Biology subjects

CUBRY, P.

Publications and source records attributed to CUBRY, P..

4 recordsLinked to original sources

bioRxiv2024

Genome-wide association analysis of flowering date in a collection of cultivated olive tree

1.Flowering date in perennial fruit trees is an important trait for fruit production. Depending on the winter and spring temperatures, flowering of olive may be advanced, delayed, or even suppressed. Deciphering the genetic control of flowering date is thus key to help selecting cultivars better adapted to the current climate context. Here, we investigated the genetic determinism of full flowering date stage in cultivated olive based on capture sequencing data of 318 genotypes from the worldwide olive germplasm bank of Marrakech, Morocco. The genetic structure of this collection was organized in three clusters that were broadly attributed to eastern, central, and western Mediterranean regions, based on the presumed origin of genotypes. Flowering dates, collected over seven years, were used to estimate the genotypic best linear unbiased predictors, which were then analyzed in a genome-wide association study. Loci with small effects were significantly associated with the studied trait, by either a single- or a multi-locus approach. The three most robust loci were located on chromosomes 01 and 04, and on a scaffold, and explained 7.1%, 6.2%, and 6.5 % of the trait variance, respectively. A significantly higher accuracy in the best linear unbiased predictors of flowering date prediction was reported with Ridge-compared to LASSO-based genomic prediction model. Along with genomic association results, this suggests a complex polygenic determinism of flowering date, as seen in many other fruit perennials. These results and the screening of associated regions for candidate genes open perspectives for further studies and breeding programs targeting flowering date.

genetics↗

bioRxiv2023

A quantitative theory for genomic offset statistics

Genomic offset statistics predict the maladaptation of populations to rapid habitat alteration based on association of genotypes with environmental variation. Despite substantial evidence for empirical validity, genomic offset statistics have well-identified limitations, and lack a theory that would facilitate interpretations of predicted values. Here, we clarified the theoretical relationships between genomic offset statistics and unobserved fitness traits controlled by environmentally selected loci, and proposed a geometric measure to predict fitness after rapid change in local environment. he predictions of our theory were verified in computer simulations and in empirical data on African pearl millet (Cenchrus americanus) obtained from a common garden experiment. Our results proposed a unified perspective on genomic offset statistics, and provided a theoretical foundation necessary when considering their potential application in conservation management in the face of environmental change.

evolutionary biology↗

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

Genome wide association study pinpoints key agronomic QTLs in African rice Oryza glaberrima

BackgroundAfrican rice, Oryza glaberrima, is an invaluable resource for rice cultivation and for the improvement of biotic and abiotic resistance properties. Since its domestication in the inner Niger delta ca. 2500 years BP, African rice has colonized a variety of ecologically and climatically diverse regions. However, little is known about the genetic basis of quantitative traits and adaptive variation of agricultural interest for this species. ResultsUsing a reference set of 163 fully re-sequenced accessions, we report the results of a Genome Wide Association Study carried out for African rice. We investigated a diverse panel of traits, including flowering date, panicle architecture and resistance to Rice yellow mottle virus. For this, we devised a pipeline using complementary statistical association methods. First, using flowering time as a target trait, we demonstrated that we could successfully retrieve known genes from the rice flowering pathway, and identified new genomic regions that would deserve more study. Then we applied our pipeline to panicle- and resistance-related traits, highlighting some interesting QTLs and candidate genes (including Rymv1 for resistance and SP1, Ghd7.1, APO1 and OsMADS1 for panicle architecture). Lastly, using a high-resolution climate database, we performed an association analysis based on climatic variables, searching for genomic regions that might be involved in adaptation to climatic variations. ConclusionOur results collectively provide insights into the extent to which adaptive variation is governed by sequence diversity within the O. glaberrima genome, paving the way for in-depth studies of the genetic basis of traits of interest that might be useful to the rice breeding community.

plant biology↗