Low-density liquid-phase chip for

1 . A liquid-phase chip for Gossypium hirsutum L. constructed by using a targeted capture sequencing technology, wherein the liquid-phase chip is a whole genome SNP chip of Gossypium hirsutum L. consisting of probes for detecting 894 SNP loci and 14 major transgenes; wherein the 14 major transgenes comprise: A1Bt, referring to Bacillus thuringiensis gene comprising of SEQ ID NO. 15; A2CPTI, referring to Cowpea Trypsin Inhibitor comprising of SEQ ID NO. 16; A3CP4-epsps, referring to 5-enolpyruvylshikimate-3-phosphate synthase gene derived from Agrobacterium sp. Cp-4 and comprising of SEQ ID NO. 17; A4CP4-epsps, referring to 5-enolpyruvylshikimate-3-phosphate synthase gene derived from Agrobacterium sp. Cp-4 2 and comprising of SEQ ID NO. 18; A5bar, referring to bialaphos resistance gene comprising of SEQ ID NO. 19; A6pat, referring to phosphinthricin acetyltransferase gene comprising of SEQ ID NO. 20; A7CdP450, referring to Cytochrome P450 comprising of SEQ ID NO. 21; A8cp4-epsps, referring to 5-enolpyruvylshikimate-3-phosphate synthase gene derived from Agrobacterium sp. Cp-4 and comprising of SEQ ID NO. 22; B.1CaMV35S, referring to 35S promoter from cauliflower mosaic virus comprising of SEQ ID NO. 23; B.2FMV35S, referring to 35S promoter from figwort mosaic virus comprising of SEQ ID NO. 24; B.3NOS, referring to promoter of nopaline synthase gene comprising of SEQ ID NO. 25; B.4NOS, referring to terminator of nopaline synthase gene comprising of SEQ ID NO. 26; B.5CaMV35S, referring to 35S terminator from the cauliflower mosaic virus comprising of SEQ ID NO. 27; and NPTII, referring to neomycin-3′-phosphotransferase gene comprising of SEQ ID NO. 28; and the 894 SNP loci comprises: SNP No. 001 at Genome position 110747518 of Chromosome A01 with Ref C and Alt T, which is a functional locus; SNP No. 002 at Genome position 11727109 of Chromosome A03 with Ref T and Alt C, which is a functional locus; SNP No. 003 at Genome position 20665441 of Chromosome A03 with Ref A and Alt G, which is a functional locus; SNP No. 004 at Genome position 2166240 of Chromosome A03 with Ref A and Alt G, which is a functional locus; SNP No. 005 at Genome position 22543857 of Chromosome A03 with Ref C and Alt T, which is a functional locus; SNP No. 006 at Genome position 8450966 of Chromosome A03 with Ref A and Alt T, which is a functional locus; SNP No. 007 at Genome position 766233 of Chromosome A05 with Ref C and Alt A, which is a functional locus; SNP No. 008 at Genome position 111125064 of Chromosome A10 with Ref A and Alt G, which is a functional locus; SNP No. 009 at Genome position 111437317 of Chromosome A10 with Ref G and Alt A, which is a functional locus; SNP No. 010 at Genome position 112338179 of Chromosome A10 with Ref A and Alt T, which is a functional locus; SNP No. 011 at Genome position 112651380 of Chromosome A10 with Ref T and Alt G, which is a functional locus; SNP No. 012 at Genome position 112940238 of Chromosome A10 with Ref G and Alt A, which is a functional locus; SNP No. 013 at Genome position 113053553 of Chromosome A10 with Ref G and Alt A, which is a functional locus; SNP No. 014 at Genome position 30523772 of Chromosome A11 with Ref A and Alt G, which is a functional locus; SNP No. 015 at Genome position 87529643 of Chromosome A12 with Ref A and Alt G, which is a functional locus; SNP No. 016 at Genome position 103027858 of Chromosome A13 with Ref C and Alt A, which is a functional locus; SNP No. 017 at Genome position 4110390 of Chromosome D02 with Ref T and Alt G, which is a functional locus; SNP No. 018 at Genome position 15331946 of Chromosome D03 with Ref G and Alt A, which is a functional locus; SNP No. 019 at Genome position 31088497 of Chromosome D03 with Ref C and Alt T, which is a functional locus; SNP No. 020 at Genome position 34610610 of Chromosome D03 with Ref A and Alt G, which is a functional locus; SNP No. 021 at Genome position 39193206 of Chromosome D03 with Ref C and Alt T, which is a functional locus; SNP No. 022 at Genome position 39600506 of Chromosome D03 with Ref A and Alt T, which is a functional locus; SNP No. 023 at Genome position 40070059 of Chromosome D03 with Ref G and Alt A, which is a functional locus; SNP No. 024 at Genome position 43229382 of Chromosome D03 with Ref A and Alt G, which is a functional locus; SNP No. 025 at Genome position 43511381 of Chromosome D03 with Ref A and Alt G, which is a functional locus; SNP No. 026 at Genome position 43821808 of Chromosome D03 with Ref A and Alt G, which is a functional locus; SNP No. 027 at Genome position 44126802 of Chromosome D03 with Ref T and Alt C, which is a functional locus; SNP No. 028 at Genome position 45101555 of Chromosome D03 with Ref G and Alt A, which is a functional locus; SNP No. 029 at Genome position 45114135 of Chromosome D03 with Ref A and Alt G, which is a functional locus; SNP No. 030 at Genome position 45162922 of Chromosome D03 with Ref A and Alt T, which is a functional locus; SNP No. 031 at Genome position 45219545 of Chromosome D03 with Ref C and Alt T, which is a functional locus; SNP No. 032 at Genome position 45904637 of Chromosome D03 with Ref A and Alt C, which is a functional locus; SNP No. 033 at Genome position 46030279 of Chromosome D03 with Ref A