scholarly journals Transcriptome Analysis of Ten Days Post Anthesis Elongating Fiber in the Upland Cotton (<i>Gossypium hirsutum</i>) Chromosome Substitution Line CS-B25

2018 ◽  
Vol 09 (06) ◽  
pp. 1334-1361 ◽  
Author(s):  
Chuan-Yu Hsu ◽  
Mark A. Arick ◽  
Qing Miao ◽  
Sukumar Saha ◽  
Johnie N. Jenkins ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Transcriptome Analysis ◽  
Upland Cotton ◽  
Substitution Line ◽  
Chromosome Substitution ◽  
Chromosome Substitution Line

scholarly journals Comparative transcriptome analysis of fiber and nonfiber tissues to identify the genes preferentially expressed in fiber development in Gossypium hirsutum

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jiangtao Yang ◽  
Lihua Gao ◽  
Xiaojing Liu ◽  
Xiaochun Zhang ◽  
Xujing Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gossypium Hirsutum ◽  
Rna Sequencing ◽  
Transcriptome Analysis ◽  
Cotton Fiber ◽  
Upland Cotton ◽  
Fiber Quality ◽  
Fiber Development ◽  
Comparative Transcriptome

AbstractCotton is an important natural fiber crop and economic crop worldwide. The quality of cotton fiber directly determines the quality of cotton textiles. Identifying cotton fiber development-related genes and exploring their biological functions will not only help to better understand the elongation and development mechanisms of cotton fibers but also provide a theoretical basis for the cultivation of new cotton varieties with excellent fiber quality. In this study, RNA sequencing technology was used to construct transcriptome databases for different nonfiber tissues (root, leaf, anther and stigma) and fiber developmental stages (7 days post-anthesis (DPA), 14 DPA, and 26 DPA) of upland cotton Coker 312. The sizes of the seven transcriptome databases constructed ranged from 4.43 to 5.20 Gb, corresponding to approximately twice the genome size of Gossypium hirsutum (2.5 Gb). Among the obtained clean reads, 83.32% to 88.22% could be compared to the upland cotton TM-1 reference genome. By analyzing the differential gene expression profiles of the transcriptome libraries of fiber and nonfiber tissues, we obtained 1205, 1135 and 937 genes with significantly upregulated expression at 7 DPA, 14 DPA and 26 DPA, respectively, and 124, 179 and 213 genes with significantly downregulated expression. Subsequently, Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analyses were performed, which revealed that these genes were mainly involved in catalytic activity, carbohydrate metabolism, the cell membrane and organelles, signal transduction and other functions and metabolic pathways. Through gene annotation analysis, many transcription factors and genes related to fiber development were screened. Thirty-six genes were randomly selected from the significantly upregulated genes in fiber, and expression profile analysis was performed using qRT-PCR. The results were highly consistent with the gene expression profile analyzed by RNA-seq, and all of the genes were specifically or predominantly expressed in fiber. Therefore, our RNA sequencing-based comparative transcriptome analysis will lay a foundation for future research to provide new genetic resources for the genetic engineering of improved cotton fiber quality and for cultivating new transgenic cotton germplasms for fiber quality improvement.

Introgression of wheat chromosome 2D or 5D into tritordeum leads to free-threshing habit

Genome ◽  
2007 ◽  
Vol 50 (11) ◽  
pp. 994-1000 ◽  
Author(s):  
S. G. Atienza ◽  
A. C. Martín ◽  
A. Martín
Keyword(s):  
Mitotic Chromosome ◽  
Wheat Chromosome ◽  
Substitution Line ◽  
Hordeum Chilense ◽  
Chromosome Substitution ◽  
D Genome ◽  
Chromosome Substitution Line ◽  
New Crop ◽  
Free Threshing

Hexaploid tritordeum is the amphiploid derived from the cross between the diploid wild barley Hordeum chilense and durum wheat. The non-free-threshing habit is a constraint to this species becoming a new crop. Three tritordeum lines (HT374, HT376, and HT382) showing the free-threshing habit were selected from crosses between tritordeum and bread wheat. All three lines were euploids, as revealed by mitotic chromosome counting. Genomic in situ hybridization analysis made it possible to distinguish differences among these lines. While the line HT382 carries only 10 chromosomes from H. chilense, the lines HT374 and HT376 have 12. These results suggest that HT382 is a double chromosome substitution line between H. chilense and the wheat D genome, while HT374 and HT376 each have one pair of H. chilense (Hch) chromosomes substituted by wheat D chromosomes. Molecular characterization revealed that HT382 is a 1D/(1Hch), 2D/(2Hch) chromosome substitution line, whereas HT374 and HT376 have 5D/(5Hch) substitutions. On the basis of previous knowledge, it seems that the absence of chromosome 2Hch or 5Hch is more important for producing the free-threshing habit than the presence of chromosome 2D or 5D, while chromosome 1Hch seems to be unrelated to the trait. These free-threshing tritordeum lines constitute an important advance in the tritordeum breeding program.

