Effects of NaCl stress on the biochemical substances in Bt cotton as well as on the growth and development and adult oviposition selectivity of Helicoverpa armigera


Recently, due to the development of food security strategies, cotton has been planted in inland saline-alkali dry soils or in coastal some saline-alkali soils in China. Under the condition, to comprehensively prevent and control Helicoverpa armigera in cotton fields with saline-alkali soils, it is important to study the larval growth and development of H. armigera and to study adult oviposition selectivity in H. armigera adults that feed on NaCl-stressed cotton plants.


In this study, Bt cotton GK19 was used for the experimental group and its nontransgenic parent Simian 3 was used for the control to study the effects of biochemical substances in cotton as well as larval growth and development and adult oviposition selectivity of H. armigera. The experiments were performed by growing cotton indoors under NaCl stress at concentrations of 0 mmol·L− 1, 75 mmol·L− 1 and 150 mmol·L− 1, respectively. The results showed that the expression of Bt protein was significantly inhibited for NaCl-stressed Bt cotton. The content of soluble protein and K+ in the leaves of cotton were decreased, while the content of gossypol and Na+ were increased. In addition, the 5th instar H. armigera larvae exhibited shorten the life span in a 13-day trial period. Under enclosure treatments and at different female densities, the adult oviposition of H. armigera decreased on high NaCl-stressed nontransgenic cotton, while the oviposition on Bt cotton tended to first increase but then decrease under low, moderate and high NaCl stress treatments.


Under certain content ranges of NaCl stress treatments, larval of H. armigera growth and development, and adult oviposition were no significant difference in the change for a certain period. However, under high NaCl stress, larval growth, development and adult oviposition were affected, which may provide insights for the prevention and control of H. armigera for Bt cotton in saline-alkali soils.


Effects of NaCl stress on the biochemical substances in Bt cotton as well as on the growth and development and adult oviposition selectivity of Helicoverpa armigera

LUO Junyu, ZHANG Shuai, ZHU Xiangzhen, JI Jichao, ZHANG Kaixin, WANG Chunyi, ZHANG Lijuan, WANG Li and CUI Jiniie

Journal of Cotton Research. 2019; 2:4




JCR-Genome-wide identification of Gossypium INDETERMINATE DOMAIN genes and their expression profiles in ovule development and abiotic stress responses


INDETERMINATE DOMAIN (IDD) transcription factors form one of the largest and most conserved gene families in plant kingdom and play important roles in various processes of plant growth and development, such as flower induction in term of flowering control. Till date, systematic and functional analysis of IDDgenes remained infancy in cotton.


In this study, we identified total of 162 IDD genes from eight different plant species including 65 IDD genes in Gossypium hirsutum. Phylogenetic analysis divided IDDs genes into seven well distinct groups. The gene structures and conserved motifs of GhIDD genes depicted highly conserved exon-intron and protein motif distribution patterns. Gene duplication analysis revealed that among 142 orthologous gene pairs, 54 pairs have been derived by segmental duplication events and four pairs by tandem duplication events. Further, Ka/Ksvalues of most of orthologous/paralogous gene pairs were less than one suggested the purifying selection pressure during evolution. Spatiotemporal expression pattern by qRT-PCR revealed that most of the investigated GhIDD genes showed higher transcript levels in ovule of seven days post anthesis, and upregulated response under the treatments of multiple abiotic stresses.


Evolutionary analysis revealed that IDD gene family was highly conserved in plant during the rapid phase of evolution. Whole genome duplication, segmental as well as tandem duplication significantly contributed to the expansion of IDDgene family in upland cotton. Some distinct genes evolved into special subfamily and indicated potential role in the allotetraploidy Gossypium hisutum evolution and development. High transcript levels of GhIDD genes in ovules illustrated their potential roles in seed and fiber development. Further, upregulated responses of GhIDD genes under the treatments of various abiotic stresses suggested them as important genetic regulators to improve stress resistance in cotton breeding.

