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ARS Home » Plains Area » Lubbock, Texas » Cropping Systems Research Laboratory » Plant Stress and Germplasm Development Research » Research » Publications at this Location » Publication #317681

Research Project: Enhancing Plant Resistance to Water-Deficit and Thermal Stresses in Economically Important Crops

Location: Plant Stress and Germplasm Development Research

Title: DNA sequences of Pima (Gossypium barbadense L.) cotton leaf for examining transcriptome diversity and SNP biomarker discovery

Author
item Ulloa, Mauricio
item Kottapalli, Pratibha - Texas Tech University
item Kottapalli, K. Rao - Texas Tech University
item Payton, Paxton
item Burke, John

Submitted to: National Center for Biotechnology Information (NCBI)
Publication Type: Other
Publication Acceptance Date: 8/20/2015
Publication Date: 10/3/2016
Citation: Ulloa, M., Kottapalli, P., Kottapalli, K., Payton, P.R., Burke, J.J. 2016. DNA sequences of Pima (Gossypium barbadense L.) cotton leaf for examining transcriptome diversity and SNP biomarker discovery. National Center for Biotechnology Information (NCBI). Genebank. SRA accession:SRP063349 and PRJNA 290525.

Interpretive Summary:

Technical Abstract: As an initial step to explore the transcriptome genetic diversity and to discover single nucleotide polymorphic (SNP)-biomarkers for marker assisted breeding within Pima (Gossypium barbadense L.) cotton, leaves from 25 day plants of three diverse genotypes were used to develop cDNA libraries. Using the next generation sequencing (NGS) Illumina MiSeq, 9,946,184 reads were obtained for Pima-S6 (PS6); 9,960,492 reads were obtained for Pima-S7 (PS7); and 8,963,102 reads were obtained for Pima 3-79 (P3-79). A total of 28.9 million reads (average read length of 138 bp) were generated by sequencing the cDNA libraries of these three genotypes. The de novo assembly of reads generated transcriptome sets of 26,369 contigs for PS6; 25,870 contigs for PS7; and 24,796 contigs for P3-79. A Pima leaf reference transcriptome was generated consisting of 42,695 contigs. Annotated contigs or transcripts revealed genes of major metabolic pathways that might explain the gene pool diversity of these Pima genotypes. Additionally, more than 10,000 single nucleotide polymorphisms (SNPs) were identified between genotypes. These sequence-reads will be deposited in GenBank (NCBI: http://www.ncbi.nlm.nih.gov). NGS data will provide additional insight into Pima transcriptome and will help us in identifying SNP-biomarkers for characterizing genetic diversity, genotyping, and eventually in breeding through marker-assisted selection.