Publications by authors named "Wangzhen Guo"

108 Publications

Cotton Fiber Development Requires the Pentatricopeptide Repeat Protein GhIm for Splicing of Mitochondrial nad7 mRNA.

Genetics 2021 Mar;217(1):1-17

State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China.

Pentatricopeptide repeat (PPR) proteins encoded by nuclear genomes can bind to organellar RNA and are involved in the regulation of RNA metabolism. However, the functions of many PPR proteins remain unknown in plants, especially in polyploidy crops. Here, through a map-based cloning strategy and Clustered regularly interspaced short palindromic repeats/cas9 (CRISPR/cas9) gene editing technology, we cloned and verified an allotetraploid cotton immature fiber (im) mutant gene (GhImA) encoding a PPR protein in chromosome A03, that is associated with the non-fluffy fiber phenotype. GhImA protein targeted mitochondrion and could bind to mitochondrial nad7 mRNA, which encodes the NAD7 subunit of Complex I. GhImA and its homolog GhImD had the same function and were dosage-dependent. GhImA in the im mutant was a null allele with a 22 bp deletion in the coding region. Null GhImA resulted in the insufficient GhIm dosage, affected mitochondrial nad7 pre-mRNA splicing, produced less mature nad7 transcripts, and eventually reduced Complex I activities, up-regulated alternative oxidase metabolism, caused reactive oxygen species (ROS) burst and activation of stress or hormone response processes. This study indicates that the GhIm protein participates in mitochondrial nad7 splicing, affects respiratory metabolism, and further regulates cotton fiber development via ATP supply and ROS balance.
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http://dx.doi.org/10.1093/genetics/iyaa017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8045684PMC
March 2021

Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum.

BMC Genomics 2021 Jan 6;22(1):26. Epub 2021 Jan 6.

Provincial Key Laboratory of Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, China.

Background: Cotton is more resistant to salt and drought stresses as compared to other field crops, which makes itself as a pioneer industrial crop in saline-alkali lands. However, abiotic stresses still negatively affect its growth and development significantly. It is therefore important to breed salt tolerance varieties which can help accelerate the improvement of cotton production. The development of molecular markers linked to causal genes has provided an effective and efficient approach for improving salt tolerance.

Results: In this study, a genome-wide association study (GWAS) of salt tolerance related traits at seedling stage was performed based on 2 years of phenotype identification for 217 representative upland cotton cultivars by genotyping-by-sequencing (GBS) platform. A total of 51,060 single nucleotide polymorphisms (SNPs) unevenly distributed among 26 chromosomes were screened across the cotton cultivars, and 25 associations with 27 SNPs scattered over 12 chromosomes were detected significantly (-log > 4) associated with three salt tolerance related traits in 2016 and 2017. Among these, the associations on chromosome A13 and D08 for relative plant height (RPH), A07 for relative shoot fresh matter weight (RSFW), A08 and A13 for relative shoot dry matter weight (RSDW) were expressed in both environments, indicating that they were likely to be stable quantitative trait loci (QTLs). A total of 12 salt-induced candidate genes were identified differentially expressed by the combination of GWAS and transcriptome analysis. Three promising genes were selected for preliminary function verification of salt tolerance. The increase of GH_A13G0171-silenced plants in salt related traits under salt stress indicated its negative function in regulating the salt stress response.

Conclusions: These results provided important genetic variations and candidate genes for accelerating the improvement of salt tolerance in cotton.
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http://dx.doi.org/10.1186/s12864-020-07321-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7789578PMC
January 2021

NST- and SND-subgroup NAC proteins coordinately act to regulate secondary cell wall formation in cotton.

Plant Sci 2020 Dec 4;301:110657. Epub 2020 Sep 4.

State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China. Electronic address:

Secondary cell wall (SCW) has a strong impact on plant growth and adaptation to the environments. Previous studies have shown that NAC (NAM, ATAF1/2, and CUC2) transcription factors act as key regulators of SCW biosynthesis. However, the regulatory network triggered by NAC proteins is largely unknown, especially in cotton, a model plant for SCW development studies. Here, we show that several cotton NAC transcription factors are clustered in the same group with Arabidopsis secondary wall NACs (SWNs), including secondary wall-associated NAC domain protein1 (SND1) and NAC secondary wall thickening promoting factor1/2 (NST1/2), so we name these cotton orthologs as SND1s and NST1s. We found that simultaneous silencing of SND1s and NST1s led to severe xylem and phloem developmental defect in cotton stems, however silencing either SND1s or NST1s alone had no visible phenotype. Silencing both SND1s and NST1s but not one subgroup caused decreased expression of a set of SCW-associated genes, while over-expression of cotton SWNs in tobacco leaves resulted in SCW deposition. SWNs could bind the promoter of MYB46 and MYB83, which are highly expressed in SCW-rich tissues of cotton. In total, our data provide evidence that cotton SWNs positively and coordinately regulate SCW formation.
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http://dx.doi.org/10.1016/j.plantsci.2020.110657DOI Listing
December 2020

Genome-wide association analysis reveals loci and candidate genes involved in fiber quality traits in sea island cotton (Gossypium barbadense).

BMC Plant Biol 2020 Jun 22;20(1):289. Epub 2020 Jun 22.

State Key Laboratory of Crop Genetics and Germplasm Enhancement, Engineering Research Center of Hybrid Cotton Development (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China.

Background: Sea island cotton (Gossypium barbadense) has markedly superior high quality fibers, which plays an important role in the textile industry and acts as a donor for upland cotton (G. hirsutum) fiber quality improvement. The genetic characteristics analysis and the identification of key genes will be helpful to understand the mechanism of fiber development and breeding utilization in sea island cotton.

