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Journal of Integrative Agriculture  2023, Vol. 22 Issue (2): 325-340    DOI: 10.1016/j.jia.2022.08.080
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Analyses and identifications of quantitative trait loci and candidate genes controlling mesocotyl elongation in rice

ZHANG Xi-juan1, 2, LAI Yong-cai1, 2, MENG Ying1, 2, TANG Ao1, 2, DONG Wen-jun1, 2, LIU You-hong1, 2, LIU Kai2, WANG Li-zhi1, 2, YANG Xian-li1, 2, WANG Wen-long1, DING Guo-hua1, 2, JIANG Hui2, REN Yang2, JIANG Shu-kun1, 2, 3

1 Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, P.R.China

2 Northeast Branch of National Salt–Alkali Tolerant Rice Technology Innovation Center, Harbin 150086, P.R.China

3 Qiqihar Branch, Heilongjiang Academy of Agricultural Sciences, Qiqihar 161006, P.R.China

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摘要  由于水稻直播在节约劳动力、节约水资源、保护环境和大幅减少温室气体排放等方面具有巨大潜力。因此,正成为许多国家水稻生产的主要栽培技术。挖掘和利用中胚轴伸长基因是加快直播稻育种和满足直播水稻生产要求的最有效途径之一。黑龙江省农业科学院利用丽江新团黑谷(LTH)和沈农265(SN265)衍生的144个重组自交系(RIL)群体及其配套的包含2,828个bin标记的连锁图谱分别在2019年和2020年检测了与中胚轴长度相关的数量性状基因座(QTL)。采用30°C黑暗环境下培养10天后测量中胚轴长度。在第1(2)、2(4)、3(2)、4、5、6、7、9、11(2)和12号染色体上共鉴定出16个中胚轴长度QTL。其中7个QTLs可以在两年中被重复检测到,包括qML1aqML1bqML2dqML3aqML3bqML5qML11b。主效QTL-qML3a还可以在不同作图方法中被重复检测到。进一步分析发现,qML3a被定位在88.18kb的范围内,这一区间包含13个预测基因。利用近等基因系也证明了qML3a的真实存在和调控中胚轴伸长的效果。最后,通过分析SN265、LTH 和日本晴之间的DNA序列变异,表明LOC_Os03g50550qML3a的候选基因。该基因编码有丝分裂原活化的蛋白激酶。使用qRT-RCR分析进一步揭示了LTH中胚轴中LOC_Os03g50550基因的表达水平显著低于SN265中胚轴中的表达水平。这些结果进一步加强了我们对水稻中胚轴伸长遗传机制的认识,也将有助于加快直播专用新品种的育种进程。


Rice direct seeding has the significant potential to save labor and water, conserve environmental resources, and reduce greenhouse gas emissions tremendously.  Therefore, rice direct seeding is becoming the major cultivation technology applied to rice production in many countries.  Identifying and utilizing genes controlling mesocotyl elongation is an effective approach to accelerate breeding procedures and meet the requirements for direct-seeded rice (DSR) production.  This study used a permanent mapping population with 144 recombinant inbred lines (RILs) and 2 828 bin-markers to detect quantitative trait loci (QTLs) associated with mesocotyl length in 2019 and 2020.  The mesocotyl lengths of the rice RILs and their parents, Lijiangxintuanheigu (LTH) and Shennong 265 (SN265), were measured in a growth chamber at 30°C in a dark environment.  A total of 16 QTLs for mesocotyl length were identified on chromosomes 1(2), 2(4), 3(2), 4, 5, 6, 7, 9, 11(2), and 12.  Seven of these QTLs, including qML1a, qML1b, qML2d, qML3a, qML3b, qML5, and qML11b, were reproducibly detected in both years via the interval mapping method.  The major QTL, qML3a, was reidentified in two years via the composite interval mapping method.  A total of 10 to 413 annotated genes for each QTL were identified in their smallest genetic intervals of 37.69 kb to 2.78 Mb, respectively.  Thirteen predicted genes within a relatively small genetic interval (88.18 kb) of the major mesocotyl elongation QTL, qML3a, were more thoroughly analyzed.  Finally, the coding DNA sequence variations among SN265, LTH, and Nipponbare indicated that the LOC_Os03g50550 gene was the strongest candidate gene for the qML3a QTL controlling the mesocotyl elongation.  This LOC_Os03g50550 gene encodes a mitogen-activated protein kinase.  Relative gene expression analysis using qRT-RCR further revealed that the expression levels of the LOC_Os03g50550 gene in the mesocotyl of LTH were significantly lower than in the mesocotyl of SN265.  In conclusion, these results further strengthen our knowledge about rice’s genetic mechanisms of mesocotyl elongation.  This investigation’s discoveries will help to accelerate breeding programs for new DSR variety development.

Keywords:  japonica rice       direct-seeded rice (DSR)       mesocotyl elongation       quantitative trait loci       candidate gene  
Received: 15 November 2021   Accepted: 24 January 2022

This work was supported by grants from the Natural Science Foundation of Heilongjiang Province, China (LH2020C098), the Fundamental Research Funds for the Research Institutes of Heilongjiang Province, China (CZKYF2020A001), the National Key Research and Development Program of China (2016YFD0300104), and the Heilongjiang Province Agricultural Science and Technology Innovation Project, China (2020JCQN001, 2019JJPY007, 2020FJZX049, 2021QKPY009, 2021CQJC003).

About author:  ZHANG Xi-juan, E-mail:; Correspondence JIANG Shu-kun, E-mail:; LAI Yong-cai, E-mail:

Cite this article: 

ZHANG Xi-juan, LAI Yong-cai, MENG Ying, TANG Ao, DONG Wen-jun, LIU You-hong, LIU Kai, WANG Li-zhi, YANG Xian-li, WANG Wen-long, DING Guo-hua, JIANG Hui, REN Yang, JIANG Shu-kun. 2023. Analyses and identifications of quantitative trait loci and candidate genes controlling mesocotyl elongation in rice. Journal of Integrative Agriculture, 22(2): 325-340.

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