海岛棉叶绿素含量的全基因组关联分析及候选基因预测

doi:10.3864/j.issn.0578-1752.2025.10.002

Abstract

Abstract:

【Objective】 Chlorophyll, as the core pigment of plant photosynthesis, directly affects the photosynthetic efficiency and yield of plants. By mining molecular markers and candidate genes related to chlorophyll in Sea-island cotton, we can provide a theoretical basis for the improvement of Sea-island cotton varieties. 【Method】 Using 203 sea-island cotton varieties as research objects, the chlorophyll content of sea-island cotton in three stages (budding stage, flowering stage, and boll stage) was measured in 4 environments (2 points in 2 years), and the chlorophyll content of sea-island cotton in 4 environments was measured. Correlation analysis was performed on the chlorophyll content, and the whole-genome resequencing data and the BLUP value of the chlorophyll content were used for genome-wide correlation analysis to screen candidate genes related to chlorophyll content. 【Result】 Descriptive statistics of chlorophyll content in the four environments showed that the chlorophyll content at bud stage, flowering stage and bell stage were normally distributed across years and locations, indicating that the trait is a quantitative trait controlled by multiple genes. Chlorophyll content varied significantly across growth periods and was significantly affected by environment, with correlation coefficients of 0.021-0.287 for chlorophyll content at bud stage, 0.017-0.180 at flowering stage and -0.118-0.212 at bell stage. GWAS research results screened out a total of 52 significant SNPs sites. Among them, 20, 20 and 12 significant SNP sites were screened in the bud stage, flowering stage and boll stage respectively, mainly distributed on chromosomes such as A05, A06, D05, D06 and D10. By annotating significant sites, a total of 80 candidate genes were annotated, including GB_A05G0103, GB_A05G0104, GB_A05G0105, GB_A05G0106, GB_A05G0107, GB_A05G0108, GB_A05G0109, GB_A05G0110, GB_A05G0111 and GB_A 05G0112 and other 10 genes are in type I (4 environments) The flowering stage and the flowering stage of type Ⅱ (two environments in northern Xinjiang) are all annotated. GB_A06G1512 and GB_A06G1513 are annotated in the flowering stage and boll stage of typeⅠand the flowering stage of typeⅡ. GB_D09G0836, GB_D09G0837 and GB_D09G0838 are annotated in the florescence and boll stage of typeⅠand typeⅡ. The flowering stages are all annotated. Nine genes related to chlorophyll content were identified through relative expression analysis. Among them, genes such as GB_A05G0097, GB_A05G0093 and GB_D05G0109 play important roles in chlorophyll metabolism, photosynthesis and plant stress resistance. 【Conclusion】 There are significant differences in the chlorophyll content of sea-island cotton at different growth stages, and are significantly affected by the environment. A total of 52 loci related to the chlorophyll content of sea-island cotton were detected, and nine genes were found to be candidate genes for chlorophyll in sea-island cotton.

Key words: Gossypium barbadense, chlorophyll, genome-wide association analysis, bud stage, flowering stage, boll stage

SHI ShunYu, YANG Tao, PANG Bo, LI Jing, LIN YiFeng, WANG ZhengRui, FU LinCheng, ABUDUBEK Zalgamali, GAO WenWei, WU PengHao. Genome-Wide Association Analysis and Prediction of Candidate Genes for Chlorophyll Content in Gossypium barbadense[J].Scientia Agricultura Sinica, 2025, 58(10): 1878-1895.

