1
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Fu J, Ren Y, Jiang F, Wang L, Yu X, Du SK. Effects of pulsed ultrasonic treatment on the structure and functional properties of cottonseed protein isolate. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.114143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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2
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Kumar M, Hasan M, Choyal P, Tomar M, Gupta OP, Sasi M, Changan S, Lorenzo JM, Singh S, Sampathrajan V, Dhumal S, Pandiselvam R, Sharma K, Satankar V, Waghmare R, Senapathy M, Sayed AA, Radha, Dey A, Amarowicz R, Kennedy JF. Cottonseed feedstock as a source of plant-based protein and bioactive peptides: Evidence based on biofunctionalities and industrial applications. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.107776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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3
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Song J, Pei W, Wang N, Ma J, Xin Y, Yang S, Wang W, Chen Q, Zhang J, Yu J, Wu M, Qu Y. Transcriptome analysis and identification of genes associated with oil accumulation in upland cotton. Physiol Plant 2022; 174:e13701. [PMID: 35526222 DOI: 10.1111/ppl.13701] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/25/2022] [Accepted: 05/05/2022] [Indexed: 06/14/2023]
Abstract
Cotton is not only the most important fiber crop but also the fifth most important oilseed crop in the world because of its oil-rich seeds as a byproduct of fiber production. By comparative transcriptome analysis between two germplasms with diverse oil accumulation, we reveal pieces of the gene expression network involved in the process of oil synthesis in cottonseeds. Approximately, 197.16 Gb of raw data from 30 RNA sequencing samples with 3 biological replicates were generated. Comparison of the high-oil and low-oil transcriptomes enabled the identification of 7682 differentially expressed genes (DEGs). Based on gene expression profiles relevant to triacylglycerol (TAG) biosynthesis, we proposed that the Kennedy pathway (diacylglycerol acyltransferase-catalyzed diacylglycerol to TAG) is the main pathway for oil production, rather than the phospholipid diacylglycerol acyltransferase-mediated pathway. Using weighted gene co-expression network analysis, 5312 DEGs were obtained and classified into 14 co-expression modules, including the MEblack module containing 10 genes involved in lipid metabolism. Among the DEGs in the MEblack module, GhCYSD1 was identified as a potential key player in oil biosynthesis. The overexpression of GhCYSD1 in yeast resulted in increased oil content and altered fatty acid composition. This study may not only shed more light on the underlying molecular mechanism of oil accumulation in cottonseed oil, but also provide a set of new gene for potential enhancement of oil content in cottonseeds.
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Affiliation(s)
- Jikun Song
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Urumqi, China
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, China
| | - Wenfeng Pei
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Urumqi, China
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, China
| | - Nuohan Wang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Jianjiang Ma
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, China
| | - Yue Xin
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, China
| | - Shuxian Yang
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, China
| | - Wei Wang
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Urumqi, China
| | - Quanjia Chen
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Urumqi, China
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, New Mexico, USA
| | - Jiwen Yu
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Urumqi, China
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, China
| | - Man Wu
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, China
| | - Yanying Qu
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Urumqi, China
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4
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Wu M, Pei W, Wedegaertner T, Zhang J, Yu J. Genetics, Breeding and Genetic Engineering to Improve Cottonseed Oil and Protein: A Review. Front Plant Sci 2022; 13:864850. [PMID: 35360295 PMCID: PMC8961181 DOI: 10.3389/fpls.2022.864850] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 02/15/2022] [Indexed: 05/17/2023]
Abstract
Upland cotton (Gossypium hirsutum) is the world's leading fiber crop and one of the most important oilseed crops. Genetic improvement of cotton has primarily focused on fiber yield and quality. However, there is an increased interest and demand for enhanced cottonseed traits, including protein, oil, fatty acids, and amino acids for broad food, feed and biofuel applications. As a byproduct of cotton production, cottonseed is an important source of edible oil in many countries and could also be a vital source of protein for human consumption. The focus of cotton breeding on high yield and better fiber quality has substantially reduced the natural genetic variation available for effective cottonseed quality improvement within Upland cotton. However, genetic variation in cottonseed oil and protein content exists within the genus of Gossypium and cultivated cotton. A plethora of genes and quantitative trait loci (QTLs) (associated with cottonseed oil, fatty acids, protein and amino acids) have been identified, providing important information for genetic improvement of cottonseed quality. Genetic engineering in cotton through RNA interference and insertions of additional genes of other genetic sources, in addition to the more recent development of genome editing technology has achieved considerable progress in altering the relative levels of protein, oil, fatty acid profile, and amino acids composition in cottonseed for enhanced nutritional value and expanded industrial applications. The objective of this review is to summarize and discuss the cottonseed oil biosynthetic pathway and major genes involved, genetic basis of cottonseed oil and protein content, genetic engineering, genome editing through CRISPR/Cas9, and QTLs associated with quantity and quality enhancement of cottonseed oil and protein.
