A genome-wide identification of the BLH gene family reveals BLH1 involved in cotton fiber development

[Background] Cotton is the world’s largest and most important source of renewable natural fiber. BEL1-like homeodomain (BLH) genes are ubiquitous in plants and have been reported to contribute to plant development. However, there is no comprehensive characterization of this gene family in cotton. In this study, 32, 16, and 18 BLH genes were identified from the G. hirsutumG. arboreum, and G. raimondii genome, respectively. In addition, we also studied the phylogenetic relationships, chromosomal location, gene structure, and gene expression patterns of the BLH genes.

[Result] The results indicated that these BLH proteins were divided into seven distinct groups by phylogenetic analysis. Among them, 25 members were assigned to 15 chromosomes. Furthermore, gene structure, chromosomal location, conserved motifs, and expression level of BLH genes were investigated in G. hirsutum. Expression profiles analysis showed that four genes (GhBLH1_3GhBLH1_4GhBLH1_5, and GhBLH1_6) from BLH1 subfamily were highly expressed during the fiber cell elongation period. The expression levels of these genes were significantly induced by gibberellic acid and brassinosteroid, but not auxin. Exogenous application of gibberellic acid significantly enhanced GhBLH1_3GhBLH1_4, and GhBLH1_5transcripts. Expression levels of GhBLH1_3 and GhBLH1_4 genes were significantly increased under brassinosteroid treatment.

[Conclusion] The BLH gene family plays a very important role in many biological processes during plant growth and development. This study deepens our understanding of the role of the GhBLH1gene involved in fiber development and will help us in breeding better cotton varieties in the future.

[Title] A genome-wide identification of the BLH gene family reveals BLH1 involved in cotton fiber development

[Authors] LIU Cuixia, LI Zhifang, DOU Lingling, Yi YUAN, ZOU Changsong, SHANG Haihong, CUI Langjun & XIAO  Guanghui

Journal of Cotton Research 2020, 326

https://doi.org/10.1186/s42397-020-00068-y

Global identification of genes associated with xylan biosynthesis in cotton fiber

[Background] Mature cotton fiber secondary cell wall comprises largely of cellulose (> 90%) and small amounts of xylan and lignin. Little is known about the cotton fiber xylan biosynthesis by far.

[Result] To comprehensively survey xylan biosynthetic genes in cotton fiber, we identified five IRX9, five IRX10, one IRX14, six IRX15, two FRA8, one PARVUS, eight GUX, four GXM, two RWA, two AXY9, 13 TBL genes by using phylogenetic analysis coupled with expression profile analysis and co-expression analyses. In addition, we also identified two GT61 members, two GT47 members, and two DUF579 family members whose homologs in Arabidopsis were not functionally characterized. These 55 genes were regarded as the most probable genes to be involved in fiber xylan biosynthesis. Further complementation analysis indicated that one IRX10 like and two FRA8 related genes were able to partially recover the irregular xylem phenotype conferred by the xylan deficiency in their respective Arabidopsis mutant. We conclude that these genes are functional orthologs of respective genes that are implicated in GX biosynthesis.

[Conclusion] The list of 55 cotton genes presented here provides not only a solid basis to uncover the biosynthesis of xylan in cotton fiber, but also a genetic resource potentially useful for future studies aiming at fiber improvement via biotechnological approaches.

[Title] Global identification of genes associated with xylan biosynthesis in cotton fiber

[Authors] CHEN Feng, GUO Yanjun, CHEN Li, GAN Xinli, LIU Min, LI Juan & XU Wenliang

Journal of Cotton Research 2020, 325

https://doi.org/10.1186/s42397-020-00063-3

Development and application of perfect SSR markers in cotton

[Background] This study aimed to develop a set of perfect simple sequence repeat (SSR) markers with a single copy in the cotton genome, to construct a DNA fingerprint database suitable for authentication of cotton cultivars. We optimized the polymerase chain reaction (PCR) system for multi-platform compatibility and improving detection efficiency. Based on the reference genome of upland cotton and 10× resequencing data of 48 basic cotton germplasm lines, single-copy polymorphic SSR sites were identified and developed as diploidization SSR markers. The SSR markers were detected by denaturing polyacrylamide gel electrophoresis (PAGE) for initial screening, then fluorescence capillary electrophoresis for secondary screening. The final perfect SSR markers were evaluated and verified using 210 lines from different sources among Chinese cotton regional trials.

