Search

Interspecific breeding in cotton takes advantage of genetic recombination among desirable genes from different parental lines. However, the expression new alleles (ENAs) from crossovers within genic regions and their significance in fibre length (FL) improvement are currently not understood. Here, we generated resequencing genomes of 191 interspecific backcross inbred lines derived from CRI36 (Gossypium hirsutum) × Hai7124 (Gossypium barbadense) and 277 dynamic fibre transcriptomes to identify the ENAs and extremely expressed genes (eGenes) potentially influencing FL, and uncovered the dynamic regulatory network of fibre elongation. Of 35 420 eGenes in developing fibres, 10 366 ENAs were identified and preferentially distributed in chromosomes subtelomeric regions. In total, 1056-1255 ENAs showed transgressive expression in fibres at 5-15 dpa (days post-anthesis) of some BILs, 520 of which were located in FL-quantitative trait locus (QTLs) and GhFLA9 (recombination allele) was identified with a larger effect for FL than GhFLA9 of CRI36 allele. Using ENAs as a type of markers, we identified three novel FL-QTLs. Additionally, 456 extremely eGenes were identified that were preferentially distributed in recombination hotspots. Importantly, 34 of them were significantly associated with FL. Gene expression quantitative trait locus analysis identified 1286, 1089 and 1059 eGenes that were colocalized with the FL trait at 5, 10 and 15 dpa, respectively. Finally, we verified the Ghir_D10G011050 gene linked to fibre elongation by the CRISPR-cas9 system. This study provides the first glimpse into the occurrence, distribution and expression of the developing fibres genes (especially ENAs) in an introgression population, and their possible biological significance in FL.

A backcross inbred line population of cotton was evaluated for Fusarium wilt race 4 resistance at different days after inoculation (DAI). Both constitutively expressed and developmentally regulated QTLs were detected. The soil-borne fungus Fusarium oxysporum f. sp. vasinfectum (FOV) race 4 (FOV4) causes Fusarium wilt including seedling mortality in cotton. A backcross inbred line (BIL) population of 181 lines, derived from a bi-parental cross of moderately resistant non-recurrent Hai 7124 (Gossypium barbadense) and recurrent parent CCRI 36 (G. hirsutum), was evaluated under temperature-controlled conditions for FOV4 resistance with artificial inoculations. Based on three replicated tests evaluated at 7, 14, 21, and 28 days after inoculation (DAI), only 2-5 BILs showed lower disease severity ratings (DSR) than the parents while 22-50 BILs were more susceptible, indicating transgressive segregation toward susceptibility. Although DSR were overall congruent between DAI, there were many BILs displaying different responses to FOV4 across DAI. Genetic mapping using 7709 SNP markers identified 42 unique QTLs for four evaluation parameters- disease incidence (DI), DSR, mortality rate (MR), and area under disease progress curve (AUDPC), including 26 for two or more parameters. All five QTLs for AUDPC were co-localized with QTLs for DI, DSR, and/or MR at one or two DAI, indicating the unnecessary use of AUDPC in QTL mapping for FOV4 resistance. Those common QTLs explained the significant positive associations between parameters observed. Ten common QTLs with negative or positive additive effects were detected between DAI. DAI-specific and consistent QTLs were detected between DAI in cotton for the first time, suggesting the existence of both constitutively expressed and developmentally regulated QTLs for FOV4 resistance and the importance of evaluating genetic populations for FOV4 resistance at different growth stages.

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 20∼25 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). Conclusions This study provides a genetic reference for genetic improvement of cotton fiber micronaire and a foundation for verification of the functions of GhFLA9.