and Alt C, which is a functional locus; SNP No. 034 at Genome position 53296491 of Chromosome D04 with Ref T and Alt A, which is a functional locus; SNP No. 035 at Genome position 53338317 of Chromosome D04 with Ref A and Alt G, which is a functional locus; SNP No. 036 at Genome position 55873730 of Chromosome D04 with Ref G and Alt T, which is a functional locus; SNP No. 037 at Genome position 55895101 of Chromosome D04 with Ref A and Alt T, which is a functional locus; SNP No. 038 at Genome position 11366732 of Chromosome D06 with Ref G and Alt T, which is a functional locus; SNP No. 039 at Genome position 7626032 of Chromosome D09 with Ref T and Alt C, which is a functional locus; SNP No. 040 at Genome position 5613642 of Chromosome D10 with Ref C and Alt T, which is a functional locus; SNP No. 041 at Genome position 65188256 of Chromosome D10 with Ref T and Alt C, which is a functional locus; SNP No. 042 at Genome position 171062 of Chromosome D11 with Ref T and Alt C, which is a functional locus; SNP No. 043 at Genome position 23848335 of Chromosome D11 with Ref T and Alt C, which is a functional locus; SNP No. 044 at Genome position 23889334 of Chromosome D11 with Ref T and Alt C, which is a functional locus; SNP No. 045 at Genome position 23957256 of Chromosome D11 with Ref A and Alt T, which is a functional locus; SNP No. 046 at Genome position 24042912 of Chromosome D11 with Ref C and Alt T, which is a functional locus; SNP No. 047 at Genome position 9255660 of Chromosome D11 with Ref C and Alt T, which is a functional locus; SNP No. 048 at Genome position 4503413 of Chromosome D13 with Ref G and Alt A, which is a functional locus; SNP No. 049 at Genome position 103887986 of Chromosome A02 with Ref G and Alt A, which is a functional locus; SNP No. 050 at Genome position 103969684 of Chromosome A02 with Ref T and Alt C, which is a functional locus; SNP No. 051 at Genome position 103980780 of Chromosome A02 with Ref A and Alt G, which is a functional locus; SNP No. 052 at Genome position 7639601 of Chromosome A03 with Ref A and Alt G, which is a functional locus; SNP No. 053 at Genome position 4584038 of Chromosome A04 with Ref G and Alt A, which is a functional locus; SNP No. 054 at Genome position 4584101 of Chromosome A04 with Ref C and Alt T, which is a functional locus; SNP No. 055 at Genome position 69623179 of Chromosome A05 with Ref C and Alt T, which is a functional locus; SNP No. 056 at Genome position 28180129 of Chromosome A06 with Ref G and Alt G, which is a functional locus; SNP No. 057 at Genome position 28338559 of Chromosome A06 with Ref T and Alt G, which is a functional locus; SNP No. 058 at Genome position 28760155 of Chromosome A06 with Ref A and Alt G, which is a functional locus; SNP No. 059 at Genome position 37577336 of Chromosome A06 with Ref T and Alt C, which is a functional locus; SNP No. 060 at Genome position 10774519 of Chromosome A07 with Ref G and Alt A, which is a functional locus; SNP No. 061 at Genome position 89225727 of Chromosome A07 with Ref T and Alt C, which is a functional locus; SNP No. 062 at Genome position 90178382 of Chromosome A07 with Ref T and Alt C, which is a functional locus; SNP No. 063 at Genome position 90300535 of Chromosome A07 with Ref G and Alt T, which is a functional locus; SNP No. 064 at Genome position 90432981 of Chromosome A07 with Ref T and Alt C, which is a functional locus; SNP No. 065 at Genome position 90438470 of Chromosome A07 with Ref G and Alt A, which is a functional locus; SNP No. 066 at Genome position 90497386 of Chromosome A07 with Ref C and Alt T, which is a functional locus; SNP No. 067 at Genome position 4830640 of Chromosome A09 with Ref G and Alt A, which is a functional locus; SNP No. 068 at Genome position 77528103 of Chromosome A09 with Ref G and Alt T, which is a functional locus; SNP No. 069 at Genome position 109602998 of Chromosome A10 with Ref G and Alt A, which is a functional locus; SNP No. 070 at Genome position 112187864 of Chromosome A10 with Ref C and Alt A, which is a functional locus; SNP No. 071 at Genome position 112213784 of Chromosome A10 with Ref T and Alt C, which is a functional locus; SNP No. 072 at Genome position 75431311 of Chromosome A10 with Ref A and Alt G, which is a functional locus; SNP No. 073 at Genome position 75517245 of Chromosome A10 with Ref C and Alt G, which is a functional locus; SNP No. 074 at Genome position 7883291 of Chromosome A10 with Ref T and Alt C, which is a functional locus; SNP No. 075 at Genome position 114890178 of Chromosome A11 with Ref C and Alt T, which is a functional locus; SNP No. 076 at Genome position 15811782 of Chromosome A11 with Ref G and Alt A, which is a functional locus; SNP No. 077 at Genome position 23909944 of Chromosome A11 with Ref C and Alt, which is a functional locus; SNP No. 078 at Genome position 360614 of Chromosome A11 with Ref A and Alt C, which is a functional locus; SNP No. 079 at Genome position 90244406 of Chromosome A11 with Ref C and Alt A, which is a functional locus; SNP No. 080 at Genome position 57229716 of Chromosome A12 with Ref A and Alt G, which is a functional locus; SNP No. 081 at Genome position 88694205 of Chromosome A12 with Ref C and Alt T, which is a functional locus; SNP No. 082 at Genome position 90492050 of