Systematic analysis of cotton non-specific lipid transfer proteins revealed a clade of genes that play an important role in fiber development Cheng-sheng Meng1,2, Yuan-yuan Yan1,2, Zheng-wen Liu1, Li-ting Chen1, Yan Zhang1, Xiu-xin Li1, Li-qiang Wu1, Gui-yin Zhang1, Xing-fen Wang1* and Zhi-ying Ma1* 1College of Agronomy, North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center For Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, Hebei 071001, China 2 These authors contributed equally to this work *Correspondence: mzhy@hebau.edu.cn; cotton@hebau.edu.cn It makes great sense to investigate the regulatory mechanism of fiber development of cotton as it supports an important economic industry-textile. Plant non-specific lipid transfer proteins (nsLTPs) are capable to bind in vitro to various phospholipids including phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol and galactolipids with broad specificity. Multiple physiological functions of nsLTPs have been suggested, including membrane and liposome biogenesis, somatic embryogenesis, pollen development, stress resistance, defence and signal transduction. Although some nsLTPs were isolated from cotton fibers and supposed to regulate fiber development, little progress has been achieved on how nsLTPs regulate fiber development. In the present study, nsLTP genes were strictly identified from cotton genome with 138 members in G. hirsutum, 65 members in G. arboreum and 70 members in G. raimondii. These cotton nsLTP genes could be clustered into ten subgroups according to the number of flanking amino acid residues within the conserved ECM domain. Interestingly, type Ⅺ extremely expanded in G. hirsutum genome to be the largest subgroup, which is different from Arabidopsis, cacao，grape， rape and rice whose genome contain most members belonging to type Ⅰ or type Ⅱ. Sequence analysis revealed that GhLtpⅪs were evolutionally close to GhLtpⅡ12-15, and duplication pairs were indentified between GhLtpⅪs and GhLtpⅡs, indicating that type Ⅺ genes of G. hirsutum are likely to diverge from type Ⅱ genes. A large amount of tandem duplication events and non-reciprocal DNA exchanges were found within GhLtpⅪs, which might contribute to the tremendous expansion of type Ⅺ genes. Transcriptional analysis showed that GhLtps were highly transcribed in ovules and fibers, especially GhLtpⅪs whose transcription was significantly higher during fiber elongation in upland cotton cultivars with long fibers, suggesting an essential role of GhLtpⅪs in fiber elongation. Additionally, analysis of the published transcriptome data suggested that most of GhLtpⅪs, ignoring 12 genes that were scarcely detected, were significantly differentially transcribed in ovules at 10 and 20DPA compared with their orthologs in genome A or D, indicating a correlation of cotton type Ⅺ genes with fiber evolution. As fibers are trichomes of the outer epidermis of a single ovule, GhLtpⅪ17, 24, 27 and 28 were cloned and ectopically expressed in Arabidopsis. And significantly elongated trichomes of GhLtpⅪs overexpressed Arabidopsis suggested functional roles of GhLtpⅪs in promoting cell elongation. Our results implied a clade of nsLTP genes regulating fiber elongation and provide new insights into the phenotypic evolution of Gossypium species.

For ICGI 2018. Cotton fiber is the most important sustainable fiber source for textile industry. It is a single cell organ derived from the epidermis of the cotton ovule or seed. To understand the molecular basis of plant cell differentiation pattern, the cotton fiber cell is a good model system. Non-coding RNA is emerging as one of the most important regulators for the gene expression in response to multiple biological transitions and environmental stimuli. We systematically investigate the non-coding RNA behavior in the fiber cell differentiation progress. The major data indicate both small RNA and long non-coding RNA (lncRNA) play critical roles in fiber cell development. First of all, the fiber cell generates a unique group of small RNA in the fiber initiation stage. For example, the miR828 and miR858 trigger the target gene GhMYB2 to generate tasiRNAs in fiber cell fate determination. Another MIXTA MYB transcriptional factor coding gene, GhMML3 can generate an antisense transcript on the 3’ end of the gene loci. Together with the sense and antisense transcripts, a double strand RNA come into being to derive small RNAs. These secondary generated small RNAs interfere the cell fate determination in the mml3 mutant in stimulating the fiberless seed phenotype. On the other hand, the long non-coding RNAs are also found to take parts in the fiber cell differentiation by small RNA generation. We therefore conclude noncoding RNAs directly impact the fiber cell development in multiple aspects of molecular regulation.

The cotton genus (Gossypium) is remarkable for its extraordinary natural diversity as well as its importance to humankind. More than 50 species are recognized, including several recently described, which collectively are distributed in arid to semi-arid regions of the tropics and subtropics. Diversity in Gossypium has been promoted by two seemingly unlikely processes: trans-oceanic, long-distance dispersal, and wide hybridization among lineages that presently are widely separated geographically. Included are four species that were independently domesticated for their seed fiber, two diploids from Africa-Asia and two allopolyploids from the Americas. As Gossypium spread worldwide, it experienced remarkable morphological, cytogenetic and genomic diversification, spawning eight monophyletic groups of diploid (n = 13) species (“genome groups” A through G, and K) and 8 allopolyploids (n = 26; AD-genome), the latter resulting from an improbable trans-oceanic dispersal of an A-genome taxon to the New World 1-2 million years ago and subsequent hybridization with an indigenous D-genome diploid. The extraordinary diversity in the genus represents a largely untapped genomic reservoir for agronomic exploration. From a genomic perspective, cotton has a marvelously complex evolutionary history. We now understand that modern allopolyploid species are descended from diploid ancestors which themselves were once polyploid, with this cycle of polyploidization followed by diploidization being repeated many times. This history of “genomic superimpositions” will be described, as will some of the many implications that derive from this understanding.

Upland cotton (Gossypium hirsutum) is the most widely cultivated species, with over 90% of the global cotton production. Owing to long-term natural selection and artificial breeding under diverse climatic and cultivated conditions, plentiful germplasm resources have been produced for sustainable genetic improvement. Thus, to detect genetic factors contributing to the important traits in a genome-wide scale is indispensable based on these germplasm resources. In the present study, on the basis of approximately 3.66 million SNPs, we conducted genome-wide association study with 419 accessions in three important traits including days to flowering (FD), fiber length (FL) and strength (FS). The results showed that there were 1199, 1661 and 735 SNPs (P < 10-6) significantly associated with FD, FL and FS. We identified 528 FD, 456 FL and 301 FS genes in the 50-kb region surrounding the associated SNPs. For FD, we observed that 94.6% of the associated SNPs (1,199) were located on Dt03 with a strong peak. Among the identified FL-associated SNPs, 646 (38.9%) and 755 (45.5%) were located in At10 and Dt11 with strong association signals, respectively. For FS, 391 (53.1%) SNPs were located in At07. Therefore, we focused on these chromosomes to detect the new genes. We adopted the method that combines peak SNPs and SNP type in GWAS with transcriptome data, functional annotation of the orthologues in Arabidopsis to rapidly identify candidate genes associated with the traits. Through phenotypic significance analysis of haplotypes, qRT-PCR using two types of varieties with different haplotypes, transgenic method and VIGS technology, we found that GhCIP1 and GhUCE are the new genes contributing to FD and fiber initiation in cotton. GhFL1 in At10 and GhFL2 in Dt11 are the new genes controlling fiber elongation. Gh_A07G1769 is a causal gene underpinning the fiber strength of cotton. These results provide targets for molecular selection and genetic manipulation in cotton improvement.