Results: In this study, 279 sea island cotton accessions were collected from different origins for genotyping and phenotyping fiber quality traits. A set of 6303 high quality single nucleotide polymorphisms (SNPs) were obtained by high-density CottonSNP80K array. The population characteristics showed that the sea island cotton accessions had wide genetic diversity and were clustered into three groups, with Group1 closely related to Menoufi, an original sea island cotton landrace, and Group2 and Group3 related to widely introduced accessions from Egypt, USA and Former Soviet Union. Further, we used 249 accessions and evaluated five fiber quality traits under normal and salt environments over 2 years. Except for fiber uniformity (FU), fiber length (FL) and fiber elongation (FE) were significantly decreased in salt conditions, while fiber strength (FS) and fiber micronaire (MIC) were increased. Based on 6303 SNPs and genome-wide association study (GWAS) analysis, a total of 34 stable quantitative trait loci (QTLs) were identified for the five fiber quality traits with 25 detected simultaneously under normal and salt environments. Gene Ontology (GO) analysis indicated that candidate genes in the 25 overlapped QTLs were enriched mostly in "cellular and biological process". In addition, "xylem development" and "response to hormone" pathways were also found. Haplotype analyses found that GB_A03G0335 encoding an E3 ubiquitin-protein ligase in QTL TM6004 had SNP variation (A/C) in gene region, was significantly correlated with FL, FS, FU, and FE, implying a crucial role in fiber quality.

Conclusions: The present study provides a foundation for genetic diversity of sea island cotton accessions and will contribute to fiber quality improvement in breeding practice.
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http://dx.doi.org/10.1186/s12870-020-02502-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7310526PMC
June 2020

A cotton NAC transcription factor GhirNAC2 plays positive roles in drought tolerance via regulating ABA biosynthesis.

Plant Sci 2020 Jul 13;296:110498. Epub 2020 Apr 13.

State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China. Electronic address:

NAC protein is a large plant specific transcription factor family, which plays important roles in the response to abiotic stresses. However, the regulation mechanism of most NAC proteins in drought stress remains to be further uncovered. In this study, we elucidated the molecular functions of a NAC protein, GhirNAC2, in response to drought stress in cotton. GhirNAC2 was greatly induced by drought and phytohormone abscisic acid (ABA). Subcellular localization demonstrated that GhirNAC2 was located in the nucleus. Co-suppression of GhirNAC2 in cotton led to larger stomata aperture, elevated water loss and finally reduced transgenic plants tolerance to drought stress. Furthermore, the endogenous ABA content was significantly lower in GhirNAC2-suppressed transgenic plant leaves compared to wild type. in vivo and in vitro studies showed that GhirNAC2 directly binds to the promoter of GhNCED3a/3c, key genes in ABA biosynthesis, which were both down-regulated in GhirNAC2-suppressed transgenic lines. Transient silencing of GhNCED3a/3c also significantly reduced the resistance to drought stress in cotton plants. However, ectopic expression of GhirNAC2 in tobacco significantly enhanced seed germination, root growth and plant survival under drought stress. Taken together, GhirNAC2 plays a positive role in cotton drought tolerance, which functions by modulating ABA biosynthesis and stomata closure via regulating GhNCED3a/3c expression.
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http://dx.doi.org/10.1016/j.plantsci.2020.110498DOI Listing
July 2020

A cotton α1,3-/4-fucosyltransferase-encoding gene, FucT4, plays an important role in cell elongation and is significantly associated with fiber quality.

Mol Genet Genomics 2020 Sep 27;295(5):1141-1153. Epub 2020 May 27.

State Key Laboratory of Crop Genetics and Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China.

Fucosylation, one of the key posttranslational modifications, plays an important role in plants. It is involved in the development, signal transduction, reproduction, and disease resistance. α1,3-/4-Fucosyltransferase is responsible for transferring L-fucose from GDP-L-fucose to the N-glycan to exert fucosylational functions. However, the roles of the fucosyltransferase gene in cotton remain unknown. This study provided a comprehensive investigation of its possible functions. A genome-wide analysis identified four, four, eight, and eight FucT genes presented in the four sequenced cotton species, diploid Gossypium raimondii, G. arboreum, tetraploid G. hirsutum acc. TM-1, and G. barbadense cv. H7124, respectively. These FucTs were classified into two groups, with FucT4 homologs alone as a group. We isolated FucT4 in TM-1 and H7124, and named it GhFucT4 and GbFucT4, respectively. Quantitative RT-PCR and transcriptome data demonstrated that GhFucT4 had the highest expression levels in fibers among all GhFucT genes. Association studies and QTL co-localization supported the possible involvement of GhFucT4 in cotton fiber development. GhFucT4 and GbFucT4 shared high sequence identities, and FucT4 had higher expression in H7124 fiber tissues compared with TM-1. Furthermore, ectopic expression of FucT4 in transgenic Arabidopsis promoted root cell elongation, upregulated expression of genes related to cell wall loosening, and led to longer primary root. These results collectively indicate that FucT4 plays an important role in promoting cell elongation and modulating fiber development, which could be utilized to improve fiber quality traits in cotton breeding.
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http://dx.doi.org/10.1007/s00438-020-01687-5DOI Listing
September 2020

Genome-wide association reveals genetic variation of lint yield components under salty field conditions in cotton (Gossypium hirsutum L.).

BMC Plant Biol 2020 Jan 14;20(1):23. Epub 2020 Jan 14.

State Key Laboratory of Crop Genetics and Germplasm Enhancement, Engineering Research Center of Hybrid Cotton Development (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China.

Background: Salinity is one of the most significant environmental factors limiting the productivity of cotton. However, the key genetic components responsible for the reduction in cotton yield in saline-alkali soils are still unclear.

