Angélique D'Hont's research while affiliated with Université de Montpellier and other places

Black Leaf Streak Disease (BLSD), caused by the fungus Pseudocercospora fijiensis, is a recent pandemic and the most economically and environmentally important leaf disease of banana. To assist breeding of varieties with durable resistance to the rapidly evolving P. fijiensis, we used a diploid genitor ‘IDN 110’ with partial resistance to BLSD to search for QTLs. We assessed diploid progeny of 73 hybrids between ‘IDN 110’ and the diploid cultivar ‘Khai Nai On’, which is susceptible to BLSD. Hybrids were phenotyped with artificial inoculation under controlled conditions. This method allowed us to focus on resistance in the early stages of the interaction already identified as strongly influencing BLSD epidemiology. Progeny were genotyped by sequencing. As both parents are heterozygous for large reciprocal translocations, the distribution of recombination was assessed and revealed regions with low recombination rates. Fourteen non-overlapping QTLs of resistance to BLSD were identified of which four main QTLs from the ‘IDN110‘ parent, located on chromosomes 06, 07, 08, and 09, were shown to be of interest for marker-assisted selection. Genes that underline those four QTLs are discussed in the light of previous literature.

Societal impact statement Bananas are nutritious fruits of major importance in the tropics and subtropics. Characterizing their diversity is essential to ensure their conservation and use. A catalogue showcasing cultivated bananas genomic diversity was compiled and is to be used as a tool to support the classification of banana cultivars. This research revealed that cultivated banana groups are not all made of identical clones. Materials from recent collecting missions indicated that more banana diversity is expected to be found as the exploration of the banana gene pool continues. These discoveries will drive dynamic conservation strategies for banana genetic resources and will increase their use. Summary Banana is an important food crop cultivated in many tropical and subtropical regions around the world. Due to their low fertility, banana landraces are clonally propagated. However, different factors, such as synonymy and the effects of environment, make their assignment to described sets of clones, or cultivar groups, difficult. Consequently, passport data of accessions in genebanks is often uncomplete and sometimes inaccurate. With the recent advances in genomics, a new powerful tool was developed enabling the fine-scale characterization of banana’s ancestry along chromosomes, i.e. in silico chromosome painting. We applied this method to a high-throughput genotyping data set obtained from 317 banana accessions spanning most of the known cultivar groups. This set included both genebank and new uncharacterized materials. By comparing curated morphological assignation to the genomic patterns resulting from in silico chromosome painting, we were able to compile a catalogue referencing the chromosome painting patterns of most of the described cultivar groups. Examining the genomic patterns obtained, we discovered intra-cultivar group variability. In some cultivar groups, mitotic recombination or deletions were clonally accumulated in cultivars. In addition, we identified at least 4 cultivar groups in which cultivars likely resulting from distinct sexual events co-existed, notably Pisang Awak in which 5 distinct genomic patterns of two ploidy levels were identified. New patterns were also discovered in the newest materials of the set, showing that a wider diversity of clones still exist on farm .

Abstract Background: In French Polynesia, traditional tō (Saccharum officinarum) have been re-exploited in the recent years to produce organic certified rum. Former botanists have described the sugarcane which were spread by Polynesians during their migrations of the Eastern Pacific. One of them, referred by botanists as Otahiti was the main cultivar grown for sugar production until the 1880s. Methods: Between 2013 and 2017, we collected 15 sugarcane accessions in the Society Islands and examined their taxonomic status to establish the correspondence with those described by former botanists. Nine morphological traits were repeatedly measured including stalk colour, tillering, stalk height, stalk diameter, and internode lengths. We also analyzed them using flow cytometry, PCR markers and in one case molecular cytogenetics. Results: The results showed 4 modern hybrids cultivars, 9 traditional S. officinarum and one intergeneric hybrid between S. officinarum and the wild genus Miscanthus floridulus, Tō 'ā'eho. Among the traditional S. officinarum sugarcane cultivars, we suggested that Polynesian sugarcane called Tō ‘irimotu and Tō re’are’a could correspond to Otahiti. Conclusions: The studies of processing characteristics also revealed the high Brix of the Tō 'ā'eho and its potential for producing rum. These types of hybrids support the hypothesis of Pacific being a satellite center of sugarcane diversity. Key words: Saccharum officinarum, noble sugarcane, Saccharum maximum, French Polynesia, Otahiti

Sugarcane, the world’s most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide¹. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued². The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype (‘monoploid’) representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.