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Figures/Tables 12

Table 1

Table 2

Fig. 1

Fig. 2

Fig. 3

Fig. 4

Table 3

GWAS analysis of SNP loci significant"

时期 Stage	染色体 Chr.	位点 SNP	位置 Position (bp)	域值 Log₁₀(P)	贡献率 R² (%)
typeⅠ-蕾期 type I-BU	D06	D06__45046684	45046684	5.23E-07	11.71
	D06	D06__45046727	45046727	7.35E-07	11.48
	A06	A06__97133658	97133658	1.11E-06	11.13
	D06	D06__45046692	45046692	1.18E-06	11.07
	A06	A06__97133639	97133639	1.48E-06	10.88
	A06	A06__75682296	75682296	1.53E-06	11.00
	A05	A05__1015344	1015344	1.88E-06	10.68
	D06	D06__45048679	45048679	2.33E-06	10.45
	A06	A06__77381986	77381986	3.19E-06	10.18
	A06	A06__77425996	77425996	5.30E-06	9.79
	D12	D12__30721282	30721282	5.37E-06	9.82
	D12	D12__30721261	30721261	5.59E-06	9.83
	A06	A06__77244172	77244172	6.70E-06	9.63
	A06	A06__77234476	77234476	7.13E-06	9.53
	D05	D05__1148688	1148688	9.08E-06	9.28
	D03	D03__20289762	20289762	9.22E-06	9.27
	A06	A06__79031976	79031976	1.05E-05	9.16
typeⅠ-花期 typeⅠ-FL	A01	A01__90389165	90389165	2.89E-07	12.32
	A05	A05__1143105	1143105	4.33E-07	11.87
	D06	D06__9609452	9609452	2.01E-06	10.62
	D06	D06__9609444	9609444	2.88E-06	10.31
	D06	D06__9594267	9594267	5.55E-06	9.93
	D06	D06__9596411	9596411	5.65E-06	9.69
	A06	A06__84839696	84839696	6.52E-06	9.70
	A06	A06__84839628	84839628	6.80E-06	9.62
	D06	D06__9596396	9596396	7.66E-06	9.43
	D06	D06__9596403	9596403	7.66E-06	9.43
	D06	D06__9609329	9609329	7.70E-06	9.51
	A07	A07__40303394	40303394	8.30E-06	9.40
	A07	A07__33782171	33782171	8.44E-06	9.39
	D06	D06__9607739	9607739	9.09E-06	9.41
	D06	D06__9609239	9609239	1.01E-05	9.19
	A07	A07__33782163	33782163	1.04E-05	9.21
typeⅠ-铃期 typeⅠ-BO	D09	D09__33492473	33492473	2.30E-06	10.51
	D11	D11__9159215	9159215	6.86E-06	9.61
	A06	A06__84839696	84839696	8.56E-06	9.46
typeⅡ-蕾期 type II-BU	D06	D06__9609329	9609329	7.21E-06	9.57
	D06	D06__9609356	9609356	7.92E-06	9.44
	D06	D06__9609239	9609239	8.91E-06	9.30
typeⅡ-花期 typeⅡ-FL	A06	A06__84839628	84839628	7.19E-06	9.57
	A05	A05__29811660	29811660	7.60E-06	9.65
	A05	A05__1143105	1143105	8.55E-06	9.33
	D09	D09__7822269	7822269	9.98E-06	9.37
typeⅡ-铃期 typeⅡ-BO	A02	A02__75978101	75978101	3.33E-07	12.26
	D09	D09__1283330	1283330	2.89E-06	10.40
	A02	A02__75978116	75978116	4.05E-06	10.06
	D10	D10__33330685	33330685	6.28E-06	9.73
	D11	D11__54219214	54219214	9.19E-06	9.49
	D09	D09__33492473	33492473	1.02E-05	9.23
typeⅢ-铃期 typeⅢ-BO	A05	A05__25568668	25568668	8.35E-06	9.61
	A11	A11__111767796	111767796	8.81E-06	9.70
	D04	D04__33010594	33010594	1.03E-05	9.26

Table 3

Fig. 5

Fig. 6

Fig. 7

Table 4

Candidate genes annotated by GWAS analysis"

