With the recent completion of draft sequencing of diploid cotton Gossypium raimondii and G. arboreum genomes published in Nature Genetics, and the first “gold-standard” version of G. raimondii genome published in Nature, cotton research community enjoyed the pick of many seminal research results that have provided a glorious opportunity to study orthologous and paralogous genes and gene families in allotetraploid cotton.
These successes and great achievements in ancestral diploid genome sequencing further resulted in decoding of the representative genome of widely grown allotetraploid Upland (G. hirsutum L.) cotton, Texas Marker-1.
Two independent research papers published in Nature Biotechnology by Zhang et al. and Li et al. in this week issue described the complex allotetraploid TM-1 genome that further entered cotton research to an era of “golden” opportunities providing the first insights into allotetraploid cotton genome structure, genome rearrangements, gene evolution, cotton fiber biology and biotechnology that will help to rapidly translate the genomics “knowledge” to an “economic impact”!
Congratulation to all cotton community with these latest achievements, high impact journal seminal publications, and hard work to foster cotton research!
[Background] Cotton fibers are single-celled extensions of the seed epidermis, a model tissue for studying cytoskeleton. Tubulin genes play a critical role in synthesizing the microtubules (MT) as a core element of the cytoskeleton. However, there is a lack of studies concerning the systematic characterization of the tubulin gene family in cotton. Therefore, the identification and portrayal of G. hirsutum tubulin genes can provide key targets for molecular manipulation in cotton breeding.
[Results] In this study, we investigated all tubulin genes from different plant species and identified 98 tubulin genes in G. hirsutum. Phylogenetic analysis showed that tubulin family genes were classified into three subfamilies. The protein motifs and gene structure of α-, β-tubulin genes are more conserved compared with γ-tubulin genes. Most tubulin genes are located at the proximate ends of the chromosomes. Spatiotemporal expression pattern by transcriptome and qRT-PCR analysis revealed that 12 α-tubulin and 7 β-tubulin genes are specifically expressed during different fiber development stages. However, Gh.A03G027200, Gh.D03G169300, and Gh.A11G258900 had differential expression patterns at distinct stages of fiber development in varieties J02508 and ZRI015.
[Conclusion] In this study, the evolutionary analysis showed that the tubulin genes were divided into three clades. The genetic structures and molecular functions were highly conserved in different plants. Three candidate genes, Gh.A03G027200, Gh.D03G169300, and Gh.A11G258900 may play a key role during fiber development complementing fiber length and strength.
[Title] Identification and expression analysis of Tubulin gene family in upland cotton
[Authors] CHEN Baojun, ZHAO Junjie, FU Guoyong, PEI Xinxin, PAN Zhaoe, LI Hongge, AHMED Haris, HE Shoupu & DU Xiongming
Journal of Cotton Research 2021, 4: 20
Better Together -International Partnerships Can Solve Threats to Cotton Production
Speaker: Dr. Jodi Scheffler. Research Geneticist Plants. USDA-ARS. Stoneville, Mississippi, United States
When the seed breaks, when the fibre sticks… Some contaminants of cotton
Speakers: Dr Bruno Bachelier. Assistant Unit Director, Cotton Supply Chain Correspondent, CIRAD France. & Dr Jean-Paul Gourlot. Co-leader of the Cotton Sector Group, CIRAD, France.
[Background] Micronaire is a comprehensive index reflecting the fineness and maturity of cotton fiber. Micronaire is one of the important internal quality indicators of the cotton fiber and is closely related to the value of the cotton fiber. Understanding the genetic basis of micronaire is required for the genetic improvement of the trait. However, the genetic architecture of micronaire at the genomic level is unclear. The present genome-wide association study (GWAS) aimed to identify the genetic mechanism of the micronaire trait in 83 representative upland cotton lines grown in multiple environments.
[Results] GWAS of micronaire used 83 upland cotton accessions assayed by a Cotton 63 K Illumina Infinium single nucleotide polymorphism (SNP) array. A total of 11 quantitative trait loci (QTLs) for micronaire were detected on 10 chromosomes. These 11 QTLs included 27 identified genes with specific expression patterns. A novel QTL, qFM-A12–1, included 12 significant SNPs, and GhFLA9 was identified as a candidate gene based on haplotype block analysis and on strong and direct linkage disequilibrium between the significantly related SNPs and gene. GhFLA9 was expressed at a high level during secondary wall thickening at 20∼25 days post-anthesis. The expression level of GhFLA9 was significantly higher in the low micronaire line (Msco-12) than that in the high micronaire line (Chuangyou-9).
