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Jindal S, Pathak D, Dutt T, Rathore P. Genetic analysis and molecular validation of gene conferring petal spot phenotype in interspecific crosses of cotton. Heliyon 2024; 10:e31538. [PMID: 38826732 PMCID: PMC11141370 DOI: 10.1016/j.heliyon.2024.e31538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 05/10/2024] [Accepted: 05/17/2024] [Indexed: 06/04/2024] Open
Abstract
Cotton (Gossypium species) has received considerable interest from the geneticists, cytologists and evolutionary biologists since the last more than a century. Here, we explore the genetics of petal spot in the interspecific derivatives involving tetraploid and diploid cottons; and confirm the location of gene governing petal spot phenotype on chromosome A7 by demonstrating co-segregation of SSR marker NAU 2186 with petal spot phenotype. The presence of petal spot was observed to be dominant over its absence. Petal spot inheritance showed significant deviation from the expected Mendelian ratio in all the segregating populations indicating segregation distortion. The distortion was biased towards the hirsutum parent which has important implications from introgression point of view. We also report a strong association between petal spot and petal margin coloration phenotypes. Extant American cotton varieties generally lack petal spot and margin coloration phenotypes. These petal characteristics can serve as morphological markers during germplasm characterization.
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Affiliation(s)
- Salil Jindal
- Department of Plant Breeding & Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Dharminder Pathak
- Department of Plant Breeding & Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Tanvir Dutt
- Department of Plant Breeding & Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Pankaj Rathore
- Punjab Agricultural University Regional Research Station, Faridkot, Punjab, India
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2
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Khidirov MT, Ernazarova DK, Rafieva FU, Ernazarova ZA, Toshpulatov AK, Umarov RF, Kholova MD, Oripova BB, Kudratova MK, Gapparov BM, Khidirova MM, Komilov DJ, Turaev OS, Udall JA, Yu JZ, Kushanov FN. Genomic and Cytogenetic Analysis of Synthetic Polyploids between Diploid and Tetraploid Cotton ( Gossypium) Species. PLANTS (BASEL, SWITZERLAND) 2023; 12:4184. [PMID: 38140511 PMCID: PMC10748080 DOI: 10.3390/plants12244184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023]
Abstract
Cotton (Gossypium spp.) is the most important natural fiber source in the world. The genetic potential of cotton can be successfully and efficiently exploited by identifying and solving the complex fundamental problems of systematics, evolution, and phylogeny, based on interspecific hybridization of cotton. This study describes the results of interspecific hybridization of G. herbaceum L. (A1-genome) and G. mustelinum Miers ex Watt (AD4-genome) species, obtaining fertile hybrids through synthetic polyploidization of otherwise sterile triploid forms with colchicine (C22H25NO6) treatment. The fertile F1C hybrids were produced from five different cross combinations: (1) G. herbaceum subsp. frutescens × G. mustelinum; (2) G. herbaceum subsp. pseudoarboreum × G. mustelinum; (3) G. herbaceum subsp. pseudoarboreum f. harga × G. mustelinum; (4) G. herbaceum subsp. africanum × G. mustelinum; (5) G. herbaceum subsp. euherbaceum (variety A-833) × G. mustelinum. Cytogenetic analysis discovered normal conjugation of bivalent chromosomes in addition to univalent, open, and closed ring-shaped quadrivalent chromosomes at the stage of metaphase I in the F1C and F2C hybrids. The setting of hybrid bolls obtained as a result of these crosses ranged from 13.8-92.2%, the fertility of seeds in hybrid bolls from 9.7-16.3%, and the pollen viability rates from 36.6-63.8%. Two transgressive plants with long fiber of 35.1-37.0 mm and one plant with extra-long fiber of 39.1-41.0 mm were identified in the F2C progeny of G. herbaceum subsp. frutescens × G. mustelinum cross. Phylogenetic analysis with 72 SSR markers that detect genomic changes showed that tetraploid hybrids derived from the G. herbaceum × G. mustelinum were closer to the species G. mustelinum. The G. herbaceum subsp. frutescens was closer to the cultivated form, and its subsp. africanum was closer to the wild form. New knowledge of the interspecific hybridization and synthetic polyploidization was developed for understanding the genetic mechanisms of the evolution of tetraploid cotton during speciation. The synthetic polyploids of cotton obtained in this study would provide beneficial genes for developing new cotton varieties of the G. hirsutum species, with high-quality cotton fiber and strong tolerance to biotic or abiotic stress. In particular, the introduction of these polyploids to conventional and molecular breeding can serve as a bridge of transferring valuable genes related to high-quality fiber and stress tolerance from different cotton species to the new cultivars.
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Affiliation(s)
- Mukhammad T. Khidirov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Dilrabo K. Ernazarova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
- Department of Genetics, National University of Uzbekistan, Tashkent 100174, Uzbekistan;
| | - Feruza U. Rafieva
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Ziraatkhan A. Ernazarova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Abdulqahhor Kh. Toshpulatov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Ramziddin F. Umarov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Madina D. Kholova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Barno B. Oripova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Mukhlisa K. Kudratova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | - Bunyod M. Gapparov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
| | | | - Doniyor J. Komilov
- Department of Biology, Namangan State University, Uychi Street-316, Namangan 160100, Uzbekistan;
| | - Ozod S. Turaev
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
- Department of Genetics, National University of Uzbekistan, Tashkent 100174, Uzbekistan;
| | - Joshua A. Udall
- United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, TX 77845, USA;
| | - John Z. Yu
- United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, TX 77845, USA;
| | - Fakhriddin N. Kushanov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent 111226, Uzbekistan; (M.T.K.); (D.K.E.); (F.U.R.); (Z.A.E.); (A.K.T.); (R.F.U.); (M.D.K.); (B.B.O.); (M.K.K.); (B.M.G.); (O.S.T.)
- Department of Genetics, National University of Uzbekistan, Tashkent 100174, Uzbekistan;
- Department of Biology, Namangan State University, Uychi Street-316, Namangan 160100, Uzbekistan;
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Naveed S, Gandhi N, Billings G, Jones Z, Campbell BT, Jones M, Rustgi S. Alterations in Growth Habit to Channel End-of-Season Perennial Reserves towards Increased Yield and Reduced Regrowth after Defoliation in Upland Cotton ( Gossypium hirsutum L.). Int J Mol Sci 2023; 24:14174. [PMID: 37762483 PMCID: PMC10532291 DOI: 10.3390/ijms241814174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/03/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Cotton (Gossypium spp.) is the primary source of natural textile fiber in the U.S. and a major crop in the Southeastern U.S. Despite constant efforts to increase the cotton fiber yield, the yield gain has stagnated. Therefore, we undertook a novel approach to improve the cotton fiber yield by altering its growth habit from perennial to annual. In this effort, we identified genotypes with high-expression alleles of five floral induction and meristem identity genes (FT, SOC1, FUL, LFY, and AP1) from an Upland cotton mini-core collection and crossed them in various combinations to develop cotton lines with annual growth habit, optimal flowering time, and enhanced productivity. To facilitate the characterization of genotypes with the desired combinations of stacked alleles, we identified molecular markers associated with the gene expression traits via genome-wide association analysis using a 63 K SNP Array. Over 14,500 SNPs showed polymorphism and were used for association analysis. A total of 396 markers showed associations with expression traits. Of these 396 markers, 159 were mapped to genes, 50 to untranslated regions, and 187 to random genomic regions. Biased genomic distribution of associated markers was observed where more trait-associated markers mapped to the cotton D sub-genome. Many quantitative trait loci coincided at specific genomic regions. This observation has implications as these traits could be bred together. The analysis also allowed the identification of candidate regulators of the expression patterns of these floral induction and meristem identity genes whose functions will be validated.
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Affiliation(s)
- Salman Naveed
- Department of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education Center, Florence, SC 29506, USA; (S.N.); (M.J.)
| | - Nitant Gandhi
- Department of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education Center, Florence, SC 29506, USA; (S.N.); (M.J.)
| | - Grant Billings
- Department of Crop & Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Zachary Jones
- Department of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education Center, Florence, SC 29506, USA; (S.N.); (M.J.)
| | - B. Todd Campbell
- USDA-ARS Coastal Plains Soil, Water, and Plant Research Center, Florence, SC 29501, USA;
| | - Michael Jones
- Department of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education Center, Florence, SC 29506, USA; (S.N.); (M.J.)
| | - Sachin Rustgi
- Department of Plant and Environmental Sciences, Clemson University Pee Dee Research and Education Center, Florence, SC 29506, USA; (S.N.); (M.J.)