基因Gene	位置Position (bp)	功能注释Annotation
GB_A01G1746	A01:90339165-90439165	玉米野生近缘种（大刍草）颖壳结构1 Teosinte glume architecture 1
GB_A01G1747	A01:90339165-90439165	-
GB_A01G1748	A01:90339165-90439165	-
GB_A02G1377	A02:75928101-76028101	-
GB_A05G0095	A05:965344-1065344	真核翻译起始因子4G异构体1 Eukaryotic translation initiation factor isoform 4G-1
GB_A05G0096	A05:965344-1065344	基因沉默抑制蛋白3 Protein suppressor of gene silencing 3
GB_A05G0097	A05:965344-1065344	叶绿体腺苷酸核苷转运体BT1 Adenine nucleotide transporter BT1, chloroplastic
GB_A05G0098	A05:965344-1065344	未表征蛋白At2g34160 Uncharacterized protein At2g34160
GB_A05G0099	A05:965344-1065344	纤维素合成酶A催化亚基1 Cellulose synthase A catalytic subunit 1
GB_A05G0100	A05:965344-1065344	未表征RNA结合蛋白C17H9.04c Uncharacterized RNA-binding protein C17H9.04c
GB_A05G0101	A05:965344-1065344	富含亮氨酸重复序列的类受体丝氨酸LRR receptor-like serine
GB_A05G0092	A05:965344-1065344	E3泛素-蛋白连接酶CIP8 E3 ubiquitin-protein ligase CIP8
GB_A05G0093	A05:965344-1065344	纤维素合成酶A催化亚基1 Cellulose synthase A catalytic subunit 1
GB_A05G0094	A05:965344-1065344	纤维素合成酶A催化亚基7 Cellulose synthase A catalytic subunit 7
GB_A05G0103	A05:1093105-1193105	含EG45样结构域的蛋白EG45-like domain containing protein
GB_A05G0104	A05:1093105-1193105	葡聚糖内切-1,3-β-葡糖苷酶Glucan endo-1,3-beta-glucosidase
GB_A05G0105	A05:1093105-1193105	蛋白磷酸酶2C 22 Probable protein phosphatase 2C 22
GB_A05G0106	A05:1093105-1193105	吲哚-3-丙酮酸单加氧酶YUCCA4 Probable indole-3-pyruvate monooxygenase YUCCA4
GB_A05G0107	A05:1093105-1193105	TIFY 8蛋白 Protein TIFY 8
GB_A05G0108	A05:1093105-1193105	细胞周期蛋白A2-2 Cyclin-A2-2
GB_A05G0109	A05:1093105-1193105	E3泛素-蛋白连接酶At1g12760 E3 ubiquitin-protein ligase At1g12760
GB_A05G0110	A05:1093105-1193105	PHD指蛋白3 PHD finger protein 3
GB_A05G0111	A05:1093105-1193105	DnaJ同源亚家族B成员4 DnaJ homolog subfamily B member 4
GB_A05G0112	A05:1093105-1193105	-
GB_A05G2749	A05:29761660-29861660	MYB蛋白1的靶标 Target of MYB protein 1
GB_A05G2750	A05:29761660-29861660	转录延伸因子SPT5 Transcription elongation factor SPT5
GB_A05G2751	A05:29761660-29861660	-
GB_A05G2752	A05:29761660-29861660	硬脂酰-[酰基载体蛋白]9-去饱和酶6，叶绿体 Stearoyl-[acyl-carrier-protein] 9-desaturase 6, chloroplastic
GB_A05G2753	A05:29761660-29861660	UDP-葡糖醛酸：木聚糖α-葡糖醛酸转移酶1 UDP-glucuronate:xylan alpha-glucuronosyltransferase 1
GB_A06G1449	A06:77331986-77431986	未表征蛋白At2g29880 Uncharacterized protein At2g29880
GB_A06G1588	A06:97083639-97183639	鸟苷酸结合蛋白7 Guanylate-binding protein 7
GB_A06G1512	A06:84789628-84889628	SET结构域组40蛋白 Protein SET DOMAIN GROUP 40
GB_A06G1513	A06:84789628-84889628	-
GB_A07G1593	A07:33732163-33832163	贝壳杉烯酮还原酶Vestitone reductase
