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Ma J, Jia B, Bian Y, Pei W, Song J, Wu M, Wang W, Kashif, Shahzad, Wang L, Zhang B, Feng P, Yang L, Zhang J, Yu J. Genomic and co-expression network analyses reveal candidate genes for oil accumulation based on an introgression population in Upland cotton (Gossypium hirsutum). Theor Appl Genet 2024; 137:23. [PMID: 38231256 DOI: 10.1007/s00122-023-04527-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 12/11/2023] [Indexed: 01/18/2024]
Abstract
KEY MESSAGE Integrated QTL mapping and WGCNA condense the potential gene regulatory network involved in oil accumulation. A glycosyl hydrolases gene (GhHSD1) for oil biosynthesis was confirmed in Arabidopsis, which will provide useful knowledge to understand the functional mechanism of oil biosynthesis in cotton. Cotton is an economical source of edible oil for the food industry. The genetic mechanism that regulates oil biosynthesis in cottonseeds is essential for the genetic enhancement of oil content (OC). To explore the functional genomics of OC, this study utilized an interspecific backcross inbred line population to dissect the quantitative trait locus (QTL) interlinked with OC. In total, nine OC QTLs were identified, four of which were novel, and each QTL explained 3.62-34.73% of the phenotypic variation of OC. The comprehensive transcript profiling of developing cottonseeds revealed 3,646 core genes differentially expressed in both inbred parents. Functional enrichment analysis determined 43 genes were annotated with oil biosynthesis processes. Implementation of weighted gene co-expression network analysis showed that 803 differential genes had a significant correlation with the OC phenotype. Further integrated analysis identified seven important genes located in OC QTLs. Of which, the GhHSD1 gene located in stable QTL qOC-Dt3-1 exhibited the highest functional linkages with the other network genes. Phylogenetic analysis showed significant evolutionary differences in the HSD1 sequences between oilseed- and starch- crops. Furthermore, the overexpression of GhHSD1 in Arabidopsis yielded almost 6.78% higher seed oil. This study not only uncovers important genetic loci for oil accumulation in cottonseed, but also provides a set of new candidate genes that potentially influence the oil biosynthesis pathway in cottonseed.
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Affiliation(s)
- Jianjiang Ma
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Anyang, China
- State Key Laboratory of Cotton Biology, Zhengzhou Research Base, Zhengzhou University, Zhengzhou, China
| | - Bing Jia
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Anyang, China
| | - Yingying Bian
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Anyang, China
| | - Wenfeng Pei
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Anyang, China
| | - Jikun Song
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Anyang, China
| | - Man Wu
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Anyang, China
| | - Wenkui Wang
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Anyang, China
| | | | - Shahzad
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Anyang, China
| | - Li Wang
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Anyang, China
| | - Bingbing Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Anyang, China
| | - Pan Feng
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Anyang, China
| | - Liupeng Yang
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Anyang, China
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, USA.
| | - Jiwen Yu
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Anyang, China.
- State Key Laboratory of Cotton Biology, Zhengzhou Research Base, Zhengzhou University, Zhengzhou, China.
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Alam B, Liu R, Gong J, Li J, Yan H, Ge Q, Xiao X, Pan J, Shang H, Shi Y, Yuan Y, Gong W. Hub Genes in Stable QTLs Orchestrate the Accumulation of Cottonseed Oil in Upland Cotton via Catalyzing Key Steps of Lipid-Related Pathways. Int J Mol Sci 2023; 24:16595. [PMID: 38068920 PMCID: PMC10706765 DOI: 10.3390/ijms242316595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/10/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023] Open
Abstract
Upland cotton is the fifth-largest oil crop in the world, with an average supply of nearly 20% of vegetable oil production. Cottonseed oil is also an ideal alternative raw material to be efficiently converted into biodiesel. However, the improvement in kernel oil content (KOC) of cottonseed has not received sufficient attention from researchers for a long time, due to the fact that the main product of cotton planting is fiber. Previous studies have tagged QTLs and identified individual candidate genes that regulate KOC of cottonseed. The regulatory mechanism of oil metabolism and accumulation of cottonseed are still elusive. In the current study, two high-density genetic maps (HDGMs), which were constructed based on a recombinant inbred line (RIL) population consisting of 231 individuals, were used to identify KOC QTLs. A total of forty-three stable QTLs were detected via these two HDGM strategies. Bioinformatic analysis of all the genes harbored in the marker intervals of the stable QTLs revealed that a total of fifty-one genes were involved in the pathways related to lipid biosynthesis. Functional analysis via coexpression network and RNA-seq revealed that the hub genes in the co-expression network that also catalyze the key steps of fatty acid synthesis, lipid metabolism and oil body formation pathways (ACX4, LACS4, KCR1, and SQD1) could jointly orchestrate oil accumulation in cottonseed. This study will strengthen our understanding of oil metabolism and accumulation in cottonseed and contribute to KOC improvement in cottonseed in the future, enhancing the security and stability of worldwide food supply.
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Affiliation(s)
- Beena Alam
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China (Y.S.)
| | - Ruixian Liu
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China (Y.S.)
| | - Juwu Gong
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China (Y.S.)
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Junwen Li
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China (Y.S.)
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Haoliang Yan
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China (Y.S.)
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Qun Ge
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China (Y.S.)
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Xianghui Xiao
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China (Y.S.)
| | - Jingtao Pan
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China (Y.S.)
| | - Haihong Shang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China (Y.S.)
