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The indigenous peoples of South America contributed substantially to the domestication of the pineapple, probably through the selection of spontaneous mutations expressing desirable traits. The types growing in and around villages usually exhibit desirable traits, e.g. improved palatability, improved fruit size, seedlessness, smooth leaves and, in some cases, improved leaf fibre properties which are not commonly found in wild types. To adapt the crop to intensive cultivation and current standards, pineapple breeders have attempted to remove the remaining undesirable ‘wild’ traits, i.e. natural flower initiation, small fruit size, excessive vegetativeness and long peduncles from parental stock (Leal and Coppens d’Eeckenbrugge, 1996; Coppens d’Eeckenbrugge et al., 2011). Pineapple breeding has become increasingly demanding as selection criteria have expanded to include not only preferences of growers and consumers, but also what packers and marketers want; therefore, a stepwise improvement programme must build on desirable attributes already existing in many of the current pineapple hybrids used as base parents (Chan, 2011).

Pineapple taxonomy was revised and simplified by Coppens d’Eeckenbrugge and Leal (2003) to two species (A. comosus, diploid, and Ananas macrodontes, tetraploid) and five botanical varieties (‘Abacaxi’, ‘Cayenne’, ‘Perolera’, ‘Queen’ and ‘Spanish’) with morphological and biochemical data supported by molecular studies (Duval et al., 2001, 2003). Coppens d’Eeckenbrugge and Leal (2003) hypothesized that A. comosus var. ananassoides is likely the progenitor of cultivated pineapple and its domestication occurred in the Guiana Shield, with a second hot spot in the upper Amazon (Coppens d’Eeckenbrugge et al., 2011). Zhou et al. (2015) suggest another possible site of domestication with var. bracteatus in the Parana-Paraguay river drainage area based on their study with 57 single nucleotide polymorphism (SNP) markers. Geographically disparate origins of crop domestication are not uncommon in the Americas.

Most domesticated pineapple cultivars are highly heterozygous; heterozygosity is naturally maintained in pineapple through strong self-incompatibility. Incompatibility in pineapple is gametophytic and is thought to be controlled by at least two loci. Incompatibility favours outcrossing and hence higher genetic variability.

Sanewski et al. (2011) considers the best pineapple breeding system is one that maintains genetic variability in the breeding population but allows the frequency of desirable genes and gene combinations to increase. In heterozygotic species such as pineapple, outcrossing with simple recurrent selection will shift the mean for characters under selection in the direction of selection but without changing the heterozygosity so long as the breeding population is not diluted with unimproved cultivars. The best parents in a recurrent selection programme will usually be late generation selections; however, it is important to be able to quickly assess selections so the best can be used as parents in the next generation. In the PRI programme, at least 7, and up to 13, years were required before selections could be used as parents. Strategies for decreasing the interval between generations are critical to making rapid progress. New approaches such as genome-wide marker selection might be worth evaluating (Volz et al., 2009).

There are few detailed genetic studies in pineapple, and heritability estimates for a few traits of common interest indicate they are often quantitative and controlled by multiple genes. Fruit weight, total soluble solids, peduncle length and root rot resistance fall into this category (Collins, 1960; Smith, 1966; Cabot, 1987; Chan, 1989). Some traits, i.e. presence of slips and suckers, are qualitative with low heritability and a strong environmental influence (Loison-Cabot, 1990).

Many pineapple-producing countries now conduct small- to medium-scale hybridization and selection programmes. Most breeding has utilized ‘Smooth Cayenne’, ‘Queen’, ‘Mordilona’, ‘Spanish’ and ‘Pernambuco’ or hybrids thereof to produce segregating populations of seedlings for screening and selection.