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The importance of cotton genomics research for the U. S. cotton industry

1.  Economic impact and seeking a competitive advantage:

World cotton commerce of about $20 billion annually is made possible by the unusual ability of certain members of the cotton genus (Gossypium) to produce single-celled, seed-borne, epidermal trichomes(lint fibers) that can reach as much as 5-6 cm in length. In the USA alone, cotton is typically grown on about 5 million hectares per year, more than all crops except maize, wheat, or soybean (USDA-NASS, 2002). The value of cotton fiber grown in the USA is typically about $6 billion/yr, while cottonseed oil and meal add another $500 million/yr.  Also, cotton fiber exports account for about $4 billion/yr of the US trade surplus (Meyer et al., 2005) and business revenue stimulated by this crop is estimated at about $120 billion (National Cotton Council,  To sustain these statistics, the US is increasingly reliant on global markets for sale of its cotton, where it must compete with highly uniform man-made fibers as well as with foreign-produced cottons, many of which are harvested and/or processed by hand.

2.  Two key factors important for achieving a stable competitive advantage:

Fiber Uniformity: Fiber uniformity and quality are increasingly important due to their global impact on textile manufacture, processing and end-product value.  Increased fiber uniformity will confer a competitive advantage for US cottons in the world market.  Improvements of fiber uniformity are likely to involve changes in plant architecture, boll distribution, fiber initiation, elongation, diameter, maturation, strength, and other traits.  These changes will be best made with knowledge gained from genomics-based trait genetic dissection, QTL definition, and functional genomic inquiries.  These research techniques begin by identifying the genes that influence these important traits and through generating an understanding of their effects and the dynamics of their expression during the critical periods for fiber development. These approaches are leading to an improved physiological understanding of fiber uniformity traits, their relationships to each other and to agricultural production.

Threats to yield stability: The US cotton gene pool is genetically impoverished as a result of at least four genetic bottlenecks.  All cottons cultivated in the USA are tetraploid, thought to have arisen in the New World about 1-2 million years ago as a result of an unusual hybridization event between an immigrant A-genome diploid genotype and an indigenous D-genome diploid.  Polyploid cottons are thought to be monophyletic, representing the first genetic bottleneck.  A second bottleneck was associated with the domestication of cotton from a small subset of the wild genotypes.  A third bottleneck was imposed by human sampling of tetraploid cotton genotypes from their center of diversity in Mexico and Central America, and spread northward into the USA, and also to China, India, Egypt, Australia, and other countries.  Finally, a fourth bottleneck results from the recent widespread use of transgenes in only a small number of genotypes.  Such low genetic diversity may have contributed to reduced yields that have been associated with a reduction in the plasticity of crops to respond to pathogens, infestations, climactic changes and agriculture practices.

Growing concern about genetic vulnerability of the cotton gene pool to a wide range of biotic and abiotic hazards is exemplified by recent investigation of trends in yield improvement.  A ‘Blue Ribbon Committee’ of public and private scientists convened by the National Cotton Council (Helms, 2000) determined that indeed, US cotton yields peaked in 1992 and by 1998 had reached a disturbing rate of decline of about 16.8 kg ha-1 yr-1 (3.3% annual rate). Accompanying this yield decline, year-to-year variations in yield were almost four times greater in the period from 1980–1998 than in 1960–1979.  This increased volatility in yield translates directly into higher risk for the grower. 

3.  Genomics research contributions: 

Building an understanding important to controlling fiber uniformity: Cotton is not only the world’s most important fiber plant and a mainstay of the US economy, but it has become a model for developmental and evolutionary studies. There is nothing in nature that resembles the long, strong, and fine fibers of modern cotton cultivars that have resulted from a long history of both natural and human-mediated selection from ancestors whose seeds bore much shorter, coarser and tightly adherent or non-spinnable lint. Ongoing research efforts are clarifying this evolutionary history and discovering the steps that were involved in transforming primitive trichomes to the economically important fibers of modern cotton cultivars. By studying the different stages in this morphological series, research efforts are generating unparalleled insights into the genes involved in evolutionary transformations of cotton fiber during species divergence, initial domestication and modern crop improvement. In addition, cotton is unique in the annals of plant domestication in that four different species were independently developed from different wild ancestors, two in the Old World, which are diploids, and two in the New World, which are allopolyploids. Thus the “experiment” of domestication has been replicated at two ploidy levels and on opposite sides of the globe by aboriginal peoples. This offers a marvelous opportunity to explore the comparative genetics of plant domestication and the extent to which parallel selection has led to convergent or parallel patterns of gene expression change.  These experimental investigations promise new insights into the comparative basis of fiber development, an essential component of understanding the processes that are important for controlling fiber uniformity.

Future research efforts will likely build upon the developed knowledge of critical genes and expression profiles with studies that compare the transcriptome, proteome, and metabolome of a range of cotton genotypes that differ in the uniformity of fiber physical properties and tolerance to stress. Common mechanisms for temporal and spatial regulation of these genes will need to be investigated and correlated with distinct fiber properties. From these studies, it will be possible to construct predictive models that correlate expression of fiber genes and/or pathways with particular fiber traits as a framework for the design and implementation of strategies for the genetic improvement of cotton fiber quality and stress tolerance.

Yield stability and genetic diversity: The past decade of genomics research has yielded a high-resolution cotton molecular map that has been linked to more than 400 QTLs, influencing 26 traits related to plant growth, development, and morphology, reproductive biology; fiber yield and quality, disease resistance and the preservation of productivity and quality under drought stress. At least six high quality BAC libraries exist, for G. barbadense, G. raimondii, G. arboreum, G. longicalyx, and two strains of G. hirsutum.  Genomic tools have been employed toward development of strategies for genetic improvement, analyses of genetic diversity and many other areas.  Research efforts focused on analyses of genetic diversity and the development of genomic resources to establish the context for diversity studies are particularly important for cotton.  This body of data and the improved genomics techniques are continually improving the molecular toolbox for cotton genomics research efforts to advance cotton germplasm. Researchers are fortunate that producers in the U.S. are receptive to cotton germplasm enhancement using genomic and biotechnological approaches. 


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