Identification and characterization of a fast-neutron-induced mutant with elevated seed protein content in soybean.
Chromosome 12
Deletion
Fast neutrons
Mutant
Protein content
Soybeans
Journal
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
ISSN: 1432-2242
Titre abrégé: Theor Appl Genet
Pays: Germany
ID NLM: 0145600
Informations de publication
Date de publication:
Nov 2019
Nov 2019
Historique:
received:
17
02
2019
accepted:
11
07
2019
pubmed:
22
7
2019
medline:
6
2
2020
entrez:
21
7
2019
Statut:
ppublish
Résumé
Protein content of soybean is critical for utility of soybean meal. A fast-neutron-induced deletion on chromosome 12 was found to be associated with increased protein content. Soybean seed composition affects the utility of soybean, and improving seed composition is an essential breeding goal. Fast neutron radiation introduces genomic mutations resulting in novel variation for traits of interest. Two elite soybean lines were irradiated with fast neutrons and screened for altered seed composition. Twenty-three lines with altered protein, oil, or sucrose content were selected based on near-infrared spectroscopy data from five environments and yield tested at five locations. Mutants with significantly increased protein averaged 19.1-36.8 g kg
Identifiants
pubmed: 31324928
doi: 10.1007/s00122-019-03399-w
pii: 10.1007/s00122-019-03399-w
doi:
Substances chimiques
Plant Proteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
2965-2983Références
Anderson JE, Michno J-M, Kono TJY, Stec AO, Campbell BW, Curtin SJ, Stupar RM (2016) Genomic variation and DNA repair associated with soybean transgenesis: a comparison to cultivars and mutagenized plants. BMC Biotechnol 16:41
doi: 10.1186/s12896-016-0271-z
pubmed: 4866027
pmcid: 4866027
Andrews S (2014) FastQC a quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Bandillo N, Jarquin D, Song Q, Nelson R, Cregan P, Specht J, Lorenz A (2015) A population structure and genome-wide association analysis on the usda soybean germplasm collection. Plant Genome 8
Barthelson R (2014a) HTProcess_trimmomatic_0.32. rogerab. CyVerse https://de.cyverse.org/de/?type=apps&app-id=93820714-89b7-4008-a9d1-98cb35ae3b09&system-id=de
Barthelson R (2014b) HTProcess-prepare_directories-and-run_fastqc-0.1. rogerab. CyVerse. https://de.cyverse.org/de/?type=apps&app-id=b4d15ab5-81b6-47e1-8637-26824e1f1679&system-id=de
Barthelson R (2016) SAM-to-sorted-BAM. rogerab. CyVerse. https://pods.iplantcollaborative.org/wiki/display/DEapps/Convert+SAM-to-sorted-BAM
Belfield E, Gan X, Mithani A, Brown C, Jiang C, Franklin K, Alvey E, Wibowo A, Jung M, Bailey K, Kalwani S, Ragoussis J, Mott R, Harberd N (2012) Genome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thaliana. Genome Res 22:1306–1315
doi: 10.1101/gr.131474.111
pubmed: 3396371
pmcid: 3396371
Boerma HR, Hussey RS, Phillips DV, Wood ED, Rowan GB, Finnerty SL (1997) Registration of ‘Benning’ soybean. Crop Sci 37:1982
doi: 10.2135/cropsci1997.0011183X003700060061x
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinform 30(15):2114–2120
doi: 10.1093/bioinformatics/btu170
Bolon Y-T, Haun WJ, Xu WW, Grant D, Stacey MG, Nelson RT, Gerhardt DJ, Jeddeloh JA, Stacey G, Muehlbauer GJ, Orf JH, Naeve SL, Stupar RM, Vance CP (2011) Phenotypic and genomic analyses of a fast neutron mutant population resource in soybean. Plant Physiol 156:240–253
doi: 10.1104/pp.110.170811
pubmed: 3091049
pmcid: 3091049
Bolon Y-T, Stec AO, Michno J-M, Roessler J, Bhaskar PB, Ries L, Dobbels AA, Campbell BW, Young NP, Anderson JE, Grant DM, Orf JH, Naeve SL, Muehlbauer GJ, Vance CP, Stupar RM (2014) Genome resilience and prevalence of segmental duplications following fast neutron irradiation of soybean. Genetics 198:967–981
