QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
Theor Appl Genet. 2010 May;120(8):1547-57. doi: 10.1007/s00122-010-1275-z. Epub 2010 Feb 10.
Backcrossed inbred lines (BILs) and a set of reciprocal chromosome segment substitution lines (CSSLs) derived from crosses between japonica rice cultivars Nipponbare and Koshihikari were used to detect quantitative trait loci (QTLs) for pre-harvest sprouting resistance. In the BILs, we detected one QTL on chromosome 3 and one QTL on chromosome 12. The QTL on the short arm of chromosome 3 accounted for 45.0% of the phenotypic variance and the Nipponbare allele of the QTL increased germination percentage by 21.3%. In the CSSLs, we detected seven QTLs, which were located on chromosomes 2, 3 (two), 5, 8 and 11 (two). All Nipponbare alleles of the QTLs were associated with an increased rate of germination. The major QTL for pre-harvest sprouting resistance on the short arm of chromosome 3 was localized to a 474-kbp region in the Nipponbare genome by the SSR markers RM14240 and RM14275 by using 11 substitution lines to replace the different short chromosome segments on chromosome 3. This QTL co-localized with the low-temperature germinability gene qLTG3-1. The level of germinability under low temperature strongly correlated with the level of pre-harvest sprouting resistance in the substitution lines. Sequence analyses revealed a novel functional allele of qLTG3-1 in Nipponbare and a loss-of-function allele in Koshihikari. The allelic difference in qLTG3-1 between Nipponbare and Koshihikari is likely to be associated with differences in both pre-harvest sprouting resistance and low-temperature germinability.
回交系（BILs）和一套由粳稻品种 Nipponbare 和 Koshihikari 杂交衍生的相互染色体片段替换系（CSSLs）被用于检测抗穗发芽的数量性状位点（QTLs）。在 BILs 中，我们在第 3 号染色体上检测到一个 QTL，在第 12 号染色体上检测到一个 QTL。第 3 号染色体短臂上的 QTL 占表型方差的 45.0%，该 QTL 的 Nipponbare 等位基因使发芽率提高了 21.3%。在 CSSLs 中，我们检测到七个 QTL，它们位于第 2、3（两个）、5、8 和 11（两个）号染色体上。所有 QTL 的 Nipponbare 等位基因都与发芽率的提高有关。第 3 号染色体短臂上抗穗发芽的主 QTL 被 RM14240 和 RM14275 两个 SSR 标记定位到 Nipponbare 基因组的 474-kbp 区域，该 QTL 由 11 个替换系替换第 3 号染色体上的不同短染色体片段。这个 QTL 与低温发芽性基因 qLTG3-1 共定位。替换系中低温发芽率与穗发芽抗性水平强烈相关。序列分析显示，Nipponbare 中有一个 qLTG3-1 的新功能等位基因，而 Koshihikari 中有一个失活等位基因。Nipponbare 和 Koshihikari 之间 qLTG3-1 的等位基因差异可能与抗穗发芽性和低温发芽性的差异有关。