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Yuzhen Shi
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China (Y.S.)
| | - Youlu Yuan
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China (Y.S.)
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Wankui Gong
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China (Y.S.)
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Liu L, Wang D, Hua J, Kong X, Wang X, Wang J, Si A, Zhao F, Liu W, Yu Y, Chen Z. Genetic and Morpho-Physiological Differences among Transgenic and No-Transgenic Cotton Cultivars. Plants (Basel) 2023; 12:3437. [PMID: 37836177 PMCID: PMC10574747 DOI: 10.3390/plants12193437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/22/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023]
Abstract
Three carbon-chain extension genes associated with fatty acid synthesis in upland cotton (Gossypium hirsutum), namely GhKAR, GhHAD, and GhENR, play important roles in oil accumulation in cotton seeds. In the present study, these three genes were cloned and characterized. The expression patterns of GhKAR, GhHAD, and GhENR in the high seed oil content cultivars 10H1014 and 10H1041 differed somewhat compared with those of 10H1007 and 2074B with low seed oil content at different stages of seed development. GhKAR showed all three cultivars showed higher transcript levels than that of 2074B at 10-, 40-, and 45-days post anthesis (DPA). The expression pattern of GhHAD showed a lower transcript level than that of 2074B at both 10 and 30 DPA but a higher transcript level than that of 2074B at 40 DPA. GhENR showed a lower transcript level than that of 2074B at both 15 and 30 DPA. The highest transcript levels of GhKAR and GhENR were detected at 15 DPA in 10H1007, 10H1014, and 10H1041 compared with 2074B. From 5 to 45 DPA cotton seed, the oil content accumulated continuously in the developing seed. Oil accumulation reached a peak between 40 DPA and 45 DPA and slightly decreased in mature seed. In addition, GhKAR and GhENR showed different expression patterns in fiber and ovule development processes, in which they showed high expression levels at 20 DPA during the fiber elongation stage, but their expression level peaked at 15 DPA during ovule development processes. These two genes showed the lowest expression levels at the late seed maturation stage, while GhHAD showed a peak of 10 DPA in fiber development. Compared to 2074B, the oil contents of GhKAR and GhENR overexpression lines increased 1.05~1.08 folds. These results indicated that GhHAD, GhENR, and GhKAR were involved in both seed oil synthesis and fiber elongation with dual biological functions in cotton.
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Affiliation(s)
- Li Liu
- Cotton Institute, Xinjiang Academy of Agricultural and Reclamation Science/Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding, Shihezi 832000, China; (L.L.); (X.K.); (X.W.); (J.W.); (A.S.); (F.Z.); (W.L.)
| | - Dan Wang
- Laboratory of Cotton Genetics, Genomics and Breeding/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (D.W.); (J.H.)
| | - Jinping Hua
- Laboratory of Cotton Genetics, Genomics and Breeding/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (D.W.); (J.H.)
| | - Xianhui Kong
- Cotton Institute, Xinjiang Academy of Agricultural and Reclamation Science/Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding, Shihezi 832000, China; (L.L.); (X.K.); (X.W.); (J.W.); (A.S.); (F.Z.); (W.L.)
| | - Xuwen Wang
- Cotton Institute, Xinjiang Academy of Agricultural and Reclamation Science/Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding, Shihezi 832000, China; (L.L.); (X.K.); (X.W.); (J.W.); (A.S.); (F.Z.); (W.L.)
| | - Juan Wang
- Cotton Institute, Xinjiang Academy of Agricultural and Reclamation Science/Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding, Shihezi 832000, China; (L.L.); (X.K.); (X.W.); (J.W.); (A.S.); (F.Z.); (W.L.)
| | - Aijun Si
- Cotton Institute, Xinjiang Academy of Agricultural and Reclamation Science/Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding, Shihezi 832000, China; (L.L.); (X.K.); (X.W.); (J.W.); (A.S.); (F.Z.); (W.L.)
| | - Fuxiang Zhao
- Cotton Institute, Xinjiang Academy of Agricultural and Reclamation Science/Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding, Shihezi 832000, China; (L.L.); (X.K.); (X.W.); (J.W.); (A.S.); (F.Z.); (W.L.)
| | - Wenhao Liu
- Cotton Institute, Xinjiang Academy of Agricultural and Reclamation Science/Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding, Shihezi 832000, China; (L.L.); (X.K.); (X.W.); (J.W.); (A.S.); (F.Z.); (W.L.)
| | - Yu Yu
- Cotton Institute, Xinjiang Academy of Agricultural and Reclamation Science/Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding, Shihezi 832000, China; (L.L.); (X.K.); (X.W.); (J.W.); (A.S.); (F.Z.); (W.L.)
