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Genetic diversity and subgroups of apricot (Prunus armeniaca L.) from North China using a model-based method with simple sequence repeats

Liu, S., Liu, D. C., Zhang, Q. P., Liu, N., Zhang, A. M., Liu, W. S.
Acta horticulturae 2018 no.1214 pp. 285-298
Prunus armeniaca, alleles, apricots, computer software, ecology, gene flow, gene pool, genetic variation, germplasm, heterozygosity, linkage groups, loci, microsatellite repeats, multidimensional scaling, provenance, watersheds, China, Yellow River
Twenty-nine apricot accessions from North China were analyzed with 55 simple sequence repeat (SSR) markers from a T×E map. All the SSR markers were analyzed throughout the genome and compared among eight linkage groups. Linkage group 4 performed well in number of alleles per locus (Na) and effective number of alleles (Ne), in which marker BPPCT040 was prominent, with an Ne of 8.46 and Na of 10. For assessment of genetic diversity, the observed (Ho) and expected (He) heterozygosity were measured, resulting in average values of 0.419 and 0.644, respectively. Furthermore, the highest values occurred in linkage group 4 compared with all chromosomes. The mean values of Shannon's information index ranged from 0.9859 in linkage group 2 to 1.4773 in linkage group 8, with an average of 1.2025. All the apricot accessions were calculated under K=4 and grouped into four clusters according to the Q value inferred by STRUCTURE software, using a model-based method. More than 85% of apricot accessions had a maximum Q, which was more than 0.80 for the four inferred Q values. Four subgroups of 29 apricot accessions were irregular in their geographical origins, based on the results from STRUCTURE. Principal coordinates analysis (PCoA) indicated that the three inferred subgroup gene pools were closely related. The north Chinese apricot gene flow in the Yellow River Basin area is very complex and frequent. The reason is likely the introduction of cultivation and selection by humans of North China during their long history, and the complexity between the various eco-geographical groups for germplasm penetration.