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Hu G, Grover CE, Vera DL, Lung PY, Girimurugan SB, Miller ER, Conover JL, Ou S, Xiong X, Zhu D, Li D, Gallagher JP, Udall JA, Sui X, Zhang J, Bass HW, Wendel JF. Evolutionary dynamics of chromatin structure and duplicate gene expression in diploid and allopolyploid cotton. Mol Biol Evol 2024:msae095. [PMID: 38758089 DOI: 10.1093/molbev/msae095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 04/10/2024] [Accepted: 05/10/2024] [Indexed: 05/18/2024] Open
Abstract
Polyploidy is a prominent mechanism of plant speciation and adaptation, yet the mechanistic understandings of duplicated gene regulation remain elusive. Chromatin structure dynamics are suggested to govern gene regulatory control. Here we characterized genome-wide nucleosome organization and chromatin accessibility in allotetraploid cotton, Gossypium hirsutum (AADD, 2n=4X=52), relative to its two diploid parents (AA or DD genome) and their synthetic diploid hybrid (AD), using DNS-seq. The larger A-genome exhibited wider average nucleosome spacing in diploids, and this inter-genomic difference diminished in the allopolyploid but not hybrid. Allopolyploidization also exhibited increased accessibility at promoters genome-wide and synchronized cis-regulatory motifs between subgenomes. A prominent cis-acting control was inferred for chromatin dynamics and demonstrated by transposable element removal from promoters. Linking accessibility to gene expression patterns, we found distinct regulatory effects for hybridization and later allopolyploid stages, including nuanced establishment of homoeolog expression bias and expression level dominance. Histone gene expression and nucleosome organization are coordinated through chromatin accessibility. Our study demonstrates the capability to track high resolution chromatin structure dynamics and reveals their role in the evolution of cis-regulatory landscapes and duplicate gene expression in polyploids, illuminating regulatory ties to subgenomic asymmetry and dominance.
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Affiliation(s)
- Guanjing Hu
- State Key Laboratory of Cotton Bio-breeding and Integrated, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China 455000
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China 518120
| | - Corrinne E Grover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa, USA 50011
| | - Daniel L Vera
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA 32306
| | - Pei-Yau Lung
- Department of Statistics, Florida State University, Tallahassee, Florida, USA 32306
| | | | - Emma R Miller
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa, USA 50011
| | - Justin L Conover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa, USA 50011
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, USA 85721
- Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA 85721
| | - Shujun Ou
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio, USA 43210
| | - Xianpeng Xiong
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China 518120
| | - De Zhu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China 518120
| | - Dongming Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China 450000
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China 518120
| | - Joseph P Gallagher
- Forage Seed and Cereal Research Unit, USDA/Agricultural Research Service, Corvallis, Oregon, USA 97331
| | - Joshua A Udall
- Crop Germplasm Research Unit, USDA/Agricultural Research Service, College Station, Texas, USA 77845
| | - Xin Sui
- Department of Statistics, Florida State University, Tallahassee, Florida, USA 32306
| | - Jinfeng Zhang
- Department of Statistics, Florida State University, Tallahassee, Florida, USA 32306
| | - Hank W Bass
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA 32306
| | - Jonathan F Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa, USA 50011
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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) 2023; 12:4184. [PMID: 38140511 PMCID: PMC10748080 DOI: 10.3390/plants12244184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [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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Morales KY, Bridgeland AH, Hake KD, Udall JA, Thomson MJ, Yu JZ. Homology-based identification of candidate genes for male sterility editing in upland cotton ( Gossypium hirsutum L.). Front Plant Sci 2022; 13:1006264. [PMID: 36589117 PMCID: PMC9795482 DOI: 10.3389/fpls.2022.1006264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
Upland cotton (Gossypium hirsutum L.) accounts for more than 90% of the world's cotton production, providing natural material for the textile and oilseed industries worldwide. One strategy for improving upland cotton yields is through increased adoption of hybrids; however, emasculation of cotton flowers is incredibly time-consuming and genetic sources of cotton male sterility are limited. Here we review the known biochemical modes of plant nuclear male sterility (NMS), often known as plant genetic male sterility (GMS), and characterized them into four groups: transcriptional regulation, splicing, fatty acid transport and processing, and sugar transport and processing. We have explored protein sequence homology from 30 GMS genes of three monocots (maize, rice, and wheat) and three dicots (Arabidopsis, soybean, and tomato). We have analyzed evolutionary relationships between monocot and dicot GMS genes to describe the relative similarity and relatedness of these genes identified. Five were lowly conserved to their source species, four unique to monocots, five unique to dicots, 14 highly conserved among all species, and two in the other category. Using this source, we have identified 23 potential candidate genes within the upland cotton genome for the development of new male sterile germplasm to be used in hybrid cotton breeding. Combining homology-based studies with genome editing may allow for the discovery and validation of GMS genes that previously had no diversity observed in cotton and may allow for development of a desirable male sterile mutant to be used in hybrid cotton production.
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Affiliation(s)
- Karina Y. Morales
- USDA-ARS, Southern Plains Agricultural Research Center, College Station, TX, United States
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Aya H. Bridgeland
- USDA-ARS, Southern Plains Agricultural Research Center, College Station, TX, United States
| | - Kater D. Hake
- Cotton Incorporated, Agricultural and Environment Research, Cary, NC, United States
| | - Joshua A. Udall
- USDA-ARS, Southern Plains Agricultural Research Center, College Station, TX, United States
| | - Michael J. Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - John Z. Yu
- USDA-ARS, Southern Plains Agricultural Research Center, College Station, TX, United States
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Grover CE, Arick MA, Thrash A, Sharbrough J, Hu G, Yuan D, Snodgrass S, Miller ER, Ramaraj T, Peterson DG, Udall JA, Wendel JF. Dual Domestication, Diversity, and Differential Introgression in Old World Cotton Diploids. Genome Biol Evol 2022; 14:6890153. [PMID: 36510772 PMCID: PMC9792962 DOI: 10.1093/gbe/evac170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/19/2022] [Accepted: 12/01/2022] [Indexed: 12/15/2022] Open
Abstract
Domestication in the cotton genus is remarkable in that it has occurred independently four different times at two different ploidy levels. Relatively little is known about genome evolution and domestication in the cultivated diploid species Gossypium herbaceum and Gossypium arboreum, due to the absence of wild representatives for the latter species, their ancient domestication, and their joint history of human-mediated dispersal and interspecific gene flow. Using in-depth resequencing of a broad sampling from both species, we provide support for their independent domestication, as opposed to a progenitor-derivative relationship, showing that diversity (mean π = 6 × 10-3) within species is similar, and that divergence between species is modest (FST = 0.413). Individual accessions were homozygous for ancestral single-nucleotide polymorphisms at over half of variable sites, while fixed, derived sites were at modest frequencies. Notably, two chromosomes with a paucity of fixed, derived sites (i.e., chromosomes 7 and 10) were also strongly implicated as having experienced high levels of introgression. Collectively, these data demonstrate variable permeability to introgression among chromosomes, which we propose is due to divergent selection under domestication and/or the phenomenon of F2 breakdown in interspecific crosses. Our analyses provide insight into the evolutionary forces that shape diversity and divergence in the diploid cultivated species and establish a foundation for understanding the contribution of introgression and/or strong parallel selection to the extensive morphological similarities shared between species.
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Affiliation(s)
| | - Mark A Arick
- Biocomputing & Biotechnology, Institute for Genomics, Mississippi State University, Mississippi, USA
| | - Adam Thrash
- Biocomputing & Biotechnology, Institute for Genomics, Mississippi State University, Mississippi, USA
| | - Joel Sharbrough
- Biology Department, New Mexico Institute of Mining and Technology, Socorro, New Mexico 87801, USA
| | - Guanjing Hu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Daojun Yuan
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan Hubei 430070, China
| | - Samantha Snodgrass
- Ecology, Evolution, and Organismal Biology Department, Iowa State University, Ames, Iowa 5001, USA
| | - Emma R Miller
- Ecology, Evolution, and Organismal Biology Department, Iowa State University, Ames, Iowa 5001, USA
| | - Thiruvarangan Ramaraj
- School of Computing, College of Computing and Digital Media, DePaul University, Chicago, Illinois 6060, USA
| | - Daniel G Peterson
- Biocomputing & Biotechnology, Institute for Genomics, Mississippi State University, Mississippi, USA
| | - Joshua A Udall
- Crop Germplasm Research Unit, USDA/Agricultural Research Service, 2881 F&B Road, College Station, Texas 77845, USA
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Ramaraj T, Grover CE, Mendoza AC, Arick MA, Jareczek JJ, Leach AG, Peterson DG, Wendel JF, Udall JA. The Gossypium herbaceum L. Wagad genome as a resource for understanding cotton domestication. G3 (Bethesda) 2022; 13:6858943. [PMID: 36454094 PMCID: PMC9911056 DOI: 10.1093/g3journal/jkac308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 10/14/2022] [Accepted: 10/23/2022] [Indexed: 12/05/2022]
Abstract
Gossypium herbaceum is a species of cotton native to Africa and Asia that is one of the 2 domesticated diploids. Together with its sister-species G. arboreum, these A-genome taxa represent models of the extinct A-genome donor of modern polyploid cotton, which provide about 95% of cotton grown worldwide. As part of a larger effort to characterize variation and improve resources among diverse diploid and polyploid cotton genomes, we sequenced and assembled the genome of G. herbaceum cultivar (cv.) Wagad, representing the first domesticated accession for this species. This chromosome-level genome was generated using a combination of PacBio long-read technology, HiC, and Bionano optical mapping and compared to existing genome sequences in cotton. We compare the genome of this cultivar to the existing genome of wild G. herbaceum subspecies africanum to elucidate changes in the G. herbaceum genome concomitant with domestication and extend these analyses to gene expression using available RNA-seq. Our results demonstrate the utility of the G. herbaceum cv. Wagad genome in understanding domestication in the diploid species, which could inform modern breeding programs.
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Affiliation(s)
- Thiruvarangan Ramaraj
- School of Computing, Jarvis College of Computing and Digital Media, DePaul University, Chicago, IL 60605, USA
| | - Corrinne E Grover
- Ecology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA 50011, USA
| | - Azalea C Mendoza
- School of Computing, Jarvis College of Computing and Digital Media, DePaul University, Chicago, IL 60605, USA
| | - Mark A Arick
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Josef J Jareczek
- Ecology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA 50011, USA
| | - Alexis G Leach
- Ecology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA 50011, USA
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Jonathan F Wendel
- Ecology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA 50011, USA
| | - Joshua A Udall
- *Corresponding author: Crop Germplasm Research Unit, USDA/Agricultural Research Service, 2881 F&B Rd., College Station, TX 77845, USA.
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Parris SM, Jeffers SN, Olvey JM, Olvey JM, Adelberg JW, Wen L, Udall JA, Coleman JJ, Jones DC, Saski CA. An In Vitro Co-Culture System for Rapid Differential Response to Fusarium oxysporum f. sp. vasinfectum Race 4 in Three Cotton Cultivars. Plant Dis 2022; 106:990-995. [PMID: 34705484 DOI: 10.1094/pdis-08-21-1743-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Fusarium oxysporum f. sp. vasinfectum race 4 (FOV4) is a devastating fungus pathogen that causes Fusarium wilt in both domesticated cotton species, Gossypium hirsutum (Upland) and G. barbadense (Pima). Greenhouse and field-based pathogenicity assays can be a challenge because of nonuniform inoculum levels, the presence of endophytes, and varying environmental factors. Therefore, an in vitro coculture system was designed to support the growth of both domesticated cotton species and FOV4 via an inert polyphenolic foam substrate with a liquid medium. A Fusarium wilt-susceptible Pima cotton cultivar, G. barbadense 'GB1031'; a highly resistant Pima cotton cultivar, G. barbadense 'DP348RF'; and a susceptible Upland cotton cultivar, G. hirsutum 'TM-1', were evaluated for 30 days during coculture with FOV4 in this foam-based system. Thirty days after inoculation, disease symptoms were more severe in both susceptible cultivars, which displayed higher percentages of foliar damage, and greater plant mortality than observed in 'DP348RF', the resistant Pima cotton cultivar. This foam-based in vitro system may be useful for screening cotton germplasm for resistance to a variety of fungus pathogens and may facilitate the study of biotic interactions in domesticated cotton species under controlled environmental conditions.
