[Objective] CLE (CLAVATA3/Embryo surrounding region-related), a class of small secreted protein, plays an important role in sustaining the balance between cell proliferation and differentiation during the progress of plant growth and development. CLE gene family is the largest peptide family which has been identified so far, and it is also the hotspot of plant peptide studies. Although the study of CLE has made a great progress in Arabidopsis and rice, the CLE peptides in cotton have rarely been studied. Genome-wide analysis of CLE peptides in cotton will helpful to understand the evolutionary history and the regulation mechanism of peptides in cotton. [Method] In this study, we identified the members of CLE peptide family in the genomes of four cotton species using bioinformatics methods. [Result] One hundred and forty-eight CLE genes were identified in the four cotton species. The number of CLE gene in Gossypium hirsutum L. and G. barbadense L. are twice as much as in both G. arboreum and G. raimondii, respectively. These genes were divided into five clusters by phylogenetic analysis. The Ka/Ks ratios of most orthologs were less one, suggesting that most genes likely underwent purifying selection. We also detected eleven homologous gene pairs under positive selection. Using online published transcriptome data, we found that most CLE genes were expressed at low levels, and only six genes (GhCLE34, GhCLE9, GaCLE4, GbCLE39, GbCLE13, and GbCLE43) showed relatively high expression level. The conserved motif analysis showed that there are 12 specific CLE peptides in cotton, two of which derived from genes that under positive selection, which should be paid more attention in the future study. [Conclusion] Using bioinformatics methods and comparative genomics, we identified and characterized the CLE genes in cotton. These results may be useful for future studies of functions and regulation mechanism of CLE peptides in cotton.
[Objective] This article aims to provide a theoretical basis for molecular marker-assisted breeding by quantitative trait loci (QTLs) mapping and gene function annotation of fiber quality. [Method] F2 populations were constructed using the two cotton cultivars (lines), CCRI 49 and 396289, as parents. Based on high-density genetic maps, the F2:3 families with three environments were included in the F2 population. The QTL mapping of seven fiber quality traits including fineness and maturity, etc., was performed using the Clusters of orthologous groups (COG), Gene ontology (GO), and Kyoto encyclopedia of genes and genomes (KEGG) databases to annotate QTLs for gene function. [Result] A total of 157 QTLs related to fiber quality were obtained and distributed on 20 chromosomes. QTLs with more traits on A03, A04, D02, A11 and D07 chromosomes clustered and may be the key chromosomes controlling fiber quality traits. A total of 13 stable QTLs were obtained, of which qFL-A03-1 and qFin-A11-4 were repeated in three environments, and nine other QTLs were repeated in two environments. And 4 763 candidate genes were annotated, with 2 416, 4 188, and 2 512 genes being annotated in COG, GO, and KEGG, respectively. Among them, 429 genes were annotated in stable QTLs. Some of these genes may be closely related to fiber quality. [Conclusion] The high-density genetic map obtained by high-throughput sequencing can help to obtain more QTLs, which is beneficial to the screening of candidate genes related to fiber quality and the improvement of fiber traits, and improves the breeding efficiency.
[Objective] Dimorphic InDel markers can be used for cotton variety identification and purity detection, to improve the accuracy and efficiency of cotton seed testing, and to play a role in molecular breeding of cotton. [Method] Based on the whole genome sequencing of 121 cotton varieties from different sources, the InDel markers with high polymorphism were developed according to polymorphism information content(PIC) and were applied in the genetic distance analysis and cluster analysis by using 66 cotton varieties in China. [Result] Totally 10 967 InDel were identified based on the next generation sequencing data of 121 cotton varieties. Among the 85 pairs of InDel primers synthesized, 64 were selected including 35 from At group and 29 from Dt group. The minimum average allelic frequency(MAF) of At and Dt chromosomes were 0.45 and 0.32, respectively, while the PIC were 0.49 and 0.40, respectively. The genetic distances of the 66 cotton varieties ranged from 0.04 to 0.65 centimorgan (cM), with an average of 0.39 cM. The two varieties with the largest genetic distance were Simian 3 and CCRI 36, and the two varieties with the smallest genetic distance were Xumian 18 and Xuza 3. [Conclusion] The 64 cotton dimorphic InDel markers can effectively reveal the relationships among varieties based on the genetic distance, and distinguish cotton varieties from different sources, which has certain theoretical significance and application value.
[Objective] Calmodulin-like protein (CML) is an important Ca2+ sensor and plays an important role in regulating plant stress response mechanism. Genome-wide analysis of CML gene family provides a basis for further study of the role of CML genes in cotton under stress. [Method] The members of CML family in cotton were identified by bioinformatics. The expression patterns of CML genes in upland cotton under salt stress were analyzed by the transcriptome data and real-time reverse transcription-polymerase chain reaction. Virus-induced gene silencing (VIGS) was used to silence GhCML44-2 gene and to verify its function. [Result] 154, 74 and 78 CML proteins were obtained from Gossypium hirsutum L., G. raimondii Ulbrich and G. arboreum L., respectively. Evolutionary tree and conservative motif analysis showed that GhCML proteins were divided into eight subgroups, all containing conserved EF-hand domain. Under salt stress, 107 GhCML genes were differentially expressed with different expression patterns in leaves and roots. Promoter analysis showed that there were many different stress response elements in these gene promoters, and cotton plants were more salt-tolerant than control plants after silencing the expression of GhCML44-2 successfully by using VIGS. [Conclusion] The results of this study are helpful to understand the evolution and function of CML gene family in cotton, and provide a theoretical basis and reference for the follow-up study of their specific functions in cotton.
