Article
Genetics & Heredity
Minqiang Tang, Juanling Li, Xu Hu, Lu Sun, M. M. U. Helal, Jianguo Chen, Yuanyuan Zhang
Summary: This study comprehensively analyzed the DNA and RNA variations of two Brassica napus inbred lines and found significant differences in SNP transmission between the A(n) and C-n subgenomes, which may contribute to the asymmetrical gene expression in polyploid B. napus. The SNPs transmitted from DNA to RNA could be an important complement feature in comparative genomics, and they may play important roles in asymmetrical genome evolution in polyploidy.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Kai Zheng, Yongsheng Cai, Yanying Qu, Lu Teng, Chaoyue Wang, Jie Gao, Quanjia Chen
Summary: In this study, the whole genome identification and bioinformatics analysis of the HCT gene family were performed in G. barbadense. The results showed that the GbHCT114 gene regulates plant trichome development, which is closely related to cotton fiber quality. Gene silencing and overexpression experiments confirmed the important role of GbHCT114 gene in cotton fiber morphology, lignin content, and secondary xylem duct cell wall development. Transcriptomic analysis identified differentially expressed genes associated with lignin synthesis and fiber development.
Article
Plant Sciences
Juncheng Zhang, Huan Mei, Hejun Lu, Rui Chen, Yan Hu, Tianzhen Zhang
Summary: By integrating a large number of samples and time points, this study reveals the genetic basis of fiber quality differences between Gossypium hirsutum and Gossypium barbadense. Key genes involved in fiber development were identified, providing a theoretical basis for breeding high-quality cotton and gene function analysis.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Plant Sciences
Chunji Liu, You-Gan Wang
Summary: Polyploids, common in flowering plants, often have wider distribution ranges than their diploid progenitors. Previous studies have shown that polyploidy leads to novel changes and differences in gene number, gene expression levels, and epigenetic alteration between subgenomes of allopolyploid species. Contrary to popular belief, subgenome biases mainly reflect legacy from the progenitors and can be detected before polyploidization is complete.
Article
Multidisciplinary Sciences
Sakshi Arora, Amarjeet Kumar Singh, Bhupendra Chaudhary
Summary: This study demonstrates that the diminution of Gh-miR167 expression in cotton leads to developmental abnormalities in floral and fiber development. Dosage-dependent deformities were observed in anther development, pollen maturation, and boll formation. The decreased expression of Gh-miR167 also affected the expression of other miRNAs related to hormone signaling and flavonoid biosynthesis.
Article
Developmental Biology
Kazuya Yamada, Akiteru Maeno, Soh Araki, Morimichi Kikuchi, Masato Suzuki, Mizuki Ishizaka, Koumi Satoh, Kagari Akama, Yuki Kawabe, Kenya Suzuki, Daiki Kobayashi, Nanami Hamano, Akinori Kawamura
Summary: This study isolated all seven hox cluster loss-of-function alleles in zebrafish using the CRISPR-Cas9 system, revealing species-specific functional contributions and shared general principles of homologous Hox clusters along different axes.
Article
Plant Sciences
Sakshi Arora, Bhupendra Chaudhary
Summary: The study reveals that the majority of miRNAs with functional attributes have been recruited independently and in parallel during the millennia of human selection, impacting the transcriptional dynamicity of key miRNAs. These DEmiRs play crucial roles in fiber initiation and elongation stages, with A-subgenome-specific DEmiRs showing expression dominance in allopolyploid genetic backgrounds. The evolutionarily favored DEmiRs, including miR167, are involved in the transcriptional regulation of numerous genes during cotton evolution for enhanced fiber-associated agronomic traits.
Article
Multidisciplinary Sciences
Giacomo Potente, Rebecca L. Stubbs, Narjes Yousefi, Walter Pirovano, Peter Szoevenyi, Elena Conti
Summary: This study discovered homologous genes involved in the control of distyly in distantly related taxa for the first time. Comparative analysis of transcriptomes revealed that brassinosteroids and auxin are the main hormones controlling style elongation in Primula veris and Fagopyrum esculentum, respectively. Shared biochemical pathways and the recruitment of genes related to the phytochrome-interacting factor (PIF) signaling network may underlie the expression of distyly in distantly related species.
SCIENTIFIC REPORTS
(2022)
Article
Agricultural Engineering
Mengyu Li, Pengbo Hao, Jingjing Zhang, Xu Yang, Aimin Wu, Meng Zhang, Hengling Wei, Xiaokang Fu, Hantao Wang, Shuxun Yu
Summary: This study identified and analyzed the AIFs gene family in cotton and other species, showing conservation in the protein sequences and a possible amplification mechanism through fragment and tandem replication in cotton. The expression analysis of GhAIFs revealed high expression at the fiber initiation stage. Additionally, GhAIFs may be involved in regulating abiotic stress according to the results of selected gene expression under various stress conditions.