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Huo WQ, Zhang ZQ, Ren ZY, Zhao JJ, Song CX, Wang XX, Pei XY, Liu YG, He KL, Zhang F, Li XY, Li W, Yang DG, Ma XF. Unraveling genomic regions and candidate genes for multiple disease resistance in upland cotton using meta-QTL analysis. Heliyon 2023; 9:e18731. [PMID: 37576216 PMCID: PMC10412778 DOI: 10.1016/j.heliyon.2023.e18731] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/15/2023] [Accepted: 07/25/2023] [Indexed: 08/15/2023] Open
Abstract
Verticillium wilt (VW), Fusarium wilt (FW) and Root-knot nematode (RKN) are the main diseases affecting cotton production. However, many reported quantitative trait loci (QTLs) for cotton resistance have not been used for agricultural practices because of inconsistencies in the cotton genetic background. The integration of existing cotton genetic resources can facilitate the discovery of important genomic regions and candidate genes involved in disease resistance. Here, an improved and comprehensive meta-QTL analysis was conducted on 487 disease resistant QTLs from 31 studies in the last two decades. A consensus linkage map with genetic overall length of 3006.59 cM containing 8650 markers was constructed. A total of 28 Meta-QTLs (MQTLs) were discovered, among which nine MQTLs were identified as related to resistance to multiple diseases. Candidate genes were predicted based on public transcriptome data and enriched in pathways related to disease resistance. This study used a method based on the integration of Meta-QTL, known genes and transcriptomics to reveal major genomic regions and putative candidate genes for resistance to multiple diseases, providing a new basis for marker-assisted selection of high disease resistance in cotton breeding.
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Affiliation(s)
- Wen-Qi Huo
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhi-Qiang Zhang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhong-Ying Ren
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Jun-Jie Zhao
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Cheng-Xiang Song
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xing-Xing Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiao-Yu Pei
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yan-Gai Liu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Kun-Lun He
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Fei Zhang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xin-Yang Li
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wei Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China
| | - Dai-Gang Yang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China
| | - Xiong-Feng Ma
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China
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Liu Z, Sun Z, Ke H, Chen B, Gu Q, Zhang M, Wu N, Chen L, Li Y, Meng C, Wang G, Wu L, Zhang G, Ma Z, Zhang Y, Wang X. Transcriptome, Ectopic Expression and Genetic Population Analysis Identify Candidate Genes for Fiber Quality Improvement in Cotton. Int J Mol Sci 2023; 24:8293. [PMID: 37175999 PMCID: PMC10179096 DOI: 10.3390/ijms24098293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Comparative transcriptome analysis of fiber tissues between Gossypium barbadense and Gossypium hirsutum could reveal the molecular mechanisms underlying high-quality fiber formation and identify candidate genes for fiber quality improvement. In this study, 759 genes were found to be strongly upregulated at the elongation stage in G. barbadense, which showed four distinct expression patterns (I-IV). Among them, the 346 genes of group IV stood out in terms of the potential to promote fiber elongation, in which we finally identified 42 elongation-related candidate genes by comparative transcriptome analysis between G. barbadense and G. hirsutum. Subsequently, we overexpressed GbAAR3 and GbTWS1, two of the 42 candidate genes, in Arabidopsis plants and validated their roles in promoting cell elongation. At the secondary cell wall (SCW) biosynthesis stage, 2275 genes were upregulated and exhibited five different expression profiles (I-V) in G. barbadense. We highlighted the critical roles of the 647 genes of group IV in SCW biosynthesis and further picked out 48 SCW biosynthesis-related candidate genes by comparative transcriptome analysis. SNP molecular markers were then successfully developed to distinguish the SCW biosynthesis-related candidate genes from their G. hirsutum orthologs, and the genotyping and phenotyping of a BC3F5 population proved their potential in improving fiber strength and micronaire. Our results contribute to the better understanding of the fiber quality differences between G. barbadense and G. hirsutum and provide novel alternative genes for fiber quality improvement.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Yan Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China; (Z.L.); (Z.S.); (H.K.); (B.C.); (Q.G.); (M.Z.); (N.W.); (G.Z.); (Z.M.)
| | - Xingfen Wang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China; (Z.L.); (Z.S.); (H.K.); (B.C.); (Q.G.); (M.Z.); (N.W.); (G.Z.); (Z.M.)
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Kushanov FN, Komilov DJ, Turaev OS, Ernazarova DK, Amanboyeva RS, Gapparov BM, Yu JZ. Genetic Analysis of Mutagenesis That Induces the Photoperiod Insensitivity of Wild Cotton Gossypium hirsutum Subsp. purpurascens. PLANTS (BASEL, SWITZERLAND) 2022; 11:3012. [PMID: 36432741 PMCID: PMC9698681 DOI: 10.3390/plants11223012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/22/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
Cotton genus Gossypium L., especially its wild species, is rich in genetic diversity. However, this valuable genetic resource is barely used in cotton breeding programs. In part, due to photoperiod sensitivities, the genetic diversity of Gossypium remains largely untapped. Herein, we present a genetic analysis of morphological, cytological, and genomic changes from radiation-mediated mutagenesis that induced plant photoperiod insensitivity in the wild cotton of Gossypium hirsutum. Several morphological and agronomical traits were found to be highly inheritable using the progeny between the wild-type G. hirsutum subsp. purpurascens (El-Salvador) and its mutant line (Kupaysin). An analysis of pollen mother cells (PMCs) revealed quadrivalents that had an open ring shape and an adjoining type of divergence of chromosomes from translocation complexes. Using 336 SSR markers and 157 F2 progenies that were grown with parental genotypes and F1 hybrids in long day and short night conditions, five quantitative trait loci (QTLs) associated with cotton flowering were located on chromosomes At-05, At-11, and Dt-07. Nineteen candidate genes related to the flowering traits were suggested through molecular and in silico analysis. The DNA markers associated with the candidate genes, upon future functional analysis, would provide useful tools in marker-assisted selection (MAS) in cotton breeding programs for early flowering and maturity.
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Affiliation(s)
- Fakhriddin N. Kushanov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Qibray QFY, Yuqori-Yuz, Qibray District, Tashkent 111226, Uzbekistan
- Department of Biology, National University of Uzbekistan, University Street-4, Olmazor District, Tashkent 100174, Uzbekistan
- Department of Biotechnology, Namangan State University, Uychi Street-316, Namangan 160100, Uzbekistan
| | - Doniyor J. Komilov
- Department of Biotechnology, Namangan State University, Uychi Street-316, Namangan 160100, Uzbekistan
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, University Street-2, Qibray District, Tashkent 111215, Uzbekistan
| | - Ozod S. Turaev
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Qibray QFY, Yuqori-Yuz, Qibray District, Tashkent 111226, Uzbekistan
- Department of Biology, National University of Uzbekistan, University Street-4, Olmazor District, Tashkent 100174, Uzbekistan
| | - Dilrabo K. Ernazarova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Qibray QFY, Yuqori-Yuz, Qibray District, Tashkent 111226, Uzbekistan
- Department of Biology, National University of Uzbekistan, University Street-4, Olmazor District, Tashkent 100174, Uzbekistan
| | - Roza S. Amanboyeva
- Department of Biology, National University of Uzbekistan, University Street-4, Olmazor District, Tashkent 100174, Uzbekistan
- Faculty of Natural Sciences, Gulistan State University, 4th Microregion, Gulistan 120100, Uzbekistan
| | - Bunyod M. Gapparov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Qibray QFY, Yuqori-Yuz, Qibray District, Tashkent 111226, Uzbekistan
| | - John Z. Yu
- United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, TX 77845, USA
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Si Z, Jin S, Chen J, Wang S, Fang L, Zhu X, Zhang T, Hu Y. Construction of a high-density genetic map and identification of QTLs related to agronomic and physiological traits in an interspecific (Gossypium hirsutum × Gossypium barbadense) F2 population. BMC Genomics 2022; 23:307. [PMID: 35428176 PMCID: PMC9013169 DOI: 10.1186/s12864-022-08528-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/21/2022] [Indexed: 02/06/2023] Open
Abstract
Abstract
Background
Advances in genome sequencing technology, particularly restriction-site associated DNA sequence (RAD-seq) and whole-genome resequencing, have greatly aided the construction of cotton interspecific genetic maps based on single nucleotide polymorphism (SNPs), Indels, and other types of markers. High-density genetic maps can improve accuracy of quantitative trait locus (QTL) mapping, narrow down location intervals, and facilitate identification of the candidate genes.
Result
In this study, 249 individuals from an interspecific F2 population (TM-1 and Hai7124) were re-sequenced, yielding 6303 high-confidence bin markers spanning 5057.13 cM across 26 cotton chromosomes. A total of 3380 recombination hot regions RHRs were identified which unevenly distributed on the 26 chromosomes. Based on this map, 112 QTLs relating to agronomic and physiological traits from seedling to boll opening stage were identified, including 15 loci associated with 14 traits that contained genes harboring nonsynonymous SNPs. We analyzed the sequence and expression of these ten candidate genes and discovered that GhRHD3 (GH_D10G0500) may affect fiber yield while GhGPAT6 (GH_D04G1426) may affect photosynthesis efficiency.
Conclusion
Our research illustrates the efficiency of constructing a genetic map using binmap and QTL mapping on the basis of a certain size of the early-generation population. High-density genetic map features high recombination exchanges in number and distribution. The QTLs and the candidate genes identified based on this high-density genetic map may provide important gene resources for the genetic improvement of cotton.
