Rice Science ›› 2021, Vol. 28 ›› Issue (1): 58-68.DOI: 10.1016/j.rsci.2020.11.007
• Research Papers • Previous Articles Next Articles
Xun Xu1,2, Song Ge1,2, Fumin Zhang1,2()
Received:
2020-04-07
Accepted:
2020-06-20
Online:
2021-01-28
Published:
2021-01-28
Xun Xu, Song Ge, Fumin Zhang. Genetic and Geographic Patterns of Duplicate DPL Genes Causing Genetic Incompatibility Within Rice: Implications for Multiple Domestication Events in Rice[J]. Rice Science, 2021, 28(1): 58-68.
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Species/Population/ Group | Number | Frequency (%) | S | π | h | Hd | Tajima’s D | |||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
DPL1- | DPL2- | DPL1- | DPL2- | DPL1 | DPL2 | DPL1 | DPL2 | DPL1 | DPL2 | DPL1 | DPL2 | DPL1 | DPL2 | |||||||
O. nivara | 91 | 0 | 37.0 | 0.0 | 41 | 12 | 0.00336 | 0.00090 | 23 | 9 | 0.819 | 0.267 | -1.73831 | -1.85460* | ||||||
O. rufipogon | 16 | 18 | 5.0 | 4.9 | 79 | 34 | 0.00421 | 0.00290 | 53 | 25 | 0.914 | 0.429 | -2.19350** | -2.11384** | ||||||
O. sativa | 15 | 49 | 10.2 | 30.4 | 11 | 6 | 0.00118 | 0.00363 | 7 | 4 | 0.223 | 0.571 | -1.21896 | 1.04607 | ||||||
nIND | 18 | 0 | 45.0 | 0.0 | 12 | 5 | 0.00210 | 0.00140 | 6 | 5 | 0.638 | 0.410 | -1.18432 | -1.17921 | ||||||
rIND | 2 | 0 | 11.8 | 0.0 | 17 | 8 | 0.00422 | 0.00292 | 9 | 7 | 0.955 | 0.584 | -1.31101 | -1.22445 | ||||||
nTHA | 5 | 0 | 62.5 | 0.0 | 6 | 3 | 0.00370 | 0.00105 | 3 | 3 | 0.762 | 0.295 | 1.59761 | -1.65231 | ||||||
rTHA | 2 | 0 | 13.3 | 0.0 | 12 | 3 | 0.00345 | 0.00110 | 5 | 3 | 0.813 | 0.362 | -1.08464 | -1.34917 | ||||||
nKHM | 29 | 0 | 93.5 | 0.0 | 11 | 1 | 0.00202 | 0.00014 | 5 | 2 | 0.743 | 0.125 | -1.19393 | -1.14244 | ||||||
rKHM | 6 | 0 | 22.2 | 0.0 | 6 | 0 | 0.00182 | 0.00000 | 5 | 4 | 0.667 | 0.200 | -0.48253 | NA | ||||||
nMMR | 0 | 0 | 0.0 | 0.0 | 0 | 3 | 0.00000 | 0.00050 | 1 | 2 | 0.000 | 0.063 | NA | -1.56135 | ||||||
rMMR | 0 | 0 | 0.0 | 0.0 | 22 | 10 | 0.00429 | 0.00361 | 9 | 1 | 0.714 | 0.000 | -1.52558 | -1.00632 | ||||||
nNEP | 0 | 0 | 0.0 | 0.0 | 4 | 1 | 0.00083 | 0.00028 | 3 | 3 | 0.530 | 0.170 | -0.76705 | -0.77374 | ||||||
rNEP | 2 | 0 | 7.1 | 0.0 | 5 | 3 | 0.00123 | 0.00071 | 3 | 7 | 0.574 | 0.696 | -0.51862 | -1.37016 | ||||||
nLAO1 | 20 | 0 | 100.0 | 0.0 | 13 | 1 | 0.00341 | 0.00015 | 4 | 2 | 0.591 | 0.067 | 1.061730 | -1.14700 | ||||||
rLAO1 | 0 | 0 | 0.0 | 0.0 | 12 | 13 | 0.00278 | 0.00240 | 8 | 5 | 0.837 | 0.261 | -1.04354 | -2.24274** | ||||||
nLAO2 | 19 | 0 | 90.5 | 0.0 | 8 | 0 | 0.00142 | 0.00000 | 4 | 1 | 0.348 | 0.000 | -1.54473 | NA | ||||||
