Genetic costs of domestication and improvement

Moyers, Brook T.; Morrell, Peter L.; McKay, John

doi:10.1101/122093

Cited by 36 publications

(68 citation statements)

References 145 publications

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“…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., ) and papaya Carica papaya ( F IS = 0.58; Matos et al., ). Domestication and crop improvement often involve increased inbreeding (Robinson, ; Moyers et al., ). 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., ; Montes‐Hernández and Eguiarte, ), in which flowers may be fertilized with the pollen of a male flower from the same plant (Hessing, ).…”

Section: Discussionmentioning

confidence: 99%

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

Hernández-Rosales

Castellanos‐Morales

Vega

et al. 2020

American J of Botany

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Premise Domestication usually involves local adaptation to environmental conditions. Cucurbita species are a promising model for studying these processes. Cucurbita moschata is the third major crop in the genus because of its economic value and because it displays high landrace diversity, but research about its genetic diversity, population structure, and phylogeography is limited. We aimed at understanding how geography and elevation shape the distribution of genetic diversity in C. moschata landraces in Mexico. Methods We sampled fruits from 24 localities throughout Mexico. We assessed 11 nuclear microsatellite loci, one mtDNA region, and three cpDNA regions but found no variation in cpDNA. We explored genetic structure with cluster analysis, and phylogeographic relationships with haplotype network analysis. Results Mitochondrial genetic diversity was high, and nuclear genetic differentiation among localities was intermediate compared to other domesticated Cucurbita. We found high levels of inbreeding. We recovered two mitochondrial lineages: highland (associated with the Trans‐Mexican Volcanic Belt) and lowland. Nuclear microsatellites show that localities from the Yucatan Peninsula constitute a well‐differentiated group. Conclusions Mexico is an area of high diversity for C. moschata, and these landraces represent important plant genetic resources. In Mexico this species is characterized by divergence processes linked to an elevational gradient, which could be related to adaptation and may be of value for applications in agriculture. The Isthmus of Tehuantepec may be a partial barrier to gene flow. Morphological variation, agricultural management, and cultural differences may be related to this pattern of genetic structure, but further studies are needed.

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Section: Discussionmentioning

confidence: 99%

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

Hernández-Rosales

Castellanos‐Morales

Vega

et al. 2020

American J of Botany

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“…Domesticated species are an excellent model to investigate the consequences of population bottlenecks on genetic and deleterious variation. This is because their demographic history is characterized by multiple population contractions associated with domestication, breed formation and intense selective breeding (Bosse, Megens, Derks, Cara, & Groenen, ; Makino et al, ; Mardsen et al, ; Moyers, Morrell, & McKay, ). Domestication involves the (partial or complete) isolation of a number of individuals from a wild progenitor population and entails drastic changes in the nature and strength of selective forces acting on the population, as well as its size (Larson & Fuller, ).…”

Section: Introductionmentioning

confidence: 99%

The type of bottleneck matters: Insights into the deleterious variation landscape of small managed populations

Bortoluzzi

Bosse

Derks

et al. 2019

Evolutionary Applications

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Predictions about the consequences of a small population size on genetic and deleterious variation are fundamental to population genetics. As small populations are more affected by genetic drift, purifying selection acting against deleterious alleles is predicted to be less efficient, therefore increasing the risk of inbreeding depression. However, the extent to which small populations are subjected to genetic drift depends on the nature and time frame in which the bottleneck occurs. Domesticated species are an excellent model to investigate the consequences of population bottlenecks on genetic and deleterious variation in small populations. This is because their history is dominated by known bottlenecks associated with domestication, breed formation and intense selective breeding. Here, we use whole-genome sequencing data from 97 chickens representing 39 traditional fancy breeds to directly examine the consequences of two types of bottlenecks for deleterious variation: the severe domestication bottleneck and the recent population decline accompanying breed formation. We find that recently bottlenecked populations have a higher proportion of deleterious variants relative to populations that have been kept at small population sizes since domestication. We also observe that long tracts of homozygous genotypes (runs of homozygosity) are proportionally more enriched in deleterious variants than the rest of the genome. This enrichment is particularly evident in recently bottlenecked populations, suggesting that homozygosity of these variants is likely to occur due to genetic drift and recent inbreeding. Our results indicate that the timing and nature of population bottlenecks can substantially shape the deleterious variation landscape in small populations. K E Y W O R D S deleterious variants, domestication, effective population size, population bottleneck, runs of homozygosity, small population | 331 BORTOLUZZI eT aL.

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“…In many previous studies, it has been shown that crop plants experienced a strong selection pressure during the domestication process (Gepts, ; Zohary, ; Purugganan and Fuller, ), which often results in the independent appearance of multiple spontaneous adaptive mutations, most of which are base substitutions (Hall, ). The process of increased prevalence (an increase in the number, frequency and/or proportion) of deleterious mutations in domesticated species, has been described as the ‘cost of domestication’ (Kono et al ., ; Moyers et al ., ). An excess of non‐synonymous substitutions was observed in different domesticated germplasm (Liu et al .…”

Section: Discussionmentioning

confidence: 97%

“…Recently, the effects of domestication on the genome have been presented as the ‘cost of domestication’ hypothesis. According to this, domesticated species have acquired an increased prevalence (an increase in the number, frequency and/or proportion) in deleterious genetic variants during the process of domestication (Kono et al ., ; Moyers et al ., ). In different crop species (rice, maize, barley, soybean and sunflower), an increased proportion of non‐synonymous mutations in domesticated taxa relative to their wild progenitors has been documented (Mezmouk and Ross‐Ibarra, ; Renaut and Rieseberg, ; Kono et al ., ; Liu et al .…”

Section: Introductionmentioning

confidence: 97%

Identification of candidate domestication‐related genes with a systematic survey of loss‐of‐function mutations

et al. 2018

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Domestication is an important key co-evolutionary process through which humans have extensively altered the genomic make-up and appearance of both plants and animals. The identification of domesticationrelated genes remains very arduous. In this study, we present a systematic analytical approach that harnesses two recent advances in genomics, whole-genome sequencing (WGS) and prediction of loss-offunction (LOF) mutations, to greatly facilitate the assembly of an enriched catalogue of domesticationrelated candidate genes. Using WGS data for 296 cultivated (Glycine max) and 64 wild soybean accessions, we identified 8699 LOF variants, and 116 genes that are uniquely fixed for one or more LOF allele(s) in domesticated soybeans. Existing soybean transcriptomic data led us to overcome analytical challenges associated with whole-genome duplications and to identify neo-or subfunctionalized genes. This systematic approach allowed us to identify 110 candidate domestication-related genes in an efficient and rapid way. This catalogue contains previously well characterized domestication genes in soybean, as well as some orthologs from other domesticated crop species. In addition, it comprises many promising candidate domestication genes. Overall, this collection of candidate domestication-related genes in soybean is almost twice as large as the sum of all previously reported candidate genes in all other crops. We believe this systematic approach could readily be used in wide range of species.

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Genetic costs of domestication and improvement

Cited by 36 publications

References 145 publications

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

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

The type of bottleneck matters: Insights into the deleterious variation landscape of small managed populations

Identification of candidate domestication‐related genes with a systematic survey of loss‐of‐function mutations

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