Sexual reproduction in plants is the main pathway for creating new genetic combinations in modern agriculture. In heterozygous plants, after the identification of a plant with desired traits, vegetative propagation (cloning) is the primary path to create genetically uniform plants. Another natural plant mechanism that creates genetically uniform plants (clones) is apomixis. In fruit crops like citrus and mango, sporophytic apomixis results in polyembryony, where seeds contain multiple embryos, one of which is sexually originated and the others are vegetative clones of the parent mother tree. Utilizing the mango genome and genetic analysis of a diverse germplasm collection, we identified MiRWP as the gene that causes polyembryony in mango. There is a strong correlation between a specific insertion in the gene’s promoter region and altered expression in flowers and developing fruitlets, inducing multiple embryos. The MiRWP gene is an ortholog of CitRWP that causes polyembryony in citrus. Based on the data, we speculate that promoter insertion events, which occurred independently in citrus and mango, induced nucellar embryogenesis. The results suggest convergent evolution of polyembryony in the two species. Further work is required to demonstrate the utility of these genes (mango and citrus) in other biological systems as a tool for the clonal production of other crops.

The Pacific countries of Fiji, Samoa, Solomon Islands, and Vanuatu account for less than 2% of the world’s cacao dry bean production. To capitalise on the rapidly expanding origin craft cocoa market, understanding the genetic attributes of Theobroma cacao in the Pacific is essential. A six‐year ACIAR‐funded project collected 1647 dried leaf samples from research stations and smallholder farms to identify the population ancestry of T. cacao in the partner countries. Using SNP marker profiling, the study identified germplasm high in Amelonado, which represents the majority of material throughout the Pacific. However, the study also identified samples high in the remaining nine genetic groups, including Criollo, Nanay, IMC (Iquitos), Guiana, Parinari (Marañón), Nacional, Ucayali (Contamana), LCT EEN (Curaray), and Purus, which were distributed throughout the Pacific. The results, if utilised in local selection trials, could reposition growers in the Pacific countries, allowing them to supply the growing origin craft cocoa market, with genetically unique beans. Cocoa genetics was one aspect of a project incorporating production and postharvest research to refocus the commodity based cocoa industry to a supplier of high‐quality beans of unique Pacific cocoa origin to the rapidly expanding craft ‘bean to bar’ cocoa industry.

Mango (Mangifera indica L.) cultivars display a wide range of ripe flesh colours, from deep-orange to pale-yellow, largely linked to differences in carotenoid profiles. This study examined the relationship between carotenoid profile and flesh colour across 25 mango cultivars. Flesh colour was measured using chroma (intensity) and hue angle (colour) and correlated with carotenoid content quantified using ultra-high performance liquid chromatography with diode-array detection (UHPLC-DAD). Chroma and hue angle displayed a second-order inverse polynomial relationship with chroma increasing as hue angle decreased. At lower hue angles, a wider range of chroma values was observed. Regression analysis showed that chroma correlated most strongly with total carotenoid concentration (TCC) (R² = 0.54), followed by total orange carotenoid concentration (R² = 0.47) and all-trans β-carotene concentration (R² = 0.45). Hue angle correlated most strongly with the total orange carotenoid concentration (R² = 0.76), then all-trans β-carotene concentration (R² = 0.73) and TCC (R² = 0.64). Interestingly, pale-yellow cultivars often exhibited low carotenoid concentrations, high titratable acidity and low soluble solids, suggesting incomplete ripening may also contribute to their pale colouration. These results provide insight into carotenoid-colour relationships and offer direction for phytochemical-based breeding programmes targeting mango flesh colour traits.

Chromosomal inversions can preserve combinations of favorable alleles by suppressing recombination. Simultaneously, they reduce the effectiveness of purifying selection enabling deleterious alleles to accumulate. This study explores how areas of low recombination, including centromeric regions and chromosomal inversions, contribute to the accumulation of deleterious and favorable loci in 225 Mangifera indica genomes from the Australian Mango Breeding Program. Here, we identify 17 chromosomal inversions that cover 7.7% (29.7Mb) of the M. indica genome: eight pericentric (inversion includes the centromere) and nine paracentric (inversion is on one arm of the chromosome). Our results show that these large pericentric inversions are accumulating deleterious loci, while the paracentric inversions show deleterious levels above and below the genome wide average. We find that despite their deleterious load, chromosomal inversions contain small effect loci linked to variation in crucial breeding traits, indicating that chromosomal inversions have likely facilitated their selection. The results from this study have important implications for selective breeding of favorable combinations of alleles in regions of low recombination. Significance Statement: Chromosomal inversions and other low recombination regions of the genome can drive trait evolution. Fewer recombination events can assist in maintaining favorable combinations of alleles, but it can also make disentangling favorable and deleterious alleles difficult. Understanding whether these low recombination regions contain favorable or deleterious loci could drive our decision to increase or decrease the frequency of these regions in target breeding populations. Breeding for large segments of the genome based on presence or absence of an inversion can rapidly drive large trait differences within few generations. Harnessing the impact of large low recombination regions of the genome could have major implications for future genetic improvement in breeding.

Cocoa (Theobroma cacao L.) is an important agricultural export of South Pacific countries, providing livelihoods for an estimated 310,000 people. The wet tropical coast of Far North Queensland has also started producing cocoa for a local boutique chocolate making industry. Although the volumes of cocoa produced are small by global standards, Pacific island and north Australian cocoa is well placed to compete in the high-value, low-volume markets—based on fine flavour, unusual genetic resources and novel ‘single origin’ branding. A member of the Malvaceae family, cocoa has its origins in Central and South America. First domesticated over 2000 years ago, cocoas’ global dispersal was mediated by humans and cultivation is now widespread across the humid tropics. The use of molecular markers to characterize the diversity of genetic resources available and identify superior genetic material is vital to the continued improvement and selection of clones. This work used single nucleotide polymorphism (SNP) markers to identify the parentage of Pacific island cocoa selections in relation to the 10 distinct cocoa families formerly identified from the original Central and South American populations. On farm collections from Pacific island countries has revealed distinct geographic cocoa populations. Specific populations show strong Criollo parentage, a source of fine flavour qualities, while others exhibit a high component of Amelonado parentage. Small populations showed a higher percentage of IMC, Parinari, National or Scavina parentage. Production and quality data linked to these populations assists to identify superior parentage to enable local programs to rapidly bring these into commercial production thereby improving cocoa productivity and quality in the Pacific.