中国高粱株高和节间数全基因组关联分析及候选基因预测

doi:10.3724/SP.J.1006.2025.44051

Abstract

Abstract:

An appropriate reduction in plant height is essential for improving nutrient utilization efficiency and lodging resistance, both of which significantly contribute to achieving high and stable yields. This study investigated 242 Chinese sorghum accessions to elucidate the genetic mechanisms underlying plant height. A genome-wide association study (GWAS) was performed using 2,015,850 single nucleotide polymorphisms (SNPs) to analyze plant height, internode number, and internode length across seven environments. The results showed that the phenotypic variation coefficients for plant height, internode number, and internode length ranged from 13.47% to 30.06%, with absolute skewness and kurtosis values less than 1 under all conditions. Using two association models (Blink and FarmCPU), the GWAS identified 118 quantitative trait nucleotides (QTNs) significantly associated with the three traits across 10 chromosomes. Specifically, 60, 37, and 32 QTNs were significantly associated with plant height, internode number, and internode length, respectively. Eight QTNs were co-located for both plant height and internode number, while three QTNs were co-located for internode length. Through sequence analysis and functional annotation of candidate genes, 14 genes related to plant height and internode number were identified within or near the confidence intervals of 12 QTNs. These genes were homologous to those involved in sugar metabolism, hormone synthesis and signaling, and cell division in rice and maize. Selective sweep analysis revealed strong selection pressure on the candidate gene Sobic.001G510400 on chromosome 1 in Chinese sorghum populations, resulting in the formation of Hap1, which is dominant in northern dwarf sorghum, and Hap2, which is dominant in southern tall sorghum. Significant expression differences of this gene were observed between the northern accession 871255 (Hap1) and the southern accession Hongyingzi (Hap2). These findings provide a theoretical foundation for the genetic improvement of plant height in Chinese sorghum varieties.

Key words: sorghum, plant height, internode number, genome-wide association analysis, GWAS, candidate genes

XU Jian-Xia, DING Yan-Qing, CAO Ning, CHENG Bin, GAO Xu, LI Wen-Zhen, ZHANG Li-Yi. Genome-wide association analysis and prediction of candidate genes for plant height and internode number in Chinese sorghum[J].Acta Agronomica Sinica, 2025, 51(3): 568-585.

Figures/Tables 17

Table 1

Table 2

Fig. 1

Fig. 2

Table 3

Table 4

Summary of significantly associated loci for plant height, internode number, and internode length across different environments"