Chromosome A12 with Ref C and Alt T, which is a functional locus; SNP No. 083 at Genome position 98576530 of Chromosome A12 with Ref C and Alt T, which is a functional locus; SNP No. 084 at Genome position 105476632 of Chromosome A13 with Ref G and Alt T, which is a functional locus; SNP No. 085 at Genome position 105477213 of Chromosome A13 with Ref G and Alt A, which is a functional locus; SNP No. 086 at Genome position 105486165 of Chromosome A13 with Ref G and Alt A, which is a functional locus; SNP No. 087 at Genome position 105603690 of Chromosome A13 with Ref T and Alt C, which is a functional locus; SNP No. 088 at Genome position 64087028 of Chromosome D01 with Ref G and Alt C, which is a functional locus; SNP No. 089 at Genome position 1013903 of Chromosome D02 with Ref T and Alt C, which is a functional locus; SNP No. 090 at Genome position 1396386 of Chromosome D02 with Ref T and Alt C, which is a functional locus; SNP No. 091 at Genome position 43272859 of Chromosome D03 with Ref G and Alt C, which is a functional locus; SNP No. 092 at Genome position 43289074 of Chromosome D03 with Ref A and Alt T, which is a functional locus; SNP No. 093 at Genome position 23684485 of Chromosome D05 with Ref C and Alt A, which is a functional locus; SNP No. 094 at Genome position 5720265 of Chromosome D05 with Ref G and Alt T, which is a functional locus; SNP No. 095 at Genome position 57485276 of Chromosome D05 with Ref C and Alt A, which is a functional locus; SNP No. 096 at Genome position 58079007 of Chromosome D05 with Ref G and Alt A, which is a functional locus; SNP No. 097 at Genome position 58177617 of Chromosome D05 with Ref C and Alt T, which is a functional locus; SNP No. 098 at Genome position 12003138 of Chromosome D06 with Ref G and Alt A, which is a functional locus; SNP No. 099 at Genome position 17773574 of Chromosome D06 with Ref A and Alt G, which is a functional locus; SNP No. 100 at Genome position 60207647 of Chromosome D06 with Ref G and Alt C, which is a functional locus; SNP No. 101 at Genome position 8776619 of Chromosome D06 with Ref G and Alt, which is a functional locus; SNP No. 102 at Genome position 19075384 of Chromosome D07 with Ref A and Alt G, which is a functional locus; SNP No. 103 at Genome position 51856497 of Chromosome D07 with Ref T and Alt C, which is a functional locus; SNP No. 104 at Genome position 6729179 of Chromosome D07 with Ref A and Alt C, which is a functional locus; SNP No. 105 at Genome position 2896926 of Chromosome D08 with Ref A and Alt C, which is a functional locus; SNP No. 106 at Genome position 2901847 of Chromosome D08 with Ref A and Alt G, which is a functional locus; SNP No. 107 at Genome position 2904400 of Chromosome D08 with Ref A and Alt G, which is a functional locus; SNP No. 108 at Genome position 5505113 of Chromosome D08 with Ref G and Alt T, which is a functional locus; SNP No. 109 at Genome position 63065133 of Chromosome D08 with Ref G and Alt C, which is a functional locus; SNP No. 110 at Genome position 6549285 of Chromosome D09 with Ref G and Alt A, which is a functional locus; SNP No. 111 at Genome position 2524436 of Chromosome D10 with Ref C and Alt A, which is a functional locus; SNP No. 112 at Genome position 57041068 of Chromosome D11 with Ref C and Alt T, which is a functional locus; SNP No. 113 at Genome position 58261390 of Chromosome D11 with Ref A and Alt C, which is a functional locus; SNP No. 114 at Genome position 64752270 of Chromosome D11 with Ref C and Alt A, which is a functional locus; SNP No. 115 at Genome position 64756382 of Chromosome D11 with Ref T and Alt C, which is a functional locus; SNP No. 116 at Genome position 64904998 of Chromosome D11 with Ref G and Alt C, which is a functional locus; SNP No. 117 at Genome position 64926164 of Chromosome D11 with Ref C and Alt T, which is a functional locus; SNP No. 118 at Genome position 64930470 of Chromosome D11 with Ref T and Alt C, which is a functional locus; SNP No. 119 at Genome position 64937064 of Chromosome D11 with Ref G and Alt C, which is a functional locus; SNP No. 120 at Genome position 65065455 of Chromosome D11 with Ref C and Alt A, which is a functional locus; SNP No. 121 at Genome position 53158662 of Chromosome D12 with Ref G and Alt A, which is a functional locus; SNP No. 122 at Genome position 60059695 of Chromosome D12 with Ref T and Alt C, which is a functional locus; SNP No. 123 at Genome position 1774748 of Chromosome D13 with Ref C and Alt T, which is a functional locus; SNP No. 124 at Genome position 229536 of Chromosome D13 with Ref C and Alt G, which is a functional locus; SNP No. 125 at Genome position 45090184 of Chromosome D13 with Ref T and Alt G, which is a functional locus; SNP No. 126 at Genome position 53340754 of Chromosome D13 with Ref A and Alt C, which is a functional locus; SNP No. 127 at Genome position 8371110 of Chromosome D13 with Ref A and Alt C, which is a functional locus; SNP No. 128 at Genome position 39098148 of Chromosome seq1 with Ref T and Alt A, which is a functional locus; SNP No. 129 at Genome position 39098165 of Chromosome seq1 with Ref A and Alt C, which is a functional locus; SNP No. 130 at Genome position 39098173 of Chromosome seq1 with Ref G and Alt C, which is a functional locus; SNP No. 131 at Genome