Lycium ruthenicum Murr. is an econo-ecological tree species that abounds in the Qinghai–Tibet Plateau, which is located in the Chaka Salt Lake region of Qinghai Province, China. This study compared the phenotypes and main inclusions in two-shaped berries (flat peach and sphere types) at different developmental stages of L. ruthenicum Murr. to provide first-hand information for targeted breeding toward higher quality and stronger stress resistance of the fruit. Results showed the distinct advantage of the quality characters of flat peach-type fruits over the sphere-type with regard to the length of bearing shoot, internode, peduncle, single fruit weight, and 100-pod weight. In terms of inclusions, the anthocyanin contents in two-shaped fruits showed no significant difference at S5. Anthocyanin accumulated in the developing fruits, and the amount peaked at S4 and then gradually decreased. The expression profiles of the key genes in anthocyanin biosynthesis were correlated with anthocyanin accumulation during fruit development, and the high expressions of flavonoid 3′,5′-hydroxylase gene and dihydroflavonol 4-reductase gene were found to be the critical factors of specific delphinidin accumulation. Sphere-type mature fruits had considerable higher total polyphenol level than flat peach fruits, but the opposite result was observed for polysaccharides. The contents of Ca, Co, Cr, Cu, K, Li, Mn, P, Ti, V, and Al presented no considerable differences, whereas B, Mg, Na, Si, and Zn exhibited evident advantages in sphere-type fruits. α-Toc was the most abundant component in both fruits and no evident difference in its content was observed. The data on nutritional contents provide a theoretical basis for different breeding goals of L. ruthenicum and its further utilization as health food.
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