[Result] Using bioinformatics techniques, 1 246 SSR markers were designed from 26 626 single-copy SSR loci. Adopting a stepwise (primary and secondary) screening strategy, a set of 60 perfect SSR markers was selected with high amplification efficiency and stability, easy interpretation of peak type, multiple allelic variations, high polymorphism information content (PIC) value, uniform chromosome distribution, and single-copy characteristics. A multiplex PCR system was established with ten SSR markers using capillary electrophoresis detection.

[Conclusion] A set of perfect SSR markers of cotton was developed and a high-throughput SSR marker detection system was established. This study lays a foundation for large-scale and standardized construction of a cotton DNA fingerprint database for authentication of cotton varieties.

[Title] Development and application of perfect SSR markers in cotton

[Authors] WU Yuzhen, HUANG Longyu, ZHOU Dayun, FU Xiaoqiong, LI Chao, WEI Shoujun, PENG Jun & KUANG Meng

Journal of Cotton Research 2020, 321

https://doi.org/10.1186/s42397-020-00066-0

QTL and genetic analysis controlling fiber quality traits using paternal backcross population in upland cotton

[Background] Genetic improvement in fiber quality is one of the main challenges for cotton breeders. Quantitative trait loci (QTL) mapping provides a powerful approach to dissect the molecular mechanism in fiber quality traits. In present study, F14recombinant inbred line (RIL) population was backcrossed to paternal parent for a paternal backcross (BC/P) population, deriving from one upland cotton hybrid. Three repetitive BC/P field trials and one maternal backcross (BC/M) field trial were performed including both two BC populations and the original RIL population.

[Result] In total, 24 novel QTLs are detected for fiber quality traits and among which 13 QTLs validated previous results. Thirty-five QTLs in BC/P populations explain 5.01%–22.09% of phenotype variation (PV). Among the 35 QTLs, 23 QTLs are detected in BC/P population alone. Present study provides novel alleles of male parent for fiber quality traits with positive genetic effects. Particularly, qFS-Chr3–1 explains 22.09% of PV in BC/P population, which increaseds 0.48 cN·tex− 1 for fiber strength. A total of 7, 2, 8, 2 and 6 QTLs explain over 10.00% of PV for fiber length, fiber uniformity, fiber strength, fiber elongation and fiber micronaire, respectively. In RIL population, six common QTLs are detected in more than one environment: qFL-Chr1–2qFS-Chr5–1qFS-Chr9–1qFS-Chr21–1qFM-Chr9–1 and qFM-Chr9–2. Two common QTLs of qFE-Chr2–2(TMB2386-SWU12343) and qFM-Chr9–1 (NAU2873-CGR6771) explain 22.42% and 21.91% of PV. The region between NAU4034 and TMB1296 harbor 30 genes (379 kb) in A05 and 42 genes (49 kb) in D05 for fiber length along the QTL qFL-Chr5–1 in BC/P population, respectively. In addition, a total of 142 and 46 epistatic QTLs and QTL × environments (E-QTLs and QQEs) are identified in recombinant inbred lines in paternal backcross (RIL-P) and paternal backcross (BC/P) populations, respectively.