Results: Here, we evaluated three main components of lint yield, single boll weight (SBW), lint percentage (LP) and boll number per plant (BNPP), across 316 G. hirsutum accessions under four salt conditions over two years. Phenotypic analysis indicated that LP was unchanged under different salt conditions, however BNPP decreased significantly and SBW increased slightly under high salt conditions. Based on 57,413 high-quality single nucleotide polymorphisms (SNPs) and genome-wide association study (GWAS) analysis, a total of 42, 91 and 25 stable quantitative trait loci (QTLs) were identified for SBW, LP and BNPP, respectively. Phenotypic and QTL analysis suggested that there was little correlation among the three traits. For LP, 8 stable QTLs were detected simultaneously in four different salt conditions, while fewer repeated QTLs for SBW or BNPP were identified. Gene Ontology (GO) analysis indicated that their regulatory mechanisms were also quite different. Via transcriptome profile data, we detected that 10 genes from the 8 stable LP QTLs were predominantly expressed during fiber development. Further, haplotype analyses found that a MYB gene (GhMYB103), with the two SNP variations in cis-regulatory and coding regions, was significantly correlated with lint percentage, implying a crucial role in lint yield. We also identified that 40 candidate genes from BNPP QTLs were salt-inducible. Genes related to carbohydrate metabolism and cell structure maintenance were rich in plants grown in high salt conditions, while genes related to ion transport were active in plants grown in low salt conditions, implying different regulatory mechanisms for BNPP at high and low salt conditions.

Conclusions: This study provides a foundation for elucidating cotton salt tolerance mechanisms and contributes gene resources for developing upland cotton varieties with high yields and salt stress tolerance.
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http://dx.doi.org/10.1186/s12870-019-2187-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6961271PMC
January 2020

Genetic Basis of Fiber Improvement and Decreased Stress Tolerance in Cultivated Versus Semi-Domesticated Upland Cotton.

Front Plant Sci 2019 29;10:1572. Epub 2019 Nov 29.

State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, China.

Crop domestication from wild ancestors has resulted in the wide adaptation coupled with improved yield and quality traits. However, the genetic basis of many domesticated characteristics remains to be explored. Upland cotton () is the most important tetraploid cotton species, accounting for about 90% of world cotton commerce. Here, we reveal the effects of domestication on fiber and stress traits through comprehensive analyses of semi-domesticated races and cultivated cotton accessions. A total of 416 cotton accessions were genotyped, and a decrease in genetic diversity from races to landraces and modern cultivars was detected. Furthermore, 71 domestication selective sweeps (DSS) and 14 improvement selective sweeps (ISS) were identified, with the Dt sub-genome experiencing stronger selection than the At sub-genome during the both selection types. The more expressed genes and a delay in the expression peak of genes related to secondary cell wall (SCW) development in modern cultivars compared to semi-domesticated cotton races, may have contributed to long fibers in these plants. However, down-regulation of genes related to stress response was responsible for decreasing stress tolerance in modern cultivars. We further experimentally confirmed that silencing of and , genes that showed higher expression in the semi-domesticated races, drastically compromised cotton resistance to . Our results reveal fiber improvement and decreased stress tolerance as a result of the domestication of modern upland cotton cultivars.
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http://dx.doi.org/10.3389/fpls.2019.01572DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6895062PMC
November 2019

Retraction Note: Genetic regulation of salt stress tolerance revealed by RNA-Seq in cotton diploid wild species, Gossypium davidsonii.

Sci Rep 2019 Aug 16;9(1):12205. Epub 2019 Aug 16.

State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China.

This article has been retracted.
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http://dx.doi.org/10.1038/s41598-019-45848-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6697700PMC
August 2019

Combining genome-wide and transcriptome-wide analyses reveal the evolutionary conservation and functional diversity of aquaporins in cotton.

BMC Genomics 2019 Jul 1;20(1):538. Epub 2019 Jul 1.

State Key Laboratory of Crop Genetics & Germplasm Enhancement, Engineering Research Center of Hybrid Cotton Development Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, People's Republic of China.

Background: Aquaporins (AQPs) are integral membrane proteins from a larger family of major intrinsic proteins (MIPs) and function in a huge variety of processes such as water transport, plant growth and stress response. The availability of the whole-genome data of different cotton species allows us to study systematic evolution and function of cotton AQPs on a genome-wide level.

Results: Here, a total of 53, 58, 113 and 111 AQP genes were identified in G. arboreum, G. raimondii, G. hirsutum and G. barbadense, respectively. A comprehensive analysis of cotton AQPs, involved in exon/intron structure, functional domains, phylogenetic relationships and gene duplications, divided these AQPs into five subfamilies (PIP, NIP, SIP, TIP and XIP). Comparative genome analysis among 30 species from algae to angiosperm as well as common tandem duplication events in 24 well-studied plants further revealed the evolutionary conservation of AQP family in the organism kingdom. Combining transcriptome analysis and Quantitative Real-time PCR (qRT-PCR) verification, most AQPs exhibited tissue-specific expression patterns both in G. raimondii and G. hirsutum. Meanwhile, a bias of time to peak expression of several AQPs was also detected after treating G. davidsonii and G. hirsutum with 200 mM NaCl. It is interesting that both PIP1;4 h/i/j and PIP2;2a/e showed the highly conserved tandem structure, but differentially contributed to tissue development and stress response in different cotton species.

Conclusions: These results demonstrated that cotton AQPs were structural conservation while experienced the functional differentiation during the process of evolution and domestication. This study will further broaden our insights into the evolution and functional elucidation of AQP gene family in cotton.
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http://dx.doi.org/10.1186/s12864-019-5928-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6604486PMC
July 2019

GbCYP86A1-1 from Gossypium barbadense positively regulates defence against Verticillium dahliae by cell wall modification and activation of immune pathways.

Plant Biotechnol J 2020 01 26;18(1):222-238. Epub 2019 Jun 26.

State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu Province, China.

