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Cheng X, Xie H, Zhang K, Wen J. Enabling Medicago truncatula forward genetics: identification of genetic crossing partner for R108 and development of mapping resources for Tnt1 mutants. Plant J 2022; 111:608-616. [PMID: 35510429 DOI: 10.1111/tpj.15797] [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] [Received: 02/11/2022] [Revised: 04/19/2022] [Accepted: 05/01/2022] [Indexed: 06/14/2023]
Abstract
Though Medicago truncatula Tnt1 mutants are widely used by researchers in the legume community, they are mainly used for reverse genetics because of the availability of the BLAST-searchable large-scale flanking sequence tags database. However, these mutants should have also been used extensively for forward genetic screens, an effort that has been hindered due to the lack of a compatible genetic crossing partner for the M. truncatula genotype R108, from which Tnt1 mutants were generated. In this study, we selected three Medicago HapMap lines (HM017, HM018 and HM022) and performed reciprocal genetic crosses with R108. After phenotypic analyses in F1 and F2 progenies, HM017 was identified as a compatible crossing partner with R108. By comparing the assembled genomic sequences of HM017 and R108, we developed and confirmed 318 Indel markers evenly distributed across the eight chromosomes of the M. truncatula genome. To validate the effectiveness of these markers, by employing the map-based cloning approach, we cloned the causative gene in the dwarf mutant crs isolated from the Tnt1 mutant population, identifying it as gibberellin 3-β-dioxygenase 1, using some of the confirmed Indel markers. The primer sequences and the size difference of each marker were made available for users in the web-based database. The identification of the crossing partner for R108 and the generation of Indel markers will enhance the forward genetics and the overall usage of the Tnt1 mutants.
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Affiliation(s)
- Xiaofei Cheng
- Noble Research Institute, LLC, Ardmore, OK, 73401, USA
| | - Hongli Xie
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, Shandong, 266109, China
| | - Kuihua Zhang
- Noble Research Institute, LLC, Ardmore, OK, 73401, USA
| | - Jiangqi Wen
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, 74078, USA
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK, 73401, USA
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Nandety RS, Serrani‐Yarce JC, Gill US, Oh S, Lee H, Zhang X, Dai X, Zhang W, Krom N, Wen J, Zhao PX, Mysore KS. Insertional mutagenesis of Brachypodium distachyon using the Tnt1 retrotransposable element. Plant J 2020; 103:1924-1936. [PMID: 32410353 PMCID: PMC7496502 DOI: 10.1111/tpj.14813] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 04/29/2020] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
Brachypodium distachyon is an annual C3 grass used as a monocot model system in functional genomics research. Insertional mutagenesis is a powerful tool for both forward and reverse genetics studies. In this study, we explored the possibility of using the tobacco retrotransposon Tnt1 to create a transposon-based insertion mutant population in B. distachyon. We developed transgenic B. distachyon plants expressing Tnt1 (R0) and in the subsequent regenerants (R1) we observed that Tnt1 actively transposed during somatic embryogenesis, generating an average of 6.37 insertions per line in a population of 19 independent R1 regenerant plants analyzed. In seed-derived progeny of R1 plants, Tnt1 segregated in a Mendelian ratio of 3:1 and no new Tnt1 transposition was observed. A total of 126 flanking sequence tags (FSTs) were recovered from the analyzed R0 and R1 lines. Analysis of the FSTs showed a uniform pattern of insertion in all the chromosomes (1-5) without any preference for a particular chromosome region. Considering the average length of a gene transcript to be 3.37 kb, we estimated that 29 613 lines are required to achieve a 90% possibility of tagging a given gene in the B. distachyon genome using the Tnt1-based mutagenesis approach. Our results show the possibility of using Tnt1 to achieve near-saturation mutagenesis in B. distachyon, which will aid in functional genomics studies of other C3 grasses.
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Affiliation(s)
| | - Juan C. Serrani‐Yarce
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
- Present address:
Department of Biological SciencesUniversity of North TexasDentonTX76203USA
| | - Upinder S. Gill
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
- Present address:
Department of Plant PathologyNorth Dakota State UniversityFargoND58102USA
| | - Sunhee Oh
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
| | - Hee‐Kyung Lee
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
| | - Xinji Zhang
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
| | - Xinbin Dai
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
| | - Wenchao Zhang
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
| | - Nick Krom
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
| | - Jiangqi Wen
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
| | - Patrick X. Zhao
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
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Sun L, Gill US, Nandety RS, Kwon S, Mehta P, Dickstein R, Udvardi MK, Mysore KS, Wen J. Genome-wide analysis of flanking sequences reveals that Tnt1 insertion is positively correlated with gene methylation in Medicago truncatula. Plant J 2019; 98:1106-1119. [PMID: 30776165 DOI: 10.1111/tpj.14291] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 12/04/2018] [Revised: 02/07/2019] [Accepted: 02/14/2019] [Indexed: 05/07/2023]
Abstract
From a single transgenic line harboring five Tnt1 transposon insertions, we generated a near-saturated insertion population in Medicago truncatula. Using thermal asymmetric interlaced-polymerase chain reaction followed by sequencing, we recovered 388 888 flanking sequence tags (FSTs) from 21 741 insertion lines in this population. FST recovery from 14 Tnt1 lines using the whole-genome sequencing (WGS) and/or Tnt1-capture sequencing approaches suggests an average of 80 insertions per line, which is more than the previous estimation of 25 insertions. Analysis of the distribution pattern and preference of Tnt1 insertions showed that Tnt1 is overall randomly distributed throughout the M. truncatula genome. At the chromosomal level, Tnt1 insertions occurred on both arms of all chromosomes, with insertion frequency negatively correlated with the GC content. Based on 174 546 filtered FSTs that show exact insertion locations in the M. truncatula genome version 4.0 (Mt4.0), 0.44 Tnt1 insertions occurred per kb, and 19 583 genes contained Tnt1 with an average of 3.43 insertions per gene. Pathway and gene ontology analyses revealed that Tnt1-inserted genes are significantly enriched in processes associated with 'stress', 'transport', 'signaling' and 'stimulus response'. Surprisingly, gene groups with higher methylation frequency were more frequently targeted for insertion. Analysis of 19 583 Tnt1-inserted genes revealed that 59% (1265) of 2144 transcription factors, 63% (765) of 1216 receptor kinases and 56% (343) of 616 nucleotide-binding site-leucine-rich repeat genes harbored at least one Tnt1 insertion, compared with the overall 38% of Tnt1-inserted genes out of 50 894 annotated genes in the genome.
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Affiliation(s)
- Liang Sun
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Upinder S Gill
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | | | - Soonil Kwon
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Perdeep Mehta
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Rebecca Dickstein
- Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203, USA
| | - Michael K Udvardi
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | | | - Jiangqi Wen
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
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