Seedling vigor, which is controlled by many quantitative trait loci (QTLs), is one of several important agronomic traits for direct-seedling rice systems. However, isolating these QTL genes is laborious and expensive. Here, we combined QTL mapping and microarray profiling to identify QTL genes for seedling vigor. By performing QTL mapping using 82 backcross inbred lines (BILs) of the Koshihikari (japonica) and Habataki (indica) cultivars for the rice initial growth, we identified two QTLs, early-stage plant development1/2 (qEPD1 and qEPD2), whose Koshihikari alleles promote plant height and/or leaf sheath length. Phenotypic analysis of the two substituted lines carrying the Habataki qEPD1 or qEPD2 allele revealed that qEPD2 functioned more dominantly for the initial growth of rice. From the microarray experiment, 55 and 45 candidate genes were found in the qEPD1 and qEPD2 genomic regions, which are expressed differentially between each substitution line (SL) and Koshihikari. Gibberellin 20 oxidase-2 (OsGA20ox2), which is identical to Semi Dwarf1 (SD1), was included among the 55 candidate genes of qEPD1, whereas its paralog, OsGA20ox1, was included among the 45 candidate genes of qEPD2. Consistently, introduction of the Koshihikari OsGA20ox1 allele into SLqEPD2 increaseed its plant height and leaf sheath length significantly relative to the introduction of the Habataki OsGA20ox1 allele. Therefore, microarray profiling could be useful for rapidly screening QTL candidate genes. We concluded that OsGA20ox1 and OsGA20ox2 (SD1) function during the initial growth of rice, but OsGA20ox1 plays a dominant role in increasing plant height and leaf sheath length at the initial growth stage.
幼苗活力，受多個(gè)數(shù)量性狀基因位點(diǎn)（QTLs）控制，是直播水稻的重要農(nóng)藝性狀之一。然而，分離這些QTL是一項(xiàng)費(fèi)時(shí)費(fèi)力的工作。本研究，我們結(jié)合QTL定位和基因芯片分析，鑒定幼苗活力QTL。利用來源于粳稻Koshihikari和秈稻Habataki的82個(gè)回交自交系（BILs）進(jìn)行了水稻初生生長性狀的QTL定位，鑒定到2個(gè)QTLs，qEPD1和qEPD2，Koshihikari等位基因促進(jìn)植株的高度和/或葉鞘的長度。對(duì)2個(gè)攜帶Habataki qEPD1或qEPD2等位基因替換系進(jìn)行了表型分析，結(jié)果顯示qEPD2對(duì)水稻的初生生長具有更顯著的功能。基因芯片分析數(shù)據(jù)顯示，在qEPD1和qEPD2基因組定位區(qū)間內(nèi)，分別有55和45個(gè)候選基因在代換系和Koshihikari之間存在表達(dá)差異。赤霉素20氧化酶基因OsGA20ox2，也就是半矮稈基因SD1，包含在qEPD1的55個(gè)候選基因中，它的一個(gè)同源基因OsGA20ox1，包含在qEPD2的45個(gè)候選基因中。與導(dǎo)入Habataki OsGA20ox1等位基因相比，Koshihikari OsGA20ox1等位基因?qū)隨LqEPD2能夠顯著提高植株高度和葉鞘長度。所以，基因芯片分析對(duì)快速發(fā)現(xiàn)QTL的候選基因十分有用。OsGA20ox1和OsGA20ox2 (SD1)在水稻初生生長中起作用，但是在初生生長期，OsGA20ox1是促進(jìn)植株長高和葉鞘生長的主效基因。