Showing papers by "Shuxun Yu published in 2021"

Genomic analyses reveal the genetic basis of early maturity and identification of loci and candidate genes in upland cotton (Gossypium hirsutum L.).

Abstract: Although upland cotton (Gossypium hirsutism L.) originated in the tropics, this early maturity cotton can be planted as far north as 46°N in China due to the accumulation of numerous phenotypic and physiological adaptations during domestication. However, how the genome of early maturity cotton has been altered by strong human selection remains largely unknown. Herein, we report a cotton genome variation map generated by the resequencing of 436 cotton accessions. Whole-genome scans for sweep regions identified 357 putative selection sweeps covering 4.94% (112 Mb) of the upland cotton genome, including 5184 genes. These genes were functionally related to flowering time control, hormone catabolism, ageing and defence response adaptations to environmental changes. A genome-wide association study (GWAS) for seven early maturity traits identified 307 significant loci, 22.48% (69) of which overlapped with putative selection sweeps that occurred during the artificial selection of early maturity cotton. Several previously undescribed candidate genes associated with early maturity were identified by GWAS. This study provides insights into the genetic basis of early maturity in upland cotton as well as breeding resources for cotton improvement.

Multi-Omics-Based Identification and Functional Characterization of Gh_A06G1257 Proves Its Potential Role in Drought Stress Tolerance in Gossypium hirsutum.

Abstract: Cotton is one of the most important fiber crops globally. Despite this, various abiotic stresses, including drought, cause yield losses. We used transcriptome profiles to investigate the co-expression patterns of gene networks associated with drought stress tolerance. We identified three gene modules containing 3,567 genes highly associated with drought stress tolerance. Within these modules, we identified 13 hub genes based on intramodular significance, for further validation. The yellow module has five hub genes (Gh_A07G0563, Gh_D05G0221, Gh_A05G3716, Gh_D12G1438, and Gh_D05G0697), the brown module contains three hub genes belonging to the aldehyde dehydrogenase (ALDH) gene family (Gh_A06G1257, Gh_A06G1256, and Gh_D06G1578), and the pink module has five hub genes (Gh_A02G1616, Gh_D12G2599, Gh_D07G2232, Gh_A02G0527, and Gh_D07G0629). Based on RT-qPCR results, the Gh_A06G1257 gene has the highest expression under drought stress in different plant tissues and it might be the true candidate gene linked to drought stress tolerance in cotton. Silencing of Gh_A06G1257 in cotton leaves conferred significant sensitivity in response to drought stress treatments. Overexpression of Gh_A06G1257 in Arabidopsis also confirms its role in drought stress tolerance. L-valine, Glutaric acid, L-proline, L-Glutamic acid, and L-Tryptophan were found to be the most significant metabolites playing roles in drought stress tolerance. These findings add significantly to existing knowledge of drought stress tolerance mechanisms in cotton.

Overexpression of GhMPK3 from Cotton Enhances Cold, Drought, and Salt Stress in Arabidopsis

Abstract: Cotton production is hampered by a variety of abiotic stresses that wreak havoc on the growth and development of plants, resulting in significant financial losses. According to reports, cotton production areas have declined around the world as a result of the ongoing stress. Therefore, plant breeding programs are concentrating on abiotic stress-tolerant cotton varieties. Mitogen-activated protein kinase (MAPK) cascades are involved in plant growth, stress responses, and the hormonal signaling pathway. In this research, three abiotic stresses (cold, drought, and salt) were analyzed on GhMPK3 transformed Arabidopsis plants. The transgenic plant’s gene expression and morphologic analysis were studied under cold, drought, and salt stress. Physiological parameters such as relative leaf water content, excised leaf water loss, chlorophyll content, and ion leakage showed that overexpressed plants possess more stable content under stress conditions compared with the WT plants. Furthermore, GhMPK3 overexpressed plants had greater antioxidant activities and weaker oxidant activities. Silencing GhMPK3 in cotton inhibited its tolerance to drought stress. Our research findings strongly suggest that GhMPK3 can be regarded as an essential gene for abiotic stress tolerance in cotton plants.

Comprehensive identification and expression analysis of B-Box genes in cotton.

Abstract: B-BOX (BBX) proteins are zinc-finger transcription factors with one or two BBX domains and sometimes a CCT domain. These proteins play an essential role in regulating plant growth and development, as well as in resisting abiotic stress. So far, the BBX gene family has been widely studied in other crops. However, no one has systematically studied the BBX gene in cotton. In the present study, 17, 18, 37 and 33 BBX genes were detected in Gossypium arboreum, G. raimondii, G. hirsutum and G. barbadense, respectively, via genome-wide identification. Phylogenetic analysis showed that all BBX genes were divided into 5 main categories. The protein motifs and exon/intron structures showed that each group of BBX genes was highly conserved. Collinearity analysis revealed that the amplification of BBX gene family in Gossypium spp. was mainly through segmental replication. Nonsynonymous (Ka)/ synonymous (Ks) substitution ratios indicated that the BBX gene family had undergone purification selection throughout the long-term natural selection process. Moreover, transcriptomic data showed that some GhBBX genes were highly expressed in floral organs. The qRT-PCR results showed that there were significant differences in GhBBX genes in leaves and shoot apexes between early-maturing materials and late-maturing materials at most periods. Yeast two-hybrid results showed that GhBBX5/GhBBX23 and GhBBX8/GhBBX26 might interact with GhFT. Transcriptome data analysis and qRT-PCR verification showed that different GhBBX genes had different biological functions in abiotic stress and phytohormone response. Our comprehensive analysis of BBX in G. hirsutum provided a basis for further study on the molecular role of GhBBXs in regulating flowering and cotton resistance to abiotic stress.

