Biology subjects

Lacombe, T.

Publications and source records attributed to Lacombe, T..

3 recordsLinked to original sources

bioRxiv2025

Evolution of crop phenotypic spaces through domestication

O_LIWe used domestication as an in vivo replicated experiment to investigate how divergent selection has shaped the evolution of multivariate phenotypic spaces. C_LIO_LIWe measured 11 to 57 qualitative and quantitative traits in 13 species, either unique or shared between species, and established a framework for cross-species comparisons. C_LIO_LIOur results revealed significant convergence that translated into a cross-species domestication syndrome. Most species exhibited a reduction of the multivariate phenotypic space during domestication. We brought evidence that Near Infrared spectra measured on leaves reflect phenotypic evolution unrelated with domestication, enabling its use as a control for sampling effects across species. Building on this, we developed a multivariate Phenotypic Divergence Index (mPDI) to rank species by the extent of phenotypic divergence under domestication. We found a high disjunction of wild and domestic phenotypic spaces in all species. Neither the mPDI nor the relative size of wild versus domestic multivariate phenotypic spaces was influenced by the domestication timing or mating system. Lastly, we observed a progressive decoupling of trait correlations with increasing time since domestication. C_LIO_LIIn addition to introducing a new index that can be applied for cross-species comparisons, our study uncovers recurring patterns shared among species, pointing to general principles underlying plant domestication. C_LI

evolutionary biology↗

bioRxiv2020

Genome-wide association and prediction studies using a grapevine diversity panel give insights into the genetic architecture of several traits of interest

To cope with the challenges faced by agriculture, speeding-up breeding programs is a worthy endeavor, especially for perennials such as grapevine, but requires understanding the genetic architecture of target traits. To go beyond the mapping of quantitative trait locus (QTL) in bi-parental crosses, we exploited a diverse panel of 279 Vitis vinifera L. cultivars. This panel planted in five blocks in the vineyard was phenotyped over several years for 127 traits including yield components, organic acids, aroma precursors, polyphenols, and a water stress indicator. The panel was genotyped for 63k single nucleotide polymorphisms (SNPs) by combining an 18K microarray and genotyping-by-sequencing (GBS). The experimental design allowed to reliably assess the genotypic values for most traits. Marker densification via GBS markedly increased the proportion of genetic variance explained by SNPs, and two multi-SNP models identified QTLs not found by a SNP-by-SNP model. Overall, 489 reliable QTLs were detected for 41% more response variables than by a SNP-by-SNP model with microarray-only SNPs, many new ones compared to the results from bi-parental crosses. Prediction accuracy higher than 0.42 was obtained for 50% of the response variables. Our overall approach as well as QTL and prediction results provide insights into the genetic architecture of target traits. New candidate genes and the application in breeding are discussed.

genetics↗

bioRxiv2019

Berry and pip form covariation in wild and domesticated grapevines: eco-evo-devo implications and archaeobotanical perspectives

The phenotypic changes that occurred during the domestication and diversification of grapevine are well known, particularly changes in seed morphology, but the functional causes and consequences behind these variations are poorly understood. Wild and domesticate grapes differ, among others, in the form of their pips: wild grapes produce roundish pips with short stalks and cultivated varieties have more elongated pips with longer stalks. Such variations of form are of first importance for archaeobotany since the pip form is, most often, the only remaining information in archaeological settings. This study aims to enlight archaeobotanical record and grapevine pip development by better understanding how size and shape (co)variates between pip and berry in both wild and domesticated Vitis vinifera. The covariation of berry size, number of seeds per berry ("piposity"), pip size and pip shape were explored on 49 grapevine accessions sampled among Euro-Mediterranean traditional cultivars and wild grapevines. We show that for wild grapevine, the higher the piposity, the bigger the berry and the more elongated the pip. For both wild and domesticated grapevine, the longer is the pip, the more it has a "domesticated" shape. Consequences for archaeobotanical studies are tested and discussed, and these covariations allowed the inference of berry dimensions from archaeological pips from a Southern France Roman site. This systematic exploration sheds light on new aspects of pip-berry relationship, in both size and shape, on grapevine eco-evo-devo changes during domestication, and invites to explore further the functional ecology of grapevine pip and berry and notably the impact of cultivation practices and human selection on grapevine morphology.

plant biology↗