Transition From Wild to Domesticated Pearl Millet (Pennisetum glaucum) Revealed in Ceramic Temper at Three Middle Holocene Sites in Northern Mali.

Imprints of domesticated pearl millet (Pennisetum glaucum (L.) R. Br.) spikelets, observed as temper in ceramics dating to the third millennium BC, provide the earliest evidence for the cultivation and domestication process of this crop in northern Mali. Additional sherds from the same region dating to the fifth and fourth millennium BC were examined and found to have pearl millet chaff with wild morphologies. In addition to studying sherds by stereomicroscopy and subjecting surface casts to scanning electron microscopy (SEM), we also deployed X-ray microcomputed tomography (microCT) on eleven sherds. This significantly augmented the total dataset of archaeological pearl millet chaff remains from which to document the use of the wild pearl millet as ceramic temper and the evolution of its morphology over time. Grain sizes were also estimated from spikelets preserved in the ceramics. Altogether, we are now able to chart the evolution of domesticated pearl millet in western Africa using three characteristics: the evolution of nonshattering stalked involucres; the appearance of multiple spikelet involucres, usually paired spikelets; and the increase in grain size. By the fourth millennium BC, average grain breadth had increased by 28%, although spikelet features otherwise resemble the wild type. In the third millennium BC, the average width of seeds is 38% greater than that of wild seeds, while other qualitative features of domestication are indicated by the presence of paired spikelets and the appearance of nondehiscent, stalked involucres. Nonshattering spikelets had probably become fixed by around 2000 BC, while increases in average grain size continued into the second millennium BC. These data now provide a robust sequence for the morphological evolution of domesticated pearl millet, the first indigenous crop domesticated in western Africa. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10437-021-09428-8.

Des empreintes d'épillets de mil domestiqué (Pennisetum glaucum (L.) R. Br.) observées dans des céramiques datées du 3e millénaire av. J.-C. provenant du nord du Mali constituent les plus anciens témoins de la mise en culture et de la domestication de cette céréale. Des tessons supplémentaires issus de la même région se rapportant aux 5e et 4e millénaires av. J.-C. ont été examinés et ont révélé des empreintes de balle de mil de morphologies sauvages. En plus de l'observation de leurs surfaces par stéréo-microscopie, et de l'observation des moulages d'empreintes au microscope à balayage, onze d'entre eux ont fait l'objet des micro-tomographies aux rayons X (microCT). Ces examens enrichissent considérablement l'ensemble des données archéologiques concernant l'utilisation du mil sauvage comme dégraissant végétal et son évolution morphologique à travers le temps. La taille des grains a aussi été estimée à partir des épillets conservés dans la céramique. En tenant compte des données enregistrées lors d'études antérieures, nous pouvons désormais retracer l'évolution du mil domestiqué en Afrique de l'Ouest à travers trois caractéristiques : l'évolution des involucres pédonculés à égrenage non-spontané; l'apparition d'involucres multiples par épillets, des épillets appariés le plus souvent; l'augmentation de la taille des grains au vu de leur largeur. Déjà au 4e millénaire avant J.-C., la largeur moyenne des grains a augmenté de 28% bien que les caractéristiques de l'épillet ressemblent au type sauvage. Au 3e millénaire avant J.-C., elle est 38% supérieure à celle du morphotype sauvage, tandis que des caractéristiques qualitatives de la domestication sont avérées par la présence d'épillets appariés et par celle d'involucres pédonculés à égrenage non-spontané. La non-déhiscence des épillets est un caractéristique de la domesticité qui s'est probablement fixé vers 2000 avant J.-C., tandis que l'augmentation de la taille moyenne des grains s'est poursuivie tout au long du 2e millénaire av. J.-C. Ces données fournissent désormais une séquence robuste concernant l'évolution morphologique du mil, la première céréale indigène domestiquée en Afrique de l'Ouest.

A western Sahara centre of domestication inferred from pearl millet genomes.

There have been intense debates over the geographic origin of African crops and agriculture. Here, we used whole-genome sequencing data to infer the domestication origin of pearl millet (Cenchrus americanus). Our results supported an origin in western Sahara, and we dated the onset of cultivated pearl millet expansion in Africa to 4,900 years ago. We provided evidence that wild-to-crop gene flow increased cultivated genetic diversity leading to diversity hotspots in western and eastern Sahel and adaptive introgression of 15 genomic regions. Our study reconciled genetic and archaeological data for one of the oldest African crops.

The Rise and Fall of African Rice Cultivation Revealed by Analysis of 246 New Genomes.

African rice (Oryza glaberrima) was domesticated independently from Asian rice. The geographical origin of its domestication remains elusive. Using 246 new whole-genome sequences, we inferred the cradle of its domestication to be in the Inner Niger Delta. Domestication was preceded by a sharp decline of most wild populations that started more than 10,000 years ago. The wild population collapse occurred during the drying of the Sahara. This finding supports the hypothesis that depletion of wild resources in the Sahara triggered African rice domestication. African rice cultivation strongly expanded 2,000 years ago. During the last 5 centuries, a sharp decline of its cultivation coincided with the introduction of Asian rice in Africa. A gene, PROG1, associated with an erect plant architecture phenotype, showed convergent selection in two rice cultivated species, Oryza glaberrima from Africa and Oryza sativa from Asia. In contrast, a shattering gene, SH5, showed selection signature during African rice domestication, but not during Asian rice domestication. Overall, our genomic data revealed a complex history of African rice domestication influenced by important climatic changes in the Saharan area, by the expansion of African agricultural society, and by recent replacement by another domesticated species.

Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments.

Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ∼1.79 Gb draft whole genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for wax biosynthesis genes, which may contribute to heat and drought tolerance in this crop. We resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication. We use these resequencing data to establish marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance. We believe that these resources should empower researchers and breeders to improve this important staple crop.