Identification and expression analysis of phosphatidy ethanolamine-binding protein (PEBP) gene family in cotton.

The phosphatidy ethanolamine-binding proteins (PEBP) play an important role in controlling flower development and phase change. Here, a total of 61 PEBP genes were identified, in which 20, 21, 10, and 10 were from tetraploid Gossypium hirsutum (AD1) and G. barbadense (AD2), and diploid G. raimondii (D5) and G. arboreum (A2), respectively. In G. hirsutum, 20 identified PEBP genes were unevenly distributed on 12 chromosomes. The identified PEBP genes were classified into four groups (TFL1, MFT, FT and FT-like). Among those, FT-like group are unique to cotton. The majority of PEBP genes had similar intron/exon distribution, whereas the divergence of PEBP genes suggests the possibility of functional diversification. The expression of PEBP genes varied among different tissues. This study brings new insights into the integrated genome-wide identification of PEBP genes in cotton and provides a foundation for breeding cotton cultivars with early maturation.

Differential expression of microRNAs during fiber development between fuzzless-lintless mutant and its wild-type allotetraploid cotton.

Cotton is one of the most important textile crops but little is known how microRNAs regulate cotton fiber development. Using a well-studied cotton fiberless mutant Xu-142-fl, we compared 54 miRNAs for their expression between fiberless mutant and its wildtype. In wildtype Xu-142, 26 miRNAs are involved in cotton fiber initiation and 48 miRNAs are related to primary wall synthesis and secondary wall thickening. Thirty three miRNAs showed different expression in fiber initiation between Xu-142 and Xu-142-fl. These miRNAs potentially target 723 protein-coding genes, including transcription factors, such as MYB, ARF, and LRR. ARF18 was newly predicted targets of miR160a, and miR160a was expressed at higher level in -2DPA of Xu-142-fl compared with Xu-142. Furthermore, the result of Gene Ontology-based term classification (GO), EuKaryotic Orthologous Groups (KOG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis shows that miRNA targets were classified to 222 biological processes, 64 cellular component and 42 molecular functions, enriched in 22 KOG groups, and classified into 28 pathways. Together, our study provides evidence for better understanding of miRNA regulatory roles in the process of fiber development, which is helpful to increase fiber yield and improve fiber quality.