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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] [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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Kushanov FN, Turaev OS, Ernazarova DK, Gapparov BM, Oripova BB, Kudratova MK, Rafieva FU, Khalikov KK, Erjigitov DS, Khidirov MT, Kholova MD, Khusenov NN, Amanboyeva RS, Saha S, Yu JZ, Abdurakhmonov IY. Genetic Diversity, QTL Mapping, and Marker-Assisted Selection Technology in Cotton ( Gossypium spp.). FRONTIERS IN PLANT SCIENCE 2021; 12:779386. [PMID: 34975965 PMCID: PMC8716771 DOI: 10.3389/fpls.2021.779386] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 11/23/2021] [Indexed: 02/05/2023]
Abstract
Cotton genetic resources contain diverse economically important traits that can be used widely in breeding approaches to create of high-yielding elite cultivars with superior fiber quality and adapted to biotic and abiotic stresses. Nevertheless, the creation of new cultivars using conventional breeding methods is limited by the cost and proved to be time consuming process, also requires a space to make field observations and measurements. Decoding genomes of cotton species greatly facilitated generating large-scale high-throughput DNA markers and identification of QTLs that allows confirmation of candidate genes, and use them in marker-assisted selection (MAS)-based breeding programs. With the advances of quantitative trait loci (QTL) mapping and genome-wide-association study approaches, DNA markers associated with valuable traits significantly accelerate breeding processes by replacing the selection with a phenotype to the selection at the DNA or gene level. In this review, we discuss the evolution and genetic diversity of cotton Gossypium genus, molecular markers and their types, genetic mapping and QTL analysis, application, and perspectives of MAS-based approaches in cotton breeding.
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Affiliation(s)
- Fakhriddin N. Kushanov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
| | - Ozod S. Turaev
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Dilrabo K. Ernazarova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
| | - Bunyod M. Gapparov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Barno B. Oripova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
| | - Mukhlisa K. Kudratova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Feruza U. Rafieva
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Kuvandik K. Khalikov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Doston Sh. Erjigitov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Mukhammad T. Khidirov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Madina D. Kholova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Naim N. Khusenov
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Roza S. Amanboyeva
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
| | - Sukumar Saha
- Crop Science Research Laboratory, USDA-ARS, Washington, DC, United States
| | - John Z. Yu
- Southern Plains Agricultural Research Center, USDA-ARS, Washington, DC, United States
| | - Ibrokhim Y. Abdurakhmonov
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
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10
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Rashid MHO, Li PT, Chen TT, Palanga KK, Gong WK, Ge Q, Gong JW, Liu AY, Lu QW, Diouf L, Sarfraz Z, Jamshed M, Shi YZ, Yuan YL. Genome-wide quantitative trait loci mapping on Verticillium wilt resistance in 300 chromosome segment substitution lines from Gossypium hirsutum × Gossypium barbadense. G3-GENES GENOMES GENETICS 2021; 11:6128683. [PMID: 33846710 PMCID: PMC8104949 DOI: 10.1093/g3journal/jkab027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 02/02/2021] [Indexed: 02/07/2023]
Abstract
Cotton Verticillium wilt (VW) is a devastating disease seriously affecting fiber yield and quality, and the most effective and economical prevention measure at present is selection and extension of Gossypium varieties harboring high resistance to VW. However, multiple attempts to improve the VW resistance of the most widely cultivated upland cottons have made little significant progress. The introduction of chromosome segment substitution lines (CSSLs) provide the practical solutions for merging the superior genes related with high yield and wide adaptation from Gossypium hirsutum and VW resistance and the excellent fiber quality from Gossypium barbadense. In this study, 300 CSSLs were chosen from the developed BC5F3:5 CSSLs constructed from CCRI36 (G. hirsutum) and Hai1 (G. barbadense) to conduct quantitative trait locus (QTL) mapping of VW resistance, and a total of 40 QTL relevant to VW disease index (DI) were identified. Phenotypic data were obtained from a 2-year investigation in two fields with two replications per year. All the QTL were distributed on 21 chromosomes, with phenotypic variation of 1.05%-10.52%, and 21 stable QTL were consistent in at least two environments. Based on a meta-analysis, 34 novel QTL were identified, while 6 loci were consistent with previously identified QTL. Meanwhile, 70 QTL hotspot regions were detected, including 44 novel regions. This study concentrates on QTL identification and screening for hotspot regions related with VW in the 300 CSSLs, and the results lay a solid foundation not only for revealing the genetic and molecular mechanisms of VW resistance but also for further fine mapping, gene cloning and molecular designing in breeding programs for resistant cotton varieties.
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Affiliation(s)
- Md Harun Or Rashid
- State Key Laboratory of Cotton Biology, Research Base, Anyang Institute of Technology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.,Senior Scientific Officer, Breeding Division, Bangladesh Jute Research Institute, Dhaka-1207, Bangladesh
| | - Peng-Tao Li
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China
| | - Ting-Ting Chen
- State Key Laboratory of Cotton Biology, Research Base, Anyang Institute of Technology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.,College of Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Koffi Kibalou Palanga
- State Key Laboratory of Cotton Biology, Research Base, Anyang Institute of Technology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.,Institut Supérieur des Métiers de l'Agriculture- Université de Kara (ISMA-UK), Kara, Togo
| | - Wan-Kui Gong
- State Key Laboratory of Cotton Biology, Research Base, Anyang Institute of Technology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Research Base, Anyang Institute of Technology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Ju-Wu Gong
- State Key Laboratory of Cotton Biology, Research Base, Anyang Institute of Technology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Ai-Ying Liu
- State Key Laboratory of Cotton Biology, Research Base, Anyang Institute of Technology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Quan-Wei Lu
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China
| | - Latyr Diouf
- State Key Laboratory of Cotton Biology, Research Base, Anyang Institute of Technology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Zareen Sarfraz
- State Key Laboratory of Cotton Biology, Research Base, Anyang Institute of Technology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Muhammad Jamshed
- State Key Laboratory of Cotton Biology, Research Base, Anyang Institute of Technology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Yu-Zhen Shi
- State Key Laboratory of Cotton Biology, Research Base, Anyang Institute of Technology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - You-Lu Yuan
- State Key Laboratory of Cotton Biology, Research Base, Anyang Institute of Technology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
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11
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Fang L, Zhao T, Hu Y, Si Z, Zhu X, Han Z, Liu G, Wang S, Ju L, Guo M, Mei H, Wang L, Qi B, Wang H, Guan X, Zhang T. Divergent improvement of two cultivated allotetraploid cotton species. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1325-1336. [PMID: 33448110 PMCID: PMC8313128 DOI: 10.1111/pbi.13547] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/24/2020] [Accepted: 01/03/2021] [Indexed: 05/21/2023]
Abstract
Interspecific genomic variation can provide a genetic basis for local adaptation and domestication. A series of studies have presented its role of interspecific haplotypes and introgressions in adaptive traits, but few studies have addressed their role in improving agronomic character. Two allotetraploid Gossypium species, Gossypium barbadense (Gb) and G. hirsutum (Gh) originating from the Americas, are cultivated independently. Here, through sequencing and the comparison of one GWAS panel in 229 Gb accessions and two GWAS panels in 491 Gh accessions, we found that most associated loci or functional haplotypes for agronomic traits were highly divergent, representing the strong divergent improvement between Gb and Gh. Using a comprehensive interspecific haplotype map, we revealed that six interspecific introgressions from Gh to Gb were significantly associated with the phenotypic performance of Gb, which could explain 5%-40% of phenotypic variation in yield and fibre qualities. In addition, three introgressions overlapped with six associated loci in Gb, indicating that these introgression regions were under further selection and stabilized during improvement. A single interspecific introgression often possessed yield-increasing potential but decreased fibre qualities, or the opposite, making it difficult to simultaneously improve yield and fibre qualities. Our study not only has proved the importance of interspecific functional haplotypes or introgressions in the divergent improvement of Gb and Gh, but also supports their potential value in further human-mediated hybridization or precision breeding.
