” in genetics) that houses genes responsible for improved fiber strength. Since the last report, the same researchers analyzed the entire DNA sequences of 550 cotton lines differing in fiber strength, and identified three genes that are likely responsible for the stronger fiber. To further validate the function of these genes, ARS scientists at New Orleans, Louisiana reduced the expression of two genes using a technology called virus-induced gene silencing (VIGS). The VIGS-plants were grown in a greenhouse, and their fibers were collected and measured for strength. The gene Gh_A07G1731 was found by ARS scientists at New Orleans, Louisiana to play an important role in improving fiber strength. The next step will be to inset a superior version of this gene into a weak fiber cotton line to further confirm its ability in improving fiber strength.
Also in support of Objective 1, to aid breeders in the selection of quantitative traits (e.g., fiber strength), ARS researchers in New Orleans, Louisiana had previously identified a major locus on chromosome A07 that has great effect on improving fiber strength. The stability and transferability of this locus using 10 new populations derived from crossing cotton lines with different genetic backgrounds was also confirmed at that time. Since the last report, ARS researchers in New Orleans collaborated with a ARS cotton breeder in Stoneville, Mississippi to select cotton plants using the DNA markers associated with high fiber strength. Selection with additional assistance from DNA markers greatly improved fiber strength of the selected lines when comparing with trait selection alone. The selected cotton lines will be further evaluated by ARS scientists at New Orleans, Louisiana in multi-field experiments. Progress was made by ARS researchers at New Orleans, Louisiana under the agreement with Cotton Incorporated.
Previously (as part of Objective 2), a fuzzless cotton plant mutant that has normal long fiber but without short fuzz fiber was created after ARS scientists at New Orleans, Louisiana treated cotton seeds with a mutagenic chemical reagent. Fuzz is short fiber that strongly adheres to the seed surface. Fuzz is considered as an inferior trait because more energy is required to gin a cotton variety with heavy fuzz fibers. Since the last report, ARS researchers in New Orleans, Louisiana crossed the mutant with a normal cotton line, and evaluated the fiber quality properties of 602 progeny offsprings. It was concluded by ARS researchers at New Orleans, Louisiana that the fuzzless phenotype is controlled by a single recessive locus, and the fuzzless mutation locus was located on chromosome D04. In this region seven genes showed expression difference between the fuzzless mutant and normal cotton. Future research by ARS scientists at New Orleans, Louisiana will be needed to identify candidate gene(s) responsible for the fuzzless phenotype.
Also in support of Objective 2, ARS researchers in New Orleans, Louisiana used a short fiber mutant called Ligon lintless-2 (Li2) to study how cotton fiber elongates. Li2 is a naturally occurring cotton mutant that produces very short lint fiber. What causes the Li2 short fiber phenotype is unknown. Previously ARS researchers in New Orleans, Louisiana located the mutation locus on the chromosome D13. Recently, ARS researchers at New Orleans, Louisiana observed a 177 kilobase (kb) deletion and a 221 kb duplication positioned as a tandem inverted repeat in the mutant as compared to a regular cotton line. ARS researchers at New Orleans, Louisiana identified the gene encoding RanBP1 that is located at junction of the duplicated region as the causative gene for the short fiber phenotype in the Li2 mutant. The RanBP1 is a part of the complex that transfers molecules between different compartments of a cell. Deficiency of RanBP1 protein disrupts transport of molecules and consequently prevents elongation of cotton fibers. This discovery provides the knowledge about cotton fiber development.
In order to efficiently characterize fiber wall thickness and as part of Objective 3, a traditional microscopic method was compared by ARS reseachers at New Orleans, Louisiana with quicker, less labor-intensive method using an instrument called CottonScope. Using the two methods, ARS researchers in New Orleans, Louisiana measured a large number of fiber samples representing a broad range of known maturities. It was determined by ARS researchers that the immature fiber content values obtained from both methods were highly correlated, but CottonScope method was five times faster. ARS reseachers conclude that a CottonScope will be useful for cotton scientists to evaluate fiber maturity variations within-and among- large number of samples for future genetic analysis. Progress was made by ARS researchers under the agreement with Cotton Incorporated.
Also in support of Objective 3, ARS researchers in New Orleans, Louisiana made progress to validate a genetic locus related to fiber maturity. ARS researchers at New Orleans, Louisiana identified a group of DNA markers on chromosome A13 that are potentially associated with immature fiber content. Using this information, ARS researchers crossed two cotton lines that differed in fiber maturity and DNA marker profile in the genomic region of interest. The resulting progeny plants were grown in a field by ARS researchers to collect fiber samples and will be evaluated for fiber maturity using a CottonScope, and the DNA markers will be further investigated to see if they can be used in practical breeding.
Accomplishments
1. Release of seven upland Cotton lines with superior fiber strength and/or length. ARS scientists at New Orleans, Louisiana, believe High quality (stronger, longer and finer) cotton fiber commands premium price, and brings extra profit to farmers. Yet high cotton yield and superior quality do not normally go together and breaking this negative relationship has been a major goal in world-wide cotton breeding programs. In order to explore options, ARS researchers in Starkville, Mississippi, first used a technique called random-mating to create a unique cotton population consisting of 550 lines. Later, ARS researchers in New Orleans, Louisiana, used this population to identify DNA markers associated with fiber quality traits especially strength and length. The researchers in New Orleans used both DNA markers and field data to have selected seven cotton lines showing improved fiber strength and /or length. They have acceptable yield and other agronomic traits when compared with their parents. In 2021, these seven cotton lines were released to the public as novel materials for future cotton varietal improvement.
Review Publications
Fang, D.D., Zeng, L., Thyssen, G.N., Delhom, C.D., Bechere, E., Jones, D.C., Li, P. 2021. Stability and transferability assessment of the cotton fiber strength QTL qFS-c7-1 on chromosome A07. The Crop Journal. 9(2):380-386. https://doi.org/10.1016/j.cj.2020.06.016.
Naoumkina, M.A., Thyssen, G.N., Fang, D.D., Li, P., Florane, C.B. 2020. Elucidation of sequence polymorphism in fuzzless-seed cotton lines. Molecular Genetics and Genomics. 296(1):193–206. https://doi.org/10.1007/s00438-020-01736-z.
Abdelraheem, A., Thyssen, G.N., Fang, D.D., Jenkins, J.N., McCarty, J.C., Wedegaertner, T., Zhang, J. 2020. GWAS reveals consistent QTL for drought and salt tolerance in a MAGIC population of 550 lines derived from intermating of 11 Upland cotton (Gossypium hirsutum) parents. Molecular Genetics and Genomics. 296(1):119-129. https://doi.org/10.1007/s00438-020-01733-2.
Naoumkina, M., Thyssen, G.N., Fang, D.D., Bechere, E., Li, P., Florane, C.B. 2021. Mapping-by-sequencing the locus of EMS-induced mutation responsible for tufted-fuzzless seed phenotype in cotton. Molecular Genetics and Genomics. https://doi.org/10.1007/s00438-021-01802-0.