rLAO2 | 1 | 0 | 3.4 | 0.0 | 13 | 2 | 0.00297 | 0.00102 | 7 | 2 | 0.817 | 0.228 | -0.78196 | -0.24788 | ||||||
nLKA04 | 0 | 0 | 0.0 | 0.0 | 1 | 0 | 0.00023 | 0.00000 | 2 | 1 | 0.200 | 0.000 | -1.11173 | NA | ||||||
nLKA05 | 0 | 0 | 0.0 | 0.0 | 3 | 0 | 0.00187 | 0.00000 | 2 | 1 | 0.533 | 0.000 | 1.83053* | NA | ||||||
nLKA07 | 0 | 0 | 0.0 | 0.0 | 2 | 0 | 0.00047 | 0.00000 | 3 | 1 | 0.378 | 0.000 | -1.40085 | NA | ||||||
nLKA08 | 0 | 0 | 0.0 | 0.0 | 1 | 0 | 0.00026 | 0.00000 | 2 | 1 | 0.222 | 0.000 | -1.88230 | NA | ||||||
nLKA09 | 0 | 0 | 0.0 | 0.0 | 0 | 0 | 0.00000 | 0.00000 | 1 | 1 | 0.000 | 0.000 | NA | NA | ||||||
nLKA10 | 0 | 0 | 0.0 | 0.0 | 0 | 3 | 0.00000 | 0.00198 | 1 | 3 | 0.000 | 0.600 | NA | -0.65748 | ||||||
nLKA11 | 0 | 0 | 0.0 | 0.0 | 3 | 0 | 0.00098 | 0.00000 | 3 | 1 | 0.417 | 0.000 | -0.93613 | NA | ||||||
nLKA12 | 0 | 0 | 0.0 | 0.0 | 4 | 2 | 0.00201 | 0.00091 | 2 | 1 | 0.429 | 0.000 | 0.48523 | -1.40085 | ||||||
rLKA01 | 0 | 0 | 0.0 | 0.0 | 3 | 1 | 0.00195 | 0.00076 | 4 | 2 | 1.000 | 0.333 | 0.16766 | -0.93302 | ||||||
rLKA06 | 0 | 0 | 0.0 | 0.0 | 1 | 0 | 0.00033 | 0.00000 | 1 | 1 | 0.000 | 0.000 | -1.00623 | NA | ||||||
rLKA13 | 0 | 0 | 0.0 | 0.0 | 0 | 1 | 0.00000 | 0.00046 | 1 | 1 | 0.000 | 0.000 | NA | -1.11173 | ||||||
rGDGZ | 0 | 10 | 0.0 | 47.6 | 8 | 4 | 0.00152 | 0.00354 | 7 | 3 | 0.569 | 0.648 | -1.48037 | 1.12924 | ||||||
rGXBH | 0 | 0 | 0.0 | 0.0 | 6 | 2 | 0.00285 | 0.00198 | 2 | 2 | 1.000 | 0.400 | -0.49605 | -0.05002 | ||||||
rGXHZ | 0 | 8 | 0.0 | 34.8 | 8 | 4 | 0.00213 | 0.00236 | 6 | 4 | 0.748 | 0.679 | -0.60490 | -0.12320 | ||||||
rGXTD | 0 | 0 | 0.0 | 0.0 | 18 | 2 | 0.00440 | 0.00230 | 11 | 2 | 0.912 | 0.500 | -1.13215 | 1.81115 | ||||||
rHNCL | 0 | 0 | 0.0 | 0.0 | 7 | 2 | 0.00235 | 0.00249 | 4 | 3 | 0.810 | 0.607 | -0.85010 | 1.82766 | ||||||
rHNJY | 0 | 0 | 0.0 | 0.0 | 11 | 3 | 0.00407 | 0.00294 | 3 | 3 | 0.600 | 0.679 | -0.38658 | 0.77501 | ||||||
rHNDZ | 0 | 0 | 0.0 | 0.0 | 8 | 4 | 0.00306 | 0.00370 | 2 | 3 | 0.476 | 0.733 | -0.51253 | 0.56555 | ||||||
rHNWC | 0 | 0 | 0.0 | 0.0 | 11 | 5 | 0.00332 | 0.00332 | 7 | 4 | 0.944 | 0.750 | -0.23157 | -0.56682 | ||||||
rJXDX | 0 | 0 | 0.0 | 0.0 | 8 | 2 | 0.00331 | 0.00213 | 6 | 2 | 0.952 | 0.533 | -0.25553 | 1.03299 | ||||||
rYNJH | 0 | 0 | 0.0 | 0.0 | 5 | 1 | 0.00251 | 0.00046 | 5 | 2 | 0.806 | 0.200 | 0.28702 | -1.11173 | ||||||
rIDN | 0 | 0 | 0.0 | 0.0 | 5 | 4 | 0.00304 | 0.00365 | 4 | 3 | 1.000 | 0.700 | 0.56199 | -1.09380 | ||||||
rPNG | 3 | 0 | 60.0 | 0.0 | 5 | 2 | 0.00281 | 0.00178 | 3 | 2 | 0.700 | 0.400 | 0.00000 | 0.19590 | ||||||