| | - Zhiwen Chen
- Key Laboratory of Graphene Forestry Application of National Forest and Grass Administration, Engineering Research Center of Coal-Based Ecological Carbon Sequestration Technology of the Ministry of Education, Shanxi Datong University, Datong 037009, China
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Maryum Z, Luqman T, Nadeem S, Khan SMUD, Wang B, Ditta A, Khan MKR. An overview of salinity stress, mechanism of salinity tolerance and strategies for its management in cotton. Front Plant Sci 2022; 13:907937. [PMID: 36275563 PMCID: PMC9583260 DOI: 10.3389/fpls.2022.907937] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 09/20/2022] [Indexed: 05/14/2023]
Abstract
Salinity stress is one of the primary threats to agricultural crops resulting in impaired crop growth and development. Although cotton is considered as reasonably salt tolerant, it is sensitive to salt stress at some critical stages like germination, flowering, boll formation, resulting in reduced biomass and fiber production. The mechanism of partial ion exclusion (exclusion of Na+ and/or Cl-) in cotton appears to be responsible for the pattern of uptake and accumulation of harmful ions (Na+ and Cl) in tissues of plants exposed to saline conditions. Maintaining high tissue K+/Na+ and Ca2+/Na+ ratios has been proposed as a key selection factor for salt tolerance in cotton. The key adaptation mechanism in cotton under salt stress is excessive sodium exclusion or compartmentation. Among the cultivated species of cotton, Egyptian cotton (Gossypium barbadense L.) exhibit better salt tolerance with good fiber quality traits as compared to most cultivated cotton and it can be used to improve five quality traits and transfer salt tolerance into Upland or American cotton (Gossypium hirsutum L.) by interspecific introgression. Cotton genetic studies on salt tolerance revealed that the majority of growth, yield, and fiber traits are genetically determined, and controlled by quantitative trait loci (QTLs). Molecular markers linked to genes or QTLs affecting key traits have been identified, and they could be utilized as an indirect selection criterion to enhance breeding efficiency through marker-assisted selection (MAS). Transfer of genes for compatible solute, which are an important aspect of ion compartmentation, into salt-sensitive species is, theoretically, a simple strategy to improve tolerance. The expression of particular stress-related genes is involved in plant adaptation to environmental stressors. As a result, enhancing tolerance to salt stress can be achieved by marker assisted selection added with modern gene editing tools can boost the breeding strategies that defend and uphold the structure and function of cellular components. The intent of this review was to recapitulate the advancements in salt screening methods, tolerant germplasm sources and their inheritance, biochemical, morpho-physiological, and molecular characteristics, transgenic approaches, and QTLs for salt tolerance in cotton.
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Affiliation(s)
- Zahra Maryum
- Nuclear Institute for Agriculture and Biology-Constituent College (NIAB-C), Pakistan Institute of Engineering and Applied Science Nilore, Islamabad, Pakistan
| | - Tahira Luqman
- Nuclear Institute for Agriculture and Biology-Constituent College (NIAB-C), Pakistan Institute of Engineering and Applied Science Nilore, Islamabad, Pakistan
| | - Sahar Nadeem
- Nuclear Institute for Agriculture and Biology-Constituent College (NIAB-C), Pakistan Institute of Engineering and Applied Science Nilore, Islamabad, Pakistan
| | - Sana Muhy Ud Din Khan
- Plant Breeding and Genetics Division, Cotton Group, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Baohua Wang
- School of Life Sciences, Nantong University, Nantong, China
| | - Allah Ditta
- Nuclear Institute for Agriculture and Biology-Constituent College (NIAB-C), Pakistan Institute of Engineering and Applied Science Nilore, Islamabad, Pakistan
- Plant Breeding and Genetics Division, Cotton Group, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Muhammad Kashif Riaz Khan
- Nuclear Institute for Agriculture and Biology-Constituent College (NIAB-C), Pakistan Institute of Engineering and Applied Science Nilore, Islamabad, Pakistan
- Plant Breeding and Genetics Division, Cotton Group, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
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Wu L, Jia B, Pei W, Wang L, Ma J, Wu M, Song J, Yang S, Xin Y, Huang L, Feng P, Zhang J, Yu J. Quantitative Trait Locus Analysis and Identification of Candidate Genes Affecting Seed Size and Shape in an Interspecific Backcross Inbred Line Population of Gossypium hirsutum × Gossypium barbadense. Front Plant Sci 2022; 13:837984. [PMID: 35392518 PMCID: PMC8981304 DOI: 10.3389/fpls.2022.837984] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Seed size and shape are key agronomic traits affecting seedcotton yield and seed quality in cotton (Gossypium spp.). However, the genetic mechanisms that regulate the seed physical traits in cotton are largely unknown. In this study, an interspecific backcross inbred line (BIL) population of 250 BC1F7 lines, derived from the recurrent parent Upland CRI36 (Gossypium hirsutum) and Hai7124 (Gossypium barbadense), was used to investigate the genetic basis of cotton seed physical traits via quantitative trait locus (QTL) mapping and candidate gene identification. The BILs were tested in five environments, measuring eight seed size and shape-related traits, including 100-kernel weight, kernel length width and their ratio, kernel area, kernel girth, kernel diameter, and kernel roundness. Based on 7,709 single nucleotide polymorphic (SNP) markers, a total of 49 QTLs were detected and each explained 2.91-35.01% of the phenotypic variation, including nine stable QTLs mapped in at least three environments. Based on pathway enrichment, gene annotation, genome sequence, and expression analysis, five genes encoding starch synthase 4, transcription factor PIF7 and MYC4, ubiquitin-conjugating enzyme E27, and THO complex subunit 4A were identified as candidate genes that might be associated with seed size and shape. Our research provides valuable information to improve seed physical traits in cotton breeding.
