Skip to main content
ARS Home » Southeast Area » New Orleans, Louisiana » Southern Regional Research Center » Cotton Fiber Bioscience Research » Research » Research Project #435004

Research Project: Molecular Characterization and Phenotypic Assessments of Cotton Fiber Quality Traits

Location: Cotton Fiber Bioscience Research

2022 Annual Report

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. 1.C.Develop and test DNA markers associated with cotton leaf roll dwarf virus resistance to enhance host plant resistance. 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.

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 fourth annual progress report of the Project 6054-21000-018-000D that started on May 29, 2018. Progress was made 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. Under Objective 1, ARS researchers at New Orleans, Louisiana, re-analyzed DNA sequence data of the previously characterized 550 Upland cotton recombinant inbred lines using the newly published cotton reference genome (a genome is the collection of all DNAs in a living organism), and conducted genome-wide association study for the fiber traits. In addition, we collected young fibers at various development stages from parents and a few progeny plants of a population containing DNA segments from Pima cotton. Under Objective 2, we obtained transgenic plants containing actin gene that affects fiber length and fineness. Under Objective 3, we studied the effects of environment factors such as high temperature on fiber development using a fiber mutant. Overall, our research progress is in line with the project plan. Detail progress for each objective is described below. Also in support of Objective 1, we sequenced the genomes of 180 recombinant inbred lines (RILs) of a population derived from crosses using 21 Upland cotton lines as parents. These 21 cotton lines contain portions of DNA from premium Pima cotton. Pima cotton exhibits superior fiber traits, but has a lower crop yield than Upland cotton. Breeders have long been searching for lines that combine the favorable attributes of both. We obtained DNA sequence data for all 180 RILs and 21 parents. Further, we sequenced the RNAs from developing cotton fiber cells at various development stages of the 21 parents. Currently, we are conducting genome wide association study to identify the Pima DNA regions and genomic locations responsible for fiber traits. Analysis of the RNA sequences data is ongoing, which is expected to reveal key gene networks and synergistic interactions between Upland cotton and Pima cotton genes. Combining analysis of the DNA and RNA sequencing data with measurements of fiber quality will result in a better understanding of cotton fiber bioscience and the development of genetic markers that will allow breeders to improve the quality of U.S. cotton varieties. Part of this progress was made under the agreement # 0000070312 with Cotton Incorporated. For Objective 2, we had previously identified an actin gene (GhACT_Li1) on chromosome D04 as the cause for the short fiber mutation in Ligon-lintless 1 mutant. Actin is an intracellular protein present in all plant and animal cells and plays a pivotal role in muscle contraction as well as in cell movements. To further understand how this actin gene affects other fiber quality attributes besides length, we overexpressed the actin gene through transformation (a process of inserting a target gene into another cotton cell artificially). Transgenic lines with excessive expression of actin showed reduction in fineness of cotton fibers. This knowledge may help breeders to improve the fineness of a cotton variety with coarse fiber in breeding. Also in support of Objective 2, we discovered a variant of an actin gene that profoundly impacts the length of cotton fiber. The organization of the cytoskeleton and secondary cell wall affect the length and strength of the individual fibers, and the quality of the end-use characteristics of yarn and textiles. Recently, we designed and built a vector for transformation of cotton that is proceeding through a cooperation with Texas A&M University Plant Biotechnology Center. This line is designed to fluorescently label the actin cytoskeleton in a transgenic plant. This will substantially simplify the observation of the organization of the cytoskeleton in developing fiber cells. Additionally, this line can be crossed with cotton strains with superior or inferior fiber traits and permit the cytoskeleton of the resulting lines to be easily investigated by fluorescent microscopy. As part of Objective 3, we studied the impacts of genes and environment on cotton fiber maturity. We compared how cotton immature fiber mutant and its wild type responded to heat stress. The immature fiber mutant produces thin-walled fibers while the wild type generates normal fibers with thick-walls. Under stress-free conditions, both mutant and the wild type showed the same photosynthetic performance. However, high temperature stress reduced photosynthesis more severely in the immature fiber mutant plant leaves by closing stomata disproportionately more than in the wild type, and consequently decreased maturity of fibers from a mutant plant. These findings provide insight into how the environmental stresses may involve in amplifying the immature fiber phenotype by meddling with photosynthetic activity. The pair of cotton lines differing in stress tolerance may be used in the future for studying the effect of global warming and climate changes on fiber maturity or understanding heat acclimation mechanisms of cotton plants. Part of this progress was made under the agreement # 0000070455 with Cotton Incorporated. Also in support of Objective 3, we obtained a transgenic cotton plant overly expressing the gene causing immature fiber in cooperation with University of North Texas with a financial support from Cotton Incorporated. Right now, we are growing it in a greenhouse in New Orleans for further evaluation. Another type of transgenic plants designed to suppress the immature fiber mutant gene by RNA interference are also being regenerated in Texas A&M University. Part of this progress was made under the agreement # 0000070455 with Cotton Incorporated. In an effort of improving cotton fiber maturity measurement method and identifying quantitative trait loci (QTL) responsible for fiber maturity as a part of Objective 3, we compared three methods including microscopic cross-sections, Advanced Fiber Information System, and Cottonscope that can measure average fiber maturity and immature fiber content. We found that the average fiber maturity represented a mixture of mature, immature, and severely immature fibers. The complex trait caused difficulties of identifying QTL accurately with genetic approaches. In contrast, the immature fiber content representing a single trait from severely immature fibers within a sample provided a reliable and sensitive way of identifying QTLs. Thus, the Cottonscope measurement of immature fiber content showed more reliability and efficiency over others and will be used in the future. Part of this progress was made under the agreement #0000070455 with Cotton Incorporated.

