Zekraoui, L. | bioRxiv Science

bioRxiv2020

Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

Sustainable food production in the context of climate change necessitates diversification of agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we established high-quality genomic resources to facilitate fonio improvement through molecular breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population structure, and domestication. Fonio diversity is shaped by climatic, geographic, and ethnolinguistic factors. Two genes associated with seed size and shattering showed signatures of selection. Most known domestication genes from other cereal models however have not experienced strong selection in fonio, providing direct targets to rapidly improve this crop for agriculture in hot and dry environments.

plant biology↗

bioRxiv2020

Transferability, development of Single Sequence Repeat (SSR) markers and application to the analysis of genetic diversity and population structure of the African fan palm (Borassus aethiopum Mart.) in Benin

In Sub-Saharan Africa, the fan palm Borassus aethiopum Mart. is an important non-timber forest product-providing palm that faces multiple anthropogenic threats to its genetic diversity. However, this species is so far under-studied, which prevents its sustainable development as a resource. The present work is a first attempt at characterizing the genetic diversity of this palm species as well as its spatial structuration in Benin, West Africa. During a first phase we implemented a microsatellite markers-based approach relying on the reported transferability of primers developed in other palm species and found that, in disagreement with previously published results, only 22.5% of the 80 markers tested enabled amplification of African fan palm DNA and polymorphism detection was insufficient. During a second phase, we therefore generated a B. aethiopum-specific genomic dataset through high-throughput sequencing and used it for the de novo detection of potential microsatellite markers. Among these, 11 enabled polymorphism detection and were further used for analyzing genetic diversity in nine B. aethiopum populations. Our results show that genetic diversity of Beninese fan palm populations is low, with an overall average expected heterozygosity (He) of 0.354. Moreover, the positive values of the fixation index (F) in populations from both the Central (Soudano-Guinean) and the Southern (Guinean) regions suggest limited gene flows. Our analysis show that sampled B. aethiopum populations are clustered into two groups, one spanning populations from both the Southern and most of the Central region, and the other including the Central population of Save (which also has the highest He) and populations from the North. In light of our results, we discuss the use of inter-species transfer vs. de novo development of microsatellite markers in genetic diversity analyses targeting under-studied species. We also suggest future applications for the molecular resources generated through the present study.

genetics↗