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Affiliation(s)
- Stephen M Parris
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29631
| | - Steven N Jeffers
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29631
| | | | | | - Jeffrey W Adelberg
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29631
| | - Li Wen
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29631
| | - Joshua A Udall
- USDA-ARS Southern Plains Agricultural Research Center, College Station, TX 77845
| | - Jeffrey J Coleman
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849
| | | | - Christopher A Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29631
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Perkin LC, Bell A, Hinze LL, Suh CPC, Arick MA, Peterson DG, Udall JA. Genome assembly of two nematode-resistant cotton lines ( Gossypium hirsutum L.). G3 Genes|Genomes|Genetics 2021; 11. [PMID: 34849785 PMCID: PMC8527472 DOI: 10.1093/g3journal/jkab276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Abstract
Upland cotton (Gossypium hirsutum L.) is susceptible to damage by the root-knot and the reniform nematodes, causing yield losses greater than 4% annually in the United States. In addition, these nematodes are synergistic with seeding disease and root rot pathogens that exacerbate diseases and subsequent yield losses. Production practices to minimize nematode damage include crop rotation and nematicides, but these techniques need to be repeated and are expensive. The use of resistant cultivars is deemed the most effective and economical approach for managing nematodes in cotton. Here, we describe the genomes of two nematode-resistant lines of cotton, BARBREN-713 and BAR 32-30. These genomes may expedite the development of DNA markers that can be used to efficiently introduce nematode resistance into commercially valuable Upland lines.
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Affiliation(s)
- Lindsey C Perkin
- USDA Agricultural Research Service, Insect Control and Cotton Disease Research Unit, College Station, TX 77845, USA
| | - Al Bell
- USDA Agricultural Research Service, Insect Control and Cotton Disease Research Unit, College Station, TX 77845, USA
| | - Lori L Hinze
- USDA Agricultural Research Service, Crop Germplasm Research Unit, College Station, TX 77845, USA
| | - Charles P -C Suh
- USDA Agricultural Research Service, Insect Control and Cotton Disease Research Unit, College Station, TX 77845, USA
| | - Mark A Arick
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Joshua A Udall
- USDA Agricultural Research Service, Crop Germplasm Research Unit, College Station, TX 77845, USA
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Grover CE, Yuan D, Arick MA, Miller ER, Hu G, Peterson DG, Wendel JF, Udall JA. The Gossypium anomalum genome as a resource for cotton improvement and evolutionary analysis of hybrid incompatibility. G3 Genes|Genomes|Genetics 2021; 11:jkab319. [PMID: 34549783 PMCID: PMC8527517 DOI: 10.1093/g3journal/jkab319] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/30/2021] [Indexed: 11/14/2022]
Abstract
Cotton is an important crop that has been the beneficiary of multiple genome sequencing efforts, including diverse representatives of wild species for germplasm development. Gossypium anomalum is a wild African diploid species that harbors stress-resistance and fiber-related traits with potential application to modern breeding efforts. In addition, this species is a natural source of cytoplasmic male sterility and a resource for understanding hybrid lethality in the genus. Here, we report a high-quality de novo genome assembly for G. anomalum and characterize this genome relative to existing genome sequences in cotton. In addition, we use the synthetic allopolyploids 2(A2D1) and 2(A2D3) to discover regions in the G. anomalum genome potentially involved in hybrid lethality, a possibility enabled by introgression of regions homologous to the D3 (Gossypium davidsonii) lethality loci into the synthetic 2(A2D3) allopolyploid.
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Affiliation(s)
- Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50010, USA
| | - Daojun Yuan
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Mark A Arick
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, MS 39762, USA
| | - Emma R Miller
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50010, USA
| | - Guanjing Hu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Shenzhen 518120, China
- Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, MS 39762, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50010, USA
| | - Joshua A Udall
- USDA/Agricultural Research Service, Crop Germplasm Research Unit, College Station, TX 77845, USA
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Yuan D, Grover CE, Hu G, Pan M, Miller ER, Conover JL, Hunt SP, Udall JA, Wendel JF. Parallel and Intertwining Threads of Domestication in Allopolyploid Cotton. Adv Sci (Weinh) 2021; 8:2003634. [PMID: 34026441 PMCID: PMC8132148 DOI: 10.1002/advs.202003634] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 02/02/2021] [Indexed: 05/09/2023]
Abstract
The two cultivated allopolyploid cottons, Gossypium hirsutum and Gossypium barbadense, represent a remarkable example of parallel independent domestication, both involving dramatic morphological transformations under selection from wild perennial plants to annualized row crops. Deep resequencing of 643 newly sampled accessions spanning the wild-to-domesticated continuum of both species, and their allopolyploid relatives, are combined with existing data to resolve species relationships and elucidate multiple aspects of their parallel domestication. It is confirmed that wild G. hirsutum and G. barbadense were initially domesticated in the Yucatan Peninsula and NW South America, respectively, and subsequently spread under domestication over 4000-8000 years to encompass most of the American tropics. A robust phylogenomic analysis of infraspecific relationships in each species is presented, quantify genetic diversity in both, and describe genetic bottlenecks associated with domestication and subsequent diffusion. As these species became sympatric over the last several millennia, pervasive genome-wide bidirectional introgression occurred, often with striking asymmetries involving the two co-resident genomes of these allopolyploids. Diversity scans revealed genomic regions and genes unknowingly targeted during domestication and additional subgenomic asymmetries. These analyses provide a comprehensive depiction of the origin, divergence, and adaptation of cotton, and serve as a rich resource for cotton improvement.
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Affiliation(s)
- Daojun Yuan
- Department of EcologyEvolution, and Organismal Biology (EEOB)Bessey HallIowa State UniversityAmesIA50011USA
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubei430070China
| | - Corrinne E. Grover
- Department of EcologyEvolution, and Organismal Biology (EEOB)Bessey HallIowa State UniversityAmesIA50011USA
| | - Guanjing Hu
- Department of EcologyEvolution, and Organismal Biology (EEOB)Bessey HallIowa State UniversityAmesIA50011USA
| | - Mengqiao Pan
- State Key Laboratory of Crop Genetics and Germplasm EnhancementCotton Hybrid R & D Engineering CenterNanjing Agricultural UniversityNanjing210095China
| | - Emma R. Miller
- Department of EcologyEvolution, and Organismal Biology (EEOB)Bessey HallIowa State UniversityAmesIA50011USA
| | - Justin L. Conover
- Department of EcologyEvolution, and Organismal Biology (EEOB)Bessey HallIowa State UniversityAmesIA50011USA
| | | | - Joshua A. Udall
- Crop Germplasm Research UnitUSDA‐ARSCollege StationTX77845USA
| | - Jonathan F. Wendel
- Department of EcologyEvolution, and Organismal Biology (EEOB)Bessey HallIowa State UniversityAmesIA50011USA
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10
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Grover CE, Yuan D, Arick MA, Miller ER, Hu G, Peterson DG, Wendel JF, Udall JA. The Gossypium stocksii genome as a novel resource for cotton improvement. G3 Genes|Genomes|Genetics 2021; 11:6237488. [DOI: 10.1093/g3journal/jkab125] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/07/2021] [Indexed: 12/17/2022]
Abstract
Abstract
Cotton is an important textile crop whose gains in production over the last century have been challenged by various diseases. Because many modern cultivars are susceptible to several pests and pathogens, breeding efforts have included attempts to introgress wild, naturally resistant germplasm into elite lines. Gossypium stocksii is a wild cotton species native to Africa, which is part of a clade of vastly understudied species. Most of what is known about this species comes from pest resistance surveys and/or breeding efforts, which suggests that G. stocksii could be a valuable reservoir of natural pest resistance. Here, we present a high-quality de novo genome sequence for G. stocksii. We compare the G. stocksii genome with resequencing data from a closely related, understudied species (Gossypium somalense) to generate insight into the relatedness of these cotton species. Finally, we discuss the utility of the G. stocksii genome for understanding pest resistance in cotton, particularly resistance to cotton leaf curl virus.
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Affiliation(s)
- Corrinne E Grover
- Ecology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA 50010, USA
| | - Daojun Yuan
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Mark A Arick
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Emma R Miller
- Ecology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA 50010, USA
| | - Guanjing Hu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Jonathan F Wendel
- Ecology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA 50010, USA
| | - Joshua A Udall
- Crop Germplasm Research Unit, USDA/Agricultural Research Service, College Station, TX 77845, USA
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11
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Iqbal MM, Huynh M, Udall JA, Kilian A, Adhikari KN, Berger JD, Erskine W, Nelson MN. The first genetic map for yellow lupin enables genetic dissection of adaptation traits in an orphan grain legume crop. BMC Genet 2019; 20:68. [PMID: 31412771 PMCID: PMC6694670 DOI: 10.1186/s12863-019-0767-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 07/17/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Yellow lupin (Lupinus luteus L.) is a promising grain legume for productive and sustainable crop rotations. It has the advantages of high tolerance to soil acidity and excellent seed quality, but its current yield potential is poor, especially in low rainfall environments. Key adaptation traits such as phenology and enhanced stress tolerance are often complex and controlled by several genes. Genomic-enabled technologies may help to improve our basic understanding of these traits and to provide selective markers in breeding. However, in yellow lupin there are very limited genomic resources to support research and no published information is available on the genetic control of adaptation traits. RESULTS We aimed to address these deficiencies by developing the first linkage map for yellow lupin and conducting quantitative trait locus (QTL) analysis of yield under well-watered (WW) and water-deficit (WT) conditions. Two next-generation sequencing marker approaches - genotyping-by-sequencing (GBS) and Diversity Array Technology (DArT) sequencing - were employed to genotype a recombinant inbred line (RIL) population developed from a bi-parental cross between wild and domesticated parents. A total of 2,458 filtered single nucleotide polymorphism (SNP) and presence / absence variation (PAV) markers were used to develop a genetic map comprising 40 linkage groups, the first reported for this species. A number of significant QTLs controlling total biomass and 100-seed weight under two water (WW and WD) regimes were found on linkage groups YL-03, YL-09 and YL-26 that together explained 9 and 28% of total phenotypic variability. QTLs associated with length of the reproductive phase and time to flower were found on YL-01, YL-21, YL-35 and YL-40 that together explained a total of 12 and 44% of total phenotypic variation. CONCLUSION These genomic resources and the QTL information offer significant potential for use in marker-assisted selection in yellow lupin.
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Affiliation(s)
- Muhammad Munir Iqbal
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia.
- Centre for Plant Genetics and Breeding and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia.
| | - Mark Huynh
- The College of Life Sciences, Brigham Young University, Provo, UT, USA
| | - Joshua A Udall
- USDA-ARS Southern Plains Agricultural Research Center, 2881 F&B Rd., College Station, TX, 77845, USA
| | - Andrzej Kilian
- Diversity Arrays Technology, University of Canberra, Canberra, Australia
| | - Kedar N Adhikari
- School of Life and Environmental Sciences, I A Watson Grains Research Centre, The University of Sydney, Narrabri, NSW, Australia
| | | | - William Erskine
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- Centre for Plant Genetics and Breeding and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Matthew N Nelson
- Agriculture and Food, CSIRO, Floreat, WA, Australia
- The UWA Institute of Agriculture, Perth, WA, Australia
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12
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Udall JA, Long E, Ramaraj T, Conover JL, Yuan D, Grover CE, Gong L, Arick MA, Masonbrink RE, Peterson DG, Wendel JF. The Genome Sequence of Gossypioides kirkii Illustrates a Descending Dysploidy in Plants. Front Plant Sci 2019; 10:1541. [PMID: 31827481 PMCID: PMC6890844 DOI: 10.3389/fpls.2019.01541] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 11/05/2019] [Indexed: 05/20/2023]
Abstract
One of the extraordinary aspects of plant genome evolution is variation in chromosome number, particularly that among closely related species. This is exemplified by the cotton genus (Gossypium) and its relatives, where most species and genera have a base chromosome number of 13. The two exceptions are sister genera that have n = 12 (the Hawaiian Kokia and the East African and Madagascan Gossypioides). We generated a high-quality genome sequence of Gossypioides kirkii (n = 12) using PacBio, Bionano, and Hi-C technologies, and compared this assembly to genome sequences of Kokia (n = 12) and Gossypium diploids (n = 13). Previous analysis demonstrated that the directionality of their reduced chromosome number was through large structural rearrangements. A series of structural rearrangements were identified comparing the de novo G. kirkii genome sequence to genome sequences of Gossypium, including chromosome fusions and inversions. Genome comparison between G. kirkii and Gossypium suggests that multiple steps are required to generate the extant structural differences.
