JCR | Zinc finger transcription factor ZAT family genes confer multi-tolerances in Gossypium hirsutum L.

[Abstract] ZAT (Zinc Finger of Arabidopsis thaliana) proteins are composed of a plant-specific transcription factor family, which play an important role in plant growth, development, and stress resistance. To study the potential function of ZAT family in cotton, the whole genome identification, expression, and structure analysis of ZAT gene family were carried out. In this study, our analysis revealed the presence of 115, 56, 59, and 115 ZAT genes in Gossypium hirsutumG. raimondiiG. arboreum and G. barbadense, respectively. According to the number of domains and phylogenetic characteristics, we divided ZAT genes of four Gossypium species into 4 different clades, and further divided them into 11 subfamilies. The results of collinearity analysis showed that segmental duplication was the main method to amplify the cotton ZAT genes family. Analysis of cis-elements of promoters indicated that most GhZAT genes contained cis-elements related to plant hormones and abiotic stress. According to heatmap analysis, the expression patterns of GhZAT genes under different stresses indicated that GhZAT genes were significantly involved in the response to cold, heat, salt, and PEG stress, possibly through different mechanisms. Among the highly expressed genes, we cloned a G. hirsutum gene GhZAT67. Through virus-induced gene silencing (VIGS), we found that its expression level decreased significantly after being silenced. Under alkaline treatment, the wilting degree of silenced plants was even greater than the wild type, which proved that GhZAT67 gene was involved in the response to alkaline stress.

[Title] Zinc finger transcription factor ZAT family genes confer multi-tolerances in Gossypium hirsutum L.

[Authors] FAN Yapeng, ZHANG Yuexin, RUI Cun, XU Nan, ZHANG Hong, WANG Jing, MALIK Waqar Afzal, HAN Mingge, ZHAO Lanjie, LU Xuke, CHEN Xiugui, CHEN Chao & YE Wuwei

Journal of Cotton Research 2021, 424

https://doi.org/10.1186/s42397-021-00098-0

JCR | Improved Gossypium raimondii genome using a Hi-C-based proximity-guided assembly

[Introduction] Genome sequence plays an important role in both basic and applied studies. Gossypium raimondii, the putative contributor of the D subgenome of upland cotton (G. hirsutum), highlights the need to improve the genome quality rapidly and efficiently.

[Methods] We performed Hi-C sequencing of G. raimondii and reassembled its genome based on a set of new Hi-C data and previously published scaffolds. We also compared the reassembled genome sequence with the previously published G. raimondii genomes for gene and genome sequence collinearity.

[Result] A total of 98.42% of scaffold sequences were clustered successfully, among which 99.72% of the clustered sequences were ordered and 99.92% of the ordered sequences were oriented with high-quality. Further evaluation of results by heat-map and collinearity analysis revealed that the current reassembled genome is significantly improved than the previous one (Nat Genet 44:98–1103, 2012).

[Conclusion] This improvement in G. raimondii genome not only provides a better reference to increase study efficiency but also offers a new way to assemble cotton genomes. Furthermore, Hi-C data of G. raimondii may be used for 3D structure research or regulating analysis.

[Title] Improved Gossypium raimondii genome using a Hi-C-based proximity-guided assembly

[Authors] YANG Qiuhong, ZUO Dongyun, CHENG Hailiang, ZHANG Youping, WANG Qiaolian, JAVARIA Ashraf, FENG Xiaoxu, LI Simin, CHEN Xiaoqin, LIU Shang & SONG Guoli

Journal of Cotton Research 2021, 423

https://doi.org/10.1186/s42397-021-00096-2

JCR | Research progress in the population differentiation and geographical adaptation of cotton

[Abstract] Recently, Du and his team revealed the genomic basis of population differentiation and geographical distribution of Chinese cultivated G. hirsutum(upland cotton). Our previous study showed that the large-scale inversions on chromosome A08 are widely distributed in a core collection of upland cotton and have driven population differentiation in G. hirsutum. With 3248 tetraploid cotton germplasms, He et al. identified new inversions on chromosome A06, and found these inversions together with those in chromosome A08 caused subpopulation differentiation Chinese cultivars that were highly consistent with their corresponding geographical distributions. This work provides new perspectives to further understand environmental adaptation of Chinese upland cotton germplasms.

[Title] Research progress in the population differentiation and geographical adaptation of cotton

[Authors] LI Fuguang

Journal of Cotton Research 2021, 421

https://doi.org/10.1186/s42397-021-00095-3

JCR | Evolution of pectin synthesis relevant galacturonosyltransferase gene family and its expression during cotton fiber development

[Background] Pectin is a key substance involved in cell wall development, and the galacturonosyltransferases (GAUTs) gene family is a critical participant in the pectin synthesis pathway. Systematic and comprehensive research on GAUTshas not been performed in cotton. Analysis of the evolution and expression patterns of the GAUT gene family in different cotton species is needed to increase knowledge of the function of pectin in cotton fiber development.

[Results] In this study, we have identified 131 GAUT genes in the genomes of four Gossypium species (G. raimondiiG. barbadenseG. hirsutum, and G. arboreum), and classified them as GAUT-AGAUT-B and GAUT-C, which coding probable galacturonosyltransferases. Among them, the GAUT genes encode proteins GAUT1 to GAUT15. All GAUT proteins except for GAUT7 contain a conserved glycosyl transferase family 8 domain (H-DN-A-SVV-S-V-H-T-F). The conserved sequence of GAUT7 is PLN (phospholamban) 02769 domain. According to cis-elemet analysis, GAUT genes transcript levels may be regulated by hormones such as JA, GA, SA, ABA, Me-JA, and IAA. The evolution and transcription patterns of the GAUT gene family in different cotton species and the transcript levels in upland cotton lines with different fiber strength were analyzed. Peak transcript level of GhGAUT genes have been observed before 15 DPA. In the six materials with high fiber strength, the transcription of GhGAUT genes were concentrated from 10 to 15 DPA; while the highest transcript levels in low fiber strength materials were detected between 5 and 10 DPA. These results lays the foundation for future research on gene function during cotton fiber development.

[Conclusion] The GAUT gene family may affect cotton fiber development, including fiber elongation and fiber thickening. In the low strength fiber lines, GAUTs mainly participate in fiber elongation, whereas their major effect on cotton with high strength fiber is related to both elongation and thickening.

[Title] Evolution of pectin synthesis relevant galacturonosyltransferase gene family and its expression during cotton fiber development

[Authors] FAN Senmiao, LIU Aiying, ZOU Xianyan, ZHANG Zhen, GE Qun, GONG Wankui, LI Junwen, GONG Juwu, SHI Yuzhen, DENG Xiaoying, JIA Tingting, YUAN Youlu & SHANG Haihong

Journal of Cotton Research 2021, 422

https://doi.org/10.1186/s42397-021-00099-z