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United States Department of Agriculture

Agricultural Research Service

Research Project: COTTON GENOMICS AND GENETIC ANALYSIS

Location: Crop Germplasm Research

Title: Sampling nucleotide diversity in cotton

Authors
item Van Deynze, Allen -
item Stoffel, Kevin -
item Lee, Mike -
item Kozik, Alexander -
item Wilkins, Thea -
item Cantrell, Roy -
item Yu, John
item Kohel, Russell
item Stelly, David -

Submitted to: Biomed Central (BMC) Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 20, 2009
Publication Date: October 20, 2009
Citation: Van Deynze, A., Stoffel, K., Lee, M., Wilkins, T.A., Kozik, A., Cantrell, R.G., Yu, J., Kohel, R.J., Stelly, D.M. 2009. Sampling nucleotide diversity in cotton. BMC Plant Biology. 9:Article 125.

Interpretive Summary: DNA markers have been shown to be useful in accelerating the transfer of novel traits into elite backgrounds. The vast majority of markers useful in cotton breeding are as simple sequence repeat (SSR) markers. Informative, abundant, high-throughput markers associated with genes such as single nucleotide polymorphisms (SNPs) or insertion/deletions (indels) are desirable for both breeding and genetic analyses. This study reports a strategy to efficiently identify and characterize SNP markers that are useful to manipulate and transfer novel alleles to breeding germplasm in cotton. SNP and indel diversity was characterized for 270 single-copy polymorphic loci in cotton. Diversity was characterized in a broad set of 24 breeding lines and exotic lines representing a standard germplasm panel. A moderate amount of variation associated with genes exists in breeding germplasm at the nucleotide level. Distribution of SNP markers in the cotton genome was characterized among the 26 chromosomes. The study demonstrates that sufficient SNP diversity exists in cotton populations for genetic and breeding studies and it can be efficiently assayed.

Technical Abstract: Informative, abundant, high-throughput markers associated with genes such as SNPs or insertion/deletions (indels) are desirable for both breeding and genetic analyses. Expressed genes are available as templates to study variation. In G. arboreum, 24,597 non-redundant transcripts are available; with 27,355 in G. raimondii; and 63,138 in G. hirsutum. The current report describes a strategy to efficiently identify and characterize SNP markers that are useful to manipulate and transfer novel alleles to breeding germplasm in cotton. Different DNA templates were evaluated for their specificity to amplify single-copy loci, and polymorphism within and among species, with emphasis on cultivated cotton. We demonstrate that single-copy loci can be efficiently amplified in cotton despite redundancy conferred by its allopolyploid origin, and that they can be mapped to specific genomes. In this research, SNP and indel diversity is characterized for 270 single-copy polymorphic loci in cotton. The strategy for SNP discovery is described to pre-screen loci for copy number and polymorphism. Diversity was characterized in a broad set of breeding lines and exotic lines representing a standard germplasm panel indicating that G. barbadense is much more diverse than G. hirsutum. Our data also indicate that the A and D genomes in both diploid and tetraploid cotton remain distinct from each other such that homoeologs can be distinguished.

Last Modified: 9/20/2014
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