TABLE 3

Summary of interspecific, intraspecific, and subgenomic SNPs discovered

Rate of variation per nucleotide (%)
STSTotal nta analyzedHomeologous (subgenomic)Intraspecific G. barbadense (K101 vs. Pima)Intraspecific G. hirsutum (Palmeri vs. Maxxa)Interspecific (G. hirsutum vs. barbadense)Variation due to SNPsVariation due to indelsLength of indels (nt)
A11074200.950.4800.481000
A1110550000000
A11262851.0500066.733.337
A11315021.5900.2066.733.31, 2, and 3
A11485050000.21000
A1152422000000
A11674500.890.4400.4466.633.31 and 4
A1174470n.d001.2783.316.77
A136448001.041.041.041000
PAR00604802.52.080090.99.13 and 22
PAR08273853.6400.260.5293.86.211
PCK460n.d0.430.220.2210006 and 18
Average % of variation1.060.370.140.3572.311.9

Sequences with subgenomic affinity cannot be positively identified, due to either a high divergence between the A-genome probe sequence and the PCR-amplified tetraploid genome sequences or no diploid genome sequence being available (PCK primers were designed from a G. barbadense cDNA clone sequence that preferentially expressed in fiber tissues). Sequences are available from GenBank, accession nos. CC737118–CC737319.

  • a The total nucleotides analyzed may be different from the PCR fragment length because of poor sequence quality, particularly in reads beyond 500 nucleotides.