Cotton fiber is one of the most important natural raw materials in the world textile industry. Improving fiber yield and quality has always been the main goal. MicroRNAs, as typical small noncoding RNAs, could affect fiber length during different stages of fiber development. Based on differentially expressed microRNA in the two interspecific backcross inbred lines (BILs) with a significant difference in fiber length, we identified the miR396 gene family in the two tetraploid cotton genomes and found MIR396b_D13 as the functional precursor to produce mature miR396 during the fiber elongation stage. Among 46 target genes regulated by miR396b, the GROWTH-REGULATING FACTOR 5 gene (GRF5, Gh_A10G0492) had a differential expression level in the two BILs during fiber elongation stage. The expression patterns indicated that the miR396b-GRF5 regulatory module has a critical role in fiber development. Furthermore, virus-induced gene silencing (VIGS) of miR396b significantly produced longer fiber than the wild type, and the expression level of GRF5 showed the reverse trends of the miR396b expression level. The analysis of co-expression network for the GRF5 gene suggested that a cytochrome P450 gene functions as an allene oxide synthase (Gh_D06G0089, AOS), which plays a critical role in jasmonate biosynthetic pathway. In conclusion, our results revealed that the miR396b-GRF5 module has a critical role in fiber development. These findings provide a molecular foundation for fiber quality improvement in the future.

Cotton is not only the most important fiber crop but also the fifth most important oilseed crop in the world because of its oil-rich seeds as a byproduct of fiber production. By comparative transcriptome analysis between two germplasms with diverse oil accumulation, we reveal pieces of the gene expression network involved in the process of oil synthesis in cottonseeds. Approximately, 197.16 Gb of raw data from 30 RNA sequencing samples with 3 biological replicates were generated. Comparison of the high-oil and low-oil transcriptomes enabled the identification of 7682 differentially expressed genes (DEGs). Based on gene expression profiles relevant to triacylglycerol (TAG) biosynthesis, we proposed that the Kennedy pathway (diacylglycerol acyltransferase-catalyzed diacylglycerol to TAG) is the main pathway for oil production, rather than the phospholipid diacylglycerol acyltransferase-mediated pathway. Using weighted gene co-expression network analysis, 5312 DEGs were obtained and classified into 14 co-expression modules, including the MEblack module containing 10 genes involved in lipid metabolism. Among the DEGs in the MEblack module, GhCYSD1 was identified as a potential key player in oil biosynthesis. The overexpression of GhCYSD1 in yeast resulted in increased oil content and altered fatty acid composition. This study may not only shed more light on the underlying molecular mechanism of oil accumulation in cottonseed oil, but also provide a set of new gene for potential enhancement of oil content in cottonseeds.

Seed size and shape are key agronomic traits affecting seedcotton yield and seed quality in cotton (

Main conclusion The MIR160 family in Gossypium hirsutum and G. barbadense was characterized, and miR160a_A05 was found to increase cotton-fiber length by downregulating its target gene (ARF17) and several GH3 genes. Abstract Cotton fiber is the most important raw material for the textile industry. MicroRNAs are involved in regulating cotton-fiber development, but a role in fiber elongation has not been demonstrated. In this study, miR160a was found to be differentially expressed in elongating fibers between two interspecific (between Gossypium hirsutum and G. barbadense) backcross inbred lines (BILs) with different fiber lengths. The gene MIR160 colocalized with a previously mapped fiber-length quantitative trait locus. Its target gene ARF17 was differentially expressed between the two BILs during fiber elongation, but in the inverse fashion. Bioinformatics was used to analyze the MIR160 family in both G. hirsutum and G. barbadense. Moreover, qRT–PCR analysis identified MIR160a as the functional MIR160 gene encoding the miR160a precursor during fiber elongation. Using virus-induced gene silencing and overexpression, overexpressed MIR160a_A05 resulted in significantly longer fibers compared with wild type, whereas suppression of miR160 resulted in significantly shorter fibers. Expression levels of the target gene auxin-response factor 17 (ARF17) and related genes GH3 in the two BILs and/or the virus-infected plants demonstrated similar changes in response to modulation of miR160a level. Finally, overexpression or suppression of miR160 increased or decreased, respectively, the cellular level of indole-3-acetic acid, which is involved in fiber elongation. These results describe a specific regulatory mechanism for fiber elongation in cotton that can be utilized for future crop improvement.

