ABSTRACT
Genetic diversity and population structure of Australian-descent and open-pollinated macadamia accessions in Indonesia revealed by SSR markers

Nur Kholilatul Izzah1*, Meynarti Sari Dewi Ibrahim1*, Nur Kholis Firdaus1, Cici Tresniawati1, Susilawati Susilawati1, Rubiyo Rubiyo1, Enny Randriani1, Dani Dani1, Eko Heri Purwanto2, and Dini Hervani3
 
Macadamia (Macadamia integrifolia Maiden & Betche) is a highly prized global commodity that thrives in Indonesia’s agroclimatic condition. To support germplasm characterization and breeding strategies, the genetic diversity and population structure of 80 macadamia accessions were evaluated using simple sequence repeat (SSR) markers. Of the 20 SSR markers tested, 18 were polymorphic and selected for further analysis. A total of 117 alleles were detected, with an average of 6.5 alleles per locus, indicating moderate to high genetic variability. The mean observed heterozygosity (Ho = 0.67) slightly exceeded the expected heterozygosity (He = 0.63), suggesting a heterozygote excess likely associated with outcrossing and admixture. Polymorphic information content (PIC) values ranged from 0.10 to 0.87, with an average of 0.59, confirming that most markers were highly informative. Cluster analysis based on unweighted pair group method with arithmetic mean (UPGMA) grouped the accessions into three main clusters, largely reflecting their geographic origin and breeding background. Australian-descent accessions predominantly clustered together, while open-pollinated accessions exhibited broader genetic distribution, indicating greater variability. Population structure (K = 3) supported these groupings and revealed admixed genotypes, highlighting gene flow and shared ancestry among accessions. Genetic distance analysis identified several highly divergent genotype combinations, which are promising candidates for parental selection in breeding programs. Overall, the results demonstrate substantial genetic variation within populations and relatively weak differentiation among populations, consistent with the biology of outcrossing perennial species. The SSR markers used proved effective for genetic characterization, providing valuable insights for the conservation and improvement of macadamia germplasm.
Key words: Breeding strategy, genetic characterization, genetic distance analysis, germplasm, heterozygosity, Macadamia sp.
1National Research and Innovation Agency (BRIN), Research Center for Estate Crops, Cibinong-Bogor, Indonesia.
2National Research and Innovation Agency (BRIN), Research Center for Food Technology and Processing, Yogyakarta, Indonesia.
3Andalas University, Faculty of Agriculture, Padang, Indonesia.
*Corresponding author (meyn001@brin.go.id; nurk010@brin.go.id).
Received: 20 May 2026; Accepted: 30 August 2026, Available online: 29 October 2026.