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Affiliation(s)
- Lei Fang
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Ting Zhao
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Yan Hu
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Zhanfeng Si
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Xiefei Zhu
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina
| | - Zegang Han
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Guizhen Liu
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina
- Henan Province Seed StationZhengzhouChina
| | - Sen Wang
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina
- Institute of Food CropsJiangsu Academy of Agricultural SciencesNanjingChina
| | - Longzhen Ju
- State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina
| | - Menglan Guo
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Huan Mei
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Luyao Wang
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Bowen Qi
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Heng Wang
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Xueying Guan
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Tianzhen Zhang
- Zhejiang Provincial Key Laboratory of Crop Genetic ResourcesInstitute of Crop SciencePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
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12
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Zhang K, Kuraparthy V, Fang H, Zhu L, Sood S, Jones DC. High-density linkage map construction and QTL analyses for fiber quality, yield and morphological traits using CottonSNP63K array in upland cotton (Gossypium hirsutum L.). BMC Genomics 2019; 20:889. [PMID: 31771502 PMCID: PMC6878679 DOI: 10.1186/s12864-019-6214-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 10/22/2019] [Indexed: 12/14/2022] Open
Abstract
Background Improving fiber quality and yield are the primary research objectives in cotton breeding for enhancing the economic viability and sustainability of Upland cotton production. Identifying the quantitative trait loci (QTL) for fiber quality and yield traits using the high-density SNP-based genetic maps allows for bridging genomics with cotton breeding through marker assisted and genomic selection. In this study, a recombinant inbred line (RIL) population, derived from cross between two parental accessions, which represent broad allele diversity in Upland cotton, was used to construct high-density SNP-based linkage maps and to map the QTLs controlling important cotton traits. Results Molecular genetic mapping using RIL population produced a genetic map of 3129 SNPs, mapped at a density of 1.41 cM. Genetic maps of the individual chromosomes showed good collinearity with the sequence based physical map. A total of 106 QTLs were identified which included 59 QTLs for six fiber quality traits, 38 QTLs for four yield traits and 9 QTLs for two morphological traits. Sub-genome wide, 57 QTLs were mapped in A sub-genome and 49 were mapped in D sub-genome. More than 75% of the QTLs with favorable alleles were contributed by the parental accession NC05AZ06. Forty-six mapped QTLs each explained more than 10% of the phenotypic variation. Further, we identified 21 QTL clusters where 12 QTL clusters were mapped in the A sub-genome and 9 were mapped in the D sub-genome. Candidate gene analyses of the 11 stable QTL harboring genomic regions identified 19 putative genes which had functional role in cotton fiber development. Conclusion We constructed a high-density genetic map of SNPs in Upland cotton. Collinearity between genetic and physical maps indicated no major structural changes in the genetic mapping populations. Most traits showed high broad-sense heritability. One hundred and six QTLs were identified for the fiber quality, yield and morphological traits. Majority of the QTLs with favorable alleles were contributed by improved parental accession. More than 70% of the mapped QTLs shared the similar map position with previously reported QTLs which suggest the genetic relatedness of Upland cotton germplasm. Identification of QTL clusters could explain the correlation among some fiber quality traits in cotton. Stable and major QTLs and QTL clusters of traits identified in the current study could be the targets for map-based cloning and marker assisted selection (MAS) in cotton breeding. The genomic region on D12 containing the major stable QTLs for micronaire, fiber strength and lint percentage could be potential targets for MAS and gene cloning of fiber quality traits in cotton.
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Affiliation(s)
- Kuang Zhang
- Crop & Soil Sciences Department, North Carolina State University, Raleigh, NC, 27695, USA
| | - Vasu Kuraparthy
- Crop & Soil Sciences Department, North Carolina State University, Raleigh, NC, 27695, USA.
| | - Hui Fang
- Crop & Soil Sciences Department, North Carolina State University, Raleigh, NC, 27695, USA
| | - Linglong Zhu
- Crop & Soil Sciences Department, North Carolina State University, Raleigh, NC, 27695, USA
| | - Shilpa Sood
- Crop & Soil Sciences Department, North Carolina State University, Raleigh, NC, 27695, USA.,4 Cityplace drive, The Climate Corporation (Bayer U.S. Crop Science), St. Louis, MO, 63141, USA
| | - Don C Jones
- Cotton Incorporated, 6399 Weston Parkway, Cary, NC, 27513, USA
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13
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Enhancing Upland cotton for drought resilience, productivity, and fiber quality: comparative evaluation and genetic dissection. Mol Genet Genomics 2019; 295:155-176. [PMID: 31620883 DOI: 10.1007/s00438-019-01611-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/22/2019] [Indexed: 01/09/2023]
Abstract
To provision the world sustainably, modern society must increase overall crop production, while conserving and preserving natural resources. Producing more with diminishing water resources is an especially daunting endeavor. Toward the goal of genetically improving drought resilience of cultivated Upland cotton (Gossypium hirsutum L.), this study addresses the genetics of differential yield components referred to as productivity and fiber quality traits under regular-water versus low-water (LW) field conditions. We used ten traits to assess water stress deficit, which included six productivity and four fiber quality traits on two recombinant inbred line (RIL) populations from reciprocally crossed cultivars, Phytogen 72 and Stoneville 474. To facilitate genetic inferences, we genotyped RILs with the CottonSNP63K array, assembled high-density linkage maps of over 7000 SNPs and then analyzed quantitative trait variations. Analysis of variance revealed significant differences for all traits (p < 0.05) in these RIL populations. Although the LW irrigation regime significantly reduced all traits, except lint percent, the RILs exhibited a broad phenotypic spectrum of heritable differences across the water regimes. Transgressive segregation occurred among the RILs, suggesting the possibility of genetic gain through phenotypic selection for drought resilience and perhaps through marker-based selection. Analyses revealed more than 150 quantitative trait loci (QTLs) associated with productivity and fiber quality traits (p < 0.005) on different genomic regions of the cotton genome. The multiple-QTL models analysis with LOD > 3.0 detected 21 QTLs associated with productivity and 22 QTLs associated with fiber quality. For fiber traits, strong clustering and QTL associations occurred in c08 and its homolog c24 as well as c10, c14, and c21. Using contemporary genome sequence assemblies and bioinformatically related information, the identification of genomic regions associated with responses to plant stress/drought elevates the possibility of using marker-assisted and omics-based selection to enhance breeding for drought resilient cultivars and identifying candidate genes and networks. RILs with different responses to drought indicated that it is possible to maintain high fiber quality under LW conditions or reduce the of LW impact on quality. The heritable variation among elite bi-parental RILs for productivity and quality under field drought conditions, and their association of QTLs, and thus specific genomic regions, indicate opportunities for breeding-based gains in water resource conservation, i.e., enhancing cotton's agricultural sustainability.
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14
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Shi Y, Liu A, Li J, Zhang J, Zhang B, Ge Q, Jamshed M, Lu Q, Li S, Xiang X, Gong J, Gong W, Shang H, Deng X, Pan J, Yuan Y. Dissecting the genetic basis of fiber quality and yield traits in interspecific backcross populations of Gossypium hirsutum × Gossypium barbadense. Mol Genet Genomics 2019; 294:1385-1402. [PMID: 31201519 DOI: 10.1007/s00438-019-01582-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 05/29/2019] [Indexed: 12/31/2022]
Abstract
Fiber quality and yield are important traits of cotton. Quantitative trait locus (QTL) mapping is a prerequisite for marker-assisted selection (MAS) in cotton breeding. To identify QTLs for fiber quality and yield traits, 4 backcross-generation populations (BC1F1, BC1S1, BC2F1, and BC3F0) were developed from an interspecific cross between CCRI36 (Gossypium hirsutum L.) and Hai1 (G. barbadense L.). A total of 153 QTLs for fiber quality and yield traits were identified based on data from the BC1F1, BC1S1, BC2F1 and BC3F0 populations in the field and from the BC2F1 population in an artificial disease nursery using a high-density genetic linkage map with 2292 marker loci covering 5115.16 centimorgans (cM) from the BC1F1 population. These QTLs were located on 24 chromosomes, and each could explain 4.98-19.80% of the observed phenotypic variations. Among the 153 QTLs, 30 were consistent with those identified previously. Specifically, 23 QTLs were stably detected in 2 or 3 environments or generations, 6 of which were consistent with those identified previously and the other 17 of which were stable and novel. Ten QTL clusters for different traits were found and 9 of them were novel, which explained the significant correlations among some phenotypic traits in the populations. The results including these stable or consensus QTLs provide valuable information for marker-assisted selection (MAS) in cotton breeding and will help better understand the genetic basis of fiber quality and yield traits, which can then be used in QTL cloning.
