Cotton supplies a great majority of natural fiber for the global textile industry. The negative correlation between yield and fiber quality has hindered breeders’ ability to improve these traits simultaneously. A multi-parent advanced generation inter-cross (MAGIC) population developed through random-mating of multiple diverse parents has the ability to break this negative correlation. Genotyping-by-sequencing (GBS) is a method that can rapidly identify and genotype a large number of single nucleotide polymorphisms (SNP). Genotyping a MAGIC population using GBS technologies will enable us to identify marker-trait associations with high resolution. An Upland cotton MAGIC population was developed through random-mating of 11 diverse cultivars for five generations. In this study, fiber quality data obtained from four environments and 6071 SNP markers generated via GBS and 223 microsatellite markers of 547 recombinant inbred lines (RILs) of the MAGIC population were used to conduct a genome wide association study (GWAS). By employing a mixed linear model, GWAS enabled us to identify markers significantly associated with fiber quantitative trait loci (QTL). We identified and validated one QTL cluster associated with four fiber quality traits [short fiber content (SFC), strength (STR), length (UHM) and uniformity (UI)] on chromosome A07. We further identified candidate genes related to fiber quality attributes in this region. Gene expression and amino acid substitution analysis suggested that a regeneration of bulb biogenesis 1 (GhRBB1_A07) gene is a candidate for superior fiber quality in Upland cotton. The DNA marker CFBid0004 designed from an 18 bp deletion in the coding sequence of GhRBB1_A07 in Acala Ultima is associated with the improved fiber quality in the MAGIC RILs and 105 additional commercial Upland cotton cultivars. Using GBS and a MAGIC population enabled more precise fiber QTL mapping in Upland cotton. The fiber QTL and associated markers identified in this study can be used to improve fiber quality through marker assisted selection or genomic selection in a cotton breeding program. Target manipulation of the GhRBB1_A07 gene through biotechnology or gene editing may potentially improve cotton fiber quality.

Individual fiber strength is an important quality attribute that greatly influences the strength of the yarn spun from cotton fibers. Fiber strength is usually measured from bundles of fibers due to the difficulty of reliably measuring strength from individual cotton fibers. However, bundle fiber strength (BFS) is not always correlated with yarn strength since it is affected by multiple fiber properties involved in fiber-to-fiber interactions within a bundle in addition to the individual fiber strength. Molecular mechanisms responsible for regulating individual fiber strength remain unknown. Gossypium hirsutum near isogenic lines (NILs), MD52ne and MD90ne showing variations in BFS provide an opportunity for dissecting the regulatory mechanisms involved in individual fiber strength. Comprehensive fiber property analyses of the NILs revealed that the superior bundle strength of MD52ne fibers resulted from high individual fiber strength with minor contributions from greater fiber length. Comparative transcriptome analyses of the NILs showed that the superior bundle strength of MD52ne fibers was potentially related to two signaling pathways: one is ethylene and the interconnected phytohormonal pathways that are involved in cotton fiber elongation, and the other is receptor-like kinases (RLKs) signaling pathways that are involved in maintaining cell wall integrity. Multiple RLKs were differentially expressed in MD52ne fibers and localized in genomic regions encompassing the strength quantitative trait loci (QTLs). Several candidate genes involved in crystalline cellulose assembly were also up-regulated in MD52ne fibers while the secondary cell wall was produced. Comparative phenotypic and transcriptomic analyses revealed differential expressions of the genes involved in crystalline cellulose assembly, ethylene and RLK signaling pathways between the MD52ne and MD90ne developing fibers. Ethylene and its phytohormonal network might promote the elongation of MD52ne fibers and indirectly contribute to the bundle strength by potentially improving fiber-to-fiber interactions. RLKs that were suggested to mediate a coordination of cell elongation and SCW biosynthesis in other plants might be candidate genes for regulating cotton fiber cell wall assembly and strength.

Cotton fiber length is very important to the quality of textiles. Understanding the genetics and physiology of cotton fiber elongation can provide valuable tools to the cotton industry by targeting genes or other molecules responsible for fiber elongation. Ligon Lintless-1 (Li 1 ) is a monogenic mutant in Upland cotton (Gossypium hirsutum) which exhibits an early cessation of fiber elongation resulting in very short fibers (< 6 mm) at maturity. This presents an excellent model system for studying the underlying molecular and cellular processes involved with cotton fiber elongation. Previous reports have characterized Li 1 at early cell wall elongation and during later secondary cell wall synthesis, however there has been very limited analysis of the transition period between these developmental time points. Physical and morphological measurements of the Li 1 mutant fibers were conducted, including measurement of the cellulose content during development. Affymetrix microarrays were used to analyze transcript profiles at the critical developmental time points of 3 days post anthesis (DPA), the late elongation stage of 12 DPA and the early secondary cell wall synthesis stage of 16 DPA. The results indicated severe disruption to key hormonal and other pathways related to fiber development, especially pertaining to the transition stage from elongation to secondary cell wall synthesis. Gene Ontology enrichment analysis identified several key pathways at the transition stage that exhibited altered regulation. Genes involved in ethylene biosynthesis and primary cell wall rearrangement were affected, and a primary cell wall-related cellulose synthase was transcriptionally repressed. Linkage mapping using a population of 2,553 F2 individuals identified SSR markers associated with the Li 1 genetic locus on chromosome 22. Linkage mapping in combination with utilizing the diploid G. raimondii genome sequences permitted additional analysis of the region containing the Li 1 gene. The early termination of fiber elongation in the Li 1 mutant is likely controlled by an early upstream regulatory factor resulting in the altered regulation of hundreds of downstream genes. Several elongation-related genes that exhibited altered expression profiles in the Li 1 mutant were identified. Molecular markers closely associated with the Li 1 locus were developed. Results presented here will lay the foundation for further investigation of the genetic and molecular mechanisms of fiber elongation.

Cotton fiber maturity is an important factor for determining the commercial value of cotton. How fiber cell wall development affects fiber maturity is not well understood. A comparison of fiber cross-sections showed that an immature fiber (im) mutant had lower fiber maturity than its near isogenic wild type, Texas marker-1 (TM-1). The availability of the im mutant and TM-1 provides a unique way to determine molecular mechanisms regulating cotton fiber maturity.