Yang Jing, Yang Guili, Yang Meng, Su Ling, Xia Aoyun, Li Dandan, Huang Cuihong, Zhou Danhua, Liu Yongzhu, Wang Hui, Chen Zhiqiang, Guo Tao
National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China.
Front Plant Sci. 2019 Dec 13;10:1582. doi: 10.3389/fpls.2019.01582. eCollection 2019.
Seed germination and early seedling growth are important agricultural traits for developing populations of both irrigated and directly seeded rice (DSR). To investigate the genetic mechanisms underlying seed germination and early seedling growth in rice, 275 recombinant inbred lines (RILs) were genotyped in this study the genotyping-by-sequencing (GBS) approach to construct a high-density linkage bin map based on the parent-independent genotyping method. Quantitative trait loci (QTLs) for 12 traits related to seed germination and early seedling growth were analyzed. Totally, 22 additive loci were detected, after analysis of the interaction between additive QTLs and environments, five stable additive loci were obtained. Among them, loci 4, 5, 12 and 14 exhibited clear pleiotropic effects that were associated with multiple traits. Analysis of the effects of the five additive stable loci showed that a single locus increased the corresponding phenotypic value. Ten of the 275 RILs pyramided the excellent alleles of the five stable genetic loci. Most phenotypic values of the ten RILs were greater than the average values. Four RILs (G260, G342, G371, and G401) with more excellent phenotypic values were subsequently selected; these RILs could serve as donor parents of favorable alleles in the breeding process. Due to the existence of pleiotropy, the use of these genetic loci for pyramid breeding can further increase the efficiency to reach breeding goals. In addition, these five stable loci have an average physical interval of only 170 kb, we also further identified five promising candidate genes by qRT-PCR, which provides us with a basis for future cloning of these genes. Overall, this work will help broaden our understanding of the genetic control of seed germination and early seedling growth, and this study provides both a good theoretical basis and a new genetic resource for the breeding of direct-seeded rice.
种子萌发和幼苗早期生长是灌溉水稻和直播水稻（DSR）群体发育的重要农艺性状。为了研究水稻种子萌发和幼苗早期生长的遗传机制，本研究对275个重组自交系（RIL）进行了基因分型，采用简化基因组测序（GBS）方法，基于独立于亲本的基因分型方法构建了高密度连锁图谱。分析了与种子萌发和幼苗早期生长相关的12个性状的数量性状位点（QTL）。共检测到22个加性位点，通过分析加性QTL与环境之间的相互作用，获得了5个稳定的加性位点。其中，位点4、5、12和14表现出明显的多效性，与多个性状相关。对这5个加性稳定位点的效应分析表明，单个位点可增加相应的表型值。275个RIL中有10个聚合了5个稳定遗传位点的优异等位基因。这10个RIL的大多数表型值均大于平均值。随后选择了4个表型值更优异的RIL（G260、G342、G371和G401）；这些RIL可作为育种过程中有利等位基因的供体亲本。由于存在多效性，利用这些基因位点进行聚合育种可进一步提高实现育种目标的效率。此外，这5个稳定位点的平均物理间隔仅为170 kb，我们还通过qRT-PCR进一步鉴定了5个有前景的候选基因，为今后这些基因的克隆提供了依据。总体而言，本研究有助于拓宽我们对种子萌发和幼苗早期生长遗传控制的理解，为直播水稻育种提供了良好的理论基础和新的遗传资源。