数量性状核苷酸 QTN	染色体 Chr.	位置 Position	次等等位基因频率 MAF	效应值 Effect	-log₁₀(P)- value	性状 Trait	环境+模型 Environment + Model
QTN1.2405118	Chr.01	2,405,118	0.29	-0.27	8.62	IN	2018GY (FarmCPU)
QTN1.2551955	Chr.01	2,551,955	0.49	-0.14	7.90	IN	BLUP (FarmCPU)
QTN1.4569288	Chr.01	4,569,288	0.02	-1.36	15.28	IN	2019HZ (FarmCPU)
QTN1.5144542	Chr.01	5,144,542	0.30	12.59	8.33	PH	2020GY (FarmCPU)
QTN1.5629263	Chr.01	5,629,263	0.20	10.10	8.22	PH	BLUP (FarmCPU)
QTN1.7184266	Chr.01	7,184,266	0.01	1.86	9.32	IN	2019LS (FarmCPU), 2021GY (Blink, FarmCPU)
QTN1.19414155	Chr.01	19,414,155	0.25	1.64	8.20	IL	2021GY (FarmCPU)
QTN1.23001725	Chr.01	23,001,725	0.01	2.16	7.36	IN	2019LS (FarmCPU)
QTN1.52105747	Chr.01	52,105,747	0.01	-39.48	7.42	PH	2018GY (FarmCPU)
QTN1.57894341	Chr.01	57,894,341	0.23	0.55	18.60	IN	2021GY (FarmCPU)
QTN1.73232722	Chr.01	73,232,722	0.08	17.86	8.08	PH	BLUP (FarmCPU)
QTN1.75754022	Chr.01	75,754,022	0.02	NA	9.10	PH	2019HZ (Blink)
QTN1.75986905	Chr.01	75,986,905	0.18	8.14	8.77	PH	2020LD (FarmCPU)
QTN1.77964551	Chr.01	77,964,551	0.48	NA	11.19	PH	2019GY (Blink), 2020GY (FarmCPU), 2021GY (Blink, FarmCPU)
QTN2.5369719	Chr.02	5,369,719	0.38	-10.54	8.52	PH	2018GY (FarmCPU)
QTN2.5571151	Chr.02	5,571,151	0.45	11.61	13.47	PH	BLUP (FarmCPU, Blink)
QTN2.10544191	Chr.02	10,544,191	0.08	NA	7.72	IL	2019HZ (Blink)
QTN2.36051465	Chr.02	36,051,465	0.11	-1.98	7.83	IL	2021GY (FarmCPU)
QTN2.61222038	Chr.02	61,222,038	0.15	0.45	13.64	IN	2018GY (FarmCPU), 2020LD (FarmCPU)
QTN2.61222038	Chr.02	61,222,038	0.15	0.45	13.64	PH	2019HZ (Blink), 2020LD (FarmCPU), BLUP (FarmCPU)
QTN2.61553618	Chr.02	61,553,618	0.07	0.59	9.66	IN	2020GY (FarmCPU), 2021GY (FarmCPU)
QTN2.71720401	Chr.02	71,720,401	0.05	NA	7.22	PH	2019HZ (Blink)
QTN3.3169459	Chr.03	3,169,459	0.06	-27.36	12.20	PH	2018GY (Blink, FarmCPU)
QTN3.3838811	Chr.03	3,838,811	0.04	3.35	7.39	IL	2020GY (FarmCPU)
QTN3.9730138	Chr.03	9,730,138	0.17	-1.64	6.77	IL	2021GY (FarmCPU)
QTN3.27015392	Chr.03	27,015,392	0.01	41.33	6.75	PH	2021GY (FarmCPU)
QTN3.36482112	Chr.03	36,482,112	0.08	-26.89	8.80	PH	202119 (FarmCPU)
QTN3.47562291	Chr.03	47,562,291	0.05	NA	6.69	PH	2019GY (Blink)
QTN3.51305296	Chr.03	51,305,296	0.02	-45.60	7.36	PH	2020GY (FarmCPU)
QTN3.52695022	Chr.03	52,695,022	0.17	NA	8.14	IN	BLUP(Blink)
QTN3.53396433	Chr.03	53,396,433	0.18	NA	13.06	IN	2020GY (Blink, FarmCPU)
QTN3.53699753	Chr.03	53,699,753	0.15	0.78	14.87	PH	2019GY(FarmCPU)
QTN3.53699753	Chr.03	53,699,753	0.15	0.78	14.87	IN	2019HZ (FarmCPU)
QTN3.66783610	Chr.03	66,783,610	0.25	0.31	7.84	IN	2020LD (FarmCPU)
QTN3.67461402	Chr.03	67,461,402	0.03	2.74	11.86	IN	2019GY (FarmCPU)
QTN3.69982563	Chr.03	69,982,563	0.07	0.52	18.31	IN	BLUP (Blink, FarmCPU)
QTN3.71309333	Chr.03	71,309,333	0.44	0.69	9.21	IL	BLUP (FarmCPU)
QTN3.72489056	Chr.03	72,489,056	0.03	NA	8.78	IL	2020LD
QTN3.72974611	Chr.03	72,974,611	0.24	NA	7.06	PH	2019GY (Blink)
QTN4.21358166	Chr.04	21,358,166	0.03	-7.55	6.91	IL	2021GY (FarmCPU)
QTN4.24740647	Chr.04	24,740,647	0.03	-7.58	6.94	IL	2020GY (FarmCPU)
QTN4.39744627	Chr.04	39,744,627	0.06	-3.06	10.06	IL	2019LS (Blink), 2019LS (FarmCPU), 2021GY (FarmCPU)
QTN4.51304388	Chr.04	51,304,388	0.19	-16.98	9.16	PH	2019GY (FarmCPU)
