Danièle Roques

Genetic dissection of a modern sugarcane cultivar (Saccharum spp.). I. Genome mapping with AFLP markers

Abstractu2002Sugarcane cultivars are polyploid, aneuploid clones derived from interspecific hybridization between Saccharum officinarum and S. spontaneum. Their genome has recently started to be unravelled as a result of the development of molecular markers. We constructed an AFLP genetic map based on a selfing population of a specific cultivar, R570.Using 37 AFLP primer pairs, we detected 1,185 polymorphic markers of which 939 were simplex (segregated 3:1); these were used to construct the map. Of those 939, 887 were distributed on 120 cosegregation groups (CGs) based on linkages in coupling, while 52 remained unlinked. The cumulative length of all the groups was 5,849 cM, which is probably around one-third of the total genome length. Comparison with reference S. officinarum clones enabled us to assign 11 and 79 CGs to S. spontaneum and S. officinarum,respectively, whereas 11 CGs were probably derived from recombination between chromosomes of the two ancestral species. The patchy size of the groups, which ranges from 1 to 232 cM, illustrates the difficulty to access large portions of chromosomes, particularly those inherited from S. officinarum. Repulsion phase linkages suggested a high preferential pairing for 13 CG pairs. Out of the 120 CGs, 34 could be assigned to one of the 10 homo(eo)logy groups already defined in a previous RFLP map owing to the use of a small common marker set. The genome coverage was significantly increased in the map reported here. Implications for quantitative trait loci (QTL) research and marker-assisted breeding perspectives are discussed.

A putative major gene for rust resistance linked with a RFLP marker in sugarcane cultivar 'R570'

Inheritance of resistance to rust was investigated in the self progeny of the sugarcane cultivar ‘R570’ also used to build a RFLP genetic map. Resistance was evaluated through both field and controlled greenhouse trials. A clear-cut 3 (resistant) ∶ 1 (susceptible) segregation indicative of a probable dominant resistant gene was observed. This is the first documented report of a monogenic inheritance for disease resistance in sugarcane. This gene was found linked at 10 cM with an RFLP marker revealed by probe CDSR29. Other minor factors involved in the resistance were also detected.

Targeted mapping of a sugarcane rust resistance gene (Bru1) using bulked segregant analysis and AFLP markers.

The presence of a major resistance gene (Bru1) for brown rust in the sugarcane cultivar R570 (2n about 115) was confirmed by analyzing segregation of rust resistance in a large population of 658 individuals, derived from selfing of clone R570. A subset of this population was analyzed with AFLP and bulked segregant analysis (BSA) to develop a detailed genetic map around the resistance gene. Four hundred and forty three primer pairs were used resulting in the identification of eight AFLP markers surrounding the resistance gene in an interval of 10xa0cM, with the closest markers located at 1.9 and 2.2xa0cM on each side of the gene. Efficiency of the AFLP/BSA applied to the complex polyploid genome of sugarcane is discussed, as well as the potential of the newly identified AFLP markers for developing a map-based cloning approach exploiting, synteny conservation with sorghum.

Genetic mapping in sugarcane, a high polyploid, using bi-parental progeny: identification of a gene controlling stalk colour and a new rust resistance gene

Modern sugarcane cultivars (Saccharum spp) are highly polyploïd and aneuploid interspecific hybrids (2n=100–130). Two genetic maps were constructed using a population of 198 progeny from a cross between R570, a modern cultivar, and MQ76-53, an old Australian clone derived from a cross between Trojan (a modern cultivar) and SES528 (a wild Saccharum spontaneum clone). A total of 1,666 polymorphic markers were produced using 37 AFLP primer combinations, 46 SSRs and 9 RFLP probes. Linkage analysis led to the construction of 86 cosegregation groups for R570 and 105 cosegregation groups for MQ76-53 encompassing 424 and 536 single dose markers, respectively. The cumulative length of the R570 map was 3,144xa0cM, while that of the MQ76-53 map was 4,329xa0cM. Here, we integrated mapping information obtained on R570 in this study with that derived from a previous map based on a selfed R570 population. Two new genes controlling Mendelian traits were localized on the MQ76-53 map: a gene controlling the red stalk colour was linked at 6.5xa0cM to an AFLP marker and a new brown rust resistance gene was linked at 23xa0cM to an AFLP marker. Besides another previously identified brown rust resistance gene (Bru1), these two genes are the only other major genes to be identified in sugarcane so far.

Comparative genome mapping of sugar cane with other species within the Andropogoneae tribe

Comparative mapping within the tribe Andropogoneae has recently progressed with the development of mapped maize genomic probes that can be used for sorghum and sugar cane genomes. In the present study, data from previous reports were used to locate various linkage groups of sugar cane and sorghum on the genomic map of maize. Syntenic genome regions in the three plants were determined according to existing bridge-loci. The distribution of these synteny clusters closely matched the duplication pattern in maize. In several cases, the two arms of a single maize chromosome corresponded to at least two synteny clusters. There seem to be common chromosome rearrangements between maize and sugar cane and between maize and sorghum. In this respect, sugar cane and sorghum appear to be more closely related than either one with maize. A more detailed analysis of two synteny clusters was undertaken using recent sugar cane data to compare gene orders and recombination rates of the three plants. The three genomes showed colinearity in these regions. Distances between genes were similar in maize and sorghum, whereas sugar cane tended to display less recombination, at least in the varietal progeny investigated.