The sugarcane ( Saccharum spp.) genome is one of the most complex of all. Modern varieties are highly polyploid and aneuploid as a result of hybridization between Saccharum officinarum and S. spontaneum . Little research has been done on meiotic control in polyploid species, with the exception of the wheat Ph1 locus harboring the ZIP4 gene ( TaZIP4 ‐B2) which promotes pairing between homologous chromosomes while suppressing crossover between homeologs. In sugarcane, despite its interspecific origin, bivalent association is favored, and multivalents, if any, are resolved at the end of prophase I. Thus, our aim herein was to investigate the purported genetic control of meiosis in the parental species and in sugarcane itself. We investigated the ZIP4 gene and immunolocalized meiotic proteins, namely synaptonemal complex proteins Zyp1 and Asy1. The sugarcane ZIP4 gene is located on chromosome 2 and expressed more abundantly in flowers, a similar profile to that found for TaZIP4 ‐B2. ZIP4 expression is higher in S. spontaneum a neoautopolyploid, with lower expression in S. officinarum , a stable octoploid species. The sugarcane Zip4 protein contains a TPR domain, essential for scaffolding. Its 3D structure was also predicted, and it was found to be very similar to that of TaZIP4 ‐B2, reflecting their functional relatedness. Immunolocalization of the Asy1 and Zyp1 proteins revealed that S. officinarum completes synapsis. However, in S. spontaneum and SP80‐3280 (a modern variety), no nuclei with complete synapsis were observed. Importantly, our results have implications for sugarcane cytogenetics, genetic mapping, and genomics.

Key message Six QTLs of resistance to sugarcane orange rust were identified in modern interspecific hybrids by GWAS. For five of them, the resistance alleles originated from S. spontaneum. Altogether, they efficiently predict disease resistance. Abstract Sugarcane orange rust (SOR) is a threatening emerging disease in many sugarcane industries worldwide. Improving the genetic resistance of commercial cultivars remains the most promising solution to control this disease. In this study, an association panel of 568 modern interspecific sugarcane hybrids (Saccharum officinarum x S. spontaneum) from Réunion’s breeding program was evaluated for its resistance to SOR under natural conditions of infection. Two genome-wide association studies (GWAS) were conducted between disease reactions and 183,842 single nucleotide polymorphism (SNP) markers obtained by targeted genotyping-by-sequencing. Five resistance quantitative trait loci (QTLs), named Oru1, Oru2, Oru3, Oru4 and Oru5, were identified using a single-locus GWAS (SL-GWAS). These five QTLs all originated from the species S. spontaneum. A multi-locus GWAS (ML-GWAS) uncovered an additional but less significant resistance QTL named Oru6, which originated from S. officinarum. All six QTLs had a moderate to major phenotypic effect on disease resistance. Prediction accuracy estimated with linear regression models based on each of the five QTLs identified by SL-GWAS was between 0.16-0.41. Altogether, these five QTLs provided a relatively high prediction accuracy of 0.60. In comparison, accuracies obtained with six genome-wide prediction models (i.e., GBLUP, Bayes-A, Bayes-B, Bayes-C, Bayesian Lasso and RKHS) reached only 0.65. The good prediction accuracy of disease resistance provided by the QTLs and the predominant S. spontaneum origin of their resistance alleles pave the way for effective marker-assisted breeding strategies.

Banana breeding faces numerous challenges, such as sterility and low seed viability. Enhancing our understanding of banana genetics, notably through next-generation sequencing, can help mitigate these challenges. The genotyping datasets currently available from genebanks were used to decipher cultivated bananas’ genetic makeup of natural cultivars using genome ancestry mosaic painting. This article presents the application of this method to breeding materials by analyzing the chromosome segregation at the origin of ‘Gold Finger’ (FHIA-01), a successful improved tetraploid variety that was developed in the 1980s. First, the method enabled us to clarify the variety’s intricate genetic composition from ancestral wild species. Second, it enabled us to infer the parental gametes responsible for the formation of this hybrid. It thus revealed 16 recombinations in the haploid male gamete and 10 in the unreduced triploid female gamete. Finally, we could deduce the meiotic mechanism lying behind the transmission of unreduced gametes (i.e., FDR). While we show that the method is a powerful tool for the visualization and inference of gametic contribution in hybrids, we also discuss its advantages and limitations to advance our comprehension of banana genetics in a breeding context.