QTN4.56405572	Chr.04	56,405,572	0.44	0.17	6.87	IN	2020LD (FarmCPU)
QTN4.57121231	Chr.04	57,121,231	0.15	-1.48	9.36	IL	2021GY (FarmCPU)
QTN4.57121231	Chr.04	57,121,231	0.15	-1.48	9.36	PH	2019LS (Blink)
QTN4.62261029	Chr.04	62,261,029	0.50	1.22	9.06	IL	2020GY (FarmCPU)
QTN4.63570248	Chr.04	63,570,248	0.04	-0.36	7.12	IN	BLUP (FarmCPU)
QTN4.65266850	Chr.04	65,266,850	0.43	11.00	12.76	PH	2018GY (FarmCPU)
QTN4.65266850	Chr.04	65,266,850	0.43	11.00	12.76	IL	2020LD (FarmCPU), BLUP (FarmCPU)
QTN4.65863171	Chr.04	65,863,171	0.4	14.04	13.22	IN	BLUP (FarmCPU)
QTN4.65863171	Chr.04	65,863,171	0.4	14.04	13.22	PH	2020GY (Blink, FarmCPU), 2021GY (FarmCPU), BLUP (FarmCPU)
QTN5.225941	Chr.05	225,941	0.06	-29.88	9.55	PH	2018GY (FarmCPU)
QTN5.17438732	Chr.05	17,438,732	0.06	2.29	7.77	IL	2021GY (FarmCPU)
QTN5.20666756	Chr.05	20,666,756	0.01	78.55	9.92	PH	2019GY (FarmCPU)
QTN5.35025393	Chr.05	35,025,393	0.15	1.66	7.36	IL	2021GY (FarmCPU)
QTN5.61015103	Chr.05	61,015,103	0.24	-16.48	7.93	PH	2021GY (FarmCPU)
QTN5.65444056	Chr.05	65,444,056	0.01	-56.28	7.83	PH	2018GY (FarmCPU)
QTN5.70860912	Chr.05	70,860,912	0.25	-18.44	11.54	PH	2018GY (FarmCPU), 2019GY (FarmCPU), 2021GY (FarmCPU)
QTN5.70860912	Chr.05	70,860,912	0.25	-18.44	11.54	IN	2018GY (FarmCPU)
QTN6.6070840	Chr.06	6,070,840	0.01	1.54	7.26	IN	2019HZ (FarmCPU)
QTN6.6720303	Chr.06	6,720,303	0.05	-3.41	8.91	IL	2020GY (FarmCPU)
QTN6.11512672	Chr.06	11,512,672	0.08	-21.11	9.44	PH	2018GY (FarmCPU)
QTN6.14112048	Chr.06	14,112,048	0.03	NA	9.66	IL	2021GY (Blink)
QTN6.17354113	Chr.06	17,354,113	0.10	-0.89	12.69	IN	2019HZ (FarmCPU)
QTN6.19368812	Chr.06	19,368,812	0.03	0.47	7.00	IN	BLUP (FarmCPU)
QTN6.20384517	Chr.06	20,384,517	0.04	3.43	8.71	IL	2020GY (FarmCPU,Blink)
QTN6.21804125	Chr.06	21,804,125	0.12	-0.52	8.37	IN	2019HZ (FarmCPU)
QTN6.30195457	Chr.06	30,195,457	0.01	NA	10.43	IN	2018GY (Blink)
QTN6.39969911	Chr.06	39,969,911	0.31	NA	7.65	IN	2018GY (Blink)
QTN6.47858747	Chr.06	47,858,747	0.17	NA	7.38	PH	BLUP (Blink)
QTN6.51781734	Chr.06	51,781,734	0.34	1.58	10.43	IL	2021GY (FarmCPU)
QTN6.58083889	Chr.06	58,083,889	0.07	2.31	7.53	IL	2021GY (FarmCPU)
QTN7.1772505	Chr.07	1,772,505	0.31	1.09	7.83	IL	2021GY (FarmCPU)
QTN7.2186032	Chr.07	2,186,032	0.07	NA	9.09	PH	2019LS (Blink)
QTN7.26630649	Chr.07	26,630,649	0.01	54.39	17.39	PH	2020LD (Blink, FarmCPU)
QTN7.42714173	Chr.07	42,714,173	0.15	-1.03	8.73	IL	BLUP (FarmCPU)
QTN7.42714173	Chr.07	42,714,173	0.15	-1.03	8.73	PH	2018GY (FarmCPU)
QTN7.49687684	Chr.07	49,687,684	0.09	NA	8.32	IL	2019HZ (FarmCPU, Blink)
QTN7.55183398	Chr.07	55,183,398	0.04	-3.34	6.92	IL	2020GY (FarmCPU)
QTN7.56139617	Chr.07	56,139,617	0.01	NA	10.10	IN	2019HZ (Blink, FarmCPU)
QTN7.58438538	Chr.07	58,438,538	0.34	0.51	10.74	IN	2018GY (FarmCPU)
QTN7.59393707	Chr.07	59,393,707	0.02	NA	12.03	PH	BLUP (Blink)
QTN7.59653890	Chr.07	59,653,890	0.20	NA	10.82	PH	2019LS (Blink), 2020LD (FarmCPU)
QTN7.59721216	Chr.07	59,721,216	0.15	21.54	7.48	PH	2019GY (FarmCPU), 2020GY (FarmCPU), BLUP (FarmCPU)
QTN7.60501279	Chr.07	60,501,279	0.04	26.10	10.81	PH	2018GY (Blink, FarmCPU)
QTN7.60940816	Chr.07	60,940,816	0.10	-1.92	8.70	IL	2020GY (FarmCPU)
