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Wang F, Das P, Pal N, Bhawal R, Zhang S, Bhattacharyya MK. A Phosphoproteomics Study of the Soybean root necrosis 1 Mutant Revealed Type II Metacaspases Involved in Cell Death Pathway. FRONTIERS IN PLANT SCIENCE 2022; 13:882561. [PMID: 35928708 PMCID: PMC9344878 DOI: 10.3389/fpls.2022.882561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
The soybean root necrosis 1 (rn1) mutation causes progressive browning of the roots soon after germination and provides increased tolerance to the soil-borne oomycete pathogen Phytophthora sojae in soybean. Toward understanding the molecular basis of the rn1 mutant phenotypes, we conducted tandem mass tag (TMT)-labeling proteomics and phosphoproteomics analyses of the root tissues of the rn1 mutant and progenitor T322 line to identify potential proteins involved in manifestation of the mutant phenotype. We identified 3,160 proteins. When the p-value was set at ≤0.05 and the fold change of protein accumulation between rn1 and T322 at ≥1.5 or ≤0.67, we detected 118 proteins that showed increased levels and 32 proteins decreased levels in rn1 as compared to that in T322. The differentially accumulated proteins (DAPs) are involved in several pathways including cellular processes for processing environmental and genetic information, metabolism and organismal systems. Five pathogenesis-related proteins were accumulated to higher levels in the mutant as compared to that in T322. Several of the DAPs are involved in hormone signaling, redox reaction, signal transduction, and cell wall modification processes activated in plant-pathogen interactions. The phosphoproteomics analysis identified 22 phosphopeptides, the levels of phosphorylation of which were significantly different between rn1 and T322 lines. The phosphorylation levels of two type II metacaspases were reduced in rn1 as compared to T322. Type II metacaspase has been shown to be a negative regulator of hypersensitive cell death. In absence of the functional Rn1 protein, two type II metacaspases exhibited reduced phosphorylation levels and failed to show negative regulatory cell death function in the soybean rn1 mutant. We hypothesize that Rn1 directly or indirectly phosphorylates type II metacaspases to negatively regulate the cell death process in soybean roots.
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Affiliation(s)
- Feifei Wang
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Priyanka Das
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Narinder Pal
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Ruchika Bhawal
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, United States
| | - Sheng Zhang
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, United States
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Sandhu D, Ghosh J, Johnson C, Baumbach J, Baumert E, Cina T, Grant D, Palmer RG, Bhattacharyya MK. The endogenous transposable element Tgm9 is suitable for generating knockout mutants for functional analyses of soybean genes and genetic improvement in soybean. PLoS One 2017; 12:e0180732. [PMID: 28797084 PMCID: PMC5552171 DOI: 10.1371/journal.pone.0180732] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 06/20/2017] [Indexed: 11/19/2022] Open
Abstract
In soybean, variegated flowers can be caused by somatic excision of the CACTA-type transposable element Tgm9 from Intron 2 of the DFR2 gene encoding dihydroflavonol-4-reductase of the anthocyanin pigment biosynthetic pathway. DFR2 was mapped to the W4 locus, where the allele containing Tgm9 was termed w4-m. In this study we have demonstrated that previously identified morphological mutants (three chlorophyll deficient mutants, one male sterile-female fertile mutant, and three partial female sterile mutants) were caused by insertion of Tgm9 following its excision from DFR2. Analyses of Tgm9 insertion sites among 105 independent mutants demonstrated that Tgm9 hops to all 20 soybean chromosomes from its original location on Chromosome 17. Some genomic regions are prone to increased Tgm9-insertions. Tgm9 transposed over 25% of the time into exon or intron sequences. Tgm9 is therefore suitable for generating an indexed insertional mutant collection for functional analyses of most soybean genes. Furthermore, desirable Tgm9-induced stable knockout mutants can be utilized in generating improved traits for commercial soybean cultivars.
