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Title: Transcriptome‐wide association and prediction for carotenoids and tocochromanols in fresh sweet corn kernels
Abstract

Sweet corn (Zea maysL.) is consistently one of the most highly consumed vegetables in the United States, providing a valuable opportunity to increase nutrient intake through biofortification. Significant variation for carotenoid (provitamin A, lutein, zeaxanthin) and tocochromanol (vitamin E, antioxidants) levels is present in temperate sweet corn germplasm, yet previous genome‐wide association studies (GWAS) of these traits have been limited by low statistical power and mapping resolution. Here, we employed a high‐quality transcriptomic dataset collected from fresh sweet corn kernels to conduct transcriptome‐wide association studies (TWAS) and transcriptome prediction studies for 39 carotenoid and tocochromanol traits. In agreement with previous GWAS findings, TWAS detected significant associations for four causal genes,β‐carotene hydroxylase(crtRB1),lycopene epsilon cyclase(lcyE),γ‐tocopherol methyltransferase(vte4), andhomogentisate geranylgeranyltransferase(hggt1) on a transcriptome‐wide level. Pathway‐level analysis revealed additional associations fordeoxy‐xylulose synthase2(dxs2),diphosphocytidyl methyl erythritol synthase2(dmes2),cytidine methyl kinase1(cmk1), andgeranylgeranyl hydrogenase1(ggh1), of which,dmes2,cmk1, andggh1have not previously been identified through maize association studies. Evaluation of prediction models incorporating genome‐wide markers and transcriptome‐wide abundances revealed a trait‐dependent benefit to the inclusion of both genomic and transcriptomic data over solely genomic data, but both transcriptome‐ and genome‐wide datasets outperformed a priori candidate gene‐targeted prediction models for most traits. Altogether, this study represents an important step toward understanding the role of regulatory variation in the accumulation of vitamins in fresh sweet corn kernels.

 
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NSF-PAR ID:
10393694
Author(s) / Creator(s):
 ;  ;  ;  ;  ;  ;  ;  ;  
Publisher / Repository:
Wiley Blackwell (John Wiley & Sons)
Date Published:
Journal Name:
The Plant Genome
Volume:
15
Issue:
2
ISSN:
1940-3372
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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