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Affiliation(s)
- Luyao Wu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Bing Jia
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Wenfeng Pei
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Li Wang
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jianjiang Ma
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Man Wu
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jikun Song
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shuxian Yang
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yue Xin
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Li Huang
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Pan Feng
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of 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
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
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6
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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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7
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Zhang Z, Gong J, Zhang Z, Gong W, Li J, Shi Y, Liu A, Ge Q, Pan J, Fan S, Deng X, Li S, Chen Q, Yuan Y, Shang H. Identification and analysis of oil candidate genes reveals the molecular basis of cottonseed oil accumulation in Gossypium hirsutum L. Theor Appl Genet 2022; 135:449-460. [PMID: 34714356 DOI: 10.1007/s00122-021-03975-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/15/2021] [Indexed: 05/14/2023]
Abstract
Based on the integration of QTL-mapping and regulatory network analyses, five high-confidence stable QTL regions, six candidate genes and two microRNAs that potentially affect the cottonseed oil content were discovered. Cottonseed oil is increasingly becoming a promising target for edible oil with its high content of unsaturated fatty acids. In this study, a recombinant inbred line (RIL) cotton population was constructed to detect quantitative trait loci (QTLs) for the cottonseed oil content. A total of 39 QTLs were detected across eight different environments, of which five QTLs were stable. Forty-three candidate genes potentially involved in carbon metabolism, fatty acid synthesis and triacylglycerol biosynthesis processes were further obtained in the stable QTL regions. Transcriptome analysis showed that nineteen of these candidate genes expressed during the developing cottonseed ovules and may affect the cottonseed oil content. Besides, transcription factor (TF) and microRNA (miRNA) co-regulatory network analyses based on the nineteen candidate genes suggested that six genes, two core miRNAs (ghr-miR2949b and ghr-miR2949c), and one TF GhHSL1 were considered to be closely associated with the cottonseed oil content. Moreover, four vital genes were validated by quantitative real-time PCR (qRT-PCR). These results provide insights into the oil accumulation mechanism in developing cottonseed ovules through the construction of a detailed oil accumulation model.
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Affiliation(s)
- Zhibin Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450000, China
| | - Juwu Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, Ürümqi, 830001, China
| | - Zhen Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wankui Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Junwen Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yuzhen Shi
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Aiying Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Jingtao Pan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Senmiao Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiaoying Deng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Shaoqi Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Quanjia Chen
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, Ürümqi, 830001, China
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450000, China.
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, Ürümqi, 830001, China.
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450000, China.
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8
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Li Y, Mo T, Ran L, Zeng J, Wang C, Liang A, Dai Y, Wu Y, Zhong Z, Xiao Y. Genome resequencing-based high-density genetic map and QTL detection for yield and fiber quality traits in diploid Asiatic cotton (Gossypium arboreum). Mol Genet Genomics 2022; 297:199-212. [PMID: 35048185 DOI: 10.1007/s00438-021-01848-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 03/11/2021] [Accepted: 12/14/2021] [Indexed: 10/19/2022]
Abstract
Cotton is the most important fiber crop in the world. Asiatic cotton (Gossypium arboreum, genome A2) is a diploid cotton species producing spinnable fibers and important germplasm for cotton breeding and a significant model for fiber biology. However, the genetic map of Asiatic cotton has been lagging behind tetraploid cottons, as well as other stable crops. This study aimed to construct a high-density SNP genetic map and to map QTLs for important yield and fiber quality traits. Using a recombinant inbred line (RIL) population and genome resequencing technology, we constructed a high-density genetic map that covered 1980.17 cM with an average distance of 0.61 cM between adjacent markers. QTL analysis revealed a total of 297 QTLs for 13 yield and fiber quality traits in three environments, explaining 5.0-37.4% of the phenotypic variance, among which 75 were stably detected in two or three environments. Besides, 47 QTL clusters, comprising 131 QTLs for representative traits, were identified. Our works laid solid foundation for fine mapping and cloning of QTL for yield and fiber quality traits in Asiatic cotton.
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Affiliation(s)
- Yaohua Li
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Southwest University Southern Campus, Tiansheng Rd No. 2, Beibei, Chongqing, 400716, China
| | - Tong Mo
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Southwest University Southern Campus, Tiansheng Rd No. 2, Beibei, Chongqing, 400716, China
| | - Lingfang Ran
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Southwest University Southern Campus, Tiansheng Rd No. 2, Beibei, Chongqing, 400716, China
| | - Jianyan Zeng
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Southwest University Southern Campus, Tiansheng Rd No. 2, Beibei, Chongqing, 400716, China
| | - Chuannan Wang
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Southwest University Southern Campus, Tiansheng Rd No. 2, Beibei, Chongqing, 400716, China
| | - Aimin Liang
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Southwest University Southern Campus, Tiansheng Rd No. 2, Beibei, Chongqing, 400716, China
| | - Yonglu Dai
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Southwest University Southern Campus, Tiansheng Rd No. 2, Beibei, Chongqing, 400716, China
| | - Yiping Wu
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Southwest University Southern Campus, Tiansheng Rd No. 2, Beibei, Chongqing, 400716, China
| | - Ziman Zhong
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Southwest University Southern Campus, Tiansheng Rd No. 2, Beibei, Chongqing, 400716, China
| | - Yuehua Xiao
- Biotechnology Research Center, Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Southwest University, Southwest University Southern Campus, Tiansheng Rd No. 2, Beibei, Chongqing, 400716, China.