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Affiliation(s)
- Devinder Sandhu
- USDA-ARS, US Salinity Laboratory, Riverside, CA, United States of America
| | - Jayadri Ghosh
- Department of Agronomy, Iowa State University, Ames, IA, United States of America
| | - Callie Johnson
- Department of Biology, University of Wisconsin-Stevens Point, Stevens Point, WI, United States of America
| | - Jordan Baumbach
- Department of Agronomy, Iowa State University, Ames, IA, United States of America
| | - Eric Baumert
- Department of Biology, University of Wisconsin-Stevens Point, Stevens Point, WI, United States of America
| | - Tyler Cina
- Department of Biology, University of Wisconsin-Stevens Point, Stevens Point, WI, United States of America
| | - David Grant
- Department of Agronomy, Iowa State University, Ames, IA, United States of America
- USDA-ARS Corn Insects and Crop Genomics Research Unit, Ames, IA, United States of America
| | - Reid G. Palmer
- Department of Agronomy, Iowa State University, Ames, IA, United States of America
- USDA-ARS Corn Insects and Crop Genomics Research Unit, Ames, IA, United States of America
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Campbell BW, Hofstad AN, Sreekanta S, Fu F, Kono TJY, O'Rourke JA, Vance CP, Muehlbauer GJ, Stupar RM. Fast neutron-induced structural rearrangements at a soybean NAP1 locus result in gnarled trichomes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1725-38. [PMID: 27282876 PMCID: PMC4983299 DOI: 10.1007/s00122-016-2735-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/28/2016] [Indexed: 05/20/2023]
Abstract
KEY MESSAGE Three adjacent and distinct sequence rearrangements were identified at a NAP1 locus in a soybean mutant. Genetic dissection and validation revealed the function of this gene in soybean trichome development. A soybean (Glycine max (L.) Merr.) gnarled trichome mutant, exhibiting stunted trichomes compared to wild-type, was identified in a fast neutron mutant population. Genetic mapping using whole genome sequencing-based bulked segregant analysis identified a 26.6 megabase interval on chromosome 20 that co-segregated with the phenotype. Comparative genomic hybridization analysis of the mutant indicated that the chromosome 20 interval included a small structural variant within the coding region of a soybean ortholog (Glyma.20G019300) of Arabidopsis Nck-Associated Protein 1 (NAP1), a regulator of actin nucleation during trichome morphogenesis. Sequence analysis of the candidate allele revealed multiple rearrangements within the coding region, including two deletions (approximately 1-2 kb each), a translocation, and an inversion. Further analyses revealed that the mutant allele perfectly co-segregated with the phenotype, and a wild-type soybean NAP1 transgene functionally complemented an Arabidopsis nap1 mutant. In addition, mapping and exon sequencing of NAP1 in a spontaneous soybean gnarled trichome mutant (T31) identified a frame shift mutation resulting in a truncation of the coding region. These data indicate that the soybean NAP1 gene is essential for proper trichome development and show the utility of the soybean fast neutron population for forward genetic approaches for identifying genes.
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Affiliation(s)
- Benjamin W Campbell
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Anna N Hofstad
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Suma Sreekanta
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Fengli Fu
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Thomas J Y Kono
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Jamie A O'Rourke
- USDA-ARS, Corn Insects and Crop Genetics Research, Iowa State University, Ames, IA, 50011, USA
| | - Carroll P Vance
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
- Department of Plant Biology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA.
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Campbell BW, Stupar RM. Soybean (Glycine max) Mutant and Germplasm Resources: Current Status and Future Prospects. ACTA ACUST UNITED AC 2016; 1:307-327. [PMID: 30775866 DOI: 10.1002/cppb.20015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Genetic bottlenecks during domestication and modern breeding limited the genetic diversity of soybean (Glycine max (L.) Merr.). Therefore, expanding and diversifying soybean genetic resources is a major priority for the research community. These resources, consisting of natural and induced genetic variants, are valuable tools for improving soybean and furthering soybean biological knowledge. During the twentieth century, researchers gathered a wealth of genetic variation in the forms of landraces, Glycine soja accessions, Glycine tertiary germplasm, and the U.S. Department of Agriculture (USDA) Type and Isoline Collections. During the twenty-first century, soybean researchers have added several new genetic and genomic resources. These include the reference genome sequence, genotype data for the USDA soybean germplasm collection, next-generation mapping populations, new irradiation and transposon-based mutagenesis populations, and designer nuclease platforms for genome engineering. This paper briefly surveys the publicly accessible soybean genetic resources currently available or in development and provides recommendations for developing such genetic resources in the future. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Benjamin W Campbell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota
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Baumbach J, Pudake RN, Johnson C, Kleinhans K, Ollhoff A, Palmer RG, Bhattacharyya MK, Sandhu D. Transposon Tagging of a Male-Sterility, Female-Sterility Gene, St8, Revealed that the Meiotic MER3 DNA Helicase Activity Is Essential for Fertility in Soybean. PLoS One 2016; 11:e0150482. [PMID: 26930200 PMCID: PMC4773125 DOI: 10.1371/journal.pone.0150482] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 02/14/2016] [Indexed: 11/19/2022] Open
Abstract
The W4 locus in soybean encodes a dihydroflavonol-4-reductase (DFR2) that regulates pigmentation patterns in flowers and hypocotyl. The mutable w4-m allele that governs variegated flowers has arisen through insertion of a CACTA-type transposable element, Tgm9, in DFR2. In the w4-m line, reversion from variegated to purple flower indicates excision of Tgm9, and its insertion at a new locus. Previously, we have identified a male-sterile, female-sterile mutant among the selfed progenies of a revertant plant carrying only purple flowers. Co-segregation between Tgm9 and the sterility phenotype suggested that the mutant was generated by insertion of Tgm9 at the St8 locus. The transposon was localized to exon 10 of Glyma.16G072300 that shows high identity to the MER3 DNA helicase involved in crossing over. Molecular analysis of fertile branches from two independent revertant plants confirmed precise excision of Tgm9 from the st8 allele, which restored fertility. In soybean, the gene is expressed in flower-buds, trifoliate leaves and stem. Phylogenetic analysis placed St8 in a clade with the Arabidopsis and rice MER3 suggesting that St8 is most likely the orthologous MER3 soybean gene. This study established the utility of Tgm9 in gene identification as well as in forward and reverse genetics studies.
