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United States Department of Agriculture

Agricultural Research Service

Title: Wide-Cross Whole-Genome Radiation Hybrid (Wwrh) Mapping of Cotton (G. Hirsutum L.)

Authors
item Gao, Wenxiang - DEPT SOIL & CROP SCIENCES
item Chen, Jeffrey - DEPT SOIL & CROP SCIENCES
item Yu, John
item Raska, Dwaine - DEPT SOIL & CROP SCIENCES
item Kohel, Russell
item Womack, James - DEPT VETERINARY PATH
item Stelly, David - DEPT SOIL & CROP SCIENCES

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 9, 2003
Publication Date: October 9, 2003
Citation: Gao, W., Chen, J., Yu, J., Raska, D., Kohel, R.J., Womack, J.E., Stelly, D.M. 2003. Wide-cross whole-genome radiation hybrid (WWRH) mapping of cotton (G. hirsutum L.). Genetics. 167:1317-1329.

Interpretive Summary: Radiation hybrid mapping is a new technology to map genes. In contrast to natural recombination, radiation-induced recombination frequencies and map resolution can be modulated by modifying radiation doses. However, this mapping technology has been used widely in animals. Our study of cotton is the first application of such a technology on plants, and thus it provide a new possibility to complement plant genome mapping. After preliminary observations on seed production, germination, and genotyping with DNA markers, gamma-irradiation (5-krad) of cotton flowers was chosen for more detailed examination of 101 F1 hybrids derived from a cross between TM-1 x 3-79, two cotton parents. About 93 treated hybrids were genotyped with 102 DNA markers. Sixteen groups were obtained from the mapping. The findings indicate that the approach complements traditional linkage mapping efforts and it can be extended to other plants.

Technical Abstract: Radiation hybrid mapping has been used widely to help describe genomes of humans and certain other animals, but not plants. Whereas radiation hybrid mapping of animal genomes has relied on in vitro radiation hybrid cell lines that comprise individual radiation hybrid panels targeted at specific chromosomes or whole genomes, we created an in vivo "wide-cross whole-genome radiation hybrid" (WWRH) panel from the genome of cotton (Gossypium hirsutum L.). We used G. barbadense egg cells (n = 26) to rescue chromosomal segments of G. hirsutum sperm nuclei. Genomes of G. hirsutum (n = 26) were segmented by 1.5, 5, 15 or 30 krad g-irradiation. After preliminary observations on seed production, germination and genotyping with 33 SSR markers from four chromosomes and one unidentified linkage group, we selected the 5-krad treatment for more detailed examination. To characterize retention, we screened 101 5-krad WWRHs with eight micro-satellite markers in cotton linkage group 9 (LG-9). Marker retention frequencies from the 5-krad g-ray treatment were relatively high (87% - 94%), but results were nevertheless informative. For example, SSR markers BNL0625 and BNL2805 had been co-localized in the traditional linkage map of LG-9, but were ordered by differential loss and retention among the WWRH plants. The marker-to-marker distance correlation coefficient between traditional linkage map and the WWRH map for LG-9 was 0.49. A 5-krad g-ray WWRH mapping panel (N = 93) was constructed and genotyped with 102 SSR markers. The program RHMAP was used to analyze the genotypic data. At LOD score four, 52 out of 102 SSR markers were resolved into 16 syntenic groups. Linkage groups LG-9 and LG-13 of the traditional linkage map were combined by WWRH mapping into one syntenic group by RHMAP two-point analysis. A WWRH map of this syntenic group was generated by maximum likelihood analysis using the RHMAP general retention model. Tests with monosomic and monotelodisomic hypoaneuploid interspecific hybrids confirmed the synteny and assigned both LG-9 and LG-13 to the short arm of chromosome 17. The WWRH mapping method also corrected the chromosome location of marker BNL4053 to the long arm of chromosome 9, instead of its previous assignment to chromosome 1 in the traditional linkage map. The correction was also confirmed by cytogenetic analysis. The findings indicate that WWRH mapping will work in cotton, and that the approach complements traditional linkage mapping, as well as cytogenetic methods. We anticipate that optimized retention frequencies for cotton WWRHs will require higher rates of chromosome breakage, and that the WWRH approach can be extended to genomes of some other plant taxa.

Last Modified: 10/24/2014
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