ABSTRACTCompetition with manmade fibers has increased focus on upland cotton (Gossypium hirsutum L.) fiber quality, especially upper half mean length (FL), for industry stakeholders and breeders. The purpose of this study was to characterize the effect of qFL‐Chr.25, a quantitative trait locus (QTL) introgressed from G. barbadense L. originally identified in ‘Sealand 883’. The QTL was deployed within four genetic backgrounds: Acala SJ4, Paymaster HS26, Deltapine 50 (DP 50), and Georgia 2004089 (GA089), each representing the gene pools of the major US cotton‐growing regions: the US Southwest, Texas High Plains, Mississippi Delta, and US Southeast, respectively. In highly related bulked sister lines (BSLs), the effect of qFL‐Chr.25 was significant in the DP 50 (1.4 mm) and GA089 (1 mm) backgrounds in trials grown in Tifton, GA, in 2014 and 2015. In multilocation trials planted across the Cotton Belt in 2011 of 25 lines from each of the four backgrounds carrying the G. barbadense allele and 25 without the introgressed allele, FL of the QTL(+) lines were numerically higher than the QTL(−) lines by 0.9 mm, though not statistically significant. Recombinant genotypes recovered from the Paymaster HS26 and GA089 backgrounds, and development of additional simple sequence repeat (SSR) markers within the QTL region, allowed further refinement of the qFL‐Chr.25 region's boundaries from ∼2.2 to 0.8 Mb. Although variable effects were seen from this QTL, observation in a more isogenic state such as the BSLs and recombinant lines made the effect of the QTL more apparent. Incorporation of this QTL into breeding programs aided by these newly developed SSR markers should help in the utilization of this introgression to improve cotton fiber quality.

Evidence that supports a relation between AOX expression and improvement in plant height, internode length, and total leaf area under cool temperature is shown. Cell expansion and elongation appear to be enhanced when AOX expression was increased.

Cotton exhibits moderately high vegetative tolerance to water-deficit stress but lint production is restricted by the available rainfed and irrigation capacity. We have described the impact of water-deficit stress on the genetic and metabolic control of fiber quality and production. Here we examine the association of tentative consensus sequences (TCs) derived from various cotton tissues under irrigated and water-limited conditions with stress-responsive QTLs. Three thousand sixteen mapped sequence-tagged-sites were used as anchored targets to examine sequence homology with 15,784 TCs to test the hypothesis that putative stress-responsive genes will map within QTLs associated with stress-related phenotypic variation more frequently than with other genomic regions not associated with these QTLs. Approximately 1,906 of 15,784 TCs were mapped to the consensus map. About 35% of the annotated TCs that mapped within QTL regions were genes involved in an abiotic stress response. By comparison, only 14.5% of the annotated TCs mapped outside these QTLs were classified as abiotic stress genes. A simple binomial probability calculation of this degree of bias being observed if QTL and non-QTL regions are equally likely to contain stress genes was P (x ≥ 85) = 7.99  × 10−15. These results suggest that the QTL regions have a higher propensity to contain stress genes.

The complex genetic and environmental control of lint fiber yield and quality of cotton has long motivated interest in whether information from genetically-simpler trichome variations might contribute knowledge salient to cotton improvement. To investigate this question, from 3164 M5 lines resulting from EMS mutagenesis of two Gossypium hirsutum breeding lines, TAM 94L25 and Acala 1517-99, 106 lines with leaf and stem trichome variations and 55 control lines were further studied to investigate associations between trichome variation and lint fiber development. Although only weak correlation was found between stem/leaf trichome and fiber traits, we still found that among nine fiber traits measured in replicated trials, lines with mutations affecting stem trichome development had significant alterations for seven traits in the TAM 94L25 mutants, and six in the Acala 1517-99 mutants. While the small number of leaf trichome mutants found offered only minimal statistical power to resolve differences, mutant lines had significant alterations for three of the nine traits in the TAM 94L25 mutants, and two in the Acala 1517-99 mutants. In summary, mutants in leaf and/or stem trichome development often have altered lint fiber characteristics, supporting the hypothesis that there is considerable overlap in the sets of genetic factors acting in the development of these analogous organs. Moreover, visual selection of trichome mutants may be an effective screen to identify potential new alleles affecting lint fiber development.

Genetic improvements for many fiber traits are obtained by mutagenesis of elite cottons, mitigating genetic uniformity in this inbred polyploid by contributing novel alleles important to ongoing crop improvement.