BackgroundMicronaire is a comprehensive index reflecting fineness and maturity of cotton fibers. It is one of the important internal quality indicators of cotton fibers and is closely related to the use value of cotton fibers. Understanding the genetic basis of micronaire is required for the genetic improvement of the trait. However, the underlying genetic architecture at the genomic level is not yet clear. The aim of this study was to use GWAS to dissect the genetic mechanism underlying the micronaire trait in 83 representative upland cotton lines grown in multiple environments.ResultsThe GWAS of micronaire was conducted using 83 upland cotton accessions and the Cotton 63K Illumina Infinium SNP array. A total of 11 quantitative trait loci (QTLs) on 10 chromosomes for micronaire were detected. Among these 11 QTLs, 27 genes with specific expression patterns were identified and selected. One novel QTL, qFM-A12-1, included 12 significant SNPs, and GhFLA9 was identified as a candidate gene based on the strong, direct LD relationships between the significantly related SNPs and the gene and a haplotype block analysis. GhFLA9 was highly expressed during secondary wall thickening at 20-25 days post-anthesis (DPA). Its expression level was significantly higher in low-micronaire line (Msco-12) than in high-micronaire line (Chuangyou-9).Conclusions This study provides a genetic reference for the genetic improvement of cotton fiber micronaire (FM) and lays a foundation for the functional verification of GhFLA9.

Active natural productscan be valuable lead compounds and numerous drugs derived from natural products have successfully entered the clinic. Arenobufagin, one of the important active components of toad venom, indicates significant antitumor activities with limited preclinical development for its strong cardiotoxicity. Ten 3-monopeptide substituted arenobufagin derivatives have been designed and synthesized. Antitumor activity and cardiotoxicity assays lead to the discovery of compound ZM226 as a potent antitumor agent with low cardiotoxicity. These findings suggest optimization of arenobufagin on position 3 maybe an efficacious strategy for the development of antitumor drug candidates derived from arenobufagin.

Cottonseed oil is one of the most important renewable resources for edible oil and biodiesel. To detect QTLs associated with cottonseed oil content (OC) and identify candidate genes that regulate oil biosynthesis, a panel of upland cotton germplasm lines was selected among those previously used to perform GWASs in China. In the present study, 13 QTLs associated with 53 common SNPs on 13 chromosomes were identified in multiple environments based on 15,369 polymorphic SNPs using the Cotton63 KSNP array. Of these, the OC QTL qOC-Dt5-1 delineated by nine SNPs occurred in a confidence interval of 4 SSRs with previously reported OC QTLs. A combined transcriptome and qRT-PCR analysis revealed that a peroxidase gene (GhPRXR1) was predominantly expressed during the middle-late stage (20–35 days post anthesis) of ovule development. The overexpression of GhPRXR1 in yeast significantly increased the OC by 20.01–37.25 %. Suppression of GhPRXR1 gene expression in the virus-induced gene-silenced cotton reduced the OC by 18.11%. Our results contribute to identifying more OC QTLs and verifying a candidate gene that influences cottonseed oil biosynthesis.

Cotton (Gossypium spp.) is the most important natural fiber crop in the world. The R2R3-MYB gene family is a large gene family involved in many plant functions including cotton fiber development. Although previous studies have reported its phylogenetic relationships, gene structures, and expression patterns in tetraploid G. hirsutum and diploid G. raimondii, little is known about the sequence variation of the members between G. hirsutum and G. barbadense and their involvement in the natural quantitative variation in fiber quality and yield. In this study, a comprehensive genome-wide comparative analysis was performed among the four Gossypium species using whole genome sequences, i.e., tetraploid G. hirsutum (AD1) and G. barbadense (AD2) as well as their likely ancestral diploid extants G. raimondii (D5) and G. arboreum (A2), leading to the identification of 406, 393, 216, and 213 R2R3-MYB genes, respectively. To elucidate whether the R2R3-MYB genes are genetically associated with fiber quality traits, 86 R2R3-MYB genes were co-localized with quantitative trait loci (QTL) hotspots for fiber quality and yield, including 42 genes localized within the fiber length QTL hotspots, in interspecific G. hirsutum × G. barbadense populations. There were 20 interspecific nonsynonymous single-nucleotide polymorphism (SNP) sites between the two tetraploid cultivated species, of which 16 developed from 11 R2R3-MYB genes were significantly correlated with fiber quality and yield in a backcross inbred population (BIL) of G. hirsutum × G. barbadense in at least one of the four field tests. Taken together, these results indicate that the sequence variation in these 11 R2R3-MYB genes is associated with the natural variation (i.e., QTL) in fiber quality and yield. Moreover, the functional SNPs of five R2R3-MYB allele pairs from the AD1 and AD2 genomes were significantly correlated with the gene expression related to fiber quality in fiber development. The results will be useful in further elucidating the role of the R2R3-MYB genes during fiber development.

