Accuracy of Genomic Prediction of Yield and Sugar Traits in Saccharum spp. Hybrids

Md. S. Islam (), Per McCord, Quentin D. Read, Lifang Qin, Alexander E. Lipka, Sushma Sood, James Todd and Marcus Olatoye
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Md. S. Islam: Sugarcane Field Station, USDA-ARS, Canal Point, FL 33834, USA
Per McCord: Sugarcane Field Station, USDA-ARS, Canal Point, FL 33834, USA
Quentin D. Read: Southeast Area, USDA-ARS, Raleigh, NC 38776, USA
Lifang Qin: Sugarcane Field Station, USDA-ARS, Canal Point, FL 33834, USA
Alexander E. Lipka: Department of Crop Sciences, University of Illinois, Urbana-Champaign, IL 61820, USA
Sushma Sood: Sugarcane Field Station, USDA-ARS, Canal Point, FL 33834, USA
James Todd: Sugarcane Research, USDA-ARS, Houma, LA 70360, USA
Marcus Olatoye: Forage Seed and Cereal Research Unit, USDA ARS, Prosser, WA 97331, USA

Agriculture, 2022, vol. 12, issue 9, 1-22

Abstract: Genomic selection (GS) has been demonstrated to enhance the selection process in breeding programs. The objectives of this study were to experimentally evaluate different GS methods in sugarcane hybrids and to determine the prospect of GS in future breeding approaches. Using sugar and yield-related trait data from 432 sugarcane clones and 10,435 single nucleotide polymorphisms (SNPs), a study was conducted using seven different GS models. While fivefold cross-validated prediction accuracy differed by trait and by crop cycle, there were only small differences in prediction accuracy among the different models. Prediction accuracy was on average 0.20 across all traits and crop cycles for all tested models. Utilizing a trait-assisted GS model, we could effectively predict the fivefold cross-validated genomic estimated breeding value of ratoon crops using both SNPs and trait values from the plant cane crop. We found that the plateau of prediction accuracy could be achieved with 4000 to 5000 SNPs. Prediction accuracy did not decline with decreasing size of the training population until it was reduced below 60% (259) to 80% (346) of the original number of clones. Our findings suggest that GS is possibly a new direction for improving sugar and yield-related traits in sugarcane.

Keywords: genomic selection; prediction accuracy; Saccharum spp. hybrid; sugar and yield trait; sugarcane (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2022
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