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Affiliation(s)
- Joshua A. Udall
- Crop Germplasm Research, USDA, College Station, TX, United States
- *Correspondence: Joshua A. Udall, ; Jonathan F. Wendel,
| | - Evan Long
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
| | - Thiruvarangan Ramaraj
- National Center of Genome Resources, Santa Fe, NM, United States
- School of Computing, DePaul University, Chicago, IL, United States
| | | | - Daojun Yuan
- EEOB Department, Iowa State University, Ames, IA, United States
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | | | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, China
| | - Mark A. Arick
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS, United States
| | - Rick E. Masonbrink
- Genome Informatics Facility, Iowa State University, Ames, IA, United States
| | - Daniel G. Peterson
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS, United States
| | - Jonathan F. Wendel
- EEOB Department, Iowa State University, Ames, IA, United States
- *Correspondence: Joshua A. Udall, ; Jonathan F. Wendel,
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13
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Wang M, Tu L, Yuan D, Zhu D, Shen C, Li J, Liu F, Pei L, Wang P, Zhao G, Ye Z, Huang H, Yan F, Ma Y, Zhang L, Liu M, You J, Yang Y, Liu Z, Huang F, Li B, Qiu P, Zhang Q, Zhu L, Jin S, Yang X, Min L, Li G, Chen LL, Zheng H, Lindsey K, Lin Z, Udall JA, Zhang X. Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense. Nat Genet 2018; 51:224-229. [PMID: 30510239 DOI: 10.1038/s41588-018-0282-x] [Citation(s) in RCA: 350] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 10/19/2018] [Indexed: 11/09/2022]
Abstract
Allotetraploid cotton species (Gossypium hirsutum and Gossypium barbadense) have long been cultivated worldwide for natural renewable textile fibers. The draft genome sequences of both species are available but they are highly fragmented and incomplete1-4. Here we report reference-grade genome assemblies and annotations for G. hirsutum accession Texas Marker-1 (TM-1) and G. barbadense accession 3-79 by integrating single-molecule real-time sequencing, BioNano optical mapping and high-throughput chromosome conformation capture techniques. Compared with previous assembled draft genomes1,3, these genome sequences show considerable improvements in contiguity and completeness for regions with high content of repeats such as centromeres. Comparative genomics analyses identify extensive structural variations that probably occurred after polyploidization, highlighted by large paracentric/pericentric inversions in 14 chromosomes. We constructed an introgression line population to introduce favorable chromosome segments from G. barbadense to G. hirsutum, allowing us to identify 13 quantitative trait loci associated with superior fiber quality. These resources will accelerate evolutionary and functional genomic studies in cotton and inform future breeding programs for fiber improvement.
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Affiliation(s)
- Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Daojun Yuan
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.,Plant and Wildlife Science Department, Brigham Young University, Provo, UT, USA
| | - De Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Chao Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jianying Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Fuyan Liu
- Biomarker Technologies Corporation, Beijing, China
| | - Liuling Pei
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Pengcheng Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Guannan Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zhengxiu Ye
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Hui Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Feilin Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Lin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Min Liu
- Biomarker Technologies Corporation, Beijing, China
| | - Jiaqi You
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yicheng Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zhenping Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Fan Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Baoqi Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Ping Qiu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xiyan Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Ling Min
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Guoliang Li
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Ling-Ling Chen
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | | | - Keith Lindsey
- Department of Biosciences, Durham University, Durham, UK.
| | - Zhongxu Lin
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
| | - Joshua A Udall
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA.
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
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14
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Udall JA, Dawe RK. Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping. Plant Cell 2018; 30:7-14. [PMID: 29263086 PMCID: PMC5810561 DOI: 10.1105/tpc.17.00514] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 11/21/2017] [Accepted: 12/20/2017] [Indexed: 05/02/2023]
Abstract
Long-read single-molecule sequencing, Hi-C sequencing, and improved bioinformatic tools are ushering in an era where complete genome assembly will become common for species with few or no classical genetic resources. There are no guidelines for how to proceed in such cases. Ideally, such genomes would be sequenced by two different methods so that one assembly serves as confirmation of the other; however, cost constraints make this approach unlikely. Overreliance on synteny as a means of confirming and ordering contigs will lead to compounded errors. Optical mapping is an accessible and relatively mature technology that can be used for genome assembly validation. We discuss how optical mapping can be used as a validation tool for genome assemblies and how to interpret the results. In addition, we discuss methods for using optical map data to enhance genome assemblies derived from both traditional sequence contigs and Hi-C pseudomolecules.
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Affiliation(s)
- Joshua A Udall
- Plant and Wildlife Science Department, Brigham Young University, Provo, Utah 84602
| | - R Kelly Dawe
- Department of Genetics, University of Georgia, Athens, Georgia 30602
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15
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Osorio CE, Udall JA, Salvo-Garrido H, Maureira-Butler IJ. Development and characterization of InDel markers for Lupinus luteus L. (Fabaceae) and cross-species amplification in other Lupin species. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2017.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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16
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Grover CE, Arick MA, Conover JL, Thrash A, Hu G, Sanders WS, Hsu CY, Naqvi RZ, Farooq M, Li X, Gong L, Mudge J, Ramaraj T, Udall JA, Peterson DG, Wendel JF. Comparative Genomics of an Unusual Biogeographic Disjunction in the Cotton Tribe (Gossypieae) Yields Insights into Genome Downsizing. Genome Biol Evol 2017; 9:3328-3344. [PMID: 29194487 PMCID: PMC5737505 DOI: 10.1093/gbe/evx248] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2017] [Indexed: 12/19/2022] Open
Abstract
Long-distance insular dispersal is associated with divergence and speciation because of founder effects and strong genetic drift. The cotton tribe (Gossypieae) has experienced multiple transoceanic dispersals, generating an aggregate geographic range that encompasses much of the tropics and subtropics worldwide. Two genera in the Gossypieae, Kokia and Gossypioides, exhibit a remarkable geographic disjunction, being restricted to the Hawaiian Islands and Madagascar/East Africa, respectively. We assembled and use de novo genome sequences to address questions regarding the divergence of these two genera from each other and from their sister-group, Gossypium. In addition, we explore processes underlying the genome downsizing that characterizes Kokia and Gossypioides relative to other genera in the tribe. Using 13,000 gene orthologs and synonymous substitution rates, we show that the two disjuncts last shared a common ancestor ∼5 Ma, or half as long ago as their divergence from Gossypium. We report relative stasis in the transposable element fraction. In comparison to Gossypium, there is loss of ∼30% of the gene content in the two disjunct genera and a history of genome-wide accumulation of deletions. In both genera, there is a genome-wide bias toward deletions over insertions, and the number of gene losses exceeds the number of gains by ∼2- to 4-fold. The genomic analyses presented here elucidate genomic consequences of the demographic and biogeographic history of these closest relatives of Gossypium, and enhance their value as phylogenetic outgroups.
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Affiliation(s)
- Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA
| | - Mark A Arick
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS
| | - Justin L Conover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA
| | - Adam Thrash
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS
| | - Guanjing Hu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA
| | - William S Sanders
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS
- Department of Computer Science & Engineering, Mississippi State University, Mississippi State, MS
- The Jackson Laboratory, Connecticut, Farmington, CT
| | - Chuan-Yu Hsu
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS
| | - Rubab Zahra Naqvi
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Punjab, Pakistan
| | - Muhammad Farooq
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Punjab, Pakistan
| | - Xiaochong Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, P.R. China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, P.R. China
| | - Joann Mudge
- National Center for Genome Resources, Santa Fe, New Mexico
| | | | - Joshua A Udall
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA
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17
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Hinze LL, Hulse-Kemp AM, Wilson IW, Zhu QH, Llewellyn DJ, Taylor JM, Spriggs A, Fang DD, Ulloa M, Burke JJ, Giband M, Lacape JM, Van Deynze A, Udall JA, Scheffler JA, Hague S, Wendel JF, Pepper AE, Frelichowski J, Lawley CT, Jones DC, Percy RG, Stelly DM. Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array. BMC Plant Biol 2017; 17:37. [PMID: 28158969 PMCID: PMC5291959 DOI: 10.1186/s12870-017-0981-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 01/23/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Cotton germplasm resources contain beneficial alleles that can be exploited to develop germplasm adapted to emerging environmental and climate conditions. Accessions and lines have traditionally been characterized based on phenotypes, but phenotypic profiles are limited by the cost, time, and space required to make visual observations and measurements. With advances in molecular genetic methods, genotypic profiles are increasingly able to identify differences among accessions due to the larger number of genetic markers that can be measured. A combination of both methods would greatly enhance our ability to characterize germplasm resources. Recent efforts have culminated in the identification of sufficient SNP markers to establish high-throughput genotyping systems, such as the CottonSNP63K array, which enables a researcher to efficiently analyze large numbers of SNP markers and obtain highly repeatable results. In the current investigation, we have utilized the SNP array for analyzing genetic diversity primarily among cotton cultivars, making comparisons to SSR-based phylogenetic analyses, and identifying loci associated with seed nutritional traits. RESULTS The SNP markers distinctly separated G. hirsutum from other Gossypium species and distinguished the wild from cultivated types of G. hirsutum. The markers also efficiently discerned differences among cultivars, which was the primary goal when designing the CottonSNP63K array. Population structure within the genus compared favorably with previous results obtained using SSR markers, and an association study identified loci linked to factors that affect cottonseed protein content. CONCLUSIONS Our results provide a large genome-wide variation data set for primarily cultivated cotton. Thousands of SNPs in representative cotton genotypes provide an opportunity to finely discriminate among cultivated cotton from around the world. The SNPs will be relevant as dense markers of genome variation for association mapping approaches aimed at correlating molecular polymorphisms with variation in phenotypic traits, as well as for molecular breeding approaches in cotton.
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Affiliation(s)
- Lori L. Hinze
- USDA-ARS, Crop Germplasm Research Unit, College Station, TX 77845 USA
| | - Amanda M. Hulse-Kemp
- Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, CA 95616 USA
| | - Iain W. Wilson
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Qian-Hao Zhu
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Danny J. Llewellyn
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Jen M. Taylor
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Andrew Spriggs
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - David D. Fang
- USDA-ARS, Cotton Fiber Bioscience Research Unit, New Orleans, LA 70124 USA
| | - Mauricio Ulloa
- USDA-ARS, Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Research Unit, Lubbock, TX 79415 USA
| | - John J. Burke
- USDA-ARS, Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Research Unit, Lubbock, TX 79415 USA
| | - Marc Giband
- CIRAD, UMR AGAP, Montpellier, F34398 France
- EMBRAPA, Algodão, Nucleo Cerrado, 75.375-000 Santo Antônio de Goias, GO Brazil
| | | | - Allen Van Deynze
- Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, CA 95616 USA
| | - Joshua A. Udall
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602 USA
| | - Jodi A. Scheffler
- USDA-ARS, Jamie Whitten Delta States Research Center, Stoneville, MS 38776 USA
| | - Steve Hague
- Department of Soil & Crop Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011 USA
| | - Alan E. Pepper
- Department of Biology, Texas A&M University, College Station, TX 77843 USA
- Interdisciplinary Department of Genetics, Texas A&M University, College Station, TX 77843 USA
| | | | - Cindy T. Lawley
- Illumina Inc., 499 Illinois Street, San Francisco, CA 94158 USA
| | - Don C. Jones
- Cotton Incorporated, Agricultural Research, Cary, NC 27513 USA
| | - Richard G. Percy
- USDA-ARS, Crop Germplasm Research Unit, College Station, TX 77845 USA
| | - David M. Stelly
- Department of Soil & Crop Sciences, Texas A&M University, College Station, TX 77843 USA
- Interdisciplinary Department of Genetics, Texas A&M University, College Station, TX 77843 USA
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18
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Reddy UK, Nimmakayala P, Abburi VL, Reddy CVCM, Saminathan T, Percy RG, Yu JZ, Frelichowski J, Udall JA, Page JT, Zhang D, Shehzad T, Paterson AH. Genome-wide divergence, haplotype distribution and population demographic histories for Gossypium hirsutum and Gossypium barbadense as revealed by genome-anchored SNPs. Sci Rep 2017; 7:41285. [PMID: 28128280 PMCID: PMC5269598 DOI: 10.1038/srep41285] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 12/19/2016] [Indexed: 11/08/2022] Open
Abstract
Use of 10,129 singleton SNPs of known genomic location in tetraploid cotton provided unique opportunities to characterize genome-wide diversity among 440 Gossypium hirsutum and 219 G. barbadense cultivars and landrace accessions of widespread origin. Using the SNPs distributed genome-wide, we examined genetic diversity, haplotype distribution and linkage disequilibrium patterns in the G. hirsutum and G. barbadense genomes to clarify population demographic history. Diversity and identity-by-state analyses have revealed little sharing of alleles between the two cultivated allotetraploid genomes, with a few exceptions that indicated sporadic gene flow. We found a high number of new alleles, representing increased nucleotide diversity, on chromosomes 1 and 2 in cultivated G. hirsutum as compared with low nucleotide diversity on these chromosomes in landrace G. hirsutum. In contrast, G. barbadense chromosomes showed negative Tajima's D on several chromosomes for both cultivated and landrace types, which indicate that speciation of G. barbadense itself, might have occurred with relatively narrow genetic diversity. The presence of conserved linkage disequilibrium (LD) blocks and haplotypes between G. hirsutum and G. barbadense provides strong evidence for comparable patterns of evolution in their domestication processes. Our study illustrates the potential use of population genetic techniques to identify genomic regions for domestication.
