Deep gene exchange break among Konosirus punctatus populations across the Northwestern Pacific inferred from AFLP and ISSR markers
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Abstract: The correct understanding of fish population structure plays a positive role in their fishery management. The dotted gizzard shad, Konosirus punctatus, is widely distributed in the coastal waters of the Northwestern Pacific. With the over-exploitation of economically important fishes, its importance is increasingly prominent. To further examine the population genetic structure of K. punctatus across the Northwestern Pacific, the amplified fragment length polymorphism (AFLP) and the inter-simple sequence repeats (ISSRs) were employed to perform genetic variation analysis. The results showed that the combination of polyacrylamide gel electrophoresis and silver staining can effectively detect genetic variation for K. punctatus populations. The average proportions of polymorphic loci were 46.26% and 87.13% for AFLP and ISSR markers, respectively, and the genetic diversity parameters showed no obvious differences among populations. Both AMOVA and pairwise Fst suggested that there was significant genetic differentiation between Chinese and Japanese populations. All samples also clustered into two clades based on the UPGMA tree by two markers, which indicated significant genetic differentiation among populations. Consistent with the previous studies, there are two highly differentiated groups at the nuclear gene level and they were suggested to be treated as two separate genetic management units. The results of the present study could provide the genetic management strategy for this important economic species.
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Key words:
- Konosirus punctatus /
- population genetic differentiation /
- AFLP /
- ISSR
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Figure 2. UPGMA tree based on genetic distance among individuals of K. punctatus by AFLP (left) and ISSR (right) markers.
Table 1. Sample information and genetic diversity information of K. punctatus
Populations ID Date of
collectionn Number
of lociNumber of
polymorphic
lociProportion of
polymorphic
loci/%Nei’s genetic
diversityShannon’s
diversity indexAFLP Aomori AM 2006-05 17 192 62 32.29 0.091 8 0.140 1 Tokyo Bay TB 2007-06 27 196 67 34.18 0.080 1 0.126 8 Nagasaki NG 2007-06 27 191 66 34.55 0.077 1 0.123 1 Qingdao QD 2006-04 17 198 70 35.35 0.079 7 0.128 6 Yellow River
EstuaryYR 2007-04 14 195 62 31.79 0.069 5 0.112 8 Zhoushan ZS 2006-05 14 196 65 33.16 0.091 8 0.141 9 Chengshantou CS 2007-05 19 196 74 37.75 0.089 1 0.142 0 Kongdong Island KI 2007-05 16 195 62 31.79 0.061 7 0.102 4 Daya Bay DB 2006-04 15 182 50 27.47 0.062 6 0.099 7 Total 166 214 99 46.26 ISSR Aomori AM 2006-05 18 168 120 71.42 0.179 1 0.277 Nagasaki NG 2007-06 17 167 126 75.44 0.191 1 0.292 3 Qingdao QD 2006-04 18 168 128 76.19 0.182 3 0.284 Zhoushan ZS 2006-05 17 163 118 72.39 0.182 7 0.280 8 Daya Bay DB 2006-04 18 165 127 76.96 0.184 5 0.287 7 Total 202 176 87.13 
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Table 2. Polymorphism information of primers based on two markers
AFLP primers E-ACC/
M-CTAE-AGA/
M-CTGE-AGG/
M-CTTE-ACG/
M-CTCE-AGA/
M-CTATotal Number of loci 42 71 39 23 39 214 Polymorphic loci 19 31 17 12 20 99 Proportion of polymorphic loci/% 45.23 43.66 43.59 52.17 51.28 46.26 ISSR primers UBC834 ISSR4 UBC841 ISSR62 Total Number of loci 41 58 62 41 \ 202 Noumber of polymorphic loci 39 54 50 33 \ 176 Proportion of polymorphic loci/% 95.12 93.10 80.65 80.49 \ 87.13
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Table 3. Pairwise Fst values (below) and genetic distance (above) among K. punctatus populations by AFLP marker
AM TB NG QD ZS YR KI CS DB AM 0.006 8 0.006 2 0.062 6 0.060 9 0.058 9 0.060 7 0.063 4 0.067 8 TB 0.034 49* 0.001 4 0.067 8 0.069 4 0.068 8 0.068 9 0.070 9 0.074 7 NG 0.032 46* −0.006 05 0.067 1 0.068 9 0.066 3 0.064 9 0.067 2 0.071 1 QD 0.337 90** 0.352 47** 0.361 87** 0.002 9 0.003 6 0.002 8 0.002 6 0.005 5 ZS 0.338 42** 0.362 06** 0.373 36** −0.008 73 0.003 2 0.004 8 0.005 5 0.008 YR 0.333 09** 0.362 11** 0.366 64** −0.001 66 −0.007 83 0.004 1 0.003 0.008 3 KI 0.351 59** 0.371 7** 0.370 26** −0.004 98 0.012 15 0.006 18 0.004 4 0.007 CS 0.351 59** 0.375 12** 0.374 37** −0.005 03 0.019 2* −0.003 76 0.013 26 0.004 8 DB 0.351 59** 0.413 14** 0.415 39** 0.0257 2*0.052 09* 0.0567 4*0.047 01* 0.022 2 Note: * Significant values after Bonferroni correct at 5% (P<0.05); ** significant values after Bonferroni correct at 1% (P<0.01).
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Table 4. Pairwise Fst value (below) and genetic distance (above) between K. punctatus populations by ISSR marker
AM NG QD ZS DB AM 0.005 6 0.105 6 0.109 6 0.127 9 NG −0.006 8 0.109 0.116 0.129 6 QD 0.284 66* 0.273 59* 0.004 7 0.014 9 ZS 0.291 24* 0.284 81* −0.01 0.015 7 DB 0.323 67* 0.307 88* 0.032 21* 0.034 13* Note: * Significant values after Bonferroni correct at 5% (P<0.05); ** significant values after Bonferroni correct at 1% (P<0.01).
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Table 5. AMOVA of K. punctatus by AFLP and ISSR markers
Source of variation AFLP ISSR Df Sum of squares Variance components Percentage of variation/% Df Sum of squares Variance components Percentage of variation/% All populations Among groups 1 492.437 5.898 97 36.42 1 368.878 8.188 28 36.42 Among populations within groups 7 88.605 0.139 72 0.86 3 71.015 0.212 04 0.86 Within populations 157 1 594.434 10.155 63 62.71 83 1 654.971 19.939 40 62.71 Total 165 2 175.476 16.194 02 87 2 094.864 28.339 73 Japanese group Among populations 2 29.287 0.175 5 1.63 1 18.024 −0.138 11 −0.68 Within populations 68 718.911 10.572 22 98.37 33 674.490 20.439 10 100.68 Total 70 748.197 10.747 71 34 692.514 20.300 98 Chinese group Among populations 5 59.319 0.128 31 1.29 2 52.991 0.389 91 1.95 Within populations 89 875.523 9.837 34 98.71 50 980.480 19.609 61 Total 94 934.842 9.965 65 52 1 033.472 19.999 52
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