Genetic assessment of philippine milkfish (Chanos chanos) stocks based on novel microsatellites for markeraided broodstock management

Abstract

Reports on genetic diversity within/among milkfish populations using DNA markers are sparse. Earlier work dealt with evolutionary relationships among wild populations to define management units in the Indo-Pacific region where milkfish naturally abound. However, application of milkfish genetic markers in broodstock development and management remains to be investigated. Here, nine novel microsatellites developed by NGS were utilized to (a) describe the genetic structure of Philippine wild and hatchery-bred milkfish; (b) monitor the impact of domestication selection and inbreeding; and (c) formulate marker-aided broodstock management methods, a prerequisite to genetic improvement. Milkfish samples from three wild populations: Claveria (CLA), Currimao (CUR), Camiguin (CAM); eleven local hatchery stocks: SEAFDEC Integrated Hatchery (SIH), SEAFDEC Big Hatchery-Igang batches 1 and 2 (SBH-I1 and SBH-I2), SEAFDEC Big Hatchery-Dumangas (SBH-D), Hautea Hatchery (HH), Sual Pangasinan Hatchery (SPH), BFAR Dagupan Hatchery (BDH), BFAR Bohol Hatchery (BoH), BFAR Palawan Hatchery (PAL), Zambales Hatchery-P0 (ZH-P0), Zambales Hatchery-F1 (ZH-F1); and a hatchery stock from West Java in Indonesia (WJH), were examined. An Indonesian stock was included since in the Philippines, Indonesian milkfish fingerlings are imported and farmed for having purportedly better production traits. Genetic diversity indices such as expected heterozygosity (He) and allele frequency (A) ranged from 0.655 to 0.697 and 9.2 to 11.1, respectively. AMOVA showed significant but low genetic differentiation among the milkfish populations (FST = 0.013; P=0.000,) since much of the variation is attributed to intrapopulation differences (98.6%). The oldest hatchery stock SIH (30-35 years) had relatively moderate genetic variability (He = 0.66, A = 10.6), which is lower than that of 5-year old SBH-I1 (He= 0.687, A= 11.5) considering that both stocks originally came from the same source in the wild. A reduction in genetic diversity was seen when a local hatchery stock (ZH-P0;He = 0.66 and A= 10.8) was monitored after one generation (ZH-F1; He = 0.65, A=9.3). Finally, the Indonesian stock WJH had genetic variability levels (He= 0.66; A= 10.5) comparable with local stocks. Results of genetic analyses are herein discussed in the context of promoting effective milkfish broodstock management practices for the production of good quality seed stock.