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Affiliation(s)
- Umesh K. Reddy
- Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA
| | - Padma Nimmakayala
- Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA
| | - Venkata Lakshmi Abburi
- Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA
| | - C. V. C. M. Reddy
- Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA
| | - Thangasamy Saminathan
- Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, WV 25112-1000, USA
| | - Richard G. Percy
- USDA–ARS, Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, TX 77845, USA
| | - John Z. Yu
- USDA–ARS, Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, TX 77845, USA
| | - James Frelichowski
- USDA–ARS, Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, TX 77845, USA
| | - Joshua A. Udall
- WIDB, Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602, USA
| | - Justin T. Page
- WIDB, Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602, USA
| | - Dong Zhang
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Room 228, Athens, GA 30605, USA
| | - Tariq Shehzad
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Room 228, Athens, GA 30605, USA
| | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Room 228, Athens, GA 30605, USA
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19
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Hu G, Hovav R, Grover CE, Faigenboim-Doron A, Kadmon N, Page JT, Udall JA, Wendel JF. Evolutionary Conservation and Divergence of Gene Coexpression Networks in Gossypium (Cotton) Seeds. Genome Biol Evol 2016; 8:3765-3783. [PMID: 28062755 PMCID: PMC5585989 DOI: 10.1093/gbe/evw280] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2016] [Indexed: 12/18/2022] Open
Abstract
The cotton genus (Gossypium) provides a superior system for the study of diversification, genome evolution, polyploidization, and human-mediated selection. To gain insight into phenotypic diversification in cotton seeds, we conducted coexpression network analysis of developing seeds from diploid and allopolyploid cotton species and explored network properties. Key network modules and functional associations were identified related to seed oil content and seed weight. We compared species-specific networks to reveal topological changes, including rewired edges and differentially coexpressed genes, associated with speciation, polyploidy, and cotton domestication. Network comparisons among species indicate that topologies are altered in addition to gene expression profiles, indicating that changes in transcriptomic coexpression relationships play a role in the developmental architecture of cotton seed development. The global network topology of allopolyploids, especially for domesticated G. hirsutum, resembles the network of the A-genome diploid more than that of the D-genome parent, despite its D-like phenotype in oil content. Expression modifications associated with allopolyploidy include coexpression level dominance and transgressive expression, suggesting that the transcriptomic architecture in polyploids is to some extent a modular combination of that of its progenitor genomes. Among allopolyploids, intermodular relationships are more preserved between two different wild allopolyploid species than they are between wild and domesticated forms of a cultivated cotton, and regulatory connections of oil synthesis-related pathways are denser and more closely clustered in domesticated vs. wild G. hirsutum. These results demonstrate substantial modification of genic coexpression under domestication. Our work demonstrates how network inference informs our understanding of the transcriptomic architecture of phenotypic variation associated with temporal scales ranging from thousands (domestication) to millions (speciation) of years, and by polyploidy.
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Affiliation(s)
- Guanjing Hu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames
| | - Ran Hovav
- Agricultural Research Organization (Volcani Center), Bet Dagan, Israel
| | - Corrinne E. Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames
| | | | - Noa Kadmon
- Agricultural Research Organization (Volcani Center), Bet Dagan, Israel
| | | | | | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames
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20
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Niederhuth CE, Bewick AJ, Ji L, Alabady MS, Kim KD, Li Q, Rohr NA, Rambani A, Burke JM, Udall JA, Egesi C, Schmutz J, Grimwood J, Jackson SA, Springer NM, Schmitz RJ. Widespread natural variation of DNA methylation within angiosperms. Genome Biol 2016; 17:194. [PMID: 27671052 DOI: 10.1101/045880] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/09/2016] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND DNA methylation is an important feature of plant epigenomes, involved in the formation of heterochromatin and affecting gene expression. Extensive variation of DNA methylation patterns within a species has been uncovered from studies of natural variation. However, the extent to which DNA methylation varies between flowering plant species is still unclear. To understand the variation in genomic patterning of DNA methylation across flowering plant species, we compared single base resolution DNA methylomes of 34 diverse angiosperm species. RESULTS By analyzing whole-genome bisulfite sequencing data in a phylogenetic context, it becomes clear that there is extensive variation throughout angiosperms in gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. The Brassicaceae have reduced CHG methylation levels and also reduced or loss of CG gene body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Furthermore, low levels of CHH methylation are observed in a number of species, especially in clonally propagated species. CONCLUSIONS These results reveal the extent of variation in DNA methylation in angiosperms and show that DNA methylation patterns are broadly a reflection of the evolutionary and life histories of plant species.
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Affiliation(s)
- Chad E Niederhuth
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA
| | - Adam J Bewick
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA
| | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Magdy S Alabady
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Kyung Do Kim
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
| | - Qing Li
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Nicholas A Rohr
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA
| | - Aditi Rambani
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, USA
| | - John M Burke
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Joshua A Udall
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Chiedozie Egesi
- National Root Crops Research Institute (NRCRI), Umudike, Km 8 Ikot Ekpene Road, PMB 7006, Umuahia, 440001, Nigeria
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
| | - Nathan M Springer
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA.
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21
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Niederhuth CE, Bewick AJ, Ji L, Alabady MS, Kim KD, Li Q, Rohr NA, Rambani A, Burke JM, Udall JA, Egesi C, Schmutz J, Grimwood J, Jackson SA, Springer NM, Schmitz RJ. Widespread natural variation of DNA methylation within angiosperms. Genome Biol 2016; 17:194. [PMID: 27671052 PMCID: PMC5037628 DOI: 10.1186/s13059-016-1059-0] [Citation(s) in RCA: 313] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/09/2016] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND DNA methylation is an important feature of plant epigenomes, involved in the formation of heterochromatin and affecting gene expression. Extensive variation of DNA methylation patterns within a species has been uncovered from studies of natural variation. However, the extent to which DNA methylation varies between flowering plant species is still unclear. To understand the variation in genomic patterning of DNA methylation across flowering plant species, we compared single base resolution DNA methylomes of 34 diverse angiosperm species. RESULTS By analyzing whole-genome bisulfite sequencing data in a phylogenetic context, it becomes clear that there is extensive variation throughout angiosperms in gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. The Brassicaceae have reduced CHG methylation levels and also reduced or loss of CG gene body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Furthermore, low levels of CHH methylation are observed in a number of species, especially in clonally propagated species. CONCLUSIONS These results reveal the extent of variation in DNA methylation in angiosperms and show that DNA methylation patterns are broadly a reflection of the evolutionary and life histories of plant species.
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Affiliation(s)
- Chad E Niederhuth
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA
| | - Adam J Bewick
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA
| | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Magdy S Alabady
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Kyung Do Kim
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
| | - Qing Li
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Nicholas A Rohr
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA
| | - Aditi Rambani
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, USA
| | - John M Burke
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Joshua A Udall
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Chiedozie Egesi
- National Root Crops Research Institute (NRCRI), Umudike, Km 8 Ikot Ekpene Road, PMB 7006, Umuahia, 440001, Nigeria
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
| | - Nathan M Springer
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA.
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22
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Chaney L, Sharp AR, Evans CR, Udall JA. Genome Mapping in Plant Comparative Genomics. Trends Plant Sci 2016; 21:770-780. [PMID: 27289181 DOI: 10.1016/j.tplants.2016.05.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 04/27/2016] [Accepted: 05/12/2016] [Indexed: 05/10/2023]
Abstract
Genome mapping produces fingerprints of DNA sequences to construct a physical map of the whole genome. It provides contiguous, long-range information that complements and, in some cases, replaces sequencing data. Recent advances in genome-mapping technology will better allow researchers to detect large (>1kbp) structural variations between plant genomes. Some molecular and informatics complications need to be overcome for this novel technology to achieve its full utility. This technology will be useful for understanding phenotype responses due to DNA rearrangements and will yield insights into genome evolution, particularly in polyploids. In this review, we outline recent advances in genome-mapping technology, including the processes required for data collection and analysis, and applications in plant comparative genomics.
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Affiliation(s)
- Lindsay Chaney
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, UT 84602, USA
| | - Aaron R Sharp
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, UT 84602, USA
| | - Carrie R Evans
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, UT 84602, USA
| | - Joshua A Udall
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, UT 84602, USA.
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23
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Abstract
BACKGROUND Physical mapping of DNA with restriction enzymes allows for the characterization and assembly of much longer molecules than is feasible with sequencing. However, assemblies of physical map data are sensitive to input parameters, which describe noise inherent in the data collection process. One possible way to determine the parameter values that best describe a dataset is by trial and error. RESULTS Here we present OMWare, a tool that efficiently generated 405 de novo map assemblies of a single datasets collected from the cotton species Gossypium raimondii. The assemblies were generated using various input parameter values, and were completed more efficiently by re-using compatible intermediate results. These assemblies were assayed for contiguity, internal consistency, and accuracy. CONCLUSIONS Resulting assemblies had variable qualities. Although highly accurate assemblies were found, contiguity and internal consistency metrics were poor predictors of accuracy.
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Affiliation(s)
- Aaron R Sharp
- College of Life Sciences, Brigham Young University, Provo, UT, 84602-2400, USA.
| | - Joshua A Udall
- College of Life Sciences, Brigham Young University, Provo, UT, 84602-2400, USA
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24
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Renny-Byfield S, Page JT, Udall JA, Sanders WS, Peterson DG, Arick MA, Grover CE, Wendel JF. Independent Domestication of Two Old World Cotton Species. Genome Biol Evol 2016; 8:1940-7. [PMID: 27289095 PMCID: PMC4943200 DOI: 10.1093/gbe/evw129] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2016] [Indexed: 11/16/2022] Open
Abstract
Domesticated cotton species provide raw material for the majority of the world's textile industry. Two independent domestication events have been identified in allopolyploid cotton, one in Upland cotton (Gossypium hirsutum L.) and the other to Egyptian cotton (Gossypium barbadense L.). However, two diploid cotton species, Gossypium arboreum L. and Gossypium herbaceum L., have been cultivated for several millennia, but their status as independent domesticates has long been in question. Using genome resequencing data, we estimated the global abundance of various repetitive DNAs. We demonstrate that, despite negligible divergence in genome size, the two domesticated diploid cotton species contain different, but compensatory, repeat content and have thus experienced cryptic alterations in repeat abundance despite equivalence in genome size. Evidence of independent origin is bolstered by estimates of divergence times based on molecular evolutionary analysis of f7,000 orthologous genes, for which synonymous substitution rates suggest that G. arboreum and G. herbaceum last shared a common ancestor approximately 0.4-2.5 Ma. These data are incompatible with a shared domestication history during the emergence of agriculture and lead to the conclusion that G. arboreum and G. herbaceum were each domesticated independently.
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Affiliation(s)
- Simon Renny-Byfield
- Department of Ecology, Evolution and Organismal Biology, Iowa State University DuPont Pioneer, Johnston, IA
| | - Justin T Page
- Plant and Wildlife Science Department, Brigham Young University
| | - Joshua A Udall
- Plant and Wildlife Science Department, Brigham Young University
| | - William S Sanders
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University Department of Computer Science and Engineering, Mississippi State University
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University Department of Plant and Soil Sciences, Mississippi State University
| | - Mark A Arick
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University
| | - Corrinne E Grover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University
| | - Jonathan F Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University
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25
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Page JT, Liechty ZS, Alexander RH, Clemons K, Hulse-Kemp AM, Ashrafi H, Van Deynze A, Stelly DM, Udall JA. DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton. PLoS Genet 2016; 12:e1006012. [PMID: 27168520 PMCID: PMC4864293 DOI: 10.1371/journal.pgen.1006012] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/06/2016] [Indexed: 01/08/2023] Open
Abstract
Allotetraploid cotton species are a vital source of spinnable fiber for textiles. The polyploid nature of the cotton genome raises many evolutionary questions as to the relationships between duplicated genomes. We describe the evolution of the cotton genome (SNPs and structural variants) with the greatly improved resolution of 34 deeply re-sequenced genomes. We also explore the evolution of homoeologous regions in the AT- and DT-genomes and especially the phenomenon of conversion between genomes. We did not find any compelling evidence for homoeologous conversion between genomes. These findings are very different from other recent reports of frequent conversion events between genomes. We also identified several distinct regions of the genome that have been introgressed between G. hirsutum and G. barbadense, which presumably resulted from breeding efforts targeting associated beneficial alleles. Finally, the genotypic data resulting from this study provides access to a wealth of diversity sorely needed in the narrow germplasm of cotton cultivars.
