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Title: Lessons Learned and Challenges Ahead for Cotton Genome Mapping.

Author
item Ulloa, Mauricio
item Saha, Sukumar
item Yu, John
item Jenkins, Johnie
item Meredith Jr, William
item Kohel, Russell

Submitted to: World Cotton Research Conference Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 10/30/2007
Publication Date: 12/1/2008
Citation: Ulloa, M., Saha, S., Yu, J., Jenkins, J.N., Meredith Jr, W.R., Kohel, R.J. 2008. Lessons Learned and Challenges Ahead for Cotton Genome Mapping. World Cotton Res. Conf. (Proc) paper no. 1798.

Interpretive Summary: Recently developed DNA technology has allowed plant breeders to better understand and manipulate plant characteristics (or traits) that are under complex genetic control. Identification of genes controlling a specific trait, and understanding how those genes function in relation to other genes, provides the means to better manipulate desired traits in crop plants. An important advancement in DNA technology is the ability to use molecular markers as a tool for crop improvement. A molecular marker is a small piece of DNA that can be detected chemically. When a marker consistently occurs in association with a given plant trait, it is said to be linked, and its presence indicates the gene(s) responsible for the trait may also be present. In this paper we present an overview of the use of molecular markers in cotton improvement and challenges ahead. Before 1994 genetic linkage mapping in cotton relied on the linkage of desired traits to other characters that could be directly observed (morphological traits). Use of morphological linkages required the plants be grown to the desired stage (often crop maturity) before selections were made. Still, the cropping environment could influence plant development and thereby complicate the selection process. Since 1994, 27 major efforts to map the cotton genome (the sum of genetic material in the plant) have placed molecular markers on 26 linkage groups, often on specific chromosomes. The International Cotton Genome Initiative and the Cotton Marker Database have provided a means for researchers to share marker data, and to integrate their findings into common, or consensus, maps. Consensus maps, in turn, are facilitating efforts to expand genetic maps of use in cotton improvement. We conclude that molecular markers and linkage maps will be primary tools of cotton breeders in the next decade.

Technical Abstract: The goal of genetic linkage mapping is to discover genes for improving trait performance. The process of manipulating the cotton genome is complex because the cotton fibers (lint) used in textiles are derived from the seed trichomes (hairs) of four Gossypium species. In just over a decade, our understanding of the structure of the cotton genome has expanded tremendously. Prior to 1994, genetic linkage mapping in cotton was limited to linkage detection among morphological markers and the placement of those markers on chromosomes using cytogenetic stocks. Since then, approximately 27 major mapping efforts in Gossypium have emerged. In addition, PCR-based markers, such as microsatellites, have been placed on 26 cotton linkage groups/chromosomes. Over the past decade new tools have emerged (e.g., BAC physical mapping, differential display, microarrays, and SNPs), providing new avenues for gene discovery that circumvent some of the limitations of genetic linkage mapping. Global research efforts, such as the International Cotton Genome Initiative (ICGI) and Cotton Marker Database (CMD), have also provided opportunity for wide collaboration. However, difficulties have risen from the use of different electrophoretic systems (RFLP, gel systems, and dye-primers) for calling alleles on mapping populations. In addition, the need for standard nomenclature in naming molecular markers, as well as in identifying quantitative trait loci (QTL) in the cotton genome, continues to exist. Real gains in cotton improvement will require an unprecedented understanding of the molecular genetics of complex traits, and expanded genetic linkage maps that can be used to manipulate the cotton genome in ways that were previously inconceivable. Herein, we provided an overview of the progress, future, and challenges facing genetic mapping efforts in cotton.