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Affiliation(s)
- Yuzhen Shi
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Aiying Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Junwen Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Baocai Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Muhammad Jamshed
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Quanwei Lu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Shaoqi Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Xianghui Xiang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Juwu Gong
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Wankui Gong
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Xiaoying Deng
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Jingtao Pan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
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15
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Li PT, Rashid MHO, Chen TT, Lu QW, Ge Q, Gong WK, Liu AY, Gong JW, Shang HH, Deng XY, Li JW, Li SQ, Xiao XH, Liu RX, Zhang Q, Duan L, Zou XY, Zhang Z, Jiang X, Zhang Y, Peng RH, Shi YZ, Yuan YL. Transcriptomic and biochemical analysis of upland cotton (Gossypium hirsutum) and a chromosome segment substitution line from G. hirsutum × G. barbadense in response to Verticillium dahliae infection. BMC PLANT BIOLOGY 2019; 19:19. [PMID: 30634907 PMCID: PMC6329193 DOI: 10.1186/s12870-018-1619-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 12/26/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Verticillium wilt (VW), also known as "cotton cancer," is one of the most destructive diseases in global cotton production that seriously impacts fiber yield and quality. Despite numerous attempts, little significant progress has been made in improving the VW resistance of upland cotton. The development of chromosome segment substitution lines (CSSLs) from Gossypium hirsutum × G. barbadense has emerged as a means of simultaneously developing new cotton varieties with high-yield, superior fiber, and resistance to VW. RESULTS In this study, VW-resistant investigations were first conducted in an artificial greenhouse, a natural field, and diseased nursery conditions, resulting in the identification of one stably VW-resistant CSSL, MBI8255, and one VW-susceptible G. hirsutum, CCRI36, which were subsequently subjected to biochemical tests and transcriptome sequencing during V991 infection (0, 1, and 2 days after inoculation). Eighteen root samples with three replications were collected to perform multiple comparisons of enzyme activity and biochemical substance contents. The findings indicated that VW resistance was positively correlated with peroxidase and polyphenol oxidase activity, but negatively correlated with malondialdehyde content. Additionally, RNA sequencing was used for the same root samples, resulting in a total of 77,412 genes, of which 23,180 differentially expressed genes were identified from multiple comparisons between samples. After Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis on the expression profiles identified using Short Time-series Expression Miner, we found that the metabolic process in the biological process, as well as the pathways of phenylpropanoid biosynthesis and plant hormone signal transduction, participated significantly in the response to VW. Gene functional annotation and expression quantity analysis indicated the important roles of the phenylpropanoid metabolic pathway and oxidation-reduction process in response to VW, which also provided plenty of candidate genes related to plant resistance. CONCLUSIONS This study concentrates on the preliminary response to V991 infection by comparing the VW-resistant CSSL and its VW-susceptible recurrent parent. Not only do our findings facilitate the culturing of new resistant varieties with high yield and superior performance, but they also broaden our understanding of the mechanisms of cotton resistance to VW.
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Affiliation(s)
- Peng-tao Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, 455000 Henan China
| | - Md. Harun or Rashid
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Ting-ting Chen
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong China
| | - Quan-wei Lu
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, 455000 Henan China
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Wan-kui Gong
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Ai-ying Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Ju-wu Gong
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Hai-hong Shang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Xiao-ying Deng
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Jun-wen Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Shao-qi Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Xiang-hui Xiao
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Rui-xian Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Qi Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Li Duan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Xian-yan Zou
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Zhen Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Xiao Jiang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - Ya Zhang
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, 455000 Henan China
| | - Ren-hai Peng
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, 455000 Henan China
| | - Yu-zhen Shi
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
| | - You-lu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000 Henan China
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16
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Li PT, Rashid MHO, Chen TT, Lu QW, Ge Q, Gong WK, Liu AY, Gong JW, Shang HH, Deng XY, Li JW, Li SQ, Xiao XH, Liu RX, Zhang Q, Duan L, Zou XY, Zhang Z, Jiang X, Zhang Y, Peng RH, Shi YZ, Yuan YL. Transcriptomic and biochemical analysis of upland cotton (Gossypium hirsutum) and a chromosome segment substitution line from G. hirsutum × G. barbadense in response to Verticillium dahliae infection. BMC PLANT BIOLOGY 2019; 19:19. [PMID: 30634907 DOI: 10.1186/s12870-018-1619-1614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 12/26/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Verticillium wilt (VW), also known as "cotton cancer," is one of the most destructive diseases in global cotton production that seriously impacts fiber yield and quality. Despite numerous attempts, little significant progress has been made in improving the VW resistance of upland cotton. The development of chromosome segment substitution lines (CSSLs) from Gossypium hirsutum × G. barbadense has emerged as a means of simultaneously developing new cotton varieties with high-yield, superior fiber, and resistance to VW. RESULTS In this study, VW-resistant investigations were first conducted in an artificial greenhouse, a natural field, and diseased nursery conditions, resulting in the identification of one stably VW-resistant CSSL, MBI8255, and one VW-susceptible G. hirsutum, CCRI36, which were subsequently subjected to biochemical tests and transcriptome sequencing during V991 infection (0, 1, and 2 days after inoculation). Eighteen root samples with three replications were collected to perform multiple comparisons of enzyme activity and biochemical substance contents. The findings indicated that VW resistance was positively correlated with peroxidase and polyphenol oxidase activity, but negatively correlated with malondialdehyde content. Additionally, RNA sequencing was used for the same root samples, resulting in a total of 77,412 genes, of which 23,180 differentially expressed genes were identified from multiple comparisons between samples. After Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis on the expression profiles identified using Short Time-series Expression Miner, we found that the metabolic process in the biological process, as well as the pathways of phenylpropanoid biosynthesis and plant hormone signal transduction, participated significantly in the response to VW. Gene functional annotation and expression quantity analysis indicated the important roles of the phenylpropanoid metabolic pathway and oxidation-reduction process in response to VW, which also provided plenty of candidate genes related to plant resistance. CONCLUSIONS This study concentrates on the preliminary response to V991 infection by comparing the VW-resistant CSSL and its VW-susceptible recurrent parent. Not only do our findings facilitate the culturing of new resistant varieties with high yield and superior performance, but they also broaden our understanding of the mechanisms of cotton resistance to VW.
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Affiliation(s)
- Peng-Tao Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, Henan, China
| | - Md Harun Or Rashid
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Ting-Ting Chen
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Quan-Wei Lu
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, Henan, China
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Wan-Kui Gong
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Ai-Ying Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Ju-Wu Gong
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Hai-Hong Shang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Xiao-Ying Deng
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Jun-Wen Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Shao-Qi Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Xiang-Hui Xiao
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Rui-Xian Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Qi Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Li Duan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Xian-Yan Zou
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Zhen Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Xiao Jiang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China
| | - Ya Zhang
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, Henan, China
| | - Ren-Hai Peng
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, Henan, China
| | - Yu-Zhen Shi
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China.
| | - You-Lu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, 455000, Henan, China.
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17
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Sun Q, Qiao J, Zhang S, He S, Shi Y, Yuan Y, Zhang X, Cai Y. Changes in DNA methylation assessed by genomic bisulfite sequencing suggest a role for DNA methylation in cotton fruiting branch development. PeerJ 2018; 6:e4945. [PMID: 29915693 PMCID: PMC6004305 DOI: 10.7717/peerj.4945] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 05/18/2018] [Indexed: 12/20/2022] Open
Abstract
Cotton plant architecture, including fruit branch formation and flowering pattern, influences plant light exploitation, cotton yield and planting cost. DNA methylation has been widely observed at different developmental stages in both plants and animals and is associated with regulation of gene expression, chromatin remodelling, genome protection and other functions. Here, we investigated the global epigenetic reprogramming during the development of fruiting branches and floral buds at three developmental stages: the seedling stage, the pre-squaring stage and the squaring stage. We first identified 22 cotton genes which potentially encode DNA methyltransferases and demethylases. Among them, the homologous genes of CMT, DRM2 and MET1 were upregulated at pre-squaring and squaring stages, suggesting that DNA methylation is involved in the development of floral buds and fruit branches. Although the global methylation at all of three developmental stages was not changed, the CHG-type methylation of non-expressed genes was higher than those of expressed genes. In addition, we found that the expression of the homologous genes of the key circadian rhythm regulators, including CRY, LHY and CO, was associated with changes of DNA methylation at three developmental stages.
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Affiliation(s)
- Quan Sun
- Henan University, State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Kaifeng, Henan, China.,Chongqing University of Posts and Telecommunications, College of Bioinformation, ChongQing, China
| | - Jing Qiao
- Henan University, State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Kaifeng, Henan, China
| | - Sai Zhang
- Henan University, State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Kaifeng, Henan, China
| | - Shibin He
- Henan University, State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Kaifeng, Henan, China
| | - Yuzhen Shi
- Cotton Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Youlu Yuan
- Cotton Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Xiao Zhang
- Henan University, State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Kaifeng, Henan, China.,Cotton Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Yingfan Cai
- Henan University, State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Kaifeng, Henan, China
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18
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Huang C, Nie X, Shen C, You C, Li W, Zhao W, Zhang X, Lin Z. Population structure and genetic basis of the agronomic traits of upland cotton in China revealed by a genome-wide association study using high-density SNPs. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1374-1386. [PMID: 28301713 PMCID: PMC5633765 DOI: 10.1111/pbi.12722] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 03/08/2017] [Accepted: 03/10/2017] [Indexed: 05/18/2023]
Abstract
Gossypium hirsutum L. represents the largest source of textile fibre, and China is one of the largest cotton-producing and cotton-consuming countries in the world. To investigate the genetic architecture of the agronomic traits of upland cotton in China, a diverse and nationwide population containing 503 G. hirsutum accessions was collected for a genome-wide association study (GWAS) on 16 agronomic traits. The accessions were planted in four places from 2012 to 2013 for phenotyping. The CottonSNP63K array and a published high-density map based on this array were used for genotyping. The 503 G. hirsutum accessions were divided into three subpopulations based on 11 975 quantified polymorphic single-nucleotide polymorphisms (SNPs). By comparing the genetic structure and phenotypic variation among three genetic subpopulations, seven geographic distributions and four breeding periods, we found that geographic distribution and breeding period were not the determinants of genetic structure. In addition, no obvious phenotypic differentiations were found among the three subpopulations, even though they had different genetic backgrounds. A total of 324 SNPs and 160 candidate quantitative trait loci (QTL) regions were identified as significantly associated with the 16 agronomic traits. A network was established for multieffects in QTLs and interassociations among traits. Thirty-eight associated regions had pleiotropic effects controlling more than one trait. One candidate gene, Gh_D08G2376, was speculated to control the lint percentage (LP). This GWAS is the first report using high-resolution SNPs in upland cotton in China to comprehensively investigate agronomic traits, and it provides a fundamental resource for cotton genetic research and breeding.