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Affiliation(s)
- Jordan Baumbach
- Department of Biology, University of Wisconsin-Stevens Point, Stevens Point, Wiconsin, 54481, United States of America
- Department of Agronomy, Iowa State University, Ames, Iowa, 50011, United States of America
| | - Ramesh N. Pudake
- Department of Agronomy, Iowa State University, Ames, Iowa, 50011, United States of America
| | - Callie Johnson
- Department of Biology, University of Wisconsin-Stevens Point, Stevens Point, Wiconsin, 54481, United States of America
| | - Kaylin Kleinhans
- Department of Biology, University of Wisconsin-Stevens Point, Stevens Point, Wiconsin, 54481, United States of America
| | - Alexandrea Ollhoff
- Department of Biology, University of Wisconsin-Stevens Point, Stevens Point, Wiconsin, 54481, United States of America
| | - Reid G. Palmer
- Department of Agronomy, Iowa State University, Ames, Iowa, 50011, United States of America
| | - Madan K. Bhattacharyya
- Department of Agronomy, Iowa State University, Ames, Iowa, 50011, United States of America
| | - Devinder Sandhu
- Department of Biology, University of Wisconsin-Stevens Point, Stevens Point, Wiconsin, 54481, United States of America
- USDA-ARS Salinity Lab., 450 W. Big Springs Rd., Riverside, California, 92507, United States of America
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Raval J, Baumbach J, Ollhoff AR, Pudake RN, Palmer RG, Bhattacharyya MK, Sandhu D. A candidate male-fertility female-fertility gene tagged by the soybean endogenous transposon, Tgm9. Funct Integr Genomics 2013; 13:67-73. [PMID: 23184475 DOI: 10.1007/s10142-012-0304-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 10/29/2012] [Accepted: 11/12/2012] [Indexed: 10/27/2022]
Abstract
In soybean, the W4 gene encoding dihydroflavonol-4-reductase controls anthocyanin pigment biosynthesis in flowers. The mutant allele, w4-m, is characterized by variegated flowers and was evolved from the insertion of an endogenous transposable element, Tgm9, in intron II of the W4 gene. In the w4-m mutant line, reversion of the unstable allele from variegated to normal purple flower in revertants would indicate Tgm9's excision accompanied by its insertion into a second locus. We identified a male-sterile, female-sterile mutant from such germinal revertant bearing purple flowers. The objectives of our investigation were to map the sterility locus, identify candidate genes for the male-fertile, female-fertile phenotype, and then determine if sterility is associated with the insertion of Tgm9 in the sterility locus. We used bulked segregant analysis to map the locus to molecular linkage group J (chromosome 16). Fine mapping enabled us to flank the locus to a 62-kb region that contains only five predicted genes. One of the genes in that region, Glyma16g07850.1, codes for a helicase. A rice homolog of this gene has been shown to control crossing over and fertility phenotype. Thus, Glyma16g07850.1 is most likely the gene regulating the male and female fertility phenotype in soybean. DNA blot analysis of the segregating individuals for Tgm9 showed perfect association between sterility and the presence of the transposon. Most likely, the sterility mutation was caused by the insertion of Tgm9. The transposable element should facilitate identification of the male- and female-fertility gene. Characterization of the fertility gene will provide vital molecular insight on the reproductive biology of soybean and other plants.
