Association study of tree size and male sterility in a F2 Coffea Arabica population

RATIONALE Male sterility and tree size are two major traits for breeders. Male sterility enables to decrease the mass multiplication costs of FI hybrids. Indeed, two types of Arabica varieties can be produced: fixed lines or FI hybrids. FI hybrids are more vigorous, resilient and less affected by diseases than fixed lines. However, it is more difficult to reproduce them making the cost of mass production higher. Producing FI hybrid seems to be a good alternative to face the ongoing climate change and the rust crisis and using male sterility could enable limiting the costs. Breeding for dwarf leads to production of coffee trees well adapted to mechanization. The objective of this study was to find markers associated to dwarf and male sterility in order to set up marker assisted breeding and to speed up varietal creation. METHODS A F2 population has been created by crossing the dwarf sarchimor IAPAR59 and a tall male sterile coffee tree. 277 coffee progeny as well as the FI and two parents were genotyped using GBS and the restriction enzyme Pstl for complexity reduction. DNA from the coffee samples was restricted with PstI and a 12 bp unique barcode identifier was ligated to the cut-site prior to pooling for Illumina template preparation. 150 bp single end reads were collected on an Illumina HiSeq 2500. Seventy-two barcoded samples were pooled per lane on the Illumina flow cell and 150 bp single-end reads were collected. An average of 2.8M reads per sample was obtained for the 277 progenies. The two parents were blasted against the C. canephora genome to identify sequence polymorphisms between them. 871 markers were identified. The association between dwarf trait, male sterility and SNPs markers was tested by a Chi-squared test. RESULTS A region containing 100 markers situated on the scaffold 612 on the chromosome 7 has been identified in association with male sterility. A PCoA performed on those markers showed a good discrimination between male sterile and male fertile genotypes. A selection based on those markers will enable to be more efficient through an early selection of male sterile plants in a segregating population. A SNP marker of dwarfism has been identified on chromosome 3. One version of this SNP is totally absent in tall genotypes. CONCLUSIONS & PERSPECTIVES An association has been found between a chromosom 7 region and male sterility. It could help breeder to enrich their working population with male sterile and then to reduce hybrid F 1 production cost. A more precise study of this region has to be performed. A marker of dwarfism which could be usefull to breed for mechanization adapted coffee trees has been discovered.