sARO | 0 | 1 | 0.0 | 25.0 | 0 | 4 | 0.00000 | 0.00456 | 1 | 2 | 0.000 | 0.500 | NA | -0.78012 | ||||||
sAUS | 12 | 1 | 70.6 | 4.8 | 7 | 3 | 0.00286 | 0.00068 | 4 | 2 | 0.596 | 0.100 | 0.61839 | -1.72331 | ||||||
sINDI | 2 | 5 | 3.0 | 7.5 | 5 | 5 | 0.00035 | 0.00135 | 2 | 3 | 0.060 | 0.252 | -1.64155 | -0.99668 | ||||||
sRAY | 0 | 2 | 0.0 | 66.7 | 1 | 3 | 0.00078 | 0.00456 | 2 | 2 | 0.667 | 0.667 | NA | NA | ||||||
sTEJ | 0 | 36 | 0.0 | 87.8 | 1 | 4 | 0.00007 | 0.00172 | 2 | 3 | 0.056 | 0.292 | -1.13321 | -0.46012 | ||||||
sTRJ | 1 | 4 | 4.8 | 16.0 | 7 | 5 | 0.00078 | 0.00417 | 3 | 4 | 0.186 | 0.684 | -2.13123* | 1.11236 |
Table 1 Nucleotide polymorphism and results of neutral test in O. rufipogon, O. nivara and O. sativa.
Species/Population/ Group | Number | Frequency (%) | S | π | h | Hd | Tajima’s D | |||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
DPL1- | DPL2- | DPL1- | DPL2- | DPL1 | DPL2 | DPL1 | DPL2 | DPL1 | DPL2 | DPL1 | DPL2 | DPL1 | DPL2 | |||||||
O. nivara | 91 | 0 | 37.0 | 0.0 | 41 | 12 | 0.00336 | 0.00090 | 23 | 9 | 0.819 | 0.267 | -1.73831 | -1.85460* | ||||||
O. rufipogon | 16 | 18 | 5.0 | 4.9 | 79 | 34 | 0.00421 | 0.00290 | 53 | 25 | 0.914 | 0.429 | -2.19350** | -2.11384** | ||||||
O. sativa | 15 | 49 | 10.2 | 30.4 | 11 | 6 | 0.00118 | 0.00363 | 7 | 4 | 0.223 | 0.571 | -1.21896 | 1.04607 | ||||||
nIND | 18 | 0 | 45.0 | 0.0 | 12 | 5 | 0.00210 | 0.00140 | 6 | 5 | 0.638 | 0.410 | -1.18432 | -1.17921 | ||||||
rIND | 2 | 0 | 11.8 | 0.0 | 17 | 8 | 0.00422 | 0.00292 | 9 | 7 | 0.955 | 0.584 | -1.31101 | -1.22445 | ||||||
nTHA | 5 | 0 | 62.5 | 0.0 | 6 | 3 | 0.00370 | 0.00105 | 3 | 3 | 0.762 | 0.295 | 1.59761 | -1.65231 | ||||||
rTHA | 2 | 0 | 13.3 | 0.0 | 12 | 3 | 0.00345 | 0.00110 | 5 | 3 | 0.813 | 0.362 | -1.08464 | -1.34917 | ||||||
nKHM | 29 | 0 | 93.5 | 0.0 | 11 | 1 | 0.00202 | 0.00014 | 5 | 2 | 0.743 | 0.125 | -1.19393 | -1.14244 | ||||||
rKHM | 6 | 0 | 22.2 | 0.0 | 6 | 0 | 0.00182 | 0.00000 | 5 | 4 | 0.667 | 0.200 | -0.48253 | NA | ||||||
nMMR | 0 | 0 | 0.0 | 0.0 | 0 | 3 | 0.00000 | 0.00050 | 1 | 2 | 0.000 | 0.063 | NA | -1.56135 | ||||||
rMMR | 0 | 0 | 0.0 | 0.0 | 22 | 10 | 0.00429 | 0.00361 | 9 | 1 | 0.714 | 0.000 | -1.52558 | -1.00632 | ||||||
nNEP | 0 | 0 | 0.0 | 0.0 | 4 | 1 | 0.00083 | 0.00028 | 3 | 3 | 0.530 | 0.170 | -0.76705 | -0.77374 | ||||||
rNEP | 2 | 0 | 7.1 | 0.0 | 5 | 3 | 0.00123 | 0.00071 | 3 | 7 | 0.574 | 0.696 | -0.51862 | -1.37016 | ||||||
nLAO1 | 20 | 0 | 100.0 | 0.0 | 13 | 1 | 0.00341 | 0.00015 | 4 | 2 | 0.591 | 0.067 | 1.061730 | -1.14700 | ||||||