QTN7.62144455	Chr.07	62,144,455	0.06	-4.42	14.15	IL	2021GY (FarmCPU)
QTN8.2105446	Chr.08	2,105,446	0.11	-18.15	8.47	PH	BLUP (FarmCPU)
QTN8.4977795	Chr.08	4,977,795	0.07	27.21	11.93	PH	2018GY (FarmCPU), 2019HZ (Blink), 2021GY (FarmCPU)
QTN08.8249188	Chr.08	8,249,188	0.34	13.21	9.24	PH	BLUP (FarmCPU)
QTN8.8955240	Chr.08	8,955,240	0.01	72.34	11.00	PH	2020GY (FarmCPU)
QTN8.13232192	Chr.08	13,232,192	0.04	-97.42	7.04	PH	2020GY (FarmCPU)
QTN8.13747177	Chr.08	13,747,177	0.12	-17.00	10.04	PH	2020LD (FarmCPU)
QTN8.18073491	Chr.08	18,073,491	0.18	0.36	8.72	IN	2020LD (FarmCPU)
QTN8.46279959	Chr.08	46,279,959	0.24	15.75	6.66	PH	2021GY (FarmCPU)
QTN8.50392737	Chr.08	50,392,737	0.41	10.55	10.18	PH	2018GY (FarmCPU)
QTN8.57976551	Chr.08	57,976,551	0.38	6.20	8.01	PH	2020LD (FarmCPU)
QTN8.57976551	Chr.08	57,976,551	0.38	6.20	8.01	IN	BLUP (Blink)
QTN8.59708198	Chr.08	59,708,198	0.46	22.46	20.80	PH	2019GY (Blink, FarmCPU), 2020GY (Blink, FarmCPU), 2021GY (FarmCPU), BLUP (FarmCPU)
QTN8.59708198	Chr.08	59,708,198	0.46	22.46	20.80	IN	2018GY (FarmCPU), 2019GY (Blink), 2019HZ (FarmCPU), 2020GY (FarmCPU), 2021GY (FarmCPU), BLUP (FarmCPU)
QTN8.60514221	Chr.08	60,514,221	0.04	4.24	11.16	IL	2021GY (FarmCPU)
QTN8.61141049	Chr.08	61,141,049	0.10	NA	6.72	PH	2020LD (Blink)
QTN9.9011331	Chr.09	9,011,331	0.04	NA	8.04	IL	2021GY (Blink)
QTN9.9723995	Chr.09	9,723,995	0.02	-1.26	9.13	IN	2020GY (FarmCPU)
QTN9.13457659	Chr.09	13,457,659	0.02	-2.20	7.58	IL	BLUP (FarmCPU)
QTN9.14023575	Chr.09	14,023,575	0.04	-6.79	7.28	IL	2019GY (FarmCPU)
QTN9.16091197	Chr.09	16,091,197	0.03	4.48	6.90	IN	2019HZ (Blink)
QTN9.21770577	Chr.09	21,770,577	0.04	21.71	6.75	PH	BLUP (FarmCPU)
QTN9.24272625	Chr.09	24,272,625	0.03	-92.74	7.08	IN	2019LS (FarmCPU)
QTN9.26282863	Chr.09	26,282,863	0.12	-21.59	7.89	PH	2019GY (FarmCPU)
QTN9.40913786	Chr.09	40,913,786	0.06	NA	9.21	PH	2019HZ (Blink)
QTN9.45916233	Chr.09	45,916,233	0.06	2.86	7.86	IL	2020GY (FarmCPU)
QTN9.51292519	Chr.09	51,292,519	0.01	-63.41	7.17	PH	2019GY (FarmCPU)
QTN9.53210328	Chr.09	53,210,328	0.05	31.32	6.94	PH	2020GY (FarmCPU)
QTN9.59349793	Chr.09	59,349,793	0.49	2.91	9.54	IL	2020GY (FarmCPU), BLUP (FarmCPU, Blink)
QTN10.1694341	Chr.10	1,694,341	0.19	0.96	14.00	IN	2019GY (FarmCPU)
QTN10.1694341	Chr.10	1,694,341	0.19	0.96	14.00	PH	2018GY (Blink, FarmCPU)
QTN10.3945045	Chr.10	3,945,045	0.07	NA	8.06	IN	BLUP (Blink)
QTN10.12448273	Chr.10	12,448,273	0.11	-0.53	10.57	PH	2019GY (FarmCPU)
QTN10.12448273	Chr.10	12,448,273	0.11	-0.53	10.57	IN	2020GY (Blink, FarmCPU), 2021GY (Blink), BLUP (FarmCPU)
QTN10.12598609	Chr.10	12,598,609	0.15	16.40	10.00	PH	2020GY (FarmCPU, Blink)
QTN10.13745644	Chr.10	13,745,644	0.01	52.08	8.78	PH	2018GY (FarmCPU)
QTN10.19774145	Chr.10	19,774,145	0.02	41.69	9.73	PH	2018GY (FarmCPU)
QTN10.26748555	Chr.10	26,748,555	0.02	47.76	8.41	PH	2020GY (FarmCPU)
QTN10.34601077	Chr.10	34,601,077	0.04	0.33	7.74	IN	BLUP (FarmCPU)
QTN10.55997217	Chr.10	55,997,217	0.45	-0.16	9.49	IN	BLUP (FarmCPU)
QTN10.57784636	Chr.10	57,784,636	0.04	29.25	7.78	PH	2019GY (FarmCPU)
QTN10.60576093	Chr.10	60,576,093	0.01	31.62	6.62	PH	2020LD (FarmCPU)