[Conclusion] The present studies provide informative basis for improving cotton fiber quality in different populations.
[Title] QTL and genetic analysis controlling fiber quality traits using paternal backcross population in upland cotton

[Authors] MA LingLing, SU Ying, NIE Hushuai, CUI Yupeng, CHENG Cheng, IJAZ Babar & HUA  Jinping

Journal of Cotton Research 2020, 322

https://doi.org/10.1186/s42397-020-00060-6

Overexpressing rice lesion simulating disease 1-like gene (OsLOL1) in Gossypium hirsutum promotes somatic embryogenesis and plant regeneration

[Background] Cotton somatic embryogenesis is difficult or rarely frequent to present, which has limited gene function identification and biotechnological utility. Here, we employed a rice key somatic embryogenesis-related gene, rice lesion simulating disease 1-like gene (OsLOL1), to develop transgenic cotton callus for evaluating its function in ectopic plants.

[Result] Overexpressing OsLOL1 can promote cotton callus to form embryogenic callus, not only shortening time but also increasing transition of somatic callus cells to embryogenic callus cells. And the regenerating plantlets per transgenic OsLOL1 embryogenic callus were significantly higher than those in the control transformed with empty vector. Analysis of physiological and biochemical showed that OsLOL1 can repress cotton superoxide dismutase 1 gene (GhSOD1) expression, possibly resulting in reactive oxidant species (ROS) accumulation in transgenic callus cells. And OsLOL1-overexpressed embryogenic callus exhibited higher α-amylase activity compared with the control, resulting from the promotion of OsLOL1 to cotton amylase 7 gene (GhAmy7) and GhAmy8 expression.

[Conclusion] The data showed that OsLOL1 could be used as a candidate gene to transform cotton to increase its somatic embryogenesis capacity, facilitating gene function analysis and molecular breeding in cotton.
[Title] Overexpressing rice lesion simulating disease 1-like gene (OsLOL1) in Gossypium hirsutum promotes somatic embryogenesis and plant regeneration

[Authors] WANG Zhian, WANG Peng, HU Guang, XIAO Juanli, ZHANG Anhong, LUO Xiaoli & WU Jiahe

Journal of Cotton Research 2020, 319

https://doi.org/10.1186/s42397-020-00062-4

Unraveling the puzzle of the origin and evolution of cotton A-genome

[Abstract] Gossypium hirsutum, the most widely planted cotton species, its evolution has long been an unsolved puzzle because of its hybrid origin from D-genome and A-genome species. To better understand the genetic component of cotton, Huang et al. recently sequenced and assembled the first A1-genome G. herbaceum, and updated the A2-genome G. arboreum and (AD)1-genome G. hirsutum. On the basis of the three reference genomes, they resolved existing controversial concepts and provided novel evolutionary insights surrounding the A-genome.

[Title] Unraveling the puzzle of the origin and evolution of cotton A-genome

[Authors] MA Zhiying

Journal of Cotton Research 3, Article number: 17 (2020)

https://doi.org/10.1186/s42397-020-00056-2

Succinate dehydrogenase SDH1–1 positively regulates cotton resistance to Verticillium dahliae through a salicylic acid pathway

Journal of Cotton Research

[Background] Verticillium wilt, caused by the soil-borne fungus of Verticillium dahliae Kleb., is one of the most devastating diseases of cotton. The complex mechanism underlying cotton resistance to Verticillium wilt remains uncharacterized. Identifying an endogenous resistance gene may be helpful to control this disease. Previous studies revealed that succinate dehydrogenase (SDH) is involved in reactive oxygen species (ROS)-induced stress signaling pathway that is likely to be triggered by salicylic acid (SA). Here, through the metabolomics and differential expression analyses in wilt-inoculated cotton (Gossypium hirsutum), we noticed that GhSDH1–1gene in cotton may play an important role in the resistance to V. dahlia. Then we reported GhSDH1–1 gene and its functional analysis in relation to the resistance of cotton to V. dahliae.

[Results] The GhSDH1–1 gene in cotton root was significantly up-regulated after V. dahlia inoculation, and its expression level peaked at 12 and 24 h post-infection. SA can also induce the up-regulation of GhSDH1–1. Additionally, the functional analysis showed that GhSDH1–1-silenced cotton was more susceptible to V. dahliae than the control because of the significant decrease in abundance of immune-related molecules and severe damage to the SA-signaling pathway. In Arabidopsis thaliana, high expression of GhSDH1–1 conferred high resistance to V. dahliaeArabidopsis that overexpressed GhSDH1–1 had higher resistance to V. dahliae infection compared with the wild-type.