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Affiliation(s)
- Cong Huang
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Sciences & TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Xinhui Nie
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Sciences & TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang BingtuanAgricultural CollegeShihezi UniversityShiheziXinjiangChina
| | - Chao Shen
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Sciences & TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Chunyuan You
- Cotton Research InstituteShihezi Academy of Agriculture ScienceShiheziXinjiangChina
| | - Wu Li
- Economic Crop Research InstituteHenan Academy of Agricultural SciencesZhengzhouHenanChina
| | - Wenxia Zhao
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Sciences & TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Xianlong Zhang
- 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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19
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Kushanov FN, Buriev ZT, Shermatov SE, Turaev OS, Norov TM, Pepper AE, Saha S, Ulloa M, Yu JZ, Jenkins JN, Abdukarimov A, Abdurakhmonov IY. QTL mapping for flowering-time and photoperiod insensitivity of cotton Gossypium darwinii Watt. PLoS One 2017; 12:e0186240. [PMID: 29016665 PMCID: PMC5633191 DOI: 10.1371/journal.pone.0186240] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/27/2017] [Indexed: 02/05/2023] Open
Abstract
Most wild and semi-wild species of the genus Gossypium are exhibit photoperiod-sensitive flowering. The wild germplasm cotton is a valuable source of genes for genetic improvement of modern cotton cultivars. A bi-parental cotton population segregating for photoperiodic flowering was developed by crossing a photoperiod insensitive irradiation mutant line with its pre-mutagenesis photoperiodic wild-type G. darwinii Watt genotype. Individuals from the F2 and F3 generations were grown with their parental lines and F1 hybrid progeny in the long day and short night summer condition (natural day-length) of Uzbekistan to evaluate photoperiod sensitivity, i.e., flowering-time during the seasons 2008-2009. Through genotyping the individuals of this bi-parental population segregating for flowering-time, linkage maps were constructed using 212 simple-sequence repeat (SSR) and three cleaved amplified polymorphic sequence (CAPS) markers. Six QTLs directly associated with flowering-time and photoperiodic flowering were discovered in the F2 population, whereas eight QTLs were identified in the F3 population. Two QTLs controlling photoperiodic flowering and duration of flowering were common in both populations. In silico annotations of the flanking DNA sequences of mapped SSRs from sequenced cotton (G. hirsutum L.) genome database has identified several potential 'candidate' genes that are known to be associated with regulation of flowering characteristics of plants. The outcome of this research will expand our understanding of the genetic and molecular mechanisms of photoperiodic flowering. Identified markers should be useful for marker-assisted selection in cotton breeding to improve early flowering characteristics.
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Affiliation(s)
- Fakhriddin N. Kushanov
- Laboratory of Structural and Functional Genomics, Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Zabardast T. Buriev
- Laboratory of Structural and Functional Genomics, Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Shukhrat E. Shermatov
- Laboratory of Structural and Functional Genomics, Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Ozod S. Turaev
- Laboratory of Structural and Functional Genomics, Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Tokhir M. Norov
- Laboratory of Structural and Functional Genomics, Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Alan E. Pepper
- Department of Biology, Texas A&M University, Colleges Station, Texas, United States of America
| | - Sukumar Saha
- Crop Science Research Laboratory, United States Department of Agriculture-Agricultural Research Services, Starkville, Mississippi, United States of America
| | - Mauricio Ulloa
- Plant Stress and Germplasm Development Research, United States Department of Agriculture-Agricultural Research Services, Lubbock, Texas, United States of America
| | - John Z. Yu
- Southern Plains Agricultural Research Center, United States Department of Agriculture-Agricultural Research Services, College Station, Texas, United States of America
| | - Johnie N. Jenkins
- Crop Science Research Laboratory, United States Department of Agriculture-Agricultural Research Services, Starkville, Mississippi, United States of America
| | - Abdusattor Abdukarimov
- Laboratory of Structural and Functional Genomics, Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Ibrokhim Y. Abdurakhmonov
- Laboratory of Structural and Functional Genomics, Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
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20
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Li PT, Wang M, Lu QW, Ge Q, Rashid MHO, Liu AY, Gong JW, Shang HH, Gong WK, Li JW, Song WW, Guo LX, Su W, Li SQ, Guo XP, Shi YZ, Yuan YL. Comparative transcriptome analysis of cotton fiber development of Upland cotton (Gossypium hirsutum) and Chromosome Segment Substitution Lines from G. hirsutum × G. barbadense. BMC Genomics 2017; 18:705. [PMID: 28886694 PMCID: PMC5591532 DOI: 10.1186/s12864-017-4077-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 08/21/2017] [Indexed: 12/15/2022] Open
Abstract
Background How to develop new cotton varieties possessing high yield traits of Upland cotton and superior fiber quality traits of Sea Island cotton remains a key task for cotton breeders and researchers. While multiple attempts bring in little significant progresses, the development of Chromosome Segment Substitution Lines (CSSLs) from Gossypium barbadense in G. hirsutum background provided ideal materials for aforementioned breeding purposes in upland cotton improvement. Based on the excellent fiber performance and relatively clear chromosome substitution segments information identified by Simple Sequence Repeat (SSR) markers, two CSSLs, MBI9915 and MBI9749, together with the recurrent parent CCRI36 were chosen to conduct transcriptome sequencing during the development stages of fiber elongation and Secondary Cell Wall (SCW) synthesis (from 10DPA and 28DPA), aiming at revealing the mechanism of fiber development and the potential contribution of chromosome substitution segments from Sea Island cotton to fiber development of Upland cotton. Results In total, 15 RNA-seq libraries were constructed and sequenced separately, generating 705.433 million clean reads with mean GC content of 45.13% and average Q30 of 90.26%. Through multiple comparisons between libraries, 1801 differentially expressed genes (DEGs) were identified, of which the 902 up-regulated DEGs were mainly involved in cell wall organization and response to oxidative stress and auxin, while the 898 down-regulated ones participated in translation, regulation of transcription, DNA-templated and cytoplasmic translation based on GO annotation and KEGG enrichment analysis. Subsequently, STEM software was performed to explicate the temporal expression pattern of DEGs. Two peroxidases and four flavonoid pathway-related genes were identified in the “oxidation-reduction process”, which could play a role in fiber development and quality formation. Finally, the reliability of RNA-seq data was validated by quantitative real-time PCR of randomly selected 20 genes. Conclusions The present report focuses on the similarities and differences of transcriptome profiles between the two CSSLs and the recurrent parent CCRI36 and provides novel insights into the molecular mechanism of fiber development, and into further exploration of the feasible contribution of G. barbadense substitution segments to fiber quality formation, which will lay solid foundation for simultaneously improving fiber yield and quality of upland cotton through CSSLs. Electronic supplementary material The online version of this article (10.1186/s12864-017-4077-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Peng-Tao Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Mi Wang
- College of Agriculture, Yangtze University, Jingzhou, Hubei, 434025, China
| | - Quan-Wei Lu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China
| | - Md Harun Or Rashid
- State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China
| | - Ai-Ying Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China
| | - Ju-Wu Gong
- State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China
| | - Hai-Hong Shang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China
| | - Wan-Kui Gong
- State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China
| | - Jun-Wen Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China
| | - Wei-Wu Song
- State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China
| | - Li-Xue Guo
- State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China
| | - Wei Su
- State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China.,College of Agriculture, Yangtze University, Jingzhou, Hubei, 434025, China
| | - Shao-Qi Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China
| | - Xiao-Ping Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Yu-Zhen Shi
- State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China.
| | - You-Lu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biologiacl and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China.