INDUSTRIAL CROPS AND PRODUCTS
(2021)
Review
Biochemistry & Molecular Biology
Masood Jan, Zhixin Liu, Chenxi Guo, Xuwu Sun
Summary: This review focuses on the genes and mechanisms involved in cotton fiber development, discussing the regulatory roles of plant hormones in fiber cell differentiation and elongation, as well as the functions of genes involved in hormone biosynthesis and signaling pathways in cotton fiber development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Jing Zheng, Shuhan Wen, Zhipeng Yu, Keyan Luo, Junkang Rong, Mingquan Ding
Summary: Cotton is a valuable cash crop that serves as an excellent model for understanding cell differentiation. Alternative splicing (AS) is a common regulatory process in plants that is essential for growth and development, but its role in cotton fiber formation is still largely unknown.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Jiasen He, Zhongyang Xu, Muhammad Tehseen Azhar, Zhen Zhang, Pengtao Li, Juwu Gong, Xiao Jiang, Senmiao Fan, Qun Ge, Youlu Yuan, Haihong Shang
Summary: This study used comparative transcriptomics to analyze the transcriptome data of cotton fibers and revealed the expression patterns of key genes during fiber development. The molecular mechanisms affecting fiber quality and yield were identified. The findings provide new information for improving fiber quality and yield in upland cotton genotypes.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Abdul Hafeez, Qun Ge, Qi Zhang, Junwen Li, Juwu Gong, Ruixian Liu, Yuzhen Shi, Haihong Shang, Aiying Liu, Muhammad S. Iqbal, Xiaoying Deng, Abdul Razzaq, Muharam Ali, Youlu Yuan, Wankui Gong
Summary: O-methyltransferases (OMTs) in Gossypium species play important roles in phenolics and flavonoid pathways, defending cellulose fiber and promoting plant cell wall strength and growth. Analysis of a 192-member OMT gene family in G. hirsutum, G. arboreum, and G. raimondii reveals their involvement in growth, development, defense against stresses, and their correlations with fiber quality and salt stress response. Specific OMT genes show responses to salt stress and fiber development stages, suggesting their potential contributions to salt tolerance and fiber quality formation in Gossypium.
Article
Genetics & Heredity
Ya-Qian Zhu, Lu Qiu, Lu-Lu Liu, Lei Luo, Xin-Pei Han, Yao-Hua Zhai, Wen-Jing Wang, Mao-Zhi Ren, Ya-Di Xing
Summary: The EXO70 gene is a key component of the exocytosis complex and plays critical roles in various biological processes. Through analysis of cotton databases, 165 EXO70 genes were identified and grouped into eight subgroups, with EXO70A potentially having the most important functions. The silencing of GhEXO70A1-A significantly impacted gene expression and metabolic signaling pathways in cotton, highlighting the vital role of the EXO70 gene in cotton physiological functions.
Article
Biochemistry & Molecular Biology
Yue Him Wong, Niklas Dreyer, HaoCheng Liu, Yi Lan, Jamie J. J. Chen, Jin Sun, Wei-Peng Zhang, Pei-Yuan Qian, Benny K. K. Chan
Summary: In this study, the authors identified 30 larval and 27 adult cement proteins of the epibiotic turtle barnacle Chelonibia testudinaria. The results showed that the larval and adult cement systems evolved independently and both emerged from co-option of existing genes and de novo formation, duplication and functional divergence of lineage-specific cement protein genes. These findings provide important insights into the evolutionary mechanisms of bioadhesives in sessile marine invertebrates.
Article
Materials Science, Textiles
Yali Sun, Zhaoe Pan, Yunfang Qu, Shoupu He, Yinhua Jia, Liru Wang, Baoyin Pang, Hongge Li, Jinlong Zhang, Xiongming Du, Jinling Huang
Summary: The genetic diversity and population structure analysis of cotton breeding revealed wide variation in agronomic traits, especially lint percentage. High genetic diversity was found at the DNA level using SSR markers, and GWAS identified 3 SSR markers associated with lint percentage, providing a theoretical basis for improving fiber yield.
JOURNAL OF NATURAL FIBERS
(2022)
Article
Plant Sciences
Chenhui Ma, Abdul Rehman, Hong Ge Li, Zi Bo Zhao, Gaofei Sun, Xiong Ming Du
Summary: The study successfully identified a candidate QTL for plant height in a Co-60 gamma treated upland cotton semi-dwarf mutant, Ari1327. Using bulk segregant analysis and genotyping by sequencing, the QTL was located on chromosome D01 in two F-2 populations. Comparative analysis of RNA-seq between mutant and wild variety revealed an important gene, Gh_D01G0592, responsible for dwarfness. Additionally, the study showed that the use of partial separation markers in QTL mapping can enhance linkage information. Overall, the results provide a basis for further research on candidate genes and utilization of dwarf genetic resources.
