The bracteatus pineapple genome and domestication of clonally propagated crops

Domestication of clonally propagated crops such as pineapple from South America was hypothesized to be a 'one-step operation'. We sequenced the genome of Ananas comosus var. bracteatus CB5 and assembled 513 Mb into 25 chromosomes with 29,412 genes. Comparison of the genomes of CB5, F153 and MD2 elucidated the genomic basis of fiber production, color formation, sugar accumulation and fruit maturation. We also resequenced 89 Ananas genomes. Cultivars 'Smooth Cayenne' and 'Queen' exhibited ancient and recent admixture, while 'Singapore Spanish' supported a one-step operation of domestication. We identified 25 selective sweeps, including a strong sweep containing a pair of tandemly duplicated bromelain inhibitors. Four candidate genes for self-incompatibility were linked in F153, but were not functional in self-compatible CB5. Our findings support the coexistence of sexual recombination and a one-step operation in the domestication of clonally propagated crops. This work guides the exploration of sexual and asexual domestication trajectories in other clonally propagated crops

DArTseq molecular markers associated with the piping leaf margin phenotype in pineapple (Ananas comosus L.)

This study sought to understand the genetic basis of the piping leaf margin phenotype in pineapple. To achieve this aim, a genome-wide association study (GWAS) using mixed linear regression and logistic regression analysis was conducted on three pineapple diversity panels including seedling populations segregating for spiny, spiny-tip and piping leaf margins. This study identified single nucleotide polymorphism (SNP) markers associated with the piping and spiny-tip leaf margin phenotypes. A broad quantitative trait locus (QTL) positioned on chromosome 23 between positions 240,475 and 2,369,197 bp was the most highly associated with piping leaf margin in all analyses. Major candidate genes proposed are a Zinc finger protein 2, a Zinc finger protein 3, a WUSCHEL-related homeobox 2, a WUSCHEL-related homeobox 1 and a Zinc finger protein CONSTANS-like. Some other genes of a lower association, linked or nearby genes of interest, are also considered potentially involved to varying degrees. All candidate genes are known to be involved in aspects of stem cell maintenance, cell proliferation, epidermal cell differentiation, organogenesis, leaf polarity, cell wall modification or hormone signalling. It is possible each plays a role in either differentiation or morphological aspects of the spiny-tip and piping leaf margin phenotypes. It is expected the relative role of each associated gene might vary with genetic background

The History of Pineapple Improvement

Man has been directing the genome of pineapple for a very long time. There is some evidence to suggest the domestication process started around 6000 years ago. The methods for breeding have of course changed considerably from the earliest times of pineapple domestication, but we still are seeking much the same goals. So much so that one of the cultivars to emerge from that early domestication, ‘Smooth Cayenne’, is still the predominant processing pineapple worldwide. The most modern pineapple genotypes today are only about eight generations removed from the early pre-Columbian village cultivars. These early pre-Columbian cultivars have in fact been the source of genetics for most pineapple breeding programs. There has been little effort to incorporate wild genetics into modern pineapple. There is in fact little need given the substantial level of heterozygosity that domestic pineapple exhibits. The high level of heterozygosity in pineapple has both been a great source of diversity for breeders and also a major bottleneck in progress. Almost all modern approaches to genome manipulation or breeding have been attempted in pineapple to overcome the problems associated with high heterozygosity including inbreeding, ploidy manipulation, mutation breeding and gene modification. Only gene editing and marker-assisted breeding have yet to make their impact in pineapple. This chapter looks at the history of pineapple breeding, the approaches used and lessons learnt in the hope we build on their successes to provide the world with more examples of the great diversity in pineapple

DArTseq Molecular Markers Associated with the Spiny-Tip Leaf Margin in Pineapple (Ananas comosus L.)

A genome-wide association study (GWAS) and quantitative trait loci (QTL) analysis using two bi-parental (parental cultivars Smooth Cayenne and MD-2) pineapple seedling populations segregating for spiny and spiny-tip leaf margin and 12 wild and pre-Columbian domesticated genotypes were used to identify single nucleotide polymorphism (SNP) and silicoDArT markers associated with the spiny-tip leaf margin phenotype in pineapple. One QTL between the nucleotide positions 14,355,639 and 14,368,806 on linkage group six (LG06) was identified using SNP markers and one QTL between the nucleotide positions 14,330,844 and 14,346,378 using silicoDArT markers. GWAS and QTL analysis methods identified the same most significantly associated SNP and silicoDArT markers. The most significantly associated SNP and silicoDArT markers were positioned at 14,355,639 and 14,341,745 bp respectively, on or very near, a zeaxanthin epoxidase (ZEP) gene, a key gene in the abscisic acid (ABA) pathway. Other associated genes with a high significance by GWAS analysis using at least two algorithms include a detoxification 33-like (DTX) and a resistance gene analog (RGA2-like). It is proposed that a polymorphism in the putative ZEP gene is the main causal variant associated with the spiny-tip leaf margin in ‘Smooth Cayenne’ pineapple and its descendants including ‘MD-2’