Genetic mapping of Fusarium wilt resistance in a wild banana Musa acuminata ssp. malaccensis accession

Abstract

Banana is an important fruit and food crop, but is threatened by Fusarium wilt, one of the most devastating soil-borne fungal diseases. Only host resistance facilitates banana cultivation in infested soils around the world, but the genetic basis of Fusarium wilt of banana (FWB) is unknown. We selfed a heterozygous wild banana accession Musa acuminata ssp. malaccensis (Mam, AA, 2n = 22) to generate a mapping population and to investigate the inheritance of resistance to Race 1 and tropical race 4 (TR4) that cause FWB. Phenotyping (N = 217) revealed segregation for resistance, and genotyping by sequencing resulted in 2802 high-quality single-nucleotide polymorphic markers (SNPs) that were used for genetic mapping. Combined analyses of these data showed that a single dominant resistance locus controls resistance to Race 1 and maps near the distal part of chromosome 10. Recombinants, together with the position of the putative resistance gene, were further analysed using graphical genotyping, which retrieved markers flanking a 360 kb genetic region that associates with Race 1 resistance. The region contains 165 putative genes on the reference genome, including 19 leucine-rich repeat receptor-like kinase-like genes. At the same position and phase, we also identified a QTL for TR4 resistance, showing that the locus for resistance against Race 1 provided partial resistance to TR4. However, this effect was far less significant and hence not included in the mapping. These data support the breeding of new banana varieties with resistance to Fusarium wilt.

Fig. 1

Frequency distribution of disease severity scores for Fusarium wilt in leaves and rhizomes upon inoculations with Race 1 and TR4. Musa acuminata ssp. malaccensis is the heterozygous parent of the segregating population. Cavendish ‘Grand Naine’ is the control for resistance to Race 1 and for susceptibility to TR4. ‘Gros Michel’ is the susceptible control for Race 1

Fig. 2

Distribution of SNP markers across the 11 chromosomes according to their physical positions on the reference genome of Musa acuminata ssp. malaccensis (Mam) DH ‘Pahang’, version 2, released January 2016 (http://banana-genome-hub.southgreen.fr/organism/Musa/acuminata). All chromosomes are covered by segregating markers, which means all chromosomes are heterozygous in the Mam parent that was self-pollinated in this study, thus allowing genetic mapping of all chromosomes in the segregating population

Fig. 3

Interval mapping for Fusarium wilt resistance on chromosome 10 to Race 1 and TR4 on Musa acuminata ssp. malaccensis chromosomes according to leaf and rhizome severity scores. Horizontal lines represent LOD threshold (4.1) value for α = 0.05 after 1000 permutations. Markers above the threshold line indicate a significant association with disease score

Fig. 4

Graphical genotyping of Fusarium wilt resistance to Race 1 on chromosome 10, using rhizomes scores, and DArTseq SNP markers that were significantly associated with resistance. By sorting the selected progeny of selfed Musa acuminata ssp. malaccensis (Mam) according to the recombination events on chromosome 10 of Mam, the Race 1 resistance could be located in the range of 0–4.3 Mbp at the distal end of the chromosome. The physical positions of the markers on the reference genome (http://banana-genome-hub.southgreen.fr/organism/Musa/acuminata) are shown in the groups of co-segregating markers at the top of the figure