A western Sahara centre of domestication inferred from pearl millet genomes

Burgarella, Concetta; Cubry, Philippe; Kane, Ndjido Ardo; Varshney, Rajeev K.; Mariac, Cédric; Liu, Xin; Shi, Chengcheng; Thudi, Mahendar; Couderc, Marie; Xu, Xun; Chitikineni, Annapurna; Scarcelli, Nora; Barnaud, Adéline; Rhoné, Bénédicte; Dupuy, Christian; Ochsenbein, F.; Berthouly‐Salazar, Cécile; Vigouroux, Yves

doi:10.1038/s41559-018-0643-y

Cited by 104 publications

(95 citation statements)

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“…These regions, related to adaptive traits, such as the quantity of leaf macrohairs and pigmentation intensity, could have helped maize to adapt to high altitude (Hufford et al, 2013). Recent study suggested that wild-to-crop gene flow significantly genetic diversity and possibly lead to introgressions of local adaptation in pearl millet, a major staple African crops (Burgarella et al, in press).…”

Section: Gene Flow In Crops: Challenges and Opportunitiesmentioning

confidence: 99%

Adaptive introgression: an untapped evolutionary mechanism for crop adaptation

Burgarella

Barnaud

Kane

et al. 2018

Preprint

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29Global environmental changes strongly impact wild and domesticated species biology and their 30 associated ecosystem services. For crops, global warming has led to significant changes in terms of 31 phenology and/or yield. To respond to the agricultural challenges of this century, there is a strong 32 need for harnessing the genetic variability of crops and adapting them to new conditions. Gene 33 flow, from either the same species or a different species, may be an immediate primary source to 34 widen genetic diversity and adaptions to various environments. When the incorporation of a foreign 35 variant leads to an increase of the fitness of the recipient pool, it is referred to as "adaptive 36 introgression". Crop species are excellent case studies of this phenomenon since their genetic 37 variability has been considerably reduced over space and time but most of them continue 38 exchanging genetic material with their wild relatives. In this paper, we review studies of adaptive 39 introgression, presenting methodological approaches and challenges to detecting it. We pay 40 particular attention to the potential of this evolutionary mechanism for the adaptation of crops. 41Furthermore, we discuss the importance of farmers' knowledge and practices in shaping wild-to-42 crop gene flow. Finally, we argue that screening the wild introgression already existing in the 43 cultivated gene pool may be an effective strategy for uncovering wild diversity relevant for crop 44 adaptation to current environmental changes and for informing new breeding directions. 45 46 93 94 In the context of species conservation and management a large body of literature discuss how gene 95 flow could also be associated with negative effects. Undesirable consequences of gene flow are 96 4 associated with the risks of invasiveness (Ellstrand and Schierenbeck, 2000; Whitney et al., 2006), 97 transgene escape (Ellstrand et al., 2013 and references therein), or genetic erosion of native 98 populations (Wolf et al., 2001). Little attention has been paid to the potential of managed gene flow 99to increase genetic variation for species rescue (Hedrick, 2009) and adaptation (Aitken and 100 Whitlock, 2013). Up to now, the potential of adaptive introgression as a source of adaptation to on-101 going global changes for domesticated species has been overlooked. 103In this paper, we review studies of adaptive introgression, paying particular attention to the potential 104 of this evolutionary mechanism for the adaptation of crops. By the term 'introgression' we mean the 105 consequence of gene flow, at both the interspecific and the intraspecific level, i.e. independently of 106 the taxonomic classification of the gene pools exchanging genetic material. We focus on sexually 107 reproductive organisms; and we did not directly discuss horizontal gene transfer (reviewed in 108 Arnold and Kunte, 2017). Within this framework, we report on 34 case studies addressing adaptive 109 introgression ( Table 1). After discussing methodological approaches and challenges ...

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Section: Gene Flow In Crops: Challenges and Opportunitiesmentioning

confidence: 99%

Adaptive introgression: an untapped evolutionary mechanism for crop adaptation

Burgarella

Barnaud

Kane

et al. 2018

Preprint

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“…The prehistory of populations living in the savanna belt of the Sahel was shaped by demographic expansions in the Sahara during the last African Humid Period (Manning & Timpson, ), when a culture known as the “African cattle complex” spread into this region some eight thousand years ago (di Lernia et al, ; Dunne et al, ; Jesse, Keding, Lenssen‐Erz, & Pöllath, ). In Africa, pastoralism probably preceded farming by several thousand years (Marshall & Hildebrand, ; Neumann, ; Neumann, ), whereby the cultivation of pearl millet has a long tradition, especially in the western region (Burgarella et al, ), and the cultivation of sorghum has been present in eastern parts of the Sahara for over five thousand years (Winchell, Stevens, Murphy, Champion, & Fuller, ). It has been proposed that the first cultivators in the Sahel were Saharan pastoralists who shifted to agropastoralism in the Niger Bend some five thousand years ago (Ozainne et al, ).…”

