Characterization of Proteome Variation During Modern Maize Breeding*

Abstract

The integrated multi-omics analysis provides insights into variation at different gene expression levels during the adaption of modern maize from tropical to temperate regions. Population-specific proteome variation mirrors genetic variation better than mRNA levels, and a class of cis-QTLs were identified that regulate protein abundance with little or no effect on mRNA levels. Thus, the discordance between protein and mRNA levels indicates far greater evolutionary stability of proteome during modern maize breeding.

Exploiting Interdata Relationships in Next-generation Proteomics Analysis

“…For example, they detected several pQTLs that affected protein levels in trans , illustrating how pQTLs can identify effects hidden at the mRNA level (40). Other studies found several pQTLs acting in cis and reported substantial overlap between pQTLs and cis-eQTLs—contrasting what had been observed before (41–43).…”

5Gs for crop genetic improvement

“…One goal of systems biology is to discover emergent properties derived from molecular interactions that will further our understanding of the entirety of processes that occur in a biological system. In furtherance of this goal, gene expression atlases [ 38 , 39 , 40 , 41 , 42 ], epigenome maps [ 43 , 44 , 45 ], proteome maps [ 46 , 47 , 48 ] and metabolome maps [ 49 , 50 , 51 ] have been developed in some crop species. Availability of these resources will accelerate the use of systems biology approaches to understand the molecular mechanism of complex traits such as drought tolerance [ 52 ] or heterosis [ 53 ].…”

Genomic, Transcriptomic and Epigenomic Tools to Study the Domestication of Plants and Animals: A Field Guide for Beginners

“…Whole-genome sequencing can be used in almost any population-level test of interest ( Schreiber et al, 2018 ). Common practices recommend a sequencing depth around 30× per individual, but empirical studies in pigs suggests that even 10x is enough to cover up to 99% of a genome with accurate detection of variant sites ( Jiang L.G. et al, 2019 ).…”