[Conclusion] This study provides a genetic reference for genetic improvement of cotton fiber micronaire and a foundation for verification of the functions of GhFLA9.
[Title] Genome-wide association study of micronaire using a natural population of representative upland cotton (Gossypium hirsutum L.)
[Authors] SONG Jikun, PEI Wenfeng, MA Jianjiang, YANG Shuxian, JIA Bing, BIAN Yingying, XIN Yue, WU Luyao, ZANG Xinshan, QU Yanying, ZHANG Jinfa, WU Man & YU Jiwen
Journal of Cotton Research 2021, 4: 14
[Background] In order to uncover the mechanism of significantly reduced insect resistance at the late developmental stage in cotton (Gossypium hirsutum L.), the relationship between boll setting rate under different planting densities and Bacillus thuringiensis (Bt) insecticidal concentrations in the boll wall were investigated in the present study. Two studies were arranged at Yangzhou, China during the 2017–2018 cotton growth seasons. Five planting densities (15 000, 25 000, 45 000, 60 000 and 75 000 plants per hectare) and the flower-removal treatment were imposed separately on Bt cotton cultivar Sikang3 to arrange different boll setting rates, and the boll setting rates and Bt toxin content were compared.
[Results] Higher boll setting rate together with lower Bt toxin contents in boll wall was observed under low planting density, whereas lower boll setting rate and higher Bt toxin contents were found under high planting density. Also, higher Bt protein concentration was associated with higher soluble protein content, glutamic-pyruvic transaminase (GPT), and glutamic oxaloacetate transaminase (GOT) activities, but lower amino acid content, and protease and peptidase activities. It was further confirmed that a higher boll setting rate with lower Bt protein content under flower-removal.
[Conclusion] This study demonstrated that the insecticidal efficacy of boll walls was significantly impacted by boll formation. Reduced protein synthesis and enhanced protein degradation were related to the reduced Bt toxin concentration.
[Title] Increasing plant density increases Bt toxin concentration of boll wall in cotton by decreasing boll setting speed
[Authors] ZHOU Mingyuan, CHEN Chen, TAMBEL Leila I. M., CHEN Yuan, ZHANG Xiang, CHEN Yuan & CHEN Dehua
Journal of Cotton Research 2021, 4: 12
[Background] Soil salt stress seriously restricts the yield and quality of cotton worldwide. To investigate the molecular mechanism of cotton response to salt stress, a main cultivated variety Gossypium hirsutum L. acc. Xinluzhong 54 was used to perform transcriptome and proteome integrated analysis.
[Results] Through transcriptome analysis in cotton leaves under salt stress for 0 h (T0), 3 h (T3) and 12 h (T12), we identified 8 436, 11 628 and 6 311 differentially expressed genes (DEGs) in T3 vs. T0, T12 vs. T0 and T12 vs. T3, respectively. A total of 459 differentially expressed proteins (DEPs) were identified by proteomic analysis, of which 273, 99 and 260 DEPs were identified in T3 vs. T0, T12 vs. T0 and T12 vs. T3, respectively. Metabolic pathways, biosynthesis of secondary metabolites, photosynthesis and plant hormone signal transduction were enriched among the identified DEGs or DEPs. Detail analysis of the DEGs or DEPs revealed that complex signaling pathways, such as abscisic acid (ABA) and jasmonic acid (JA) signaling, calcium signaling, mitogen-activated protein kinase (MAPK) signaling cascade, transcription factors, activation of antioxidant and ion transporters, were participated in regulating salt response in cotton.
[Conclusion] Our research not only contributed to understand the mechanism of cotton response to salt stress, but also identified nine candidate genes, which might be useful for molecular breeding to improve salt-tolerance in cotton.
[Title] Integrated transcriptome and proteome analysis reveals complex regulatory mechanism of cotton in response to salt stress
[Authors] CHEN Lin, SUN Heng, KONG Jie, XU Haijiang & YANG Xiyan
Journal of Cotton Research 2021, 4: 11
[Background] Cotton fiber yield is a complex trait, which can be influenced by multiple agronomic traits. Unravelling the genetic basis of cotton fiber yield-related traits contributes to genetic improvement of cotton.