scholarly journals Transcriptome Analysis of Ten-DPA Fiber in an Upland Cotton (<i>Gossypium hirsutum</i>) Line with Improved Fiber Traits from Phytochrome A1 RNAi Plants

2017 ◽  
Vol 08 (10) ◽  
pp. 2530-2553 ◽  
Author(s):  
Qing Miao ◽  
Peng Deng ◽  
Sukumar Saha ◽  
Johnie N. Jenkins ◽  
Chuan-Yu Hsu ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Transcriptome Analysis ◽  
Upland Cotton ◽  
Fiber Traits

scholarly journals Genome-Wide Analysis of the Cytochrome P450 Gene Family Involved in Salt Tolerance in Gossypium hirsutum

2021 ◽  
Vol 12 ◽  
Author(s):  
Kangtai Sun ◽  
Hui Fang ◽  
Yu Chen ◽  
Zhimin Zhuang ◽  
Qi Chen ◽  
...  
Keyword(s):  
Cytochrome P450 ◽  
Salt Tolerance ◽  
Gossypium Hirsutum ◽  
Gene Family ◽  
Gene Structure ◽  
Transcriptome Analysis ◽  
Upland Cotton ◽  
Chromosomal Localization ◽  
P450 Gene ◽  
Qrt Pcr

Plant cytochrome P450 (P450) participates in a wide range of biosynthetic reactions and targets a variety of biological molecules. These reactions lead to various fatty acid conjugates, plant hormones, secondary metabolites, lignin, and various defensive compounds. In our previous research, transcriptome analysis was performed on the salt-tolerant upland cotton “Tongyan No. 1.” Many differentially expressed genes (DEGs) belong to the P450 family, and their domains occur widely in plants. In this current research, P450 genes were identified in Gossypium hirsutum with the aid of bioinformatics methods for investigating phylogenetic relations, gene structure, cis-elements, chromosomal localization, and collinearity within a genome. qRT-PCR was conducted to analyze P450 gene expression patterns under salt stress. The molecular weights of the 156 P450 genes were in the range of 5,949.6–245,576.3 Da, and the length of the encoded amino acids for all the identified P450 genes ranged from 51 to 2,144. P450 proteins are divided into four different subfamilies based on phylogenetic relationship, gene structure, and chromosomal localization of gene replication. The length of P450 genes in upland cotton differs greatly, ranging from 1,500 to 13,000 bp. The number of exons in the P450 family genes ranged from 1 to 9, while the number of introns ranged from 0 to 8, and there were similar trends within clusters. A total of 31 cis-acting elements were identified by analyzing 1,500 bp promoter sequences. Differences were found in cis-acting elements among genes. The consistency between qRT-PCR and previous transcriptome analysis of salt tolerance DEGs indicated that they were likely to be involved in the salt tolerance of cotton seedlings. Our results provide valuable information on the evolutionary relationships of genes and functional characteristics of the gene family, which is beneficial for further study of the cotton P450 gene family.

scholarly journals Quantitative Trait Loci and Transcriptome Analysis Reveal Genetic Basis of Fiber Quality Traits in CCRI70 RIL Population of Gossypium hirsutum

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiao Jiang ◽  
Juwu Gong ◽  
Jianhong Zhang ◽  
Zhen Zhang ◽  
Yuzhen Shi ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Gossypium Hirsutum ◽  
Transcriptome Analysis ◽  
Quantitative Trait ◽  
Upland Cotton ◽  
Fiber Quality ◽  
Quality Traits ◽  
High Quality ◽  
Fiber Quality Traits ◽  
Ril Population

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 transcriptome analysis for two parents and two RILs, 24,941 unique differentially expressed genes (DEGs) were identified, 473 of which were promising genes. For the fiber strength (FS) QTLs, 320 DEGs were identified, suggesting that pectin synthesis, phenylpropanoid biosynthesis, and plant hormone signaling pathways could influence FS, and several transcription factors may regulate fiber development, such as GAE6, C4H, OMT1, AFR18, EIN3, bZIP44, and GAI. Notably, the marker D13_56413025 in qFS-chr18-4 provides a potential basis for enhancing fiber quality of upland cotton via marker-assisted breeding and gene cloning of important fiber quality traits.

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