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Si Z, Jin S, Chen J, Wang S, Fang L, Zhu X, Zhang T, Hu Y. Construction of a high-density genetic map and identification of QTLs related to agronomic and physiological traits in an interspecific (Gossypium hirsutum × Gossypium barbadense) F2 population. BMC Genomics 2022; 23:307. [PMID: 35428176 PMCID: PMC9013169 DOI: 10.1186/s12864-022-08528-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/21/2022] [Indexed: 02/06/2023] Open
Abstract
Abstract
Background
Advances in genome sequencing technology, particularly restriction-site associated DNA sequence (RAD-seq) and whole-genome resequencing, have greatly aided the construction of cotton interspecific genetic maps based on single nucleotide polymorphism (SNPs), Indels, and other types of markers. High-density genetic maps can improve accuracy of quantitative trait locus (QTL) mapping, narrow down location intervals, and facilitate identification of the candidate genes.
Result
In this study, 249 individuals from an interspecific F2 population (TM-1 and Hai7124) were re-sequenced, yielding 6303 high-confidence bin markers spanning 5057.13 cM across 26 cotton chromosomes. A total of 3380 recombination hot regions RHRs were identified which unevenly distributed on the 26 chromosomes. Based on this map, 112 QTLs relating to agronomic and physiological traits from seedling to boll opening stage were identified, including 15 loci associated with 14 traits that contained genes harboring nonsynonymous SNPs. We analyzed the sequence and expression of these ten candidate genes and discovered that GhRHD3 (GH_D10G0500) may affect fiber yield while GhGPAT6 (GH_D04G1426) may affect photosynthesis efficiency.
Conclusion
Our research illustrates the efficiency of constructing a genetic map using binmap and QTL mapping on the basis of a certain size of the early-generation population. High-density genetic map features high recombination exchanges in number and distribution. The QTLs and the candidate genes identified based on this high-density genetic map may provide important gene resources for the genetic improvement of cotton.
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2
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Graham BP, Haigler CH. Microtubules exert early, partial, and variable control of cotton fiber diameter. PLANTA 2021; 253:47. [PMID: 33484350 DOI: 10.1007/s00425-020-03557-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/30/2020] [Indexed: 05/07/2023]
Abstract
Variable cotton fiber diameter is set early in anisotropic elongation by cell-type-specific processes involving the temporal and spatial regulation of microtubules in the apical region. Cotton fibers are single cells that originate from the seed epidermis of Gossypium species. Then, they undergo extreme anisotropic elongation and limited diametric expansion. The details of cellular morphogenesis determine the quality traits that affect fiber uses and value, such as length, strength, and diameter. Lower and more consistent diameter would increase the competitiveness of cotton fiber with synthetic fiber, but we do not know how this trait is controlled. The complexity of the question is indicated by the existence of fibers in two major width classes in the major commercial species: broad and narrow fibers exist in commonly grown G. hirsutum, whereas G. barbadense produces only narrow fiber. To further understand how fiber diameter is controlled, we used ovule cultures, morphology measurements, and microtubule immunofluorescence to observe the effects of microtubule antagonists on fiber morphology, including shape and diameter within 80 µm of the apex. The treatments were applied at either one or two days post-anthesis during different stages of fiber morphogenesis. The results showed that inhibiting the presence and/or dynamic activity of microtubules caused larger diameter tips to form, with greater effects often observed with earlier treatment. The presence and geometry of a microtubule-depleted-zone below the apex were transiently correlated with the apical diameter of the narrow tip types. Similarly, the microtubule antagonists had somewhat different effects between tip types. Overall, the results demonstrate cell-type-specific mechanisms regulating fiber expansion within 80 µm of the apex, with variation in the impact of microtubules between tip types and over developmental time.
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Affiliation(s)
- Benjamin P Graham
- Department of Crop and Soil Sciences and Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Candace H Haigler
- Department of Crop and Soil Sciences and Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA.
