Genetic Costs of Domestication and Improvement

Abstract

The "cost of domestication" hypothesis posits that the process of domesticating wild species can result in an increase in the number, frequency, and/or proportion of deleterious genetic variants that are fixed or segregating in the genomes of domesticated species. This cost may limit the efficacy of selection and thus reduce genetic gains in breeding programs for these species. Understanding when and how deleterious mutations accumulate can also provide insight into fundamental questions about the interplay of demography and selection. Here we describe the evolutionary processes that may contribute to deleterious variation accrued during domestication and improvement, and review the available evidence for "the cost of domestication" in animal and plant genomes. We identify gaps and explore opportunities in this emerging field, and finally offer suggestions for researchers and breeders interested in understanding or avoiding the consequences of an increased number or frequency of deleterious variants in domesticated species.

Purging of deleterious mutations during domestication in the predominant selfing crop soybean

“…Mutation burden was further decreased in improved lines from modern soybean breeding. The results are in contrast to the cost of domestication hypothesis that deleterious alleles (the genetic load) that happen to be present in the neighborhood background of the strongly selected allele in the presence of selective sweeps may become more prevalent than those in other neutral backgrounds 32,33 . Purging of deleterious alleles from the domesticated soybean has been further enhanced in selective sweep regions.…”

“…Deleterious alleles that are tightly linked to the strongly selected allele on selective sweeps may be less effectively purged relative to those on neutral backgrounds. Studies with several predominant or mandatory outcrossing species 21,[29][30][31] showed that process of domestication have resulted in an increased number of deleterious variants in the domesticated genome, providing a basis for the "cost of domestication" hypothesis 32,33 . Here, to quantify the extent of purifying selection on deleterious alleles in the self-compatible, predominantly selfing plant soybean, we used Sorting Intolerant From Tolerant (SIFT) 34 and GERP 35 scores.…”

Phylogeographic and population genetic analyses ofCucurbita moschatareveal divergence of two mitochondrial lineages linked to an elevational gradient

“…However, the inbreeding coefficient in C. moschata was lower than that reported for other domesticated plants native to Mesoamerica, such as common bean Phaseolus vulgaris L. (F IS = 0.81; Blair et al, 2011) and papaya Carica papaya (F IS = 0.58; Matos et al, 2013). Domestication and crop improvement often involve increased inbreeding (Robinson, 2008;Moyers et al, 2018). For instance, in order to increase crop productivity (by ensuring pollination) or to reduce variability in the crop, farmers sometimes select geitonogamous individuals (Escalante et al, 1994;Montes-Hernández and Eguiarte, 2002), in which flowers may be fertilized with the pollen of a male flower from the same plant (Hessing, 1988).…”

Genetic differentiation and intrinsic genomic features explain variation in recombination hotspots among cocoa tree populations

“…The identification of ten genetically differentiated populations of the cocoa tree, Theobroma 108 cacao, (Motamayor et al 2008, Cornejo et al 2017) can be leveraged to study population-level 109 dynamics of recombination patterns. The ten T. Cacao populations originate from different 110 regions of South and Central America, and include one fully domesticated population (Criollo), 111 used in the production of fine chocolate, and nine wilder, more resilient populations which 112 generate higher cocoa yield than the Criollo variety ( recombination plays an important role in the segregation of traits, and for this reason it has been 117 hypothesized that recombination rates will increase during the process of domestication 118 (Moyers et al 2018). Domestication can be a rapid process and there is theoretical evidence for 119 the increase of recombination rates during periods of rapid evolutionary change (Otto and 120 Barton 1997).…”