1. Rearrangement of chromosome DNA causes short cotton fibers. Fiber length is one of the most important quality attributes and cotton with longer fiber can demand premium price. Ligon-lintless 2 is a naturally occurring cotton mutant that produces very short fibers, but what causes the short fiber phenotype has been unknown until now. ARS researchers in New Orleans, Louisiana, discovered that a large structural rearrangement had occurred in the mutant on the chromosome called D13. As a result of the rearrangement, the transport of enzymes that cause fiber elongation is hindered. With this knowledge, we can now focus on increasing the transport of this enzyme in normal cotton, which in turn may cause longer fibers in cotton. This may be accomplished with traditional breeding or biotechnological tools.

Review Publications
Kim, H.J., Kato, N., Ndathe, R., Thyssen, G.N., Jones, D.C., Ratnayaka, H. 2021. Evidence for thermosensitivity of the cotton (Gossypium hirsutum L.) immature fiber (im) mutant via hypersensitive stomatal activity. PLoS ONE. 16(12):e0259562.
Wang, M., Qi, Z., Thyssen, G.N., Naoumkina, M.A., Jenkins, J.N., McCarty, J.C., Xiao, Y., Li, J., Zhang, X., Fang, D.D. 2022. Genomic interrogation of a MAGIC population highlights genetic factors controlling fiber quality traits in cotton. Communications Biology. 5:60.
Pei, L., Huang, X., Liu, Z., Tian, X., You, J., Li, J., Fang, D.D., Lindsey, K., Zhu, L., Zhang, X., Wang, M. 2022. Dynamic 3D genome architecture of cotton fiber reveals subgenome-coordinated chromatin topology for 4-staged single-cell differentiation. Genome Biology. 23:45.
Kim, H.J., Delhom, C.D., Liu, Y., Jones, D.C., Xu, B. 2021. Characterizations of a distributional parameter that evaluates contents of immature fibers within and among cotton samples. Cellulose. 28:9023-9038.
Zhu, Y., Thyssen, G.N., Abdelraheem, A., Teng, Z., Fang, D.D., Jenkins, J.N., Mccarty Jr, J.C., Wedegaertner, T., Hake, K., Zhang, J. 2022. A GWAS identified a major QTL for resistance to Fusarium wilt (Fusarium oxysporum f. sp. vasinfectum) race 4 in a MAGIC population of Upland cotton and a meta-analysis of QTLs for Fusarium wilt resistance. Theoretical and Applied Genetics. 135:2297-2312.