Suberin acts as stress-induced antipathogen barrier in the root cell wall. CYP86A1 encodes cytochrome P450 fatty acid ω-hydroxylase, which has been reported to be a key enzyme for suberin biosynthesis; however, its role in resistance to fungi and the mechanisms related to immune responses remain unknown. Here, we identified a disease resistance-related gene, GbCYP86A1-1, from Gossypium barbadense cv. Hai7124. There were three homologs of GbCYP86A1 in cotton, which are specifically expressed in roots and induced by Verticillium dahliae. Among them, GbCYP86A1-1 contributed the most significantly to resistance. Silencing of GbCYP86A1-1 in Hai7124 resulted in severely compromised resistance to V. dahliae, while heterologous overexpression of GbCYP86A1-1 in Arabidopsis improved tolerance. Tissue sections showed that the roots of GbCYP86A1-1 transgenic Arabidopsis had more suberin accumulation and significantly higher C16-C18 fatty acid content than control. Transcriptome analysis revealed that overexpression of GbCYP86A1-1 not only affected lipid biosynthesis in roots, but also activated the disease-resistant immune pathway; genes encoding the receptor-like kinases (RLKs), receptor-like proteins (RLPs), hormone-related transcription factors, and pathogenesis-related protein genes (PRs) were more highly expressed in the GbCYP86A1-1 transgenic line than control. Furthermore, we found that when comparing V. dahliae -inoculated and noninoculated plants, few differential genes related to disease immunity were detected in the GbCYP86A1-1 transgenic line; however, a large number of resistance genes were activated in the control. This study highlights the role of GbCYP86A1-1 in the defence against fungi and its underlying molecular immune mechanisms in this process.
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http://dx.doi.org/10.1111/pbi.13190DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6920168PMC
January 2020

Inheritance of Transgenes in Transgenic Bt Lines Resistance to Helicoverpa armigera in Upland Cotton.

Methods Mol Biol 2019 ;1902:199-210

Agronomy Department, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China.

Six transgenic Bt cotton cultivars (lines) including GKsu12, GK19, MR1, GK5, 109B, and SGK1 are highly resistant to bollworm from the seedling to boll-setting stages in bioassays with detached cotton leaves, though there are differences in resistant level and Bt toxin content in these transgenic cottons. Genetics analysis reveals that the resistance to Helicoverpa armigera in these six transgenic Bt cotton cultivars (lines) are controlled by one pair of dominant genes. Allelic tests further demonstrate some populations are in Mendel segregation for two nonallelic genes, i.e., the inserted Bt gene in GKsu12 is nonallelic to that of SGK1, GK5, 109B, and GK19, and Bt genes in GK19 and SGK1 are likely inserted in the same or in close proximity (genetically closely linked), while some F produce abnormal segregation patterns, with a segregation of resistance to Helicoverpa armigera which vary between 15:1 and 3:1, though their Bt segregation fit into 15:1 by PCR analysis, suggesting Bt gene silence in these populations. Two genes silence may occur in these populations due to the homologous sequence by crossing since the silenced individuals accounted for 1/16 of the F populations for allelic test. To those silenced populations, one of their parents all showed high resistance to bollworm.
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http://dx.doi.org/10.1007/978-1-4939-8952-2_17DOI Listing
June 2019

Tobacco Rattle Virus-Induced Gene Silencing in Cotton.

Methods Mol Biol 2019 ;1902:105-119

State Key Laboratory of Crop Genetics & Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu, China.

Virus-induced gene silencing (VIGS), as a tool for plant reverse genetics, has been widely used in cotton for target gene function analysis. Compared with genetically transformed plants, the target gene expression level is reduced in the newly emerged leaves and can carry out phenotype identification after a few weeks of Agrobacterium infiltration. In this chapter, we describe a detailed protocol for Agrobacterium-mediated TRV-VIGS system for cotton gene function studies, with focus on designing primers, constructing TRV-target gene vectors via homologous recombination method, preparing and infiltrating Agrobacterium with TRV-VIGS, and identifying target gene silencing.
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http://dx.doi.org/10.1007/978-1-4939-8952-2_9DOI Listing
June 2019

Genome-Wide Association Studies Reveal Genetic Variation and Candidate Genes of Drought Stress Related Traits in Cotton ( L.).

Front Plant Sci 2018 3;9:1276. Epub 2018 Sep 3.

State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, China.

Cotton is an important industrial crop worldwide and upland cotton ( L.) is most widely cultivated in the world. Due to ever-increasing water deficit, drought stress brings a major threat to cotton production. Thus, it is important to reveal the genetic basis under drought stress and develop drought tolerant cotton cultivars. To address this issue, in present study, 319 upland cotton accessions were genotyped by 55,060 single nucleotide polymorphisms (SNPs) from high-density CottonSNP80K array and phenotyped nine drought tolerance related traits. The two datasets were used to identify quantitative trait nucleotides (QTNs) for the above nine traits using multi-locus random-SNP-effect mixed linear model method. As a result, a total of 20 QTNs distributed on 16 chromosomes were found to be significantly associated with six drought tolerance related traits. Of the 1,326 genes around the 20 QTNs, 205 were induced after drought stress treatment, and 46 were further mapped to Gene ontology (GO) term "response to stress." Taken genome-wide association study (GWAS) analysis, RNA-seq data and qRT-PCR verification, four genes, encoding a response to desiccation 2 protein, encoding a homeobox-leucine zipper protein, encoding a plasma membrane intrinsic protein 2, and encoding a protein phosphatase 2C, were proposed to be potentially important for drought tolerance in cotton. These results will deepen our understanding of the genetic basis of drought stress tolerance in cotton and provide candidate markers to accelerate the development of drought-tolerant cotton cultivars.
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http://dx.doi.org/10.3389/fpls.2018.01276DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6129771PMC
September 2018

Retraction Note to: Overexpression of a cotton annexin gene, GhAnn1, enhances drought and salt stress tolerance in transgenic cotton.

Plant Mol Biol 2018 09;98(1-2):185

State Key Laboratory of Crop Genetics and Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, People's Republic of China.

The authors are retracting this article because irregularities were involved in the reuse of stomatal images in Figure 9.
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http://dx.doi.org/10.1007/s11103-018-0775-0DOI Listing
September 2018

Ectopic expression of GhCOBL9A, a cotton glycosyl-phosphatidyl inositol-anchored protein encoding gene, promotes cell elongation, thickening and increased plant biomass in transgenic Arabidopsis.

Mol Genet Genomics 2018 Oct 5;293(5):1191-1204. Epub 2018 Jun 5.

State Key Laboratory of Crop Genetics and Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.

