title: Identification and evidence of positive selection upon resistance gene analogs in cotton (Gossypium hirsutumL.).
abstract: Upland cotton (Gossypium hirsutumL.) is an important fiber crop species, which is intensively plagued by a plethora of phytopathogenic fungi such asFusarium oxysporumf. sp.vasinfectum(Fov) causing severe wilt disease. Resistance gene analogs (RGAs) are the largest class of potential resistance (R) genes depicting highly conserved domains and structures in plants. Additionally,RGAs are pivotal components of breeding projects towards host disease resistance, serving as useful functional markers linked toRgenes. In this study, a cloning approach based on conservedRGAs motifs was used in order to amplify 38RGAs from two upland cotton cultivars differing in theirFovsusceptibility. Besides, we assessed the phylogenetic expansion and the evolutionary pressures acting upon 127RGAhomologues, which were previously deposited in GenBank along with the 38RGAs from this study. A total of 165RGAs sequences were clustered according to their BLAST(P) similarities in ten paralogous genes groups (PGGs). TheseRGAs exhibited intensive signs of positive selection as it was revealed by inferring various maximum likelihood analyses. The results showed robust signs of positive selection, acting in almost all PGGs across the phylogeny. The evolutionary analysis revealed the existence of 42 positively selected residue sites across the PGG lineages, putatively affecting their ligand-binding specificities. AsRGAs derived markers are in close linkage toRgenes, these results could be used in ongoing breeding programs of upland cotton.
authors.affiliation: Laboratory of Genetics and Plant Breeding, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, P.O. Box 261, 54124 Thessaloníki, Greece.
authors.forename: Antonios
authors.initials: A
authors.lastname: Zambounis
authors.affiliation: Laboratory of Forest Genetics and Tree Breeding, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, P.O. Box 238, 54006 Thessaloníki, Greece.
authors.forename: Ioannis
authors.initials: I
authors.lastname: Ganopoulos
authors.affiliation: Plant Breeding and Phytogenetic Resources Institute, Hellenic Agricultural Organization "Demeter", 5700 Thermi, Thessaloníki, Greece.
authors.forename: Apostolos
authors.initials: A
authors.lastname: Kalivas
authors.affiliation: Laboratory of Genetics and Plant Breeding, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, P.O. Box 261, 54124 Thessaloníki, Greece ; Institute of Applied Biosciences, CERTH, 570 01 Thermi, Thessaloníki, Greece.
authors.forename: Athanasios
authors.initials: A
authors.lastname: Tsaftaris
authors.affiliation: Institute of Applied Biosciences, CERTH, 570 01 Thermi, Thessaloníki, Greece.
authors.forename: Panagiotis
authors.initials: P
authors.lastname: Madesis
keywords: Fungal diseases; Molecular breeding; Non-synonymous nucleotide substitution