Fusarium wilt of banana is a devastating disease that has decimated banana production worldwide. Host resistance to Fusarium oxysporum f. sp. Cubense (Foc), the causal agent of this disease , is genetically dissected in this study using two Musa acuminata ssp. Malaccensis segregating populations, segregating for Foc Tropical (TR4) and Subtropical (STR4) race 4 resistance. Marker loci and trait association using 11 SNP-based PCR markers allowed the candidate region to be delimited to a 12.9 cM genetic interval corresponding to a 959 kb region on chromosome 3 of 'DH-Pahang' reference assembly v4. Within this region, there was a cluster of pattern recognition receptors , namely leucine-rich repeat ectodomain containing receptor-like protein kinases, cysteine-rich cell-wall-associated protein kinases, and leaf rust 10 disease-resistance locus receptor-like proteins, positioned in an interspersed arrangement. Their transcript levels were rapidly upregulated in the resistant progenies but not in the susceptible F2 progenies at the onset of infection. This suggests that one or several of these genes may control resistance at this locus. To confirm the segregation of single-gene resistance, we generated an inter-cross between the resistant parent 'Ma850' and a susceptible line 'Ma848', to show that the STR4 resistance co-segregated with marker '28820' at this Citation: Chen, A.; Sun, J.; Viljoen, A.; Mostert, D.; Xie, Y.; Mangila, L.; Bothma, S.; Lyons, R.; Hřibová, E.; Christelová, P.; et al.

Background and aims: Cultivated bananas resulted from inter-(sub-)specific hybridizations involving Musa species and subspecies (M. acuminata subspecies, M. schizocarpa, M. balbisiana) and the subsequent selection, centuries ago, of hybrids with parthenocarpic, seedless fruits. Cultivars have low fertility and are vegetatively propagated, forming groups of somaclones. Relatively few of them, mainly triploids, are grown on a large scale and characterization of their parental relationships may be useful for breeding strategies. Here, we investigate parental relationships and gamete-type contributions among diploid and polyploid banana cultivars. Methods: We used SNP genotyping data from whole genome sequencing of 178 banana individuals including 111 cultivars, 55 wild bananas and 12 synthetic F1 hybrids. We analysed the proportion of SNP sites in accordance with direct parentage with a global statistic and along chromosomes for selected individuals. Key results: We characterised parentage relationships for seven diploid, eleven triploid and one tetraploid cultivars. Results showed that both diploid and triploid cultivars could have contributed gametes to other banana cultivars. Diploids may have contributed 1x or 2x gametes and triploids, 1x to 3x gametes. The Mchare diploid cultivars group nowadays only found in East Africa, was found as parent of 2 diploid and 8 triploid cultivars. In five of its identified triploid offspring, corresponding to main export or locally popular dessert bananas, Mchare contributed a 2x gamete with full genome restitution without recombination. Analyses of remaining haplotypes in these Mchare offspring suggested ancestral pedigree relationships between different interspecific banana cultivars. Conclusions: Current cultivated banana resulted from different pathways of formation, with implication of recombined or un-recombined unreduced gametes produced by diploid or triploid cultivars. Identification of dessert banana's parents and the type of their contributed gametes should support the design of breeding strategies.

Fusarium wilt of banana is a devastating disease that has decimated banana production worldwide. Host resistance to Fusarium oxysporum f. sp. cubense (Foc), the causal agent of this disease, is genetically dissected in this study using two Musa acuminata ssp. malaccensis segregating populations segregating for Foc Tropical (TR4) and Subtropical (STR4) race 4 resistance. Marker loci and trait association using 11 SNP-based PCR markers allowed the candidate region to be delimited to a 12.9 cM genetic interval corresponding to a 959 kb region on Chromosome 3 of ‘DH-Pahang’ reference assembly v4. Within this region, there is a cluster of pattern recognition receptors, namely leucine rich repeat ectodomain containing receptor-like protein kinases, cysteine-rich cell wall associated protein kinases, and leaf rust 10 disease-resistance locus receptor-like proteins positioned in an interspersed arrangement. Their transcript levels were rapidly upregulated in the resistant but not in susceptible F2 progenies at the onset of infection. This suggests that one or several of these genes may control resistance at this locus. To confirm the segregation of single-gene resistance, we generated an inter-cross between the resistant parent ‘Ma850’ and a susceptible line ‘Ma848’, to show that the STR4 resistance co-segregated with marker ‘28820’ at this locus. Finally, an informative SNP marker 29730 allowed the locus specific resistance to be assessed in a collection of diploid and polyploid banana plants. Out of the 60 lines screened, 22 lines were predicted to carry resistance at this locus, including lines known to be TR4 resistant, such as ‘Pahang’, ‘SH-3362’, ‘SH-3217’, ‘Ma-ITC0250’, and ‘DH-Pahang/CIRAD 930’. Additional screening in the International Institute for Tropical Agriculture’s collection suggests that the dominant allele is common among in the elite ‘Matooke’ NARITA hybrids, as well as in other triploid or tetraploid hybrids derived from East African highland bananas. Fine-mapping and candidate gene identification will allow characterization of molecular mechanisms underlying TR4 resistance. The markers developed in this study can now aid the marker-assisted selection of TR4 resistance in breeding programs around the world.