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Theoretical and Applied Genetics

, Volume 132, Issue 11, pp 2965–2983 | Cite as

Identification and characterization of a fast-neutron-induced mutant with elevated seed protein content in soybean

  • Elizabeth M. Prenger
  • Alexandra Ostezan
  • M. A. Rouf Mian
  • Robert M. Stupar
  • Travis Glenn
  • Zenglu LiEmail author
Original Article

Abstract

Key message

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.

Abstract

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−1 more protein than the parents across 10 environments. Comparative genomic hybridization (CGH) identified putative mutations in a mutant, G15FN-12, that has 36.8 g kg−1 higher protein than the parent genotype, and whole genome sequencing (WGS) of the mutant has confirmed these mutations. An F2:3 population was developed from G15FN-12 to determine association between genomic changes and increased protein content. Bulked segregant analysis of the population using the SoySNP50K BeadChip identified a CGH- and WGS-confirmed deletion on chromosome 12 to be responsible for elevated protein content. The population was genotyped using a KASP marker designed at the mutation region, and significant association (P < 0.0001) between the deletion on chromosome 12 and elevated protein content was observed and confirmed in the F3:4 generation. The F2 segregants homozygous for the deletion averaged 27 g kg−1 higher seed protein and 8 g kg−1 lower oil than homozygous wild-type segregants. Mutants with altered seed composition are a new resource for gene function studies and provide elite materials for genetic improvement of seed composition.

Keywords

Fast neutrons Mutant Protein content Soybeans Deletion Chromosome 12 

Abbreviations

BAM

Binary alignment map

BLAST

Basic local alignment search tool

BLUP

Best linear unbiased predictor

BSA

Bulked segregant analysis

BWA

Burrows-Wheeler aligner

CGH

Comparative genomic hybridization

CNV

Copy number variation

CRISPR

Clustered regularly interspaced short palindromic repeats

FN

Fast neutron

GWAS

Genome-wide association study

IGV

Integrative Genomics Viewer

KASP

Kompetitive allele specific PCR

MG

Maturity Group

NIL

Near-isogenic line

NIR

Near-infrared

PCR

Polymerase chain reaction

PI

Plant introduction

QTL

Quantitative trait locus

RFO

Raffinose family of oligosaccharides

RIL

Recombinant inbred line

RT-PCR

Reverse transcription polymerase chain reaction

SAM

Sequence alignment/map format

SNP

Single nucleotide polymorphism

WGS

Whole genome sequencing

Notes

Acknowledgements

We thank the United Soybean Board and the John Ingle Innovation in Plant Breeding Award for funding this research. Thanks to Dale Wood, Earl Baxter, Brice Wilson, Jeremy Nation, Greg Gokalp, Ricky Zoller, Tatyana Nienow, Troy Kieran, and Swarnali Louha from University of Georgia, and Adrian Stec and Jean-Michel Michno from University of Minnesota for their technical support. Thanks to Blair Buckley for growing the yield trial at Bossier, LA. Thanks to Drs. Henry Nguyen and Tri Vuong from University of Missouri for analyzing the sugar content.

Author Contribution statement

EMP conducted the experiment, analyzed the data, and drafted the manuscript; RMS and TG conducted comparative genomic hybridization and whole genome sequencing, respectively; MARM performed field tests; AO conducted seed composition analysis; and ZL designed and organized the experiment, interpreted the results, and edited the manuscript.

Compliance with ethical standards

Conflict of interest

On behalf of all authors, the corresponding author states that there is no conflict of interest.

Supplementary material

122_2019_3399_MOESM1_ESM.docx (40 kb)
Supplementary material 1 (DOCX 39 kb)
122_2019_3399_MOESM2_ESM.tif (58.9 mb)
Fig. S1. Protein differences among genotypes in the F3 Benning × G15FN-12 populationProtein content is reported in g kg-1 on a dry matter basis. P<.0001. An “n” indicates the number of F3 families measured for each corresponding genotype. (TIFF 60353 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Crop and Soil Sciences and Institute of Plant Breeding, Genetics, and GenomicsUniversity of GeorgiaAthensUSA
  2. 2.Soybean and Nitrogen Fixation Research UnitUSDA-ARSRaleighUSA
  3. 3.Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulUSA
  4. 4.Deparment of GeneticsUniversity of GeorgiaAthensUSA

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