Decrease of gene expression diversity during domestication of animals and plants

Abstract

BackgroundThe genetic mechanisms underlying the domestication of animals and plants have been of great interest to biologists since Darwin. To date, little is known about the global pattern of gene expression changes during domestication.ResultsWe generated and collected transcriptome data for seven pairs of domestic animals and plants including dog, silkworm, chicken, rice, cotton, soybean and maize and their wild progenitors and compared the expression profiles between the domestic and wild species. Intriguingly, although the number of expressed genes varied little, the domestic species generally exhibited lower gene expression diversity than did the wild species, and this lower diversity was observed for both domestic plants and different kinds of domestic animals including insect, bird and mammal in the whole-genome gene set (WGGS), candidate selected gene set (CSGS) and non-CSGS, with CSGS exhibiting a higher degree of decreased expression diversity. Moreover, different from previous reports which found 2 to 4% of genes were selected by human, we identified 6892 candidate selected genes accounting for 7.57% of the whole-genome genes in rice and revealed that fewer than 8% of the whole-genome genes had been affected by domestication.ConclusionsOur results showed that domestication affected the pattern of variation in gene expression throughout the genome and generally decreased the expression diversity across species, and this decrease may have been associated with decreased genetic diversity. This pattern might have profound effects on the phenotypic and physiological changes of domestic animals and plants and provide insights into the genetic mechanisms at the transcriptome level other than decreased genetic diversity and increased linkage disequilibrium underpinning artificial selection.Electronic supplementary materialThe online version of this article (10.1186/s12862-018-1340-9) contains supplementary material, which is available to authorized users.

Evolutionary transcriptomics reveals the origins of olives and the genomic changes associated with their domestication

“…In contrast with the nucleotide diversity, however, we did not find a significant reduction in the diversity of gene expression. While such a reduction is reported for annual crops such as rice (5.1% reduction; Liu et al ., ) or common bean (18% reduction; Bellucci et al ., ), it might be a result of the generally weaker domestication syndrome in perennial plants. However, an important limitation of our result is the restricted number of samples used for the expression analysis, and further observations might provide a more robust outcome.…”

Involvement of homocastasterone, salicylic and abscisic acids in the regulation of drought and freezing tolerance in doubled haploid lines of winter barley

“…During evolution, the accuracy and efficiency of stress defence has been predestining the success of a particular plant species. This natural process was disturbed by domestication and conventional breeding, which diminished biological variation and resulted in the production of highyield, high-input cultivars with decreased environmental acclimation ability (Liu et al 2019). Based on transcriptome data it was shown that domestication and artificial selection affected the pattern of variation in gene expression throughout the genome and decreased the expression diversity across several examined animal and plant species.…”

Variation under domestication in animal models: the case of the Mexican axolotl

“…Given the impoverished state of the Xochimilco axolotl population, critically endangered and having suffered dramatic reductions in population size for many years [ 16 , 17 ], the wild populations could no longer reflect the variation of the wild source from which domestic populations arose. Breeding management strategies have shaped genetic variation of laboratory animal populations, causing in some cases large genetic differences plausibly not only between natural and laboratory animals, but also among laboratory strains, that can affect experimental reproducibility, including studies of gene expression [ 7 , 8 , 35 ]. The genetic differences found here need to be further investigated to address whether this variation is affecting biological processes.…”