position 9660644 of Chromosome seq1 with Ref C and Alt G, which is a functional locus; SNP No. 132 at Genome position 2102346 of Chromosome A01 with Ref T and Alt C, which is a functional locus; SNP No. 133 at Genome position 8820452 of Chromosome A01 with Ref A and Alt C, which is a functional locus; SNP No. 134 at Genome position 1689682 of Chromosome A02 with Ref C and Alt T, which is a functional locus; SNP No. 135 at Genome position 51260473 of Chromosome A03 with Ref T and Alt A, which is a functional locus; SNP No. 136 at Genome position 6518897 of Chromosome A04 with Ref C and Alt T, which is a functional locus; SNP No. 137 at Genome position 11730945 of Chromosome A05 with Ref G and Alt A, which is a functional locus; SNP No. 138 at Genome position 75751203 of Chromosome A05 with Ref T and Alt C, which is a functional locus; SNP No. 139 at Genome position 8750649 of Chromosome A06 with Ref T and Alt C, which is a functional locus; SNP No. 140 at Genome position 1032070 of Chromosome A07 with Ref A and Alt C, which is a functional locus; SNP No. 141 at Genome position 1032071 of Chromosome A07 with Ref G and Alt T, which is a functional locus; SNP No. 142 at Genome position 12032478 of Chromosome A07 with Ref C and Alt T, which is a functional locus; SNP No. 143 at Genome position 95507309 of Chromosome A07 with Ref C and Alt G, which is a functional locus; SNP No. 144 at Genome position 989813 of Chromosome A07 with Ref T and Alt A, which is a functional locus; SNP No. 145 at Genome position 117118370 of Chromosome A08 with Ref A and Alt G, which is a functional locus; SNP No. 146 at Genome position 119190686 of Chromosome A08 with Ref T and Alt C, which is a functional locus; SNP No. 147 at Genome position 124176460 of Chromosome A08 with Ref A and Alt G, which is a functional locus; SNP No. 148 at Genome position 6187342 of Chromosome A08 with Ref T and Alt C, which is a functional locus; SNP No. 149 at Genome position 97074019 of Chromosome A08 with Ref C and Alt T, which is a functional locus; SNP No. 150 at Genome position 13706113 of Chromosome A09 with Ref T and Alt C, which is a functional locus; SNP No. 151 at Genome position 109236405 of Chromosome A10 with Ref A and Alt G, which is a functional locus; SNP No. 152 at Genome position 114220963 of Chromosome A10 with Ref C and Alt T, which is a functional locus; SNP No. 153 at Genome position 94150095 of Chromosome A12 with Ref C and Alt T, which is a functional locus; SNP No. 154 at Genome position 106412709 of Chromosome A13 with Ref C and Alt T, which is a functional locus; SNP No. 155 at Genome position 109879969 of Chromosome A13 with Ref C and Alt T, which is a functional locus; SNP No. 156 at Genome position 6433021 of Chromosome A13 with Ref T and Alt C, which is a functional locus; SNP No. 157 at Genome position 1150200 of Chromosome D01 with Ref T and Alt A, which is a functional locus; SNP No. 158 at Genome position 18933398 of Chromosome D01 with Ref C and Alt T, which is a functional locus; SNP No. 159 at Genome position 600285 of Chromosome D01 with Ref C and Alt T, which is a functional locus; SNP No. 160 at Genome position 12661527 of Chromosome D02 with Ref T and Alt C, which is a functional locus; SNP No. 161 at Genome position 1920733 of Chromosome D02 with Ref C and Alt G, which is a functional locus; SNP No. 162 at Genome position 1946913 of Chromosome D02 with Ref A and Alt G, which is a functional locus; SNP No. 163 at Genome position 44762375 of Chromosome D02 with Ref T and Alt C, which is a functional locus; SNP No. 164 at Genome position 6392666 of Chromosome D02 with Ref G and Alt A, which is a functional locus; SNP No. 165 at Genome position 68951786 of Chromosome D02 with Ref C and Alt A, which is a functional locus; SNP No. 166 at Genome position 2487227 of Chromosome D03 with Ref A and Alt G, which is a functional locus; SNP No. 167 at Genome position 1347244 of Chromosome D04 with Ref A and Alt G, which is a functional locus; SNP No. 168 at Genome position 52647897 of Chromosome D04 with Ref A and Alt G, which is a functional locus; SNP No. 169 at Genome position 26764654 of Chromosome D05 with Ref C and Alt T, which is a functional locus; SNP No. 170 at Genome position 45810951 of Chromosome D05 with Ref A and Alt G, which is a functional locus; SNP No. 171 at Genome position 1497967 of Chromosome D06 with Ref G and Alt A, which is a functional locus; SNP No. 172 at Genome position 1624645 of Chromosome D06 with Ref A and Alt C, which is a functional locus; SNP No. 173 at Genome position 54504155 of Chromosome D06 with Ref A and Alt T, which is a functional locus; SNP No. 174 at Genome position 59180787 of Chromosome D06 with Ref G and Alt A, which is a functional locus; SNP No. 175 at Genome position 61085437 of Chromosome D06 with Ref T and Alt A, which is a functional locus; SNP No. 176 at Genome position 46303166 of Chromosome D07 with Ref A and Alt G, which is a functional locus; SNP No. 177 at Genome position 61439658 of Chromosome D08 with Ref G and Alt A, which is a functional locus; SNP No. 178 at Genome position 68631323 of Chromosome D08 with Ref C and Alt T, which is a functional locus; SNP No. 179 at Genome position 9335830 of Chromosome D08 with Ref C and Alt T, which is a functional locus; SNP