Section: Introductionmentioning

confidence: 99%

Subsistence strategy was the main factor driving population differentiation in the bidirectional corridor of the African Sahel

Nováčková

Čížková

Mokhtar

et al. 2020

American J Phys Anthropol

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Objectives: The Sahel belt is occupied by populations who use two types of subsistence strategy, nomadic pastoralism and sedentary farming, and who belong to three linguistic families, Niger-Congo, Nilo-Saharan, and Afro-Asiatic. Little is known, however, about the origins of these two populations and their mutual genetic relationships. Materials and Methods:We have built a large dataset of mitochondrial DNA sequences and Y chromosomal STR haplotypes of pastoralists and farmers belonging to all three linguistic phyla in the western, central, and eastern parts of the Sahel. We calculated pairwise genetic, geographic, and linguistic distances between populations and analyzed the effects of geography, language, and subsistence on population genetic structure.Results: We found that subsistence mode significantly contributed to the generally low population structure in the Sahel and that language affiliation plays a more important role for pastoralists than for farmers. We also demonstrated that geographic isolation significantly influenced the population structure of sedentary farmers but not of nomadic pastoralists. Finally, we found haplotypes shared between the Fulani and Arabic-speaking Baggara, supporting the theory of Baggarization, which explains the recent adaptation of Arabic-speaking nomads in the Sahel region through contact with autochthonous sub-Saharan populations.

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“…Crops and their wild relatives can often intercross in the wild and exchange adaptive traits (Janzen et al 2018). In a number of major crops such as maize (Hufford et al 2013), barley (Poets et al 2015), rice Meyer et al 2016) and pearl millet (Burgarella et al 2018) adaptive introgression from wild relatives has been observed. Adaptive introgression requires several generations of backcrossing to the crop in order to remove linkage drag (reviewed in Janzen et al 2018).…”

Section: Gene Flow Between Wild and Domesticated Amaranthsmentioning

confidence: 99%

Convergent seed color adaptation during repeated domestication of an ancient new world grain

Stetter

Vidal-Villarejo

Schmid

2019

Preprint

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Out of the almost 2,000 plants that have been selected as crops, only a few are fully domesticated, and many intermediates between wild plants and domesticates exist. Genetic constraints might be the reason why incompletely domesticated plants have few characteristic crop traits, and retained numerous wild plant features. Here, we investigate the incomplete domestication of an ancient grain from the Americas, amaranth. We sequenced 121 genomes of the crop and its wild ancestors to show that grain amaranth has been selected three times independently from a single wild ancestor, but has not been fully domesticated. While only few domestication traits have been adapted during amaranth domestication, the seed color converted from dark seeds to white seeds between the ancestor and the crops. To investigate the seed color adaptation in amaranth we produced a mapping population between wild and domesticated amaranth, a whole genome sequenced bulked segregant population and perform genome wide association mapping in our divers panel. All three methods agree on two quantitative trait loci controlling the trait. We identify a MYB-like transcription factor gene, a known regulator for seed color variation in other plant species, within one of the significant regions and shows that the trait was independently converted in Central and South America. We propose that a low effective population size at the time of domestication might have contributed to the lack of adaptation of complex domestication traits. Our results show how genetic constraints influenced domestication and might have set the fate of hundreds of crops. SignificanceEarly farmers cultivated hundreds of plant species and altered their morphological and physiological characteristics during domestication to be well suited for human consumption. Despite long cultivation histories, many crops remained of minor importance, because they were limited in their adaptation to agro-ecological systems. We investigate the domestication history of the ancient minor crop amaranth and show that it was independently domesticated three times from the same ancestor. In all three domesticates, white seed color, which is controlled by only two genes, was independently selected. In contrast, more complex domestication traits like seed size were not changed during domestication, and our analyses suggest that this may have resulted from a lack of functional genetic variation in the ancestor during domestication.

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A western Sahara centre of domestication inferred from pearl millet genomes

Cited by 104 publications

References 32 publications

Adaptive introgression: an untapped evolutionary mechanism for crop adaptation

Adaptive introgression: an untapped evolutionary mechanism for crop adaptation

Subsistence strategy was the main factor driving population differentiation in the bidirectional corridor of the African Sahel

Convergent seed color adaptation during repeated domestication of an ancient new world grain

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