Figure S2. Genome-wide association study (GWAS) of dynamic fiber length. The lowercase letters a through e represent Manhattan plots of the GLM at 10, 15, 20 and 25 DPA and maturity in 2014; f through l represent Manhattan plots of the GLM at 10, 15, 20 and 25 DPA and maturity in 2015; and m through q represent Manhattan plots of the GLM at 10, 15, 20 and 25 DPA and maturity in 2016, respectively. (PDF 893â kb)

Sequence variations in the predicted LPAAT genes between the sequenced G. hirsutum (TM-1) and G. barbadense (3â 79 and Xinhai 21). The boxes indicate the variations of the A- and D- subgenomes and the ellipses indicate the SNPs between the two cultivated species; Gb1 and Gb2 indicate 3â 79 and Xinhai21 respectively. (PDF 22277 kb)

Background Lysophosphatidic acid acyltransferase (LPAAT) encoded by a multigene family is a rate-limiting enzyme in the Kennedy pathway in higher plants. Cotton is the most important natural fiber crop and one of the most important oilseed crops. However, little is known on genes coding for LPAATs involved in oil biosynthesis with regard to its genome organization, diversity, expression, natural genetic variation, and association with fiber development and oil content in cotton. Results In this study, a comprehensive genome-wide analysis in four Gossypium species with genome sequences, i.e., tetraploid G. hirsutum- AD1 and G. barbadense- AD2 and its possible ancestral diploids G. raimondii- D5 and G. arboreum- A2, identified 13, 10, 8, and 9 LPAAT genes, respectively, that were divided into four subfamilies. RNA-seq analyses of the LPAAT genes in the widely grown G. hirsutum suggest their differential expression at the transcriptional level in developing cottonseeds and fibers. Although 10 LPAAT genes were co-localised with quantitative trait loci (QTL) for cottonseed oil or protein content within a 25-cM region, only one single strand conformation polymorphic (SSCP) marker developed from a synonymous single nucleotide polymorphism (SNP) of the At-Gh13LPAAT5 gene was significantly correlated with cottonseed oil and protein contents in one of the three field tests. Moreover, transformed yeasts using the At-Gh13LPAAT5 gene with the two sequences for the SNP led to similar results, i.e., a 25–31% increase in palmitic acid and oleic acid, and a 16–29% increase in total triacylglycerol (TAG). Conclusions The results in this study demonstrated that the natural variation in the LPAAT genes to improving cottonseed oil content and fiber quality is limited; therefore, traditional cross breeding should not expect much progress in improving cottonseed oil content or fiber quality through a marker-assisted selection for the LPAAT genes. However, enhancing the expression of one of the LPAAT genes such as At-Gh13LPAAT5 can significantly increase the production of total TAG and other fatty acids, providing an incentive for further studies into the use of LPAAT genes to increase cottonseed oil content through biotechnology. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3594-9) contains supplementary material, which is available to authorized users.

Two novel Fe(II) diimine complexes have been synthesized. In combination with MAO, they generate active catalytic systems that oligomerize ethylene with both high catalytic activity and high selectivity for α-olefins. The effects of substituents on the aryl ring, reaction temperatures and molar ratios of Al/Fe on catalytic activity and product distribution are studied.