[Objective] This study aims to identify quantitative trait loci (QTLs) associated with cotton fruit branch length by using the combination of bulked-segregant analysis (BSA) and next-generation sequencing (NGS) method. [Method] In this study, the cotton F2 segregating population was developed with the short branch line Sujimian 125 and long-branch variety Sikang 1 as cross parents. According to the average internode length of fruit branches in middle, extreme individuals in F2 population were divided into two groups to generate the bulked DNA samples. The whole-genome resequencing of two DNA bulks was applied to analyze the single nucleotide polymorphism (SNP) and insertion-deletion (InDel) between two groups, and the fruit branch internode length related QTLs were detected using Euclidean distance (ED). [Result] With SNP data obtained from sequencing, a 0.8 Mbp range associated region on chromosome A3 was identified; with InDel data obtained from sequencing, a 1.09 Mbp range associated region on chromosome A3 was identified. Two regions overlapped, and the overlapped range was 0.77 Mbp. [Conclusion] This result suggested that the difference between I-type fruit branch and zero-type was due to different genetic locus and pattern rather than dosage effect of the same gene.
[Objective] The aim of this study was to map quantitative trait loci (QTLs) of Verticillium wilt resistance in cotton. [Method] In this study, with the cultivar Lumianyan 28(Gossypium hirsutum L.) as the recipient parent and the F1 generation obtained from the cross Hai7124 (G. barbadense) and TM-1(G. hirsutum L.) as the donor parent, an interspecific advanced backcross population was constructed. Compared with the integrated high density genetic linkage map published, simple sequence repeat(SSR) markers of polymorphism were used to construct genetic linkage map. QTLs detection was conducted by composite interval mapping method in field and disease nursery. [Result] 216 simple sequence repeated (SSR) markers of polymorphism were assigned to 26 Chromosomes with a total map distance of 3 380 cM and an average distance of about 15.77 cM between two adjacent markers. Six QTLs located on 6 chromosomes had been detected and could explain phenotypic variance with 8.56%~20.26%. Five of Six QTLs were consistent with the previous study. Moreover, one novel QTL which located on Chromosome 1 was detected in this study. These results maybe helpful for the marker-assisted development of new cultivars which were resistant to Verticillium wilt. [Conclusion] Six QTLs were detected, one of them is a new QTL on chromosome 1.
[Objective] Based on the representative 236 cotton varieties in Xinjiang, the resistance of cotton to mites was identified, and the waxy content and waxy components of leaves were analyzed to lay a foundation for cotton breeding. [Method] In the cotton seedling stage, the waxy content of the leaves of different cotton varieties was determined, and the waxy components of the leaves were analyzed by gas chromatography-mass spectrometry. [Result] Most cotton varieties are sensitive to the damage of cotton mites. There were 2 high resistance varieties, 3 resistant materials, 22 medium resistant materials, 207 sensitive materials and 2 high-sensitivity materials in 236 cotton materials. The waxy content on the surface of cotton leaves was significantly negatively correlated with leaf damage levels. The waxy components of cotton leaves were mainly alkane compounds, containing a small amount of esters, ethers and fatty acids. The content of alkanes and esters in waxy leaves of high-resistance cotton germplasm materials was higher than that of high-sensitivity materials. The compound with the largest difference in content are C24H50, C35H72 and C17H36. [Conclusion]These results lay a foundation for further study on the effects of waxy content on host selection and mite resistance of cotton mites.
Cotton is one of the major field crops which are seriously threatened by pests and diseases. In recent years, the ecological management of cotton pests and diseases with intercropping has become to be an interesting approach. Intercropping possibly increases the population of natural enemies and finally reduces the population density of pests as a result of changes in ecological structure and environmental conditions of farmland. Intercropping thus has been considered an important alternative in controlling pests and diseases. However, cotton field intercropping also has some limitations in controlling pests and diseases. Unreasonable intercropping system has many risks such as increasing labor input, increasing the difficulty of pests’ control, and aggravating pests and diseases. In this paper, the effects and the underlying mechanisms of cotton intercropping on cotton pests and diseases were reviewed. The possible risks and countermeasures used for ecological control of intercropping were also put forward, and the future and application of ecological management of cotton pests and diseases with intercropping were prospected.
Naturally colored cotton is a special type cotton, which contains pigment in cotton fiber. Up to date, there are only two kinds of commercial colored cotton varieties in the world, brown cotton and green cotton. In order to breed new colored varieties and meet people’s need for different colors, many researches on pigment in naturally colored cotton fiber were studied. This review summarizes the molecular mechanism of the pigment formation of naturally colored cotton fiber. In this paper, the fiber development, pigment accumulation and composition of colored cotton are introduced in detail. The results of the composition analyzed in the colored fiber showed that the pigment was related to the flavonoid biosynthesis pathway, which was the important secondary metabolites pathway. Therefore, the structural genes and transcription regulator factors of the flavonoid biosynthesis pathway are mainly reviewed. It may provide important theory basis for colored cotton breeding and improvement by using the genetic engineering technology.