rLAO1 | 0 | 0 | 0.0 | 0.0 | 12 | 13 | 0.00278 | 0.00240 | 8 | 5 | 0.837 | 0.261 | -1.04354 | -2.24274** | ||||||
nLAO2 | 19 | 0 | 90.5 | 0.0 | 8 | 0 | 0.00142 | 0.00000 | 4 | 1 | 0.348 | 0.000 | -1.54473 | NA | ||||||
rLAO2 | 1 | 0 | 3.4 | 0.0 | 13 | 2 | 0.00297 | 0.00102 | 7 | 2 | 0.817 | 0.228 | -0.78196 | -0.24788 | ||||||
nLKA04 | 0 | 0 | 0.0 | 0.0 | 1 | 0 | 0.00023 | 0.00000 | 2 | 1 | 0.200 | 0.000 | -1.11173 | NA | ||||||
nLKA05 | 0 | 0 | 0.0 | 0.0 | 3 | 0 | 0.00187 | 0.00000 | 2 | 1 | 0.533 | 0.000 | 1.83053* | NA | ||||||
nLKA07 | 0 | 0 | 0.0 | 0.0 | 2 | 0 | 0.00047 | 0.00000 | 3 | 1 | 0.378 | 0.000 | -1.40085 | NA | ||||||
nLKA08 | 0 | 0 | 0.0 | 0.0 | 1 | 0 | 0.00026 | 0.00000 | 2 | 1 | 0.222 | 0.000 | -1.88230 | NA | ||||||
nLKA09 | 0 | 0 | 0.0 | 0.0 | 0 | 0 | 0.00000 | 0.00000 | 1 | 1 | 0.000 | 0.000 | NA | NA | ||||||
nLKA10 | 0 | 0 | 0.0 | 0.0 | 0 | 3 | 0.00000 | 0.00198 | 1 | 3 | 0.000 | 0.600 | NA | -0.65748 | ||||||
nLKA11 | 0 | 0 | 0.0 | 0.0 | 3 | 0 | 0.00098 | 0.00000 | 3 | 1 | 0.417 | 0.000 | -0.93613 | NA | ||||||
nLKA12 | 0 | 0 | 0.0 | 0.0 | 4 | 2 | 0.00201 | 0.00091 | 2 | 1 | 0.429 | 0.000 | 0.48523 | -1.40085 | ||||||
rLKA01 | 0 | 0 | 0.0 | 0.0 | 3 | 1 | 0.00195 | 0.00076 | 4 | 2 | 1.000 | 0.333 | 0.16766 | -0.93302 | ||||||
rLKA06 | 0 | 0 | 0.0 | 0.0 | 1 | 0 | 0.00033 | 0.00000 | 1 | 1 | 0.000 | 0.000 | -1.00623 | NA | ||||||
rLKA13 | 0 | 0 | 0.0 | 0.0 | 0 | 1 | 0.00000 | 0.00046 | 1 | 1 | 0.000 | 0.000 | NA | -1.11173 | ||||||
rGDGZ | 0 | 10 | 0.0 | 47.6 | 8 | 4 | 0.00152 | 0.00354 | 7 | 3 | 0.569 | 0.648 | -1.48037 | 1.12924 | ||||||
rGXBH | 0 | 0 | 0.0 | 0.0 | 6 | 2 | 0.00285 | 0.00198 | 2 | 2 | 1.000 | 0.400 | -0.49605 | -0.05002 | ||||||
rGXHZ | 0 | 8 | 0.0 | 34.8 | 8 | 4 | 0.00213 | 0.00236 | 6 | 4 | 0.748 | 0.679 | -0.60490 | -0.12320 | ||||||
rGXTD | 0 | 0 | 0.0 | 0.0 | 18 | 2 | 0.00440 | 0.00230 | 11 | 2 | 0.912 | 0.500 | -1.13215 | 1.81115 | ||||||
rHNCL | 0 | 0 | 0.0 | 0.0 | 7 | 2 | 0.00235 | 0.00249 | 4 | 3 | 0.810 | 0.607 | -0.85010 | 1.82766 | ||||||
rHNJY | 0 | 0 | 0.0 | 0.0 | 11 | 3 | 0.00407 | 0.00294 | 3 | 3 | 0.600 | 0.679 | -0.38658 | 0.77501 | ||||||
rHNDZ | 0 | 0 | 0.0 | 0.0 | 8 | 4 | 0.00306 | 0.00370 | 2 | 3 | 0.476 | 0.733 | -0.51253 | 0.56555 | ||||||
rHNWC | 0 | 0 | 0.0 | 0.0 | 11 | 5 | 0.00332 | 0.00332 | 7 | 4 | 0.944 | 0.750 | -0.23157 | -0.56682 | ||||||
rJXDX | 0 | 0 | 0.0 | 0.0 | 8 | 2 | 0.00331 | 0.00213 | 6 | 2 | 0.952 | 0.533 | -0.25553 | 1.03299 | ||||||
rYNJH | 0 | 0 | 0.0 | 0.0 | 5 | 1 | 0.00251 | 0.00046 | 5 | 2 | 0.806 | 0.200 | 0.28702 | -1.11173 | ||||||