Cellulose is a major component of plant cell walls and is necessary for plant morphogenesis and biomass. COBL (COBRA-Like) proteins have been shown to be key regulators in the orientation of cell expansion and cellulose crystallinity status. To clarify the role of a cotton COBL gene, GhCOBL9A, we conducted the ectopic expression and functional analysis in Arabidopsis. Previous study showed that GhCOBL9A was preferentially expressed during secondary cell wall biosynthesis in cotton fibers, and showed a significant co-expression pattern with cellulose synthase genes. Here, we detected that overexpression of GhCOBL9A induced the up-regulation of genes related to cellulose synthesis and enhanced the cellulose deposition. As a result, GhCOBL9A transgenic plants displayed increased hypocotyl and root lengths in early development, and cell wall thickening at the SCW stage. Notably, overexpression of GhCOBL9A led to an erect, robust-stature phenotype and brought higher biomass in mature plants. In addition, overexpression of GhCOBL9A in Arabidopsis AtCOBL4 mutants, a paralogous gene of GhCOBL9A, also led to a stronger growth potential, but the Atcobl4 mutant phenotype could not be rescued, implying the functional divergence of GhCOBL9A and AtCOBL4 paralogs. Taken together, these results suggest that overexpression of GhCOBL9A contributes to plant cell elongation and thickening, and increased biomass, which provides references for further utilizing GhCOBL9A to improve yield and quality traits in cotton and other species.
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http://dx.doi.org/10.1007/s00438-018-1452-3DOI Listing
October 2018

Identification on mitogen-activated protein kinase signaling cascades by integrating protein interaction with transcriptional profiling analysis in cotton.

Sci Rep 2018 05 25;8(1):8178. Epub 2018 May 25.

State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China.

Plant mitogen-activated protein kinase (MAPK) cascades play important roles in development and stress responses. In previous studies, we have systematically investigated the mitogen-activated protein kinase kinase (MKK) and MAPK gene families in cotton. However, the complete interactions between MAPK gene family members in MAPK signaling cascade is poorly characterized. Herein, we investigated the mitogen-activated protein kinase kinase kinase (MAPKKK) family members and identified a total of 89 MAPKKK genes in the Gossypium raimondii genome. We cloned 51 MAPKKKs in G. hirsutum and investigated the interactions between MKK and MAPKKK proteins through yeast-two hybrid assays. A total of 18 interactive protein pairs involved in 14 MAPKKKs and six MKKs were found. Among these, 13 interactive pairs had not been reported previously. Gene expression patterns revealed that 12 MAPKKKs were involved in diverse signaling pathways triggered by hormone treatments or abiotic stresses. By combining the MKK-MAPK and MKK-MAPKKK protein interactions with gene expression patterns, 38 potential MAPK signaling modules involved in the complicated cross-talks were identified, which provide a basis on elucidating biological function of the MAPK cascade in response to hormonal and/or stress responses. The systematic investigation in MAPK signaling cascades will lay a foundation for understanding the functional roles of different MAPK cascades in signal transduction pathways, and for the improvement of various defense responses in cotton.
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http://dx.doi.org/10.1038/s41598-018-26400-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5970168PMC
May 2018

Divergence and evolution of cotton bHLH proteins from diploid to allotetraploid.

BMC Genomics 2018 02 23;19(1):162. Epub 2018 Feb 23.

National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China.

Background: Polyploidy is considered a major driving force in genome expansion, yielding duplicated genes whose expression may be conserved or divergence as a consequence of polyploidization.

Results: We compared the genome sequences of tetraploid cotton (Gossypium hirsutum) and its two diploid progenitors, G. arboreum and G. raimondii, and found that the bHLH genes were conserved over the polyploidization. Oppositely, the expression of the homeolgous gene pairs was diversified. The biased homeologous proportion for bHLH family is significantly higher (64.6%) than the genome wide homeologous expression bias (40%). Compared with cacao (T. cacao), orthologous genes only accounted for a small proportion (41.7%) of whole cotton bHLHs family. The further Ks analysis indicated that bHLH genes underwent at least two distinct episodes of whole genome duplication: a recent duplication (1.0-60.0 million years ago, MYA, 0.005 < Ks < 0.312) and an old duplication (> 60.0 MYA, 0.312 < Ks < 3.0). The old duplication event might have played a key role in the expansion of the bHLH family. Both recent and old duplicated pairs (68.8%) showed a divergent expression profile, indicating specialized functions. The expression diversification of the duplicated genes suggested it might be a universal feature of the long-term evolution of cotton.

Conclusions: Overview of cotton bHLH proteins indicated a conserved and divergent evolution from diploids to allotetraploid. Our results provided an excellent example for studying the long-term evolution of polyploidy.
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http://dx.doi.org/10.1186/s12864-018-4543-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5824590PMC
February 2018

Host-induced gene silencing of a regulator of G protein signalling gene (VdRGS1) confers resistance to Verticillium wilt in cotton.

Plant Biotechnol J 2018 Feb 12. Epub 2018 Feb 12.

State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China.

Verticillium wilt (VW), caused by soil-borne fungi of the genus Verticillium, is a serious disease affecting a wide range of plants and leading to a constant and major challenge to agriculture worldwide. Cotton (Gossypium hirsutum) is the world's most important natural textile fibre and oil crop. VW of cotton is a highly devastating vascular disease; however, few resistant germplasms have been reported in cotton. An increasing number of studies have shown that RNA interference (RNAi)-based host-induced gene silencing (HIGS) is an effective strategy for improving plant resistance to pathogens by silencing genes essential for the pathogenicity of these pathogens. Here, we have identified and characterized multifunctional regulators of G protein signalling (RGS) in the Verticillium dahliae virulence strain, Vd8. Of eight VdRGS genes, VdRGS1 showed the most significant increase in expression in V. dahliae after treating with the roots of cotton seedlings. Based on the phenotype detection of VdRGS1 deletion and complementation mutants, we found that VdRGS1 played crucial roles in spore production, hyphal development, microsclerotia formation and pathogenicity. Tobacco rattle virus-mediated HIGS in cotton plants silenced VdRGS1 transcripts in invaded V. dahliae strains and enhanced broad-spectrum resistance to cotton VW. Our data demonstrate that VdRGS1 is a conserved and essential gene for V. dahliae virulence. HIGS of VdRGS1 provides effective control against V. dahliae infection and could obtain the durable disease resistance in cotton and in other VW-susceptible host crops by developing the stable transformants.
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http://dx.doi.org/10.1111/pbi.12900DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6096726PMC
February 2018

RNA-seq analysis reveals alternative splicing under salt stress in cotton, Gossypium davidsonii.