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21
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Wang B, Draye X, Zhuang Z, Zhang Z, Liu M, Lubbers EL, Jones D, May OL, Paterson AH, Chee PW. QTL analysis of cotton fiber length in advanced backcross populations derived from a cross between Gossypium hirsutum and G. mustelinum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1297-1308. [PMID: 28349176 DOI: 10.1007/s00122-017-2889-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 03/02/2017] [Indexed: 05/09/2023]
Abstract
QTLs for fiber length mapped in three generations of advanced backcross populations derived from crossing Gossypium hirsutum and Gossypium mustelinum showed opportunities to improve elite cottons by introgression from wild relatives. The molecular basis of cotton fiber length in crosses between Gossypium hirsutum and Gossypium mustelinum was dissected using 21 BC3F2 and 12 corresponding BC3F2:3 and BC3F2:4 families. Sixty-five quantitative trait loci (QTLs) were detected by one-way analysis of variance. The QTL numbers detected for upper-half mean length (UHM), fiber uniformity index (UI), and short fiber content (SFC) were 19, 20, and 26 respectively. Twenty-three of the 65 QTLs could be detected at least twice near adjacent markers in the same family or near the same markers across different families/generations, and 32 QTLs were detected in both one-way variance analyses and mixed model-based composite interval mapping. G. mustelinum alleles increased UHM and UI and decreased SFC for five, one, and one QTLs, respectively. In addition to the main-effect QTLs, 17 epistatic QTLs were detected which helped to elucidate the genetic basis of cotton fiber length. Significant among-family genotypic effects were detected at 18, 16, and 16 loci for UHM, UI, and SFC, respectively. Six, two, and two loci showed genotype × family interaction for UHM, UI and SFC, respectively, illustrating complexities that might be faced in introgression of exotic germplasm into cultivated cotton. Co-location of many QTLs for UHM, UI, and SFC accounted for correlations among these traits, and selection of these QTLs may improve the three traits simultaneously. The simple sequence repeat (SSR) markers associated with G. mustelinum QTLs will assist breeders in transferring and maintaining valuable traits from this exotic source during cultivar development.
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Affiliation(s)
- Baohua Wang
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
- Department of Crop and Soil Sciences, University of Georgia, 2356 Rainwater Road, Tifton, GA, 31793, USA
| | - Xavier Draye
- Université catholique de Louvain, Place Croix du Sud 2/11, 1348, Louvain-la-Neuve, Belgium
| | - Zhimin Zhuang
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
- Department of Crop and Soil Sciences, University of Georgia, 2356 Rainwater Road, Tifton, GA, 31793, USA
| | - Zhengsheng Zhang
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Min Liu
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA
| | - Edward L Lubbers
- Department of Crop and Soil Sciences, University of Georgia, 2356 Rainwater Road, Tifton, GA, 31793, USA
| | - Don Jones
- Cotton Incorporated, Cary, NC, 27513, USA
| | - O Lloyd May
- Department of Crop and Soil Sciences, University of Georgia, 2356 Rainwater Road, Tifton, GA, 31793, USA
- Monsanto Cotton Breeding, Tifton, GA, 31793, USA
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA.
| | - Peng W Chee
- Department of Crop and Soil Sciences, University of Georgia, 2356 Rainwater Road, Tifton, GA, 31793, USA.
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22
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Cai C, Wu S, Niu E, Cheng C, Guo W. Identification of genes related to salt stress tolerance using intron-length polymorphic markers, association mapping and virus-induced gene silencing in cotton. Sci Rep 2017; 7:528. [PMID: 28373664 PMCID: PMC5428780 DOI: 10.1038/s41598-017-00617-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 03/06/2017] [Indexed: 12/20/2022] Open
Abstract
Intron length polymorphisms (ILPs), a type of gene-based functional marker, could themselves be related to the particular traits. Here, we developed a genome-wide cotton ILPs based on orthologs annotation from two sequenced diploid species, A-genome Gossypium arboreum and D-genome G. raimondii. We identified 10,180 putative ILP markers from 5,021 orthologous genes. Among these, 535 ILP markers from 9 gene families related to stress were selected for experimental verification. Polymorphic rates were 72.71% between G. arboreum and G. raimondii and 36.45% between G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124. Furthermore, 14 polymorphic ILP markers were detected in 264 G. hirsutum accessions. Coupled with previous simple sequence repeats (SSRs) evaluations and salt tolerance assays from the same individuals, we found a total of 25 marker-trait associations involved in nine ILPs. The nine genes, temporally named as C1 to C9, showed the various expressions in different organs and tissues, and five genes (C3, C4, C5, C7 and C9) were significantly upregulated after salt treatment. We verified that the five genes play important roles in salt tolerance. Particularly, silencing of C4 (encodes WRKY DNA-binding protein) and C9 (encodes Mitogen-activated protein kinase) can significantly enhance cotton susceptibility to salt stress.
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Affiliation(s)
- Caiping Cai
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shuang Wu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
| | - Erli Niu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chaoze Cheng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China.
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23
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Zhu S, Liu T, Dai Q, Wu D, Zheng X, Tang S, Chen J. Genetic structure and relationships of an associated population in ramie (Boehmeria nivea L. Gaud) evaluated by SSR markers. BIOTECHNOL BIOTEC EQ 2016. [DOI: 10.1080/13102818.2016.1253437] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Siyuan Zhu
- Department of Southern Forage Crop and Utilization, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, PR China
| | - Touming Liu
- Department of Southern Forage Crop and Utilization, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, PR China
| | - Qiuzhong Dai
- Department of Southern Forage Crop and Utilization, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, PR China
| | - Duanqing Wu
- Department of Southern Forage Crop and Utilization, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, PR China
| | - Xia Zheng
- Department of Southern Forage Crop and Utilization, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, PR China
| | - Shouwei Tang
- Department of Southern Forage Crop and Utilization, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, PR China
| | - Jianhua Chen
- Department of Southern Forage Crop and Utilization, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, PR China
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24
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Kushanov FN, Pepper AE, Yu JZ, Buriev ZT, Shermatov SE, Saha S, Ulloa M, Jenkins JN, Abdukarimov A, Abdurakhmonov IY. Development, genetic mapping and QTL association of cotton PHYA, PHYB, and HY5-specific CAPS and dCAPS markers. BMC Genet 2016; 17:141. [PMID: 27776497 PMCID: PMC5078887 DOI: 10.1186/s12863-016-0448-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/13/2016] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Among SNP markers that become increasingly valuable in molecular breeding of crop plants are the CAPS and dCAPS markers derived from the genes of interest. To date, the number of such gene-based markers is small in polyploid crop plants such as allotetraploid cotton that has A- and D-sub-genomes. The objective of this study was to develop and map new CAPS and dCAPS markers for cotton developmental-regulatory genes that are important in plant breeding programs. RESULTS Gossypium hirsutum and G. barbadense, are the two cultivated allotetraploid cotton species. These have distinct fiber quality and other agronomic traits. Using comparative sequence analysis of characterized GSTs of the PHYA1, PHYB, and HY5 genes of G. hirsutum and G. barbadense one PHYA1-specific Mbo I/Dpn II CAPS, one PHYB-specific Alu I dCAPS, and one HY5-specific Hinf I dCAPS cotton markers were developed. These markers have successfully differentiated the two allotetraploid genomes (AD1 and AD2) when tested in parental genotypes of 'Texas Marker-1' ('TM-1'), 'Pima 3-79' and their F1 hybrids. The genetic mapping and chromosome substitution line-based deletion analyses revealed that PHYA1 gene is located in A-sub-genome chromosome 11, PHYB gene is in A-sub-genome chromosome 10, and HY5 gene is in D-sub-genome chromosome 24, on the reference 'TM-1' x 'Pima 3-79' RIL genetic map. Further, it was found that genetic linkage map regions containing phytochrome and HY5-specific markers were associated with major fiber quality and flowering time traits in previously published QTL mapping studies. CONCLUSION This study detailed the genome mapping of three cotton phytochrome genes with newly developed CAPS and dCAPS markers. The proximity of these loci to fiber quality and other cotton QTL was demonstrated in two A-subgenome and one D-subgenome chromosomes. These candidate gene markers will be valuable for marker-assisted selection (MAS) programs to rapidly introgress G. barbadense phytochromes and/or HY5 gene (s) into G. hirsutum cotton genotypes or vice versa.