doi: 10.1534/genetics.114.170340
pubmed: 4224183
pmcid: 4224183
Brummer EC, Graef GL, Orf J, Wilcox JR, Shoemaker RC (1997) Mapping QTL for seed protein and oil content in eight soybean populations. Crop Sci 37:370–378
doi: 10.2135/cropsci1997.0011183X003700020011x
Brzostowski LF, Diers BW (2017) Agronomic evaluation of a high protein allele from PI407788A on chromosome 15 across two soybean backgrounds. Crop Sci 57:2972–2978
doi: 10.2135/cropsci2017.02.0083
Brzostowski LF, Pruski T, Specht JE, Diers BW (2017) Impact of seed protein alleles from three soybean sources on seed composition and agronomic traits. Theor Appl Genet 130:2315–2326
doi: 10.1007/s00122-017-2961-x
Burton JW (1987) Quantitative genetics: results relevant to soybean breeding. In: Wilcox JR (ed) Soybeans: improvement, production and uses, 2nd edn. ASA, CSSA, and SSSA, Madison
Campbell BW, Hofstad AN, Sreekanta S, Fu F, Kono TJY, O’Rourke JA, Vance CP, Muehlbauer GJ, Stupar RM (2016) Fast neutron-induced structural rearrangements at a soybean NAP1 locus result in gnarled trichomes. Theor Appl Genet 129:1725–1738
doi: 10.1007/s00122-016-2735-x
pubmed: 4983299
pmcid: 4983299
Chung J, Babka HL, Graef GL, Staswick PE, Lee DJ (2003) The seed protein, oil, and yield QTL on soybean linkage group I. Crop Sci 43:1053–1067
doi: 10.2135/cropsci2003.1053
Cober ER, Voldeng HD (2000) Developing high-protein, high-yield soybean populations and lines. Crop Sci 40:39–42
doi: 10.2135/cropsci2000.40139x
Cooksey A (2017) BWA mem_longreads-0.7.15. Upendra Devisetty. CyVerse. https://de.cyverse.org/de/?type=apps&app-id=e813971a-7d2d-11e7-9247-008cfa5ae621&system-id=de
DeBolt S (2010) Copy number variation shapes genome diversity in Arabidopsis over immediate family generational scales. Genome Biol Evol 2:441–453
doi: 10.1093/gbe/evq033
pubmed: 2997553
pmcid: 2997553
Devisetty UK (2016a) BWA mem 0.7.15. Upendra Devisetty. CyVerse. https://de.cyverse.org/de/?type=apps&app-id=4c7e942e-6408-11e6-a1f5-008cfa5ae621&system-id=de
Devisetty UK (2016b) SAM_to_Sorted_BAM-0.1.19 (app for workflows). Upendra Kumar Devisetty. CyVerse. https://de.cyverse.org/de/?type=apps&app-id=9b837c54-122f-11e6-98c7-dfa2ad9d9ddd&system-id=de
Diers BW, Keim P, Fehr WR, Shoemaker RC (1992) RFLP analysis of soybean seed protein and oil content. Theor Appl Genet 83:608–612
doi: 10.1007/BF00226905
Dobbels AA, Michno J-M, Campbell BW, Virdi KS, Stec AO, Muehlbauer GJ, Naeve SL, Stupar RM (2017) An induced chromosomal translocation in soybean disrupts a KASI ortholog and is associated with a high-sucrose and low-oil seed phenotype. G3 Genes Genomes Genet 7:1215–1223
Eskandari M, Cober E, Rajcan I (2013) Genetic control of soybean seed oil: II QTL and genes that increase oil concentration without decreasing protein or with increased seed yield. Theor Appl Genet 126(6):1677–1687
doi: 10.1007/s00122-013-2083-z
Fehr WR, Caviness CE (1977) Stages of soybean development. Special Report. 87. https://lib.dr.iastate.edu/specialreports/87/
Glenn TC, Nilsen RA, Kieran TJ, Finger JW Jr, Pierson TW, Bentley KE, Hoffberg SL, Louha S, García-De León FJ, Del Rio Portilla MA, Reed KD, Anderson JL, Meece JK, Aggrey SE, Rekaya R, Alabady M, Bélanger M, Winker K, Faircloth BC (2016) Adapterama I: universal stubs and primers for thousands of dual-indexed Illumina libraries (iTru & iNext). BioRxiv. https://doi.org/10.1101/049114
doi: 10.1101/049114
Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J et al (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 40((Database issue)):D1178–D1186. https://doi.org/10.1093/nar/gkr944
doi: 10.1093/nar/gkr944
pubmed: 22110026