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Affiliation(s)
- Man Wu
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute, Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Wenfeng Pei
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute, Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | | | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
| | - Jiwen Yu
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute, Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
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5
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Zhu D, Le Y, Zhang R, Li X, Lin Z. A global survey of the gene network and key genes for oil accumulation in cultivated tetraploid cottons. Plant Biotechnol J 2021; 19:1170-1182. [PMID: 33382517 PMCID: PMC8196633 DOI: 10.1111/pbi.13538] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/03/2020] [Accepted: 12/20/2020] [Indexed: 05/14/2023]
Abstract
To enrich our knowledge about gene network of fatty acid biosynthesis in cottonseed, we conducted comparative transcriptome to reveal the differences in gene expression between Gossypium hirsutum and Gossypium barbadense during cottonseed development. The prolonged expression period and increased expression abundance of oil-related genes are the main reasons for producing high seed oil content (SOC) in G. barbadense, which manifested as the bias of homeologous gene expression in Dt-subgenome after 25 day postanthesis (DPA). The dynamic expression profile showed that SAD6 and FATA are more important for oil biosynthesis in G. barbadense than that in G. hirsutum. Three key transcription factors, WRI1, NF-YB6 and DPBF2, showed their elite roles in regulating seed oil in cotton. We observed that sequence variations in the promoter region of BCCP2 genes might contribute to its divergence in expression level between the two species. Based on the quantitative trait loci (QTL) information of the seed oil content and utilizing additional G. barbadense introgression lines (ILs), we propose 21 candidate genes on the basis of their differential expression level, of which the GbSWEET and the GbACBP6 showed the potential functional to improve the oil content. Taken together, studying the different expression of oil-related genes and their genetic regulation mechanisms between G. hirsutum and G. barbadense provide new insights to understanding the mechanism of fatty acid biosynthesis network and fatty acid genetic improving breeding in cotton.
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Affiliation(s)
- De Zhu
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Sciences & TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Yu Le
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Sciences & TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Ruiting Zhang
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Sciences & TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Xiaojing Li
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Sciences & TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Sciences & TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
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6
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Snider JL, Thangthong N, Pilon C, Virk G, Tishchenko V. OJIP-fluorescence parameters as rapid indicators of cotton (Gossypium hirsutum L.) seedling vigor under contrasting growth temperature regimes. Plant Physiol Biochem 2018; 132:249-257. [PMID: 30237089 DOI: 10.1016/j.plaphy.2018.09.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/13/2018] [Accepted: 09/11/2018] [Indexed: 06/08/2023]
Abstract
Vigorous seedling growth in cotton is desirable because it minimizes the negative impact of multiple early season stresses, and seedling vigor can be impacted by early season growth temperature or cultivar. OJIP fluorescence provides rapid information on a broad range of photosynthetic component processes and may be a useful surrogate for seeding vigor, but this possibility has not been evaluated previously in cotton. To this end, a controlled environment study was conducted with six cultivars selected based on seed characteristics that are widely indicative of vigor and under two growth temperature regimes (sub-optimal = 20/15 °C day/night temperature; optimal = 30/20 °C) for the first two weeks after seed germination. Thereafter multiple whole-plant vigor assessments were conducted along with extensive OJIP-fluorescence characterization in cotyledons. Growth temperature was the primary factor influencing multiple plant responses. Specifically, all whole-plant indicators of seedling vigor were negatively impacted by sub-optimal temperature as were all photosynthetic performance indices and quantum efficiencies. By comparison, most photosynthetic structural indicators or reaction center-specific fluxes were either unaffected or positively impacted by low growth temperature, largely because PSII antenna size increased. The performance index, PIABS, and the quantum efficiency, φEo, were the most sensitive to low growth temperature and exhibited the strongest relationships with whole-plant seedling vigor. Thus, OJIP parameters incorporating intersystem electron transport beyond PSII but not additional downstream processes may represent the most useful surrogates for whole-plant seedling vigor in cotton.