BMC Genomics 2018 01 23;19(1):73. Epub 2018 Jan 23.

State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China.

Background: Numerous studies have focused on the regulation of gene expression in response to salt stress at the transcriptional level; however, little is known about this process at the post-transcriptional level.

Results: Using a diploid D genome wild salinity-tolerant cotton species, Gossypium davidsonii, we analyzed alternative splicing (AS) of genes related to salt stress by comparing high-throughput transcriptomes from salt-treated and well-watered roots and leaves. A total of 14,172 AS events were identified involving 6798 genes, of which intron retention (35.73%) was the most frequent, being detected in 3492 genes. Under salt stress, 1287 and 1228 differential alternative splicing (DAS) events were identified in roots and leaves, respectively. These DAS genes were associated with specific functional pathways, such as "responses to stress", "metabolic process" and "RNA splicing", implying that AS represents an important pathway of gene regulation in response to salt stress. Several salt response genes, such as pyrroline-5-carboxylate synthase (P5CS), K channel outward (KCO1), plasma membrane intrinsic protein (PIP) and WRKY33 which were involved in osmotic balance, ion homeostasis, water transportation and transcriptional regulation, respectively, were identified with differential alternative splicing under salt stress. Moreover, we revealed that 13 genes encoding Ser/Arg-rich (SR) proteins related to AS regulation were differentially alternatively spliced under salt stress.

Conclusion: This study first provide a comprehensive view of AS in G. davidsonii, and highlight novel insights into the potential roles of AS in plant responses to salt stress.
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http://dx.doi.org/10.1186/s12864-018-4449-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5782385PMC
January 2018

Genome-wide identification and characterization of SPL transcription factor family and their evolution and expression profiling analysis in cotton.

Sci Rep 2018 01 15;8(1):762. Epub 2018 Jan 15.

Department of Biology, East Carolina University, Greenville, NC, 27858, USA.

Plant specific transcription factors, SQUAMOSA promoter-binding protein-like (SPL), are involved in many biological processes. However, no systematical study has been reported in cotton. In this study, a total of 177 SPL genes were identified, including 29, 30, 59 and 59 SPLs in Gossypium arboreum, G. raimondii, G. barbadense, and G. hirsutum, respectively. These SPL genes were classified into eight phylogenetical groups. The gene structure, conserved motif, and clustering were highly conserved within each orthologs. Two zinc finger-like structures (Cys3His and Cys2HisCys) and NLS segments were existed in all GrSPLs. Segmental duplications play important roles in SPL family expansion, with 20 genes involved in segmental duplications and 2 in tandem duplications, and ten ortholog pairs in syntenic regions between G. raimondii and A. thaliana. Several putative cis-elements, involved in light, stresses and phytohormones response, were found in the promoter regions of GhSPLs, suggesting that plant responses to those environmental changes may be induced through targeting SPL transcription factors. RNA-seq analysis shows that SPL genes were differentially expressed in cotton; some were highly expressed during fiber initiation and early development. Comparing with other plants, SPL genes show subfunctionalization, lost and/or gain functions in cotton during long-term domestication and evolution.
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http://dx.doi.org/10.1038/s41598-017-18673-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5768680PMC
January 2018

Genetics and evolution of MIXTA genes regulating cotton lint fiber development.

New Phytol 2018 01 16;217(2):883-895. Epub 2017 Oct 16.

State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.

Cotton, with cellulose-enriched mature fibers, is the largest source of natural textiles. Through a map-based cloning strategy, we isolated an industrially important lint fiber development gene (Li ) that encodes an MYB-MIXTA-like transcription factor (MML) on chromosome D12 (GhMML4_D12). Virus-induced gene silencing or decreasing the expression of the GhMML4_D12 gene in n NSM plants resulted in a significant reduction in epidermal cell prominence and lint fiber production. GhMML4_D12 is arranged in tandem with GhMML3, another MIXTA gene responsible for fuzz fiber development. These two very closely related MIXTA genes direct fiber initiation production in two specialized cell forms: lint and fuzz fibers. They may control the same metabolic pathways in different cell types. The MIXTAs expanded in Malvaceae during their evolution and produced a Malvaceae-specific family that regulates epidermal cell differentiation, different from the gene family that regulates leaf hair trichome development. Cotton has developed a unique transcriptional regulatory network for fiber development. Characterization of target genes regulating fiber production has provided insights into the molecular mechanisms underlying cotton fiber development and has allowed the use of genetic engineering to increase lint yield by inducing more epidermal cells to develop into lint rather than fuzz fibers.
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http://dx.doi.org/10.1111/nph.14844DOI Listing
January 2018

The lysin motif-containing proteins, Lyp1, Lyk7 and LysMe3, play important roles in chitin perception and defense against Verticillium dahliae in cotton.

BMC Plant Biol 2017 Sep 4;17(1):148. Epub 2017 Sep 4.

State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, People's Republic of China.

Background: Lysin motif (LysM)-containing proteins are important pattern recognition receptors (PRRs) in plants, which function in the perception of microbe-associated molecular patterns (MAMPs) and in the defense against pathogenic attack. To date, the LysM genes have not been systematically analyzed in cotton or effectively utilized for disease resistance.

