Upland cotton is the most widely planted for natural fiber around the world, and either lint perc... more Upland cotton is the most widely planted for natural fiber around the world, and either lint percentage (LP) or fiber length (FL) is the crucial component tremendously affecting cotton yield and fiber quality, respectively. In this study, two lines MBZ70-053 and MBZ70-236 derived from G. hirsutum CCRI70 recombinant inbred line (RIL) population presenting different phenotypes in LP and FL traits were chosen to conduct RNA sequencing on ovule and fiber samples, aiming at exploring the differences of molecular and genetic mechanisms during cotton fiber initiation and elongation stages. As a result, 249/128, 369/206, 4296/1198 and 3547/2129 up-/down- regulated differentially expressed genes (DGEs) in L2 were obtained at −3, 0, 5 and 10 days post-anthesis (DPA), respectively. Seven gene expression profiles were discriminated using Short Time-series Expression Miner (STEM) analysis; seven modules and hub genes were identified using weighted gene co-expression network analysis. The DEGs we...
Peroxiredoxin (PRX) is a ubiquitous thioredoxin-dependent peroxidase that can eliminate excessive... more Peroxiredoxin (PRX) is a ubiquitous thioredoxin-dependent peroxidase that can eliminate excessive free radicals produced by stress and protect cells from oxidative damage. PRXs are also involved in reactive oxygen species (ROS)- and redox-dependent signaling by performing redox interactions with other proteins and modify their redox status. At present, PRX family identification, evolution and regulation research has been conducted in some plants; however, systematic research about this family is lacking in cotton. In this study, a total of 44 PRXs were identified in the cotton genome. Phylogenetic and conserved active site analyses showed that the PRXs were divided into six subfamilies according to the conserved site (PxxxTxxC…S…W/F) and conserved cysteinyl residues positions. Segmental duplication and polyploid events were the main methods for PRX family expansion, and the PRXs of diploid G. arboreum were the donors of PRXs in the D subgenomes of allotetraploid G. hirsutum and G. b...
Identification of hub genes through co-expression network of major QTLs of fiber length and strength traits in multiple RIL populations of cotton
Genomics
The present study demonstrated a de novo correlation among fiber quality genes in multiple RIL po... more The present study demonstrated a de novo correlation among fiber quality genes in multiple RIL populations including sGK9708 × 0-153, LMY22 × LY343 and Lumianyan28 × Xinluzao24. The current study was conducted to identify the major common QTLs including fiber length and strength, and to identify the co-expression networks of fiber length and strength QTLs harbored genes to target the hub genes. The RNA-seq data of sGK9708 × 0-153 population highlighted 50 and 48 candidate genes of fiber length and fiber strength QTLs. A total of 29 and 21 hub genes were identified in fiber length and strength co-expression network modules. The absolute values of correlation coefficient close to 1 resulted highly positive correlation among hub genes. Results also suggested that the gene correlation significantly influence the gene expression at different fiber development stages. These results might provide useful reference for further experiments in multiple RIL populations and suggest potential candidate genes for functional studies in cotton.
In this study, a total of 66 UDP-glucose pyrophosphorylase (UGP) (EC 2.7.7.9) genes were identifi... more In this study, a total of 66 UDP-glucose pyrophosphorylase (UGP) (EC 2.7.7.9) genes were identified from the genomes of four cotton species, which are the members of Pfam glycosyltransferase family (PF01702) and catalyze the reaction between glucose-1-phosphate and UTP to produce UDPG. The analysis of evolutionary relationship, gene structure, and expression provides the basis for studies on function of UGP genes in cotton. The evolutionary tree and gene structure analysis revealed that the UGP gene family is evolutionarily conserved. Collinearity and Ka/Ks analysis indicated that amplification of UGP genes is due to repetitive crosstalk generating between new family genes, while being under strong selection pressure. The analysis of cis-acting elements exhibited that UGP genes play important role in cotton growth, development, abiotic and hormonal stresses. Six UGP genes that were highly expressed in cotton fiber at 15 DPA were screened by transcriptome data and qRT-PCR analysis. T...
Additional file 1: Table S1. of Genome-wide identification, phylogeny, and expression analysis of pectin methylesterases reveal their major role in cotton fiber development
PMEs genes identified from the three cotton species. (XLSX 36 kb)
Additional file 3: of Quantitative trait loci analysis of Verticillium wilt resistance in interspecific backcross populations of Gossypium hirsutum × Gossypium barbadense
The genotype datasets of 135 BC1F1 plants of CCRI36× Hai1. (XLSX 1247 kb)
Additional file 1: Table S1. of Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.)
Distribution of the SNP markersâ type on the genetic map. (XLSX 9Â kb)
Additional file 10: Table S8. of Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.)
The KEGG annotation result of all the candidate genes of the stable QTLs of cotton boll weight. (... more The KEGG annotation result of all the candidate genes of the stable QTLs of cotton boll weight. (XLSX 15Â kb)
Additional file 3: Table S3. of Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.)
The X2_value and P_value of all the markers in the genetic map. (XLSX 233Â kb)
Additional file 12: Table S10. of Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.)
The KOG annotation result all the candidate genes of the stable QTLs of cotton boll weight. (XLSX... more The KOG annotation result all the candidate genes of the stable QTLs of cotton boll weight. (XLSX 15Â kb)
Additional file 13: Table S11. of Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.)