[Conclusions] Our findings provide new insights into the role of GhSDH1–1; it positively regulates cotton resistance to Verticillium wilt. The regulatory mechanism of GhSDH1–1 is closely related to SA-related signaling pathway.

[Title] Succinate dehydrogenase SDH1–1 positively regulates cotton resistance to Verticillium dahliae through a salicylic acid pathway
[Authors] ZHANG Xiangyue, FENG Zili, ZHAO Lihong, LIU Shichao, WEI Feng, SHI Yongqiang, FENG Hongjie & ZHU Heqin

https://doi.org/10.1186/s42397-020-00052-6

GbAt11 gene cloned from Gossypium barbadense mediates resistance to Verticillium wilt in Gossypium hirsutum

Journal of Cotton Research

[Background] Gossypium hirsutum is highly susceptible to Verticillium wilt, and once infected Verticillium wilt, its yield is greatly reduced. But G. barbadense is highly resistant to Verticillium wilt. It is possible that transferring some disease-resistant genes from G. barbadense to G. hirsutummay contribute to G. hirsutum resistance to Verticillium wilt.

[Results] Here, we described a new gene in G. barbadense encoding AXMN Toxin Induced Protein-11, GbAt11, which is specifically induced by Verticillium dahliae in G. barbadense and enhances Verticillium wilt resistance in G. hirsutum. Overexpression in G. hirsutum not only significantly improves resistance to Verticillium wilt, but also increases the boll number per plant. Transcriptome analysis and real-time polymerase chain reaction showed that GbAt11overexpression can simultaneously activate FLS2BAK1 and other genes, which are involved in ETI and PTI pathways in G. hirsutum.

[Conclusions] These data suggest that GbAt11 plays a very important role in resistance to Verticillium wilt in cotton. And it is significant for improving resistance to Verticillium wilt and breeding high-yield cotton cultivars.

[Title] GbAt11 gene cloned from Gossypium barbadense mediates resistance to Verticillium wilt in Gossypium hirsutum

[Authors] QIU Tingting, WANG Yanjun, JIANG Juan, ZHAO Jia, WANG Yanqing & QI Junsheng

https://doi.org/10.1186/s42397-020-00047-3

Towards complete deconstruction of cotton transcriptional landscape

Journal of Cotton Research

Abstract: Recently, Wang et al. systematically explored the transcription landscape in diploid cotton Gossypium arboreum. In the study, they integrated four high-throughput sequencing techniques, including Pacbio sequencing, strand-specific RNA sequencing (ssRNA-seq), Cap analysis gene expression sequencing (CAGE-seq), and PolyA sequencing (PolyA-seq) to profile the RNA transcriptome of G. arboreum. They developed a pipeline, IGIA to construct accurate gene structure annotation based on the updated genome of G. arboreum and the multi-strategic RNA-seq data. Their study revealed some intriguing phenomena and potential novel mechanisms in the regulation of RNA transcription in plants, and also provided valuable resources for further functional genomic research in cotton.

[Title] Towards complete deconstruction of cotton transcriptional landscape

[Author] LI Fuguang

https://doi.org/10.1186/s42397-020-00050-8

Extrafloral nectary–the sleeping beauty of plant science

Journal of Cotton Research

Abstract: Cotton is one of the most important cash crops, its growth season coincides with a high incidence of diverse groups of pests, leading to heavy use of pesticides. Recent identification of a signaling protein as a candidate regulator of cotton extrafloral nectary provides a new insight into the formation of sophisticated defense mechanisms in plants.

[Title] Extrafloral nectary–the sleeping beauty of plant science

[Author] CHEN Xiaoya

https://doi.org/10.1186/s42397-020-00051-7