preprints.org > biology and life sciences > agricultural science and agronomy > doi: 10.20944/preprints202304.1235.v1

Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Version 1 : Received: 27 April 2023 / Approved: 29 April 2023 / Online: 29 April 2023 (10:11:10 CEST)

Marker-assisted selection (MAS) and genomic selection (GS) have been used to select individuals with desirable traits. MAS used a few markers associated with a specific trait to select individuals with desirable traits, which are determined after a Genome-wide association studies (GWAS). On the contrary, GS uses a large number of markers distributed across the genome to predict the genomic breeding values for a further selection of the individuals. In general, MAS has shown a high prediction accuracy but is not suitable for traits that are controlled for multiple genes, and has another constraint, it is required the phenotypic data; on the contrary, GS has not shown the highest prediction accuracy as MAS but it takes into account the effect of multiple genes controlling a target trait and it can be used without phenotypic data. Including GWAS-selected markers in GS can enhance the reduced prediction accuracy that GS shows in comparison with MAS. Thus, the objective of this study was to compare the prediction accuracy of MAS, and some models of genomic prediction (gBLUP, gBLUP including GWAs-selected markers, and some Bayesian models such as Bayes A, Bayes B, Bayes LASSO and Bayesian Ridge Regression) with GWAS-selected markers incorporated in gBLUP in order to confirm if the incorporation of GWAS in GS increases the prediction accuracy of GS. As a model for this study, it was used data from Sorghum which has shown population structure, to evaluate if the incorporation of GWAs-selected markers into GS improves prediciton accuracy. It was used a sample of 6000 SNPs out of the 265.487 reported in the study conducted by Morris et al (2013), and also it was considered some parameters that affect the efficiency of the selection such as the size of the training population, the heritability, and the number of QTNs. The GWAS-selected SNPs were identified after using the model BLINK. The results showed that the incorporation of GWAS-selected markers enhanced the performance of the genomic selection with similar prediction accuracy as MAS, the number of QTNs and size of the training population affected the accuracy, with higher accuracy with a bigger size of the training population and with a lower number of QTNs, but it seems that the heritability does not have any impact in the model where GWAS-selected SNPs were included in gBLUP.

Genomic prediction; flavonoid pigmentation; Sorghum bicolor; prediction accuracy; marker-assisted selection

Biology and Life Sciences, Agricultural Science and Agronomy

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