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Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal Publication Acceptance Date: 9/15/2014 Publication Date: 12/5/2014 Citation: Islam, M.S., Thyssen, G.N., Jenkins, J.N., Fang, D.D. 2014. Detection, validation, and application of genotyping-by-sequencing based single nucleotide polymorphisms in upland cotton. The Plant Genome. 8(1):1-10. Interpretive Summary: DNA markers are useful to tag genes controlling agronomic traits such as yield. The cultivated Upland cotton is a tetraploid (having four sets of chromosomes) plant originated from a cross between two diploid species about 1-2 million years ago. As a result, the genetic base of the Upland cotton is very low, and identification of polymorphic DNA markers within the cotton species (Gossypium hirsutum) is very difficult. Genotyping by sequencing (GBS) is a rapid way to identify single nucleotide polymorphism (SNP) markers; however, these SNPs may be specific to the sequenced cotton lines. In this research, we selected 11 diverse cultivars and their random-mated recombinant inbred progeny for SNP marker development via GBS. Two different GBS methodologies were used by Data2Bio, LLC, and the Institute for Genome Diversity, at Cornell University, to identify 4441 and 1176 polymorphic SNPs with minor allele frequency of =0.1, respectively. We further filtered the SNPs and aligned their sequences to the G. raimondii genome. We were able to use homeologous SNPs to assign 1071 SNP loci to the At sub-genome and 1223 to the Dt sub-genome. These filtered SNPs were located in genic regions about twice as frequently as expected by chance. We tested 111 of the SNPs in 154 diverse Upland cotton lines which confirmed the utility of the SNP markers developed in such approach. Not only were the SNPs identified in the 11 cultivars present in the 154 cotton lines, no two cultivars had identical SNP genotypes. We conclude that GBS can be easily used to discover SNPs in Upland cotton which can be converted to functional genotypic assays for use in breeding and genetic studies. Technical Abstract: The presence of two closely related sub-genomes in the allotetraploid Upland cotton (Gossypium hirsutum L.) combined with a narrow genetic base of the cultivated varieties has hindered the identification of polymorphic genetic markers and their utilization in improving this important crop. Genotyping by sequencing (GBS) is a rapid way to identify single nucleotide polymorphism (SNP) markers; however, these SNPs may be specific to the sequenced cotton lines. Our objective was to obtain a large set of polymorphic SNPs with broad applicability to the cultivated cotton germplasm. We selected 11 diverse cultivars and their random-mated recombinant inbred progeny for SNP marker development via GBS. Two different GBS methodologies were used by Data2Bio, LLC, and the Institute for Genome Diversity, at Cornell University, to identify 4441 and 1176 polymorphic SNPs with minor allele frequency of =0.1, respectively. We further filtered the SNPs and aligned their sequences to the G. raimondii genome. We were able to use homeologous SNPs to assign 1071 SNP loci to the At sub-genome and 1223 to the Dt sub-genome. These filtered SNPs were located in genic regions about twice as frequently as expected by chance. We tested 111 of the SNPs in 154 diverse Upland cotton lines which confirmed the utility of the SNP markers developed in such approach. Not only were the SNPs identified in the 11 cultivars present in the 154 cotton lines, no two cultivars had identical SNP genotypes. We conclude that GBS can be easily used to discover SNPs in Upland cotton which can be converted to functional genotypic assays for use in breeding and genetic studies. |
