Genome sequences of horticultural plants: past, present, and future

Abstract

Horticultural plants play various and critical roles for humans by providing fruits, vegetables, materials for beverages, and herbal medicines and by acting as ornamentals. They have also shaped human art, culture, and environments and thereby have influenced the lifestyles of humans. With the advent of sequencing technologies, there has been a dramatic increase in the number of sequenced genomes of horticultural plant species in the past decade. The genomes of horticultural plants are highly diverse and complex, often with a high degree of heterozygosity and a high ploidy due to their long and complex history of evolution and domestication. Here we summarize the advances in the genome sequencing of horticultural plants, the reconstruction of pan-genomes, and the development of horticultural genome databases. We also discuss past, present, and future studies related to genome sequencing, data storage, data quality, data sharing, and data visualization to provide practical guidance for genomic studies of horticultural plants. Finally, we propose a horticultural plant genome project as well as the roadmap and technical details toward three goals of the project.

Keywords: Plant molecular biology; Structural variation.

Fig. 1. Statistics of genome-sequenced horticultural plant species.

a Distribution of genome-sequenced horticultural plants. b Botanical distribution of genome-sequenced horticultural plants. c Annual increase in the genome-sequenced horticultural plants by botanical taxonomy. d Annual increase in the genome-sequenced horticultural plants by horticultural category. e The reported 181 horticultural plant species fall into 30 angiosperm orders. f List of the released but not reported horticultural plant species

Fig. 2. The proposed roadmap to the horticultural plant genome project (HPGP).

The first goal of HPGP is to generate all reference genome sequences for horticultural plants, after which pan-genomes and core collections will be generated as a gene bank for horticultural plants. Two recently developed methods would be applied to decode the highly ploidy and highly heterozygous horticultural genomes. The second goal is to detect the various genomic variations within a pan-genome. In addition, the mechanistic signatures leading to the variations would be explored. The third goal is to link the phenotypes with the genomic regions. Two methods would be applied: the quantitative trait locus (QTL) method to correlate genomic variations with a quantitative trait and the genome-wide association study (GWAS) method to associate genomic variation with many genomic variations from different individuals ***p < 0.001