Table 4

Fig. S1-A

Fig. S1-B

Fig. S1-C

Table 5

Functional annotation of candidate genes in important QTN intervals"

QTN	候选基因 Candidate gene	基因组位置 Genomic location	同源基因 Orthologous gene	基因名称 Gene name	蛋白注释 Proteins annotation	相似性 Similarity (%)
QTN1.4569288	Sobic.001G060100	Chr01:4502760−4511929	LOC_Os03g57940	CKI	酪蛋白激酶;抽穗期基因Casein kinase; heading stage gene	89
QTN1.4569288	Sobic.001G062900	Chr01:4700933−4706989	Zm00001d034383	VP8	调控分生组织发育 Regulate meristem development	95
QTN1.57894341	Sobic.001G298400	Chr01:57918398−57922897	LOC_Os07g15770	Ghd7	每穗粒数、株高和抽穗期多效性控制基因; 氮肥利用率Grains, height, and heading date gene; nitrogen utilization efficiency	58
QTN1.77964551	Sobic.001G510400	Chr01:77810869−77813714	LOC_Os03g04680	OsCYP96B4	细胞色素P450; 半矮秆 Cytochrome P450; semi-dwarf	77
QTN2.61222038	Sobic.002G221900	Chr02:61366555−61368022	LOC_Os09g27820	OsACO1	1-氨基环丙烷-1-羧酸氧化酶基因 1-aminocyclopropane-1-carboxylate oxidase gene	89
QTN3.3838811	Sobic.003G040900	Chr03:3821972−3830666	LOC_Os01g08700	OsGI	生物钟相关Gigantea	95.6
QTN3.67461402	Sobic.003G358400	Chr03:67621227−67632849	Zm00001d042843	NA1	油菜素内酯早期生物合成 Early step in brassinosteroid biosynthesis	95
QTN3.72974611	Sobic.003G425300	Chr03:72974769−72978763	Zm00001d011876	ELM1	光敏色素合成Photosensitive pigment synthesis	91
QTN3.72974611	Sobic.003G427600	Chr03:73106228−73116438	LOC_Os03g24220	VLN2	绒毛蛋白Villin	94
QTN4.56405572	Sobic.004G214100	Chr04:56389818−56395087	LOC_Os02g40030	OsNST1	核苷酸糖转运蛋白; 脆茎 Oryza sativa nucleotide sugar transport; brittle culm	96
QTN4.65266850	Sobic.004G317000	Chr04:65266844−65268995	LOC_Os02g53690	OsGRF1	生长调节因子 Growth regulating factor	85
QTN4.65863171	Sobic.004G323600	Chr04:65819834−65821680	LOC_Os02g54600	OsMKK4	丝裂原活化蛋白激酶;小粒 Mitogen activated protein Kinase; small grain	86
QTN7.59721216	Sobic.007G163800(Dw3)	Chr07:59821904−59829921	Zm00001d031871	BR2	生长素极性运输 Polar auxin transport	94
QTN7.59721216	Sobic.007G163800(Dw3)	Chr07:59821904−59829921	LOC_Os08g45030	SD8	矮秆基因; 三磷酸腺苷结合盒转运体B1 Semi-dwarf; ATP BINDING CASSETTE B1 transporter	93
QTN9.53210328	Sobic.009G176400	Chr09:53137542−53147354	LOC_Os05g40384	EUI1	长穗颈基因 elongated uppermost internode	88

