Comparative analysis of SIMILAR to RCD ONE(SRO)family from tetraploid cotton species and their diploid progenitors depict their significance in cotton growth and development

Background SRO(Similar to RCD1)genes family is largely recognized for their importance in the growth,develop-ment,and in responding to environmental stresses.However,genome-wide identification and functional characteri-zation of SRO genes from cotton species have not been reported so far.Results A total of 36 SRO genes were identified from four cotton species.Phylogenetic analysis divided these genes into three groups with distinct structure.Syntenic and chromosomal distribution analysis indicated uneven distribu-tion of GaSRO,GrSRO,GhSRO,and GbSRO genes on A2,D5 genomes,Gh-At,Gh-Dt,Gb-At,and Gb-Dt subgenomes,respectively.Gene duplication analysis revealed the presence of six duplicated gene pairs among GhSRO genes.In promoter analysis,several elements responsive to the growth,development and hormones were found in GhSRO genes,implying gene induction during cotton growth and development.Several miRNAs responsive to plant growth and abiotic stress were predicted to target 12 GhSRO genes.Organ-specific expression profiling demonstrated the roles of GhSRO genes in one or more tissues.In addition,specific expression pattern of some GhSRO genes dur-ing ovule development depicted their involvement in these developmental processes.Conclusion The data presented in this report laid a foundation for understanding the classification and functions of SRO genes in cotton.

Global Annotation of Small RNA and MicroRNA Mature Sequences from Developing Ovules of Gossypium hirsutum L.

The involvement of small RNAs in cotton fiber development is under explored.The objective of this work was to directly clone,annotate,and analyze small RNAs of developing ovules to reveal

A Malvaceae-specific miRNA targeting the newly duplicated GaZIP1L to regulate Zn^(2+)ion transporter capacity in cotton ovules

MicroRNAs(miRNAs)play critical roles in regulating gene expression in plants,yet their functions underlying cultivated diploid Gossypium arboreum cotton ovule development are largely unknown.Here,we acquired small RNA profiles from G.arboreum ovules and fibers collected at different growth stages,and identified 46 novel miRNAs that accounted for 23.7%of all miRNAs in G.arboreum reported in the latest plant sRNA database.Through analysis of 84(including 38 conserved)differentially expressed G.arboreum miRNAs,we detected 215 putative protein-coding genes in 26 biological processes as their potential targets.A Malvaceae-specific novel miRNA named gar-miRN44 was found to likely regulate cotton ovule growth by targeting to a newly duplicated Zn^(2+)ion transporter gene GaZIP1L.During cotton ovule development,gar-miRN44 transcript level decreased sharply after 10 to 15 days post-anthesis(DPA),while that of the GaZIP1L increased significantly,with a concomitant increase of Zn^(2+)ion concentration in late ovule developmental stages.Molecular dynamics simulation and ion absorption analysis showed that GaZIP1L has stronger Zn2+ion binding ability than the original GaZIP1,indicating that the newly evolved GaZIP1L may be more suitable for maintaining high Zn2+ion transport capacity that is likely required for cotton ovule growth via enhanced cellulose synthase activities.Our systematic miRNA profiling in G.arboreum and characterization of gar-miRN44 not only contribute to the understanding of miRNA function in cotton,but also provide potential targets for plant breeding.