Abstract
The Proteaceae genus Macadamia has a recent history of domestication as a commercial nut crop. We aimed to establish the first sequence-based haploid-correlated reference genetic linkage maps for this primarily outcrossing perennial tree crop, with marker density suitable for genome anchoring. Four first generation populations were used to maximise the segregation patterns available within full-sib, biparental and self-pollinated progeny. This allowed us to combine segregation data from overlapping subsets of >4,000 informative sequence-tagged markers to increase the effective coverage of the karyotype represented by the recombinant crossover events detected. All maps had 14 linkage groups, corresponding to the Macadamia haploid chromosome number, and enabled the anchoring and orientation of sequence scaffolds to construct a pseudo-chromosomal genome assembly for macadamia. Comparison of individual maps indicated a high level of congruence, with minor discrepancies satisfactorily resolved within the integrated maps. The combined set of maps significantly improved marker density and the proportion (70%) of the genome sequence assembly anchored. Overall, increasing our understanding of the genetic landscape and genome for this nut crop represents a substantial advance in macadamia genetics and genomics. The set of maps, large number of sequence-based markers and the reconstructed genome provide a toolkit to underpin future breeding that should help to extend the macadamia industry as well as provide resources for the long term conservation of natural populations in eastern Australia of this unique genus.
Highlights
The Proteaceae genus Macadamia has a recent history of domestication as a commercial nut crop
The introduction of generation DNA sequencing (NGS) and genotyping by sequencing (GBS) marker generation has led to the production of many revised linkage maps with increased marker density and resolution that has improved the downstream applications of linkage maps
Combining genetic maps to facilitate generation of a consensus physical map was successful and improved the proportion of the assembly anchored in comparison to individual maps
Summary
The Proteaceae genus Macadamia has a recent history of domestication as a commercial nut crop. We aimed to establish the first sequence-based haploid-correlated reference genetic linkage maps for this primarily outcrossing perennial tree crop, with marker density suitable for genome anchoring. Given that linkage maps represent the distribution of chiasmatic crossovers (COs) resulting from parental meiotic recombination, they provide valuable insights into the contribution that each set of parental alleles may make to subsequent progeny. They may be used for map-based cloning, to estimate the rate of introgression of specific alleles, and to determine the likelihood of linkage drag between loci[15]. The introduction of generation DNA sequencing (NGS) and genotyping by sequencing (GBS) marker generation has led to the production of many revised linkage maps with increased marker density and resolution that has improved the downstream applications of linkage maps
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