Combination of mixed linear model approach with selection indices in kale breeding programs

Keywords: Brassica oleracea sub acephala L.; biometry; genetic improvement; multivariate analysis; REML/BLUP.

Abstract

Utilizing selection indices is an effective strategy for the simultaneous evaluation of multiple traits in kale breeding programs. This approach allows for the selection of kale genotypes that exhibit enhanced productivity and adaptability by combining desirable attributes for the crop. In this study, we employed a mixed model approach in combination with various selection indices to estimate selection gains and recommend the most suitable index for kale breeding. The experiment was conducted at the Center of Development and Technology Transfer, Federal University of Lavras, Ijaci, MG. Thirty-four experimental genotypes were assessed in a randomized block design with three replicates, featuring four plants per plot. We evaluated several traits, including total leaf yield, number of leaves, average leaf mass, number of sprouts and chlorophyll content. Data analysis was performed at both the plot average level and the average quantity of the five harvests. Statistical analysis of mixed models confirmed the presence of genetic variability among kale genotypes. We examined the Smith and Hazel, Mulamba and Mock, Z-index, and FAI-BLUP indices. Smith and Hazel, Mulamba and Mock, as well as Z-index, were found unsuitable for leafy kale selection in breeding programs. The FAI-BLUP index demonstrated superior performance, aligning with the specific objectives of the kale breeding program and offering desirable gains. Therefore, we recommend the use of the FAI-BLUP index in kale breeding programs.

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References

Al-Ashkar, I., Sallam, M., Almutairi, K. F., Shady, M., Ibrahim, A., & Alghamdi, S. S. (2023). Detection of high-performance wheat genotypes and genetic stability to determine complex interplay between genotypes and environments. Agronomy, 13(2), 1-24. DOI: https://doi.org/10.3390/agronomy13020585

Azevedo, A. M., Andrade Júnior, V. C. D., Pedrosa, C. E., Fernandes, J. S. C., Valadares, N. R., Ferreira, M. A. M., & Martins, R. A. D. V. (2012). Desempenho agronômico e variabilidade genética em genótipos de couve. Pesquisa Agropecuária Brasileira, 47(12), 1751-1758. DOI: https://doi.org/10.1590/S0100-204X2012001200011

Azevedo, A. M., Andrade Júnior, V. C., Pedrosa, C. E., Valadares, N. R., Fernandes, J. S. C., Ferreira, M. R. A., & Martins, R. A. V. (2014). Divergência genética e importância de caracteres em genótipos de couve. Horticultura Brasileira, 32(1), 51-57. DOI: https://doi.org/10.1590/S0102-05362014000100008

Azevedo, A. M., Andrade Júnior, V. C. D., Figueiredo, J. A., Pedrosa, C. E., Viana, D. J. S., Lemos, V. T., & Neiva, I. P. (2015). Divergência genética e importância de caracteres em genótipos de batata-doce visando a produção de silagem. Revista Brasileira de Ciências Agrarias, 10(3), 479-484. DOI: https://doi.org/10.5039/agraria.v10i3a5165

Baker, R. J. (2020). Selection indices in plant breeding. Boca Raton, FL: CRC Press. DOI: https://doi.org/10.1201/9780429280498

Barth, E., Resende, J. T. V., Mariguele, K. H., Resende, M. D. V., Silva, A. L. B. R., & Ru, S. (2022). Multivariate analysis methods improve the selection of strawberry genotypes with low cold requirement. Scientific Reports, 12(1), 1-12. DOI: https://doi.org/10.1038/s41598-022-15688-4

Bates, D., Mächler, M., Bolker, B., & Walker, S. (2015). Fitting linear mixed-effects models using lme4. Journal of Statistical Software, 67(1), 1-48. DOI: https://doi.org/10.18637/jss.v067.i01

Begna, T. (2021). Role and economic importance of crop genetic diversity in food security. International Journal of Agricultural Science and Food Technology, 7(1), 164-169. DOI: https://doi.org/10.17352/2455-815X.000104