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3
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Zhang S, Jia T, Zhang Z, Zou X, Fan S, Lei K, Jiang X, Niu D, Yuan Y, Shang H. Insight into the relationship between S-lignin and fiber quality based on multiple research methods. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 147:251-261. [PMID: 31884241 DOI: 10.1016/j.plaphy.2019.12.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/18/2019] [Accepted: 12/20/2019] [Indexed: 06/10/2023]
Abstract
Cotton (Gossypium hirsutum) is an important cash crop, providing people with high quality natural fiber. Lignin is the main component of cotton fiber, second only to cellulose. As a main substance filled in the cellulose framework during the secondary wall thickening process, lignin plays a key role in the formation of cotton fiber quality. However, the mechanism behind it is still unclear. In this research, we screened candidate genes involved in lignin biosynthesis based on analysis of cotton genome and transcriptome sequence data. The authenticity of the transcriptome data was verified by qRT-PCR assay. Total 62 genes were identified from nine gene families. In the process, we found the key gene GhCAD7 that affects the biosynthesis of S-lignin and the ratio of syringyl/guaiacyl (S/G). In addition, in combination with the metabolites and transcriptome profiles of the line 0-153 with high fiber quality and the line sGK9708 with low fiber quality during cotton fiber development, we speculate that the ratio of syringyl/guaiacyl (S/G) is inseparable from the quality of cotton fiber. Finally, the S-type lignin synthesis branch may play a more important role in the formation of high-quality fiber. This work provides insights into the synthesis of lignin in cotton and lays the foundation for future research into improving fiber quality.
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Affiliation(s)
- Shuya Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Tingting Jia
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Zhen Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Xianyan Zou
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Senmiao Fan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Kang Lei
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Xiao Jiang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Doudou Niu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China; School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China; School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
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4
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Association mapping and favourable QTL alleles for fibre quality traits in Upland cotton (Gossypium hirsutum L.). J Genet 2018. [DOI: 10.1007/s12041-017-0878-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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5
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Prakash Menon M, Selvakumar R, Suresh kumar P, Ramakrishna S. Extraction and modification of cellulose nanofibers derived from biomass for environmental application. RSC Adv 2017. [DOI: 10.1039/c7ra06713e] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Cellulose nanofibers obtained from various plants and microbial sources, their extraction methods and various environmental applications are discussed.
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Affiliation(s)
| | - R. Selvakumar
- Nanobiotechnology Laboratory
- PSG Institute of Advanced Studies
- Coimbatore
- India-641004
| | - Palaniswamy Suresh kumar
- Environmental & Water Technology Centre of Innovation (EWTCOI)
- Ngee Ann Polytechnic
- Singapore-599489
| | - Seeram Ramakrishna
- Center for Nanofibers and Nanotechnology
- Department of Mechanical Engineering
- National University of Singapore
- Singapore 117576
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Li X, Jin X, Wang H, Zhang X, Lin Z. Structure, evolution, and comparative genomics of tetraploid cotton based on a high-density genetic linkage map. DNA Res 2016; 23:283-93. [PMID: 27084896 PMCID: PMC4909315 DOI: 10.1093/dnares/dsw016] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 03/17/2016] [Indexed: 01/17/2023] Open
Abstract
A high-density linkage map was constructed using 1,885 newly obtained loci and 3,747 previously published loci, which included 5,152 loci with 4696.03 cM in total length and 0.91 cM in mean distance. Homology analysis in the cotton genome further confirmed the 13 expected homologous chromosome pairs and revealed an obvious inversion on Chr10 or Chr20 and repeated inversions on Chr07 or Chr16. In addition, two reciprocal translocations between Chr02 and Chr03 and between Chr04 and Chr05 were confirmed. Comparative genomics between the tetraploid cotton and the diploid cottons showed that no major structural changes exist between DT and D chromosomes but rather between AT and A chromosomes. Blast analysis between the tetraploid cotton genome and the mixed genome of two diploid cottons showed that most AD chromosomes, regardless of whether it is from the AT or DT genome, preferentially matched with the corresponding homologous chromosome in the diploid A genome, and then the corresponding homologous chromosome in the diploid D genome, indicating that the diploid D genome underwent converted evolution by the diploid A genome to form the DT genome during polyploidization. In addition, the results reflected that a series of chromosomal translocations occurred among Chr01/Chr15, Chr02/Chr14, Chr03/Chr17, Chr04/Chr22, and Chr05/Chr19.
