GWAS Combined with WGCNA of Transcriptome and Metabolome to Excavate Key Candidate Genes for Rice Anaerobic Germination

Li, Dandan; Liu, Kai; Zhao, Chuanchao; Liang, Siyi; Yang, Jing; Peng, Ziai; Xia, Aoyun; Yang, Meng; Luo, Lixin; Huang, Cuihong; Wang, Jiafeng; Huang, Ming; Xiao, Wuming; Wang, Hui; Su, Ling; Guo, Tao

doi:10.1186/s12284-023-00667-8

Rice

Table 2 The information of 27 loci of the 317 SNP loci overlapped with the reported loci

From: GWAS Combined with WGCNA of Transcriptome and Metabolome to Excavate Key Candidate Genes for Rice Anaerobic Germination

Traits	Treatment	Chromosome	Peak position (bp)	Peak value	known loci
CD	CDAN2d	1	9,773,247	5.3599	qAGP1, Liu et al. (2021a)
	CDAN2d	2	5,392,354	5.9180	qAG2.1, Kim et al. (2019)
	CDAN4d	9	21,404,841	5.8758	qCD-9-3, Yang et al. (2019)
CL	CLAN2d	12	26,942,207	5.1454	qCSA-12-2, Yang et al. (2019)
	CLAN2d	3	32,459,894	5.4106	S3_32459722, Su et al. (2021)
	CLAN3d	3	36,409,153	5.1926	qSUR3-1Rc222-SCR-14, Ghosal et al. (2019)
CSA	CSAAN2d	1	25,169,822	5.4387	qAG1, Jeong et al. (2020); S1_25099585, Su et al. (2021)
CSA	CSAAN3d	2	26,714,756	6.5526	qSSD-2, Li et al. (2020); qAG2, Septiningsih et al. (2013)
CV	CVAN2d	1	31,418,900	6.7756	qAG-1-2, Angaji et al. (2010); S1_31006962, Hsu and Tung (2015)
	CVAN2d	1	38,223,398	8.6772	qCLN1, Liu et al. (2021a)
	CVAN2d	1	38,596,277	5.6269	qCD-1, Yang et al. (2019)
	CVAN2d	2	20,748,476	5.3130	qGS2.1, Chen et al. (2012); qAG-2, Angaji et al. (2008); qAG-2-1, Angaji et al. (2010)
	CVAN2d	3	23,491,435	5.0665	qAG3-2, Liu et al. (2021a, b)
	CVAN2d	6	9,925,796	11.7983	qCSA-6 and qCV-6-1, Yang et al. (2019)
	CVAN2d	9	10,654,108	6.3812	qAG9-3, Liu et al. (2021b)
	CVAN2d	11	3,769,274	10.0400	qAG11, Jeong et al. (2020)
	CVAN3d	1	9,390,882	5.4285	qAGP1, Liu et al. (2021a)
	CVAN3d	3	8,956,500	5.2753	qAGP3, Liu et al. (2021a)
	CVAN3d	3	27,826,611	8.1694	S3_27854371, Su et al. (2021)
	CVAN3d	3	28,227,524	7.0063	S3_28290634, Su et al. (2021)
	CVAN3d	6	30,191,930	5.7992	seq-rs3121, Zhang et al. (2017)
	CVAN3d	10	12,877,840	5.0584	qAG10-1, Liu et al. (2021b)
	CVAN4d	1	9,494,163	5.1458	qAGP1, Liu et al. (2021a)
	CVAN4d	1	26,025,387	5.9391	qAG-1-2, Angaji et al. (2010)
	CVAN4d	7	4,973,098	5.2164	seq-rs3210, Zhang et al. (2017)
	CVAN4d	8	24,896,504	5.5620	seq-rs3972, Zhang et al. (2017)
	CVAN4d	12	21,775,097	5.8391	qCL-12 and qCSA-12-1, Yang et al. (2019)

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