The Gossypium genus is used to investigate emergent consequences of polyploidy in cotton species; comparative genomic analyses reveal a complex evolutionary history including interactions among subgenomes that result in genetic novelty in elite cottons and provide insight into the evolution of spinnable fibres. A phylogenetic and genomic study of plants of the cotton genus Gossypium provides insights into the role of polyploidy in the angiosperm evolution, and specifically, in the emergence of spinnable fibres in domesticated cottons. The authors show that an abrupt five- to sixfold ploidy increase about 60 million years ago, and allopolyploidy reuniting divergent genomes approximately 1–2 million years ago, conferred a roughly 30-fold duplication of ancestral flowering plant genes in the 'elite' cottons G. hirsutum and G. barbadense compared to their presumed progenitor G. raimondii. Polyploidy often confers emergent properties, such as the higher fibre productivity and quality of tetraploid cottons than diploid cottons bred for the same environments1. Here we show that an abrupt five- to sixfold ploidy increase approximately 60 million years (Myr) ago, and allopolyploidy reuniting divergent Gossypium genomes approximately 1–2 Myr ago2, conferred about 30–36-fold duplication of ancestral angiosperm (flowering plant) genes in elite cottons (Gossypium hirsutum and Gossypium barbadense), genetic complexity equalled only by Brassica3 among sequenced angiosperms. Nascent fibre evolution, before allopolyploidy, is elucidated by comparison of spinnable-fibred Gossypium herbaceum A and non-spinnable Gossypium longicalyx F genomes to one another and the outgroup D genome of non-spinnable Gossypium raimondii. The sequence of a G. hirsutum AtDt (in which ‘t’ indicates tetraploid) cultivar reveals many non-reciprocal DNA exchanges between subgenomes that may have contributed to phenotypic innovation and/or other emergent properties such as ecological adaptation by polyploids. Most DNA-level novelty in G. hirsutum recombines alleles from the D-genome progenitor native to its New World habitat and the Old World A-genome progenitor in which spinnable fibre evolved. Coordinated expression changes in proximal groups of functionally distinct genes, including a nuclear mitochondrial DNA block, may account for clusters of cotton-fibre quantitative trait loci affecting diverse traits. Opportunities abound for dissecting emergent properties of other polyploids, particularly angiosperms, by comparison to diploid progenitors and outgroups.

Seventeen backcross-self families from crosses between two Gossypium hirsutum recurrent parent lines (CA3084, CA3093) and G. tomentosum were used to identify quantitative trait loci (QTLs) controlling fiber quality traits. A total of 28 QTLs for fiber quality traits were identified (P < 0.001), including four for fiber elongation, eight for fiber fineness, four for fiber length, four for fiber strength, six for fiber uniformity, one for boll weight, and one for boll number. Three statistically significant marker–trait associations for lint yield were found in a single environment, but need further validation. Two-way analysis of variance revealed one locus with significant genotype × family interaction (P < 0.001) for fiber strength and a second locus with significant genotype × environment interaction (P < 0.001) in the CA3084 background, and two loci with significant genotype × background interaction (P < 0.001) for the 28 common markers segregating in both of the two recurrent backgrounds. Co-location of many QTLs for fiber quality traits partially explained correlations among these traits. Some G. tomentosum alleles were associated with multiple favorable effects, offering the possibility of rapid genetic gain by introgression. Many G. tomentosum alleles were recalcitrant to homozygosity, suggesting that they might be most effectively deployed in hybrid cottons. DNA markers linked to G. tomentosum QTLs identified in the present study promise to assist breeders in transferring and maintaining valuable traits from this exotic source during Upland cotton cultivar development. This study also adds further evidence to prior studies indicating that the majority of genetic variation associated with fiber quality in tetraploid cotton traces to the D-subgenome from a diploid ancestor that does not produce spinnable fiber.

Growth, yield, and yield quality of cotton are greatly affected by water-deficit stress. We have identified the genes and associated metabolic pathways involved in the water-deficit stress response in leaf and root. Gene expression profiles were developed for leaf and root tissues subjected to slow-onset water deficit under controlled, glasshouse conditions. The water-deficit stress was characterized by leaf water potential of −23.1 bars for stressed tissue compared to −8.7 bars for fully-irrigated control plants and a corresponding decrease in net carbon assimilation to approximately 60% of the rates seen in the irrigated controls (30.3 ± 4.7 μmol CO2 m−2 s−1 compared to 17.8 ± 5.9 μmol CO2 m−2 s−1). Profiling experiments revealed 2,106 stress-responsive transcripts, 879 classified as stress-induced, 1,163 stress-repressed, and 64 showed reciprocal expression patterns in root and leaf. The majority of stress-responsive transcripts had tissue-specific expression patterns and only 173 genes showed similar patterns of stress responsive expression in both tissues. A variety of putative metabolic and regulatory pathways were identified using MapMan software and the potential targets for candidate gene selection and ectopic expression to alter these pathways and responses are discussed.

Revealing the genetic underpinnings of cotton productivity will require understanding both the prehistoric evolution of spinnable fibers, and the results of independent domestication processes in both the Old and New Worlds. Progress toward a reference sequence for the smallest Gossypium genome is a logical stepping-stone toward revealing diversity in the remaining seven genomes (A, B, C, E, F, G, K) that permitted Gossypium species to adapt to a wide range of ecosystems in warmer arid regions of the world, and toward identifying the emergent properties that account for the superior productivity and quality of tetraploid cottons. The greatest challenge facing the cotton community is not genome sequencing per se but the conversion of sequence to knowledge.