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Affiliation(s)
- John L Snider
- Department of Crop and Soil Sciences, University of Georgia, 115 Coastal Way, Tifton, GA, 31794, USA.
| | - Nuengsap Thangthong
- Department of Crop and Soil Sciences, University of Georgia, 115 Coastal Way, Tifton, GA, 31794, USA
| | - Cristiane Pilon
- Department of Crop and Soil Sciences, University of Georgia, 115 Coastal Way, Tifton, GA, 31794, USA
| | - Gurpreet Virk
- Department of Crop and Soil Sciences, University of Georgia, 115 Coastal Way, Tifton, GA, 31794, USA
| | - Viktor Tishchenko
- University of Georgia, College of Agricultural and Environmental Sciences, Griffin, GA, 30223, USA
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7
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Ma M, Ren Y, Xie W, Zhou D, Tang S, Kuang M, Wang Y, Du SK. Physicochemical and functional properties of protein isolate obtained from cottonseed meal. Food Chem 2017; 240:856-862. [PMID: 28946352 DOI: 10.1016/j.foodchem.2017.08.030] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 07/01/2017] [Accepted: 08/07/2017] [Indexed: 10/19/2022]
Abstract
To investigate the effect of preparation methods of cottonseed meals on protein properties, the physicochemical and functional properties of proteins isolated from hot-pressed solvent extraction cottonseed meal (HCM), cold-pressed solvent extraction cottonseed meal (CCM) and subcritical fluid extraction cottonseed meal (SCM) were investigated. Cottonseed proteins had two major bands (at about 45 and 50kD), two X-ray diffraction peaks (8.5° and 19.5°) and one endothermic peak (94.31°C-97.72°C). Proteins of HCM showed relatively more β-sheet (38.3%-40.5%), and less β-turn (22.2%-25.8%) and α-helix (15.8%-19.5%), indicating the presence of highly denatured protein molecules. Proteins of CCM and SCM exhibited high water/oil absorption capacity, emulsifying abilities, surface hydrophobicity and fluorescence intensity, suggesting that the proteins have potential as functional ingredients in the food industry.
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Affiliation(s)
- Mengting Ma
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanjing Ren
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wei Xie
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dayun Zhou
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, State Key Laboratory of Cotton Biology, Anyang 455000, Henan, China
| | - Shurong Tang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, State Key Laboratory of Cotton Biology, Anyang 455000, Henan, China
| | - Meng Kuang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, State Key Laboratory of Cotton Biology, Anyang 455000, Henan, China.
| | - Yanqin Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, State Key Laboratory of Cotton Biology, Anyang 455000, Henan, China
| | - Shuang-Kui Du
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China.
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8
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Sturtevant D, Horn P, Kennedy C, Hinze L, Percy R, Chapman K. Lipid metabolites in seeds of diverse Gossypium accessions: molecular identification of a high oleic mutant allele. Planta 2017; 245:595-610. [PMID: 27988885 DOI: 10.1007/s00425-016-2630-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 11/30/2016] [Indexed: 05/12/2023]
Abstract
Genetically diverse cottonseeds show altered compositions and spatial distributions of phosphatidylcholines and triacylglycerols. Lipidomics profiling led to the discovery of a novel FAD2 - 1 allele, fad2 - 1D - 1 , resulting in a high oleic phenotype. The domestication and breeding of cotton for elite, high-fiber cultivars have led to reduced variation of seed constituents within currently cultivated upland cotton genotypes. However, a recent screen of the genetically diverse U.S. National Cotton Germplasm Collection identified Gossypium accessions with marked differences in seed oil and protein content. Here, several of these accessions representing substantial variation in seed oil content were analyzed for quantitative and spatial differences in lipid compositions by mass spectrometric approaches. Results indicate considerable variation in amount and spatial distribution of pathway metabolites for triacylglycerol biosynthesis in embryos across Gossypium accessions, suggesting that this variation might be exploited by breeders for seed composition traits. By way of example, these lipid metabolite differences led to the identification of a mutant allele of the D-subgenome homolog of the delta-12 desaturase (fad2-1D-1) in a wild accession of G. barbadense that has a high oil and high oleic seed phenotype. This mutation is a 90-bp insertion in the 3' end of the FAD2-1D coding sequence and a modification of the 3' end of the gene beyond the coding sequence leading to the introduction of a premature stop codon. Given the large amounts of cottonseed produced around the world that is currently not processed into higher value products, these efforts might be one avenue to raise the overall value of the cotton crop for producers.