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9
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Gu Q, Ke H, Liu Z, Lv X, Sun Z, Zhang M, Chen L, Yang J, Zhang Y, Wu L, Li Z, Wu J, Wang G, Meng C, Zhang G, Wang X, Ma Z. A high-density genetic map and multiple environmental tests reveal novel quantitative trait loci and candidate genes for fibre quality and yield in cotton. Theor Appl Genet 2020; 133:3395-3408. [PMID: 32894321 DOI: 10.1007/s00122-020-03676-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 08/21/2020] [Indexed: 05/18/2023]
Abstract
A high-density linkage map of an intraspecific RIL population was constructed using 6187 bins to identify QTLs for fibre quality- and yield-related traits in upland cotton by whole-genome resequencing. Good fibre quality and high yield are important production goals in cotton (Gossypium hirsutum L.), which is a leading natural fibre crop worldwide. However, a greater understanding of the genetic variants underlying fibre quality- and yield-related traits is still required. In this study, a large-scale population including 588 F7 recombinant inbred lines, derived from an intraspecific cross between the upland cotton cv. Nongdamian13, which exhibits high quality, and Nongda601, which exhibits a high yield, was genotyped by using 232,946 polymorphic single-nucleotide polymorphisms obtained via a whole-genome resequencing strategy with 4.3-fold genome coverage. We constructed a high-density bin linkage map containing 6187 bin markers spanning 4478.98 cM with an average distance of 0.72 cM. We identified 58 individual quantitative trait loci (QTLs) and 25 QTL clusters harbouring 94 QTLs, and 119 previously undescribed QTLs controlling 13 fibre quality and yield traits across eight environments. Importantly, the QTL counts for fibre quality in the Dt subgenome were more than two times that in the At subgenome, and chromosome D02 harboured the greatest number of QTLs and clusters. Furthermore, we discovered 24 stable QTLs for fibre quality and 12 stable QTLs for yield traits. Four novel major stable QTLs related to fibre length, fibre strength and lint percentage, and seven previously unreported candidate genes with significantly differential expression between the two parents were identified and validated by RNA-seq. Our research provides valuable information for improving the fibre quality and yield in cotton breeding.
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Affiliation(s)
- Qishen Gu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Huifeng Ke
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Zhengwen Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Xing Lv
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Zhengwen Sun
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Man Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Liting Chen
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Jun Yang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Yan Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Liqiang Wu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Zhikun Li
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Jinhua Wu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Guoning Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Chengsheng Meng
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Guiyin Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Xingfen Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China.
| | - Zhiying Ma
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China.
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10
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Cui Y, Su Y, Wang J, Jia B, Wu M, Pei W, Zhang J, Yu J. Genome-Wide Characterization and Analysis of CIPK Gene Family in Two Cultivated Allopolyploid Cotton Species: Sequence Variation, Association with Seed Oil Content, and the Role of GhCIPK6. Int J Mol Sci 2020; 21:E863. [PMID: 32013234 PMCID: PMC7037685 DOI: 10.3390/ijms21030863] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/24/2020] [Accepted: 01/27/2020] [Indexed: 01/16/2023] Open
Abstract
Calcineurin B-like protein-interacting protein kinases (CIPKs), as key regulators, play an important role in plant growth and development and the response to various stresses. In the present study, we identified 80 and 78 CIPK genes in the Gossypium hirsutum and G. barbadense, respectively. The phylogenetic and gene structure analysis divided the cotton CIPK genes into five groups which were classified into an exon-rich clade and an exon-poor clade. A synteny analysis showed that segmental duplication contributed to the expansion of Gossypium CIPK gene family, and purifying selection played a major role in the evolution of the gene family in cotton. Analyses of expression profiles showed that GhCIPK genes had temporal and spatial specificity and could be induced by various abiotic stresses. Fourteen GhCIPK genes were found to contain 17 non-synonymous single nucleotide polymorphisms (SNPs) and co-localized with oil or protein content quantitative trait loci (QTLs). Additionally, five SNPs from four GhCIPKs were found to be significantly associated with oil content in one of the three field tests. Although most GhCIPK genes were not associated with natural variations in cotton oil content, the overexpression of the GhCIPK6 gene reduced the oil content and increased C18:1 and C18:1+C18:1d6 in transgenic cotton as compared to wild-type plants. In addition, we predicted the potential molecular regulatory mechanisms of the GhCIPK genes. In brief, these results enhance our understanding of the roles of CIPK genes in oil synthesis and stress responses.
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Affiliation(s)
- Yupeng Cui
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, China; (Y.C.); (J.W.); (B.J.); (M.W.); (W.P.)
| | - Ying Su
- Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China;
| | - Junjuan Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, China; (Y.C.); (J.W.); (B.J.); (M.W.); (W.P.)
| | - Bing Jia
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, China; (Y.C.); (J.W.); (B.J.); (M.W.); (W.P.)
| | - Man Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, China; (Y.C.); (J.W.); (B.J.); (M.W.); (W.P.)
| | - Wenfeng Pei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, China; (Y.C.); (J.W.); (B.J.); (M.W.); (W.P.)
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88003, USA;
| | - Jiwen Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, China; (Y.C.); (J.W.); (B.J.); (M.W.); (W.P.)
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11
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Ma J, Liu J, Pei W, Ma Q, Wang N, Zhang X, Cui Y, Li D, Liu G, Wu M, Zang X, Song J, Zhang J, Yu S, Yu J. Genome-wide association study of the oil content in upland cotton (Gossypium hirsutum L.) and identification of GhPRXR1, a candidate gene for a stable QTLqOC-Dt5-1. Plant Sci 2019; 286:89-97. [PMID: 31300146 DOI: 10.1016/j.plantsci.2019.05.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 02/04/2019] [Revised: 05/09/2019] [Accepted: 05/25/2019] [Indexed: 05/14/2023]
Abstract
Cottonseed oil is one of the most important renewable resources for edible oil and biodiesel. To detect QTLs associated with cottonseed oil content (OC) and identify candidate genes that regulate oil biosynthesis, a panel of upland cotton germplasm lines was selected among those previously used to perform GWASs in China. In the present study, 13 QTLs associated with 53 common SNPs on 13 chromosomes were identified in multiple environments based on 15,369 polymorphic SNPs using the Cotton63 KSNP array. Of these, the OC QTL qOC-Dt5-1 delineated by nine SNPs occurred in a confidence interval of 4 SSRs with previously reported OC QTLs. A combined transcriptome and qRT-PCR analysis revealed that a peroxidase gene (GhPRXR1) was predominantly expressed during the middle-late stage (20-35 days post anthesis) of ovule development. The overexpression of GhPRXR1 in yeast significantly increased the OC by 20.01-37.25 %. Suppression of GhPRXR1 gene expression in the virus-induced gene-silenced cotton reduced the OC by 18.11%. Our results contribute to identifying more OC QTLs and verifying a candidate gene that influences cottonseed oil biosynthesis.