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Affiliation(s)
- Ximei Li
- National Key Laboratory of Crop Genetic Improvement (Wuhan), Huazhong Agricultural University, Wuhan, Hubei 430070, China College of Agronomy and Plant Protection, Qingdao Agricultural University/Shandong Key Laboratory of Dryland Farming Technology, Qingdao, Shandong, China
| | - Xin Jin
- National Key Laboratory of Crop Genetic Improvement (Wuhan), Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Hantao Wang
- National Key Laboratory of Crop Genetic Improvement (Wuhan), Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement (Wuhan), Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement (Wuhan), Huazhong Agricultural University, Wuhan, Hubei 430070, China
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Mittal A, Jiang Y, Ritchie GL, Burke JJ, Rock CD. AtRAV1 and AtRAV2 overexpression in cotton increases fiber length differentially under drought stress and delays flowering. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 241:78-95. [PMID: 26706061 DOI: 10.1016/j.plantsci.2015.09.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 09/11/2015] [Accepted: 09/16/2015] [Indexed: 05/23/2023]
Abstract
There is a longstanding problem of an inverse relationship between cotton fiber qualities versus high yields. To better understand drought stress signaling and adaptation in cotton (Gossypium hirsutum) fiber development, we expressed the Arabidopsis transcription factors RELATED_TO_ABA-INSENSITIVE3/VIVIPAROUS1/(RAV1) and AtRAV2, which encode APETALA2-Basic3 domain proteins shown to repress transcription of FLOWERING_LOCUS_T (FT) and to promote stomatal opening cell-autonomously. In three years of field trials, we show that AtRAV1 and AtRAV2-overexpressing cotton had ∼5% significantly longer fibers with only marginal decreases in yields under well-watered or drought stress conditions that resulted in 40-60% yield penalties and 3-7% fiber length penalties in control plants. The longer transgenic fibers from drought-stressed transgenics could be spun into yarn which was measurably stronger and more uniform than that from well-watered control fibers. The transgenic AtRAV1 and AtRAV2 lines flowered later and retained bolls at higher nodes, which correlated with repression of endogenous GhFT-Like (FTL) transcript accumulation. Elevated expression early in development of ovules was observed for GhRAV2L, GhMYB25-Like (MYB25L) involved in fiber initiation, and GhMYB2 and GhMYB25 involved in fiber elongation. Altered expression of RAVs controlling critical nodes in developmental and environmental signaling hierarchies has the potential for phenotypic modification of crops.
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Affiliation(s)
- Amandeep Mittal
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, United States.
| | - Yingwen Jiang
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, United States.
| | - Glen L Ritchie
- Department of Plant and Soils Science, Texas Tech University, Lubbock, TX 79409-2122, United States.
| | - John J Burke
- USDA-ARS Plant Stress and Germplasm Laboratory, Lubbock, TX 79415, United States.
| | - Christopher D Rock
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, United States.
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Nie X, Tu J, Wang B, Zhou X, Lin Z. A BIL Population Derived from G. hirsutum and G. barbadense Provides a Resource for Cotton Genetics and Breeding. PLoS One 2015; 10:e0141064. [PMID: 26517274 PMCID: PMC4627741 DOI: 10.1371/journal.pone.0141064] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 10/05/2015] [Indexed: 11/19/2022] Open
Abstract
To provide a resource for cotton genetics and breeding, an interspecific hybridization between Gossypium hirsutum cv. Emian22 and G. barbadense acc. 3–79 was made. A population of 54 BILs (backcross inbred lines, BC1F8) was developed with the aim of transferring G. barbadense genes into G. hirsutum in order to genetically analyze these genes’ function in a G. hirsutum background and create new germplasms for breeding. Preliminary investigation of the morphological traits showed that the BILs had diverse variations in plant architecture, seed size, and fuzz color; the related traits of yield and fiber quality evaluated in 4 environments also showed abundant phenotypic variation. In order to explore the molecular diversity of the BIL population, 446 SSR markers selected at an average genetic distance of 10 cM from our interspecific linkage map were used to genotype the BIL population. A total of 393 polymorphic loci accounting for 84.4% MAF (major allele frequency) > 0.05 and 922 allele loci were detected, and the Shannon diversity index (I) was 0.417 per locus. The average introgression segment length was 16.24 cM, and an average of 29.53 segments were introgressed in each BIL line with an average background recovery of 79.8%. QTL mapping revealed 58 QTL associated with fiber quality and yield traits, and 47 favored alleles derived from the donor parent were discovered. This study demonstrated that the interspecific BIL population was enriched with much phenotypic and molecular variation which could be a resource for cotton genetics and breeding.