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Affiliation(s)
- Drew Sturtevant
- Department of Biological Sciences, Center for Plant Lipid Research, BioDiscovery Institute, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203-5217, USA
| | - Patrick Horn
- Department of Biological Sciences, Center for Plant Lipid Research, BioDiscovery Institute, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203-5217, USA
- U.S. Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
| | - Christopher Kennedy
- Department of Biological Sciences, Center for Plant Lipid Research, BioDiscovery Institute, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203-5217, USA
| | - Lori Hinze
- USDA/ARS, Southern Plains Agricultural Research Center, College Station, TX, 77845, USA
| | - Richard Percy
- USDA/ARS, Southern Plains Agricultural Research Center, College Station, TX, 77845, USA
| | - Kent Chapman
- Department of Biological Sciences, Center for Plant Lipid Research, BioDiscovery Institute, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203-5217, USA.
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Wang N, Ma J, Pei W, Wu M, Li H, Li X, Yu S, Zhang J, Yu J. A genome-wide analysis of the lysophosphatidate acyltransferase (LPAAT) gene family in cotton: organization, expression, sequence variation, and association with seed oil content and fiber quality. BMC Genomics 2017; 18:218. [PMID: 28249560 PMCID: PMC5333453 DOI: 10.1186/s12864-017-3594-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 02/15/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lysophosphatidic acid acyltransferase (LPAAT) encoded by a multigene family is a rate-limiting enzyme in the Kennedy pathway in higher plants. Cotton is the most important natural fiber crop and one of the most important oilseed crops. However, little is known on genes coding for LPAATs involved in oil biosynthesis with regard to its genome organization, diversity, expression, natural genetic variation, and association with fiber development and oil content in cotton. RESULTS In this study, a comprehensive genome-wide analysis in four Gossypium species with genome sequences, i.e., tetraploid G. hirsutum- AD1 and G. barbadense- AD2 and its possible ancestral diploids G. raimondii- D5 and G. arboreum- A2, identified 13, 10, 8, and 9 LPAAT genes, respectively, that were divided into four subfamilies. RNA-seq analyses of the LPAAT genes in the widely grown G. hirsutum suggest their differential expression at the transcriptional level in developing cottonseeds and fibers. Although 10 LPAAT genes were co-localised with quantitative trait loci (QTL) for cottonseed oil or protein content within a 25-cM region, only one single strand conformation polymorphic (SSCP) marker developed from a synonymous single nucleotide polymorphism (SNP) of the At-Gh13LPAAT5 gene was significantly correlated with cottonseed oil and protein contents in one of the three field tests. Moreover, transformed yeasts using the At-Gh13LPAAT5 gene with the two sequences for the SNP led to similar results, i.e., a 25-31% increase in palmitic acid and oleic acid, and a 16-29% increase in total triacylglycerol (TAG). CONCLUSIONS The results in this study demonstrated that the natural variation in the LPAAT genes to improving cottonseed oil content and fiber quality is limited; therefore, traditional cross breeding should not expect much progress in improving cottonseed oil content or fiber quality through a marker-assisted selection for the LPAAT genes. However, enhancing the expression of one of the LPAAT genes such as At-Gh13LPAAT5 can significantly increase the production of total TAG and other fatty acids, providing an incentive for further studies into the use of LPAAT genes to increase cottonseed oil content through biotechnology.
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Affiliation(s)
- Nuohan Wang
- National Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.,College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Jianjiang Ma
- National Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.,College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Wenfeng Pei
- National Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Man Wu
- National Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Haijing Li
- National Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xingli Li
- National Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Shuxun Yu
- National Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China. .,College of Agronomy, Northwest A&F University, Yangling, 712100, China.