No. 180 at Genome position 2749569 of Chromosome D09 with Ref A and Alt C, which is a functional locus; SNP No. 181 at Genome position 38068242 of Chromosome D09 with Ref T and Alt C, which is a functional locus; SNP No. 182 at Genome position 1280801 of Chromosome D11 with Ref G and Alt A, which is a functional locus; SNP No. 183 at Genome position 15727440 of Chromosome D12 with Ref T and Alt C, which is a functional locus; SNP No. 184 at Genome position 58551591 of Chromosome D12 with Ref C and Alt T, which is a functional locus; SNP No. 185 at Genome position 7113678 of Chromosome D12 with Ref G and Alt A, which is a functional locus; SNP No. 186 at Genome position 59655465 of Chromosome D13 with Ref T and Alt G, which is a functional locus; SNP No. 187 at Genome position 60649746 of Chromosome D13 with Ref G and Alt A, which is a functional locus; SNP No. 188 at Genome position 110967771 of Chromosome A01 with Ref A and Alt C, which is a functional locus; SNP No. 189 at Genome position 107361717 of Chromosome A02 with Ref T and Alt A, which is a functional locus; SNP No. 190 at Genome position 1707434 of Chromosome A02 with Ref G and Alt A, which is a functional locus; SNP No. 191 at Genome position 26551420 of Chromosome A02 with Ref G and Alt A, which is a functional locus; SNP No. 192 at Genome position 14504864 of Chromosome A05 with Ref C and Alt T, which is a functional locus; SNP No. 193 at Genome position 14504889 of Chromosome A05 with Ref A and Alt G, which is a functional locus; SNP No. 194 at Genome position 15429410 of Chromosome A05 with Ref C and Alt G, which is a functional locus; SNP No. 195 at Genome position 42902490 of Chromosome A07 with Ref C and Alt G, which is a functional locus; SNP No. 196 at Genome position 90603512 of Chromosome A07 with Ref T and Alt G, which is a functional locus; SNP No. 197 at Genome position 90783146 of Chromosome A07 with Ref G and Alt A, which is a functional locus; SNP No. 198 at Genome position 112071927 of Chromosome A08 with Ref C and Alt T, which is a functional locus; SNP No. 199 at Genome position 110613300 of Chromosome A10 with Ref T and Alt C, which is a functional locus; SNP No. 200 at Genome position 104539963 of Chromosome A11 with Ref T and Alt C, which is a functional locus; SNP No. 201 at Genome position 1913626 of Chromosome D02 with Ref A and Alt G, which is a functional locus; SNP No. 202 at Genome position 1915388 of Chromosome D02 with Ref T and Alt C, which is a functional locus; SNP No. 203 at Genome position 6362048 of Chromosome D02 with Ref C and Alt T, which is a functional locus; SNP No. 204 at Genome position 1546736 of Chromosome D04 with Ref T and Alt A, which is a functional locus; SNP No. 205 at Genome position 14240130 of Chromosome D05 with Ref T and Alt G, which is a functional locus; SNP No. 206 at Genome position 45390691 of Chromosome D06 with Ref C and Alt T, which is a functional locus; SNP No. 207 at Genome position 46672551 of Chromosome D06 with Ref C and Alt T, which is a functional locus; SNP No. 208 at Genome position 18841330 of Chromosome D08 with Ref A and Alt C, which is a functional locus; SNP No. 209 at Genome position 20428933 of Chromosome D11 with Ref A and Alt T, which is a functional locus; SNP No. 210 at Genome position 114857126 of Chromosome A01 with Ref G and Alt A, which is a functional locus; SNP No. 211 at Genome position 115721972 of Chromosome A01 with Ref A and Alt G, which is a functional locus; SNP No. 212 at Genome position 117760175 of Chromosome A01 with Ref T and Alt C, which is a functional locus; SNP No. 213 at Genome position 117760658 of Chromosome A01 with Ref T and Alt A, which is a functional locus; SNP No. 214 at Genome position 106224475 of Chromosome A02 with Ref A and Alt G, which is a functional locus; SNP No. 215 at Genome position 3111851 of Chromosome A02 with Ref A and Alt G, which is a functional locus; SNP No. 216 at Genome position 110233891 of Chromosome A03 with Ref A and Alt G, which is a functional locus; SNP No. 217 at Genome position 67550448 of Chromosome A04 with Ref A and Alt T, which is a functional locus; SNP No. 218 at Genome position 86560855 of Chromosome A04 with Ref C and Alt T, which is a functional locus; SNP No. 219 at Genome position 86568861 of Chromosome A04 with Ref C and Alt T, which is a functional locus; SNP No. 220 at Genome position 105715349 of Chromosome A05 with Ref A and Alt G, which is a functional locus; SNP No. 221 at Genome position 15876258 of Chromosome A05 with Ref T and Alt C, which is a functional locus; SNP No. 222 at Genome position 15876308 of Chromosome A05 with Ref C and Alt G, which is a functional locus; SNP No. 223 at Genome position 1874595 of Chromosome A05 with Ref A and Alt G, which is a functional locus; SNP No. 224 at Genome position 2124121 of Chromosome A05 with Ref C and Alt T, which is a functional locus; SNP No. 225 at Genome position 22775565 of Chromosome A05 with Ref G and Alt A, which is a functional locus; SNP No. 226 at Genome position 22924264 of Chromosome A05 with Ref T and Alt A, which is a functional locus; SNP No. 227 at Genome position 22938538 of Chromosome A05 with Ref A and Alt T, which is a functional locus; SNP No. 228 at Genome position 31423050 of Chromosome A05 with Ref T and Alt