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Affiliation(s)
- Jaydeep Raval
- Department of Biology, University of Wisconsin-Stevens Point, 800 Reserve Street, Stevens Point, WI, 54481, USA
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Xu M, Brar HK, Grosic S, Palmer RG, Bhattacharyya MK. Excision of an active CACTA-like transposable element from DFR2 causes variegated flowers in soybean [Glycine max (L.) Merr.]. Genetics 2010; 184:53-63. [PMID: 19897750 PMCID: PMC2815930 DOI: 10.1534/genetics.109.107904] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Accepted: 11/01/2009] [Indexed: 11/18/2022] Open
Abstract
Active endogenous transposable elements, useful tools for gene isolation, have not been reported from any legume species. An active transposable element was suggested to reside in the W4 locus that governs flower color in soybean. Through biochemical and molecular analyses of several revertants of the w4-m allele, we have shown that the W4 locus encodes dihydroflavonol-4-reductase 2 (DFR2). w4-m has arisen through insertion of Tgm9, a 20,548-bp CACTA-like transposable element, into the second intron of DFR2. Tgm9 showed high nucleic acid sequence identity to Tgmt*. Its 5' and 3' terminal inverted repeats start with conserved CACTA sequence. The 3' subterminal region is highly repetitive. Tgm9 carries TNP1- and TNP2-like transposase genes that are expressed in the mutable line, T322 (w4-m). The element excises at a high frequency from both somatic and germinal tissues. Following excision, reinsertions of Tgm9 into the DFR2 promoter generated novel stable alleles, w4-dp (dilute purple flowers) and w4-p (pale flowers). We hypothesize that the element is fractured during transposition, and truncated versions of the element in new insertion sites cause stable mutations. The highly active endogenous transposon, Tgm9, should facilitate genomics studies specifically that relate to legume biology.
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Affiliation(s)
- Min Xu
- Department of Agronomy, Iowa State University, Ames, Iowa 50011 and United States Department of Agriculture, Agricultural Research Service, Corn Insects and Crop Genetics Research, Department of Agronomy, Iowa State University, Ames, Iowa 50011
| | - Hargeet K. Brar
- Department of Agronomy, Iowa State University, Ames, Iowa 50011 and United States Department of Agriculture, Agricultural Research Service, Corn Insects and Crop Genetics Research, Department of Agronomy, Iowa State University, Ames, Iowa 50011
| | - Sehiza Grosic
- Department of Agronomy, Iowa State University, Ames, Iowa 50011 and United States Department of Agriculture, Agricultural Research Service, Corn Insects and Crop Genetics Research, Department of Agronomy, Iowa State University, Ames, Iowa 50011
| | - Reid G. Palmer
- Department of Agronomy, Iowa State University, Ames, Iowa 50011 and United States Department of Agriculture, Agricultural Research Service, Corn Insects and Crop Genetics Research, Department of Agronomy, Iowa State University, Ames, Iowa 50011
| | - Madan K. Bhattacharyya
- Department of Agronomy, Iowa State University, Ames, Iowa 50011 and United States Department of Agriculture, Agricultural Research Service, Corn Insects and Crop Genetics Research, Department of Agronomy, Iowa State University, Ames, Iowa 50011
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Palmer RG, Sandhu D, Curran K, Bhattacharyya MK. Molecular mapping of 36 soybean male-sterile, female-sterile mutants. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:711-9. [PMID: 18592206 DOI: 10.1007/s00122-008-0812-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Accepted: 05/21/2008] [Indexed: 05/26/2023]
Abstract
Mutability of the w(4) flower color locus in soybean [Glycine max (L.) Merr.] is conditioned by an unstable allele designated w(4)-m. Germinal revertants, purple-flower plants, recovered among self-pollinated progeny of mutable flower plants were associated with the generation of necrotic root, chlorophyll-deficiency, and sterility mutations. Thirty-seven male-sterile, female-sterile mutant lines were generated from 37 independent reversion events at the w(4)-m locus. The first germinal revertant study had one male-sterile, female-sterile mutant (st8, T352), located on Molecular Linkage Group (MLG) J. The second study had 36 germinal-revertant derived sterility mutants descended from four mutable categories of w(4)-m. The mutable categories were designated; (1) low frequency of early excisions, (2) low frequency of late excisions, (3) high frequency of early excisions, and (4) high frequency of late excisions. The objectives of the present study were to; (1) molecularly map the 36 male-sterile, female-sterile mutants, and to (2) compare map locations of these mutants with T352 (st8), identified from the first germinal revertant study. Thirty-three of 36 male-sterile, female-sterile mutations were derived from germinal reversions that were classified in the late excision categories. Thirty-five male-sterile mutants mapped to the st8 region on MLG J. The only exception mapped to MLG G. Most likely mutants were generated through insertion of a putative transposon that was excised from the w(4) locus. The location of 36 of 37 mutations to a single chromosomal region suggests preference for sequence-dependent insertion.
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Affiliation(s)
- R G Palmer
- USDA ARS CICGR, Department of Agronomy, Iowa State University, Ames, IA 50011-1010, USA.
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