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CROP BREEDING & GENETICS

AFLP-RGA Markers in Comparison with RGA and AFLP in Cultivated Tetraploid Cotton

^a Dep. of Plant and Environ. Sci., Box 30003, New Mexico State Univ., Las Cruces, NM 88003
^b Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, China Cotton Research Institute, Anyang, Henan, China
^c USDA-ARS, Southern Regional Research Center, 1100 Robert E. Lee Blvd., New Orleans, LA 70124
^d U.S. Arid-Land Agricultural Research Center, USDA-ARS, 21881 N. Cardon Lane, Maricopa, AZ 85239
^e WCIS Res. Unit, Cotton Enhancement Program, USDA, Shafter, CA 93262
^f Cotton Inc., Cary, NC 27513

^* Corresponding author (jinzhang{at}nmsu.edu)

Disease resistance (R) genes have been isolated from many plant species and R genes with domains of nucleotide binding sites (NBS) and leucine-rich repeats (LRR) represent the largest R gene family. The objective of this investigation was to test a resistance gene analog (RGA) anchored marker system, called amplified fragment length polymorphism (AFLP)-RGA in cotton (Gossypium spp.). The AFLP-RGA analysis uses one degenerate RGA primer designed from various NBS and LRR domains of R genes in combination with one selective AFLP primer in a PCR reaction. Out of a total of 446 AFLP-RGA bands amplified by 22 AFLP-RGA primer combinations, 76 (17.0%) and 37 (8.3%) were polymorphic within four G. hirsutum L. genotypes and four G. barbadense L. cotton genotypes, respectively. The number of polymorphic AFLP-RGA bands (256) between G. hirsutum and G. barbadense was much higher (57.4%). This level of polymorphism mirrors that of AFLP. The genetic similarity among the eight genotypes based on AFLP-RGA or AFLP lead to similar results in genotype grouping at the species and intraspecies level. However, RGA markers amplified by only degenerate RGA primers could not discriminate several genotypes. AFLP-RGA offers a great flexibility for numerous primer combinations in a genome-wide search for RGAs. Due to the distribution of RGAs or RGA clusters in the plant genome, genome-wide AFLP-RGA analysis provides a useful resource for candidate gene mapping of R genes for disease resistance in cotton.

Abbreviations: AFLP, amplified fragment length polymorphism • GS, genetic similarities • LRR, leucine-rich repeats • NBS, nucleotide binding sites • RGA, resistance gene analog • QTL, quantitative trait locus • SRAP, sequence-related amplified polymorphism • SSRs, simple sequence repeats • STS, sequence tagged site • TRAP, targeted region amplified polymorphism

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