Experimental assessment of the accuracy of genomic selection in sugarcane

Sugarcane cultivars are interspecific hybrids with an aneuploid, highly heterozygous polyploid genome. The complexity of the sugarcane genome is the main obstacle to the use of marker-assisted selection in sugarcane breeding. Given the promising results of recent studies of plant genomic selection, we explored the feasibility of genomic selection in this complex polyploid crop. Genetic values were predicted in two independent panels, each composed of 167 accessions representing sugarcane genetic diversity worldwide. Accessions were genotyped with 1,499 DArT markers. One panel was phenotyped in Reunion Island and the other in Guadeloupe. Ten traits concerning sugar and bagasse contents, digestibility and composition of the bagasse, plant morphology, and disease resistance were used. We used four statistical predictive models: bayesian LASSO, ridge regression, reproducing kernel Hilbert space, and partial least square regression. The accuracy of the predictions was assessed through the correlation between observed and predicted genetic values by cross validation within each panel and between the two panels. We observed equivalent accuracy among the four predictive models for a given trait, and marked differences were observed among traits. Depending on the trait concerned, within-panel cross validation yielded median correlations ranging from 0.29 to 0.62 in the Reunion Island panel and from 0.11 to 0.5 in the Guadeloupe panel. Cross validation between panels yielded correlations ranging from 0.13 for smut resistance to 0.55 for brix. This level of correlations is promising for future implementations. Our results provide the first validation of genomic selection in sugarcane.

Prospecting sugarcane resistance to Sugarcane yellow leaf virus by genome-wide association.

Key messageUsing GWAS approaches, we detected independent resistant markers in sugarcane towards a vectored virus disease. Based on comparative genomics, several candidate genes potentially involved in virus/aphid/plant interactions were pinpointed.AbstractYellow leaf of sugarcane is an emerging viral disease whose causal agent is a Polerovirus, the Sugarcane yellow leaf virus (SCYLV) transmitted by aphids. To identify quantitative trait loci controlling resistance to yellow leaf which are of direct relevance for breeding, we undertook a genome-wide association study (GWAS) on a sugarcane cultivar panel (nxa0=xa0189) representative of current breeding germplasm. This panel was fingerprinted with 3,949 polymorphic markers (DArT and AFLP). The panel was phenotyped for SCYLV infection in leaves and stalks in two trials for two crop cycles, under natural disease pressure prevalent in Guadeloupe. Mixed linear models including co-factors representing population structure fixed effects and pairwise kinship random effects provided an efficient control of the risk of inflated type-I error at a genome-wide level. Six independent markers were significantly detected in association with SCYLV resistance phenotype. These markers explained individually between 9 and 14xa0% of the disease variation of the cultivar panel. Their frequency in the panel was relatively low (8–20xa0%). Among them, two markers were detected repeatedly across the GWAS exercises based on the different disease resistance parameters. These two markers could be blasted on Sorghum bicolor genome and candidate genes potentially involved in plant–aphid or plant–virus interactions were localized in the vicinity of sorghum homologs of sugarcane markers. Our results illustrate the potential of GWAS approaches to prospect among sugarcane germplasm for accessions likely bearing resistance alleles of significant effect useful in breeding programs.

Evolution of the Banana Genome (Musa acuminata) Is Impacted by Large Chromosomal Translocations

Abstract Most banana cultivars are triploid seedless parthenocarpic clones derived from hybridization between Musa acuminata subspecies and sometimes M. balbisiana. M. acuminata subspecies were suggested to differ by a few large chromosomal rearrangements based on chromosome pairing configurations in intersubspecies hybrids. We searched for large chromosomal rearrangements in a seedy M. acuminata ssp. malaccensis banana accession through mate-pair sequencing, BAC-FISH, targeted PCR and marker (DArTseq) segregation in its progeny. We identified a heterozygous reciprocal translocation involving two distal 3 and 10u2009Mb segments from chromosomes 01 and 04, respectively, and showed that it generated high segregation distortion, reduced recombination and linkage between chromosomes 01 and 04 in its progeny. The two chromosome structures were found to be mutually exclusive in gametes and the rearranged structure was preferentially transmitted to the progeny. The rearranged chromosome structure was frequently found in triploid cultivars but present only in wild malaccensis ssp. accessions, thus suggesting that this rearrangement occurred in M. acuminata ssp. malaccensis. We propose a mechanism for the spread of this rearrangement in Musa diversity and suggest that this rearrangement could have played a role in the emergence of triploid cultivars.