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Affiliation(s)
- Justin T. Page
- Biology Department, Brigham Young University, Provo, Utah, United States of America
| | - Zach S. Liechty
- Plant and Wildlife Science Department, Brigham Young University, Provo, Utah, United States of America
| | - Rich H. Alexander
- Plant and Wildlife Science Department, Brigham Young University, Provo, Utah, United States of America
| | - Kimberly Clemons
- Plant and Wildlife Science Department, Brigham Young University, Provo, Utah, United States of America
| | - Amanda M. Hulse-Kemp
- Department of Soil & Crop Sciences, Texas A&M University and Texas A&M AgriLife Research, College Station, Texas, United States of America
| | - Hamid Ashrafi
- Seed Biotechnology Center, University of California-Davis, Davis, California, United States of America
| | - Allen Van Deynze
- Seed Biotechnology Center, University of California-Davis, Davis, California, United States of America
| | - David M. Stelly
- Department of Soil & Crop Sciences, Texas A&M University and Texas A&M AgriLife Research, College Station, Texas, United States of America
| | - Joshua A. Udall
- Plant and Wildlife Science Department, Brigham Young University, Provo, Utah, United States of America
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26
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Clouse JW, Adhikary D, Page JT, Ramaraj T, Deyholos MK, Udall JA, Fairbanks DJ, Jellen EN, Maughan PJ. The Amaranth Genome: Genome, Transcriptome, and Physical Map Assembly. Plant Genome 2016; 9. [PMID: 27898770 DOI: 10.3835/plantgenome2015.07.0062] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Amaranth ( L.) is an emerging pseudocereal native to the New World that has garnered increased attention in recent years because of its nutritional quality, in particular its seed protein and more specifically its high levels of the essential amino acid lysine. It belongs to the Amaranthaceae family, is an ancient paleopolyploid that shows disomic inheritance (2 = 32), and has an estimated genome size of 466 Mb. Here we present a high-quality draft genome sequence of the grain amaranth. The genome assembly consisted of 377 Mb in 3518 scaffolds with an N of 371 kb. Repetitive element analysis predicted that 48% of the genome is comprised of repeat sequences, of which -like elements were the most commonly classified retrotransposon. A de novo transcriptome consisting of 66,370 contigs was assembled from eight different amaranth tissue and abiotic stress libraries. Annotation of the genome identified 23,059 protein-coding genes. Seven grain amaranths (, , and ) and their putative progenitor () were resequenced. A single nucleotide polymorphism (SNP) phylogeny supported the classification of as the progenitor species of the grain amaranths. Lastly, we generated a de novo physical map for using the BioNano Genomics' Genome Mapping platform. The physical map spanned 340 Mb and a hybrid assembly using the BioNano physical maps nearly doubled the N of the assembly to 697 kb. Moreover, we analyzed synteny between amaranth and sugar beet ( L.) and estimated, using analysis, the age of the most recent polyploidization event in amaranth.
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Abstract
We report the sequencing and assembly of three transcriptomes from Big (Artemisia tridentata ssp. wyomingensis and A. tridentata ssp. tridentata) and Low (A. arbuscula ssp. arbuscula) sagebrush. The sequence reads are available in the Sequence Read Archive of NCBI. We demonstrate the utilities of these transcriptomes for gene discovery and phylogenomic analysis. An assembly of 61,883 transcripts followed by transcript identification by the program TRAPID revealed 16 transcripts directly related to terpene synthases, proteins critical to the production of multiple secondary metabolites in sagebrush. A putative terpene synthase was identified in two of our sagebrush samples. Using paralogs with synonymous mutations we reconstructed an evolutionary time line of ancient genome duplications. By applying a constant mutation rate to the data we estimate that these three ancient duplications occurred about 18, 34 and 60 million years ago. These transcriptomes offer a foundation for future studies of sagebrush, including inferences in chemical defense and the identification of species and subspecies of sagebrush for restoration and preservation of the threatened sage-grouse.
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Affiliation(s)
- Mark D. Huynh
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, United States of America
| | - Justin T. Page
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, United States of America
| | - Bryce A. Richardson
- Rocky Mountain Research Station, USDA Forest Service, Provo, UT, 84606, United States of America
| | - Joshua A. Udall
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, United States of America
- * E-mail:
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Abstract
Genome read categorization determines the genome of origin for sequence reads from an allopolyploid organism. Different techniques have been used to perform read categorization, mostly based on homoeo-SNPs identified between extant diploid relatives of allopolyploids. We present a novel technique for read categorization implemented by the software PolyDog. We demonstrate its accuracy and improved categorization relative to other methods. We discuss the situations in which one method or another might be most appropriate.
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Hulse-Kemp AM, Lemm J, Plieske J, Ashrafi H, Buyyarapu R, Fang DD, Frelichowski J, Giband M, Hague S, Hinze LL, Kochan KJ, Riggs PK, Scheffler JA, Udall JA, Ulloa M, Wang SS, Zhu QH, Bag SK, Bhardwaj A, Burke JJ, Byers RL, Claverie M, Gore MA, Harker DB, Islam MS, Jenkins JN, Jones DC, Lacape JM, Llewellyn DJ, Percy RG, Pepper AE, Poland JA, Mohan Rai K, Sawant SV, Singh SK, Spriggs A, Taylor JM, Wang F, Yourstone SM, Zheng X, Lawley CT, Ganal MW, Van Deynze A, Wilson IW, Stelly DM. Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp. G3 (Bethesda) 2015; 5:1187-209. [PMID: 25908569 PMCID: PMC4478548 DOI: 10.1534/g3.115.018416] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/11/2015] [Indexed: 11/18/2022]
Abstract
High-throughput genotyping arrays provide a standardized resource for plant breeding communities that are useful for a breadth of applications including high-density genetic mapping, genome-wide association studies (GWAS), genomic selection (GS), complex trait dissection, and studying patterns of genomic diversity among cultivars and wild accessions. We have developed the CottonSNP63K, an Illumina Infinium array containing assays for 45,104 putative intraspecific single nucleotide polymorphism (SNP) markers for use within the cultivated cotton species Gossypium hirsutum L. and 17,954 putative interspecific SNP markers for use with crosses of other cotton species with G. hirsutum. The SNPs on the array were developed from 13 different discovery sets that represent a diverse range of G. hirsutum germplasm and five other species: G. barbadense L., G. tomentosum Nuttal × Seemann, G. mustelinum Miers × Watt, G. armourianum Kearny, and G. longicalyx J.B. Hutchinson and Lee. The array was validated with 1,156 samples to generate cluster positions to facilitate automated analysis of 38,822 polymorphic markers. Two high-density genetic maps containing a total of 22,829 SNPs were generated for two F2 mapping populations, one intraspecific and one interspecific, and 3,533 SNP markers were co-occurring in both maps. The produced intraspecific genetic map is the first saturated map that associates into 26 linkage groups corresponding to the number of cotton chromosomes for a cross between two G. hirsutum lines. The linkage maps were shown to have high levels of collinearity to the JGI G. raimondii Ulbrich reference genome sequence. The CottonSNP63K array, cluster file and associated marker sequences constitute a major new resource for the global cotton research community.
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Affiliation(s)
- Amanda M Hulse-Kemp
- Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843 Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843
| | - Jana Lemm
- TraitGenetics GmbH, 06466 Gatersleben, Germany
| | | | - Hamid Ashrafi
- Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, California 95616
| | - Ramesh Buyyarapu
- Dow AgroSciences, Trait Genetics and Technologies, Indianapolis, Indiana 46268
| | - David D Fang
- USDA-ARS-SRRC, Cotton Fiber Bioscience Research Unit, New Orleans, Louisiana 70124
| | - James Frelichowski
- USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845
| | - Marc Giband
- CIRAD, UMR AGAP, Montpellier, F34398, France EMBRAPA, Algodão, Nucleo Cerrado, 75.375-000 Santo Antônio de Goias, GO, Brazil
| | - Steve Hague
- Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843
| | - Lori L Hinze
- USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845
| | - Kelli J Kochan
- Department of Animal Science, Texas A&M University, College Station, Texas 77843
| | - Penny K Riggs
- Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843 Department of Animal Science, Texas A&M University, College Station, Texas 77843
| | - Jodi A Scheffler
- USDA-ARS, Jamie Whitten Delta States Research Center, Stoneville, Mississippi 38776
| | - Joshua A Udall
- Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602
| | - Mauricio Ulloa
- USDA-ARS, PA, Plant Stress and Germplasm Development Research Unit, Lubbock, Texas 79415
| | - Shirley S Wang
- USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845
| | - Qian-Hao Zhu
- CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia
| | - Sumit K Bag
- CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India
| | - Archana Bhardwaj
- CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India
| | - John J Burke
- USDA-ARS, PA, Plant Stress and Germplasm Development Research Unit, Lubbock, Texas 79415
| | - Robert L Byers
- Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602
| | | | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
| | - David B Harker
- Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602
| | - Md S Islam
- USDA-ARS-SRRC, Cotton Fiber Bioscience Research Unit, New Orleans, Louisiana 70124
| | - Johnie N Jenkins
- USDA-ARS, Genetics and Precision Agriculture Research, Mississippi State, Mississippi 39762
| | - Don C Jones
- Cotton Incorporated, Agricultural Research, Cary, North Carolina 27513
| | | | - Danny J Llewellyn
- CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia
| | - Richard G Percy
- USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845
| | - Alan E Pepper
- Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843 Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Jesse A Poland
- Wheat Genetics Resource Center, Department of Plant Pathology and Department of Agronomy, Kansas State University, Manhattan, Kansas 66506
| | - Krishan Mohan Rai
- CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India
| | - Samir V Sawant
- CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India
| | - Sunil Kumar Singh
- CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India
| | - Andrew Spriggs
- CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia
| | - Jen M Taylor
- CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia
| | - Fei Wang
- Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843
| | - Scott M Yourstone
- Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602
| | - Xiuting Zheng
- Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843
| | | | | | - Allen Van Deynze
- Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, California 95616
| | - Iain W Wilson
- CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia
| | - David M Stelly
- Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843 Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843
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Abstract
Background Massive computational power is needed to analyze the genomic data produced by next-generation sequencing, but extensive computational experience and specific knowledge of algorithms should not be necessary to run genomic analyses or interpret their results. Findings We present BamBam, a package of tools for genome sequence analysis. BamBam contains tools that facilitate summarizing data from BAM alignment files and identifying features such as SNPs, indels, and haplotypes represented in those alignments. Conclusions BamBam provides a powerful and convenient framework to analyze genome sequence data contained in BAM files. Electronic supplementary material The online version of this article (doi:10.1186/1756-0500-7-829) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Justin T Page
- Department of Biology, Brigham Young University, Provo, UT 84602, USA.
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Abstract
BACKGROUND Massive computational power is needed to analyze the genomic data produced by next-generation sequencing, but extensive computational experience and specific knowledge of algorithms should not be necessary to run genomic analyses or interpret their results. FINDINGS We present BamBam, a package of tools for genome sequence analysis. BamBam contains tools that facilitate summarizing data from BAM alignment files and identifying features such as SNPs, indels, and haplotypes represented in those alignments. CONCLUSIONS BamBam provides a powerful and convenient framework to analyze genome sequence data contained in BAM files.
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Affiliation(s)
- Justin T Page
- Department of Biology, Brigham Young University, Provo, UT 84602, USA.
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Yurchenko OP, Park S, Ilut DC, Inmon JJ, Millhollon JC, Liechty Z, Page JT, Jenks MA, Chapman KD, Udall JA, Gore MA, Dyer JM. Genome-wide analysis of the omega-3 fatty acid desaturase gene family in Gossypium. BMC Plant Biol 2014; 14:312. [PMID: 25403726 PMCID: PMC4245742 DOI: 10.1186/s12870-014-0312-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 10/28/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND The majority of commercial cotton varieties planted worldwide are derived from Gossypium hirsutum, which is a naturally occurring allotetraploid produced by interspecific hybridization of A- and D-genome diploid progenitor species. While most cotton species are adapted to warm, semi-arid tropical and subtropical regions, and thus perform well in these geographical areas, cotton seedlings are sensitive to cold temperature, which can significantly reduce crop yields. One of the common biochemical responses of plants to cold temperatures is an increase in omega-3 fatty acids, which protects cellular function by maintaining membrane integrity. The purpose of our study was to identify and characterize the omega-3 fatty acid desaturase (FAD) gene family in G. hirsutum, with an emphasis on identifying omega-3 FADs involved in cold temperature adaptation. RESULTS Eleven omega-3 FAD genes were identified in G. hirsutum, and characterization of the gene family in extant A and D diploid species (G. herbaceum and G. raimondii, respectively) allowed for unambiguous genome assignment of all homoeologs in tetraploid G. hirsutum. The omega-3 FAD family of cotton includes five distinct genes, two of which encode endoplasmic reticulum-type enzymes (FAD3-1 and FAD3-2) and three that encode chloroplast-type enzymes (FAD7/8-1, FAD7/8-2, and FAD7/8-3). The FAD3-2 gene was duplicated in the A genome progenitor species after the evolutionary split from the D progenitor, but before the interspecific hybridization event that gave rise to modern tetraploid cotton. RNA-seq analysis revealed conserved, gene-specific expression patterns in various organs and cell types and semi-quantitative RT-PCR further revealed that FAD7/8-1 was specifically induced during cold temperature treatment of G. hirsutum seedlings. CONCLUSIONS The omega-3 FAD gene family in cotton was characterized at the genome-wide level in three species, showing relatively ancient establishment of the gene family prior to the split of A and D diploid progenitor species. The FAD genes are differentially expressed in various organs and cell types, including fiber, and expression of the FAD7/8-1 gene was induced by cold temperature. Collectively, these data define the genetic and functional genomic properties of this important gene family in cotton and provide a foundation for future efforts to improve cotton abiotic stress tolerance through molecular breeding approaches.
