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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).
Source publication
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 unde...
Context in source publication
Context 1
... ancestor of maize (66); domestication of ssp. mays from teosinte began ∼9,000 y ago, possibly in southwestern Mexico. The domestication of maize was accompanied by several substantial phenotypic changes in plant and inflorescence architecture, including increasing apical dominance, enlargement of seed-bearing ears, and kernel properties (65, 67) (Fig. ...
Citations
... This type of conservation, although important for preserving the genetic variation that supports continued innovation (SDG 9), is insufficient on its own to ensure the long-term viability of breeds and varieties (Bellon et al., 2017). Hence, maintaining the evolutionary processes and genetic diversity of cultivated plants and farmed animals is essential for ensuring their capacity for adaptation, as well as for sustainable food production systems (Andersson & Purugganan, 2022;Bernatchez et al., 2017;Scheben et al., 2016;Scherf & Pilling, 2015) (SDG 2). ...
Given the multitude of challenges Earth is facing, sustainability science is of key importance to our continued existence. Evolution is the fundamental biological process underlying the origin of all biodiversity. This phylogenetic diversity fosters the resilience of ecosystems to environmental change, and provides numerous resources to society, and options for the future. Genetic diversity within species is also key to the ability of populations to evolve and adapt to environmental change. Yet, the value of evolutionary processes and the consequences of their impairment have not generally been considered in sustainability research. We argue that biological evolution is important for sustainability and that the concepts, theory, data, and methodological approaches used in evolutionary biology can, in crucial ways, contribute to achieving the UN Sustainable Development Goals (SDGs). We discuss how evolutionary principles are relevant to understanding, maintaining, and improving Nature Contributions to People (NCP) and how they contribute to the SDGs. We highlight specific applications of evolution, evolutionary theory, and evolutionary biology's diverse toolbox, grouped into four major routes through which evolution and evolutionary insights can impact sustainability. We argue that information on both within‐species evolutionary potential and among‐species phylogenetic diversity is necessary to predict population, community, and ecosystem responses to global change and to make informed decisions on sustainable production, health, and well‐being. We provide examples of how evolutionary insights and the tools developed by evolutionary biology can not only inspire and enhance progress on the trajectory to sustainability, but also highlight some obstacles that hitherto seem to have impeded an efficient uptake of evolutionary insights in sustainability research and actions to sustain SDGs. We call for enhanced collaboration between sustainability science and evolutionary biology to understand how integrating these disciplines can help achieve the sustainable future envisioned by the UN SDGs.
... The Red junglefowl (Gallus gallus) is widely recognized as the maternal ancestor of the domestic chicken (Andersson and Purugganan, 2022;Charles, 2010). Mitochondrial DNA (mtDNA) evidence supports the existence of multiple domestication centers (Liu et al., 2006), with several subspecies of the Red junglefowl contributing to the genetic makeup of domestic chickens, except for G. g. bankiva, which is primarily found in Java, Bali, and Sumatra. ...
... Meat samples weighing 500±20mg were placed on filter paper between two acrylic plates secured found in Sri Lanka. In Southeast Asia, the Green junglefowl (Gallus varius) is endemic to Java and neighboring islands (Andersson and Purugganan, 2022). Hybridization between the Red and Grey junglefowl has been observed in their overlapping regions on the Indian subcontinent (Albuquerque et al., 2021). ...
... Notably, Morejohn successfully produced fertile F1 hybrids by crossing Red junglefowl with Grey junglefowl, followed by backcrossing with both species. The presence of Red junglefowl/domestic chicken mtDNA has been detected in captive Grey junglefowl (Andersson and Purugganan, 2022), and the yellow skin phenotype in domestic chickens likely resulted from the introgression of a chromosomal fragment from the Grey junglefowl (Albuquerque et al., 2021). Captive F1 hybrids between female domestic chickens and male Green junglefowl, known as Bekisar, are prevalent in Indonesia. ...
This study compares the physicochemical characteristics of breast meat (Pectoralis major) from conventional chicken and free-range chicken production systems. Analyses of pH, instrumental color measurement, weight loss from cooking (WLC), and water retention capacity (WRC) were carried out. Average pH values were slightly higher for conventional chicken samples. WLC did not show a significant difference between conventional and free-range chicken samples. The WRC was better and higher for the free-range chicken samples than the conventional ones. The mean values for luminosity (L*) were within the normal range, with slightly higher values for conventional chicken. In chromatids a* and b*, there was a tendency towards a more reddish color for free-range chicken samples. The differences found for types of production can be explained mainly by the difference in age at slaughter, the degree of physical activity, animal feeding, among other characteristics that differentiate an animal raised by the extensive system from the intensive system.
