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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 #375424

Research Project: Development of Economically Important Row Crops that Improve the Resilience of U.S. Agricultural Production to Present and Future Production Challenges

Location: Plant Stress and Germplasm Development Research

Title: Sequence composition of BAC clones in a transgressive root-knot nematode resistance chromosome region in tetraploid cotton

item WANG, CONGLI - Dominican University Of California
item Ulloa, Mauricio
item NICHOLS, ROBERT - Cotton, Inc
item ROBERTS, PHILLIP - Dominican University Of California

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/15/2020
Publication Date: 12/14/2020
Citation: Wang, C., Ulloa, M., Nichols, R., Roberts, P.A. 2020. Sequence composition of BAC clones in a transgressive root-knot nematode resistance chromosome region in tetraploid cotton. Frontiers in Plant Science. 11:574486.

Interpretive Summary: The root-knot nematode (RKN) is a worm that causes significant plant damage and cotton yield loss across the United States. Although possible, chemical control of nematodes is expensive and can be unreliable. Currently, crop genetic resistance to nematode infection is the most reliable means of mitigating plant damage and yield loss. In this study, ARS scientists identified specific regions of cotton chromosomes that confer resistance to RKN. This research provides new information on the mechanism of resistance to RKN in cotton and will help create new cotton varieties with improved fiber yield in RKN infested fields. Additionally, these new varieties will decrease the need for chemical control of RKN, further reducing production costs and the environmental impact of pesticide application.

Technical Abstract: Plants evolve innate immunity including resistance genes to defend against pest and pathogen attack. Our previous studies in cotton (Gossypium spp.) revealed that one telomeric segment on chromosome (Chr)11 in G. hirsutum cv. Acala NemX (rkn1 locus) contributed to transgressive resistance to the plant parasitic nematode Meloidogyne incognita, but that the highly homologous segment on homoeologous Chr 21 had no resistance contribution. To better understand the resistance mechanism, a BAC library of Acala N901 (Acala NemX resistance source) was used to select, sequence and analyze BAC clones associated with SSR markers in the complex rkn1 resistance region. Sequence alignment with the susceptible G. hirsutum cv. TM1 genome indicated that 23 BACs mapped to TM1-Chr 11 and 18 BACs mapped to TM1-Chr 21. Genetic and physical mapping confirmed less BAC sequence (52-71%) mapped with the TM1 genome in the rkn1 region on Chr 11 than to the homologous region (> 89%) on Chr 21. A 3.1 cM genetic distance between the rkn1 flanking markers CIR316 and CIR069 was mapped in a Pima S-7 x Acala NemX RIL population with a physical distance ~1 Mbp in TM1. NCBI Blast and Gene annotation indicated that both Chr 11 and Chr 21 harbor resistance gene-rich cluster regions but more multiple homologous copies of Resistance (R) proteins and of adjacent transposable elements (TE) are present within Chr11 than within Chr 21. (CC)-NB-LRR type R proteins were found in the rkn1 region close to CIR316 and (TIR)-NB-LRR type R proteins were identified in another resistance rich region 10 cM from CIR 316 (~3.1 Mbp in the TM1 genome). The identified unique insertion/deletion in NB-ARC domain, different copies of LRR domain, and multiple copies or duplication of R proteins, adjacent protein kinases or TE in the rkn1 region on Chr 11 might be major factors contributing to complex recombination and transgressive resistance.