Table 5

Table 6

Table 7

Fig. 3

Fig. 4

Fig. 5

Fig. 6

Table S1

QTN were located and QTL was reported in this study"

本研究定位到的QTN QTN located in this study			已报道的QTL QTL reported
QTN	染色体 Chromosome	SNP 位置 SNP position	QTL Id	出版 Publication	群体 Population	性状 Trait description	起始-结束 LG:Start-End (v3.0)
QTN1.2405118	Chr01	2405118	QHGHT1.37	Liu et al. 2019	Tx623 x S. virgatum	Plant height	1:0-4093151
QTN1.2551955	Chr01	2551955	QHGHT1.37	Liu et al. 2019	Tx623 x S. virgatum	Plant height	1:0-4093151
QTN1.4569288	Chr01	4569288
QTN1.5144542	Chr01	5144542	QHGHT1.2	Kebede et al. 2001	SC56/Tx7000	Height (plant height)	1:4862819-7562505
QTN1.5629263	Chr01	5629263
QTN1.7184266	Chr01	7184266
QTN1.19414155	Chr01	19414155
QTN1.23001725	Chr01	23001725
QTN1.52105747	Chr01	52105747	QHGHT1.5	Hart et al. 2001	BTx623/IS3620C	Height (plant height)	1:24186681-52681319
QTN1.57894341	Chr01	57894341	QHGHT1.8	Guan et al. 2011	Shihong137/L-Tian	Height (plant height)	1:54541207-58709704
QTN1.73232722	Chr01	73232722	QHGHT1.21	Mocoeur et al. 2015	E-Tian/Ji2731	Height (plant height)	1:69892099-74204679
QTN1.75754022	Chr01	75754022	QHGHT1.17	Wang et al. 2014a	IS8525/R931945-2-2	Height (plant height)	1:74818452-78396425
QTN1.75986905	Chr01	75986905	QHGHT1.17	Wang et al. 2014a	IS8525/R931945-2-2	Height (plant height)	1:74818452-78396425
QTN1.77964551	Chr01	77964551	QHGHT1.19	Parh 2005	IS8525/R931945-2-2	Height (plant height)	1:77677015-80878678
QTN2.5369719	Chr02	5369719
QTN2.5571151	Chr02	5571151
QTN2.10544191	Chr02	10544191
QTN2.36051465	Chr02	36051465	QHGHT2.6	Bouchet et al. 2017	Nested Association Mapping set US	Height (plant height)	2:20403133-48551270
QTN2.61222038	Chr02	61222038	QHGHT2.13	Liu et al. 2019	Tx623 / S. virgatum	Height (plant height)	2:60182134-66050977
QTN2.61553618	Chr02	61553618	QHGHT2.13	Liu et al. 2019	Tx623 / S. virgatum	Height (plant height)	2:60182134-66050977
QTN2.71720401	Chr02	71720401
QTN3.3169459	Chr03	3169459	QHGHT3.4	Phuong et al. 2013	IS2449/IS1488	Height (plant height)	3:3030648-6095949
QTN3.3838811	Chr03	3838811	QHGHT3.4	Phuong et al. 2013	IS2449/IS1488	Height (plant height)	3:3030648-6095949
QTN3.9730138	Chr03	9730138
QTN3.27015392	Chr03	27015392
QTN3.36482112	Chr03	36482112
QTN3.47562291	Chr03	47562291
QTN3.51305296	Chr03	51305296
QTN3.52695022	Chr03	52695022
QTN3.53396433	Chr03	53396433
QTN3.53699753	Chr03	53699753	qCNN3.1	xu et al. 2023	BTx623/HYZ	Internode number	3:53577719—55061159
QTN3.66783610	Chr03	66783610	QHGHT3.18	Bai et al. 2017	BTx623/Rio	Height (plant height)	3:65416545-69211928
QTN3.67461402	Chr03	67461402	QHGHT3.18 QHGHT3.20 QHGHT3.24	Bai et al. 2017 Harris-Shultz et al. 2015 Liu et al. 2019	BTx623/Rio HoneyDrip/Collier Tx623 / S. virgatum	Height (plant height)	3:65416545-69211928 3:67037126-67647534 3:67111051-72337616
QTN3.69982563	Chr03	69982563	QHGHT3.16	Nagaraja Reddy et al. 2013	M35-1/B35	Height (plant height)	3:69933510-72862046
QTN3.71309333	Chr03	71309333
QTN3.72489056	Chr03	72489056
QTN3.72974611	Chr03	72974611	QHGHT3.16	Nagaraja Reddy et al. 2013	M35-1/B35	Height (plant height)	3:69933510-72862046
QTN4.21358166	Chr04	21358166	QHGHT4.1 QHGHT4.10	Mocoeur et al. 2015 Klein et al. 2001	E-Tian/Ji2731 RTx430/Sureno	Height (plant height) Height (plant height)	4:10150746-51097958 4:13362712-50084108
QTN4.24740647	Chr04	24740647
QTN4.39744627	Chr04	39744627
QTN4.51304388	Chr04	51304388
QTN4.56405572	Chr04	56405572	qCNN4.2 QHGHT4.16 QHGHT4.13	xu et al. 2023 Mocoeur et al. 2015 Nagaraja Reddy et al. 2013	BTx623/HYZ E-Tian/Ji2731 M35-1/B35	Internode number Height (plant height) Height (plant height)	4:55918714-57111301 4:53628830-61766744 4:55962847-61572196
QTN4.57121231	Chr04	57121231	QHGHT4.16 QHGHT4.13	Mocoeur et al. 2015 Nagaraja Reddy et al. 2013	E-Tian/Ji2731 M35-1/B35	Height (plant height) Height (plant height)	4:53628830-61766744 4:55962847-61572196
QTN4.62261029	Chr04	62261029
QTN4.63570248	Chr04	63570248
QTN4.65266850	Chr04	65266850
QTN4.65863171	Chr04	65863171
QTN5.225941	Chr05	225941
QTN5.17438732	Chr05	17438732	QHGHT5.6	Shiringani et al. 2010	M71/SS79	Height (plant height)	5:11107972-52515528
QTN5.20666756	Chr05	20666756
QTN5.35025393	Chr05	35025393
QTN5.61015103	Chr05	61015103	QINTN5.1	Zhao et al. 2016	Sorghum Association Panel (SAP)	Internode number	5:60730347-61689875
QTN5.65444056	Chr05	65444056
QTN5.70860912	Chr05	70860912
QTN6.6070840	Chr06	6070840	QHGHT6.7	Wang et al. 2012	mini-core set	Height (plant height)	6:4424055-7760215
QTN6.6720303	Chr06	6720303	QHGHT6.7	Wang et al. 2012	mini-core set	Height (plant height)	6:4424055-7760215
QTN6.11512672	Chr06	11512672	QHGHT6.5 QHGHT6.6	Brown et al. 2006 Feltus et al. 2006	BTx623/IS3620C	Height (plant height)	6:3153035-14654536 6:3472068-20655330
QTN6.14112048	Chr06	14112048	QHGHT6.5	Brown et al. 2006	BTx623/IS3620C	Height (plant height)	6:3153035-14654536
QTN6.17354113	Chr06	17354113	QHGHT6.6	Feltus et al. 2006	BTx623/IS3620C	Height (plant height)	6:3472068-20655330
QTN6.19368812	Chr06	19368812
QTN6.20384517	Chr06	20384517
QTN6.21804125	Chr06	21804125	QSILN6.1	Hilley et al. 2016	Hegari/80M	Stem internode length	6:21205500-44995144
QTN6.30195457	Chr06	30195457	QHGHT6.83 QHGHT6.89	Zhao et al. 2016 Yamaguchi et al. 2016	Sorghum Association Panel (SAP) bmr-6/SIL-05	Height (plant height)	6:27834658-38482472 6:22445901-43378078