QTL mapping and candidate gene identification of lint percentage based on a recombinant inbred line population of upland cotton

Abstract: Lint percentage is a major yield component in cotton breeding programmes. To identify quantitative trait loci (QTLs) and candidate genes related to lint percentage, we used an intraspecific recombinant inbred line population of 137 lines derived from Gossypium hirsutum cv. CCRI36 and G. hirsutum acc. G2005 for QTL mapping of lint percentage. Based on a high-density genetic map and phenotype data collected in four growing environments, we identified a total of 28 QTLs for lint percentage. Three stable QTLs (qLP-At5-2, qLP-Dt7-1 and qLP-Dt7-2) were detected in at least two environments. Two genes (Gh_A05G1584 and Gh_A05G1689) containing nonsynonymous single nucleotide polymorphisms (SNPs) were identified by association analysis using published data. The quantitative real-time PCR results showed that the expression levels of Gh_A05G1584 were higher in cv. CCRI36 than in acc. G2005 during all fibre development stages; Gh_A05G1689 was mainly expressed in 15 and 25 days post-anthesis fibres and its expression level was higher in cv. CCRI36. These results suggest candidate genes for lint percentage and provide molecular information for use in cotton breeding programmes aimed at improving yield.

GhGPAT12/25 Are Essential for the Formation of Anther Cuticle and Pollen Exine in Cotton (Gossypium hirsutum L.).

Abstract: Glycerol-3-phosphate acyltransferases (GPATs), critical for multiple biological processes like male fertility, have been extensively characterized. However, their precise functions and underlying regulatory mechanism in cotton anther development are unclear. This research demonstrated the importance of GhGPAT12/25 (a paralogs pair on A12/D12 sub-chromosome of cotton) to regulate the degradation of tapetum, anther cuticle formation, and pollen exine development. GhGPAT12 and GhGPAT25 exhibited specifically detected transcripts in tapetum and pollen exine during the early anther developmental stages. GhGPAT12/25 are sn-2 glycerol-3-phosphate acyltransferases and can transfer the acyl group of palmitoyl-CoA to glycerol-3-phosphate (G3P). CRISPR/Cas9-mediated knockout identified the functional redundancy of GhGPAT12 and GhGPAT25. Knockout of both genes caused completely male sterility associated with abnormal anther cuticle, swollen tapetum, and inviable microspores with defective exine and irregular unrestricted shape. RNA-seq analysis showed that the loss of function of GhGPAT12/25 affects the processes of wax metabolic, glycerol monomer biosynthesis, and transport. Consistently, cuticular waxes were dramatically reduced in mutant anthers. Yeast one-hybrid system (Y1H), virus-induced gene silencing (VIGS), and dual-luciferase (LUC) assays illustrated that GhMYB80s are likely to directly activate the expression of GhGPAT12/25. This study provides important insights for revealing the regulatory mechanism underlying anther development in cotton.

Phylogenetic Analysis of the Membrane Attack Complex/Perforin Domain-Containing Proteins in Gossypium and the Role of GhMACPF26 in Cotton Under Cold Stress

Abstract: Membrane-attack complex/perforin (MACPF) domain-containing proteins are involved in various developmental processes, and in responding to diverse abiotic stress. The function and regulatory network of MACPF genes are rarely reported in Gossypium spp. Here, we gave the detailed identification and partial functional verification of the members of the MACPF family. Totally, 100 putative MACPF proteins containing complete MACPF domain were identified from four cotton species. They were classified into three phylogenetic groups, and underwent multifold pressure indicating that selection produced new functional differentiation. Cotton MACPF gene family members expanded mainly through whole genome duplication (WGD) /segmental, followed by the dispersed. Expression and cis-acting elements analysis revealed that MACPFs play a role in resistance to abiotic stresses, and some selected GhMACPFs were able to respond to the PEG and cold stresses. Co-expression analysis showed that GhMACPFs might interact with valine-glutamine (VQ), WRKY, and AP2/ERF domain-containing genes under cold stress. In addition, silencing endogenous GhMACPF26 in cotton by virus-induced gene silencing (VIGS) method indicated that GhMACPF26 negatively regulates cold tolerance. Our data provided a comprehensive phylogenetic evolutionary view of Gossypium MACPFs. MACPFs may work together with multiple transcriptional factors and play roles in acclimation to abiotic stress, especially cold stress in cotton.