Coupling day length data and genomic prediction tools for predicting time-related traits under complex scenarios

Genomic selection (GS) has proven to be an efficient tool for predicting crop-rank performance of untested genotypes; however, when the traits have intermediate optima (phenology stages), this implementation might not be the most convenient. GS might deliver high-rank correlations but incurring in s...

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Bibliographic Details
Published in:	Scientific reports 2020-08, Vol.10 (1), p.13382-13382, Article 13382
Main Authors:	Jarquin, Diego, Kajiya-Kanegae, Hiromi, Taishen, Chen, Yabe, Shiori, Persa, Reyna, Yu, Jianming, Nakagawa, Hiroshi, Yamasaki, Masanori, Iwata, Hiroyoshi
Format:	Article
Language:	eng
Subjects:	Adaptability Agricultural production Agriculture Agriculture - methods Bias Crops, Agricultural Developmental stages Gene-Environment Interaction Genomics - methods Genotype Genotypes Growth models Oryza - genetics Phenotype Plant Breeding Rice Selection, Genetic Time Factors
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Summary:	Genomic selection (GS) has proven to be an efficient tool for predicting crop-rank performance of untested genotypes; however, when the traits have intermediate optima (phenology stages), this implementation might not be the most convenient. GS might deliver high-rank correlations but incurring in serious bias. Days to heading (DTH) is a crucial development stage in rice for regional adaptability with a significant impact on yield potential. The objective of this research consisted in develop a novel method that accurately predicts time-related traits such as DTH in unobserved environments. For this, we propose an implementation that incorporates day length information (DL) in the prediction process for two relevant scenarios: CV0, predicting tested genotypes in unobserved environments (C method); and CV00, predicting untested genotypes in unobserved environments (CB method). The use of DL has advantages over weather data since it can be determined in advance just by knowing the location and planting date. The proposed methods showed that DL information significantly helps to improve the predictive ability of DTH in unobserved environments. Under CV0, the C method returned a root-mean-square error (RMSE) of 3.9 days, a Pearson correlation (PC) of 0.98 and the differences between the predicted and observed environmental means (EMD) ranged between -4.95 and 4.67 days. For CV00, the CB method returned an RMSE of 7.3 days, a PC of 0.93 and the EMD ranged between -6.4 and 4.1 days while the conventional GS implementation produced an RMSE of 18.1 days, a PC of 0.41 and the EMD ranged between -31.5 and 28.7 days.
ISSN:	2045-2322 2045-2322