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

Using 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. Yellow 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 (n = 189) 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 14 % of the disease variation of the cultivar panel. Their frequency in the panel was relatively low (8-20 %). 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.

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.

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 3,144 cM, while that of the MQ76-53 map was 4,329 cM. 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 6.5 cM to an AFLP marker and a new brown rust resistance gene was linked at 23 cM 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.

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 10 cM, with the closest markers located at 1.9 and 2.2 cM 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.

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.

Développement de l'anthère et du grain de pollen chez une espèce sauvage apparentée à la canne à sucre (Saccharum spontaneum)

A study of the histocytological characteristics of anthers and pollen development of fertile male genotypes of Saccharum spontaneum L. support the division of microsporogenesis into nine distinct stages: premeiosis, meiosis and tetrad, young uninucleate microsporal stage, median uninucleate microsporal stage, median vacuolized uninucleate microsporal stage, late vacuolized uninucleate microsporal stage, first pollinic mitosis, second pollinic mitosis, mature pollen. Pollen grains are subspherical, monosporal, operculated with verrucose type ornamentations. A secretory type tapetum, present from the very first microsporal stages, is covered with orbicules persisting until anthesis. Keywords: Saccharum spontaneum, microsporogenesis, pollen, tapetum. [Journal translation]

RFLP mapping in cultivated sugarcane (Saccharum spp.): genome organization in a highly polyploid and aneuploid interspecific hybrid

Sugarcane cultivars are polyploid, aneuploid, interspecific hybrids between the domesticated species Saccharum officinarum and the wild relative S. spontaneum. Cultivar chromosome numbers range from 100 to 130 with approximately 10% contributed by S. spontaneum. We have undertaken a mapping study on the progeny of a selfed cultivar, R570, to analyze this complex genome structure. A set of 128 restriction fragment length polymorphism probes and one isozyme was used. Four hundred and eight markers were placed onto 96 cosegregation groups, based on linkages in coupling only. These groups could tentatively be assembled into 10 basic linkage groups on the basis of common probes. Origin of markers was investigated for 61 probes and the isozyme, leading to the identification of 80 S. officinarum and 66 S. spontaneum derived markers, respectively. Their distribution in cosegregation groups showed better map coverage for the S. spontaneum than for the S. officinarum genome fraction and occasional recombination between the two genomes. The study of repulsions between markers suggested the prevalence of random pairing between chromosomes, typical of autopolyploids. However, cases of preferential pairing between S. spontaneum chromosomes were also detected. A tentative Saccharum map was constructed by pooling linkage information for each linkage group.