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

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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.

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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

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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.

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Authors and Affiliations

  1. Department of Crop and Soil Sciences and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, GA, 30602, USA

    Elizabeth M. Prenger, Alexandra Ostezan & Zenglu Li

  2. Soybean and Nitrogen Fixation Research Unit, USDA-ARS, Raleigh, NC, 27607, USA

    M. A. Rouf Mian

  3. Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA

    Robert M. Stupar

  4. Deparment of Genetics, University of Georgia, Athens, GA, 30602, USA

    Travis Glenn

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  1. Elizabeth M. Prenger
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Contributions

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.

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Correspondence to Zenglu Li.

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122_2019_3399_MOESM2_ESM.tif

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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Prenger, E.M., Ostezan, A., Mian, M.A.R. et al. Identification and characterization of a fast-neutron-induced mutant with elevated seed protein content in soybean. Theor Appl Genet 132, 2965–2983 (2019). https://doi.org/10.1007/s00122-019-03399-w

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