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Genome-wide association study of stem structural characteristics that extracted by a high-throughput phenotypic analysis "LabelmeP rice" in rice

文献类型： 外文期刊

作者： Li, Jianguo 1 ; Yang, Mingchong 1 ; He, Dandan 1 ; Luo, Zixuan 1 ; Li, Bo 1 ; Huang, Xiaojin 1 ; Wu, Fangxi 3 ; Xie, Guosheng 2 ; Fan, Chuchuan 2 ; Sun, Wenqiang 2 ; Yu, Sibin 2 ; Wang, Lingqiang 1 ;

作者机构： 1.Guangxi Univ, Coll Agr, State Key Lab Conservat & Utilizat Subtrop Agrobio, Nanning, Peoples R China

2.Huazhong Agr Univ, Coll Plant Sci & Technol, Natl Key Lab Crop Genet Improvement, Wuhan 430070, Peoples R China

3.Fujian Acad Agr Sci, Fujian, Peoples R China

关键词： high-throughput phenotyping; genome-wide association study; stem structure; rice

期刊名称：PLANT JOURNAL （ 影响因子：6.2； 五年影响因子：7.1 ）

ISSN： 0960-7412

年卷期： 2024 年 119 卷 4 期

页码：

收录情况： SCI

摘要： Stem is important for assimilating transport and plant strength; however, less is known about the genetic basis of its structural characteristics. In this study, a high-throughput method, "LabelmeP rice" was developed to generate 14 traits related to stem regions and vascular bundles, which allows the establishment of a stem cross-section phenotype dataset containing anatomical information of 1738 images from hand-cut transections of stems collected from 387 rice germplasm accessions grown over two successive seasons. Then, the phenotypic diversity of the rice accessions was evaluated. Genome-wide association studies identified 94, 83, and 66 significant single nucleotide polymorphisms (SNPs) for the assayed traits in 2 years and their best linear unbiased estimates, respectively. These SNPs can be integrated into 29 quantitative trait loci (QTL), and 11 of them were common in 2 years, while correlated traits shared 19. In addition, 173 candidate genes were identified, and six located at significant SNPs were repeatedly detected and annotated with a potential function in stem development. By using three introgression lines (chromosome segment substitution lines), four of the 29 QTLs were validated. LOC_Os01g70200, located on the QTL uq1.4, is detected for the area of small vascular bundles (SVB) and the rate of large vascular bundles number to SVB number. Besides, the CRISPR/Cas9 editing approach has elucidated the function of the candidate gene LOC_Os06g46340 in stem development. In conclusion, the results present a time- and cost-effective method that provides convenience for extracting rice stem anatomical traits and the candidate genes/QTL, which would help improve rice.

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