C, which is a functional locus; SNP No. 229 at Genome position 119255407 of Chromosome A06 with Ref C and Alt T, which is a functional locus; SNP No. 230 at Genome position 124093748 of Chromosome A06 with Ref C and Alt T, which is a functional locus; SNP No. 231 at Genome position 1503775 of Chromosome A06 with Ref C and Alt G, which is a functional locus; SNP No. 232 at Genome position 21563371 of Chromosome A07 with Ref C and Alt T, which is a functional locus; SNP No. 233 at Genome position 23460168 of Chromosome A07 with Ref C and Alt T, which is a functional locus; SNP No. 234 at Genome position 83188617 of Chromosome A07 with Ref G and Alt C, which is a functional locus; SNP No. 235 at Genome position 88838111 of Chromosome A07 with Ref C and Alt T, which is a functional locus; SNP No. 236 at Genome position 90625054 of Chromosome A07 with Ref C and Alt T, which is a functional locus; SNP No. 237 at Genome position 90633925 of Chromosome A07 with Ref C and Alt T, which is a functional locus; SNP No. 238 at Genome position 90639206 of Chromosome A07 with Ref T and Alt C, which is a functional locus; SNP No. 239 at Genome position 104027372 of Chromosome A08 with Ref A and Alt G, which is a functional locus; SNP No. 240 at Genome position 107661059 of Chromosome A08 with Ref T and Alt G, which is a functional locus; SNP No. 241 at Genome position 123086263 of Chromosome A08 with Ref C and Alt G, which is a functional locus; SNP No. 242 at Genome position 123101111 of Chromosome A08 with Ref T and Alt C, which is a functional locus; SNP No. 243 at Genome position 31131479 of Chromosome A08 with Ref C and Alt T, which is a functional locus; SNP No. 244 at Genome position 6469161 of Chromosome A08 with Ref T and Alt A, which is a functional locus; SNP No. 245 at Genome position 73717101 of Chromosome A09 with Ref C and Alt A, which is a functional locus; SNP No. 246 at Genome position 108187386 of Chromosome A10 with Ref C and Alt T, which is a functional locus; SNP No. 247 at Genome position 114006682 of Chromosome A10 with Ref G and Alt A, which is a functional locus; SNP No. 248 at Genome position 2516523 of Chromosome A10 with Ref C and Alt T, which is a functional locus; SNP No. 249 at Genome position 4309496 of Chromosome A10 with Ref C and Alt A, which is a functional locus; SNP No. 250 at Genome position 118950829 of Chromosome A11 with Ref A and Alt T, which is a functional locus; SNP No. 251 at Genome position 24222 of Chromosome A11 with Ref G and Alt A, which is a functional locus; SNP No. 252 at Genome position 9073286 of Chromosome A11 with Ref G and Alt A, which is a functional locus; SNP No. 253 at Genome position 99926974 of Chromosome A11 with Ref A and Alt G, which is a functional locus; SNP No. 254 at Genome position 104493499 of Chromosome A12 with Ref T and Alt A, which is a functional locus; SNP No. 255 at Genome position 95983460 of Chromosome A12 with Ref C and Alt G, which is a functional locus; SNP No. 256 at Genome position 100671788 of Chromosome A13 with Ref C and Alt T, which is a functional locus; SNP No. 257 at Genome position 104864916 of Chromosome A13 with Ref T and Alt G, which is a functional locus; SNP No. 258 at Genome position 107008682 of Chromosome A13 with Ref A and Alt G, which is a functional locus; SNP No. 259 at Genome position 5759232 of Chromosome A13 with Ref A and Alt G, which is a functional locus; SNP No. 260 at Genome position 68442801 of Chromosome A13 with Ref C and Alt A, which is a functional locus; SNP No. 261 at Genome position 89442130 of Chromosome A13 with Ref G and Alt A, which is a functional locus; SNP No. 262 at Genome position 98283310 of Chromosome A13 with Ref T and Alt C, which is a functional locus; SNP No. 263 at Genome position 19034036 of Chromosome D01 with Ref T and Alt A, which is a functional locus; SNP No. 264 at Genome position 54855218 of Chromosome D01 with Ref T and Alt C, which is a functional locus; SNP No. 265 at Genome position 54866986 of Chromosome D01 with Ref C and Alt T, which is a functional locus; SNP No. 266 at Genome position 54890106 of Chromosome D01 with Ref T and Alt C, which is a functional locus; SNP No. 267 at Genome position 54896281 of Chromosome D01 with Ref G and Alt A, which is a functional locus; SNP No. 268 at Genome position 57261588 of Chromosome D01 with Ref A and Alt G, which is a functional locus; SNP No. 269 at Genome position 58881229 of Chromosome D01 with Ref C and Alt T, which is a functional locus; SNP No. 270 at Genome position 51851185 of Chromosome D02 with Ref A and Alt G, which is a functional locus; SNP No. 271 at Genome position 52987299 of Chromosome D02 with Ref A and Alt G, which is a functional locus; SNP No. 272 at Genome position 53034743 of Chromosome D02 with Ref G and Alt T, which is a functional locus; SNP No. 273 at Genome position 53253589 of Chromosome D02 with Ref A and Alt C, which is a functional locus; SNP No. 274 at Genome position 54901956 of Chromosome D02 with Ref C and Alt T, which is a functional locus; SNP No. 275 at Genome position 63310106 of Chromosome D02 with Ref T and Alt C, which is a functional locus; SNP No. 276 at Genome position 6401616 of Chromosome D02 with Ref T and Alt A, which is a functional locus; SNP No. 277 at Genome position 68030533 of