rIDN | 0 | 0 | 0.0 | 0.0 | 5 | 4 | 0.00304 | 0.00365 | 4 | 3 | 1.000 | 0.700 | 0.56199 | -1.09380 | ||||||
rPNG | 3 | 0 | 60.0 | 0.0 | 5 | 2 | 0.00281 | 0.00178 | 3 | 2 | 0.700 | 0.400 | 0.00000 | 0.19590 | ||||||
sARO | 0 | 1 | 0.0 | 25.0 | 0 | 4 | 0.00000 | 0.00456 | 1 | 2 | 0.000 | 0.500 | NA | -0.78012 | ||||||
sAUS | 12 | 1 | 70.6 | 4.8 | 7 | 3 | 0.00286 | 0.00068 | 4 | 2 | 0.596 | 0.100 | 0.61839 | -1.72331 | ||||||
sINDI | 2 | 5 | 3.0 | 7.5 | 5 | 5 | 0.00035 | 0.00135 | 2 | 3 | 0.060 | 0.252 | -1.64155 | -0.99668 | ||||||
sRAY | 0 | 2 | 0.0 | 66.7 | 1 | 3 | 0.00078 | 0.00456 | 2 | 2 | 0.667 | 0.667 | NA | NA | ||||||
sTEJ | 0 | 36 | 0.0 | 87.8 | 1 | 4 | 0.00007 | 0.00172 | 2 | 3 | 0.056 | 0.292 | -1.13321 | -0.46012 | ||||||
sTRJ | 1 | 4 | 4.8 | 16.0 | 7 | 5 | 0.00078 | 0.00417 | 3 | 4 | 0.186 | 0.684 | -2.13123* | 1.11236 |
Fig. 1. Median-joining haplotype networks of DPL1.Sections of each circle represent the proportion species (A) or locations (B) present in each haplotype. The size of each circle corresponds to the number of sequences of each haplotype. The lengths of the gray lines correspond to the number of mutations. Nonfunctional haplotypes are indicated by hollow squares.
Fig. 2. Median-joining haplotype networks of DPL2.Sections of each circle represent the proportion species (A) or locations (B) present in each haplotype. The size of each circle corresponds to the number of sequences of each haplotype. The lengths of the gray lines correspond to the number of mutations. Nonfunctional haplotypes are indicated by hollow squares.
Fig. 3. Ratios of nucleotide diversity (π) and haplotype diversity (Hd) between groups of O. sativa and ancestral populations.AUS and TEJ indicate aus and temperate japonica rice, respectively. nIND and rGDGX indicate the ancestral populations: O. nivara from India and the two O. rufipogon populations carrying DPL2- from South China. The ratio of DPL2- nucleotide diversity between temperate japonica and the ancestral populations is represented by a blank shape, since DPL2- of temperate japonica has no diversity.
Fig. 4. Distribution of wild rice samplings, as well as functional and nonfunctional alleles of DPLs.Populations of O. nivara and O. rufipogon are indicated with spots. Triangles indicate individual samples from the International Rice Research Institute (IRRI). Red and blue lines indicate O. nivara and O. rufipogon, respectively. Circles indicate the frequencies of functional and nonfunctional alleles.
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