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Theoretical and Applied Genetics

, Volume 132, Issue 2, pp 289–300 | Cite as

Targeted recombination to increase genetic gain in self-pollinated species

  • Sushan Ru
  • Rex BernardoEmail author
Original Article

Abstract

Key message

If we can induce or select for recombination at targeted marker intervals, genetic gains for quantitative traits in self-pollinated species may be doubled.

Abstract

Targeted recombination refers to inducing or selecting for a recombination event at genomic positions that maximize genetic gain in a cross. A previous study indicated that targeted recombination could double the rate of genetic gains in maize (Zea mays L.), a cross-pollinated crop for which historical genetic gains have been large. Our objectives were to determine whether targeted recombination can sufficiently increase predicted gains in self-pollinated species, and whether prospective gains from targeted recombination vary across crops, populations, traits, and chromosomes. Genomewide marker effects were estimated from previously published marker and phenotypic data on 21 biparental populations of soybean [Glycine max (L.) Merr.], wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), and pea (Pisum sativum L.). With the predicted gain from nontargeted recombination as the baseline, the relative gains from creating a doubled haploid with up to one targeted recombination [RG(x ≤ 1)] and two targeted recombinations [RG(x ≤ 2)] per chromosome or linkage group were calculated. Targeted recombination significantly (P = 0.05) increased the predicted genetic gain compared to nontargeted recombination for all traits and all populations, except for plant height in barley. The mean RG(x ≤ 1) was 211%, whereas the mean RG(x ≤ 2) was 243%. The predicted gain varied among traits and populations. For most traits and populations, having targeted recombination on less than a third of all the chromosomes led to the same or higher predicted gain than nontargeted recombination. Together with previous findings in maize, our results suggested that targeted recombination could double the genetic gains in both self- and cross-pollinated crops.

Notes

Acknowledgements

We thank Drs. Dorrie Main, Yu Ma, and Arron Carter at Washington State University and Drs. Matthew Paul Reynolds and Sivakumar Sukumaran at CIMMYT for kindly sharing their data with us.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

122_2018_3216_MOESM1_ESM.docx (20 kb)
Supplementary material 1 (DOCX 20 kb)

References

  1. Bernardo R (2017) Prospective targeted recombination and genetic gains for quantitative traits in maize. Plant Genome.  https://doi.org/10.3835/plantgenome2016.11.0118 Google Scholar
  2. Blake VC, Birkett C, Matthews DE, Hane DL, Bradbury P, Jannink JL (2016) The Triticeae toolbox: combining phenotype and genotype data to advance small-grains breeding. Plant Genome.  https://doi.org/10.3835/plantgenome2014.12.0099 Google Scholar
  3. Bradariz S, Bernardo R (2018) Genetic gains from targeted recombination in 27 elite biparental maize populations [abstract]. In: Plant & animal genome conference XXVI, San Diego, CA, 13–17 Jan 2018. Abstract number P0849Google Scholar
  4. Broman KW, Wu H, Sen Ś, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889–890CrossRefGoogle Scholar
  5. Carter AH, Garland-Campbell K, Kidwell KK (2011) Genetic mapping of quantitative trait loci associated with important agronomic traits in the spring wheat (Triticum aestivum L.) cross ‘Louise’ × ‘Penawawa’. Crop Sci 51:84–95CrossRefGoogle Scholar
  6. Carter AH, Garland-Campbell K, Morris CF, Kidwell KK (2012) Chromosomes 3B and 4D are associated with several milling and baking quality traits in a soft white spring wheat (Triticum aestivum L.) population. Theor Appl Genet 124:1079–1096CrossRefGoogle Scholar
  7. Choi K, Henderson IR (2015) Meiotic recombination hotspots: a comparative view. Plant J 83:52–61CrossRefGoogle Scholar
  8. Endelman JB (2011) Ridge regression and other kernels for genomic selection with R package rrBLUP. Plant Genome 4:250–255CrossRefGoogle Scholar
  9. Hayes PM, Liu BH, Knapp SJ, Chen F, Jones B, Blake T, Franckowiak J, Rasmusson D, Sorrells M, Ullrich SE, Wesenberg D, Kleinhofs A (1993) Quantitative trait locus effects and environmental interaction in a sample of North American barley germplasm. Theor Appl Genet 87:392–401CrossRefGoogle Scholar
  10. Hayut SF, Bessudo CM, Levy AA (2017) Targeted recombination between homologous chromosomes for precise breeding in tomato. Nat Commun 8:15605CrossRefGoogle Scholar
  11. Loidl J, Lorenz A (2016) DNA double-strand break formation and repair in Tetrahymena meiosis. Semin Cell Dev Biol 54:126–134CrossRefGoogle Scholar
  12. Lopes MS, Reynolds MP, McIntyre CL, Mathews KL, Jalal Kamali MR, Mossad M, Feltaous Y, Tahir ISA, Chatrath R, Ogbonnaya F, Baum M (2013) QTL for yield and associated traits in the Seri/Babax population grown across several environments in Mexico, in the West Asia, North Africa, and South Asia regions. Theor Appl Genet 126:971–984CrossRefGoogle Scholar
  13. Ma Y, Coyne CJ, Grusak MA, Mazourek M, Cheng P, Main D, McGee RJ (2017) Genome-wide SNP identification, linkage map construction and QTL mapping for seed mineral concentrations and contents in pea (Pisum sativum L.). BMC Plant Biol 17:43CrossRefGoogle Scholar
  14. Margarido GRA, Souza AP, Garcia AAF (2007) OneMap: software for genetic mapping in outcrossing species. Hereditas 144:78–79CrossRefGoogle Scholar
  15. O’Sullivan H (2007) GrainGenes. In: Edwards D (ed) Plant bioinformatics. Methods in molecular biology™, vol 406. Humana Press, Totowa, pp 301–314CrossRefGoogle Scholar
  16. Peciña A, Smith KN, Mézard C, Murakami H, Ohta K, Nicolas A (2002) Targeted stimulation of meiotic recombination. Cell 111:173–184CrossRefGoogle Scholar
  17. R Core Team (2017) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. http://www.R-project.org/. Accessed 2 May 2017
  18. Sadhu MJ, Bloom JS, Day L, Kruglyak L (2016) CRISPR-directed mitotic recombination enables genetic mapping without crosses. Science 352:1113–1116CrossRefGoogle Scholar
  19. Sarno R, Vicq Y, Uematsu N, Luka M, Lapierre C, Carroll D, Bastianelli G, Serero A, Nicolas A (2017) Programming sites of meiotic crossovers using Spo11 fusion proteins. Nucleic Acids Res 45:e164CrossRefGoogle Scholar
  20. USDA NASS, Quick Stats. https://quickstats.nass.usda.gov/. Accessed 22 May 2018
  21. Wright DA, Townsend JA, Winfrey RJ, Irwin PA, Rajagopal J, Lonosky PM, Hall BD, Jondle MD, Voytas DF (2005) High-frequency homologous recombination in plants mediated by zinc-finger nucleases. Plant J 44:693–705CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulUSA

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