Genome-wide identification of Gossypium INDETERMINATE DOMAIN genes and their expression profiles in ovule development and abiotic stress responses

ALI Faiza, QANMBER Ghulam, LI Yonghui, MA Shuya, LU Lili, YANG Zuoren, WANG Zhi and LI Fuguang

Journal of Cotton Research 2019 2:3


JCR-Cotton High Speed Phenotyping Thematic Series Call For Paper

Journal of Cotton Research

Cotton High Speed Phenotyping
Thematic Series Call For Paper
Coordinator: Professor Eric F. Hequet, Texas Tech University, USA; Dr. Glen Ritchie, Texas Tech University, USA

Author’s allowance: The sponsor, Institute of Cotton Research, CAAS, grants to cover not only APC for the submission, but also the author’s allowance once published.

High speed phenotyping is critical to improve cotton research and production. It can be applied to large scale commercial fields, research fields, breeding lines, and even at the individual plant level. The main goals are to improve yield, fiber quality, stress and disease resistance, etc… Recently, advances in high speed phenotyping in cotton have been achieved. The Journal of Cotton Research is hosting a thematic series on this topic. The research community is encouraged to share original findings, methodology, results, databases, and/or software and opinions.

Scopes that may be covered in the submissions may include, but are not limited to the following:
1. Platform design: air-based and/or land-based;
2. Data capture and processing: sensors (RGB, IR, multispectral, sonic, etc.), integration of multiple sensors, information processing technologies;
3. Data analysis and Metadata: analysis of very large data sets, validation with ground truth, practical application examples (breeding programs, site specific irrigation scheduling, etc.).

Submission Deadline: April 30, 2019


Genetic diversity and population structure of Gossypium arboreum L. collected in China

[Background] Gossypium arboreum is a diploid species cultivated in the Old World. It possesses favorable characters that are valuable for developing superior cotton cultivars.

[Method] A set of 197 Gossypium arboreum accessions were genotyped using 80 genome-wide SSR markers to establish patterns of the genetic diversity and population structure. These accessions were collected from three major G. arboreum growing areas in China. A total of 255 alleles across 80 markers were identified in the genetic diversity analysis.

[Results] Three subgroups were found using the population structure analysis, corresponding to the Yangtze River Valley, North China, and Southwest China zones of G. arboreum growing areas in China. Average genetic distance and Polymorphic information content value of G. arboreum population were 0.34 and 0.47, respectively, indicating high genetic diversity in the G. arboreum germplasm pool. The Phylogenetic analysis results concurred with the subgroups identified by Structure analysis with a few exceptions. Variations among and within three groups were observed to be 13.61% and 86.39%, respectively.

[Conclusion] The information regarding genetic diversity and population structure from this study is useful for genetic and genomic analysis and systematic utilization of economically important traits in G. arboreum.

Genetic diversity and population structure of Gossypium arboreum L. collected in China
JIA Yinhua, PAN Zhaoe, HE Shoupu, GONG Wenfang, GENG Xiaoli, PANG Baoyin, WANG Liru and DU Xiongming
Journal of Cotton Research. 2018; 1:11.

Map-based cloning of a recessive gene v1 for virescent leaf expression in cotton (Gossypium spp.)

[Background] Virescence, as a recognizable phenotype in the early development stage of cotton, is not only available for research on chloroplast development and photosynthesis but also for heterosis exploitation in cotton.

[Methods] In current study, for fine mapping of virescent-1 (v1) in cotton, three populations with a total of 5 678 individuals were constructed using T582 which has the virescent trait. Tobacco rattle virus, TRV1 and TRV2 (pYL156), were used as vectors for the virus-induced gene silencing (VIGS) assay.

[Results] The v1 gene was fine-mapped to a 20 kb interval on chromosome 20 of tetraploid cotton. We identified only one candidate gene with four single nucleotide polymorphisms between parents, among which the single nucleotide polymorphism at the position of 1 082 base pair caused the change of amino acid residue from Arg (3–79) to Lys (T582). The relative expression of the candidate gene in virescent plants was extensively lower than that in normal plants. Nullification of the gene by VIGS significantly turned the green leaf of normal cotton plants into yellow. We named this candidate gene as GhRVL.

[Conclusions] This study will facilitate the further research on virescent formation, and will be useful for breeding of hybrid cottons.

Map-based cloning of a recessive gene v1 for virescent leaf expression in cotton (Gossypium spp.)
ZHANG Youping, WANG Qiaolian, ZUO Dongyun, CHENG Hailiang, LIU Ke, ASHRAF Javaria, LI Simin, FENG Xiaoxu, YU John Z. and SONG Guoli
Journal of Cotton Research. 2018; 1:10.