Article
Agronomy
Yingfei Liu, Mian Faisal Nazir, Shoupu He, Hongge Li, Zhaoe Pan, Gaofei Sun, Panhong Dai, Liyuan Wang, Xiongming Du
Summary: This study aimed to understand and explore the genomic architecture and inheritance patterns of DLP-15. Population structure and genotypic analysis revealed significant differences between different groups, and Chr-A08 exhibited a unique inheritance pattern. Haplotype analysis based on IBD segments showed significant differences between the two groups, and DLP-derived haplotypes associated with Chr-A08 were found to be significantly correlated with increased yield and fiber quality.
THEORETICAL AND APPLIED GENETICS
(2022)
Article
Plant Sciences
Zhenzhen Wang, Xiaomeng Zhang, Shoupu He, Abdul Rehman, Yinhua Jia, Hongge Li, Zhaoe Pan, Xiaoli Geng, Qiong Gao, Liru Wang, Zhen Peng, Xiongming Du
Summary: This study characterized the changes in proanthocyanidins biosynthesis components and transcripts in brown cotton fiber (BCF) variety Zong 1-61 at different stages of fiber development. The results revealed that flavonoid biosynthesis, phenylpropanoid metabolisms, and carbohydrate metabolisms dominated gene expression at 15 or 20 DPA. 63 genes, including three core genes, were identified as potentially related to flavonoid biosynthesis. Yeast one-hybrid assays confirmed the regulation of GhANS, GhANR1, and GhUFGT2 by GhMYB46, GhMYB6, and GhMYB3, respectively.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
Peng Han, Xiaomin Tian, Ying Wang, Cong Huang, Yizan Ma, Xiaofeng Zhou, Yu Yu, Dawei Zhang, Haijiang Xu, Yang Cao, Bo Zhu, Zhenxiu Feng, Shoupu He, Xiongming Du, Zhongxu Lin, Longfu Zhu, Chunyuan You, Zhenyuan Pan, Xinhui Nie
Summary: This study constructed a core germplasm bank for cotton breeding, which consisted of 85 accessions representing 16.90% of the original germplasm resources. The core bank showed slightly decreased phenotype ranges and increased coefficients of variation compared to the original bank. It also exhibited high levels of genetic diversity, with an average polymorphism information content of 0.166 and heterozygosity of 0.232, accounting for a significant portion of the values in the original bank.
GENETIC RESOURCES AND CROP EVOLUTION
(2022)
Article
Biotechnology & Applied Microbiology
Daowu Hu, Shoupu He, Gaofei Sun, Yinhua Jia, Yonghong Su, Xiaojing Ma, Washu Dev, Mian Faisal Nazir, Xiaoli Geng, Liru Wang, Zhaoe Pan, Baojun Chen, Hongge Li, Xiaoyang Wang, Baoyin Pang, Xiongming Du
Summary: In this study, a genome-wide association study was conducted on 213 Asian cotton accessions to identify SNPs and genes associated with leaf traits. Differences in leaf morphology and transcriptome between two varieties were analyzed, and two coding genes and two microRNAs were selected as candidate genes for leaf traits.
Correction
Agronomy
Yingfei Liu, Mian Faisal Nazir, Shoupu He, Hongge Li, Zhaoe Pan, Gaofei Sun, Panhong Dai, Liyuan Wang, Xiongming Du
THEORETICAL AND APPLIED GENETICS
(2022)
Article
Materials Science, Textiles
Muhammad Shahid Iqbal, Zareen Sarfraz, Mian Faisal Nazir, Yinhua Jia, Zhaoe Pan, Tahir Mahmood, Liru Wang, Xiongming Du
Summary: This study evaluated 572 cotton accessions in multiple test environments and used different evaluation methods to study genotype-environment interaction effects. The results showed that some F1 hybrid varieties had higher stability and adaptability in different environments, which contributed to increased seed cotton yield. Therefore, switching from line breeding to hybrid breeding can better adapt to different planting environments.
JOURNAL OF NATURAL FIBERS
(2022)
Article
Genetics & Heredity
Sani Muhammad Tajo, Zhaoe Pan, Shoupu He, Baojun Chen, Yusuf Km, Tahir Mahmood, Salisu Bello Sadau, Muhammad Shahid Iqbal, Teame Gereziher, Umar Suleiman Abubakar, Masha Joseph, Tajo Sammani, Xiaoli Geng, Xiongming Du
Summary: This study identified and analyzed the WOX genes in different cotton species, revealing their roles in cotton growth, development, and stress responses. The expression analysis of WOX genes in germinating hypocotyls and callus showed that most genes were up-regulated. The VIGS experiment demonstrated the importance of the Gh_A01G127500 gene in cotton growth and development, as well as its regulation of antioxidant and oxidant activities.
