Prediction accuracy of genomic selection models for earliness in tomato

Aurelio Hernandez-Bautista1, Ricardo Lobato-Ortiz1*, J. Jesus Garcia-Zavala1, Serafin Cruz-Izquierdo1, Jose Luis Chávez-Servia2, Mario Rocandio-Rodriguez3, Yolanda Del Rocio Moreno-Ramirez3, Enrique Hernandez-Leal4, Martha Hernandez-Rodriguez1, and Delfino Reyes-Lopez5
Genomic selection is considered to be an important tool in plant breeding programs. However, its application in the earliness of tomato (Solanum lycopersicum L.) has not been studied. The objective of the present study was to evaluate the prediction performance of six statistical models for six quantitative characteristics related to earliness in tomato. The study used phenotypic and genotypic data belonging to an F2 population consisting of 172 tomato plants. Simple sequence repeat (SSR) markers were obtained using genotypic information, and the genomic values were estimated by the following six different statistical models: Bayesian Lasso (BL), Bayesian ridge regression (BRR), BayesA, BayesB, BayesCπ, and reproducing kernel Hilbert spaces (RKHS) regression. The correlation values ranged from 0.17 to 0.57. The highest association values were found in days to flowering of the third inflorescence and 1000-seed weight, which were greater than 0.5. In general, all the models performed in a similar manner because only slight differences were observed among the correlation values. Specifically, BL, BayesB, and RKHS exhibited the highest Pearson correlation values for most traits. According to the results, genomic selection could be a useful tool to support tomato breeding focused on earliness.
Keywords: Genetic gain, genomic selection, Solanum lycopersicum, statistical models.
1Colegio de Postgraduados, Campus Montecillo, km 36.5 Carr. México-Texcoco, 56230, Texcoco, México.*Corresponding author (rlobato@colpos.mx).2Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR), Santa Cruz Xoxocotlán, 71230, México.3Universidad Autónoma de Tamaulipas, Instituto de Ecología Aplicada, Ciudad Victoria 87019, México.4Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Av. José Santos Valdez No. 1200 Pte. 27440, Col. Centro Matamoros, Coahuila, México.5Benemérita Universidad Autónoma de Puebla, Facultad de Ingeniería Agrohidráulica, Teziutlán, Puebla 00000, México.