ABSTRACTElectron transport in plant cells inevitably results in the creation of reactive oxygen species (ROS) that can hinder metabolic processes and cause cellular damage. In spite of the gains additional antioxidants may impart to the cotton (Gossypium hirsutum L.) photosynthetic apparatus, single time point measurements on live plants have not reflected distinguishable phenotypes for key physiological measures. Transgene efficacy may also be quantified by measuring cumulative agronomic performance (lint yield and quality) under conditions that promote photorespiration and ROS production. To test this hypothesis, cotton lines constitutively expressing the ascorbate peroxidase (APX) or glutathione reductase (GR) protein were examined in field trials (2005, 2006, and 2007) under three different irrigation treatments. Yield, gin turnout, and 23 measures of fiber quality were assessed. Transgene (APX and GR) efficacy and in vitro culture effects were estimated by comparing a line's performance with the null and wild‐type checks based on an analysis of variance using a linear mixed model to estimate general least squares and variance components. Significant effects were observed in 18 traits. Despite no significant changes in fiber maturity, all GR and APX transgenic lines produced significantly finer fibers than the wild‐type. Fiber maturity is a problem in western Texas that affects most fiber quality measures especially the fineness measurement micronaire.

The most commonly used plant DNA isolation methods use toxic and hazardous chemicals ( phenol, chloroform), which require special equipment to minimize exposure and may limit their use in certain environments. Commercial DNA extraction kits are convenient and usually safe, but their availability to certain developing countries and high cost can be limiting, especially when handing a large number of samples and considering experiments with limited financial resources. Current reports on non-phenol/chloroform protocols have not thoroughly examined the quality and suitability of the DNA for studies that require high precision. A simple, economical and rapid method is presented to isolate high quality DNA from plant and fungal species. This method uses potassium acetate to remove proteins and polysaccharides in an SDS extraction buffer. Further DNA purification is achieved using a low salt CTAB treatment. This SDS/CTAB protocol was used to isolate high quality genomic DNA subject to restriction endonuclease digestion and AFLP analysis from both plant and fungi with minimum cost and health concerns.

Black root rot (BRR), incited by the soilborne pathogen Thielaviopsis basicola has the potential to cause significant economic loss in cotton ( Gossypium spp.) production. Cultivated tetraploids of cotton ( G. hirsutum and G. barbadense ) are susceptible although resistant types have been identified in a possible tetraploid progenitor, G. herbaceum . Genetic mapping was used to detect the chromosomal locations of quantitative trait loci (QTL) that confer resistance to the BRR pathogen. A population of F 2 individuals ( G. herbaceum × G. arboreum ) and F 2:3 progeny families were examined. Phenotypic variation between resistant and susceptible reactions could be explained partly by three QTL. The BRR5.1 , BRR9.1 , and BRR13.1 QTL each explained 19.1, 10.3 and 8.5% of the total phenotypic variation, respectively. The combination of all three in a single genetic model explained 32.7% of the phenotypic variation. Comparative analysis was conducted on significant QTL regions to deduce the cotton– Arabidopsis synteny relationship and examine the correspondence between BRR QTL and Arabidopsis pathogen defense genes. Totally 20 Arabidopsis synteny segments corresponded within one of three BRR QTL regions. Each synteny segment contains many potential Arabidopsis candidate genes. A total of 624 Arabidopsis genes, including 22 pathogen defense and 36 stress response genes, could be placed within the syntenic regions corresponding to the BRR QTL. Fine mapping is needed to delineate each underlying BRR R-gene and possible Arabidopsis orthologs. Research and breeding activities to examine each QTL and underlying genes in Upland cotton ( G. hirsutum ) are ongoing.

Despite rapidly decreasing costs and innovative technologies, sequencing of angiosperm genomes is not yet undertaken lightly. Generating larger amounts of sequence data more quickly does not address the difficulties of sequencing and assembling complex genomes de novo. The cotton ( Gossypium spp.)

QTL mapping experiments yield heterogeneous results due to the use of different genotypes, environments, and sampling variation. Compilation of QTL mapping results yields a more complete picture of the genetic control of a trait and reveals patterns in organization of trait variation. A total of 432 QTL mapped in one diploid and 10 tetraploid interspecific cotton populations were aligned using a reference map and depicted in a CMap resource. Early demonstrations that genes from the non-fiber-producing diploid ancestor contribute to tetraploid lint fiber genetics gain further support from multiple populations and environments and advanced-generation studies detecting QTL of small phenotypic effect. Both tetraploid subgenomes contribute QTL at largely non-homeologous locations, suggesting divergent selection acting on many corresponding genes before and/or after polyploid formation. QTL correspondence across studies was only modest, suggesting that additional QTL for the target traits remain to be discovered. Crosses between closely-related genotypes differing by single-gene mutants yield profoundly different QTL landscapes, suggesting that fiber variation involves a complex network of interacting genes. Members of the lint fiber development network appear clustered, with cluster members showing heterogeneous phenotypic effects. Meta-analysis linked to synteny-based and expression-based information provides clues about specific genes and families involved in QTL networks.