Abstract
BackgroundDwarf cottons are more resistant to damage from wind and rain and associated with stable, increased yields, and also desirable source for breeding the machine harvest varieties. In an effort to uncover the transcripts and miRNA networks involved in plant height, the transcriptome and small RNA sequencing were performed based on dwarf mutant Ari1327 (A1), tall-culm mutant Ari3697 (A3) and wild type Ari971 (A9) in Gossypium hirsutum.MethodsThe stem apexes of wild-type upland cotton (Ari971) and its dwarf mutant (Ari1327) and tall-culm mutant (Ari3697) at the fifth true leaf stage were extracted for RNA, respectively. Transcriptome and small RNA libraries were constructed and subjected to next generation sequencing.ResultsThe transcriptome sequencing analysis showed that the enriched pathways of top 3 differentially expressed genes (DEGs) were categorized as carotenoid biosynthesis, plant-pathogen interaction and plant hormone signal transduction in both A1–A9 and A3–A9. The ABA and IAA related factors were differentially expressed in the mutants. Importantly, we found the lower expressed SAUR and elevated expressed GH3, and ABA related genes such as NCED and PP2C maybe relate to reduced growth of the plant height in Ari1327 which was consistent with the higher auxin and ABA content in this mutant. Furthermore, miRNA160 targeted to the auxin response factor (ARF) and miRNA166 (gma-miR166u and gma-miR166h-3p) targeted to ABA responsive element binding factor were related to the mutation in cotton. We have noticed that the cell growth related factors (smg7 targeted by gra-miR482 and 6 novel miRNAs and pectate-lyases targeted by osa-miR159f), the redox reactions related factors (Cytochrome P450 targeted by miR172) and MYB genes targeted by miR828, miR858 and miR159 were also involved in plant height of the cotton mutants. A total of 226 conserved miRNAs representing 32 known miRNA families were obtained, and 38 novel miRNAs corresponding to 23 unique RNA sequences were identified. Total 531 targets for 211 conserved miRNAs were obtained. Using PAREsnip, 27 and 29 miRNA/target conserved interactions were validated in A1–A9 and A3–A9, respectively. Furthermore, miRNA160, miRNA858 and miRNA172 were validated to be up-regulated in A1–A9 but down-regulated in A3–A9, whereas miRNA159 showed the opposite regulation.ConclusionsThis comprehensive interaction of the transcriptome and miRNA at tall-culm and dwarf mutant led to the discovery of regulatory mechanisms in plant height. It also provides the basis for in depth analyses of dwarf mutant genes for further breeding of dwarf cotton.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2071-6) contains supplementary material, which is available to authorized users.
Highlights
Dwarf cottons are more resistant to damage from wind and rain and associated with stable, increased yields, and desirable source for breeding the machine harvest varieties
[6] These results indicate that most dwarf mutants are controlled by recessive genes, and involve very few dominant genes, and plant hormones play significant roles in plant height decision
We found that miRNA160 and miRNA172 were upregulated in A1–A9 but down-regulated in A3–A9, whereas miRNA159 showed the opposite regulation
Summary
Dwarf cottons are more resistant to damage from wind and rain and associated with stable, increased yields, and desirable source for breeding the machine harvest varieties. Plant height is an important trait in cotton, and dwarf cottons are more resistant to damage from wind and rain and associated with stable, increased yields. Because of their agronomic importance, the different types of dwarf mutants have been isolated from rice [1], Arabidopsis [2], and wheat [3]. A cotton mutant, pag, exhibited dwarfism due to significant inhibition of cell elongation and expansion, and brassinolide (BL) treatment rescued its growth and fiber elongation [6] These results indicate that most dwarf mutants are controlled by recessive genes, and involve very few dominant genes, and plant hormones play significant roles in plant height decision
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