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 the highly homologous segment on homoeologous Chr 21 had no resistance contribution. To better understand the resistance mechanism, a bacterial chromosome (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. TM-1 genome indicated that 23 BACs mapped to TM-1-Chr11 and 18 BACs mapped to TM-1-Chr 21. Genetic and physical mapping confirmed less BAC sequence (53–84%) mapped with the TM-1 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 × Acala NemX RIL population with a physical distance ∼1 Mbp in TM-1. 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 Chr 11 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 TM-1 genome). The identified unique insertion/deletion in NB-ARC domain, different copies of LRR domain, 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.
Highlights
With plant–pathogen co-evolution, plants have evolved two types of conserved innate immune systems, pathogen- or microbe-associated molecular pattern (PAMP/MAMP)-triggered immunity (PTI) (Monaghan and Zipfel, 2012) and effectortriggered immunity (ETI) (Dangl and Jones, 2001; Eitas and Dangl, 2010), to defend pathogen invasions
The NBS-LRR class is subdivided as coiled-coil (CC)-NBS-LRR or Toll/inerleukin-1 receptor (TIR)-NBS-LRR based on N-terminal structural features that are required for downstream signaling following pathogen perception (Jones and Dangl, 2006; Qi and Innes, 2013)
A total of 293M bp clear reads was obtained for all bacterial chromosome (BAC) and 98.79% Q30 were detected after quality filtering
Summary
With plant–pathogen co-evolution, plants have evolved two types of conserved innate immune systems, pathogen- or microbe-associated molecular pattern (PAMP/MAMP)-triggered immunity (PTI) (Monaghan and Zipfel, 2012) and effectortriggered immunity (ETI) (Dangl and Jones, 2001; Eitas and Dangl, 2010), to defend pathogen invasions. High similarity of the order of marker alleles amplified from the same primer pair was shown on Chr 11 and its homoeologous region of Chr 21 in various segregating populations (Wang et al, 2015, 2017) and highly conserved sequence between the two chromosomes (Paterson et al, 2012; Wang et al, 2012; Li et al, 2014, 2015; Zhang et al, 2015) indicate the unique structure and gene combination on Chr 11 that contributes to RKN resistance. Comparisons of BACs were conducted between Chr 11 and Chr 21 in Acala NemX and between resistant Acala NemX and susceptible Acala Maxxa (Wang et al, 2015)
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