Analysis of short fruiting branch gene and Marker-assisted selection with SNP linked to its trait in upland cotton

[Background] With the rapid development of genomics, many functional genes have been targeted. Molecular marker assisted selection can accelerate the breeding process by linking selection to functional genes.

[Methods] In a study of upland cotton (Gossypium hirsutum L.), the F2 segregated population was constructed by crossing X1570 (short branches) with Ekangmian-13 (long branches) to identify the short fruiting branch gene and marker-assisted selection with SNP(Single Nucleotide Polymorphisms, SNP) linked to its trait.

[Result] The result demonstrated that linked SSR marker BNL3232 was screened by BSA(Bulked segregant analysis, BSA) method; one SNP locus was found, which was totally separated from the fruiting branches trait in upland cotton.

[Conclusion] It was verified that this SNP marker could be used for molecular assisted selection of cotton architecture.

Analysis of short fruiting branch gene and Marker-assisted selection with SNP linked to its trait in upland cotton
ZHANG Youchang, FENG Changhui, BIE Shu, WANG Xiaogang, ZHANG Jiaohai, XIA Songbo and QIN Hongde
Journal of Cotton Research. 2018; 1:5.

Designations for individual genomes and chromosomes in Gossypium

Gossypium, as the one of the biggest genera, the most diversity, and the highest economic value in field crops, is assuming an increasingly important role in studies on plant taxonomy, polyploidization, phylogeny, cytogenetics, and genomics. Here we update and provide a brief summary of the emerging picture of species relationships and diversification, and a set of the designations for individual genomes and chromosomes in Gossypium. This cytogenetic and genomic nomenclature will facilitate comparative studies worldwide, which range from basic taxonomic exploration to breeding and germplasm introgression.

Designations for individual genomes and chromosomes in Gossypium
WANG Kunbo, WENDEL Jonathan F. and HUA Jinping
Journal of Cotton Research. 2018; 1:3.

Genome-wide identification and expression analysis of Gossypium RING-H2 finger E3 ligase genes revealed their roles in fiber development, and phytohormone and abiotic stress responses

[Background] RING-H2 finger E3 ligase (RH2FE3) genes encode cysteine-rich proteins that mediate E3 ubiquitin ligase activity and degrade target substrates. The roles of these genes in plant responses to phytohormones and abiotic stresses are well documented in various species, but their roles in cotton fiber development are poorly understood. To date, genome-wide identification and expression analyses of Gossypium hirsutum RH2FE3 genes have not been reported.

[Methods] We performed computational identification, structural and phylogenetic analyses, chromosomal distribution analysis and estimated Ka/Ks values of G. hirsutum RH2FE3 genes. Orthologous and paralogous gene pairs were identified by all-versus-all BLASTP searches. We predicted cis-regulatory elements and analyzed microarray data sets to generate heatmaps at different development stages. Tissue-specific expression in cotton fiber, and hormonal and abiotic stress responses were determined by quantitative real time polymerase chain reaction (qRT-PCR) analysis.

[Results] We investigated 140 G. hirsutum, 80 G. arboreum, and 89 G. raimondii putative RH2FE3 genes and their evolutionary mechanisms and compared them with orthologs in Arabidopsis and rice. A domain-based analysis of the G. hirsutum RH2FE3 genes predicted conserved signature motifs and gene structures. Chromosomal localization showed the genes were distributed across all G. hirsutum chromosomes, and 60 duplication events (4 tandem and 56 segmental duplications) and 98 orthologs were detected. cis-elements were detected in the promoter regions of G. hirsutum RH2FE3 genes. Microarray data and qRT-PCR analyses showed that G. hirsutum RH2FE3 genes were strongly correlated with cotton fiber development. Additionally, almost all the identified genes were up-regulated in response to phytohormones (brassinolide, gibberellic acid (GA), indole-3-acetic acid (IAA), and salicylic acid (SA)) and abiotic stresses (cold, heat, drought, and salt).

