Genome-wide patterns of genetic diversity, population structure and demographic history in mānuka (Leptospermum scoparium) grown on indigenous Māori land

Abstract

Leptospermum scoparium J. R. Forst et G. Forst, known as mānuka by Māori, the indigenous people of Aotearoa (New Zealand), is a culturally and economically significant shrub species, native to New Zealand and Australia. Chemical, morphological and phylogenetic studies have indicated geographical variation of mānuka across its range in New Zealand, and genetic differentiation between New Zealand and Australia. We used pooled whole genome re-sequencing of 76 L. scoparium and outgroup populations from New Zealand and Australia to compile a dataset totalling ~2.5 million SNPs. We explored the genetic structure and relatedness of L. scoparium across New Zealand, and between populations in New Zealand and Australia, as well as the complex demographic history of this species. Our population genomic investigation suggests there are five geographically distinct mānuka gene pools within New Zealand, with evidence of gene flow occurring between these pools. Demographic modelling suggests three of these gene pools have undergone expansion events, whilst the evolutionary histories of the remaining two have been subjected to contractions. Furthermore, mānuka populations in New Zealand are genetically distinct from populations in Australia, with coalescent modelling suggesting these two clades diverged ~9 –12 million years ago. We discuss the evolutionary history of this species and the benefits of using pool-seq for such studies. Our research will support the management and conservation of mānuka by landowners, particularly Māori, and the development of a provenance story for the branding of mānuka based products.

A multiplexed plant-animal SNP array for selective breeding and species conservation applications

“…Quality filtering of the mānuka pooled sequencing datasets from Koot et al . [34] resulted in 2,006,036 SNPs. Eight classes of SNPs were identified based on their MAF values in each or a combination of gene pools (Northern North Island (NNI), the Central and Southern North Island (CNI), the East Coast North Island (ECNI), and two gene pools in the South Island representing the North-East (NESI) and South-West of the South Island (SWSI); S6 Table), and a total of 42,122 SNPs were identified that fitted into these classes.…”

“…Koot et al . [34] used pooled genome re-sequencing to study the genetic structure of mānuka collected across New Zealand. The SNP array data produced here for a subset of the populations described in Koot et al .…”

“…Mānuka samples were collected in natural stands in remote locations using silica beads in 2mL screw cap tubes as described in Koot et al . [34] and DNA was extracted using a modified CTAB protocol [39,40]. Fish DNA extractions were performed using fin clip samples collected in 96-well plates and using a proprietary automated protocol by Slipstream Automation Ltd (Palmerston North, New Zealand).…”

“…Informed consent was granted verbally by Māori landowners to re-use the reference genome of L. scoparium ‘Crimson Glory’ [33], as well as the pool-sequencing data and DNA samples of Koot et al . [34], for the purpose of developing and evaluating the SNP array in mānuka. The consent was given during a project meeting in June 2020 and minutes were documented.…”

“…Similarly, the shrub L. scoparium , which includes New Zealand mānuka, is an undomesticated species supporting the production of honeys with unique high antimicrobial properties which attract high premium prices. The recent publication of a reference genome for L. scoparium [33] and the re-sequencing of specimens from across its natural range [34] have opened new avenues for the development of genomic resources for this species to support its management and selective breeding. Emerging animal species of economic or ecological importance would also benefit from an increased application of genomic tools.…”