Mapping resistance gene analogs (RGAs) in cultivated tetraploid cotton using RGA-AFLP analysis

Abstract

Diseases cause significant losses in cotton production throughout the US Cotton Belt. Growing resistant cultivars can significantly improve cotton yields and effectively reduce production inputs. Disease resistance (R) genes have been isolated in numerous plant species and the R genes with domains of nucleotide binding sites (NB) and leucine rich repeats (LRR) represent the largest R gene family. Degenerate primers designed based on conserved motifs of plant disease resistance genes were used alone or in combination with AFLP primers to analyze disease resistance gene analogs (RGAs) in a recombinant inbred line (RIL) population of Pima (Gossypium barbadense) 3-79 and Upland cotton (G. hirsutum) line NM 24016. Eighty-eight polymorphic RGA markers were amplified by 8 pairs of RGA degenerate primers, while 131 polymorphic RGA-AFLP markers were produced from six pairs of RGA-AFLP primer combinations. Of the 219 polymorphic RGA and RGA-AFLP markers that were identified, 212 were assigned to 18 chromosomes and linkage groups based on existing SSR markers that are on known chromosomes. However, the RGA and RGA-AFLP markers are not evenly distributed among chromosomes in that 189 RGA and RGA-AFLP markers (88%) are assigned onto three ''giant'' chromosomes, i.e., C6, C12, and C15, suggesting RGA clusters in the cotton genome. Several RGA and RGA-AFLP markers were mapped to the same linkage group carrying a root-knot nematode resistance gene. The identification and mapping of RGA and RGA-AFLP markers provide a framework to facilitate marker-assisted selection of disease resistance in cotton breeding and to understand the physical relationship of cotton resistance genes.

Genetic analysis and quantitative trait locus mapping of PEG‐induced osmotic stress tolerance in cotton

“…, Niu et al. ). The development of PAAP‐RAPD (random amplified polymorphic DNA‐based promoter anchored amplified polymorphism), STS (sequence tagged sites) and cDNA‐AFLP markers was previously described by Pang () and Pang et al.…”

Genetics, Breeding, and Marker‐Assisted Selection for Verticillium Wilt Resistance in Cotton

“…The BILs were derived from an interspecific cross between the resistant Pima S-7 and the susceptible Upland Sure-Grow 747. RGA-AFLP markers, which were found to be widely distributed on the cotton genome, were also used to map root-knot nematode resistance (Niu et al, 2011). RGA-AFLP may provide candidate gene markers for disease resistance.…”

Identification and evidence of positive selection upon resistance gene analogs in cotton (Gossypium hirsutum L.)

“…Complete resistant upland cotton cultivars against Fov isolates are not reported till date. Nevertheless, numerous efforts have been previously made for assisting disease resistance breeding programs (Fang et al 2014;Hinchliffe et al 2005;Niu et al 2011), mainly by means of cloning segments of putative disease resistance (R) genes known as resistance gene analogues (RGAs).…”