... Natural selection is an evolutionary process that influences variation in the animal genome and leaves footprints in the underlying genes involved in local adaptation (Savolainen et al. 2013;Anderssona & Purugganan, 2022). Throughout evolutionary time, sheep populations have been exposed to myriad pressures from natural selection (Fariello et al. 2014). ...
Understanding how evolutionary factors related to climate adaptation and human selection have influenced the genetic architecture of domesticated animals is of great interest in biology. In the current study, by using 304 whole genomes from different geographical regions (including Europe, north Africa, Southwest Asia, east Asia, west Africa, south Asia, east Africa, Australia and Turkey), We evaluate global sheep population dynamics in terms of genetic variation and population structure. We further conducted comparative population analysis to study the genetic underpinnings of climate adaption to local environments and also morphological traits. In order to identify genomic signals under selection, we applied fixation index (FST) and also nucleotide diversity (θπ) statistical measurements. Our results revealed several candidate genes on different chromosomes under selection for local climate adaptation (e.g. HOXC12, HOXC13, IRF1, FGD2 and GNAQ), body size (PDGFA, HMGA2, PDE3A) and also morphological related traits (RXFP2). The discovered candidate genes may offer newel insights into genetic underpinning of regional adaptation and commercially significant features in local sheep.
... Peculiar colorations and morphologies have been genetically fixed in various mammals, birds and teleost species due to the attractiveness of these characteristics to humans [1][2][3][4][5][6][7][8][9][10][11] . Although these ornamental phenotypes may ultimately impair the fitness of the animal in natural conditions, the traits can be fixed in a population due to strong selection pressure applied by breeders (for example, refs 1,8,12 ). Recent genetics and genomics studies have identified the responsible alleles for many rare phenotypes in several domesticated animal species [2][3][4][5][6][7][8][9][10][11]13 . ...
Artificial selection has been widely applied to genetically fix rare phenotypic features in ornamental domesticated animals. For many of these animals, the mutated loci and alleles underlying rare phenotypes are known. However, few studies have explored whether these rare genetic mutations might have been fixed due to competition among related mutated alleles or if the fixation occurred due to contingent stochastic events. Here, we performed genetic crossing with twin-tail ornamental goldfish and CRISPR/Cas9-mutated goldfish to investigate why only a single mutated allele—chdS with a E127X stop codon (also called chdAE127X)—gives rise to the twin-tail phenotype in the modern domesticated goldfish population. Two closely related chdS mutants were generated with CRISPR/Cas9 and compared with the E127X allele in F2 and F3 generations. Both of the CRISPR/Cas9-generated alleles were equivalent to the E127X allele in terms of penetrance/expressivity of the twin-tail phenotype and viability of carriers. These findings indicate that multiple truncating mutations could have produced viable twin-tail goldfish. Therefore, the absence of polymorphic alleles for the twin-tail phenotype in modern goldfish likely stems from stochastic elimination or a lack of competing alleles in the common ancestor. Our study is the first experimental comparison of a singular domestication-derived allele with CRISPR/Cas9-generated alleles to understand how genetic fixation of a unique genotype and phenotype may have occurred. Thus, our work may provide a conceptual framework for future investigations of rare evolutionary events in domesticated animals.
... A novel classification of protein engineering strategies has been proposed for these proteins based on protein domains and highlights popular approaches to engineer critical domains to alter the functionality of CRISPR-Cas systems [60]. Genetic mutants were produced through genetic alteration, which supports the domestication of crops and the evolution of traits [4]. Traditionally, genetic differences are created at random by physical or chemical mutagenesis or natural mutations. ...
Plants with genetic diversity have a higher rate of resilience and adaptation to environmental change. Crop species need to diversify genetically if they are to produce more food for global security. Directed mutagenesis makes use of localized sequence diversification of the gene sequence to produce gene variants with desired characteristics. Using CRISPR-Cas dependent, targeted mutagenesis has recently been utilized to obtain synthetic evolution in a variety of plant species. The breadth of beneficial traits in crop species can be expanded and identified through the use of directed mutagenesis. This article focuses on efficient genome editing approaches for directed mutagenesis of plant genes with agronomic importance using the guide RNA library of CRISPR. Potential applications of cutting-edge CRISPR-Cas base editing and prime editing to introduce efficient site-directed mutation in plants are discussed. This strategy has shown considerable promise in aiding trait engineering, guided evolution, and genetic screening. Though this technology is still in its early stages, it offers a comprehensive evaluation of the existing strategies and new delivery techniques for CRISPR screens. It is possible to create superior varieties with higher yields, better nutrient content, and broad environmental tolerance with potential prospects of CRISPR screens in plants.
... It has previously been suggested that leucism mainly prevails in (Andersson & Purugganan, 2022). ...
