Genetic diversity and structure assessment of Macrobrachium nipponense populations: implications for the protection and management of genetic resources

Abstract

This article presents a study of D-loop sequences to characterize the genetic diversity of wild Macrobrachium nipponense populations in Yixing natural waters including two reservoirs (Hengshan reservoir, HS; Youche reservoir, YC), 3 brooks (Linjin Dang, LJD; Magong Dushan Dang, MDD; Yangshan Dang, YSD) and 3 shallow lakes (Dongjiu lake, DJ; Xijiu lake, XJ; Tuanjiu lake, XJ), and compared the genetic differentiation and population structure with wild populations of Taihu Lake (TH), Yangtze River (YZ), and the main local artificially bred varieties “Taihu No. 2” (TH-2). A 747 bp D-loop sequence fragment was amplified in 321 individuals and the results exhibited a higher content of A+T (80.03%) than C+G (19.97%). A total of 110 haplotypes were identified. The h and π value proved the diversity of these populations was at the same level with high genetic diversity. TH-2 and YZ showed remarkable diversity, and XJ is even better. Fst estimates suggested that YZ and TH-2 were significant differentiation with other Yixing populations (P < 0.05). Three populations from shallow lake (DJ, XJ and TJ) displayed significant differentiated with the left Yixing ones (P < 0.05). The pairwise genetic distance, as well as haplotype network results, also suggested that all these 11 populations did not diverge at the species level (<15%). The P values of Tajima's D and Fu Fs were relatively greater than 0.1 (P > 0.1) and the nucleotide mismatch distribution analysis showed multiple peaks, giving a conclusion that the populations did not exhibited expansion. All these results suggested that TH-2 and YZ have remarkable diversity, and the germplasm resources and genetic diversity of M. nipponense in Yixing are very good and are suitable for original materials of breeding.