Symposium "Cutting-edge genomics for crop improvement"
Professor Simon Krattinger
Professor Ikram Blilou
Professor Salim Al-Babili
Speaker: Jaroslav Doležel
Title: Chromosome genomics facilitates genome analysis and gene cloning in plants
Chromosome genomics is based on the ability to dissect the full nuclear genome to its individual chromosomes by flow cytometric sorting. This is a powerful approach to achieve a lossless complexity reduction and avoids problems due to the presence of homoeologs in polyploids and DNA sequence redundancy, in general. Flow cytometry requires suspensions of intact mitotic metaphase chromosomes, which are most conveniently prepared from synchronized meristem root tip cells. To date, the method has been developed for more than thirty plant species. The DNA of flow-sorted chromosomes is intact and is suitable for a wide range of molecular techniques andsequencing technologies. Chromosome genomics facilitated rapid production of draft genome assemblies in important crops with complex genomes such as wheat, barley and rye, study molecular organization of specialized chromosomes such a B chromosomes and sex chromosomes, and was found invaluable to validate whole genome shotgun assemblies in a variety of species. Other important applications include the identification of chromosomes with integrated transgenes, characterization of alien chromatin in introgression lines and development of molecular markers from particular genome regions. This allows analyzing a chromosome of interest isolated from several different genotypes and brings a significant reduction of sequencing costs. Gene cloning has become one of the most important applications of chromosome genomics, recently. The targeted approach greatly streamlines the projects and reduces costs. To date, two chromosome-based gene cloning approaches, namely MutChromSeq and TACCA (targeted chromosome-based cloning via long-range assembly) have been developed and successfully used to clone important genes. A capacity to purify mitotic chromosomes and recent progress in chromosome conformation capture techniques makes it possible to study spatial organization of DNA in condensed chromosomes. Together with the ability to sequence chromosome proteome this provides powerful approaches to understand the architecture of plant mitotic chromosomes.
Doležel is Head of the Centre of Plant Structural and Functional
Genomics of the Institute of Experimental Botany in Olomouc (Czech
Republic), Research Director of the Centre of the Region Haná for
Biotechnological and Agricultural Research in Olomouc, and Professor of
Molecular Biology and Genetics at Palacký University in Olomouc. His
research focuses on plant genome structure, function and evolution. He
has been developing flow cytometric methods to analyze, map and sequence
nuclear genomes of economically important crops. In particular, he has
pioneered chromosome genomics to facilitate the analysis of complex and
polyploid genomes, including hexaploid bread wheat. Doležel published
over 300 papers in scientific journals, edited three books and was
principal investigator and co-investigator in more than thirty national
and international research projects. He is a member of the Learned
Society of the Czech Republic and has received several prestigious
awards for his scientific achievements.
Speaker: Eva Hřibová
Title: Analysis of chromosome structure in Musaceae using oligo painting
The family Musaceae comprises genera Musa, Ensete and Musella. While Ensete (2n=18) and Musella (2n=18) are represented by a few and one endemic species, respectively, genus Musa contains about 70 different species. Based on plant morphology and basic chromosome number, Musa species are classified into four sections. The largest of them, Eumusa (x=11) comprises most of edible banana cultivars. They originated by intra- and inter-specific crosses between wild diploids M. acuminata and M. balbisiana. The section Rhodochlamys (x=11) contains ornamental species, which are closely related to those of Eumusa. The section Australimusa (x=10) is represented by species growing in Southeast Asia and contains a peculiar group of edible banana clones known as Fe‘i. The section Callimusa is the most diverse and contains species differing in basic chromosome number (x=9, 10) and species which seem to be closely related to Ensete and Musella. In order to analyze chromosome structure and karyotype evolution in Musaceae, we used the recently developed method of oligo painting FISH. Pools of chromosome arm-specific oligomers were designed using the reference genome sequence of double haploid M. acuminata 'DH Pahang'. The oligomers were labeled using reverse transcription either by hapten- or fluorescently-labeled primers and used for FISH in a set of accessions representing different subspecies of M. acuminata, in M. balbisiana, and their intra- and inter-specific hybrids. The oligo painting probes were also tested for their suitability to detect chromosome rearrangements in more distant species of the family Musaceae. The chromosome oligo painting enabled anchoring pseudomolecules to individual chromosomes, creation of molecular karyotypes and identification of large structural chromosome rearrangements. The method of oligo painting FISH thus opens avenues for comparative analysis of structural chromosome changes to shed light on karyotype evolution in Musaceae.