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Affiliation(s)
- 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, Henan 455000, China; College of Agronomy, Northwest A&F University, Yangling, Shanxi 712100, China.
| | - Ji Liu
- 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, Henan 455000, China.
| | - Wenfeng Pei
- 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, Henan 455000, China.
| | - Qifeng 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, Henan 455000, China.
| | - Nuohan Wang
- 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, Henan 455000, China; College of Agronomy, Northwest A&F University, Yangling, Shanxi 712100, China.
| | - Xia Zhang
- 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, Henan 455000, China.
| | - Yupeng Cui
- 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, Henan 455000, China.
| | - Dan Li
- 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, Henan 455000, China.
| | - Guoyuan Liu
- 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, Henan 455000, 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, Henan 455000, China.
| | - XinShan Zang
- 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, Henan 455000, China.
| | - Jikun Song
- 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, Henan 455000, China.
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, 880033, USA.
| | - Shuxun Yu
- 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, Henan 455000, China; College of Agronomy, Northwest A&F University, Yangling, Shanxi 712100, China.
| | - Jiwen Yu
- 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, Henan 455000, China.
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12
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Wang W, Sun Y, Yang P, Cai X, Yang L, Ma J, Ou Y, Liu T, Ali I, Liu D, Zhang J, Teng Z, Guo K, Liu D, Liu F, Zhang Z. A high density SLAF-seq SNP genetic map and QTL for seed size, oil and protein content in upland cotton. BMC Genomics 2019; 20:599. [PMID: 31331266 PMCID: PMC6647295 DOI: 10.1186/s12864-019-5819-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 05/21/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Cotton is a leading natural fiber crop. Beyond its fiber, cottonseed is a valuable source of plant protein and oil. Due to the much higher value of cotton fiber, there is less consideration of cottonseed quality despite its potential value. Though some QTL controlling cottonseed quality have been identified, few of them that warrant further study are known. Identifying stable QTL controlling seed size, oil and protein content is necessary for improvement of cottonseed quality. RESULTS In this study, a recombinant inbred line (RIL) population was developed from a cross between upland cotton cultivars/lines Yumian 1 and M11. Specific locus amplified fragment sequencing (SLAF-seq) technology was used to construct a genetic map that covered 3353.15 cM with an average distance between consecutive markers of 0.48 cM. The seed index, together with kernel size, oil and protein content were further used to identify QTL. In total, 58 QTL associated with six traits were detected, including 13 stable QTL detected in all three environments and 11 in two environments. CONCLUSION A high resolution genetic map including 7033 SNP loci was constructed through specific locus amplified fragment sequencing technology. A total of 13 stable QTL associated with six cottonseed quality traits were detected. These stable QTL have the potential for fine mapping, identifying candidate genes, elaborating molecular mechanisms of cottonseed development, and application in cotton breeding programs.
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Affiliation(s)
- Wenwen Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 China
| | - Ying Sun
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 China
| | - Peng Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Le Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 China
| | - Junrui Ma
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 China
| | - Yuncan Ou
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 China
| | - Tianpeng Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 China
| | - Iftikhar Ali
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 China
| | - Dajun Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 China
| | - Jian Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 China
| | - Zhonghua Teng
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 China
| | - Kai Guo
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 China
| | - Dexin Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 China
| | - Fang Liu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Zhengsheng Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 China
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13
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Du X, Liu S, Sun J, Zhang G, Jia Y, Pan Z, Xiang H, He S, Xia Q, Xiao S, Shi W, Quan Z, Liu J, Ma J, Pang B, Wang L, Sun G, Gong W, Jenkins JN, Lou X, Zhu J, Xu H. Dissection of complicate genetic architecture and breeding perspective of cottonseed traits by genome-wide association study. BMC Genomics 2018; 19:451. [PMID: 29895260 PMCID: PMC5998501 DOI: 10.1186/s12864-018-4837-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 05/29/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Cottonseed is one of the most important raw materials for plant protein, oil and alternative biofuel for diesel engines. Understanding the complex genetic basis of cottonseed traits is requisite for achieving efficient genetic improvement of the traits. However, it is not yet clear about their genetic architecture in genomic level. GWAS has been an effective way to explore genetic basis of quantitative traits in human and many crops. This study aims to dissect genetic mechanism seven cottonseed traits by a GWAS for genetic improvement. RESULTS A genome-wide association study (GWAS) based on a full gene model with gene effects as fixed and gene-environment interaction as random, was conducted for protein, oil and 5 fatty acids using 316 accessions and ~ 390 K SNPs. Totally, 124 significant quantitative trait SNPs (QTSs), consisting of 16, 21, 87 for protein, oil and fatty acids (palmitic, linoleic, oleic, myristic, stearic), respectively, were identified and the broad-sense heritability was estimated from 71.62 to 93.43%; no QTS-environment interaction was detected for the protein, the palmitic and the oleic contents; the protein content was predominantly controlled by epistatic effects accounting for 65.18% of the total variation, but the oil content and the fatty acids except the palmitic were mainly determined by gene main effects and no epistasis was detected for the myristic and the stearic. Prediction of superior pure line and hybrid revealed the potential of the QTSs in the improvement of cottonseed traits, and the hybrid could achieve higher or lower genetic values compared with pure lines. CONCLUSIONS This study revealed complex genetic architecture of seven cottonseed traits at whole genome-wide by mixed linear model approach; the identified genetic variants and estimated genetic component effects of gene, gene-gene and gene-environment interaction provide cotton geneticist or breeders new knowledge on the genetic mechanism of the traits and the potential molecular breeding design strategy.