Coat color and pattern are a distinguished feature in mammalian carnivores, shaped by climatic cycles and habitat type. It can be expressed in various ways, such as gradients , polymorphisms, and rare color variants. Although natural selection explains much of the phenotypic variation found in the wild, genetic drift and heterozygote deficiency, as prominent in small and fragmented populations, may also affect pheno-typic variability through the fixation of recessive alleles. The aim of this study was to test whether rare color variants in the wild could relate to a deficiency of heterozy-gotes, resulting from habitat fragmentation and small population size. We present an overview of all rare color variants in the order Carnivora, and compiled demographic and genetic data of the populations where they did and did not occur, to test for significant correlations. We also tested how phylogeny and body weight influenced the presence of color variants with phylogenetic generalized linear mixed models (PGLMMs). We found 40 color-variable species and 59 rare color variants. In 17 variable phenotypic populations for which genetic diversity was available, the average A R was 4.18, H O = 0.59, and H E = 0.66, and F IS = 0.086. We found that variable populations displayed a significant reduction in heterozygosity and allelic richness compared to non-variable populations across species. We also found a significant negative correlation between population size and inbreeding coefficients. Therefore, it is possible that small effective size had phenotypic consequences on the extant populations. The high frequency of the rare color variants (averaging 20%) also implies that genetic drift is locally overruling natural selection in small effective populations. As such, rare color variants could be added to the list of phenotypic consequences of inbreeding in the wild. K E Y W O R D S anomalous colouration, Carnivora, color morphs, genetic diversity, inbreeding, population bottleneck
... SV identification is crucial to understand the genetic diversity within a given population and to investigate the impact of sequence variations [1,[23][24][25]. Whole genome sequencing (WGS) with short reads still represents a cost-effective way in the circumstance. ...
Background
As an important vegetable crop, cultivated lettuce is grown worldwide and a great variety of agronomic traits have been preserved within germplasm collections. The mechanisms underlying these phenotypic variations remain to be elucidated in association with sequence variations. Compared with single nucleotide polymorphisms, structural variations (SVs) that have more impacts on gene functions remain largely uncharacterized in the lettuce genome.
Results
Here, we produced a comprehensive SV set for 333 wild and cultivated lettuce accessions. Comparison of SV frequencies showed that the SVs prevalent in L. sativa affected the genes enriched in carbohydrate derivative catabolic and secondary metabolic processes. Genome-wide association analysis of seven agronomic traits uncovered potentially causal SVs associated with seed coat color and leaf anthocyanin content.
Conclusion
Our work characterized a great abundance of SVs in the lettuce genome, and provides a valuable genomic resource for future lettuce breeding.
... Аналогичная закономерность наблюдается и у фенотипов домашних животных. Например, аллельная изменчивость KIT (tyrosine kinase receptor) -рецептора, критического для миграции популяций стволовых клеток, включая предшественники меланоцитов, и/или MC1R (рецептор меланокортина) вызывает изменение окраски у коз, свиней, лошадей, крупного рогатого скота и кур (7). ...
... Аналогичная закономерность наблюдается и у фенотипов домашних животных. Например, аллельная изменчивость KIT (tyrosine kinase receptor) -рецептора, критического для миграции популяций стволовых клеток, включая предшественники меланоцитов, и/или MC1R (рецептор меланокортина) вызывает изменение окраски у коз, свиней, лошадей, крупного рогатого скота и кур (7). ...
... To bolster production, there has been substantial economic investment geared towards achieving heightened yields and improved quality, particularly through selective breeding for resistance against pests and diseases. Maize, given its extensive study in areas like plant domestication and genome evolution, holds a pivotal role in biological research (Andersson and Purugganan, 2022). Elevating maize's tolerance to biotic stress and expanding its adaptability is crucial for both food security and livelihood enhancement. ...
To meet the rising demand for cereal-based food products, it is essential to create parent lines for hybrid development. Evaluating the sensitivity of maize genotypes to gamma rays is critical for successful mass irradiation to induce mutations. This study aimed to assess how maize genotypes respond to gamma radiation and determine an effective dosage for mutation breeding. Six maize genotypes were subjected to gamma radiation doses ranging from 0 to 750 Gy (s) 60 Co. The irradiated seeds were evaluated in controlled conditions and then planted in the field for the assessment of physio-agronomic traits. The lethal dose (LD50) was established based on the germination rate of the M1 generation. Results demonstrated a decrease in germination percentage, plant height, survival rate, root length, and plant photosynthetic rate with escalating gamma radiation doses. The mean LD 50 , determined from the germination data, was 254.3 Gy. The radiation dosage range of 206.71-301.95 Gy proved effective in influencing both quantitative and qualitative characteristics. These findings provide valuable insights into the efficient utilization of gamma radiation in expediting the development of promising parent lines, which can be instrumental in hybridization efforts to produce superior maize varieties.
