AFLP analysis of four selected generations on disease-resistance trait of Fenneropenaeus chinensis

Amplified fragment length polymorphism (AFLP) was used to detect the genetic variation of four successively selected specific-pathogen-resistance (SPR) generations. Seven EcoRⅠand MseⅠprimer combinations produced 202 polymorphic markers out of the total of 350 bands amplified. The proportions of polymorphic loci of the first,second,third and fourth generations were (39.4286%),41.4286%,33.4286% and (39.1429%),respectively. The Nei genetic diversity was 0.1197,0.1259,0.1133 and (0.1249),respectively. Shannon genetic diversity index was 0.1831,0.1917,0.1702 and 0.1896,respectively. The genetic diversity index of the third generation was low, while the index of the other three generations remains at a relatively constant level. The analysis showed that the SPR population has great potential in genetic breeding program. The genetic distance of four generations based on the Nei analysis ranged from 0.0282 to 0.0458. Partitioning of the genetic variation revealed that 80.54% is distributed within populations, which is similar to the value (86.72%)derived from AMOVA. Mantel tests showed good correlation of different genetic distance matrices. By comparing the genetic parameters obtained from different statistical methods, we recommended AMOVA the first choice in population genetics analysis with AFLP markers. Co-dominant loci were found in AFLP fingerprinting. Two fragments adjacent in gel positions were recovered, cloned and sequenced. The sequence analysis showed high similarity between them, which indicated that they belong to the same locus. Our results proved that AFLP markers were not complete dominant markers. Our study suggests that AFLP is sensitive to detect genetic variability and effective to find markers and it is useful in marker assisted selection.