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Mapping and identification of a potential candidate gene for a novel maturity locus, E10, in soybean

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Abstract

Key message

E10 is a new maturity locus in soybean and FT4 is the predicted/potential functional gene underlying the locus.

Abstract

Flowering and maturity time traits play crucial roles in economic soybean production. Early maturity is critical for north and west expansion of soybean in Canada. To date, 11 genes/loci have been identified which control time to flowering and maturity; however, the molecular bases of almost half of them are not yet clear. We have identified a new maturity locus called “E10” located at the end of chromosome Gm08. The gene symbol E10e10 has been approved by the Soybean Genetics Committee. The e10e10 genotype results in 5–10 days earlier maturity than E10E10. A set of presumed E10E10 and e10e10 genotypes was used to identify contrasting SSR and SNP haplotypes. These haplotypes, and their association with maturity, were maintained through five backcross generations. A functional genomics approach using a predicted protein–protein interaction (PPI) approach (Protein–protein Interaction Prediction Engine, PIPE) was used to investigate approximately 75 genes located in the genomic region that SSR and SNP analyses identified as the location of the E10 locus. The PPI analysis identified FT4 as the most likely candidate gene underlying the E10 locus. Sequence analysis of the two FT4 alleles identified three SNPs, in the 5′UTR, 3′UTR and fourth exon in the coding region, which result in differential mRNA structures. Allele-specific markers were developed for this locus and are available for soybean breeders to efficiently develop earlier maturing cultivars using molecular marker assisted breeding.

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Abbreviations

GO:

Gene ontology

MP-PIPE:

Massively parallel protein–protein interaction prediction engine

PIPE:

Protein–protein interaction prediction engine

PPIs:

Protein–protein interactions

QTLs:

Quantitative trait loci

SNP:

Single nucleotide polymorphism

SSR:

Simple sequence repeat

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Acknowledgements

This work was funded in part by the Canadian Field Crop Research Alliance (CFCRA) and Agriculture and Agri-Food Canada through the Growing Forward 2 Agri-Innovation Program and also by the Natural Sciences and Engineering Council of Canada (NSERC).

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Authors and Affiliations

  1. Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada

    Bahram Samanfar, Stephen J. Molnar, Martin Charette & Elroy R. Cober

  2. School of Computer Science, Carleton University, Ottawa, ON, K1S 5B6, Canada

    Andrew Schoenrock & Frank Dehne

  3. Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, K1S 5B6, Canada

    Ashkan Golshani

  4. Département de Phytologie and Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC, G1V 0A6, Canada

    François Belzile

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  1. Bahram Samanfar
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  2. Stephen J. Molnar
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  4. Andrew Schoenrock
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  8. Elroy R. Cober
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Correspondence to Elroy R. Cober.

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Communicated by V. Hahn.

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Samanfar, B., Molnar, S.J., Charette, M. et al. Mapping and identification of a potential candidate gene for a novel maturity locus, E10, in soybean. Theor Appl Genet 130, 377–390 (2017). https://doi.org/10.1007/s00122-016-2819-7

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  • DOI: https://doi.org/10.1007/s00122-016-2819-7

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