Beloti, I. F., Maciel, G. M., Juliatti, F. C., Finzi, R. R., & Cardoso, D. B. O. (2020). Genetic parameters and line selection of Cucurbita pepo based on selection indices. Bioscience Journal, 36(Suppl. 1), 205-216. DOI: https://doi.org/10.14393/BJ-v36n0a2020-53607

Brito, O. G., Andrade Júnior, V. C. D., Azevedo, A. M., Silva, N. O., Fernandes, J. S. C., & Alves, K. A. (2020). Genetic parameters selection gains and genotypic correlations in kale half-siblings progenies. Emirates Journal of Food and Agriculture, 32(8), 591-599. DOI: https://doi.org/10.9755/ejfa.2020.v32.i8.2136

Brito, O. G., Andrade Júnior, V. C. D., Azevedo, A. M. D., Donato, L. M. S., Silva, L. R., & Ferreira, M. A. M. (2019). Study of repeatability and phenotypical stabilization in kale using frequentist Bayesian and bootstrap resampling approaches. Acta Scientiarum. Agronomy, 41(1), 1-11. DOI: https://doi.org/10.4025/actasciagron.v41i1.42606

Casagrande, C. R., Mezzomo, H. C., Silva, C. M., Lima, G. W., Souza, D. J. P., Borém, A., & Nardino, M. (2022). Selection indexes based on genotypic values applied to Brazilian tropical wheat breeding. Agronomy Science and Biotechnology, 8, 1-16. DOI: https://doi.org/10.33158/ASB.r171.v8.2022

Chen, H., & Boutros, P. C. (2011). VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinformatics, 12(35), 1-7. DOI: https://doi.org/10.1186/1471-2105-12-35

Cruz, C. D. (2016). Genes software –extended and integrated with the R., Matlab and Selegen. Acta Scientiarum. Agronomy, 38(4), 547-552. DOI: https://doi.org/10.4025/actasciagron.v38i4.32629

Cruz, C. D., Regazzi, A. J., & Carneiro, P. C. S. (2012). Modelos biométricos aplicados ao melhoramento genético (1. ed). Viçosa, MG: Editora UFV.

Silva, M. J., Carneiro, P. C. S., Carneiro, J. E. S., Damasceno, C. M. B., Parrella, N. N. L. D., Pastina, M. M., ... Parrella, R. A. C. (2018). Evaluation of the potential of lines and hybrids of biomass sorghum. Industrial Crops and Products, 125, 379-385. DOI: https://doi.org/10.1016/j.indcrop.2018.08.022

Dalbosco, E. Z., Krause, W., Neves, L. G., Araújo, D. V. D., Hiega, K. M. R., & Silva, C. G. D. (2018). Parametric and non-parametric indexes applied in the selection of sour passion fruit progenies. Revista Brasileira de Fruticultura, 40(1), 1-8. DOI: https://doi.org/10.1590/0100-29452018282

Dugard, P., Todman, J., & Staines, H. (2022). Approaching multivariate analysis: A practical introduction (2nd ed.). London, UK: Routledge; Taylor & Francis.

Fadhli, N. U. R., Farid, M. U. H., Effendi, R. O. Y., Azrai, M., & Anshori, M. F. (2020). Multivariate analysis to determine secondary characters in selecting adaptive hybrid corn lines under drought stress. Biodiversitas Journal of Biological Diversity, 21(8), 3617-3624. DOI: https://doi.org/10.13057/biodiv/d210826

Hassan, S., Ahmad, T., & Hussain, B. (2022). Food preferences and consumption parameters of Cabbage butterfly, Pieris brassicae (Lepidoptera: Pieridae) on different kale genotypes. Journal of Plant Disease and Protection, 130, 45-55. DOI: https://doi.org/10.1007/s41348-022-00683-8

Hazel, L. N. (1943). The genetic basis for constructing selection indexes. Genetics, 28(6), 476-490. DOI: https://doi.org/10.1093/genetics/28.6.476

Henderson, C. R. (1984). Applications of linear models in animal breeding (v. 462). Guelph, CA: University of Guelph.