Results: Here, we identified 29, 30, 60, and 56 LysM genes in the four sequenced cotton species, diploid Gossypium raimondii, diploid G. arboreum, tetraploid G. hirsutum acc. TM-1, and G. barbadense acc. 3-79, respectively. These LysM genes were classified into four groups with different structural characteristics and a variety of expression patterns in different organs and tissues when induced by chitin or Verticillium dahliae. We further characterized three genes, Lyp1, Lyk7 and LysMe3, which showed significant increase in expression in response to chitin signals, V. dahliae challenge and several stress-related signaling compounds. Lyp1, Lyk7 and LysMe3 proteins were localized to the plasma membrane, and silencing of their expression in cotton drastically impaired salicylic acid, jasmonic acid, and reactive oxygen species generation, impaired defense gene activation, and compromised resistance to V. dahliae.

Conclusion: Our results indicate that Lyp1, Lyk7, and LysMe3 are important PRRs that function in the recognition of chitin signals to activate the downstream defense processes and induce cotton defense mechanisms against V. dahliae.
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http://dx.doi.org/10.1186/s12870-017-1096-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5583995PMC
September 2017

High-density 80 K SNP array is a powerful tool for genotyping G. hirsutum accessions and genome analysis.

BMC Genomics 2017 Aug 23;18(1):654. Epub 2017 Aug 23.

State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China.

Background: High-throughput genotyping platforms play important roles in plant genomic studies. Cotton (Gossypium spp.) is the world's important natural textile fiber and oil crop. Upland cotton accounts for more than 90% of the world's cotton production, however, modern upland cotton cultivars have narrow genetic diversity. The amounts of genomic sequencing and re-sequencing data released make it possible to develop a high-quality single nucleotide polymorphism (SNP) array for intraspecific genotyping detection in cotton.

Results: Here we report a high-throughput CottonSNP80K array and its utilization in genotyping detection in different cotton accessions. 82,259 SNP markers were selected from the re-sequencing data of 100 cotton cultivars and used to produce the array on the Illumina Infinium platform. 77,774 SNP loci (94.55%) were successfully synthesized on the array. Of them, 77,252 (99.33%) had call rates of >95% in 352 cotton accessions and 59,502 (76.51%) were polymorphic loci. Application tests using 22 cotton accessions with parent/F combinations or with similar genetic backgrounds showed that CottonSNP80K array had high genotyping accuracy, good repeatability, and wide applicability. Phylogenetic analysis of 312 cotton cultivars and landraces with wide geographical distribution showed that they could be classified into ten groups, irrelevant of their origins. We found that the different landraces were clustered in different subgroups, indicating that these landraces were major contributors to the development of different breeding populations of modern G. hirsutum cultivars in China. We integrated a total of 54,588 SNPs (MAFs >0.05) associated with 10 salt stress traits into 288 G. hirsutum accessions for genome-wide association studies (GWAS), and eight significant SNPs associated with three salt stress traits were detected.

Conclusions: We developed CottonSNP80K array with high polymorphism to distinguish upland cotton accessions. Diverse application tests indicated that the CottonSNP80K play important roles in germplasm genotyping, variety verification, functional genomics studies, and molecular breeding in cotton.
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http://dx.doi.org/10.1186/s12864-017-4062-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5569476PMC
August 2017

5-Aminolevulinic Acid Dehydratase Gene Dosage Affects Programmed Cell Death and Immunity.

Plant Physiol 2017 Sep 27;175(1):511-528. Epub 2017 Jul 27.

State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China

Programmed cell death (PCD) is an important form to protect plants from pathogen attack. However, plants must precisely control the PCD process under microbe attacks to avoid detrimental effects. The complexity of how plants balance the defense activation and PCD requires further clarification. Lesion mimic mutants constitute an excellent material to study the crosstalk between them. Here, we identified a (cotton) lesion mimic mutant (), which exhibits necrotic leaf damage and enhanced disease resistance. Map-based cloning demonstrated that , encoding 5-aminolevulinic acid dehydratase and located on chromosome D5, was responsible for the phenotype. The mutant was resulted from a nonsense mutation within the coding region of It exhibited an overaccumulation of the 5-aminolevulinic acid, elevated levels of reactive oxygen species and salicylic acid, along with constitutive expression of pathogenesis-related genes and enhanced resistance to the infection. Interestingly, plays a dosage-dependent role in regulating PCD of cotton leaves and resistance to infection. This study provides a new strategy on the modulation of plant immunity, particularly in polyploidy plants.
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http://dx.doi.org/10.1104/pp.17.00816DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5580774PMC
September 2017

Suppressing a Putative Sterol Carrier Gene Reduces Plasmodesmal Permeability and Activates Sucrose Transporter Genes during Cotton Fiber Elongation.

Plant Cell 2017 Aug 26;29(8):2027-2046. Epub 2017 Jul 26.

Agronomy Department, College of Agriculture and Biotechnology, Zhejiang University, Zhejiang 310029, China

Plasmodesmata (PDs) play vital roles in cell-to-cell communication and plant development. Emerging evidence suggests that sterols are involved in PD activity during cytokinesis. However, whether sterols contribute to PD gating between established cells remains unknown. Here, we isolated , a putative sterol carrier protein gene from elongating cotton () fibers. In contrast to wild-type fiber PDs, which opened at 5 to 10 d postanthesis (DPA) and closed only at 15 to 25 DPA, plants with suppressed expression had reduced sterol contents and closed PDs at 5 through 25 DPA The suppressed fibers exhibited callose deposition at the PDs, likely due to reduced expression of , which encodes a PD-targeting β-1,3-glucanase. Both expression and callose deposition were sensitive to a sterol biosynthesis inhibitor. Moreover, suppressing upregulated a cohort of and sucrose transporter genes in fiber cells. Collectively, our results indicate that (1) GhSCP2D is required for expression to degrade callose at the PD, thereby contributing to the establishment of the symplasmic pathway; and (2) blocking the symplasmic pathway by downregulating activates or increases the expression of and , leading to the switch from symplasmic to apoplasmic pathways.
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http://dx.doi.org/10.1105/tpc.17.00358DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5590508PMC
August 2017

Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits.

Nat Genet 2017 Jul 5;49(7):1089-1098. Epub 2017 Jun 5.

