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United States Department of Agriculture

Agricultural Research Service

Title: On the Hunt for New Molecular Markers: Evaluating Soybean (Glycine Max) Ssr's for Cotton (Gossypium Hirsutum)

Authors
item Scheffler, Jodi
item Scheffler, Brian
item Ray, Jeffery
item Taliercio, Earl

Submitted to: Indian Society for Cotton Improvement
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 23, 2006
Publication Date: June 7, 2006
Citation: Scheffler, J.A., Scheffler, B.E., Ray, J.D., Taliercio, E.W. 2006. On the hunt for new molecular markers: evaluating soybean (glycine max) ssr's for cotton (gossypium hirsutum). Indian Society for Cotton Improvement. Vol 31: 79-87

Interpretive Summary: DNA markers are small pieces of DNA that can be different lengths depending on the genetic make-up of the plant. They have been developed for many plant species, and most of the major crops have a number of available DNA markers. A marker can have a characteristic length unique for a particular variety and several of these markers together can create a 'fingerprint' for identification of the variety. If a specific marker can be associated with a gene governing resistance to a specific pest or disease, it can be used as a diagnostic tool to identify plants with potential resistance. In cotton (Gossypium hirsutum), there is a severe shortage of publicly available markers. One promising source is to use markers already developed for plant species other than cotton as markers for cotton. To test this, 240 markers developed for soybean (Glycine max) were evaluated using a group of cotton lines containing one Pima variety and seven upland cotton lines. Of the 240 markers tested, 38 were unique for the Pima variety compared to the 7 upland cotton lines, and 19 produced unique markers between the upland cotton lines. This is especially important because most of the cotton grown worldwide is upland cotton and there is a severe shortage of markers that can distinguish between the numerous upland cotton varieties. A set of 45 new markers is described that are publicly available for use by other research groups and private companies to aid in variety identification and screening for disease and pest resistance.

Technical Abstract: Molecular DNA markers have been developed for a number of plant species, and most of the major crops have well established maps that combine a number of molecular and physical markers. Initially cotton (Gossypium hirsutum L.)lagged behind in developing these resources, however, recent coordinated efforts by cotton researchers should increase the number of markers publicly available. One promising source of markers is Simple Sequence Repeats (SSR). These markers can be used for a variety of purposes including diagnostic markers for resistance genes and creating 'fingerprints' for identification of cultivars and elite material. It should be possible to use SSR markers, developed for plants outside the genus Gossypium, as markers for cotton. To test this theory, 240 soybean (Glycine max) SSRs were evaluated on a DNA test panel containing one G. barbadense and seven G. hirsutum lines. The SSR markers were evaluated using two different methods, agarose gels and an ABI 3730 DNA Analyzer (a capillary based system). Out of the 240 SSR markers tested, 57 could distinguish at least one line from the other 7 lines, and 19 produced unique markers between the G. hirsutum lines. A set of 45 new markers is described that can be used by other research groups working with cotton.

Last Modified: 10/25/2014
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