Henderson, C. R. (1986). Statistical methods in animal improvement: historical overview. In Advances in statistical methods for genetic improvement of livestock (p. 2-14). Berlin, Heidelberg, GE: Springer Berlin Heidelberg.

Hidalgo-Contreras, J. V., Salinas-Ruiz, J., Eskridge, K. M., & Baenziger, S. P. (2021). Incorporating molecular markers and causal structure among traits using a Smith-Hazel index and structural equation models. Agronomy, 11(10), 1953. DOI: https://doi.org/10.3390/agronomy11101953.

Jesus, M. S., Passos, A. R., & Diniz, R. P. (2023). Selection indexes and principal components for agronomic and bromatological traits in forage cactus. Revista Caatinga, 36(1), 189-198. DOI: https://doi.org/10.1590/1983-21252023v36n120rc

Kardos, M., Armstrong, E. E., Fitzpatrick, S. W., Hauser, S., Hedrick, P. W., Miller, J. M., ... Funk, W. C. (2021). The crucial role of genome-wide genetic variation in conservation. Perspective, 118(48), 1-10. DOI: https://doi.org/10.1073/pnas.2104642118

Lima, D. C., Abreu, Â. D. F. B., Ferreira, R. A. D. C., & Ramalho, M. A. P. (2015). Breeding common bean populations for traits using selection index. Scientia Agricola, 72(2), 132-137. DOI: https://doi.org/10.1590/0103-9016-2014-0130

Meena, K. Y., Kale, S. V., & Meena, P. O. (2014). Correlation coefficient and path analysis in coriander. International Journal of Scientific and Research Publications, 4(6), 1-4.

Meier, C., Marchioro, V. S., Meira, D., Olivoto, T., & Klein, L. A. (2021). Genetic parameters and multiple-trait selection in wheat genotypes. Pesquisa Agropecuária Tropical, 51, 1-9. DOI: https://doi.org/10.1590/1983-40632021v5167996

Mendes, F. F., Ramalho, M. A. P., & Abreu, A. D. F. B. (2009). Índice de seleção para escolha de populações segregantes de feijoeiro-comum. Pesquisa Agropecuária Brasileira, 44(10), 1312-1318. DOI: https://doi.org/10.1590/S0100-204X2009001000015

Mulamba, N. N., & Mock, J. J. (1978). Improvement of yield potential of the ETO blanco maize (Zea mays L.) population by breeding for plant traits. Egyptian Journal of Genetics Cytology, 7, 40‑51.

Neath, A. A., & Cavanaugh, J. E. (2012). The Bayesian information criterion: background derivation and applications. Wiley Interdisciplinary Reviews: Computational Statistics, 4(2), 199-203. DOI: https://doi.org/10.1002/wics.199

Olivoto, T., Lúcio, A. D., Silva, J. A., Sari, B. G., & Diel, M. I. (2019). Mean performance and stability in multi‐environment trials II: Selection based on multiple traits. Agronomy Journal, 111(6), 2961-2969. DOI: https://doi.org/10.2134/agronj2019.03.0221

Olivoto, T., & Nardino, M. (2021). MGIDI: Toward an effective multivariate selection in biological experiments. Bioinformatics, 37(10), 1383-1389. DOI: https://doi.org/10.1093/bioinformatics/btaa981

Piepho, H. P. (2009). Ridge regression and extensions for genomewide selection in maize. Crop Science, 49(4), 1165-1176. DOI: https://doi.org/10.2135/cropsci2008.10.0595

Piepho, H. P., & Möhring, J. (2005). Best linear unbiased prediction for subdivided target regions. Crop Science, 45(3), 1151-1159. DOI: https://doi.org/10.2135/cropsci2004.0398