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, 880033, USA.
| | - Jiwen Yu
- National Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
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Hinze LL, Hulse-Kemp AM, Wilson IW, Zhu QH, Llewellyn DJ, Taylor JM, Spriggs A, Fang DD, Ulloa M, Burke JJ, Giband M, Lacape JM, Van Deynze A, Udall JA, Scheffler JA, Hague S, Wendel JF, Pepper AE, Frelichowski J, Lawley CT, Jones DC, Percy RG, Stelly DM. Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array. BMC Plant Biol 2017; 17:37. [PMID: 28158969 PMCID: PMC5291959 DOI: 10.1186/s12870-017-0981-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 01/23/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Cotton germplasm resources contain beneficial alleles that can be exploited to develop germplasm adapted to emerging environmental and climate conditions. Accessions and lines have traditionally been characterized based on phenotypes, but phenotypic profiles are limited by the cost, time, and space required to make visual observations and measurements. With advances in molecular genetic methods, genotypic profiles are increasingly able to identify differences among accessions due to the larger number of genetic markers that can be measured. A combination of both methods would greatly enhance our ability to characterize germplasm resources. Recent efforts have culminated in the identification of sufficient SNP markers to establish high-throughput genotyping systems, such as the CottonSNP63K array, which enables a researcher to efficiently analyze large numbers of SNP markers and obtain highly repeatable results. In the current investigation, we have utilized the SNP array for analyzing genetic diversity primarily among cotton cultivars, making comparisons to SSR-based phylogenetic analyses, and identifying loci associated with seed nutritional traits. RESULTS The SNP markers distinctly separated G. hirsutum from other Gossypium species and distinguished the wild from cultivated types of G. hirsutum. The markers also efficiently discerned differences among cultivars, which was the primary goal when designing the CottonSNP63K array. Population structure within the genus compared favorably with previous results obtained using SSR markers, and an association study identified loci linked to factors that affect cottonseed protein content. CONCLUSIONS Our results provide a large genome-wide variation data set for primarily cultivated cotton. Thousands of SNPs in representative cotton genotypes provide an opportunity to finely discriminate among cultivated cotton from around the world. The SNPs will be relevant as dense markers of genome variation for association mapping approaches aimed at correlating molecular polymorphisms with variation in phenotypic traits, as well as for molecular breeding approaches in cotton.
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Affiliation(s)
- Lori L. Hinze
- USDA-ARS, Crop Germplasm Research Unit, College Station, TX 77845 USA
| | - Amanda M. Hulse-Kemp
- Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, CA 95616 USA
| | - Iain W. Wilson
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Qian-Hao Zhu
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Danny J. Llewellyn
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Jen M. Taylor
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Andrew Spriggs
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - David D. Fang
- USDA-ARS, Cotton Fiber Bioscience Research Unit, New Orleans, LA 70124 USA
| | - Mauricio Ulloa
- USDA-ARS, Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Research Unit, Lubbock, TX 79415 USA
| | - John J. Burke
- USDA-ARS, Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Research Unit, Lubbock, TX 79415 USA
| | - Marc Giband
- CIRAD, UMR AGAP, Montpellier, F34398 France
- EMBRAPA, Algodão, Nucleo Cerrado, 75.375-000 Santo Antônio de Goias, GO Brazil
| | | | - Allen Van Deynze
- Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, CA 95616 USA
| | - Joshua A. Udall
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602 USA
| | - Jodi A. Scheffler
- USDA-ARS, Jamie Whitten Delta States Research Center, Stoneville, MS 38776 USA
| | - Steve Hague
- Department of Soil & Crop Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011 USA
| | - Alan E. Pepper
- Department of Biology, Texas A&M University, College Station, TX 77843 USA
- Interdisciplinary Department of Genetics, Texas A&M University, College Station, TX 77843 USA
| | | | - Cindy T. Lawley
- Illumina Inc., 499 Illinois Street, San Francisco, CA 94158 USA
| | - Don C. Jones
- Cotton Incorporated, Agricultural Research, Cary, NC 27513 USA
| | - Richard G. Percy
- USDA-ARS, Crop Germplasm Research Unit, College Station, TX 77845 USA
| | - David M. Stelly
- Department of Soil & Crop Sciences, Texas A&M University, College Station, TX 77843 USA
- Interdisciplinary Department of Genetics, Texas A&M University, College Station, TX 77843 USA
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11
