Molecular genetic variation of animals and plants under domestication

Abstract

Domesticated plants and animals played crucial roles as models for evolutionary change by means of natural selection and for establishing the rules of inheritance, originally proposed by Charles Darwin and Gregor Mendel, respectively. Here, we review progress that has been made during the last 35 y in unraveling the molecular genetic variation underlying the stunning phenotypic diversity in crops and domesticated animals that inspired Mendel and Darwin. We notice that numerous domestication genes, crucial for the domestication process, have been identified in plants, whereas animal domestication appears to have a polygenic background with no obvious "domestication genes" involved. Although model organisms, such as Drosophila and Arabidopsis, have replaced domesticated species as models for basic research, the latter are still outstanding models for evolutionary research because phenotypic change in these species represents an evolutionary process over thousands of years. A consequence of this is that some alleles contributing to phenotypic diversity have evolved by accumulating multiple changes in the same gene. The continued molecular characterization of crops and farm animals with ever sharper tools is essential for future food security.

Keywords: Mendel; crops; domestic animals; domestication; genetics.

Fig. 1.

Some key Mendelian traits in domesticated plants. (A) Early genetic work in plants focused on maize, including various kernel traits, such as aleurone and pericarp color. Image credit: David Spender, United Kingdom (CC Commons Attribution 2.0 Generic license). (B) Glutinous phenotype caused by mutations at the Wx gene leads to sticky rice valued by cultures in Northeast and Southeast Asia. (C) The round vs. (D) wrinkled pea phenotype maps to the r allele first described by Mendel, with the latter caused by a 0.8-kb TE insertion into a starch branching enzyme gene. Image credit: Claire Domoney (John Innes Center, Norwich, United Kingdom). (E) Tall vs. dwarf pea plants are controlled by Mendel’s Le gene. Image credit: Julie Hofer (John Innes Center, Norwich, United Kingdom).

Fig. 2.

Comb morphology in domesticated chickens and its molecular basis. Four comb phenotypes in chickens, wild type (or single comb), Rose-comb, Pea-comb, and Walnut-comb, and immunohistochemical labeling of MNR2 and SOX5 in comb tissue sections from embryonic day (E) 6.5. Nuclei are visualized by DAPI (4′,6-diamidino-2-phenylindole). Boxed regions are shown magnified as a single color. Arrows in the Walnut-comb tissue sections indicate double-labeled cells, whereas arrowheads indicate single-labeled cells. Reproduced from ref. , which is licensed under CC BY-NC-ND.

Fig. 3.

Evolution of the Dominant white (DW) allele at the KIT locus in pigs. (A) Large white piglet with the DW phenotype. Image credit: Per Jensen (Linköping University, Linköping, Sweden). (B) Illustration of the evolution of the DW allele from the wild-type (WT) allele involving three steps: 1) a 450-kb duplication encompassing the entire KIT gene and flanking regions, 2) one or more smaller duplications of noncoding sequence (SI Appendix, Table S2), and 3) splice mutation resulting in exon skipping of exon 17 that encodes the tyrosine kinase domain in one of the two KIT copies.

Fig. 4.

Domestication traits in maize. (A, Left) An example of a Z. mays ssp. parviglumis (teosinte) ear vs. (A, Right) a domesticated Z. mays ssp. mays ear. Shoot architecture of (B) teosinte and (C) maize, which is controlled by the tb1 gene. Image credit: John Doebley (University of Wisconsin, Madison, WI).