Claire Billot

Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies

Biodiversity, phylogeography and population genetic studies will be revolutionized by access to large data sets thanks to next‐generation sequencing methods. In this study, we develop an easy and cost‐effective protocol for in‐solution enrichment hybridization capture of complete chloroplast genomes applicable at deep‐multiplexed levels. The protocol uses cheap in‐house species‐specific probes developed via long‐range PCR of the entire chloroplast. Barcoded libraries are constructed, and in‐solution enrichment of the chloroplasts is carried out using the probes. This protocol was tested and validated on six economically important West African crop species, namely African rice, pearl millet, three African yam species and fonio. For pearl millet, we also demonstrate the effectiveness of this protocol to retrieve 95% of the sequence of the whole chloroplast on 95 multiplexed individuals in a single MiSeq run at a success rate of 95%. This new protocol allows whole chloroplast genomes to be retrieved at a modest cost and will allow unprecedented resolution for closely related species in phylogeography studies using plastomes.

Phylogeographic Evidence of Crop Neodiversity in Sorghum

Sorghum has shown the adaptability necessary to sustain its improvement during time and geographical extension despite a genetic foundation constricted by domestication bottlenecks. Initially domesticated in the northeastern part of sub-Saharan Africa several millenia ago, sorghum quickly spread throughout Africa, and to Asia. We performed phylogeographic analysis of sequence diversity for six candidate genes for grain quality (Shrunken2, Brittle2, Soluble starch synthaseI, Waxy, Amylose extender1, and Opaque2) in a representative sample of sorghum cultivars. Haplotypes along 1-kb segments appeared little affected by recombination. Sequence similarity enabled clustering of closely related alleles and discrimination of two or three distantly related groups depending on the gene. This scheme indicated that sorghum domestication involved structured founder populations, while confirming a specific status for the guinea margaritiferum subrace. Allele rooted genealogy revealed derivation relationships by mutation or, less frequently, by recombination. Comparison of germplasm compartments revealed contrasts between genes. Sh2, Bt2, and SssI displayed a loss of diversity outside the area of origin of sorghum, whereas O2 and, to some extent, Wx and Ae1 displayed novel variation, derived from postdomestication mutations. These are likely to have been conserved under the effect of human selection, thus releasing valuable neodiversity whose extent will influence germplasm management strategies.

CLONAL PROPAGATION OF LAMINARIA DIGITATA (PHAEOPHYCEAE) SPOROPHYTES THROUGH A DIPLOID CELL-FILAMENT SUSPENSION

In vitro cultures of Laminaria digitata (Hudson) Lamouroux stipe medullary explants (Laminariales, Phaeophyceae) gave rise to friable morula‐like masses of pigmented cells. Upon subculture under continuous white light, they grew out as filaments, which tended to dissociate into spherical isolated cells, leading to the establishment of a suspended cell‐filament culture. Depending on culture conditions, this cell‐filament suspension underwent various forms of growth, including regeneration of morphologically normal sporophytes, and this developmental pathway was stimulated by blue light. Genotyping with nine polymorphic microsatellite markers indicated that the regenerated sporophytes and the cell‐filament suspension shared the same genotype. As assessed by flow cytometric analysis of isolated nuclei, the cell‐filament suspension exhibited a 2C nuclear DNA content, whereas the regenerated sporophytes displayed a 4C level. Chromosome counting, however, showed that both the mother suspension and the regenerated sporophytes were diploid, suggesting the involvement of polyteny in the regeneration process.

Development and characterization of nine polymorphic microsatellite markers in the Chilean kelp Lessonia nigrescens

A total of nine microsatellite loci were isolated and characterized in the Chilean kelp Lessonia nigrescens Bory. Using two different enriched libraries, we observed 1–14 alleles per locus in two samples of 21 kelp individuals each. The observed heterozygosities ranged from 0.05 to 0.80 and all loci are in Hardy–Weinberg equilibrium for one or both samples. Seventeen samples collected from different sites showed high allele diversity along the species distribution. The variation detected at these markers is currently being used for the study of populations of Lessonia nigrescens at different geographical scales.

High selfing rate inferred for white fonio [#Digitaria exilis# (Kippist.) Stapf] reproductive system opens up opportunities for breeding programs

In a context of the global major changes, it is mandatory to enlarge the range of crops supporting food security and pay great attention to neglected and underutilized species. However, basic knowledge of the biology of many neglected and underutilized species is still lacking to increase their yields. In this study, the mating system of white fonio [Digitaria exilis (Kippist.) Stapf], a West African minor and promising cereal, is assessed. Progenies arrays from both homozygous and heterozygous mothers were genotyped with microsatellites markers. The rate of genotyping errors in the experiments was assessed and a likelihood framework was used to determine the probability of different mating systems: outcrossing, self-fertilization and apomixis. The results suggested that white fonio has a highly selfing reproductive system with a possible outcrossing rate of 1.7%. Understanding the reproduction system of white fonio opens up opportunities for more effective breeding programs and a wider use of this cereal for food security improvement.

Adaptive introgression: an untapped evolutionary mechanism for crop adaptation

Global environmental changes strongly impact wild and domesticated species biology and their associated ecosystem services. For crops, global warming has led to significant changes in terms of phenology and/or yield. To respond to the agricultural challenges of this century, there is a strong need for harnessing the genetic variability of crops and adapting them to new conditions. Gene flow, from either the same species or a different species, may be an immediate primary source to widen genetic diversity and adaptions to various environments. When the incorporation of a foreign variant leads to an increase of the fitness of the recipient pool, it is referred to as “adaptive introgression”. Crop species are excellent case studies of this phenomenon since their genetic variability has been considerably reduced over space and time but most of them continue exchanging genetic material with their wild relatives. In this paper, we review studies of adaptive introgression, presenting methodological approaches and challenges to detecting it. We pay particular attention to the potential of this evolutionary mechanism for the adaptation of crops. Furthermore, we discuss the importance of farmers’ knowledge and practices in shaping wild-to-crop gene flow. Finally, we argue that screening the wild introgression already existing in the cultivated gene pool may be an effective strategy for uncovering wild diversity relevant for crop adaptation to current environmental changes and for informing new breeding directions.