Ultra-high-throughput DArTseq-based silicoDArT and SNP markers for genomic studies in macadamia

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.

Maximising recombination across macadamia populations to generate linkage maps for genome anchoring

“…In this study, heterozygosities of 0.18 ('741' , ' A268') and 0.16 (' A4') were observed in the parental genotypes. Although this was comparable to previous reports also based on codominant DArT data for macadamia breeding populations 19,30 , it is significantly lower than SNP-based estimates for other fruit crops including olive (0.44), apple (0.36) and peach (0.28) [75][76][77] . For macadamia, the relatively low level of heterozygosity detected in this study may reflect the bottleneck in recent domestication 78 .…”

“…DArTseq is is a rapid, cost-effective platform for genetic marker discovery and genotyping that targets non-repetitive regions and has been used extensively for genetic linkage mapping of plant crops 29 . Methods followed those previously optimized and described for macadamia using PstI + HhaI genome complexity reduction to generate co-dominant SNP and dominant presence-absence variant (PAV) sequence markers of 64 base pair (bp) in length 30 .…”

Bambara groundnut: an exemplar underutilised legume for resilience under climate change

“…The DArTseq platform, based on Illumina next generation sequencing, generates both dominant silicoDArT markers and co-dominant SNP markers (SNP variation within the sequence tags of the markers; Alam et al 2018;Barilli et al 2018;Kilian et al 2012). The average level of heterozygous alleles was found to range from 0.8 to 5.0% using 7894 markers after a round of single plant descent (SPD) purification from a subset of genebank accessions (n = 229), forming a good representation for a 'pure' genotype association genetics panel (S Mayes, unpublished data).…”

Genome-wide characterization of genetic diversity and population structure of Valeriana officinalis L.

“…To the best of our knowledge, in the research presented in this paper, the NGS technology was used for the first time for the analysis of intraspecies variation within the Valeriana genus. Until now, the used here, DArTseq technique has been mainly applied for the analysis of crop and animal species [30][31][32][33][34][35]. For 188 individuals of V. officinalis, representing 19 wild populations and one cultivated form, over 65 000 SNP markers and over 61 000 silicoDArT markers with a very high reproducibility coefficient were obtained using this technique.…”