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Affiliation(s)
- Xinhui Nie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jianli Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Bin Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xiaofeng Zhou
- Cotton Institute, Xinjiang Academy of Agriculture and Reclamation Science, Shihezi, 832000, Xinjiang, China
- * E-mail: (ZL); (XZ)
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- * E-mail: (ZL); (XZ)
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9
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Li X, Gao W, Guo H, Zhang X, Fang DD, Lin Z. Development of EST-based SNP and InDel markers and their utilization in tetraploid cotton genetic mapping. BMC Genomics 2014; 15:1046. [PMID: 25442170 PMCID: PMC4265408 DOI: 10.1186/1471-2164-15-1046] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Accepted: 11/14/2014] [Indexed: 12/19/2022] Open
Abstract
Background Availability of molecular markers has proven to be an efficient tool in facilitating progress in plant breeding, which is particularly important in the case of less researched crops such as cotton. Considering the obvious advantages of single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (InDels), expressed sequence tags (ESTs) were analyzed in silico to identify SNPs and InDels in this study, aiming to develop more molecular markers in cotton. Results A total of 1,349 EST-based SNP and InDel markers were developed by comparing ESTs between Gossypium hirsutum and G. barbadense, mining G. hirsutum unigenes, and analyzing 3′ untranslated region (3′UTR) sequences. The marker polymorphisms were investigated using the two parents of the mapping population based on the single-strand conformation polymorphism (SSCP) analysis. Of all the markers, 137 (10.16%) were polymorphic, and revealed 142 loci. Linkage analysis using a BC1 population mapped 133 loci on the 26 chromosomes. Statistical analysis of base variations in SNPs showed that base transitions accounted for 55.78% of the total base variations and gene ontology indicated that cotton genes varied greatly in harboring SNPs ranging from 1.00 to 24.00 SNPs per gene. Sanger sequencing of three randomly selected SNP markers revealed discrepancy between the in silico predicted sequences and the actual sequencing results. Conclusions In silico analysis is a double-edged blade to develop EST-SNP/InDel markers. On the one hand, the designed markers can be well used in tetraploid cotton genetic mapping. And it plays a certain role in revealing transition preference and SNP frequency of cotton genes. On the other hand, the developmental efficiency of markers and polymorphism of designed primers are comparatively low. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1046) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement & National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, Hubei, China.
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10
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Yu JZ, Ulloa M, Hoffman SM, Kohel RJ, Pepper AE, Fang DD, Percy RG, Burke JJ. Mapping genomic loci for cotton plant architecture, yield components, and fiber properties in an interspecific (Gossypium hirsutum L. × G. barbadense L.) RIL population. Mol Genet Genomics 2014; 289:1347-67. [PMID: 25314923 DOI: 10.1007/s00438-014-0930-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 09/20/2014] [Indexed: 12/27/2022]
Abstract
A quantitative trait locus (QTL) mapping was conducted to better understand the genetic control of plant architecture (PA), yield components (YC), and fiber properties (FP) in the two cultivated tetraploid species of cotton (Gossypium hirsutum L. and G. barbadense L.). One hundred and fifty-nine genomic regions were identified on a saturated genetic map of more than 2,500 SSR and SNP markers, constructed with an interspecific recombinant inbred line (RIL) population derived from the genetic standards of the respective cotton species (G. hirsutum acc. TM-1 × G. barbadense acc. 3-79). Using the single nonparametric and MQM QTL model mapping procedures, we detected 428 putative loci in the 159 genomic regions that confer 24 cotton traits in three diverse production environments [College Station F&B Road (FB), TX; Brazos Bottom (BB), TX; and Shafter (SH), CA]. These putative QTL loci included 25 loci for PA, 60 for YC, and 343 for FP, of which 3, 12, and 60, respectively, were strongly associated with the traits (LOD score ≥ 3.0). Approximately 17.7 % of the PA putative QTL, 32.9 % of the YC QTL, and 48.3 % of the FP QTL had trait associations under multiple environments. The At subgenome (chromosomes 1-13) contributed 72.7 % of loci for PA, 46.2 % for YC, and 50.4 % for FP while the Dt subgenome (chromosomes 14-26) contributed 27.3 % of loci for PA, 53.8 % for YC, and 49.6 % for FP. The data obtained from this study augment prior evidence of QTL clusters or gene islands for specific traits or biological functions existing in several non-homoeologous cotton chromosomes. DNA markers identified in the 159 genomic regions will facilitate further dissection of genetic factors underlying these important traits and marker-assisted selection in cotton.