[Results] In this study, 503 upland cotton varieties covering the four breeding stages (BS1–BS4, 1911–2011) in China were used for association mapping and domestication analysis. One hundred and forty SSR markers significantly associated with ten fiber yield-related traits were identified, among which, 29 markers showed an increasing trend contribution to cotton yield-related traits from BS1 to BS4, and 26 markers showed decreased trend effect. Four favorable alleles of 9 major loci (R2 ≥ 3) were strongly selected during the breeding stages, and the candidate genes of the four strongly selected alleles were predicated according to the gene function annotation and tissue expression data.
[Conclusion] The study not only uncovers the genetic basis of 10 cotton yield-related traits but also provides genetic evidence for cotton improvement during the cotton breeding process in China.
[Title] Association mapping and domestication analysis to dissect genetic improvement process of upland cotton yield-related traits in China
[Authors] GUO Chunping, PAN Zhenyuan, YOU Chunyuan, ZHOU Xiaofeng, HUANG Cong, SHEN Chao, ZHAO Ruihai, YANG Qingyong, ZHU Longfu, SHAHZAD Raheel, MENG Fande, LIN Zhongxu & NIE Xinhui
Journal of Cotton Research 2021, 4: 10
Dr. Zahoor Ahmad suffered from COVID-19 for over two weeks and died in a hospital in Islamabad, Pakistan on April 20, 2021. Dr. Ahmad was the founding Chairman of the Asian Cotton Research & Development Network, established in June/July 1999. Dr. Ahmad was Director of the Central Cotton Research Institute, Multan, Pakistan when he hosted a Regional Consultation on Insecticide Resistance Management in Cotton. The Consultation resulted in the formation of the Network, one of the strongest among the four Networks supported by the ICAC.
Dr. Ahmad was an entomologist by training. He received his Ph.D. from the Washington State University in the early 1970s and started his career in pest control on cotton at the Central Cotton Research Institute, Multan, Pakistan. He became Director of the Institute in 1979 where he served for almost 30 years. Being aware of the consequences of the insecticide use, Dr. Ahmad was one of the first to promote IPM in Pakistan. He had a high reputation as a person of new ideas and worked hardly on the containment of insecticide use in Pakistan. The Multan Institute was comparatively a new institute when he took over in the late 1970s but he led the institute to one of the most prestigious mono crop multidisciplinary research center in the country and abroad. The Food and Agriculture Organization of the United Nations hired him to implement a pest control project in Myanmar in 1981, later the FAO moved him to Africa. He worked for the FAO for about five years. Dr. Ahmad attended many meetings of the ICAC.
After retirement he kept him busy and got involved in the seed industry, particularly planting seed of cotton. He was still working as General Manager of a seed company based in Lahore. GOD bless his soul.
COTTON WEBINAR 8.00 AM to 10.00 AM (Eastern Time) 5 May 2021
Dr Eric Hequet: Topic: Importance of non-HVI (High Volume Instrument) Cotton Fiber Properties
Dr PG Patil: Topic: Wealth from Waste: Cotton By-Products Value Addition
[Abstract] Oxidative stress occurs when crop plants are exposed to extreme abiotic conditions that lead to the excessive production and accumulation of reactive oxygen species (ROS). Those extreme abiotic conditions or stresses include drought, high temperature, heavy metals, salinity, and ultraviolet radiation, and they cause yield and quality losses in crops. ROS are highly reactive species found in nature that can attack plant organelles, metabolites, and molecules by interrupting various metabolic pathways until cell death occurs. Plants have evolved defense mechanisms for the production of antioxidants to detoxify the ROS and to protect the plant against oxidative damage. Modern researches in crop plants revealed that low levels of ROS act as a signal which induces tolerance to environmental extremes by altering the expression of defensive genes. In this review, we summarized the processes involved in ROS production in response to several types of abiotic stress in cotton plants. Furthermore, we discussed the achievements in the understanding and improving oxidative stress tolerance in cotton in recent years. Researches related to plant oxidative stresses have shown excellent potential for the development of stress-tolerant crops.
[Title]Review of oxidative stress and antioxidative defense mechanisms in Gossypium hirsutum L. in response to extreme abiotic conditions
[Authors]QAMER Zainab, CHAUDHARY Muhammad Tanees, DU Xiongming, HINZE Lori & AZHAR Muhammad Tehseen
Journal of Cotton Research 2021, 4: 8