In yellow soybean, severe cold weather causes seed cracking on the dorsal side. Yellow soybeans carry the
I
or
i
i
allele of the
I
locus and have a yellow (
I
) or pigmented (
i
i
) hilum. We previously isolated an additional allele, designated as
Ic
, of the
I
locus, and reported that yellow soybeans with the
IcIc
genotype may be tolerant to cold-induced seed cracking. The
Ic
allele by itself, however, does not confer high tolerance. The association of a pubescence color gene (
T
) with suppression of low-temperature-induced seed coat deterioration has been previously reported. In the present study, we tested whether
T
is effective for the suppression of cold-induced seed cracking using two pairs of near-isogenic lines for the
T
locus in the
i
i
i
i
or
IcIc
background. In both backgrounds, the cracked seed rate of the near-isogenic line with the
TT
genotype was significantly lower than that with the
tt
genotype, which indicates that
T
has an inhibitory effect on cold-induced seed cracking. Furthermore, we also showed that gene pyramiding of
Ic
and
T
can improve tolerance to cold-induced seed cracking. Our findings should aid the development of highly SC-tolerant cultivars in soybean breeding programs.