Search

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. [ABSTRACT FROM AUTHOR]

Background: Breeding for new macadamia cultivars with high nut yield is expensive in terms of time, labour and cost. Most trees set nuts after four to five years, and candidate varieties for breeding are evaluated for at least eight years for various traits. Genome-wide association studies (GWAS) are promising methods to reduce evaluation and selection cycles by identifying genetic markers linked with key traits, potentially enabling early selection through marker-assisted selection. This study used 295 progeny from 32 full-sib families and 29 parents (18 phenotyped) which were planted across four sites, with each tree genotyped for 4113 SNPs. ASReml-R was used to perform association analyses with linear mixed models including a genomic relationship matrix to account for population structure. Traits investigated were: nut weight (NW), kernel weight (KW), kernel recovery (KR), percentage of whole kernels (WK), tree trunk circumference (TC), percentage of racemes that survived from flowering through to nut set, and number of nuts per raceme. Results: Seven SNPs were significantly associated with NW (at a genome-wide false discovery rate of < 0.05), and four with WK. Multiple regression, as well as mapping of markers to genome assembly scaffolds suggested that some SNPs were detecting the same QTL. There were 44 significant SNPs identified for TC although multiple regression suggested detection of 16 separate QTLs. Conclusions: These findings have important implications for macadamia breeding, and highlight the difficulties of heterozygous populations with rapid LD decay. By coupling validated marker-trait associations detected through GWAS with MAS, genetic gain could be increased by reducing the selection time for economically important nut characteristics. Genomic selection may be a more appropriate method to predict complex traits like tree size and yield. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Macadamia (Macadamia integrifolia Maiden & Betche, Macadamia tetraphylla L.A.S. Johnson and their hybrids) is grown commercially around the world for its high-quality edible kernel. Traditional breeding efforts involve crossing varieties to produce thousands of progeny seedlings for evaluation. Cultivar improvement for nut yield using component traits and genomics are options for macadamia breeding, but accurate knowledge of genetic diversity and structure of the breeding population is required. This study reports allelic diversity within and between families of 295 seedling offspring from 29 parents, population structure and the extent of linkage disequilibrium (LD) in the population. Genotyping generated 19,527 silicoDArT and 5329 SNP markers, and, after filtering, 16,171 silicoDArTs and 4113 SNPs were used for diversity analyses. LD decay was initially rapid at short distances, but low-level LD persisted for long distances, with an average r2 = 0.124 for SNPs within 1 kb of each other. The seedling population was relatively genetically diverse and very similar to that of the 29 parents. The diversity (HE = 0.255 for progeny and 0.250 for parents) among these individuals indicates the level of diversity at the wider population level in the breeding programme, though the population appears less diverse than other fruit crops. Macadamia progeny was moderately differentiated (FST = 0.401) and formed k = 3 distinct clusters, which represents M. integrifolia germplasm separating from two different hybrid groups. There was low to no relationship between heterozygosity and performance for nut yield among progeny. These findings will inform future genomic studies of the Australian macadamia breeding programme, such as genome-wide association studies and genomic selection, where knowledge and control of population structure are vital. [ABSTRACT FROM AUTHOR]

Macadamia integrifolia is a representative of the large basal eudicot family Proteaceae and the main progenitor species of the Australian native nut crop macadamia. Since its commercialisation in Hawaii fewer than 100 years ago, global production has expanded rapidly. However, genomic resources are limited in comparison to other horticultural crops. The first draft assembly of M. integrifolia had good coverage of the functional gene space but its high fragmentation has restricted its use in comparative genomics and association studies. Here we have generated an improved assembly of cultivar HAES 741 (4,094 scaffolds, 745 Mb, N50 413 kb) using a combination of Illumina paired and PacBio long read sequences. Scaffolds were anchored to 14 pseudo-chromosomes using seven genetic linkage maps. This assembly has improved contiguity and coverage, with >120 Gb of additional sequence. Following annotation, 34,274 protein-coding genes were predicted, representing 90% of the expected gene content. Our results indicate that the macadamia genome is repetitive and heterozygous. The total repeat content was 55% and genome-wide heterozygosity, estimated by read mapping, was 0.98% or an average of one SNP per 102 bp. This is the first chromosome-scale genome assembly for macadamia and the Proteaceae. It is expected to be a valuable resource for breeding, gene discovery, conservation and evolutionary genomics. [ABSTRACT FROM AUTHOR]