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Affiliation(s)
- Xiongming Du
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences (ICR, CAAS), State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000 People’s Republic of China
| | - Shouye Liu
- Institute of crop science and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058 People’s Republic of China
| | - Junling Sun
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences (ICR, CAAS), State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000 People’s Republic of China
| | - Gengyun Zhang
- Shenzhen Huada Gene Research Institute, Shenzhen, 518031 People’s Republic of China
| | - Yinhua Jia
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences (ICR, CAAS), State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000 People’s Republic of China
| | - Zhaoe Pan
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences (ICR, CAAS), State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000 People’s Republic of China
| | - Haitao Xiang
- Shenzhen Huada Gene Research Institute, Shenzhen, 518031 People’s Republic of China
| | - Shoupu He
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences (ICR, CAAS), State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000 People’s Republic of China
| | - Qiuju Xia
- Shenzhen Huada Gene Research Institute, Shenzhen, 518031 People’s Republic of China
| | - Songhua Xiao
- Institute of industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 People’s Republic of China
| | - Weijun Shi
- Economic Crop Research Institute, Xinjiang Academy of Agricultural Science, Urumqi, 830002 People’s Republic of China
| | - Zhiwu Quan
- Shenzhen Huada Gene Research Institute, Shenzhen, 518031 People’s Republic of China
| | - Jianguang Liu
- Institute of industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 People’s Republic of China
| | - Jun Ma
- Economic Crop Research Institute, Xinjiang Academy of Agricultural Science, Urumqi, 830002 People’s Republic of China
| | - Baoyin Pang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences (ICR, CAAS), State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000 People’s Republic of China
| | - Liru Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences (ICR, CAAS), State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000 People’s Republic of China
| | - Gaofei Sun
- Department of Computer Science and Information Engineering, Anyang Institute of Technology, Anyang, 455000 People’s Republic of China
| | - Wenfang Gong
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences (ICR, CAAS), State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, 455000 People’s Republic of China
| | | | - Xiangyang Lou
- Department of Pediatrics, Biostatistics Division Arkansas Children‘s Hospital Research Institute School of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72202 USA
| | - Jun Zhu
- Institute of crop science and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058 People’s Republic of China
| | - Haiming Xu
- Institute of crop science and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058 People’s Republic of China
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14
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Liu X, Teng Z, Wang J, Wu T, Zhang Z, Deng X, Fang X, Tan Z, Ali I, Liu D, Zhang J, Liu D, Liu F, Zhang Z. Enriching an intraspecific genetic map and identifying QTL for fiber quality and yield component traits across multiple environments in Upland cotton (Gossypium hirsutum L.). Mol Genet Genomics 2017; 292:1281-1306. [PMID: 28733817 DOI: 10.1007/s00438-017-1347-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [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: 11/28/2016] [Accepted: 06/29/2017] [Indexed: 10/19/2022]
Abstract
Cotton is a significant commercial crop that plays an indispensable role in many domains. Constructing high-density genetic maps and identifying stable quantitative trait locus (QTL) controlling agronomic traits are necessary prerequisites for marker-assisted selection (MAS). A total of 14,899 SSR primer pairs designed from the genome sequence of G. raimondii were screened for polymorphic markers between mapping parents CCRI 35 and Yumian 1, and 712 SSR markers showing polymorphism were used to genotype 180 lines from a (CCRI 35 × Yumian 1) recombinant inbred line (RIL) population. Genetic linkage analysis was conducted on 726 loci obtained from the 712 polymorphic SSR markers, along with 1379 SSR loci obtained in our previous study, and a high-density genetic map with 2051 loci was constructed, which spanned 3508.29 cM with an average distance of 1.71 cM between adjacent markers. Marker orders on the linkage map are highly consistent with the corresponding physical orders on a G. hirsutum genome sequence. Based on fiber quality and yield component trait data collected from six environments, 113 QTLs were identified through two analytical methods. Among these 113 QTLs, 50 were considered stable (detected in multiple environments or for which phenotypic variance explained by additive effect was greater than environment effect), and 18 of these 50 were identified with stability by both methods. These 18 QTLs, including eleven for fiber quality and seven for yield component traits, could be priorities for MAS.
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Affiliation(s)
- Xueying Liu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Zhonghua Teng
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Jinxia Wang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Tiantian Wu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Zhiqin Zhang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Xianping Deng
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Xiaomei Fang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Zhaoyun Tan
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Iftikhar Ali
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Dexin Liu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Jian Zhang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Dajun Liu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Fang Liu
- State Key Laboratory of Cotton Biology/Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Zhengsheng Zhang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China.