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Affiliation(s)
- Fakhriddin N. Kushanov
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, University Street-2, Qibray region Tashkent District, 111215 Uzbekistan
| | - Alan E. Pepper
- Department of Biology, Texas A&M University, Colleges Station, TX 77843 USA
| | - John Z. Yu
- USDA-ARS, Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, TX 77845 USA
| | - Zabardast T. Buriev
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, University Street-2, Qibray region Tashkent District, 111215 Uzbekistan
| | - Shukhrat E. Shermatov
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, University Street-2, Qibray region Tashkent District, 111215 Uzbekistan
| | - Sukumar Saha
- USDA-ARS, Crop Science Research Laboratory, Mississippi State, MS 39762 USA
| | - Mauricio Ulloa
- USDA-ARS, Plant Stress and Germplasm Development Research, 3810 4th Street, Lubbock, TX 79415 USA
| | - Johnie N. Jenkins
- USDA-ARS, Crop Science Research Laboratory, Mississippi State, MS 39762 USA
| | - Abdusattor Abdukarimov
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, University Street-2, Qibray region Tashkent District, 111215 Uzbekistan
| | - Ibrokhim Y. Abdurakhmonov
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, University Street-2, Qibray region Tashkent District, 111215 Uzbekistan
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25
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Zhai H, Gong W, Tan Y, Liu A, Song W, Li J, Deng Z, Kong L, Gong J, Shang H, Chen T, Ge Q, Shi Y, Yuan Y. Identification of Chromosome Segment Substitution Lines of Gossypium barbadense Introgressed in G. hirsutum and Quantitative Trait Locus Mapping for Fiber Quality and Yield Traits. PLoS One 2016; 11:e0159101. [PMID: 27603312 PMCID: PMC5014324 DOI: 10.1371/journal.pone.0159101] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 06/27/2016] [Indexed: 01/11/2023] Open
Abstract
Chromosome segment substitution lines MBI9804, MBI9855, MBI9752, and MBI9134, which were obtained by advanced backcrossing and continuously inbreeding from an interspecific cross between CCRI36, a cultivar of upland cotton (Gossypium hirsutum) as the recurrent parent, and Hai1, a cultivar of sea island cotton (G. barbadense) as the donor parent, were used to construct a multiple parent population of (MBI9804×MBI9855)×(MBI9752×MBI9134). The segregating generations of double-crossed F1 and F2 and F2:3 were used to map the quantitative trait locus (QTL) for fiber quality and yield-related traits. The recovery rate of the recurrent parent CCRI36 in the four parental lines was from 94.3%-96.9%. Each of the parental lines harbored 12-20 introgressed segments from Hai1across 21 chromosomes. The number of introgressed segments ranged from 1 to 27 for the individuals in the three generations, mostly from 9 to 18, which represented a genetic length of between 126 cM and 246 cM. A total of 24 QTLs controlling fiber quality and 11 QTLs controlling yield traits were detected using the three segregating generations. These QTLs were distributed across 11 chromosomes and could collectively explain 1.78%-20.27% of the observed phenotypic variations. Sixteen QTLs were consistently detected in two or more generations, four of them were for fiber yield traits and 12 were for fiber quality traits. One introgressed segment could significantly reduce both lint percentage and fiber micronaire. This study provides useful information for gene cloning and marker-assisted breeding for excellent fiber quality.
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Affiliation(s)
- Huanchen Zhai
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences. Anyang, Henan, China
- College of Bioengineering, Henan University of technology, Zhengzhou, Henan, China
| | - Wankui Gong
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences. Anyang, Henan, China
| | - Yunna Tan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences. Anyang, Henan, China
| | - Aiying Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences. Anyang, Henan, China
| | - Weiwu Song
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences. Anyang, Henan, China
| | - Junwen Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences. Anyang, Henan, China
| | - Zhuying Deng
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences. Anyang, Henan, China
| | - Linglei Kong
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences. Anyang, Henan, China
| | - Juwu Gong
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences. Anyang, Henan, China
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences. Anyang, Henan, China
| | - Tingting Chen
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences. Anyang, Henan, China
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences. Anyang, Henan, China
| | - Yuzhen Shi
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences. Anyang, Henan, China
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences. Anyang, Henan, China
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26
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To Be a Flower or Fruiting Branch: Insights Revealed by mRNA and Small RNA Transcriptomes from Different Cotton Developmental Stages. Sci Rep 2016; 6:23212. [PMID: 26983497 PMCID: PMC4794708 DOI: 10.1038/srep23212] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 03/02/2016] [Indexed: 12/14/2022] Open
Abstract
The architecture of the cotton plant, including fruit branch formation and flowering pattern, is the most important characteristic that directly influences light exploitation, yield and cost of planting. Nulliplex branch is a useful phenotype to study cotton architecture. We used RNA sequencing to obtain mRNA and miRNA profiles from nulliplex- and normal-branch cotton at three developmental stages. The differentially expressed genes (DEGs) and miRNAs were identified that preferentially/specifically expressed in the pre-squaring stage, which is a key stage controlling the transition from vegetative to reproductive growth. The DEGs identified were primarily enriched in RNA, protein, and signalling categories in Gossypium barbadense and Gossypium hirsutum. Interestingly, during the pre-squaring stage, the DEGs were predominantly enriched in transcription factors in both G. barbadense and G. hirsutum, and these transcription factors were mainly involved in branching and flowering. Related miRNAs were also identified. The results showed that fruit branching in cotton is controlled by molecular pathways similar to those in Arabidopsis and that multiple regulated pathways may affect the development of floral buds. Our study showed that the development of fruit branches is closely related to flowering induction and provides insight into the molecular mechanisms of branch and flower development in cotton.
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27
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Chen J, Yu R, Liu L, Wang B, Peng D. Large-scale developing of simple sequence repeat markers and probing its correlation with ramie (Boehmeria nivea L.) fiber quality. Mol Genet Genomics 2015; 291:753-61. [PMID: 26577947 DOI: 10.1007/s00438-015-1143-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 11/02/2015] [Indexed: 10/22/2022]
Abstract
Marker-assisted selection is an important component of the discipline of molecular breeding. Using DNA markers to assist in plant breeding, the efficiency and precision could be greatly increased. However, the scarcity number of identified DNA markers has hindered the research and the breeding process of ramie (Boehmeria nivea L.) in many aspects, especially fiber quality, one of the top-priority breeding objectives of ramie. In this study, 4230 SSR loci were identified in 3969 unigenes (6.80 % of 58,369), which were de novo assembled from the transcriptome involving different ramie fiber developmental stages. Among these SSRs, the dinucleotides (1599, 37.80 %) and trinucleotides (772, 18.25 %) were most abundant; the motifs AG/CT (1140, 26.94 %), AT/AT (407, 9.62 %) and AGA/TCT (246, 8.31 %) comprised the three most abundant repeats. A total of 2431 primer pairs were designed flanking the SSRs and 1050 of them were employed in PCR amplification for their usefulness using three ramie cultivars. The results showed that 88.10 % of these primers could generate positive PCR bands in any of the three cultivars. Further phylogenetic analysis that conducted from the PCR amplification of 52 specifically sifted SSR primers within 17 cultivars approved that the possible correlation may exist between the primers and ramie fiber quality. These developed SSR markers could be applied in downstream studies, like genetic and physical maps, quantitative trait loci mapping, genetic diversity studies and cultivar fingerprinting, and breeding processes of ramie with better fiber quality under further confirmation of the correlation with ramie fiber quality.
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Affiliation(s)
- Jie Chen
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Hongshan District, Wuhan, 430070, Hubei Province, China
| | - Runqing Yu
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Hongshan District, Wuhan, 430070, Hubei Province, China
| | - Lijun Liu
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Hongshan District, Wuhan, 430070, Hubei Province, China
| | - Bo Wang
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Hongshan District, Wuhan, 430070, Hubei Province, China.
| | - Dingxiang Peng
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Hongshan District, Wuhan, 430070, Hubei Province, China.
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28
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Wang H, Huang C, Guo H, Li X, Zhao W, Dai B, Yan Z, Lin Z. QTL Mapping for Fiber and Yield Traits in Upland Cotton under Multiple Environments. PLoS One 2015; 10:e0130742. [PMID: 26110526 PMCID: PMC4481505 DOI: 10.1371/journal.pone.0130742] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 05/24/2015] [Indexed: 01/30/2023] Open
Abstract
A population of 178 recombinant inbred lines (RILs) was developed using a single seed descendant from a cross between G. hirsutum. acc DH962 and G. hirsutum. cv Jimian5, was used to construct a genetic map and to map QTL for fiber and yield traits. A total of 644 polymorphic loci were used to construct a final genetic map, containing 616 loci and spanning 2016.44 cM, with an average of 3.27 cM between adjacent markers. Statistical analysis revealed that segregation distortion in the intraspecific population was more serious than that in the interspecific population. The RIL population and the two parents were phenotyped under 8 environments (two locations, six years), revealing a total of 134 QTL, including 64 for fiber qualities and 70 for yield components, independently detected in seven environments, explaining 4.40-15.28% of phenotypic variation (PV). Among the 134 QTL, 9 common QTL were detected in more than one environment, and 22 QTL and 19 new QTL were detected in combined analysis (E9). A total of 26 QTL hotspot regions were observed on 13 chromosomes and 2 larger linkage groups, and some QTL clusters related to fiber qualities or yield components were also observed. The results obtained in the present study suggested that to map accurate QTL in crops with larger plant types, such as cotton, phenotyping under multiple environments is necessary to effectively apply the obtained results in molecular marker-assisted selection breeding and QTL cloning.
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Affiliation(s)
- Hantao Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University. Wuhan 430070, Hubei, China
| | - Cong Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University. Wuhan 430070, Hubei, China
| | - Huanle Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University. Wuhan 430070, Hubei, China
| | - Ximei Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University. Wuhan 430070, Hubei, China
| | - Wenxia Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University. Wuhan 430070, Hubei, China
| | - Baosheng Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University. Wuhan 430070, Hubei, China
| | - Zhenhua Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University. Wuhan 430070, Hubei, China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University. Wuhan 430070, Hubei, China
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