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Affiliation(s)
- Olga P Yurchenko
- />USDA-ARS, US Arid-Land Agricultural Research Center, 21881 North Cardon Lane, Maricopa, AZ 85138 USA
| | - Sunjung Park
- />USDA-ARS, US Arid-Land Agricultural Research Center, 21881 North Cardon Lane, Maricopa, AZ 85138 USA
- />Department of Biological Sciences, Center for Plant Lipid Research, University of North Texas, Denton, TX 76203 USA
| | - Daniel C Ilut
- />Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853 USA
| | - Jay J Inmon
- />USDA-ARS, US Arid-Land Agricultural Research Center, 21881 North Cardon Lane, Maricopa, AZ 85138 USA
| | - Jon C Millhollon
- />USDA-ARS, US Arid-Land Agricultural Research Center, 21881 North Cardon Lane, Maricopa, AZ 85138 USA
| | - Zach Liechty
- />Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602 USA
| | - Justin T Page
- />Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602 USA
| | - Matthew A Jenks
- />Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 2650 USA
| | - Kent D Chapman
- />Department of Biological Sciences, Center for Plant Lipid Research, University of North Texas, Denton, TX 76203 USA
| | - Joshua A Udall
- />Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602 USA
| | - Michael A Gore
- />Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853 USA
| | - John M Dyer
- />USDA-ARS, US Arid-Land Agricultural Research Center, 21881 North Cardon Lane, Maricopa, AZ 85138 USA
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Yurchenko OP, Park S, Ilut DC, Inmon JJ, Millhollon JC, Liechty Z, Page JT, Jenks MA, Chapman KD, Udall JA, Gore MA, Dyer JM. Genome-wide analysis of the omega-3 fatty acid desaturase gene family in Gossypium. BMC Plant Biol 2014; 14:312. [PMID: 25403726 DOI: 10.1186/s12870-014-0312-315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 10/28/2014] [Indexed: 05/24/2023]
Abstract
BACKGROUND The majority of commercial cotton varieties planted worldwide are derived from Gossypium hirsutum, which is a naturally occurring allotetraploid produced by interspecific hybridization of A- and D-genome diploid progenitor species. While most cotton species are adapted to warm, semi-arid tropical and subtropical regions, and thus perform well in these geographical areas, cotton seedlings are sensitive to cold temperature, which can significantly reduce crop yields. One of the common biochemical responses of plants to cold temperatures is an increase in omega-3 fatty acids, which protects cellular function by maintaining membrane integrity. The purpose of our study was to identify and characterize the omega-3 fatty acid desaturase (FAD) gene family in G. hirsutum, with an emphasis on identifying omega-3 FADs involved in cold temperature adaptation. RESULTS Eleven omega-3 FAD genes were identified in G. hirsutum, and characterization of the gene family in extant A and D diploid species (G. herbaceum and G. raimondii, respectively) allowed for unambiguous genome assignment of all homoeologs in tetraploid G. hirsutum. The omega-3 FAD family of cotton includes five distinct genes, two of which encode endoplasmic reticulum-type enzymes (FAD3-1 and FAD3-2) and three that encode chloroplast-type enzymes (FAD7/8-1, FAD7/8-2, and FAD7/8-3). The FAD3-2 gene was duplicated in the A genome progenitor species after the evolutionary split from the D progenitor, but before the interspecific hybridization event that gave rise to modern tetraploid cotton. RNA-seq analysis revealed conserved, gene-specific expression patterns in various organs and cell types and semi-quantitative RT-PCR further revealed that FAD7/8-1 was specifically induced during cold temperature treatment of G. hirsutum seedlings. CONCLUSIONS The omega-3 FAD gene family in cotton was characterized at the genome-wide level in three species, showing relatively ancient establishment of the gene family prior to the split of A and D diploid progenitor species. The FAD genes are differentially expressed in various organs and cell types, including fiber, and expression of the FAD7/8-1 gene was induced by cold temperature. Collectively, these data define the genetic and functional genomic properties of this important gene family in cotton and provide a foundation for future efforts to improve cotton abiotic stress tolerance through molecular breeding approaches.
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Hulse-Kemp AM, Ashrafi H, Zheng X, Wang F, Hoegenauer KA, Maeda ABV, Yang SS, Stoffel K, Matvienko M, Clemons K, Udall JA, Van Deynze A, Jones DC, Stelly DM. Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts. BMC Genomics 2014. [PMID: 25359292 DOI: 10.1186/1471‐2164‐15‐945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cotton (Gossypium spp.) is the largest producer of natural fibers for textile and is an important crop worldwide. Crop production is comprised primarily of G. hirsutum L., an allotetraploid. However, elite cultivars express very small amounts of variation due to the species monophyletic origin, domestication and further bottlenecks due to selection. Conversely, wild cotton species harbor extensive genetic diversity of prospective utility to improve many beneficial agronomic traits, fiber characteristics, and resistance to disease and drought. Introgression of traits from wild species can provide a natural way to incorporate advantageous traits through breeding to generate higher-producing cotton cultivars and more sustainable production systems. Interspecific introgression efforts by conventional methods are very time-consuming and costly, but can be expedited using marker-assisted selection. RESULTS Using transcriptome sequencing we have developed the first gene-associated single nucleotide polymorphism (SNP) markers for wild cotton species G. tomentosum, G. mustelinum, G. armourianum and G. longicalyx. Markers were also developed for a secondary cultivated species G. barbadense cv. 3-79. A total of 62,832 non-redundant SNP markers were developed from the five wild species which can be utilized for interspecific germplasm introgression into cultivated G. hirsutum and are directly associated with genes. Over 500 of the G. barbadense markers have been validated by whole-genome radiation hybrid mapping. Overall 1,060 SNPs from the five different species have been screened and shown to produce acceptable genotyping assays. CONCLUSIONS This large set of 62,832 SNPs relative to cultivated G. hirsutum will allow for the first high-density mapping of genes from five wild species that affect traits of interest, including beneficial agronomic and fiber characteristics. Upon mapping, the markers can be utilized for marker-assisted introgression of new germplasm into cultivated cotton and in subsequent breeding of agronomically adapted types, including cultivar development.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - David M Stelly
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, USA.
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Hulse-Kemp AM, Ashrafi H, Zheng X, Wang F, Hoegenauer KA, Maeda ABV, Yang SS, Stoffel K, Matvienko M, Clemons K, Udall JA, Van Deynze A, Jones DC, Stelly DM. Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts. BMC Genomics 2014; 15:945. [PMID: 25359292 PMCID: PMC4298081 DOI: 10.1186/1471-2164-15-945] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 10/03/2014] [Indexed: 11/18/2022] Open
Abstract
Background Cotton (Gossypium spp.) is the largest producer of natural fibers for textile and is an important crop worldwide. Crop production is comprised primarily of G. hirsutum L., an allotetraploid. However, elite cultivars express very small amounts of variation due to the species monophyletic origin, domestication and further bottlenecks due to selection. Conversely, wild cotton species harbor extensive genetic diversity of prospective utility to improve many beneficial agronomic traits, fiber characteristics, and resistance to disease and drought. Introgression of traits from wild species can provide a natural way to incorporate advantageous traits through breeding to generate higher-producing cotton cultivars and more sustainable production systems. Interspecific introgression efforts by conventional methods are very time-consuming and costly, but can be expedited using marker-assisted selection. Results Using transcriptome sequencing we have developed the first gene-associated single nucleotide polymorphism (SNP) markers for wild cotton species G. tomentosum, G. mustelinum, G. armourianum and G. longicalyx. Markers were also developed for a secondary cultivated species G. barbadense cv. 3–79. A total of 62,832 non-redundant SNP markers were developed from the five wild species which can be utilized for interspecific germplasm introgression into cultivated G. hirsutum and are directly associated with genes. Over 500 of the G. barbadense markers have been validated by whole-genome radiation hybrid mapping. Overall 1,060 SNPs from the five different species have been screened and shown to produce acceptable genotyping assays. Conclusions This large set of 62,832 SNPs relative to cultivated G. hirsutum will allow for the first high-density mapping of genes from five wild species that affect traits of interest, including beneficial agronomic and fiber characteristics. Upon mapping, the markers can be utilized for marker-assisted introgression of new germplasm into cultivated cotton and in subsequent breeding of agronomically adapted types, including cultivar development. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-945) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - David M Stelly
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, USA.
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Guan X, Nah G, Song Q, Udall JA, Stelly DM, Chen ZJ. Transcriptome analysis of extant cotton progenitors revealed tetraploidization and identified genome-specific single nucleotide polymorphism in diploid and allotetraploid cotton. BMC Res Notes 2014; 7:493. [PMID: 25099166 PMCID: PMC4267057 DOI: 10.1186/1756-0500-7-493] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 07/29/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The most widely cultivated cotton (Gossypium hirsutum L., AD-genome) is derived from tetraploidization between A- and D-genome species. G. arboreum L. (A-genome) and G. raimondii Ulbr. (D-genome) are two of closely-related extant progenitors. Gene expression studies in allotetraploid cotton are complicated by the homoeologous loci of A- and D-genome origins. To develop genomic resources for gene expression and cotton breeding, we sequenced and assembled expressed sequence tags (ESTs) derived from G. arboreum and G. raimondii. RESULTS Roche/454 FLX sequencing technology was employed to sequence normalized cDNA libraries prepared from leaves, roots, bolls, ovules, and fibers in G. arboreum and G. raimondii, respectively. Sequencing reads from two independent libraries in each species were combined to assemble high-quality EST contigs. The combined sequencing reads included 1,699,776 from A-genome and 1,464,815 from D-genome, which were clustered into 89,588 contigs in the A-genome and 65,542 contigs in the D-genome. These contigs represented ~80% of EST collections in Cotton Gene Index 11 (CGI11, March 2011). Compared to the D-genome transcript database, 27,537 and 10,452 contigs were unique transcripts in A and D genomes, respectively. Further analysis using self-blastn reduced the unigene contig number by 52% in A-genome and 57% in D-genome, suggesting that 50% or more of contigs are paralogs or isoforms within each species. The majority of EST contigs (73-81%) were conserved between A- and D-genomes, whereas 27% and 19% contigs were specific to A- and D-genomes, respectively. Using these ESTs, we generated a total of 75,754 genome-specific single nucleotide polymorphism (SNP) (gSNPs or GNPs) or homoeologous-specific SNPs (hSNPs) of 10,885 contigs or genes between A and D genomes, indicating a possibility of separating allelic expression for those genes in allotetraploid cotton. CONCLUSIONS Expressed genes are highly redundant within each diploid progenitor and between A and D progenitor species, suggesting that diploid progenitors in cotton are likely ancient tetraploids. This large set of A- and D-genome ESTs and GNPs will be valuable resources for genome annotation, gene expression, and crop improvement in allotetraploid cotton.
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Affiliation(s)
| | | | | | | | | | - Z Jeffrey Chen
- Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas 78712, USA.
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Naoumkina M, Thyssen G, Fang DD, Hinchliffe DJ, Florane C, Yeater KM, Page JT, Udall JA. The Li2 mutation results in reduced subgenome expression bias in elongating fibers of allotetraploid cotton (Gossypium hirsutum L.). PLoS One 2014; 9:e90830. [PMID: 24598808 PMCID: PMC3944810 DOI: 10.1371/journal.pone.0090830] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 02/04/2014] [Indexed: 12/18/2022] Open
Abstract
Next generation sequencing (RNA-seq) technology was used to evaluate the effects of the Ligon lintless-2 (Li2) short fiber mutation on transcriptomes of both subgenomes of allotetraploid cotton (Gossypium hirsutum L.) as compared to its near-isogenic wild type. Sequencing was performed on 4 libraries from developing fibers of Li2 mutant and wild type near-isogenic lines at the peak of elongation followed by mapping and PolyCat categorization of RNA-seq data to the reference D5 genome (G. raimondii) for homeologous gene expression analysis. The majority of homeologous genes, 83.6% according to the reference genome, were expressed during fiber elongation. Our results revealed: 1) approximately two times more genes were induced in the AT subgenome comparing to the DT subgenome in wild type and mutant fiber; 2) the subgenome expression bias was significantly reduced in the Li2 fiber transcriptome; 3) Li2 had a significantly greater effect on the DT than on the AT subgenome. Transcriptional regulators and cell wall homeologous genes significantly affected by the Li2 mutation were reviewed in detail. This is the first report to explore the effects of a single mutation on homeologous gene expression in allotetraploid cotton. These results provide deeper insights into the evolution of allotetraploid cotton gene expression and cotton fiber development.