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Affiliation(s)
- John Z Yu
- USDA-ARS, Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, TX, 77845, USA,
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Ding M, Jiang Y, Cao Y, Lin L, He S, Zhou W, Rong J. Gene expression profile analysis of Ligon lintless-1 (Li1) mutant reveals important genes and pathways in cotton leaf and fiber development. Gene 2013; 535:273-85. [PMID: 24279997 DOI: 10.1016/j.gene.2013.11.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 11/02/2013] [Accepted: 11/13/2013] [Indexed: 12/14/2022]
Abstract
Ligon lintless-1 (Li1) is a monogenic dominant mutant of Gossypium hirsutum (upland cotton) with a phenotype of impaired vegetative growth and short lint fibers. Despite years of research involving genetic mapping and gene expression profile analysis of Li1 mutant ovule tissues, the gene remains uncloned and the underlying pathway of cotton fiber elongation is still unclear. In this study, we report the whole genome-level deep-sequencing analysis of leaf tissues of the Li1 mutant. Differentially expressed genes in leaf tissues of mutant versus wild-type (WT) plants are identified, and the underlying pathways and potential genes that control leaf and fiber development are inferred. The results show that transcription factors AS2, YABBY5, and KANDI-like are significantly differentially expressed in mutant tissues compared with WT ones. Interestingly, several fiber development-related genes are found in the downregulated gene list of the mutant leaf transcriptome. These genes include heat shock protein family, cytoskeleton arrangement, cell wall synthesis, energy, H2O2 metabolism-related genes, and WRKY transcription factors. This finding suggests that the genes are involved in leaf morphology determination and fiber elongation. The expression data are also compared with the previously published microarray data of Li1 ovule tissues. Comparative analysis of the ovule transcriptomes of Li1 and WT reveals that a number of pathways important for fiber elongation are enriched in the downregulated gene list at different fiber development stages (0, 6, 9, 12, 15, 18dpa). Differentially expressed genes identified in both leaf and fiber samples are aligned with cotton whole genome sequences and combined with the genetic fine mapping results to identify a list of candidate genes for Li1.
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Affiliation(s)
- Mingquan Ding
- School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China; The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, China
| | - Yurong Jiang
- School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China; The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, China
| | - Yuefen Cao
- School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China; The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, China
| | - Lifeng Lin
- Nanosphere Inc., 4088 Commercial Drive, Northbrook, IL 60062, USA
| | - Shae He
- School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China; The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, China
| | - Wei Zhou
- School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China; The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, China
| | - Junkang Rong
- School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China; The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, China.