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Hu G, Hovav R, Grover CE, Faigenboim-Doron A, Kadmon N, Page JT, Udall JA, Wendel JF. Evolutionary Conservation and Divergence of Gene Coexpression Networks in Gossypium (Cotton) Seeds. Genome Biol Evol 2016; 8:3765-3783. [PMID: 28062755 PMCID: PMC5585989 DOI: 10.1093/gbe/evw280] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2016] [Indexed: 12/18/2022] Open
Abstract
The cotton genus (Gossypium) provides a superior system for the study of diversification, genome evolution, polyploidization, and human-mediated selection. To gain insight into phenotypic diversification in cotton seeds, we conducted coexpression network analysis of developing seeds from diploid and allopolyploid cotton species and explored network properties. Key network modules and functional associations were identified related to seed oil content and seed weight. We compared species-specific networks to reveal topological changes, including rewired edges and differentially coexpressed genes, associated with speciation, polyploidy, and cotton domestication. Network comparisons among species indicate that topologies are altered in addition to gene expression profiles, indicating that changes in transcriptomic coexpression relationships play a role in the developmental architecture of cotton seed development. The global network topology of allopolyploids, especially for domesticated G. hirsutum, resembles the network of the A-genome diploid more than that of the D-genome parent, despite its D-like phenotype in oil content. Expression modifications associated with allopolyploidy include coexpression level dominance and transgressive expression, suggesting that the transcriptomic architecture in polyploids is to some extent a modular combination of that of its progenitor genomes. Among allopolyploids, intermodular relationships are more preserved between two different wild allopolyploid species than they are between wild and domesticated forms of a cultivated cotton, and regulatory connections of oil synthesis-related pathways are denser and more closely clustered in domesticated vs. wild G. hirsutum. These results demonstrate substantial modification of genic coexpression under domestication. Our work demonstrates how network inference informs our understanding of the transcriptomic architecture of phenotypic variation associated with temporal scales ranging from thousands (domestication) to millions (speciation) of years, and by polyploidy.
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Affiliation(s)
- Guanjing Hu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames
| | - Ran Hovav
- Agricultural Research Organization (Volcani Center), Bet Dagan, Israel
| | - Corrinne E. Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames
| | | | - Noa Kadmon
- Agricultural Research Organization (Volcani Center), Bet Dagan, Israel
| | | | | | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames
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Campbell B, Chapman K, Sturtevant D, Kennedy C, Horn P, Chee P, Lubbers E, Meredith W, Johnson J, Fraser D, Jones D. Genetic Analysis of Cottonseed Protein and Oil in a Diverse Cotton Germplasm. Crop Science 2016. [PMID: 0 DOI: 10.2135/cropsci2015.12.0742] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Affiliation(s)
- B.T. Campbell
- USDA-ARS Coastal Plains Soil, Water and Plant Research Center; 2611 W. Lucas St. Florence SC 29501
| | - K.D. Chapman
- Univ. of North Texas; Dep. of Biological Sciences; Denton TX 76203
| | - D. Sturtevant
- Univ. of North Texas; Dep. of Biological Sciences; Denton TX 76203
| | - C. Kennedy
- Univ. of North Texas; Dep. of Biological Sciences; Denton TX 76203
| | - P. Horn
- Michigan State Univ.; Dep. of Plant Biology; East Lansing MI 48824
| | - P.W. Chee
- Univ. of Georgia; Molecular Cotton Breeding Laboratory; Tifton GA 31794
| | - E. Lubbers
- Univ. of Georgia; Molecular Cotton Breeding Laboratory; Tifton GA 31794
| | - W.R. Meredith
- USDA-ARS; 141 Experiment Station Rd. Stoneville MS 38776
| | - J. Johnson
- PhytoGen Seed Co.; LLC, 118 Kennedy Flat Road Leland MS 38756
| | - D. Fraser
- Monsanto Company; 721 Coker Farm Rd. Hartsville SC 29550
| | - D.C. Jones
- Cotton Incorporated; 6399 Weston Pkwy Cary NC 27513
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13
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Hinze LL, Gazave E, Gore MA, Fang DD, Scheffler BE, Yu JZ, Jones DC, Frelichowski J, Percy RG. Genetic Diversity of the Two Commercial Tetraploid Cotton Species in the Gossypium Diversity Reference Set. J Hered 2016; 107:274-86. [PMID: 26774060 DOI: 10.1093/jhered/esw004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 01/04/2016] [Indexed: 11/14/2022] Open
Abstract