FRONTIERS IN GENETICS
(2022)
Article
Biotechnology & Applied Microbiology
Sani Muhammad Tajo, Zhaoe Pan, Yinhua Jia, Shoupu He, Baojun Chen, Salisu Bello Sadau, Yusuf Km, Aboleri Adijat Ajadi, Mian Faisal Nazir, Umar Auta, Xiaoli Geng, Xiongming Du
Summary: This study identified and analyzed the ORP gene family in cotton, and found that these genes play important roles in lipid metabolism, vesicular transferring and signaling, and non-vesicular sterol transport. The analysis also revealed their potential involvement in abiotic stress and provided a fundamental resource for further research.
Article
Agricultural Engineering
Tao Zhuang, Ming Xin, Qingkang Wang, Yiming Wang, Muhammad Saeed, Huixian Xing, Haijun Zhang, Yanan Zhang, Yongyan Deng, Guihua Zhang, Daowu Hu, Liming Wei, Mingshuo Cui, Yongqi Shang, Qifang Guo, Chuanban Li, Zhen Liu, Xianliang Song, Xuezhen Sun, Xiongming Du
Summary: By combining phenotypic data of seed kernel protein, oil, and fatty acid content with preprocessed near-infrared spectra, calibration models for cottonseed nutrient evaluation were established for 179 upland cotton genotypes. Results showed that 16 models had good prediction ability for seed protein, oil, and 14 fatty acids.
INDUSTRIAL CROPS AND PRODUCTS
(2023)
Article
Genetics & Heredity
Maojun Wang, Jianying Li, Zhengyang Qi, Yuexuan Long, Liuling Pei, Xianhui Huang, Corrinne E. Grover, Xiongming Du, Chunjiao Xia, Pengcheng Wang, Zhenping Liu, Jiaqi You, Xuehan Tian, Yizan Ma, Ruipeng Wang, Xinyuan Chen, Xin He, David D. Fang, Yuqiang Sun, Lili Tu, Shuangxia Jin, Longfu Zhu, Jonathan F. Wendel, Xianlong Zhang
Summary: In this study, we constructed a pan-genome of the Gossypium genus and explored the impact of transposon amplification on genome composition and evolution. We found evolutionary connections between genome size variation, chromatin structure reorganization, and chromatin interactome rewiring, as well as identified regulatory variations underlying fiber length in cotton. Our findings provide insights into the evolution of genome organization and regulation, and can inform cotton improvement strategies.
Article
Agricultural Engineering
Xiaomeng Zhang, Ruidan Dong, Yaxi Xu, Xiongming Du, Lei Ma
Summary: Cotton flowers contain a variety of flavonoids with antioxidant, anti-inflammatory, and anti-tumor effects. This study identified and quantified six macro-flavonoids in 373 G. hirsutum accessions. Candidate genes associated with specific flavonoids were identified, and the study revealed an upregulation of a certain gene and an increase in the content of a specific flavonoid in a specific genotype.
INDUSTRIAL CROPS AND PRODUCTS
(2023)
Article
Biochemistry & Molecular Biology
Zhen Peng, Abdul Rehman, Xiawen Li, Xuran Jiang, Chunyan Tian, Xiaoyang Wang, Hongge Li, Zhenzhen Wang, Shoupu He, Xiongming Du
Summary: Elevated salinity poses a significant threat to cotton growth, especially during germination and seedling stages. Utilizing primitive species of Gossypium hirsutum, such as Gossypium purpurascens, can help restore depleted genetic diversity caused by selective breeding. This study evaluated various G. purpurascens varieties and a salt-tolerant cotton variety, identifying multiple salt-tolerant and salt-resistant varieties and revealing key pathways and gene networks involved in salinity tolerance.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Hu Daowu, He Shoupu, Sun Gaofei, Jia Yinhua, Geng Xiaoli, Wang Liru, Pan Zhaoe, Chen Baojun, Li Hongge, Iqbal Zubair, Wang Xiaoyang, Zhao Zibo, Ge Yuting, Pang Baoyin, Du Xiongming
Summary: This study aimed to identify molecular markers and candidate genes associated with lateral root development in cotton and evaluate their correlation with yield and disease traits. The number of lateral roots in cotton was positively correlated with sympodial branch node and seed index traits, but negatively correlated with lint percentage. A Genome-wide association study (GWAS) identified 18 significant SNPs and 19 candidate genes related to lateral root number, and three genes (FLA12, WRKY29, and RBOHA) were found to be associated with lateral root development.
JOURNAL OF COTTON RESEARCH
(2022)
