Modeling of genetic gain for single traits from marker-assisted seedling selection in clonally propagated crops

Abstract

Seedling selection identifies superior seedlings as candidate cultivars based on predicted genetic potential for traits of interest. Traditionally, genetic potential is determined by phenotypic evaluation. With the availability of DNA tests for some agronomically important traits, breeders have the opportunity to include DNA information in their seedling selection operations-known as marker-assisted seedling selection. A major challenge in deploying marker-assisted seedling selection in clonally propagated crops is a lack of knowledge in genetic gain achievable from alternative strategies. Existing models based on additive effects considering seed-propagated crops are not directly relevant for seedling selection of clonally propagated crops, as clonal propagation captures all genetic effects, not just additive. This study modeled genetic gain from traditional and various marker-based seedling selection strategies on a single trait basis through analytical derivation and stochastic simulation, based on a generalized seedling selection scheme of clonally propagated crops. Various trait-test scenarios with a range of broad-sense heritability and proportion of genotypic variance explained by DNA markers were simulated for two populations with different segregation patterns. Both derived and simulated results indicated that marker-based strategies tended to achieve higher genetic gain than phenotypic seedling selection for a trait where the proportion of genotypic variance explained by marker information was greater than the broad-sense heritability. Results from this study provides guidance in optimizing genetic gain from seedling selection for single traits where DNA tests providing marker information are available.

References

[1] Grüneberg W, Mwanga R, Andrade M, Espinoza J . Selection methods. Part 5: breeding clonally propagated crops. In: Ceccarelli S, Guimaraes EP, Weltizien E (eds). Plant Breeding and Farmer Participation. Food and Agriculture Organization of the United Nations: Rome, Italy, 2009, 275-322.

[2] McKey D, Elias M, Pujol B, Duputié A . The evolutionary ecology of clonally propagated domesticated plants. New Phytologist 2010; 186: 318-332.

[3] Badenes ML, Byrne DH . Fruit Breeding. Springer: New York, 2012.

[4] Tester M, Langridge P . Breeding technologies to increase crop production in a changing world. Science 2010; 327: 818-822.

[5] Holland JB, Nyquist WE, Cervantes-Martínez CT . Estimating and interpreting heritability for plant breeding: an update. In: Janick J (ed). Plant Breeding Reviews, vol. 22. John Wiley & Sons, Inc.: Oxford, UK, 2010.

[6] Ru S, Main D, Evans K, Peace C . Current applications, challenges, and perspectives of marker-assisted seedling selection in Rosaceae tree fruit breeding. Tree Genet Genomes 2015; 11: 8.

[7] Mullin TJ, Park YS . Estimating genetic gains from alternative breeding strategies for clonal forestry. Can J For Res 1992; 22: 14-23.

[8] Evans K. Apple breeding in the Pacifict Northwest. Acta Hortic 2013; 976: 75-78.

[9] Dirlewanger E, Graziano E, Joobeur T, Garriga-Calderé F, Cosson P, Howad W et al. Comparative mapping and marker-assisted selection in Rosaceae fruit crops. Proc Natl Acad Sci USA 2004; 101: 9891-9896.

[10] Luby JJ, Shaw DV . Does marker-assisted selection make dollars and sense in a fruit breeding program? HortScience 2001; 36: 872-879.

[11] Collard BCY, Mackill DJ . Marker-assisted selection: An approach for precision plant breeding in the twenty-first century. Phil Trans R Soc B 2008; 363: 557-572.

[12] Dwivedi SL, Crouch JH, Mackill DJ, Xu Y, Blair MW, Ragot M et al. The molecularization of public sector crop breeding: Progress, problems, and prospects. Adv Agron 2007; 95: 163-318.

[13] Bliss FA . Marker-assisted breeding in horticultural crops. Acta Hortic 2010; 859: 339-350.

[14] Peace C, Norelli JL . Genomics approaches to crop improvement in the Rosaceae. In: Folta KM, Gardiner SE (eds). Genetics and Genomics of Rosaceae. Springer: New York, 2009, 19-53.

[15] Lande R, Thompson R . Efficiency of marker-assisted selection in the improvement of quantitative traits. Genetics 1990; 124: 743-756.

[16] Edge-Garza DA, Zhu Y, Peace CP . Enabling marker-assisted seedling selection in the Washington apple breeding program. Acta Hortic 2010; 859: 369-373.

[17] Edge-Garza DA, Luby JJ, Peace CP . Decision support for cost-efficient and logistically feasible marker-assisted seedling selection in fruit breeding. Mol Breeding 2015; 35: 223.

[18] Abalo G, Tongoona P, Derera J, Edema R . A comparative analysis of conventional and marker-assisted selection methods in breeding maize streak virus resistance in maize. Crop Sci 2009; 49: 509- 509.

[19] Asea G, Vivek B, Lipps P, Pratt R . Genetic gain and cost efficiency of marker-assisted selection of maize for improved resistance to multiple foliar pathogens. Mol Breeding 2012; 29: 515-527.

[20] Fazio G, Chung SM, Staub JE . Comparative analysis of response to phenotypic and marker-assisted selection for multiple lateral branching in cucumber (Cucumis sativus L.) . Theor Appl Genet 2003; 107: 875-883.

[21] Stromberg LD, Dudley JW, Rufener GK . Comparing conventional early generation selection with molecular marker assisted selection in maize. Crop Sci 1994; 34: 1221-1225.

[22] Yousef GG, Juvik JA . Comparison of phenotypic and marker-assisted selection for quantitative traits in sweet corn. Crop Sci 2001; 41: 645-655.

[23] Knapp SJ . Marker-assisted selection as a strategy for increasing the probability of selecting superior genotypes. Crop Sci 1998; 38: 1164-1174.

[24] Smith C . Improvement of metric traits through specific genetic loci. Anim Sci 1967; 9: 349-358.

[25] Hospital F, Moreau L, Lacoudre F, Charcosset A, Gallais A . More on the efficiency of marker-assisted selection. Theor Appl Genet 1997; 95: 1181-1189.

[26] Kuchel H, Ye G, Fox R, Jefferies S . Genetic and economic analysis of a targeted marker-assisted wheat breeding strategy. Mol Breeding 2005; 16: 67-78.

[27] Kumar S, Garrick DJ . Genetic response to within-family selection using molecular markers in some radiata pine breeding schemes. Can J For Res 2001; 31: 779-785.

[28] Han F, Romagosa I, Ullrich SE, Jones BL, Hayes PM, Wesenberg DM . Molecular marker-assisted selection for malting quality traits in barley. Mol Breeding 1997; 3: 427-437.

[29] Moreau L, Charcosset A, Hospital F, Gallais A . Marker-assisted selection efficiency in populations of finite size. Genetics 1998; 148: 1353-1365.

[30] Xie C, Xu SZ . Efficiency of multistage marker-assisted selection in the improvement of multiple quantitative traits. Heredity 1998; 80: 489-498.

[31] Xu SZ, Muir WM . Multistage selection for genetic gain by orthogonal transformation. Genetics 1991; 129: 963-974.

[32] Xu SZ, Muir WM . Selection index updating. Theor Appl Genet 1992; 83: 451-458.

[33] Gimelfarb A, Lande R . Marker-assisted selection and marker-QTL associations in hybrid populations. Theor Appl Genet 1995; 91: 522-528.