Whole-genome resequencing of Cucurbita pepo morphotypes to discover genomic variants associated with morphology and horticulturally valuable traits

[EN] Cucurbita pepo contains two cultivated subspecies, each of which encompasses four fruit-shape morphotypes (cultivar groups). The Pumpkin, Vegetable Marrow, Cocozelle, and Zucchini Groups are of subsp. pepo and the Acorn, Crookneck, Scallop, and Straightneck Groups are of subsp. ovifera. Recently, a de novo assembly of the C. pepo subsp. pepo Zucchini genome was published, providing insights into its evolution. To expand our knowledge of evolutionary processes within C. pepo and to identify variants associated with particular morphotypes, we performed whole-genome resequencing of seven of these eight C. pepo morphotypes. We report for the first time whole-genome resequencing of the four subsp. pepo (Pumpkin, Vegetable Marrow, Cocozelle, green Zucchini, and yellow Zucchini) morphotypes and three of the subsp. ovifera (Acorn, Crookneck, and Scallop) morphotypes. A high-depth resequencing approach was followed, using the BGISEQ-500 platform that enables the identification of rare variants, with an average of 33.5X. Approximately 94.5% of the clean reads were mapped against the reference Zucchini genome. In total, 3,823,977 high confidence single-nucleotide polymorphisms (SNPs) were identified. Within each accession, SNPs varied from 636,918 in green Zucchini to 2,656,513 in Crookneck, and were distributed homogeneously along the chromosomes. Clear differences between subspecies pepo and ovifera in genetic variation and linkage disequilibrium are highlighted. In fact, comparison between subspecies pepo and ovifera indicated 5710 genes (22.5%) with Fst > 0.80 and 1059 genes (4.1%) with Fst = 1.00 as potential candidate genes that were fixed during the independent evolution and domestication of the two subspecies. Linkage disequilibrium was greater in subsp. ovifera than in subsp. pepo, perhaps reflective of the earlier differentiation of morphotypes within subsp. ovifera. Some morphotype-specific genes have been localized. Our results offer new clues that may provide an improved understanding of the underlying genomic regions involved in the independent evolution and domestication of the two subspecies. Comparisons among SNPs unique to particular subspecies or morphotypes may provide candidate genes responsible for traits of high economic importance.This work has been supported by Hellenic Agricultural Organization (ELGO) Demeter. Furthermore, we thank the Conselleria de Educacio, Investigacio, Cultura i Esport (Generalitat Valenciana) for funding Project Prometeo 2017/078 "Seleccion de Variedades Tradicionales y Desarrollo de Nuevas Variedades de Cucurbitaceas Adaptadas a la Produccion Ecologica". 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Integrative epigenomic mapping defines four main chromatin states in Arabidopsis

This first comprehensive view of the Arabidopsis epigenome reveals that it is organized into four main chromatin types based on the integrative mapping of a broad set of 11 histone marks and DNA methylation in seedlings

Parallelized plant morphogenesis in a controllable microfluidic environment

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Parallelized plant morphogenesis in a controlled microfluidic environement

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Parallelized plant morphogenesis in a controllable microfluidic environement

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Caractérisation de nouveaux constituants du cytosquelette chez Arabidopsis thaliana (les protéines TON et leurs partenaires)

Le cytosquelette des cellules végétales orchestre de nombreux processus de croissance, morphogenèse et différenciation. L analyse de mutants chez Arabidopsis thaliana a permis l isolement de nouvelles protéines et de leurs partenaires et de mieux comprendre les mécanismes gouvernant la dynamique des microtubules (MTs) et des microfilaments (MFs). Les mutants tonneau et fass présentent d importants défauts morphologiques associés à une désorganisation des MTs corticaux. La protéine TON est conservée chez les plantes, et présente des homologies avec deux protéines centrosomales humaines. Nous avons montré que la fusion TON-GFP est associée aux MTs corticaux. Un crible 2-hybride avait permis d'isoler des partenaires de TON : une centrine et onze protéines inconnues, spécifiques des plantes, partageant cinq motifs conservés, et nommées TIM (TON Interactif Motif). Certains de ces motifs sont conservés chez une protéine centrosomale. La famille TIM compte une trentaine de membres dans le génome d Arabidopsis. De façon surprenante, la fusion GFP-TIM1 se lie aux MTs et/ou aux MFs et nous avons pu identifier le domaine de liaison aux MTs. Nous avons isolé des simples, doubles et quadruple mutants d une sous-famille de 4 protéines (TIM1 à TIM4) et montré que ces protéines sont importantes pour le développement de la plante. L'ensemble de ces résultats suggère que les protéines TON et TIM1 sont impliquées dans la dynamique des MTs corticaux et dans le développement de la plante. TIM1 pourrait également coordonner les réseaux de MTs et de MFs. La famille TIM pourrait se révéler essentielle dans l'organisation spatiale des structures corticales de cytosquelette végétal.The plant cell cytoskeleton is involved in many growth processes, morphogenesis and differentiation. Analysis of Arabidopsis thaliana mutants allowed us to uncover new proteins and their partners, and to better understand mechanisms that govern microtubules (MT) and microfilaments (MF) dynamics. The tonneau and fass mutants show considerable morphologic alterations associated with abnormalities in organization of cortical MTs. TON protein is strongly conserved in plants, and has similarities with two human centrosomal proteins. We have shown that a GFP-TON fusion is associated to the cortical cytoskeleton. A yeast 2-hybrid screen had previously lead to isolation of TON partners: a centrin and of 12 large unknown proteins, specific to plants, sharing 5 conserved motifs and named TIM (TON Interaction Motif). We showed that some of these motifs are conserved in CAP350, a centrosomal protein. The TIM family comprises about 30 members in the Arabidopsis genome. Interestingly, a GFP-TIM1 fusion binds both MTs and/or MFs. We have identified the TIM1 MT binding domain, which corresponds to a highly basic region. In order to study the role of these proteins in plant development, genetic study of one sub-family of 4 proteins (TIM1 to TIM4) has been undertaken. Phenotype analysis of single, double and quadruple mutants show significant defects in development. Taken together, results suggest an involvment of TON and TIM1 proteins in the dynamics of cortical MTs and in plant development. TIM1 could also coordiantes the MT and MF networks during the cell cycle. The TIM family could be essential for spatial organization of plant cortical cytoskeleton structures.ORSAY-PARIS 11-BU Sciences (914712101) / SudocSudocFranceF

Parallelized plant morphogenesis in a controlled microfluidic environement

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Parallelized plant morphogenesis in a controlled microfluidic environement

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Germination and mechanics in marchantia polymorpha gemmae

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