Grant D, Nelson RT, Cannon SB, Shoemaker RC (2010) SoyBase, the USDA-ARS soybean genetics and genomics database. Nucleic Acids Res 38(suppl 1):D843–D846. https://doi.org/10.1093/nar/gkp798
doi: 10.1093/nar/gkp798
pubmed: 20008513
Hartwig EE, Hinson K (1972) Association between chemical composition of seed and seed yield of soybeans. Crop Sci 12:829–830
doi: 10.2135/cropsci1972.0011183X001200060034x
Haun WJ, Hyten DL, Xu WW, Gerhardt DJ, Albert TJ, Richmond T, Jeddeloh JA, Jia G, Springer NM, Vance CP, Stupar RM (2011) The composition and origins of genomic variation among individuals of the soybean reference cultivar Williams 82. Plant Physiol 155:645–655
doi: 10.1104/pp.110.166736
Herman EM (2014) Soybean seed proteome rebalancing. Front Plant Sci 5(437):1–8
Hwang E-Y, Qijian S, Jia G, Specht JE, Hyten DL, Costa J, Cregan PB (2014) A genome-wide association study of seed protein and oil content in soybean. BMC Genom 15:1–25
doi: 10.1186/1471-2164-15-1
Hwang W, Kim M, Kang Y, Shim S, Stacey M, Stacey G, Lee S-H (2015) Genome-wide analysis of mutations in a dwarf soybean mutant induced by fast neutron bombardment. Euphytica 203:399–408
doi: 10.1007/s10681-014-1295-x
Hymowitz T, Collins FI, Walker WM, Panczner J (1972) Relationship between content of oil, protein, and sugar in soybean seed. Agron J 64:613
doi: 10.2134/agronj1972.00021962006400050019x
Jaureguy LM, Chen P, Scaboo AM (2011) Heritability and correlations among food-grade traits in soybean. Plant Breed 130:647–652
doi: 10.1111/j.1439-0523.2011.01887.x
Kabelka EA, Diers BW, Fehr WR, LeRoy AR, Baianu IC, You T, Neece DJ, Nelson RL (2004) Putative alleles for increased yield from soybean plant introductions. Crop Sci 44(3):784–791
doi: 10.2135/cropsci2004.7840
Keim P, Olson TC, Shoemaker RC (1988) A rapid protocol for isolating soybean DNA. Soybean Genet Newsl 18:150–152
Kim HK, Kang ST, Oh KW (2006) Mapping of putative quantitative trait loci controlling the total oligosaccharide and sucrose content of Glycine max seeds. J Plant Res 119:533–538
doi: 10.1007/s10265-006-0004-9
pubmed: 16941063
pmcid: 16941063
Kim M, Schultz S, Nelson RL, Diers BW (2016) Identification and fine mapping of a soybean seed protein QTL from PI 407788A on chromosome 15. Crop Sci 56(1):219–225. https://doi.org/10.2135/cropsci2015.06.0340
doi: 10.2135/cropsci2015.06.0340
Kuznetsova A, Brockhoff PB, Christensen RHB (2016). lmerTest: tests in linear mixed effects models. R package version 2.0-33. https://CRAN.R-project.org/package=lmerTest
Lee SH, Bailey MA, Mian MAR, Carter TE Jr, Shipe ER, Ashley DA, Parrott WA, Hussey RS, Boerma HR (1996) RFLP loci associated with soybean seed protein and oil content across populations and locations. Theor Appl Genet 93(5–6):649–657
doi: 10.1007/BF00224058
Li H (2011) A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinform 27(21):2987–2993
doi: 10.1093/bioinformatics/btr509
Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v2 (q-bio.GN)
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinform 25:1754–1760
doi: 10.1093/bioinformatics/btp324
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinform 25:2078–2079
doi: 10.1093/bioinformatics/btp352
Liang H, Yu Y, Wang S, Lian Y, Wang T, Wei Y, Gong P, Liu X, Fang X, Zhang M (2010) QTL Mapping of isoflavone, oil and protein contents in soybean (Glycine max L. Merr.). Agric Sci China 9(8):1108–1116
doi: 10.1016/S1671-2927(09)60197-8
Lu W, Wen Z, Li H, Yuan D, Li J, Zhang H, Huang Z, Cui S, Du W (2013) Identification of the quantitative trait loci (QTL) underlying water soluble protein content in soybean. Theor Appl Genet 126:425–433
doi: 10.1007/s00122-012-1990-8
Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17(1):10–12. https://doi.org/10.14806/ej.17.1.200
doi: 10.14806/ej.17.1.200
Mian R, McHale L, Li Z, Dorrance AE (2017) Registration of ‘HighPro1’ soybean with high protein and high yield developed from a north x south cross. J Plant Reg 11:51–54
doi: 10.3198/jpr2016.03.0013crc
Muñoz-Amatriaín M, Eichten SR, Wicker T, Richmond TA, Mascher M, Steuernagel B, Scholz U, Ariyadasa R, Spannagl M, Nussbaumer T, Mayer KF, Taudien S, Platzer M, Jeddeloh JA, Springer JM, Muehlbauer GJ, Stein N (2013) Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome. Genome Biol 14(6):R58. https://doi.org/10.1186/gb-2013-14-6-r58
doi: 10.1186/gb-2013-14-6-r58
pubmed: 3706897
pmcid: 3706897
Nichols DM, Glover KD, Carlson SR, Specht JE, Diers BW (2006) Fine mapping of a seed protein QTL on soybean linkage group I and its correlated effects on agronomic traits. Crop Sci 46:834–839
doi: 10.2135/cropsci2005.05-0168
Patil G, Mian R, Vuong T, Pantalone V, Song Q, Chen P, Shannon G, Carter TE, Nguyen H (2017) Molecular mapping and genomics of soybean seed protein: a review and perspective for the future. Theor Appl Genet 130:1975–1991
doi: 10.1007/s00122-017-2955-8
pubmed: 5606949
pmcid: 5606949
Pham AT, McNally K, Abdel-Haleem H, Boerma HR, Li Z (2013) Fine mapping and identification of candidate genes controlling the resistance to southern root-knot nematode in PI 96354. Theor Appl Genet 126(7):1825–1838
doi: 10.1007/s00122-013-2095-8
Phansak P, Soonsuwon W, Hyten DL, Song Q, Cregan PB, Graef GL, Specht JE (2016) Multi-population selective genotyping to identify soybean [Glycine max (L.) Merr.] seed protein and oil QTLs. G3 Genes Genomes Genet 6:1635–1648
Prenger EM, Mian R, Buckley B, Boerma HR, Li Z (2018). Introgression of a high protein allele into an elite soybean variety results in a high-protein near-isogenic line with yield parity. Chapter 3. MS thesis, University of Georgia
Qi Z, Wu Q, Han X, Sun Y-n, Du X-y, Liu C-y, Jiang H-w, Hu G-h, Chen Q-s (2011a) Soybean oil content QTL mapping and integrating with meta-analysis method for mining genes. Euphytica 179:499–514
doi: 10.1007/s10681-011-0386-1
Qi Z, Ya-nan S, Qiong W, Chun-yan L, Guo-hua H, Qing-shan C (2011b) A meta-analysis of seed protein concentration QTL in soybean. Can J Plant Sci 91:221–230
doi: 10.4141/cjps09193
Qiu BX, Arelli PR, Sleper DA (1999) RFLP markers associated with soybean cyst nematode resistance and seed composition in a ‘Peking’ x ‘Essex’ population. Theor Appl Genet 98(3–4):356–364
doi: 10.1007/s001220051080
R Core Team (2013) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0. http://www.R-project.org/
Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP (2011) Integrative genomics viewer. Nat Biotechnol 29:24–26
doi: 10.1038/nbt.1754
pubmed: 3346182
pmcid: 3346182
Schmutz et al (2010) Genome sequence of the palaeopolyploid soybean. Nat 463:178–183
doi: 10.1038/nature08670
Sebolt AM, Shoemaker RC, Diers BW (2000) Analysis of a quantitative trait locus allele from wild soybean that increases seed protein concentration in soybean. Crop Sci 40:1438–1444
doi: 10.2135/cropsci2000.4051438x
Severin AJ, Woody JL, Bolon Y-T, Joseph B, Diers BW, Farmer AD, Muehlbauer GJ, Nelson RT, Grant D, Specht JE, Graham MA, Cannon SB, May GD, Vance CP, Shoemaker RC (2010) RNA-seq atlas of glycine max: a guide to the soybean transcriptome. BMC Plant Biol 10:160
doi: 10.1186/1471-2229-10-160
pubmed: 3017786
pmcid: 3017786
Song Q, Hyten DL, Jia G, Quigley CV, Fickus EW, Nelson RL, Cregan PB (2013) Development and evaluation of SoySNP50 K, a high-density genotyping array for soybean. PLoS ONE 8:e54985
doi: 10.1371/journal.pone.0054985
pubmed: 3555945
