New ICGI co-chairs have been elected

International Cotton Genome Initiative (ICGI) has completed 2015 election process, and as a result, six new co-chairs for overall chairing and ICGI work groups have been elected for 2017-2019 terms:

ICGI Overall – Dr. John Yu (USA)

Breeding and Applied Genomics – Dr. Jodi Scheffler (USA)

Comparative Genomics and Bioinformatics – Dr. Ibrokhim Abdurakhmonov (Uzbekistan)

Functional Genomics – Dr. Guoli Song ( China)

Germplasm & Genetic Stocks – Dr. Xiongming Du (China)

Structural Genomics – Dr. Wangzhen Guo (China)

Moreover, per election results, 95-97% voters approved new Workgroup structure of ICGI and uses of ICGI funds.

Congratulations for successful election process to ICGI and its new co-chairs!

Details of ICGI election results can be fount at: http://www.cottongen.org/icgi/elections

Cotton Research enters to a period of “golden” opportunities

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!

Genome-wide association study of micronaire using a natural population of representative upland cotton (Gossypium hirsutum L.)

[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 2025 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, 414

https://doi.org/10.1186/s42397-021-00089-1

Increasing plant density increases Bt toxin concentration of boll wall in cotton by decreasing boll setting speed

[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, 412

https://doi.org/10.1186/s42397-021-00084-6

Integrated transcriptome and proteome analysis reveals complex regulatory mechanism of cotton in response to salt stress

[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, 411

https://doi.org/10.1186/s42397-021-00085-5

Association mapping and domestication analysis to dissect genetic improvement process of upland cotton yield-related traits in China

[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, 410

https://doi.org/10.1186/s42397-021-00087-3

Dr. Zahoor Ahmad, First Chairman of the Asian Cotton R & D Network Died Due to COVID-19

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.

Review of oxidative stress and antioxidative defense mechanisms in Gossypium hirsutum L. in response to extreme abiotic conditions

[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, 48

https://doi.org/10.1186/s42397-021-00086-4

Correlation analysis of stem hardness traits with fiber and yield-related traits in core collections of Gossypium hirsutum

[BackgroundStem hardness is one of the major influencing factors for plant architecture in upland cotton (Gossypium hirsutum L.). Evaluating hardness phenotypic traits is very important for the selection of elite lines for resistance to lodging in Gossypium hirsutum L. Cotton breeders are interested in using diverse genotypes to enhance fiber quality and high-yield. Few pieces of research for hardness and its relationship with fiber quality and yield were found. This study was designed to find the relationship of stem hardness traits with fiber quality and yield contributing traits of upland cotton.

[Results] Experiments were carried out to measure the bending, acupuncture, and compression properties of the stem from a collection of upland cotton genotypes, comprising 237 accessions. The results showed that the genotypic difference in stem hardness was highly significant among the genotypes, and the stem hardness traits (BL, BU, AL, AU, CL, and CU) have a positive association with fiber quality traits and yield-related traits. Statistical analyses of the results showed that in descriptive statistics result bending (BL, BU) has a maximum coefficient of variance, but fiber length and fiber strength have less coefficient of variance among the genotypes. Principal component analysis (PCA) trimmed quantitative characters into nine principal components. The first nine principal components (PC) with Eigenvalues > 1 explained 86% of the variation among 237 accessions of cotton. Both 2017 and 2018, PCA results indicated that BL, BU, FL, FE, and LI contributed to their variability in PC1, and BU, AU, CU, FD, LP, and FWPB have shown their variability in PC2.

[Conclusion] We describe here the systematic study of the mechanism involved in the regulation of enhancing fiber quality and yield by stem bending strength, acupuncture, and compression properties of G. hirsutum.

[Title] Correlation analysis of stem hardness traits with fiber and yield-related traits in core collections of Gossypium hirsutum

[Authors] RAZA Irum, HU Daowu, AHMAD Adeel, LI Hongge, HE Shoupu, NAZIR Mian Faisal, WANG Xiaoyang, JIA Yinhua, PAN Zhaoe, ZHANG Peng, YASIR Muhammad, IQBAL Muhammad Shahid, GENG Xiaoli, WANG Liru, PANG Baoyin and DU Xiongming

Journal of Cotton Research 2021, 48

https://doi.org/10.1186/s42397-021-00082-8

Identification, characterization, and expression profiles of the GASA genes in cotton

[Background] GASA (Giberellic Acid Stimulated in Arabidopsis) gene family plays a crucial role in the phytohormone signaling pathway, growth and development, and stress responses in plants. Many GASA homologs have been identified in various plants. Nevertheless, little is known about these proteins in cotton.

[Results] In the current study, we identified 19, 17, 25, 33, and 38 GASA genes via genome-wide analyses of Gossypium herbaceumG. arboreum, G. raimondiiG. barbadense, and G. hirsutum, respectively, and performed comprehensive bioinformatics and expression analyses. According to our results, 132 GASA proteins shared similar protein structures and were classified into four groups based on the phylogenetic tree. A synteny analysis suggested that segmental duplication was a key driver in the expansion of the GASA gene family. Meanwhile, the cis-element and protein interaction analyses indicated that GhGASA proteins play a significant role in the hormone responses. Transcriptomic and qRT-PCR (Quantitative real time-polymerase chain reaction) analyses revealed diverse expression profiles of the GhGASA genes in different organs under abiotic stresses, indicating that some GhGASA genes possibly participate in fiber development and abiotic-stress responses.

[Conclusion] The GASA genes in cotton were systematically identified and analyzed for the first time in this paper, and it suggested that the GASA genes are important to the development and growth of cotton. These results will support future exploration of the functions of GASA genes in cotton.

[Title] Identification, characterization, and expression profiles of the GASA genes in cotton

[Authors] QIAO Kaikai, MA Changkai, LV Jiaoyan, ZHANG Chaojun, MA Qifeng and FAN Shuli

Journal of Cotton Research 2021, 47

https://doi.org/10.1186/s42397-021-00081-9