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Affiliation(s)
- Marina Naoumkina
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, Louisiana, United States of America
- * E-mail:
| | - Gregory Thyssen
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, Louisiana, United States of America
| | - David D. Fang
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, Louisiana, United States of America
| | - Doug J. Hinchliffe
- Cotton Chemistry & Utilization Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, Louisiana, United States of America
| | - Christopher Florane
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, Louisiana, United States of America
| | - Kathleen M. Yeater
- USDA-ARS-Southern Plains Area, College Station, Texas, United States of America
| | - Justin T. Page
- Plant and Wildlife Science Department, Brigham Young University, Provo, Utah, United States of America
| | - Joshua A. Udall
- Plant and Wildlife Science Department, Brigham Young University, Provo, Utah, United States of America
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Renny-Byfield S, Gallagher JP, Grover CE, Szadkowski E, Page JT, Udall JA, Wang X, Paterson AH, Wendel JF. Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence. Genome Biol Evol 2014; 6:559-71. [PMID: 24558256 PMCID: PMC3971588 DOI: 10.1093/gbe/evu037] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2014] [Indexed: 12/25/2022] Open
Abstract
Whole genome duplication (WGD) is widespread in flowering plants and is a driving force in angiosperm diversification. The redundancy introduced by WGD allows the evolution of novel gene interactions and functions, although the patterns and processes of diversification are poorly understood. We identified ∼ 2,000 pairs of paralogous genes in Gossypium raimondii (cotton) resulting from an approximately 60 My old 5- to 6-fold ploidy increase. Gene expression analyses revealed that, in G. raimondii, 99.4% of the gene pairs exhibit differential expression in at least one of the three tissues (petal, leaf, and seed), with 93% to 94% exhibiting differential expression on a per-tissue basis. For 1,666 (85%) pairs, differential expression was observed in all tissues. These observations were mirrored in a time series of G. raimondii seed, and separately in leaf, petal, and seed of G. arboreum, indicating expression level diversification before species divergence. A generalized linear model revealed 92.4% of the paralog pairs exhibited expression divergence, with most exhibiting significant gene and tissue interactions indicating complementary expression patterns in different tissues. These data indicate massive, near-complete expression level neo- and/or subfunctionalization among ancient gene duplicates, suggesting these processes are essential in their maintenance over ∼ 60 Ma.
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Affiliation(s)
- Simon Renny-Byfield
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa
| | - Joseph P. Gallagher
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa
| | - Corrinne E. Grover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa
| | - Emmanuel Szadkowski
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa
| | - Justin T. Page
- Plant and Wildlife Science Department, Brigham Young University, Provo, Utah
| | - Joshua A. Udall
- Plant and Wildlife Science Department, Brigham Young University, Provo, Utah
| | - Xiyin Wang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia
| | | | - Jonathan F. Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa
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Tyagi P, Gore MA, Bowman DT, Campbell BT, Udall JA, Kuraparthy V. Genetic diversity and population structure in the US Upland cotton (Gossypium hirsutum L.). Theor Appl Genet 2014; 127:283-95. [PMID: 24170350 DOI: 10.1007/s00122-013-2217-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Accepted: 10/14/2013] [Indexed: 05/09/2023]
Abstract
Genetic diversity and population structure in the US Upland cotton was established and core sets of allelic richness were identified for developing association mapping populations in cotton. Elite plant breeding programs could likely benefit from the unexploited standing genetic variation of obsolete cultivars without the yield drag typically associated with wild accessions. A set of 381 accessions comprising 378 Upland (Gossypium hirsutum L.) and 3 G. barbadense L. accessions of the United States cotton belt were genotyped using 120 genome-wide SSR markers to establish the genetic diversity and population structure in tetraploid cotton. These accessions represent more than 100 years of Upland cotton breeding in the United States. Genetic diversity analysis identified a total of 546 alleles across 141 marker loci. Twenty-two percent of the alleles in Upland accessions were unique, specific to a single accession. Population structure analysis revealed extensive admixture and identified five subgroups corresponding to Southeastern, Midsouth, Southwest, and Western zones of cotton growing areas in the United States, with the three accessions of G. barbadense forming a separate cluster. Phylogenetic analysis supported the subgroups identified by STRUCTURE. Average genetic distance between G. hirsutum accessions was 0.195 indicating low levels of genetic diversity in Upland cotton germplasm pool. The results from both population structure and phylogenetic analysis were in agreement with pedigree information, although there were a few exceptions. Further, core sets of different sizes representing different levels of allelic richness in Upland cotton were identified. Establishment of genetic diversity, population structure, and identification of core sets from this study could be useful for genetic and genomic analysis and systematic utilization of the standing genetic variation in Upland cotton.
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Affiliation(s)
- Priyanka Tyagi
- Crop Science Department, North Carolina State University, Raleigh, NC, 27695, USA
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40
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Soliai MM, Meyer SE, Udall JA, Elzinga DE, Hermansen RA, Bodily PM, Hart AA, Coleman CE. De novo genome assembly of the fungal plant pathogen Pyrenophora semeniperda. PLoS One 2014; 9:e87045. [PMID: 24475219 PMCID: PMC3903604 DOI: 10.1371/journal.pone.0087045] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 12/18/2013] [Indexed: 12/31/2022] Open
Abstract
Pyrenophora semeniperda (anamorph Drechslera campulata) is a necrotrophic fungal seed pathogen that has a wide host range within the Poaceae. One of its hosts is cheatgrass (Bromus tectorum), a species exotic to the United States that has invaded natural ecosystems of the Intermountain West. As a natural pathogen of cheatgrass, P. semeniperda has potential as a biocontrol agent due to its effectiveness at killing seeds within the seed bank; however, few genetic resources exist for the fungus. Here, the genome of P. semeniperda isolate assembled from sequence reads of 454 pyrosequencing is presented. The total assembly is 32.5 Mb and includes 11,453 gene models encoding putative proteins larger than 24 amino acids. The models represent a variety of putative genes that are involved in pathogenic pathways typically found in necrotrophic fungi. In addition, extensive rearrangements, including inter- and intrachromosomal rearrangements, were found when the P. semeniperda genome was compared to P. tritici-repentis, a related fungal species.
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Affiliation(s)
- Marcus M. Soliai
- Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, United States of America
| | - Susan E. Meyer
- USDA Forest Service, Rocky Mountain Research Station, Shrub Sciences Laboratory, Provo, Utah, United States of America
| | - Joshua A. Udall
- Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, United States of America
| | - David E. Elzinga
- Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, United States of America
| | - Russell A. Hermansen
- Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, United States of America
| | - Paul M. Bodily
- Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, United States of America
| | - Aaron A. Hart
- Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, United States of America
| | - Craig E. Coleman
- Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, United States of America
- * E-mail:
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41
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Abstract
Background Genes duplicated by polyploidy (homoeologs) may be differentially expressed in plant tissues. Recent research using DNA microarrays and RNAseq data have described a cacophony of complex expression patterns during development of cotton fibers, petals, and leaves. Because of its highly canalized development, petal tissue has been used as a model tissue for gene expression in cotton. Recent advances in cotton genome annotation and assembly now permit an enhanced analysis of duplicate gene deployment in petals from allopolyploid cotton. Results Homoeologous gene expression levels were quantified in diploid and tetraploid flower petals of Gossypium using the Gossypium raimondii genome sequence as a reference. In the polyploid, most homoeologous genes were expressed at equal levels, though a subset had an expression bias of AT and DT copies. The direction of gene expression bias was conserved in natural and recent polyploids of cotton. Conservation of direction of bias and additional comparisons between the diploids and tetraploids suggested different regulation mechanisms of gene expression. We described three phases in the evolution of cotton genomes that contribute to gene expression in the polyploid nucleus. Conclusions Compared to previous studies, a surprising level of expression homeostasis was observed in the expression patterns of polyploid genomes. Conserved expression bias in polyploid petals may have resulted from cis-acting modifications that occurred prior to polyploidization. Some duplicated genes were intriguing exceptions to general trends. Mechanisms of gene regulation for these and other genes in the cotton genome warrants further investigation.
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Affiliation(s)
- Aditi Rambani
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602, USA
| | - Justin T Page
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602, USA
| | - Joshua A Udall
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602, USA
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42
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Raney JA, Reynolds DJ, Elzinga DB, Page J, A. Udall J, Jellen EN, Bonfacio A, Fairbanks DJ, Maughan PJ. Transcriptome Analysis of Drought Induced Stress in <i>Chenopodium quinoa</i>. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/ajps.2014.53047] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Bowman MJ, Park W, Bauer PJ, Udall JA, Page JT, Raney J, Scheffler BE, Jones DC, Campbell BT. RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress. PLoS One 2013; 8:e82634. [PMID: 24324815 PMCID: PMC3855774 DOI: 10.1371/journal.pone.0082634] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Accepted: 11/04/2013] [Indexed: 11/19/2022] Open
Abstract
An RNA-Seq experiment was performed using field grown well-watered and naturally rain fed cotton plants to identify differentially expressed transcripts under water-deficit stress. Our work constitutes the first application of the newly published diploid D5 Gossypium raimondii sequence in the study of tetraploid AD1 upland cotton RNA-seq transcriptome analysis. A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed root tissues, in patterns that confirm the accuracy of this technique for future studies in cotton genomics. Additionally, putative sequence based genome localization of differentially expressed transcripts detected A2 genome specific gene expression under water-deficit stress. These data will facilitate efforts to understand the complex responses governing transcriptomic regulatory mechanisms and to identify candidate genes that may benefit applied plant breeding programs.
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Affiliation(s)
- Megan J. Bowman
- USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, Florence, South Carolina, United States of America
| | - Wonkeun Park
- USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, Florence, South Carolina, United States of America
- Clemson University Pee Dee Research and Education Center, Florence, South Carolina, United States of America
| | - Philip J. Bauer
- USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, Florence, South Carolina, United States of America
| | - Joshua A. Udall
- Brigham Young University, Provo, Utah, United States of America
| | - Justin T. Page
- Brigham Young University, Provo, Utah, United States of America
| | - Joshua Raney
- Brigham Young University, Provo, Utah, United States of America
| | | | - Don. C. Jones
- Cotton Incorporated, Agricultural and Environmental Research, Cary, North Carolina, United States of America
| | - B. Todd Campbell
- USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, Florence, South Carolina, United States of America
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44
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Flagel LE, Wendel JF, Udall JA. Duplicate gene evolution, homoeologous recombination, and transcriptome characterization in allopolyploid cotton. BMC Genomics 2012. [PMID: 22768919 DOI: 10.1186/1471‐2164‐13‐302] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Modern allotetraploid cotton contains an "A" and "D" genome from an ancestral polyploidy event that occurred approximately 1-2 million years ago. Diploid A- and D-genome species can be compared to the A- and D-genomes found within these allotetraploids to make evolutionary inferences about polyploidy. In this paper we present a comprehensive EST assembly derived from diploid and model allotetraploid cottons and demonstrate several evolutionary inferences regarding genic evolution that can be drawn from these data. RESULTS We generated a set of cotton expressed sequence tags (ESTs), comprising approximately 4.4 million Sanger and next-generation (454) transcripts supplemented by approximately 152 million Illumina reads from diploid and allotetraploid cottons. From the EST alignments we inferred 259,192 genome-specific single nucleotide polymorphisms (SNPs). Molecular evolutionary analyses of protein-coding regions demonstrate that the rate of nucleotide substitution has increased among both allotetraploid genomes relative to the diploids, and that the ratio of nonsynonymous to synonymous substitutions has increased in one of the two polyploid lineages we sampled. We also use these SNPs to show that a surprisingly high percentage of duplicate genes (~7 %) show a signature of non-independent evolution in the allotetraploid nucleus, having experienced one or more episodes of nonreciprocal homoeologous recombination (NRHR). CONCLUSIONS In this study we characterize the functional and mutational properties of the cotton transcriptome, produce a large genome-specific SNP database, and detect illegitimate genetic exchanges between duplicate genomes sharing a common allotetraploid nucleus. Our findings have important implications for our understanding of the consequences of polyploidy and duplicate gene evolution. We demonstrate that cotton genes have experienced an increased rate of molecular evolution following duplication by polyploidy, and that polyploidy has enabled considerable levels of nonreciprocal exchange between homoeologous genes.