pmcid: 3555945
Song Q, Jenkins J, Jia G, Hyten DL, Pantalone V, Jackson SA, Schmutz J, Cregan PB (2016) Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01. BMC Genom 17:33
doi: 10.1186/s12864-015-2344-0
Springer NM, Ying K, Fu Y, Ji T, Yeh C-T, Jia Y, Wu W, Richmond T, Kitzman J, Rosenbaum H, Iniguez AL, Barbazuk WB, Jeddeloh JA, Nettleton D, Schnable PS (2009) Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLoS Genet 5(11):e1000734. https://doi.org/10.1371/journal.pgen.1000734
doi: 10.1371/journal.pgen.1000734
pubmed: 2780416
pmcid: 2780416
Stacey MG, Cahoon RE, Nguyen HT, Cui Y, Sato S, Nguyen CT, Phoka N, Clark KM, Liang Y, Forrester J, Batek J, Do PT, Sleper DA, Clemente TE, Cahoon EB, Stacey G (2016) Identification of homogentisate dioxygenase as a target for vitamin E biofortification in oilseeds. Plant Physiol 172:1506
doi: 10.1104/pp.16.00941
pubmed: 5100773
pmcid: 5100773
Teng W, Li W, Zhang Q, Wu D, Zhao X, Li H, Han Y, Li W (2017) Identification of quantitative trait loci underlying seed protein content of soybean including main, epistatic, and QTL × environment effects in different regions of Northeast China. Genome 60(8):649–655. https://doi.org/10.1139/gen-2016-0189
doi: 10.1139/gen-2016-0189
pubmed: 28445652
Thorne JC, Fehr WR (1970) Incorporation of high-protein, exotic germplasm into soybean populations by 2- and 3-way crosses. Crop Sci 10:652–655
doi: 10.2135/cropsci1970.0011183X001000060012x
Thorvaldsdóttir H, Robinson JT, Mesirov JP (2013) Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 14:178–192
doi: 10.1093/bib/bbs017
Valliyodan B, Shi H, Nguyen HT (2015) A simple analytical method for high-throughput screening of major sugars from soybean by normal-phase HPLC with evaporative light scattering detection. Chromatogr Res Int 15:8
van de Wiel CCM, Schaart JG, Lotz LAP, Smulders MJM (2017) New traits in crops produced by genome editing techniques based on deletions. Plant Biotechnol Rep 11:1–8. https://doi.org/10.1007/s11816-017-0425-z
doi: 10.1007/s11816-017-0425-z
pubmed: 5360818
pmcid: 5360818
Vaughn M (2012) Uncompress files with gunzip. CyVerse http://www.gnu.org/software/gzip/
Vaughn JN, Nelson RL, Song Q, Cregan PB, Li Z (2014) The genetic architecture of seed composition in soybean is refined by genome-wide association scans across multiple populations. G3 Genes Genomes Genet 4:2283–2294
Walls R (2018) Concatenate multiple files. BusyBox. CyVerse. https://de.cyverse.org/de/?type=apps&app-id=77830f32-084a-11e8-a871-008cfa5ae621&system-id=de
Warrington CV, Abdel-Haleem H, Hyten DL, Cregan PB, Orf JH, Killam AS, Bajjalieh N, Li Z, Boerma HR (2015) QTL for seed protein and amino acids in the Benning × Danbaekkong soybean population. Theor Appl Genet 128:839–850
doi: 10.1007/s00122-015-2474-4
Wilcox JR, Cavins JF (1995) Backcrossing high seed protein to a soybean cultivar. Crop Sci 35:1036–1041
doi: 10.2135/cropsci1995.0011183X003500040019x
Wilcox JR, Zhang GD (1997) Relationships between seed yield and seed protein in determinate and indeterminate soybean populations. Crop Sci 37:361–364
doi: 10.2135/cropsci1997.0011183X003700020009x
Wilson RF (2004) Seed composition. In: Boerma HR, Specht JE (eds) Soybean: improvement, production and uses, 3rd edn. ASA and CSSA, Madison, pp 671–677
Yin XH, Vyn TJ (2005) Relationships of isoflavone, oil, and protein in seed with yield of soybean. Agron J 97:1314–1321
doi: 10.2134/agronj2004.0316
Yu P, Wang C, Xu Q, Feng Y, Yuan X, Yu H, Wang Y, Tang S, Wei X (2011) Detection of copy number variations in rice using array-based comparative genomic hybridization. BMC Genom 12:372. https://doi.org/10.1186/1471-2164-12-372
doi: 10.1186/1471-2164-12-372