Hřibová is a research group leader at the Centre of Plant Structural and
Functional Genomics of the Institute of Experimental Botany in Olomouc
(Czech Republic). Her research focuses on plant genome organization,
function and evolution. In particular, she has extensive experience in
the analysis of the banana (Musa) genome using a range of molecular,
cytogenetic and bioinformatic techniques, including fluorescence in situ
hybridization and genome sequencing. She has significantly contributed
to the characterization of Musa genetic diversity using molecular
markers and its conservation. The results of her work support breeding
of improved banana cultivars. The recent research focuses on the spatial
organization of nuclear genomes and replication profiling in plants
using three-dimensional FISH and RepliSeq. Eva Hřibová published over 35
papers in scientific journals, which are frequently cited.
Speaker: Yves Vigouroux
Title: Genomics of African crops identify a hot-spot of domestication in Western Africa
While there has been progress in our understanding of the origins and history of agriculture in sub-Saharan Africa, a unified perspective is still lacking on where and how major crops were domesticated in the region. We will present the lasted results based on genomic study of major african crops: pearl millet, African rice and yam. Using whole-genome resequencing and statistical models, we infer that that the vicinity of the Niger River was a major cradle of African agriculture. The origin of the oldest crop is found in the Sahara more than 5000 years ago. Depletion of wild ressources and drying of the Sahara might have been a major driver of crop domestication in Africa. Finally, we found signature of their cultivation decreased associated with arrival of non-african crops, in the last 500 years.
Yves Vigouroux received his PhD from the University of Burgundy, France
on the study of wild/cultivated hybridization in plant. He did his
post-doctorate at the University of Madison, Wisconsin with Dr John
Doebley on maize domestication. And, subsequently, was hired as a
researcher and then Director of Research at the Institute of Research
for Development in Montpellier, France. He directed a team of 9
researchers focusing on the study of plant evolutionary history. Dr.
Yves Vigouroux has published seventy nine journal articles, mainly on
plant domestication and the genomic basis of adaptation to climate
variation. He recently led a genomic research project on domestication
process in Africa leading to new insight in several key African crops:
pearl millet, African rice, fonio, yam and sorghum.
Speaker: Adeline Barnaud
Title: Mobilizing Neglected and Underutilized Crop diversity for the future: fonio, a cereal from Western Africa
The FAO recently estimated that demand for food would increase by 70% by 2050, reflecting the effects of both population growth and the rising of per capita incomes. The challenge will not only be on increasing the food supply, but also on improving its nutritional value. Until now, despite the call for an increased use of underutilized crops to diversify alimentation and provide sustainable agriculture, those crops remain a largely untapped reservoir of agrobiodiversity. Are they really crops for the future?
In this regard, fonio (Digitaria exilis Stapf) appears as a promising crop. It is an indigenous staple cereal from Western Africa regarded as a valuable source of income, especially for small-scale farmers. It plays a crucial role in food and nutrition security: short length cycles varieties can be harvested during the shortage season, i.e. before major food crops maturity, and it presents all amino acids. Nevertheless, fonio remains largely under-studied compared to other African cereals such as sorghum, millet or rice. Here, we present recent progress in our understanding of fonio genetic diversity and evolutionary history driven by advances in genomic technologies. Further, we pinpoint and discuss existing challenges and potential opportunities for further in-depth investigation.
Barnaud is a researcher at the French National Research Institute for
Sustainable Development (IRD). She is a plant geneticist and an
ethnobotanist interested in the social, environmental and biological
factors shaping African crop diversity, evolution and adaptation.