[Conclusions] The genome-wide identification, comprehensive analysis, and characterization of conserved domains and gene structures, as well as phylogenetic analysis, cis-element prediction, and expression profile analysis of G. hirsutum RH2FE3 genes and their roles in cotton fiber development and responses to plant hormones and abiotic stresses are reported here for the first time. Our findings will contribute to the genome-wide analysis of putative RH2FE3 genes in other species and lay a foundation for future physiological and functional research on G. hirsutum RH2FE3 genes.

Genome-wide identification and expression analysis of Gossypium RING-H2 finger E3 ligase genes revealed their roles in fiber development, and phytohormone and abiotic stress responses
QANMBER Ghulam, YU Daoqian, LI Jie, WANG Lingling, MA Shuya, LU Lili, YANG Zuoren and LI Fuguang
Journal of Cotton Research. 2018; 1:1.

Genome-wide analysis of Rf-PPR-like (RFL) genes and a new InDel marker development for Rf1 gene in cytoplasmic male sterile CMS-D2 Upland cotton

[Background] Cytoplasmic male sterility in flowering plants is a convenient way to use heterosis via hybrid breeding and may be restored by nuclear restorer-of-fertility (Rf) genes. In most cases, Rf genes encoded pentatricopeptide repeat (PPR) proteins and several Rf genes are present in clusters of similar Rf-PPR-like (RFL) genes. However, the Rf genes in cotton were not fully characterized until now.

[Results] In total, 35 RFL genes were identified in G. hirsutum, 16 in G. arboreum, and 24 in G. raimondii. Additionally, four RFL-rich regions were identified; the RFL-rich region in Gh_D05 is the probable location of Rf-PPR genes in cotton and will be studied further in the future. Furthermore, an insertion sequence was identified in the promoter sequence of Gh_D05G3392 gene in the restorer line, as compared with the CMS-D2 line and maintainer lines. An InDel-R marker was then developed and could be used to distinguish the restorer line carrying Rf1 from other genotypes without the Rf1 allele.

[Conclusion] In this study, genome-wide identification and analysis of RFL genes have identified the candidate Rf-PPR genes for CMS in Gossypium. The identification and analysis of RFL genes and sequence variation analysis will be useful for cloning Rf genes in the future and also for three-line hybrid breeding in cotton.

ZHANG Bingbing, ZHANG Xuexian, GUO Liping, QI Tingxiang, WANG Hailin, TANG Huini, QIAO Xiuqin, KASHIF Shahzad, XING Chaozhu and WU Jianyong
Journal of Cotton Research. 2018; 1:12.

A genome-wide analysis of SWEET gene family in cotton and their expressions under different stresses

[Background] The SWEET (Sugars will eventually be exported transporters) gene family plays multiple roles in plant physiological activities and development process. It participates in reproductive development and in the process of sugar transport and absorption, plant senescence and stress responses and plant-pathogen interaction. However, the comprehensive analysis of SWEET genes has not been reported in cotton.

[Results] In this study, we identified 22, 31, 55 and 60 SWEET genes from the sequenced genomes of Gossypium arboreum, G. raimondii, G. hirsutum and G. barbadense, respectively. Phylogenetic tree analysis showed that the SWEET genes could be divided into four groups, which were further classified into 14 sub-clades. Further analysis of chromosomal location, synteny analysis and gene duplication suggested that the orthologs showed a good collinearity and segmental duplication events played a crucial role in the expansion of the family in cotton. Specific MtN3_slv domains were highly conserved between Arabidopsis and cotton by exon-intron organization and motif analysis. In addition, the expression pattern in different tissues indicated that the duplicated genes in cotton might have acquired new functions as a result of sub-functionalization or neo-functionalization. The expression pattern of SWEET genes showed that the different genes were induced by diverse stresses. The identification and functional analysis of SWEET genes in cotton may provide more candidate genes for genetic modification.

[Conclusion] SWEET genes were classified into four clades in cotton. The expression patterns suggested that the duplicated genes might have experienced a functional divergence. This work provides insights into the evolution of SWEET genes and more candidates for specific genetic modification, which will be useful in future research.

A genome-wide analysis of SWEET gene family in cotton and their expressions under different stresses
ZHAO Lanjie, YAO Jinbo, CHEN Wei, LI Yan, LÜ Youjun, GUO Yan, WANG Junyi, YUAN Li, LIU Ziyang and ZHANG Yongshan

Journal of Cotton Research. 2018; 1:7.