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15
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Wang H, Huang C, Zhao W, Dai B, Shen C, Zhang B, Li D, Lin Z. Identification of QTL for Fiber Quality and Yield Traits Using Two Immortalized Backcross Populations in Upland Cotton. PLoS One 2016; 11:e0166970. [PMID: 27907098 PMCID: PMC5131980 DOI: 10.1371/journal.pone.0166970] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 11/07/2016] [Indexed: 12/20/2022] Open
Abstract
Two immortalized backcross populations (DHBCF1s and JMBCF1s) were developed using a recombinant inbred line (RIL) population crossed with the two parents DH962 and Jimian5 (as the males), respectively. The fiber quality and yield component traits of the two backcross populations were phenotyped at four environments (two locations, two years). One hundred seventy-eight quantitative trait loci (QTL) were detected including 76 for fiber qualities and 102 for yield components, explaining 4.08–17.79% of the phenotypic variation (PV). Among the 178 QTL, 22 stable QTL were detected in more than one environment or population. A stable QTL, qFL-c10-1, was detected in the previous F2 population, a RIL population in 3 environments and the current two BCF1 populations in this study, explaining 5.79–37.09% of the PV. Additionally, 117 and 110 main-effect QTL (M-QTL) and 47 and 191 digenic epistatic QTL (E-QTL) were detected in the DHBCF1s and JMBCF1s populations, respectively. The effect of digenic epistasis played a more important role on lint percentage, fiber length and fiber strength. These results obtained in the present study provided more resources to obtain stable QTL, confirming the authenticity and reliability of the QTL for molecular marker-assisted selection breeding and QTL cloning.
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Affiliation(s)
- Hantao Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, China
| | - Cong Huang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Wenxia Zhao
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Baosheng Dai
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chao Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Beibei Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Dingguo Li
- Institute of Crop Genetic and Breeding, College of Agriculture, Yangtze University, Jingzhou, Hubei, China
- * E-mail: (ZXL); (DGL)
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- * E-mail: (ZXL); (DGL)
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16
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Shang L, Wang Y, Cai S, Ma L, Liu F, Chen Z, Su Y, Wang K, Hua J. Genetic analysis of Upland cotton dynamic heterosis for boll number per plant at multiple developmental stages. Sci Rep 2016; 6:35515. [PMID: 27748451 PMCID: PMC5066282 DOI: 10.1038/srep35515] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 09/06/2016] [Indexed: 01/28/2023] Open
Abstract
Yield is an important breeding target. As important yield components, boll number per plant (BNP) shows dynamic character and strong heterosis in Upland cotton. However, the genetic basis underlying the dynamic heterosis is poorly understood. In this study, we conducted dynamic quantitative trait loci (QTL) analysis for BNP and heterosis at multiple developmental stages and environments using two recombinant inbred lines (RILs) and two corresponding backcross populations. By the single-locus analysis, 23 QTLs were identified at final maturity, while 99 QTLs were identified across other three developmental stages. A total of 48 conditional QTLs for BNP were identified for the adjacent stages. QTLs detected at later stage mainly existed in the partial dominance to dominance range and QTLs identified at early stage mostly showed effects with the dominance to overdominance range during plant development. By two-locus analysis, we observe that epistasis played an important role not only in the variation of the performance of the RIL population but also in the expression of heterosis in backcross population. Taken together, the present study reveals that the genetic basis of heterosis is dynamic and complicated, and it is involved in dynamic dominance effect, epistasis and QTL by environmental interactions.
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Affiliation(s)
- Lianguang Shang
- Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yumei Wang
- Research Institute of Cash Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, Hubei, China
| | - Shihu Cai
- Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Lingling Ma
- Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Fang Liu
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang 455000, Henan, China
| | - Zhiwen Chen
- Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Ying Su
- Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Kunbo Wang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang 455000, Henan, China
| | - Jinping Hua
- Department of Plant Genetics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
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17
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Shang L, Wang Y, Wang X, Liu F, Abduweli A, Cai S, Li Y, Ma L, Wang K, Hua J. Genetic Analysis and QTL Detection on Fiber Traits Using Two Recombinant Inbred Lines and Their Backcross Populations in Upland Cotton. G3 (Bethesda) 2016; 6:2717-24. [PMID: 27342735 DOI: 10.1534/g3.116.031302] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cotton fiber, a raw natural fiber material, is widely used in the textile industry. Understanding the genetic mechanism of fiber traits is helpful for fiber quality improvement. In the present study, the genetic basis of fiber quality traits was explored using two recombinant inbred lines (RILs) and corresponding backcross (BC) populations under multiple environments in Upland cotton based on marker analysis. In backcross populations, no significant correlation was observed between marker heterozygosity and fiber quality performance and it suggested that heterozygosity was not always necessarily advantageous for the high fiber quality. In two hybrids, 111 quantitative trait loci (QTL) for fiber quality were detected using composite interval mapping, in which 62 new stable QTL were simultaneously identified in more than one environment or population. QTL detected at the single-locus level mainly showed additive effect. In addition, a total of 286 digenic interactions (E-QTL) and their environmental interactions [QTL × environment interactions (QEs)] were detected for fiber quality traits by inclusive composite interval mapping. QE effects should be considered in molecular marker-assisted selection breeding. On average, the E-QTL explained a larger proportion of the phenotypic variation than the main-effect QTL did. It is concluded that the additive effect of single-locus and epistasis with few detectable main effects play an important role in controlling fiber quality traits in Upland cotton.
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