State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R&D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, China.

Upland cotton (Gossypium hirsutum) is the most important natural fiber crop in the world. The overall genetic diversity among cultivated species of cotton and the genetic changes that occurred during their improvement are poorly understood. Here we report a comprehensive genomic assessment of modern improved upland cotton based on the genome-wide resequencing of 318 landraces and modern improved cultivars or lines. We detected more associated loci for lint yield than for fiber quality, which suggests that lint yield has stronger selection signatures than other traits. We found that two ethylene-pathway-related genes were associated with increased lint yield in improved cultivars. We evaluated the population frequency of each elite allele in historically released cultivar groups and found that 54.8% of the elite genome-wide association study (GWAS) alleles detected were transferred from three founder landraces: Deltapine 15, Stoneville 2B and Uganda Mian. Our results provide a genomic basis for improving cotton cultivars and for further evolutionary analysis of polyploid crops.
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http://dx.doi.org/10.1038/ng.3887DOI Listing
July 2017

Genome-wide characterization of the Rab gene family in Gossypium by comparative analysis.

Bot Stud 2017 Dec 2;58(1):26. Epub 2017 Jun 2.

State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, People's Republic of China.

Background: Rab protein family is the largest subfamily of small G protein family. As one of the most important families in plant, Rab family plays an important role in the process of plant growth and development. So far, the identification of 57 members of the Rab family in Arabidopsis has been completed. In cotton, the relevant family has not been reported.

Results: Here, we identified 87, 169, 136, 80 Rabs in the four sequenced cotton species, G. raimondii (D), G. hirsutum acc. TM-1 (AD), G. barbadense acc. 3-79 (AD) and G. arboreum (A), respectively. Biological information analysis showed that the number of amino acid is 200-300 aa among Rab family members in G. raimondii and the protein molecular weight is between 20 and 30 kDa, which is consistent with the characterization of the Rab protein itself. 87 GrRabs in G. raimondii are divided into eight groups. In each group, intron numbers and subcellular localization of Rab protein are basically the same. We mapped the distribution of GrRab genes on 13 chromosomes of G. raimondii except two genes. Among the 87 GrRabs in G. raimondii, we identified 60 pairs of GrRabs formed in whole genome duplication. Among all the gene pairs, the Ka/Ks values were less than 1. This indicates that it is the results of the purification selection and will help maintain the conservation of gene in structure and function. Further, 4 of the 87 GrRabs showed tandem duplication. They were GrRabA2a vs GrRabD1a and GrRabA2h vs GrRabD1b respectively. Expression patterns analysis of 169 GhRabs in G. hirsutum acc. TM-1 indicates that most Rab family members play a certain role in different tissues/organs and different growth stages of cotton, implying their potential function in the polar growth of pollen tube, root hair and fiber cell, as well as improving stress and disease tolerance.

Conclusion: The systematic investigation of Rab genes in cotton will lay a foundation for understanding the functional roles of different Rab members in the polar growth and stress tolerance.
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http://dx.doi.org/10.1186/s40529-017-0181-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5457372PMC
December 2017

Identification of genes related to salt stress tolerance using intron-length polymorphic markers, association mapping and virus-induced gene silencing in cotton.

Sci Rep 2017 04 3;7(1):528. Epub 2017 Apr 3.

State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China.

Intron length polymorphisms (ILPs), a type of gene-based functional marker, could themselves be related to the particular traits. Here, we developed a genome-wide cotton ILPs based on orthologs annotation from two sequenced diploid species, A-genome Gossypium arboreum and D-genome G. raimondii. We identified 10,180 putative ILP markers from 5,021 orthologous genes. Among these, 535 ILP markers from 9 gene families related to stress were selected for experimental verification. Polymorphic rates were 72.71% between G. arboreum and G. raimondii and 36.45% between G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124. Furthermore, 14 polymorphic ILP markers were detected in 264 G. hirsutum accessions. Coupled with previous simple sequence repeats (SSRs) evaluations and salt tolerance assays from the same individuals, we found a total of 25 marker-trait associations involved in nine ILPs. The nine genes, temporally named as C1 to C9, showed the various expressions in different organs and tissues, and five genes (C3, C4, C5, C7 and C9) were significantly upregulated after salt treatment. We verified that the five genes play important roles in salt tolerance. Particularly, silencing of C4 (encodes WRKY DNA-binding protein) and C9 (encodes Mitogen-activated protein kinase) can significantly enhance cotton susceptibility to salt stress.
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http://dx.doi.org/10.1038/s41598-017-00617-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5428780PMC
April 2017

Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons.

Genome Biol 2017 02 20;18(1):33. Epub 2017 Feb 20.

National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200233, China.

Background: Cotton has been cultivated and used to make fabrics for at least 7000 years. Two allotetraploid species of great commercial importance, Gossypium hirsutum and Gossypium barbadense, were domesticated after polyploidization and are cultivated worldwide. Although the overall genetic diversity between these two cultivated species has been studied with limited accessions, their population structure and genetic variations remain largely unknown.

Results: We resequence the genomes of 147 cotton accessions, including diverse wild relatives, landraces, and modern cultivars, and construct a comprehensive variation map to provide genomic insights into the divergence and dual domestication of these two important cultivated tetraploid cotton species. Phylogenetic analysis shows two divergent groups for G. hirsutum and G. barbadense, suggesting a dual domestication processes in tetraploid cottons. In spite of the strong genetic divergence, a small number of interspecific reciprocal introgression events are found between these species and the introgression pattern is significantly biased towards the gene flow from G. hirsutum into G. barbadense. We identify selective sweeps, some of which are associated with relatively highly expressed genes for fiber development and seed germination.

Conclusions: We report a comprehensive analysis of the evolution and domestication history of allotetraploid cottons based on the whole genomic variation between G. hirsutum and G. barbadense and between wild accessions and modern cultivars. These results provide genomic bases for improving cotton production and for further evolution analysis of polyploid crops.
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http://dx.doi.org/10.1186/s13059-017-1167-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5317056PMC
February 2017