No abstract

In 2010, a major scientific milestone was achieved for tree fruit crops: publication of the first draft whole genome sequence (WGS) for apple ( Malus domestica ). This WGS, v1.0, was valuable as the initial reference for sequence information, fine mapping, gene discovery, variant discovery, and tool development. A new, high quality apple WGS, GDDH13 v1.1, was released in 2017 and now serves as the reference genome for apple. Over the past decade, these apple WGSs have had an enormous impact on our understanding of apple biological functioning, trait physiology and inheritance, leading to practical applications for improving this highly valued crop. Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly. Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees. High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders. We understand the species, geographical, and genomic origins of domesticated apple more precisely, as well as its relationship to wild relatives. The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable, environmentally sound, productive, and consumer-desirable apple production. This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs. Recommendations for “what’s next” focus on necessary upgrades to the genome sequence data pool, as well as for use of the data, to reach new frontiers in genomics-based scientific understanding of apple.

Identifying the geographic origins of crops is important for the conservation and utilization of novel genetic variation. Even so, the origins of many food crops remain elusive. The tree nut crop macadamia has a remarkable domestication history, from subtropical rain forests in Australia through Hawaii to global cultivation all within the last century. The industry is based primarily on Macadamia integrifolia and M. integrifolia–M. tetraphylla hybrid cultivars with Hawaiian cultivars the main contributors to world production. Sequence data from the chloroplast genome assembled using a genome skimming strategy was used to determine population structure among remnant populations of the main progenitor species, M. integrifolia . Phylogenetic analysis of a 506 bp chloroplast SNP alignment from 64 wild and cultivated accessions identified phylogeographic structure and deep divergences between clades providing evidence for historical barriers to seed dispersal. High levels of variation were detected among wild accessions. Most Hawaiian cultivars, however, shared a single chlorotype that was also present at two wild sites at Mooloo and Mt Bauple from the northernmost distribution of the species in south-east Queensland. Our results provide evidence for a maternal genetic bottleneck during early macadamia domestication, and pinpoint the likely source of seed used to develop the Hawaiian cultivars. The extensive variability and structuring of M. integrifolia chloroplast genomic variation detected in this study suggests much unexploited genetic diversity is available for improvement of this recently domesticated crop.

Eucalyptus regnans is a mass flowering, tall forest tree of southeastern Australia with a mixed mating system. A field trial containing randomized single tree plots of self, outcross, and naturally open-pollinated (OP) progenies of 13 parents from two natural populations was surveyed over 15 yr. Inbreeding depression in survival at 15 years was 67% for selfs, one of the highest levels reported for a tree species, and differed little between populations. OP progenies were intermediate and the difference in fitness among the three cross types indicated that at planting, 59% were derived from outcrossing. However, with selection against the inbred progenies, this increased to 83% by 15 yr of age. Most selection against selfs occurred after four years, coincident with canopy closure and the apparent onset of intense competition.Almost twice the amount of phenotypic variability occurred among self-progenies than occurred among outcrosses with OPs again intermediate. Phenotypic variation was much greater within OP families than among families. Mortality removed the smaller trees, reducing inbreeding depression and variation both among and within OP families. In contrast, inbreeding depression and variation within OP families increased during stand development. These processes redistributed variation from among to within OP families, resulting in little overall change in phenotypic variance. Under intense competition in naturally regenerating forests, selfs are unlikely to survive to reproductive maturity. Although there was no additive variation among parents in the survival of their outcross progenies, the survival of both OP and self-progenies differed markedly among parents. However, variation in parental fitness under natural open-pollination was unrelated to estimates of fitness under outcrossing or selfing. Because parents each contributed the same number of offspring in this experiment, variation in OP fitness may instead reflect differences in outcrossing rate among families. Mixed mating may offer reproductive assurance and be advantageous in native forests if the availability of outcross pollen limits overall reproductive output.