Plants were first domesticated about 10,000 years ago, when agriculture begun with wheat, barley, lentils, and peas in what was then Mesopotamia, (now the Middle East -Iran, Iraq, Turkey, Kuwait and Syria), with very fertile valley soil between the Tigris and Euphrates rivers. Potatoes in South America and rice in Asia were among the first plants domesticated in those regions for food production. It is not clear when/where exactly olives were domesticated, the earliest was probably about 6000 years ago in the Middle East, spreading West to the Mediterranean and North Africa maybe 4500 years ago. Some plants were not cultivated for food purposes, for example cotton plants were used for their fiber to make cloth, and flowers for decoration.
Nowadays in urban settings we are often not familiar with how wild species look like, as we are only exposed to plantations and/or products of domesticates crops. This figure from a review on crop domestication (Cell 2006; 127(7):1309-21) shows striking differences between wild and domesticated species of corn, rice, wheat, tomato and sunflower.
Most dog breeds were established in the last 300-200 years, with strong artificial selection resulting in almost 500 breeds with specific morphology (body size and skull shape, tail shape, fur and pigmentation). Dog breed selection has also worked for specific behaviors such as herding, hunting, guarding, and personality including aggression.
Domestication results in genetic changes. We may not be engineering the genetic alteration in the lab (or targeting specific gene/s or using elements from other organisms), but when selecting for taste, shape, color or growth features (faster, pest-resistant, sweeter, etc) we are indeed selecting for specific gene variants and mutations. As in other biology- and medicine-related fields, recent advances in genomics and gene technologies have shed light into aspects of domestication by revealing genome (DNA) sequences of both domesticated species as well as wild ancestors (alive or extinct).
Domestication in plants has led to acquired features such as modified seed size and shattering in cereal species, and modified size and shape in vegetable crops. These modifications have been associated with specific genes in species including tomato, rice, maize, soybean, barley and wheat.
The first genome of a domesticated animal to be fully mapped was that of the chicken, in 2004 (the human genome sequence was completed and available in 2003). Gene sequence comparisons between domesticated and wild animals allow researchers to identify mutations or gene variants that are specific to domesticated animals, sometimes called “domestication genes”. One such gene in chickens is TSHR (thyroid-stimulating hormone receptor), which in wild animals coordinates reproduction with day length, resulting in breeding and egg laying restricted to spring and summer seasons. A TSHR mutation leading to one amino acid change in the receptor protein encoded by the gene in domestic chickens renders the hormone receptor inactive and enables chickens to breed and lay eggs all year long. In pigs, several gene variants/mutations have been reported, based on detailed analysis of genetic variation of local breeds (mostly European), to affect specific phenotypic traits: coat color (KIT, MC1R), production and fatness (LEPR, FTO, MC4R, LEP or MSTN), meat quality (PCK1, PRKAG3, ACACA, CAST, MTTP) and disease resistance (MUC4, GBP5). The figure below shows genes that have been shown to be directly or indirectly linked to phenotypes that distinguish dogs from wolves.