Inheritance of AFLP markers and their use for genetic diversity analysis in wild and farmed scallop (Chlamys farreri)

Inheritance patterns of amplified fragment length polymorphism (AFLP) phenotypes were tested in three full-sib families of Zhikong scallop Chlamys farreri. Overall, 9.3% of analyses exhibited non-Mendelian segregation ratios before Bonferroni correction, with 0.8% significant after correction, demonstrating that AFLP markers can be considered Mendelian traits. AFLP markers were used to investigate levels of genetic diversity within cultured stocks of C. farreri and to compare them with the wild populations. Six pairs of primers generated 293 loci among 139 individuals in four cultured and two wild populations. High polymorphism at the AFLP markers was found within both cultured and wild C. farreri populations. The expected heterozygosity ranged from 0.291 (hatcheries) to 0.295 (wild), while the percentage of polymorphic loci ranged from 92.1% (hatcheries) to 93.9% (wild), respectively. This suggests that more than 30 years of artificial cultivation have not substantially reduced the genetic variability of the cultured stocks of C. farreri. Significant genetic differentiation was observed between the cultured stocks, and between the cultured and wild populations. The information derived from this study is useful for future genetic improvement by selective breeding, and for designing suitable management guidelines for these genetic materials.