TABLE 3

Nucleotide diversity in soybean genes and genomic sequence

Coding regions and associated noncoding sequence
Noncoding regionsRandom
noncoding
genomic
sequence
Source of
sequence
Primers
designed
Successful
sequences
Coding
regions
5′- and 3′-UTRIntronsAssociated
genomic
sequence
Total
noncoding
Total
BasesSNPsBasesSNPsBasesSNPsBasesSNPsBasesSNPsBasesSNPsBasesSNPs
GenBank genes906517,913382,3251315,641715,7811923,74710341,660141
cDNAs885010,630196,933317,0922514,0255624,65575
BAC subclones13150016901694,200374,51937
SSR flanking regions155,534275,53427
Totals28,693579,2584422,902965,7811937,9411599,7346476,368280
    Synonymous6,60125
    Nonsynonymous22,09232
θ (×103)0.53 + 0.191.26 ± 0.461.11 ± 0.390.87 ± 0.351.11 ± 0.381.79 ± 0.620.97 ± 0.33
    Synonymous1.00 ± 0.39
    Nonsynonymous0.38 ± 0.15
π (×103)0.54 ± 0.261.75 ± 0.741.36 ± 0.551.14 ± 0.541.45 ± 0.562.64 ± 1.011.25 ± 0.60
    Synonymous0.79 ± 0.49
    Nonsynonymous0.41 ± 0.19
Tajima’s D0.10 NS1.49 NS0.90 NS1.05 NS1.09 NS2.00 (P < 0.10)1.08 NS
    Synonymous-0.80 NS
    Nonsynonymous0.22 NS
  • Shown are the number of bases sequenced and measures of nucleotide diversity (θ and π); Tajima’s D in coding, noncoding, and associated genomic DNA of fragments amplified from genomic DNA using PCR primers designed to GenBank-derived genes and cDNAs; and random genomic sequences from BAC subclones and SSR flanking regions determined from the sequence analysis of 25 diverse soybean genotypes. NS, not significant.