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12
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Lockhart J. Towards breeding strong but fine cotton fibers with a little help from WLIM1a. THE PLANT CELL 2013; 25:4281. [PMID: 24220633 PMCID: PMC3875715 DOI: 10.1105/tpc.113.251110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
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13
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Han LB, Li YB, Wang HY, Wu XM, Li CL, Luo M, Wu SJ, Kong ZS, Pei Y, Jiao GL, Xia GX. The dual functions of WLIM1a in cell elongation and secondary wall formation in developing cotton fibers. THE PLANT CELL 2013; 25:4421-38. [PMID: 24220634 PMCID: PMC3875727 DOI: 10.1105/tpc.113.116970] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 10/11/2013] [Accepted: 10/22/2013] [Indexed: 05/18/2023]
Abstract
LIN-11, Isl1 and MEC-3 (LIM)-domain proteins play pivotal roles in a variety of cellular processes in animals, but plant LIM functions remain largely unexplored. Here, we demonstrate dual roles of the WLIM1a gene in fiber development in upland cotton (Gossypium hirsutum). WLIM1a is preferentially expressed during the elongation and secondary wall synthesis stages in developing fibers. Overexpression of WLIM1a in cotton led to significant changes in fiber length and secondary wall structure. Compared with the wild type, fibers of WLIM1a-overexpressing plants grew longer and formed a thinner and more compact secondary cell wall, which contributed to improved fiber strength and fineness. Functional studies demonstrated that (1) WLIM1a acts as an actin bundler to facilitate elongation of fiber cells and (2) WLIM1a also functions as a transcription factor to activate expression of Phe ammonia lyase-box genes involved in phenylpropanoid biosynthesis to build up the secondary cell wall. WLIM1a localizes in the cytosol and nucleus and moves into the nucleus in response to hydrogen peroxide. Taken together, these results demonstrate that WLIM1a has dual roles in cotton fiber development, elongation, and secondary wall formation. Moreover, our study shows that lignin/lignin-like phenolics may substantially affect cotton fiber quality; this finding may guide cotton breeding for improved fiber traits.
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Affiliation(s)
- Li-Bo Han
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Plant Genomics, Beijing 100101, China
| | - Yuan-Bao Li
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Plant Genomics, Beijing 100101, China
| | - Hai-Yun Wang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Plant Genomics, Beijing 100101, China
| | - Xiao-Min Wu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Plant Genomics, Beijing 100101, China
| | - Chun-Li Li
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ming Luo
- Biotechnology Research Center, Southwest University, Chongqing 404100, China
| | - Shen-Jie Wu
- Institute of Cotton, Shanxi Academy of Agricultural Sciences, Yuncheng 044000, China
| | - Zhao-Sheng Kong
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Plant Genomics, Beijing 100101, China
| | - Yan Pei
- Biotechnology Research Center, Southwest University, Chongqing 404100, China
| | - Gai-Li Jiao
- Institute of Cotton, Shanxi Academy of Agricultural Sciences, Yuncheng 044000, China
| | - Gui-Xian Xia
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Plant Genomics, Beijing 100101, China
- Address correspondence to
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Moore JA, Chlan CA. Elucidation of Nuclear and Organellar Genomes of Gossypium hirsutum: Furthering Studies of Species Evolution and Applications for Crop Improvement. BIOLOGY 2013; 2:1224-41. [PMID: 24833222 PMCID: PMC4009799 DOI: 10.3390/biology2041224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 10/03/2013] [Accepted: 10/08/2013] [Indexed: 11/16/2022]
Abstract
Plant genomes are larger and more complex than other eukaryotic organisms, due to small and large duplication events, recombination and subsequent reorganization of the genetic material. Commercially important cotton is the result of a polyploidization event between Old and New World cottons that occurred over one million years ago. Allotetraploid cotton has properties that are dramatically different from its progenitors-most notably, the presence of long, spinnable fibers. Recently, the complete genome of a New World cotton ancestral species, Gossypium raimondii, was completed. Future genome sequencing efforts are focusing on an Old World progenitor, G. arboreum. This sequence information will enable us to gain insights into the evolution of the cotton genome that may be used to understand the evolution of other plant species. The chloroplast genomes of multiple cotton species and races have been determined. This information has also been used to gain insight into the evolutionary history of cotton. Analysis of the database of nuclear and organellar sequences will facilitate the identification of potential genes of interest and subsequent development of strategies for improving cotton.
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Affiliation(s)
- Jocelyn A Moore
- Biology Department, the University of Louisiana at Lafayette, Lafayette, LA 70504, USA.
| | - Caryl A Chlan
- Biology Department, the University of Louisiana at Lafayette, Lafayette, LA 70504, USA.
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