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

Antonios Zambounis; Ioannis Ganopoulos; Apostolos Kalivas; Athanasios Tsaftaris; Panagiotis Madesis

doi:10.1007/s12298-016-0362-2

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

Physiol Mol Biol Plants. 2016 Jul;22(3):415-421. doi: 10.1007/s12298-016-0362-2. Epub 2016 Jul 13.

Authors

Antonios Zambounis¹, Ioannis Ganopoulos², Apostolos Kalivas³, Athanasios Tsaftaris⁴, Panagiotis Madesis⁵

Affiliations

¹ Laboratory of Genetics and Plant Breeding, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, P.O. Box 261, 54124 Thessaloníki, Greece.
² 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.
³ Plant Breeding and Phytogenetic Resources Institute, Hellenic Agricultural Organization "Demeter", 5700 Thermi, Thessaloníki, Greece.
⁴ 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.
⁵ Institute of Applied Biosciences, CERTH, 570 01 Thermi, Thessaloníki, Greece.

Abstract

Upland cotton (Gossypium hirsutum L.) is an important fiber crop species, which is intensively plagued by a plethora of phytopathogenic fungi such as Fusarium oxysporum f. 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 to R genes. In this study, a cloning approach based on conserved RGAs motifs was used in order to amplify 38 RGAs from two upland cotton cultivars differing in their Fov susceptibility. Besides, we assessed the phylogenetic expansion and the evolutionary pressures acting upon 127 RGA homologues, which were previously deposited in GenBank along with the 38 RGAs from this study. A total of 165 RGAs sequences were clustered according to their BLAST(P) similarities in ten paralogous genes groups (PGGs). These RGAs 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. As RGAs derived markers are in close linkage to R genes, these results could be used in ongoing breeding programs of upland cotton.

Keywords: Fungal diseases; Molecular breeding; Non-synonymous nucleotide substitution.