QTN6.39969911	Chr06	39969911	QHGHT6.89	Yamaguchi et al. 2016	bmr-6/SIL-05	Height (plant height)	6:22445901-43378078
QTN6.47858747	Chr06	47858747	QHGHT6.58	Srinivas et al. 2009	296B/IS18551	Height (plant height)	6:47229819-48711265
QTN6.51781734	Chr06	51781734	QHGHT6.63	Kebede et al. 2001	SC56/Tx7000	Height (plant height)	6:51611228-52465988
QTN6.58083889	Chr06	58083889	QPLEN6.19	Parh 2005	IS8525/R931945-2-2	Panicle length	6:56618606-61260478
QTN7.1772505	Chr07	1772505
QTN7.2186032	Chr07	2186032
QTN7.26630649	Chr07	26630649	QHGHT7.8	Rami et al. 1998	IS2807/379	Height (plant height)	7:10020434-53294723
QTN7.42714173	Chr07	42714173	QHGHT7.8 QHGHT7.11	Rami et al. 1998 Madhusudhana and Patil 2013	IS2807/379 296B/IS18551	Height (plant height)	7:10020434-53294723 7:42199948-57729128
QTN7.49687684	Chr07	49687684	QHGHT7.8 QHGHT7.11	Rami et al. 1998 Madhusudhana and Patil 2013	IS2807/379 296B/IS18551	Height (plant height)	7:10020434-53294723 7:42199948-57729128
QTN7.55183398	Chr07	55183398	QHGHT7.11	Madhusudhana and Patil 2013	296B/IS18551	Height (plant height)	7:42199948-57729128
			QHGHT7.14	Madhusudhana and Patil 2013	296B/IS18551	Height (plant height)	7:52284804-57820875
			QSILN7.1	Hilley et al. 2016	Hegari/80M	Stem internode length	7:53924374-57857968
QTN7.56139617	Chr07	56139617	QHGHT7.14 QHGHT7.15	Madhusudhana and Patil 2013 Srinivas et al. 2009	296B/IS18551	Height (plant height)	7:52284804-57820875 7:55190663-57760757
QTN7.58438538	Chr07	58438538	QHGHT7.66 QHGHT7.67	Wang et al. 2016	Shihong137/L-Tian	Height (plant height)	7:57683232-58901776 7:57716834-58775268
QTN7.59393707	Chr07	59393707	QHGHT7.91 QHGHT7.45 QHGHT7.76 QHGHT7.46 QHGHT7.83	Liu et al. 2019 Pereira and Lee 1995 Yamaguchi et al. 2016 Madhusudhana and Patil 2013 Girma et al. 2019	Tx623 x S. virgatum CK60/PI229828 bmr-6/SIL-05 296B/IS18551 Ethiopian landraces	Height (plant height)	7:59257250-61520522 7:59531861-61538775 7:59541977-61443045 7:59551731-61527847 7:59554149-61141251
QTN7.59653890	Chr07	59653890
QTN7.59721216	Chr07	59721216
QTN7.60501279	Chr07	60501279
QTN7.60940816	Chr07	60940816
QTN7.62144455	Chr07	62144455	QHGHT7.57	Parh 2005	IS8525/R931945-2-2	Height (plant height)	7:61806978-65460255
			QHGHT7.55	Madhusudhana and Patil 2013	296B/IS18551	Height (plant height)	7:61910344-63327593
			QHGHT7.56	Feltus et al. 2006	BTx623/S. propinquum	Height (plant height)	7:61971712-64586189
QTN8.2105446	Chr08	2105446	QSLEN8.1	Wang et al. 2014b	Shihong137/L-Tian	Shoot length (seedling stage)	8:1896920-3249436
QTN8.4977795	Chr08	4977795
QTN8.8249188	Chr08	8249188	QHGHT8.2	Shiringani et al. 2010	M71/SS79	Height (plant height)	8:8198323-56470074
QTN8.8955240	Chr08	8955240
QTN8.13232192	Chr08	13232192
QTN8.13747177	Chr08	13747177
QTN8.18073491	Chr08	18073491
QTN8.46279959	Chr08	46279959
QTN8.50392737	Chr08	50392737
QTN8.57976551	Chr08	57976551	QHGHT8.4	Shehzad and Okuno 2015	Red Kafir/Takakibi (F2)	Height (plant height)	8:56697504-59292212
QTN8.59708198	Chr08	59708198	qCNN8.1	xu et al. 2023	BTx623/HYZ	Internode number	8:58253026—60762263
QTN8.60514221	Chr08	60514221	qCNN8.1	xu et al. 2023	BTx623/HYZ	Internode number	8:58253026—60762263
QTN8.61141049	Chr08	61141049
QTN9.9011331	Chr09	9011331	QHGHT9.5	Nagaraja Reddy et al. 2013	M35-1/B35	Height (plant height)	9:8157572-47755439
QTN9.9723995	Chr09	9723995
QTN9.13457659	Chr09	13457659
QTN9.14023575	Chr09	14023575
QTN9.16091197	Chr09	16091197
QTN9.21770577	Chr09	21770577
QTN9.24272625	Chr09	21554218
QTN9.26282863	Chr09	26282863
QTN9.40913786	Chr09	40913786
QTN9.45916233	Chr09	45916233
QTN9.51292519	Chr09	51292519	QHGHT9.7 QHGHT9.80	Shiringani et al. 2010 Gelli et al. 2016	M71/SS79 CK60/China17	Height (plant height)	9:50633456-52598530 9:50718886-51490320
QTN9.53210328	Chr09	53210328	QHGHT9.8 QHGHT9.10 QHGHT9.75	Feltus et al. 2006 Lin et al. 1995 Bai et al. 2017	BTx623/S.propinquum BTx623/S. propinquum BTx623/Rio	Height (plant height)	9:51845427-56983864 9:52500363-57941639 9:52719464-55273795
QTN9.59349793	Chr09	59349793	QHGHT9.79	Yamaguchi et al. 2016	bmr-6/SIL-05	Height (plant height)	9:59192467-59398238
QTN10.1694341	Chr10	1694341	QHGHT10.13	Mocoeur et al. 2015	E-Tian/Ji2731	Height (plant height)	10:1518275-8359099
QTN10.3945045	Chr10	3945045	QHGHT10.13	Mocoeur et al. 2015	E-Tian/Ji2731	Height (plant height)	10:1518275-8359099
QTN10.12448273	Chr10	12448273	QHGHT10.16	Kong et al. 2018	BTx623/IS3620C	Height (plant height)	10:10627652-13583029
QTN10.12598609	Chr10	12598609	QHGHT10.16	Kong et al. 2018	BTx623/IS3620C	Height (plant height)	10:10627652-13583029
QTN10.13745644	Chr10	13745644	QHGHT10.17 QHGHT10.5 QHGHT10.18	Liu et al. 2019 Shiringani et al. 2010 Liu et al. 2019	Tx623 x S. virgatum M71/SS79 Tx623 x S. virgatum	Height (plant height) Height (plant height) Height (plant height)	10:8044545-51747348 10:8640125-45554247 10:9185221-52571741
QTN10.19774145	Chr10	19774145
QTN10.34601077	Chr10	34601077
QTN10.26748555	Chr10	26748555
QTN10.55997217	Chr10	55997217	QHGHT10.14	Mocoeur et al. 2015	E-Tian/Ji2731	Height (plant height)	10:52112522-56441485
QTN10.55997217	Chr10	55997217	QHGHT10.8	Madhusudhana and Patil 2013	296B/IS18551	Height (plant height)	10:52619425-56427175
QTN10.57784636	Chr10	57784636	QHGHT10.11	Rajkumar et al. 2013	E36-1/SPV570	Height (plant height)	10:56548575-60429301
QTN10.60576093	Chr10	60576093

