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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 #309216
Title: Sequence composition of BAC clones and SSR markers mapped to Upland cotton chromosomes 11 and 21 targeting resistance to soil-borne pathogens

Author
item WANG, CONGLI - University Of California
item Ulloa, Mauricio
item SHI, XINYI - Chinese Academy Of Sciences
item YUAN, XIAOUHUI - Chinese Academy Of Sciences
item SASKI, CHRISTOPHERR - Clemson University
item Yu, John
item ROBERTS, PHILIP - University Of California

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/11/2015
Publication Date: 9/21/2015
Citation: Wang, C., Ulloa, M., Shi, X., Yuan, X., Saski, C., Yu, J., Roberts, P. 2015. Sequence composition of BAC clones and SSR markers mapped to Upland cotton chromosomes 11 and 21 targeting resistance to soil-borne pathogens. Frontiers in Plant Science. 6:791.

Interpretive Summary: The goal of this study was to map and to identify marker-genes on cotton chromosomes 11 and 21 responsible for resistance to root knot nematode (RKN) and Fusarium wilt (FOV). RKN and FOV cause yield losses in cotton. Interest in these two chromosomes (11 and 21) derived from the discovery of resistance (R) or pathogen-induced R genes involved in disease resistance. Simple sequence repeat (SSR) marker-sequences and DNA bacterial artificial chromosome (BAC) clones from a BAC library developed from the Upland cotton cultivar Acala Maxxa were examined. Analyses and comparisons of sequences against published databases revealed the presence of DNA regions similar to known resistance genes. BAC DNA sequences revealed the presence of genes that encode proteins containing a nucleotide-binding site (NBS) and C-terminal leucine-rich repeats (LRRs), a major class of disease R genes. Sequence information obtained through these studies can be used to develop improved tools to discover additional resistance genes, and to speed efforts to incorporate resistance genes into germplasm and breeding lines.

Technical Abstract: Genetic and physical framework mapping in cotton (Gossypium spp.) were used to discover putative gene sequences involved in resistance to common soil-borne pathogens. Chromosome (Chr) 11 and its homoeologous Chr 21 of Upland cotton (G. hirsutum) is a focus for discovery of resistance (R) or pathogen-induced R (PR) genes underlying QTLs involved in response to root-knot nematode [RKN (Meloidogyne incognita)], reniform nematode [REN (Rotylenchulus reniformis)], Fusarium wilt [FOV) (Fusarium oxysporum f.sp. vasinfectum)], Verticillium wilt [VW (Verticillium dahliae)], and black root rot [BRR (Thielaviopsis basicola)] resistance. Simple sequence repeat (SSR) markers and bacterial artificial chromosome (BAC) clones from a BAC library developed from the Upland cotton cultivar Acala Maxxa were mapped on Chr 11 and Chr 21. DNA sequence through Gene Ontology (GO) of 99 of 256 Chr 11 and 109 of 239 Chr 21 previously mapped SSRs revealed response elements to internal and external stimulus, stress, signaling process, and cell death. The reconciliation between genetic and physical mapping of gene annotations from new DNA sequences of 20 BAC clones (10 on Chr 11: 1,129,445bp and 10 on Chr 21: 974,552bp) revealed 467 (Chr 11) and 285 (Chr 21) G. hirsutum putative coding sequences (evalue equal or less than 1e-5, identity equal or more than 90 percent), plus 146 (Chr 11) and 98 (Chr 21) predicated genes. GO functional profiling of Unigenes uncovered cellular growth and development processes, transport, translation and metabolic functions, and stress response elements (SRE). BAC sequences revealed the presence of genes that encode proteins containing a nucleotide-binding site (NBS) and C-terminal leucine-rich repeats (LRRs), a major class of disease R genes. Genome sequencing, physical alignment of genomic regions into chromosomal maps, and the anchoring of genetic maps are all steps that will improve the accuracy of detecting R genes and gene functions of important biological processes in crops. The sequence information of SSR markers and BAC clones and the genetic mapping of BAC clones provide enhanced genetic and physical frameworks of the resistance gene-rich regions of the cotton genome, thereby aiding discovery of R and PR genes, whole genome assembly efforts, and breeding for resistance to cotton diseases.