Speaker: Hélène Bergès
Title: Innovative tools to characterize plants’ genome structure and link genotype and phenotype
In a context of climate change, population growth and limited energy resources, increasing plant genomes knowledge is essential for a better understanding of mechanisms driving plant adaptation and evolution. However, the exploration of plant genomes remains challenging. Indeed, among living organisms, plants display a high level of genome complexity due to their large size, variations in polyploidy levels and high percentage of repetitive elements. Moreover, due to high intra-species variability, a single reference genome is not enough to understand complex biological processes, such as resistance to biotic or abiotic stresses. A reliable sequence information linked to a trait of interest in specific genotypes is essential to understand the role of a genomic region in a phenotype. We will present an update of the various innovative tools we develop at the French Plant Genomic Center (CNRGV) in order to better characterize plants’ genome structure and link genotype and phenotype. Indeed, the CNRGV has developed various approaches combining large fragment genomic DNA library, NGS, optical map and CRISPR-CATCH targeting strategy to better characterize plant biodiversity and understand how plants adapt to their environment through the analysis of their genomes. We will more specifically highlight a new sequence capture approach aiming at targeting large DNA fragments in plants. This strategy is based on the programmable endonuclease function of the CRISPR/Cas9 system. We improved and adapted the first steps of the CATCH method (previously described by Jiang and Zhu, 2016; Jiang et al., 2015).We will present the efficiency of this strategy, based on the CRISPR/Cas9 system, to capture specific loci in Medicago truncatula and large Sunflower genomic region.
Bergès is Managing Director of the Plant Genomic Resources Center
(CNRGV) – a national infrastructure, which is part of the French
National Institute for Agricultural Research (INRA) network. Unique in
Europe, the CNRGV is a biological resource centre dedicated to plant
genomes and a research facility and service provider dedicated to the
scientific community. Employing 20 persons, the CNRGV is involved in
collaborations with more than 300 public and private laboratories
worldwide and attracts projects funded by the French government, the
French National Research Agency, and the European Union. Along other
activities, Hélène Bergès is member of the scientific committee of the
Parliamentary Office for the Evaluation of Scientific and Technological
Options (OPECST). She has received various awards, including the Legion
of Honor from the French government, the Vermal Medal from the French
Academy of Agriculture, and she’s Knight of the Order of Agricultural
Merit by the French government (Ministry of Agriculture.)
Speaker: Stéphane Cauet
Title: How optical maps can improve the understanding of plant genome’s structure
A better understanding of plant behavior will lay the foundation for new and innovative agricultural systems. Structural genomic exploration is fundamental to discover how evolution affects DNA organization and eventually plant diversity. Genomics has seen extraordinary growth but remains a challenge to understand the genome structure. With the long reads sequencing technology, such as Pacific Bioscience that produces reads of several kilobases, the genome quality assembly was largely improved with a considerable contig number reduction, a better continuity and a better resolution of repeated sequences localization. However, it remains challenging to obtain scaffold as large as chromosomes.
At the French Plant Genomic Resources Center (CNRGV), in complement to different new sequencing technologies, we use whole genome optical maps to either improve the genome assembly quality from several plant species or to highlight structural variations and sequence copy number variation in various genotypes. The Optical Mapping technology is based on the direct visualization of high molecular weight DNA (from 150kb to 2Mb) labeled on specific sequences patterns and is very useful to correct assembly organization errors (bad assembly of repeat structure for example). Using the new labelling chemistry and the Saphyr system from Bionano genomics, we generated optical maps to organize genome sequences from several species. This new approach allows us to work at the chromosome level and observe structural variation from kilobases to megabases. Here, we will present the assembly improvement of the reference sunflower genome. In addition, we will illustrate the comparison of the sunflower genotypes at the chromosome level and highlight structural variations in specific genomic region of interest.
master's degree in Computer Information System, Stéphane Cauet joined
the French Plant Genomic Resources Center (CNRGV) in 2004 as IT Manager.
The CNRGV is a national infrastructure unique in France and very rare
worldwide belonging to the French National Institute for Agricultural
Research (INRA). This Biological Resources Center (BRC) is dedicated to
all plant genomic resources of model and crop plants. The CNRGV provides
innovative and efficient genomic tools to better characterize plant
biodiversity and understand how plants adapt to their environment
through the analysis of their genomes. Stéphane Cauet is in charge of
bioinfomatic development of the lab and work on long reads sequencing,
optical map technologies and hybrid solutions to improve assemblies from
different data. In recent years he worked on species such as wheat,
maize, sunflower, passiflora, pea or barley.