Table S1

References 56

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来源地 Originated location	材料份数 Number of materials	来源地 Originated location	材料份数 Number of materials
辽宁Liaoning	39	吉林Jilin	5
山西Shanxi	28	贵州Guizhou	37
内蒙古Inner Mongolia	17	云南Yunnan	21
陕西Shaanxi	17	四川Sichuan	19
山东Shandong	12	湖北Hubei	10
河北Hebei	12	安徽Anhui	3
北京Beijing	11	广西Guangxi	2
黑龙江Heilongjiang	8	江苏Jiangsu	1

性状 Trait	环境 Environment	最小值 Min.	最大值 Max.	平均值 Mean	标准差 SD	变异系数 CV (%)	偏度 Skewness	峰度 Kurtosis
株高 PH	2018贵阳 2018GY	104.60	342.10	219.04	50.93	23.25	0.07	-0.46
	2019贵阳 2019GY	98.67	346.33	220.02	49.95	22.70	0.02	-0.41
	2019杭州 2019HZ	110.80	437.63	263.27	69.22	26.29	0.18	-0.38
	2019陵水 2019LS	104.33	316.00	195.05	39.77	20.39	0.41	0.14
	2020贵阳 2020GY	110.43	439.33	279.04	66.53	23.84	-0.25	-0.22
	2020乐东 2020LD	109.13	280.50	186.82	32.35	17.32	0.19	0.09
	2021贵阳 2021GY	128.50	375.33	244.60	52.89	21.63	-0.05	-0.35
节间数IN	2018贵阳 2018GY	3.80	10.50	6.58	1.45	21.99	0.35	-0.50
	2019贵阳 2019GY	3.00	11.75	6.54	1.56	23.92	0.28	-0.02
	2019杭州 2019HZ	4.00	15.33	9.00	2.70	30.06	0.45	-0.26
	2019陵水 2019LS	4.33	11.00	7.01	1.09	15.57	0.33	0.69
	2020贵阳 2020GY	5.14	13.33	9.04	1.38	15.26	-0.24	0.14
	2020乐东 2020LD	3.50	9.63	6.46	1.07	16.56	0.12	0.32
	2021贵阳 2021GY	4.80	12.75	7.90	1.40	17.74	0.49	0.98
节间长度 IL	2018贵阳 2018GY	19.62	49.72	33.68	6.10	18.11	-0.02	-0.52
	2019贵阳 2019GY	17.88	50.92	33.95	7.77	22.89	0.25	-0.53
	2019杭州 2019HZ	17.92	50.60	30.34	4.62	15.24	0.88	2.31
	2019陵水 2019LS	17.60	45.88	27.93	4.83	17.31	0.62	0.50
	2020贵阳 2020GY	13.14	47.13	30.77	5.76	18.73	-0.16	0.04
	2020乐东 2020LD	18.12	40.33	29.10	3.92	13.47	0.02	-0.23
	2021贵阳 2021GY	14.26	42.54	31.14	5.38	17.29	-0.36	-0.11

性状 Trait	均方 Mean square			方差Variance			F值 F-value			广义遗传力Broad-sense heritability
性状 Trait	基因型 Genotype	环境 Environment	基因型 ×环境 G×E	基因型 Genotype	环境 Environment	基因型 ×环境 G×E	基因型 Genotype	环境 Environment	基因型 ×环境 G×E	广义遗传力Broad-sense heritability
株高 PH	46,407.51	813,299.34	1867.31	2248.60	1155.41	551.77	196.32^**	3440.49^**	7.89^**	0.90
节间数 IN	30.45	868.82	4.00	1.33	1.26	1.17	58.64^**	1673.40^**	7.71^**	0.79
节间长度 IL	483.50	25,339.99	97.47	19.52	36.89	19.47	12.02^**	629.91^**	2.42^**	0.71

项目 Item	窗口数 Number of windows	前5%窗口数 Number of top 5% windows	前5%对应值 Top 5% of the value	前5%对应基因数 Top 5% of genes
南方_ Tajima’D South_ Tajima’D	60,150	3008	≤ -1.9081	1903
北方_ Tajima’D North_ Tajima’D	60,663	3033	≤ -1.8004	2834
南方/北方_Pi South/north_Pi	59,287	2964	≥ 7.5425	2674
南方/北方_Fst South/north_Fst	61,524	3076	≥ 0.5384	2478

QTN	候选基因 Candidate gene	基因组位置 Genomic location	南方_Tajima’D South_Tajima’D	北方_Tajima’D North_Tajima’D	南方/北方_Pi South/north_Pi	南方/北方_Fst South/north_Fst
QTN1.4569288	Sobic.001G060100	Chr.01: 4502760-4511929	0.63323	1.17192	0.70587	0.50171
QTN1.4569288	Sobic.001G062900	Chr.01: 4700933-4706989	—	—	—	—
QTN1.57894341	Sobic.001G298400	Chr.01: 57918398-57922897	-0.28265	3.70518	0.44059	0.20719
QTN1.77964551	Sobic.001G510400	Chr.01: 77810869-77813714	4.12955	-1.09660	240.75045	0.42020
QTN2.61222038	Sobic.002G221900	Chr.02: 61366555-61368022	1.63095	-0.83259	0.62484	0.24644
QTN3.3838811	Sobic.003G040900	Chr.03: 3821972-3830666	2.96779	-0.47567	4.26399	0.45506
QTN3.67461402	Sobic.003G358400	Chr.03: 67621227-67632849	-1.33349	2.21191	0.22586	0.12627
QTN3.72974611	Sobic.003G425300	Chr.03: 72974769-72978763	4.87495	-0.75596	3.53964	0.35919
QTN3.72974611	Sobic.003G427600	Chr.03: 73106228-73116438	4.11883	5.32407	0.91151	0.03476
QTN4.56405572	Sobic.004G214100	Chr.04: 56389818-56395087	2.65072	2.36931	0.76241	0.08865
QTN4.65266850	Sobic.004G317000	Chr.04: 65266844-65268995	2.35182	4.79370	0.73469	0.23975
QTN4.65863171	Sobic.004G323600	Chr.04: 65819834-65821680	-0.80385	4.90854	0.29065	0.41327
QTN7.59721216	Sobic.007G163800	Chr.07: 59821904-59829921	1.23952	-1.61676	7.32019	0.25767
QTN9.53210328	Sobic.009G176400	Chr.09: 53137542-53147354	1.69947	-1.47816	17.04476	0.44604

Genome-wide association analysis and prediction of candidate genes for plant height and internode number in Chinese sorghum

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