Chromosome D02 with Ref A and Alt T, which is a functional locus; SNP No. 278 at Genome position 7489387 of Chromosome D02 with Ref T and Alt G, which is a functional locus; SNP No. 279 at Genome position 7531127 of Chromosome D02 with Ref A and Alt G, which is a functional locus; SNP No. 280 at Genome position 2503186 of Chromosome D03 with Ref G and Alt T, which is a functional locus; SNP No. 281 at Genome position 52350838 of Chromosome D04 with Ref T and Alt G, which is a functional locus; SNP No. 282 at Genome position 6848742 of Chromosome D04 with Ref A and Alt C, which is a functional locus; SNP No. 283 at Genome position 6861687 of Chromosome D04 with Ref C and Alt T, which is a functional locus; SNP No. 284 at Genome position 851577 of Chromosome D04 with Ref G and Alt A, which is a functional locus; SNP No. 285 at Genome position of Chromosome D05 with 14718765 Ref A and Alt G, which is a functional locus; SNP No. 286 at Genome position of Chromosome D05 with 55154526 Ref T and Alt C, which is a functional locus; SNP No. 287 at Genome position 56805649 of Chromosome D05 with Ref A and Alt G, which is a functional locus; SNP No. 288 at Genome position 18372518 of Chromosome D06 with Ref T and Alt A, which is a functional locus; SNP No. 289 at Genome position 47311286 of Chromosome D06 with Ref G and Alt T, which is a functional locus; SNP No. 290 at Genome position 64318600 of Chromosome D06 with Ref T and Alt C, which is a functional locus; SNP No. 291 at Genome position 10130687 of Chromosome D07 with Ref G and Alt C, which is a functional locus; SNP No. 292 at Genome position 54754308 of Chromosome D07 with Ref T and Alt C, which is a functional locus; SNP No. 293 at Genome position of Chromosome D07 with 54818140 Ref G and Alt A, which is a functional locus; SNP No. 294 at Genome position 54821539 of Chromosome DO7 with Ref T and Alt A, which is a functional locus; SNP No. 295 at Genome position 2748641 of Chromosome D08 with Ref C and Alt T, which is a functional locus; SNP No. 296 at Genome position 430878 of Chromosome D08 with Ref C and Alt A, which is a functional locus; SNP No. 297 at Genome position 4868113 of Chromosome D08 with Ref C and Alt T, which is a functional locus; SNP No. 298 at Genome position 608978 of Chromosome D08 with Ref C and Alt T, which is a functional locus; SNP No. 299 at Genome position 49092148 of Chromosome D09 with Ref A and Alt G, which is a functional locus; SNP No. 300 at Genome position 6069425 of Chromosome D09 with Ref C and Alt T, which is a functional locus; SNP No. 301 at Genome position 63443095 of Chromosome D10 with Ref G and Alt C, which is a functional locus; SNP No. 302 at Genome position 63918764 of Chromosome D10 with Ref C and Alt T, which is a functional locus; SNP No. 303 at Genome position 64184291 of Chromosome D10 with Ref A and Alt T, which is a functional locus; SNP No. 304 at Genome position 826050 of Chromosome D10 with Ref A and Alt G, which is a functional locus; SNP No. 305 at Genome position 10658879 of Chromosome D11 with Ref T and Alt C, which is a functional locus; SNP No. 306 at Genome position 13890576 of Chromosome D11 with Ref T and Alt C, which is a functional locus; SNP No. 307 at Genome position 21988164 of Chromosome D11 with Ref G and Alt A, which is a functional locus; SNP No. 308 at Genome position 23924389 of Chromosome D11 with Ref T and Alt A, which is a functional locus; SNP No. 309 at Genome position 23924409 of Chromosome D11 with Ref C and Alt T, which is a functional locus; SNP No. 310 at Genome position 23944152 of Chromosome D11 with Ref C and Alt T, which is a functional locus; SNP No. 311 at Genome position 24002127 of Chromosome D11 with Ref A and Alt G, which is a functional locus; SNP No. 312 at Genome position 24004889 of Chromosome D11 with Ref C and Alt T, which is a functional locus; SNP No. 313 at Genome position 24034422 of Chromosome D11 with Ref G and Alt C, which is a functional locus; SNP No. 314 at Genome position 24036519 of Chromosome D11 with Ref A and Alt G, which is a functional locus; SNP No. 315 at Genome position 3229941 of Chromosome D11 with Ref A and Alt G, which is a functional locus; SNP No. 316 at Genome position 3230659 of Chromosome D11 with Ref C and Alt T, which is a functional locus; SNP No. 317 at Genome position 62899476 of Chromosome D11 with Ref G and Alt A, which is a functional locus; SNP No. 318 at Genome position 1201966 of Chromosome D12 with Ref C and Alt A, which is a functional locus; SNP No. 319 at Genome position position 69399954 of Chromosome A01 with Ref A and Alt G, which is not a functional locus; SNP No. 361 at Genome position 72356977 of Chromosome A01 with Ref A and Alt G, which is not a functional locus; SNP No. 362 at Genome position 73066978 of Chromosome A01 with Ref C and Alt T, which is not a functional locus; SNP No. 363 at Genome position 83056539 of Chromosome A01 with Ref G and Alt C, which is not a functional locus; SNP No. 364 at Genome position 9307886 of Chromosome A01 with Ref T and Alt C, which is not a functional locus; SNP No. 365 at Genome position 94433050 of Chromosome A01 with Ref C and Alt G, which is not a functional locus; SNP No. 366 at Genome position 97114671 of Chromosome A01 with Ref G and Alt A, which is not a functional