The number of the candidate genes in each function categories of the KOG annotation. (XLSX 11Â kb)
Fusarium wilt (FW) caused by race 4 (FOV4) of the soil-borne fungus Fusarium oxysporum f. sp. vas... more Fusarium wilt (FW) caused by race 4 (FOV4) of the soil-borne fungus Fusarium oxysporum f. sp. vasinfectum causes high cotton seedling mortality under field conditions in the west and southwest US Cotton Belt. The objectives of this study were to evaluate the dynamic responses to FOV4 infections in two introgressed Upland cotton (Gossypium hirsutum) populations using an artificial inoculation and screening method. The two populations (IL-122 with 120 introgressed lines and BIL-193 with 180 backcross inbred lines) were derived from backcrossing the same recurrent Upland parent (FOV4 resistant) to two different interspecific hybrids each with a different G. barbadense parent (FOV4 susceptible). The two populations, together with their parents and other Upland lines were evaluated in three independent replicated tests for FOV4 responses at 7, 14, 21, and 28 days after inoculation (DAI) under temperaturecontrolled conditions at 20-21°C, based on three evaluating parameters-disease incidence (DI), disease severity rating (DSR) and mortality rate (MR). Wilted seedlings were observed as the initial FW symptoms in 21% of the lines within 7 DAI, and no line had 0% DI across the three tests at 28 DAI. DI, DSR and MR were highly and significantly correlated among one another at 14, 21, and 28 DAI, and 21 DAI had the strongest correlations with 14 and 28 DAI. The results suggest that responses to FOV4 infections were overall congruent among DAI in the two cotton populations, and DSR at as early as 21 DAI can be used to assess germplasm lines for FOV4 resistance. Based on responses to FOV4 at 7, 14, 21 and 28 DAI, 17 of the 88 susceptible lines in the IL-122 population at 28 DAI showed resistant responses at 7-14 and/or 7-21 DAI, and they may provide resistant responses in early stages of FOV4 infections. Among 34 resistant (R) lines at 28 DAI, 22 lines showing susceptible (S) responses at 14 and/or 21 DAI. Similar results were observed in the BIL-193 population. The result showed that there were lines with unique responses (R or S) during different DAI and represented one of the first such studies in cotton. It provides a set of unique lines for further studies at the structural, biochemical and molecular levels and an incentive to investigate the genetic and genomic basis of the Jinfa Zhang and Abdelraheem Abdelraheems contributed equally to this work.
Upland cotton (Gossypium hirsutum) is widely planted around the world for its natural fiber, and ... more Upland cotton (Gossypium hirsutum) is widely planted around the world for its natural fiber, and producing high-quality fiber is essential for the textile industry. CCRI70 is a hybrid cotton plant harboring superior yield and fiber quality, whose recombinant inbred line (RIL) population was developed from two upland cotton varieties (sGK156 and 901-001) and were used here to investigate the source of high-quality related alleles. Based on the material of the whole population, a high-density genetic map was constructed using specific locus-amplified fragment sequencing (SLAF-seq). It contained 24,425 single nucleotide polymorphism (SNP) markers, spanning a distance of 4,850.47 centimorgans (cM) over 26 chromosomes with an average marker interval of 0.20 cM. In evaluating three fiber quality traits in nine environments to detect multiple environments stable quantitative trait loci (QTLs), we found 289 QTLs, of which 36 of them were stable QTLs and 18 were novel. Based on the transcrip...
Background Cotton (Gossypium hirsutum L.) is grown for fiber and oil purposes in tropical and sub... more Background Cotton (Gossypium hirsutum L.) is grown for fiber and oil purposes in tropical and sub-tropical areas of the world. Pakistan is the 4th largest producer of cotton. It has a significant contribution in the GDP of Pakistan. Therefore, the present study was performed to assess the genetic variations and genetic diversity of yield and fiber quality traits in cotton and to analyze the associations present among them. Results Analysis of variance exhibited significant variation for all studied traits except total number of nodes and the height to node ratio. The phenotypic coefficient of variation was higher than the genotypic coefficient of variation for all studied traits. Plant height, monopodial branches, total number of bolls, lint index, seed index, and seed cotton yield displayed high heritabilities in a broad sense with maximum genetic advance. Correlation analysis revealed that seed cotton yield had a significant positive association with plant height, the number of mo...
A RIL(recombinant inbred lines) population with 196 F6:9 lines was developed from an F2 populatio... more A RIL(recombinant inbred lines) population with 196 F6:9 lines was developed from an F2 population of upland cotton (Gossypium hirsutum L.) cross of sGK9708×0-153. sGK9708 is a commercial transgenic variety with Bt+CpTI genes resistant to budworm and 0-153 with high fibre quality. Five materials with high fibre strength and five materials with low fibre strength from the recombinant inbred lines were researched [1]. Ten materials of su per-molecular structure and fibre quality were studied by X-ray diffraction and the HVI900 technique. The results indicated that cotton matured fibre quality should mainly depend on the decrease in the orientational parameter in the crystalline section, especially the orientational separate and orientational distribution angles. The correlation of fibre maturity, linear density and the fibre super-molecular structure is an innovation in the study. Studies on the correlation of cotton fibre quality and the fibre super-molecular structure provide a scie...
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