Abstract
Macadamia (Macadamia integrifolia, M. tetraphylla and hybrids) is an Australian native nut crop and has a significant economic value in the food industries worldwide. Long juvenility along with traditional breeding strategies impede quick genetic improvement of this crop. The existing cultivars constitute only second to fourth generation of the wild germplasm in the rainforest. The utilisation of molecular markers for genomic selection and genome-wide association studies may accelerate genetic gains. Identification of a robust, reproducible, and cost-effective marker system is instrumental in increasing the efficiency of genomic studies. This study is the first to report the potential of two ultra-high-throughput diversity array technology (DArT) markers (silicoDArT and SNP) in macadamia. Both markers were used to identify the genetic diversity and population structure in 80 macadamia cultivars. Parentage analysis of 25 scions in a rootstock trial was conducted to confirm plant identity where recorded identities did not corroborate with phenotypic field observations. A total of 22,280 silicoDArT and 7,332 SNP markers were reported, of which 11,526 silicoDArT and 3,956 SNP markers were used for analyses after screening with quality control parameters including >95% call rate, >95% reproducibility, and >0.05 one ratio. The average polymorphic information content (PIC) values of silicoDArT and SNP markers were 0.29 and 0.21, respectively. Genetic variance among the cultivars ranged from 0.003 to 0.738 in silicoDArT and 0.004 to 0.412 in SNP markers. Four distinct population groups were identified from SNP data analysis. Most of the accessions used in this study were descended from two or more populations. Cluster analysis clearly separated genotypes of distinct origins, such as the Hawaii Agricultural Experiment Station and Hidden Valley Plantation accessions. Two wild accessions of Macadamia jansenii and M. ternifolia were found to be distantly related to the cultivars. Wild germplasm individuals and their hybrids with cv. ‘660’ formed separate clusters, suggesting that crossing between wild and cultivated genepools can extend genetic diversity. DArTseq-based SNP markers were successfully utilized to confirm the genetic identity of 25 scions in a rootstock trial. Our study suggests that DArT platforms are a robust system for the facilitation of genomic studies with regard to macadamia.
Highlights
Macadamia is a cross-pollinated tree and constitutes a nut crop industry with a high value kernel [1, 2]
The present study is the first to utilize the diversity array technology (DArT) platforms in macadamia; we present the development of DArT marker platforms, and compare and analyse the usefulness of silicoDArT and single nucleotide polymorphism (SNP) markers for genomic studies
Macadamia cultivars of multiple origins including from Hawaii Agricultural Experiment Station (HAES), Hidden Valley Plantation (HVP), Israeli and Australian selections, accessions from wild germplasm, and progeny from the Australian industry macadamia breeding program (Australian elite selections, dwarves, breeding progeny and hybrids of wild germplasm) were employed for genetic diversity and population structure analysis (Table 1)
Summary
Macadamia is a cross-pollinated tree and constitutes a nut crop industry with a high value kernel [1, 2]. Multipurpose uses, and long shelf life have increased the demand for macadamia nuts worldwide. The genetic improvement of Australian macadamia cultivars is still at an early stage. Worldwide macadamia improvement programs were mostly dependent on pedigree analysis and phenotypic characterization [6,7,8,9], subjected to the inaccuracy involved in the selection of elite accessions due to the effects of environment and genotype-environment interactions. To reduce inaccuracies in selection procedure and to accelerate breeding efficiency, genomic techniques may be used as a tool of macadamia breeding program [10]
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