RNA-Seq - Four Arabica genotypes -1300 m Nicaragua

Four Arabica pure line genotypes were studied. These were two Ethiopians (Geisha Especial and ET47) and two C. arabica introgressed C. canephora (T5175, a Catimor – Timor hybrids x Caturra – and Marsellesa, a Sarchimor – Timor hybrids x Villa Sarchi –). All four cultivars were cultivated at 1300 m on La Cumplida farm in Nicaragua. Three trees of each genotype were planted in barrels and randomly placed under a transparent shelter to control watering, fertilization, flowering initiation, and to reduce environmental variability. All the coffee trees were of the same age and were cultivated on homogenous soil using the same soil management, irrigation, fertilization, pruning, and disease control protocols. For each cultivar, replicate trees developed similarly. For transcriptomic analyses, beans were harvested between late 2019 and early 2020 when the fruits were yellow at around 210 days after flowering (DAF) (stage 6) and when the fruits were red at around 240 DAF (stage 7). For the transcriptomic analyses, coffee cherries harvested on a similar tree, cultivar and ripening stage constituted a sample (total of 24 samples = 3 trees x 4 genotypes x 2 ripening stages). The cherries were pulped upon harvest and the beans immediately dipped in liquid nitrogen.