TY - JOUR
T1 - Increased Predictive Accuracy of Multi-Environment Genomic Prediction Model for Yield and Related Traits in Spring Wheat (Triticum aestivum L.)
AU - Tomar, Vipin
AU - Singh, Daljit
AU - Dhillon, Guriqbal Singh
AU - Chung, Yong Suk
AU - Poland, Jesse
AU - Singh, Ravi Prakash
AU - Joshi, Arun Kumar
AU - Gautam, Yogesh
AU - Tiwari, Budhi Sagar
AU - Kumar, Uttam
N1 - Generated from Scopus record by KAUST IRTS on 2022-09-13
PY - 2021/10/8
Y1 - 2021/10/8
N2 - Genomic selection (GS) has the potential to improve the selection gain for complex traits in crop breeding programs from resource-poor countries. The GS model performance in multi-environment (ME) trials was assessed for 141 advanced breeding lines under four field environments via cross-predictions. We compared prediction accuracy (PA) of two GS models with or without accounting for the environmental variation on four quantitative traits of significant importance, i.e., grain yield (GRYLD), thousand-grain weight, days to heading, and days to maturity, under North and Central Indian conditions. For each trait, we generated PA using the following two different ME cross-validation (CV) schemes representing actual breeding scenarios: (1) predicting untested lines in tested environments through the ME model (ME_CV1) and (2) predicting tested lines in untested environments through the ME model (ME_CV2). The ME predictions were compared with the baseline single-environment (SE) GS model (SE_CV1) representing a breeding scenario, where relationships and interactions are not leveraged across environments. Our results suggested that the ME models provide a clear advantage over SE models in terms of robust trait predictions. Both ME models provided 2–3 times higher prediction accuracies for all four traits across the four tested environments, highlighting the importance of accounting environmental variance in GS models. While the improvement in PA from SE to ME models was significant, the CV1 and CV2 schemes did not show any clear differences within ME, indicating the ME model was able to predict the untested environments and lines equally well. Overall, our results provide an important insight into the impact of environmental variation on GS in smaller breeding programs where these programs can potentially increase the rate of genetic gain by leveraging the ME wheat breeding trials.
AB - Genomic selection (GS) has the potential to improve the selection gain for complex traits in crop breeding programs from resource-poor countries. The GS model performance in multi-environment (ME) trials was assessed for 141 advanced breeding lines under four field environments via cross-predictions. We compared prediction accuracy (PA) of two GS models with or without accounting for the environmental variation on four quantitative traits of significant importance, i.e., grain yield (GRYLD), thousand-grain weight, days to heading, and days to maturity, under North and Central Indian conditions. For each trait, we generated PA using the following two different ME cross-validation (CV) schemes representing actual breeding scenarios: (1) predicting untested lines in tested environments through the ME model (ME_CV1) and (2) predicting tested lines in untested environments through the ME model (ME_CV2). The ME predictions were compared with the baseline single-environment (SE) GS model (SE_CV1) representing a breeding scenario, where relationships and interactions are not leveraged across environments. Our results suggested that the ME models provide a clear advantage over SE models in terms of robust trait predictions. Both ME models provided 2–3 times higher prediction accuracies for all four traits across the four tested environments, highlighting the importance of accounting environmental variance in GS models. While the improvement in PA from SE to ME models was significant, the CV1 and CV2 schemes did not show any clear differences within ME, indicating the ME model was able to predict the untested environments and lines equally well. Overall, our results provide an important insight into the impact of environmental variation on GS in smaller breeding programs where these programs can potentially increase the rate of genetic gain by leveraging the ME wheat breeding trials.
UR - https://www.frontiersin.org/articles/10.3389/fpls.2021.720123/full
UR - http://www.scopus.com/inward/record.url?scp=85117608670&partnerID=8YFLogxK
U2 - 10.3389/fpls.2021.720123
DO - 10.3389/fpls.2021.720123
M3 - Article
C2 - 34691100
SN - 1664-462X
VL - 12
JO - Frontiers in Plant Science
JF - Frontiers in Plant Science
ER -