A diversity reference set has been constructed for the Gossypium accessions in the US National Cotton Germplasm Collection to facilitate more extensive evaluation and utilization of accessions held in the Collection. A set of 105 mapped simple sequence repeat markers was used to study the allelic diversity of 1933 tetraploid Gossypium accessions representative of the range of diversity of the improved and wild accessions of G. hirsutum and G. barbadense. The reference set contained 410 G. barbadense accessions and 1523 G. hirsutum accessions. Observed numbers of polymorphic and private bands indicated a greater diversity in G. hirsutum as compared to G. barbadense as well as in wild-type accessions as compared to improved accessions in both species. The markers clearly differentiated the 2 species. Patterns of diversity within species were observed but not clearly delineated, with much overlap occurring between races and regions of origin for wild accessions and between historical and geographic breeding pools for cultivated accessions. Although the percentage of accessions showing introgression was higher among wild accessions than cultivars in both species, the average level of introgression within individual accessions, as indicated by species-specific bands, was much higher in wild accessions of G. hirsutum than in wild accessions of G. barbadense. The average level of introgression within individual accessions was higher in improved G. barbadense cultivars than in G. hirsutum cultivars. This molecular characterization reveals the levels and distributions of genetic diversity that will allow for better exploration and utilization of cotton genetic resources.
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Affiliation(s)
- Lori L Hinze
- From the USDA-ARS, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, TX (Hinze, Yu, Frelichowski, and Percy); School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY (Gazave and Gore); USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA (Fang); USDA-ARS, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, MS (Scheffler); and Cotton Incorporated, Cary, NC (Jones).
| | - Elodie Gazave
- From the USDA-ARS, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, TX (Hinze, Yu, Frelichowski, and Percy); School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY (Gazave and Gore); USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA (Fang); USDA-ARS, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, MS (Scheffler); and Cotton Incorporated, Cary, NC (Jones)
| | - Michael A Gore
- From the USDA-ARS, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, TX (Hinze, Yu, Frelichowski, and Percy); School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY (Gazave and Gore); USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA (Fang); USDA-ARS, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, MS (Scheffler); and Cotton Incorporated, Cary, NC (Jones)
| | - David D Fang
- From the USDA-ARS, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, TX (Hinze, Yu, Frelichowski, and Percy); School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY (Gazave and Gore); USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA (Fang); USDA-ARS, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, MS (Scheffler); and Cotton Incorporated, Cary, NC (Jones)
| | - Brian E Scheffler
- From the USDA-ARS, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, TX (Hinze, Yu, Frelichowski, and Percy); School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY (Gazave and Gore); USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA (Fang); USDA-ARS, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, MS (Scheffler); and Cotton Incorporated, Cary, NC (Jones)
| | - John Z Yu
- From the USDA-ARS, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, TX (Hinze, Yu, Frelichowski, and Percy); School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY (Gazave and Gore); USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA (Fang); USDA-ARS, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, MS (Scheffler); and Cotton Incorporated, Cary, NC (Jones)
| | - Don C Jones
- From the USDA-ARS, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, TX (Hinze, Yu, Frelichowski, and Percy); School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY (Gazave and Gore); USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA (Fang); USDA-ARS, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, MS (Scheffler); and Cotton Incorporated, Cary, NC (Jones)
| | - James Frelichowski
- From the USDA-ARS, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, TX (Hinze, Yu, Frelichowski, and Percy); School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY (Gazave and Gore); USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA (Fang); USDA-ARS, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, MS (Scheffler); and Cotton Incorporated, Cary, NC (Jones)
| | - Richard G Percy
- From the USDA-ARS, Southern Plains Agricultural Research Center, Crop Germplasm Research Unit, College Station, TX (Hinze, Yu, Frelichowski, and Percy); School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY (Gazave and Gore); USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA (Fang); USDA-ARS, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, MS (Scheffler); and Cotton Incorporated, Cary, NC (Jones)
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