locus; SNP No. 367 at Genome position 9928461 of Chromosome A01 with Ref A and Alt G, which is not a functional locus; SNP No. 368 at Genome position 9992909 of Chromosome A01 with Ref T and Alt C, which is not a functional locus; SNP No. 369 at Genome position 104702522 of Chromosome A02 with Ref C and Alt G, which is not a functional locus; SNP No. 370 at Genome position 106564817 of Chromosome A02 with Ref G and Alt A, which is not a functional locus; SNP No. 371 at Genome position 126465 of Chromosome A02 with Ref A and Alt G, which is not a functional locus; SNP No. 372 at Genome position 18537125 of Chromosome A02 with Ref A and Alt G, which is not a functional locus; SNP No. 373 at Genome position 19418124 of Chromosome A02 with Ref T and Alt C, which is not a functional locus; SNP No. 374 at Genome position 3608260 of Chromosome A02 with Ref T and Alt A, which is not a functional locus; SNP No. 375 at Genome position 3753565 of Chromosome A02 with Ref C and Alt G, which is not a functional locus; SNP No. 376 at Genome position 39122586 of Chromosome A02 with Ref T and Alt C, which is not a functional locus; SNP No. 377 at Genome position 44761669 of Chromosome A02 with Ref C and Alt A, which is not a functional locus; SNP No. 378 at Genome position 44836527 of Chromosome A02 with Ref T and Alt C, which is not a functional locus; SNP No. 379 at Genome position 52198772 of Chromosome A02 with Ref A and Alt G, which is not a functional locus; SNP No. 380 at Genome position 63519897 of Chromosome A02 position 47819857 of Chromosome A07 with Ref A and Alt G, which is not a functional locus; SNP No. 502 at Genome position 54517045 of Chromosome A07 with Ref G and Alt A, which is not a functional locus; SNP No. 503 at Genome position 64238084 of Chromosome A07 with Ref C and Alt T, which is not a functional locus; SNP No. 504 at Genome position 80217572 of Chromosome A07 with Ref C and Alt T, which is not a functional locus; SNP No. 505 at Genome position 80388490 of Chromosome A07 with Ref A and Alt T, which is not a functional locus; SNP No. 506 at Genome position 82916184 of Chromosome A07 with Ref T and Alt C, which is not a functional locus; SNP No. 507 at Genome position 83105438 of Chromosome A07 with Ref G and Alt A, which is not a functional locus; SNP No. 508 at Genome position 8422752 of Chromosome A07 with Ref G and Alt C, which is not a functional locus; SNP No. 509 at Genome position 89161736 of Chromosome A07 with Ref A and Alt G, which is not a functional locus; SNP No. 510 at Genome position 9478030 of Chromosome A07 with Ref A and Alt C, which is not a functional locus; SNP No. 511 at Genome position 10429943 of Chromosome A08 with Ref C and Alt G, which is not a functional locus; SNP No. 512 at Genome position 106893339 of Chromosome A08 with Ref C and Alt T, which is not a functional locus; SNP No. 513 at Genome position 109696323 of Chromosome A08 with Ref G and Alt A, which is not a functional locus; SNP No. 514 at Genome position 112025642 of Chromosome A08 with Ref C and Alt T, which is not a functional locus; SNP No. 515 at Genome position 113464785 of Chromosome A08 with Ref A and Alt G, which is not a functional locus; SNP No. 516 at Genome position 116730869 of Chromosome A08 with Ref A and Alt G, which is not a functional locus; SNP No. 517 at Genome position 1713011 of Chromosome A08 with Ref T and Alt C, which is not a functional locus; SNP No. 518 at Genome position 19121855 of Chromosome A08 with Ref C and Alt A, which is not a functional locus; SNP No. 519 at Genome position 20388949 of Chromosome A08 with Ref G and Alt A, which is not a functional locus; SNP No. 520 at Genome position 25642734 of Chromosome A08 with Ref C and Alt T, which is not a functional locus; SNP No. 521 at Genome position 3134551 of Chromosome D13 with Ref A and Alt T, which is not a functional locus; SNP No. 885 at Genome position 39085839 of Chromosome D13 with Ref G and Alt A, which is not a functional locus; SNP No. 886 at Genome position 42257012 of Chromosome D13 with Ref A and Alt G, which is not a functional locus; SNP No. 887 at Genome position 49441679 of Chromosome D13 with Ref A and Alt G, which is not a functional locus; SNP No. 888 at Genome position 49745988 of Chromosome D13 with Ref A and Alt G, which is not a functional locus; SNP No. 889 at Genome position 55874078 of Chromosome D13 with Ref A and Alt G, which is not a functional locus; SNP No. 890 at Genome position 57525048 of Chromosome D13 with Ref T and Alt G, which is not a functional locus; SNP No. 891 at Genome position 58479149 of Chromosome D13 with Ref A and Alt G, which is not a functional locus; SNP No. 892 at Genome position 63605335 of Chromosome D13 with Ref A and Alt G, which is not a functional locus; SNP No. 893 at Genome position 64125386 of Chromosome D13 with Ref T and Alt C, which is not a functional locus; and SNP No. 894 at Genome position 9724970 of Chromosome D13 with Ref T and Alt A, which is not a functional locus, wherein, Ref represents base type of a SNP locus in a reference genome, and Alt represents base type of SNP locus in a population.

2 . The liquid-phase chip for Gossypium hirsutum L. according to claim 1 , wherein the probes for detecting the 14 major transgenes consist of SEQ ID NOs. 1-14.