Identification and Candidate Gene Evaluation of a Large Fast Neutron-Induced Deletion Associated with a High-Oil Phenotype in Soybean Seeds

Overview

Journal Genes (Basel)

Publisher MDPI

Date 2024 Jul 27

PMID 39062671

Authors

William R Serson

Mohammad Fazel Soltani Gishini

Robert M Stupar

Adrian O Stec

Paul R Armstrong

David Hildebrand

Affiliations

Soon will be listed here.

Abstract

Since the dawn of agriculture, crops have been genetically altered for desirable characteristics. This has included the selection of natural and induced mutants. Increasing the production of plant oils such as soybean () oil as a renewable resource for food and fuel is valuable. Successful breeding for higher oil levels in soybeans, however, usually results in reduced seed protein. A soybean fast neutron population was screened for oil content, and three high oil mutants with minimal reductions in protein levels were found. Three backcross F2 populations derived from these mutants exhibited segregation for seed oil content. DNA was pooled from the high-oil and normal-oil plants within each population and assessed by comparative genomic hybridization. A deletion encompassing 20 gene models on chromosome 14 was found to co-segregate with the high-oil trait in two of the three populations. Eighteen genes in the deleted region have known functions that appear unrelated to oil biosynthesis and accumulation pathways, while one of the unknown genes () may contribute to the regulation of lipid droplet formation. This high-oil trait can facilitate the breeding of high-oil soybeans without protein reduction, resulting in higher meal protein levels.

References

Kavanagh K, Jornvall H, Persson B, Oppermann U . Medium- and short-chain dehydrogenase/reductase gene and protein families : the SDR superfamily: functional and structural diversity within a family of metabolic and regulatory enzymes. Cell Mol Life Sci. 2008; 65(24):3895-906. PMC: 2792337. DOI: 10.1007/s00018-008-8588-y. View

Zhu Q, King G, Liu X, Shan N, Borpatragohain P, Baten A . Identification of SNP loci and candidate genes related to four important fatty acid composition in Brassica napus using genome wide association study. PLoS One. 2019; 14(8):e0221578. PMC: 6707581. DOI: 10.1371/journal.pone.0221578. View

Prenger E, Ostezan A, Mian M, Stupar R, Glenn T, Li Z . Identification and characterization of a fast-neutron-induced mutant with elevated seed protein content in soybean. Theor Appl Genet. 2019; 132(11):2965-2983. DOI: 10.1007/s00122-019-03399-w. View

Teaster N, Motes C, Tang Y, Wiant W, Cotter M, Wang Y . N-Acylethanolamine metabolism interacts with abscisic acid signaling in Arabidopsis thaliana seedlings. Plant Cell. 2007; 19(8):2454-69. PMC: 2002614. DOI: 10.1105/tpc.106.048702. View

Almeida J, Quadrana L, Asis R, Setta N, de Godoy F, Bermudez L . Genetic dissection of vitamin E biosynthesis in tomato. J Exp Bot. 2011; 62(11):3781-98. PMC: 3134339. DOI: 10.1093/jxb/err055. View

Le Boulch P, Poessel J, Roux D, Lugan R . Molecular mechanisms of resistance to conferred by the peach gene: A multi-omics view. Front Plant Sci. 2022; 13:992544. PMC: 9581297. DOI: 10.3389/fpls.2022.992544. View

Durufle H, Ranocha P, Balliau T, Zivy M, Albenne C, Burlat V . An integrative Study Showing the Adaptation to Sub-Optimal Growth Conditions of Natural Populations of : A Focus on Cell Wall Changes. Cells. 2020; 9(10). PMC: 7601860. DOI: 10.3390/cells9102249. View

Vanhercke T, El Tahchy A, Shrestha P, Zhou X, Singh S, Petrie J . Synergistic effect of WRI1 and DGAT1 coexpression on triacylglycerol biosynthesis in plants. FEBS Lett. 2013; 587(4):364-9. DOI: 10.1016/j.febslet.2012.12.018. View

Cvrckova F, Novotny M, Pickova D, Zarsky V . Formin homology 2 domains occur in multiple contexts in angiosperms. BMC Genomics. 2004; 5(1):44. PMC: 509240. DOI: 10.1186/1471-2164-5-44. View

10.

Vargas J, Gomez I, Vidal E, Lee C, Millar A, Jordana X . Growth Developmental Defects of Mitochondrial Iron Transporter 1 and 2 Mutants in Arabidopsis in Iron Sufficient Conditions. Plants (Basel). 2023; 12(5). PMC: 10007191. DOI: 10.3390/plants12051176. View

11.

Yang M, Zhou C, Yang H, Kuang R, Huang B, Wei Y . Genome-wide analysis of basic helix-loop-helix transcription factors in papaya ( L.). PeerJ. 2020; 8:e9319. PMC: 7341539. DOI: 10.7717/peerj.9319. View

12.

Kelley L, Mezulis S, Yates C, Wass M, Sternberg M . The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc. 2015; 10(6):845-58. PMC: 5298202. DOI: 10.1038/nprot.2015.053. View

13.

Krishnatreya D, Ray D, Baruah P, Dowarah B, Bordoloi K, Agarwal H . Identification of putative miRNAs from expressed sequence tags of L. and their cross-kingdom targets. BioTechnologia (Pozn). 2023; 102(2):179-195. PMC: 9645573. DOI: 10.5114/bta.2021.106525. View

14.

Allen D, Young J . Carbon and nitrogen provisions alter the metabolic flux in developing soybean embryos. Plant Physiol. 2013; 161(3):1458-75. PMC: 3585609. DOI: 10.1104/pp.112.203299. View

15.

Islam N, Stupar R, Qijian S, Luthria D, Garrett W, Stec A . Genomic changes and biochemical alterations of seed protein and oil content in a subset of fast neutron induced soybean mutants. BMC Plant Biol. 2019; 19(1):420. PMC: 6790046. DOI: 10.1186/s12870-019-1981-x. View

16.

Lange H, Gagliardi D . Catalytic activities, molecular connections, and biological functions of plant RNA exosome complexes. Plant Cell. 2021; 34(3):967-988. PMC: 8894942. DOI: 10.1093/plcell/koab310. View

17.

Kashima M, Kamitani M, Nomura Y, Mori-Moriyama N, Betsuyaku S, Hirata H . DeLTa-Seq: direct-lysate targeted RNA-Seq from crude tissue lysate. Plant Methods. 2022; 18(1):99. PMC: 9356424. DOI: 10.1186/s13007-022-00930-x. View

18.

Wyant S, Rodriguez M, Carter C, Parrott W, Jackson S, Stupar R . Fast neutron mutagenesis in soybean enriches for small indels and creates frameshift mutations. G3 (Bethesda). 2022; 12(2). PMC: 9335934. DOI: 10.1093/g3journal/jkab431. View

19.

Chang C, Slesak I, Jorda L, Sotnikov A, Melzer M, Miszalski Z . Arabidopsis chloroplastic glutathione peroxidases play a role in cross talk between photooxidative stress and immune responses. Plant Physiol. 2009; 150(2):670-83. PMC: 2689974. DOI: 10.1104/pp.109.135566. View

20.

Yang Z, Lasker K, Schneidman-Duhovny D, Webb B, Huang C, Pettersen E . UCSF Chimera, MODELLER, and IMP: an integrated modeling system. J Struct Biol. 2011; 179(3):269-78. PMC: 3410985. DOI: 10.1016/j.jsb.2011.09.006. View