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Affiliation(s)
- Lex E Flagel
- Department of Biology, Duke University, Durham, NC 27708, USA
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45
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Flagel LE, Wendel JF, Udall JA. Duplicate gene evolution, homoeologous recombination, and transcriptome characterization in allopolyploid cotton. BMC Genomics 2012; 13:302. [PMID: 22768919 PMCID: PMC3427041 DOI: 10.1186/1471-2164-13-302] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 07/06/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Modern allotetraploid cotton contains an "A" and "D" genome from an ancestral polyploidy event that occurred approximately 1-2 million years ago. Diploid A- and D-genome species can be compared to the A- and D-genomes found within these allotetraploids to make evolutionary inferences about polyploidy. In this paper we present a comprehensive EST assembly derived from diploid and model allotetraploid cottons and demonstrate several evolutionary inferences regarding genic evolution that can be drawn from these data. RESULTS We generated a set of cotton expressed sequence tags (ESTs), comprising approximately 4.4 million Sanger and next-generation (454) transcripts supplemented by approximately 152 million Illumina reads from diploid and allotetraploid cottons. From the EST alignments we inferred 259,192 genome-specific single nucleotide polymorphisms (SNPs). Molecular evolutionary analyses of protein-coding regions demonstrate that the rate of nucleotide substitution has increased among both allotetraploid genomes relative to the diploids, and that the ratio of nonsynonymous to synonymous substitutions has increased in one of the two polyploid lineages we sampled. We also use these SNPs to show that a surprisingly high percentage of duplicate genes (~7 %) show a signature of non-independent evolution in the allotetraploid nucleus, having experienced one or more episodes of nonreciprocal homoeologous recombination (NRHR). CONCLUSIONS In this study we characterize the functional and mutational properties of the cotton transcriptome, produce a large genome-specific SNP database, and detect illegitimate genetic exchanges between duplicate genomes sharing a common allotetraploid nucleus. Our findings have important implications for our understanding of the consequences of polyploidy and duplicate gene evolution. We demonstrate that cotton genes have experienced an increased rate of molecular evolution following duplication by polyploidy, and that polyploidy has enabled considerable levels of nonreciprocal exchange between homoeologous genes.
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Affiliation(s)
- Lex E Flagel
- Department of Biology, Duke University, Durham, NC 27708, USA
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46
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Bushakra JM, Stephens MJ, Atmadjaja AN, Lewers KS, Symonds VV, Udall JA, Chagné D, Buck EJ, Gardiner SE. Construction of black (Rubus occidentalis) and red (R. idaeus) raspberry linkage maps and their comparison to the genomes of strawberry, apple, and peach. Theor Appl Genet 2012; 125:311-27. [PMID: 22398438 DOI: 10.1007/s00122-012-1835-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 02/17/2012] [Indexed: 05/23/2023]
Abstract
The genus Rubus belongs to the Rosaceae and is comprised of 600-800 species distributed world-wide. To date, genetic maps of the genus consist largely of non-transferable markers such as amplified fragment length polymorphisms. An F(1) population developed from a cross between an advanced breeding selection of Rubus occidentalis (96395S1) and R. idaeus 'Latham' was used to construct a new genetic map consisting of DNA sequence-based markers. The genetic linkage maps presented here are constructed of 131 markers on at least one of the two parental maps. The majority of the markers are orthologous, including 14 Rosaceae conserved orthologous set markers, and 60 new gene-based markers developed for raspberry. Thirty-four published raspberry simple sequence repeat markers were used to align the new maps to published raspberry maps. The 96395S1 genetic map consists of six linkage groups (LG) and covers 309 cM with an average of 10 cM between markers; the 'Latham' genetic map consists of seven LG and covers 561 cM with an average of 5 cM between markers. We used BLAST analysis to align the orthologous sequences used to design primer pairs for Rubus genetic mapping with the genome sequences of Fragaria vesca 'Hawaii 4', Malus × domestica 'Golden Delicious', and Prunus 'Lovell'. The alignment of the orthologous markers designed here suggests that the genomes of Rubus and Fragaria have a high degree of synteny and that synteny decreases with phylogenetic distance. Our results give unprecedented insights into the genome evolution of raspberry from the putative ancestral genome of the single ancestor common to Rosaceae.
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Affiliation(s)
- J M Bushakra
- The New Zealand Institute for Plant & Food Research Limited, Batchelar Road, Private Bag 11600, Palmerston North 4442, New Zealand.
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47
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Byers RL, Harker DB, Yourstone SM, Maughan PJ, Udall JA. Development and mapping of SNP assays in allotetraploid cotton. Theor Appl Genet 2012; 124:1201-14. [PMID: 22252442 PMCID: PMC3324690 DOI: 10.1007/s00122-011-1780-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Accepted: 12/22/2011] [Indexed: 05/06/2023]
Abstract
A narrow germplasm base and a complex allotetraploid genome have made the discovery of single nucleotide polymorphism (SNP) markers difficult in cotton (Gossypium hirsutum). To generate sequence for SNP discovery, we conducted a genome reduction experiment (EcoRI, BafI double digest, followed by adapter ligation, biotin-streptavidin purification, and agarose gel separation) on two accessions of G. hirsutum and two accessions of G. barbadense. From the genome reduction experiment, a total of 2.04 million genomic sequence reads were assembled into contigs with an N(50) of 508 bp and analyzed for SNPs. A previously generated assembly of expressed sequence tags (ESTs) provided an additional source for SNP discovery. Using highly conservative parameters (minimum coverage of 8× at each SNP and 20% minor allele frequency), a total of 11,834 and 1,679 non-genic SNPs were identified between accessions of G. hirsutum and G. barbadense in genome reduction assemblies, respectively. An additional 4,327 genic SNPs were also identified between accessions of G. hirsutum in the EST assembly. KBioscience KASPar assays were designed for a portion of the intra-specific G. hirsutum SNPs. From 704 non-genic and 348 genic markers developed, a total of 367 (267 non-genic, 100 genic) mapped in a segregating F(2) population (Acala Maxxa × TX2094) using the Fluidigm EP1 system. A G. hirsutum genetic linkage map of 1,688 cM was constructed based entirely on these new SNP markers. Of the genic-based SNPs, we were able to identify within which genome ('A' or 'D') each SNP resided using diploid species sequence data. Genetic maps generated by these newly identified markers are being used to locate quantitative, economically important regions within the cotton genome.
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Affiliation(s)
- Robert L. Byers
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602 USA
| | - David B. Harker
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602 USA
| | - Scott M. Yourstone
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602 USA
| | - Peter J. Maughan
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602 USA
| | - Joshua A. Udall
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602 USA
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48
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Abstract
A narrow germplasm base and a complex allotetraploid genome have made the discovery of single nucleotide polymorphism (SNP) markers difficult in cotton (Gossypium hirsutum). To generate sequence for SNP discovery, we conducted a genome reduction experiment (EcoRI, BafI double digest, followed by adapter ligation, biotin-streptavidin purification, and agarose gel separation) on two accessions of G. hirsutum and two accessions of G. barbadense. From the genome reduction experiment, a total of 2.04 million genomic sequence reads were assembled into contigs with an N(50) of 508 bp and analyzed for SNPs. A previously generated assembly of expressed sequence tags (ESTs) provided an additional source for SNP discovery. Using highly conservative parameters (minimum coverage of 8× at each SNP and 20% minor allele frequency), a total of 11,834 and 1,679 non-genic SNPs were identified between accessions of G. hirsutum and G. barbadense in genome reduction assemblies, respectively. An additional 4,327 genic SNPs were also identified between accessions of G. hirsutum in the EST assembly. KBioscience KASPar assays were designed for a portion of the intra-specific G. hirsutum SNPs. From 704 non-genic and 348 genic markers developed, a total of 367 (267 non-genic, 100 genic) mapped in a segregating F(2) population (Acala Maxxa × TX2094) using the Fluidigm EP1 system. A G. hirsutum genetic linkage map of 1,688 cM was constructed based entirely on these new SNP markers. Of the genic-based SNPs, we were able to identify within which genome ('A' or 'D') each SNP resided using diploid species sequence data. Genetic maps generated by these newly identified markers are being used to locate quantitative, economically important regions within the cotton genome.
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Affiliation(s)
- Robert L Byers
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA
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49
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Bybee SM, Bracken-Grissom H, Haynes BD, Hermansen RA, Byers RL, Clement MJ, Udall JA, Wilcox ER, Crandall KA. Targeted amplicon sequencing (TAS): a scalable next-gen approach to multilocus, multitaxa phylogenetics. Genome Biol Evol 2011; 3:1312-23. [PMID: 22002916 PMCID: PMC3236605 DOI: 10.1093/gbe/evr106] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2011] [Indexed: 12/03/2022] Open
Abstract
Next-gen sequencing technologies have revolutionized data collection in genetic studies and advanced genome biology to novel frontiers. However, to date, next-gen technologies have been used principally for whole genome sequencing and transcriptome sequencing. Yet many questions in population genetics and systematics rely on sequencing specific genes of known function or diversity levels. Here, we describe a targeted amplicon sequencing (TAS) approach capitalizing on next-gen capacity to sequence large numbers of targeted gene regions from a large number of samples. Our TAS approach is easily scalable, simple in execution, neither time-nor labor-intensive, relatively inexpensive, and can be applied to a broad diversity of organisms and/or genes. Our TAS approach includes a bioinformatic application, BarcodeCrucher, to take raw next-gen sequence reads and perform quality control checks and convert the data into FASTA format organized by gene and sample, ready for phylogenetic analyses. We demonstrate our approach by sequencing targeted genes of known phylogenetic utility to estimate a phylogeny for the Pancrustacea. We generated data from 44 taxa using 68 different 10-bp multiplexing identifiers. The overall quality of data produced was robust and was informative for phylogeny estimation. The potential for this method to produce copious amounts of data from a single 454 plate (e.g., 325 taxa for 24 loci) significantly reduces sequencing expenses incurred from traditional Sanger sequencing. We further discuss the advantages and disadvantages of this method, while offering suggestions to enhance the approach.
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Affiliation(s)
- Seth M Bybee
- Department of Biology, Brigham Young University, USA.
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50
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Bajgain P, Richardson BA, Price JC, Cronn RC, Udall JA. Transcriptome characterization and polymorphism detection between subspecies of big sagebrush (Artemisia tridentata). BMC Genomics 2011; 12:370. [PMID: 21767398 PMCID: PMC3150299 DOI: 10.1186/1471-2164-12-370] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 07/18/2011] [Indexed: 12/14/2022] Open
Abstract
Background Big sagebrush (Artemisia tridentata) is one of the most widely distributed and ecologically important shrub species in western North America. This species serves as a critical habitat and food resource for many animals and invertebrates. Habitat loss due to a combination of disturbances followed by establishment of invasive plant species is a serious threat to big sagebrush ecosystem sustainability. Lack of genomic data has limited our understanding of the evolutionary history and ecological adaptation in this species. Here, we report on the sequencing of expressed sequence tags (ESTs) and detection of single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers in subspecies of big sagebrush. Results cDNA of A. tridentata sspp. tridentata and vaseyana were normalized and sequenced using the 454 GS FLX Titanium pyrosequencing technology. Assembly of the reads resulted in 20,357 contig consensus sequences in ssp. tridentata and 20,250 contigs in ssp. vaseyana. A BLASTx search against the non-redundant (NR) protein database using 29,541 consensus sequences obtained from a combined assembly resulted in 21,436 sequences with significant blast alignments (≤ 1e-15). A total of 20,952 SNPs and 119 polymorphic SSRs were detected between the two subspecies. SNPs were validated through various methods including sequence capture. Validation of SNPs in different individuals uncovered a high level of nucleotide variation in EST sequences. EST sequences of a third, tetraploid subspecies (ssp. wyomingensis) obtained by Illumina sequencing were mapped to the consensus sequences of the combined 454 EST assembly. Approximately one-third of the SNPs between sspp. tridentata and vaseyana identified in the combined assembly were also polymorphic within the two geographically distant ssp. wyomingensis samples. Conclusion We have produced a large EST dataset for Artemisia tridentata, which contains a large sample of the big sagebrush leaf transcriptome. SNP mapping among the three subspecies suggest the origin of ssp. wyomingensis via mixed ancestry. A large number of SNP and SSR markers provide the foundation for future research to address questions in big sagebrush evolution, ecological genetics, and conservation using genomic approaches.
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Affiliation(s)
- Prabin Bajgain
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602, USA
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