R Core Team. (2021). R: A language and environment for statistical computing. Vienna, AT: R Foundation for Statistical Computing. Retrieved on Jan. 05, 2023. from https://www.R-project.org/

Ramos, J. P., Cavalcanti, J. J., Freire, R. M., Silva, C. R., Silva, M. D. F., & Santos, R. C. D. (2022). Selection indexes and economic weights applied to runner-peanut breeding. Revista Brasileira de Engenharia Agrícola e Ambiental, 26(5), 327-334. DOI: https://doi.org/10.1590/1807-1929/agriambi.v26n5p327-334

Reda, T., Thavarajah, P., Polomski, R., Bridges, W., Shipe, E., & Thavarajah, D. (2021) Reaching the highest shelf: A review of organic production nutritional quality and shelf life of kale (Brassica oleracea var. acephala). Plants People Planet, 3, 308-318. DOI: https://doi.org/10.1002/ppp3.10183

Resende, M. D. V., & Alves, R. S. (2021). Genética: estratégias de melhoramento e métodos de seleção (3rd ed) (p. 171-202). Brasília, DF: Embrapa Florestas.

Rocha, J. R. A. S. C., Machado, J. C., & Carneiro, P. C. S. (2018). Multitrait index based on factor analysis and ideotype‐design: Proposal and application on elephant grass breeding for bioenergy. GCB-Bioenergy, 10(1), 52-60. DOI: https://doi.org/10.1111/gcbb.12443

Sellami, M. H., Lavini, A., & Pulvento, C. (2021). Phenotypic and quality traits of chickpea genotypes under rainfed conditions in south Italy. Agronomy, 11(5), 1-15. DOI: https://doi.org/10.3390/agronomy11050962

Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T, Ramage, D., Amin, N., … Ideker, T. (2003). Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research, 13(11), 2498-2504. DOI: https://doi.org/10.1101/gr.1239303

Smith, H. F. (1936). A discriminant function for plant selection. Annals of Eugenics, 7, 240-250. DOI: https://doi.org/10.1111/j.1469-1809.1936.tb02143.x

Taiz, L., Zeiger, E., Møller, I. M., & Murphy, A. (2017). Fisiologia e desenvolvimento vegetal (6. ed.). Porto Alegre, RS: Editora Artmed.

Tiwari, S., Saville, D. J., & Wratten S. D. (2019). Susceptibility of kale cultivars to the wheat bug Nysius huttoni (Hemiptera: Lygaeidae) in New Zealand. New Zealand Journal of Agricultural Research, 63(3), 467-477. DOI: https://doi.org/10.1080/00288233.2018.1562480

Trani, P. E., Tivelli, S. W., Blat, S. F., Prela-Pantano, A., Teixeira, E. P., Araújo, H. S., ... Novo, M. C. S. S. (2015). Couve-de-folha: do plantio à pós-colheita (Série Tecnologia Apta. Boletim Técnico IAC, 214). Campinas, SP: IAC.

Vieira, S. D., Souza, D. C., Martins, I. A., Ribeiro, G. H. M. R., Resende, L. V., Ferras, A. K., ... Resende, J. T. V. (2017). Selection of experimental strawberry (Fragaria x ananassa) hybrids based on selection indices. Genetics and Molecular Research, 16(1), 1-11. DOI: https://doi.org/10.4238/gmr16019052

Published
2024-11-08
How to Cite
Silva, E. A. da, Gama, A. B. N. da, Andrade Júnior, V. C. de, Brito, O. G., Costa, A. L. da, & Freire , A. I. (2024). Combination of mixed linear model approach with selection indices in kale breeding programs. Acta Scientiarum. Agronomy, 47(1), e69619. https://doi.org/10.4025/actasciagron.v47i1.69619

 

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2.0
2019CiteScore
 
 
60th percentile
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