Genomic, transcriptomic and phenomic variation reveals the complex adaptation of modern maize breeding

Abstract

The temperate-tropical division of early maize germplasm to different agricultural environments was arguably the greatest adaptation process associated with the success and near ubiquitous importance of global maize production. Deciphering this history is challenging, but new insight has been gained from the genomic, transcriptomic and phenotypic variation collected from 368 diverse temperate and tropical maize inbred lines in this study. This is the first attempt to systematically explore the mechanisms of the adaptation process. Our results indicated that divergence between tropical and temperate lines seem occur 3,400-6,700 years ago. A number of genomic selection signals and transcriptomic variants including differentially expressed individual genes and rewired co-expression networks of genes were identified. These candidate signals were found to be functionally related to stress response and most were associated with directionally selected traits, which may have been an advantage under widely varying environmental conditions faced by maize as it was migrated away from its domestication center. It’s also clear in our study that such stress adaptation could involve evolution of protein-coding sequences as well as transcriptome-level regulatory changes. This latter process may be a more flexible and dynamic way for maize to adapt to environmental changes over this dramatically short evolutionary time frame.

Molecular and phenotypic characterisation of diverse temperate maize inbred lines in Southeast Europe

“…The genetic differentiation among the groups was significant, and pair-wise fixation index ranged from 0.024 between the LSC and the IDT subpopulations to 0.191 between the mBSSS and the IDT subpopulations. The average Fst value was 0.069, larger than in breeding programs of the Corn Belt (Romay et al, 2013), between (Liu et al, 2015) and between elite Chinese lines and public US lines (Jiao et al, 2012). However, obtained Fst value in this study was smaller compared to Fst = 0.165 in a diverse panel of 284 maize inbreds (Schaefer, Bernardo, 2013).…”

Divergent selection and drift shape the genomes of two avian sister species spanning a saline–freshwater ecotone

“…The genomic era holds promise for ecological speciation research, as it has allowed for the detection of divergent signatures of selection on a genomewide scale. In recent years, the application of genomics to nonmodel systems has provided new insight into mechanisms underlying lineage-specific adaptations in a range of taxa (Cai et al, 2013;Li, Li, Jia, Caicedo, & Olsen, 2017;Liu et al, 2015;Qiu et al, 2012;Zhan et al, 2013). It has also provided insight into the genomic architecture of adaptation and speciation (Cruickshank & Hahn, 2014;Larson et al, 2017;Strasburg et al, 2012).…”

Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation

“…Among the ePAV genes, 56 (0.42%) were significantly (P < 7.49E-5, 1/n) associated with 15 agronomic traits and 1,967 (14.74%) associated with 526 metabolic traits including content of 18 amino acids (Table S9, Liu et al 2015).…”

“…Almost 34% of them were found to be associated with metabolic traits. The differences in metabolism -related genes may be associated with differential environmental effects (Liu et al 2015). The novel sequences involved in development, such as beta-tubulin, also likely contribute to adaptation.…”

“…Phenotypic variation has been explored by QTL mapping and genome-wide association studies (GWAS; Huang and Han 2014). As it becomes clear that the differences in transcript abundance are a major contributor to phenotypic evolution (Cubillos et al 2012; Albert and Kruglyak 2015; Liu et al 2015), allelic variation effects on the transcriptome, which reflect both genetic and epigenetic regulation, should be explored at a genome-wide level .…”