GB_A11G3478	A11:111717796-111817796	TMV抗性蛋白N TMV resistance protein N
GB_D04G1055	D04:32960594-33060594	丝氨酸Serine
GB_D04G1056	D04:32960594-33060594	长春碱合成酶Vinorine synthase
GB_D04G1057	D04:32960594-33060594	-
GB_D04G1058	D04:32960594-33060594	丝氨酸Serine
GB_D05G0105	D05:1098688-1198688	硼转运体4 Boron transporter 4
GB_D05G0106	D05:1098688-1198688	含EG45样结构域的蛋白EG45-like domain containing protein
GB_D05G0107	D05:1098688-1198688	葡聚糖内切-1,3-β-葡糖苷酶Glucan endo-1,3-beta-glucosidase
GB_D05G0108	D05:1098688-1198688	蛋白磷酸酶2C 22 Probable protein phosphatase 2C 22
GB_D05G0109	D05:1098688-1198688	吲哚-3-丙酮酸单加氧酶YUCCA4 Probable indole-3-pyruvate monooxygenase YUCCA4
GB_D05G0110	D05:1098688-1198688	2-氧代戊二酸依赖的双加氧酶AOP1.2 Probable 2-oxoglutarate-dependent dioxygenase AOP1.2
GB_D05G0111	D05:1098688-1198688	TIFY 8蛋白Protein TIFY 8
GB_D05G0112	D05:1098688-1198688	细胞周期蛋白A2-2 Cyclin-A2-2
GB_D05G0113	D05:1098688-1198688	E3泛素-蛋白连接酶At1g12760 E3 ubiquitin-protein ligase At1g12760
GB_D05G0114	D05:1098688-1198688	PHD指蛋白3 PHD finger protein 3
GB_D05G0115	D05:1098688-1198688	DnaJ同源亚家族B成员4 DnaJ homolog subfamily B member 4
GB_D05G0116	D05:1098688-1198688	多聚腺苷酸结合蛋白相互作用蛋白5 Polyadenylate-binding protein-interacting protein 5
GB_D06G1580	D06:44996684-45096684	含NAC结构域的蛋白73 NAC domain-containing protein 73
GB_D06G1582	D06:44996684-45096684	含EG45样结构域的蛋白EG45-like domain containing protein
GB_D09G0836	D09:33442473-33542473	线粒体含五肽重复序列的蛋白At1g61870 Pentatricopeptide repeat-containing protein At1g61870, mitochondrial
GB_D09G0837	D09:33442473-33542473	磷脂酶A I Phospholipase A I
GB_D09G0241	D09:7772269-7872269	聚半乳糖醛酸酶At3g15720 Probable polygalacturonase At3g15720
GB_D09G0242	D09:7772269-7872269	60 S核糖体输出蛋白NMD3 60S ribosomal export protein NMD3
GB_D09G0243	D09:7772269-7872269	类受体蛋白激酶At5g15080 Probable receptor-like protein kinase At5g15080
GB_D09G0244	D09:7772269-7872269	34 kDa线粒体外膜蛋白孔素Mitochondrial outer membrane protein porin of 34 kDa
GB_D09G0245	D09:7772269-7872269	果胶酸裂解酶7 Probable pectate lyase 7
GB_D09G0058	D09:1233330-1333330	-
GB_D09G0059	D09:1233330-1333330	含核糖体L1结构域的蛋白1 Ribosomal L1 domain-containing protein 1
GB_D09G0060	D09:1233330-1333330	含五肽重复序列的蛋白At4g21190 Pentatricopeptide repeat-containing protein At4g21190
GB_D09G0061	D09:1233330-1333330	氨基酸通透酶BAT1同源物Amino-acid permease BAT1 homolog
GB_D09G0838	D09:33442473-33542473	磷脂酶A 1 Phospholipase A 1
GB_D10G1608	D10:33280685-33380685	-
GB_D11G1082	D11:9109215-9209215	Rho GTPase激活蛋白3 Rho GTPase-activating protein 3
GB_D11G1083	D11:9109215-9209215	转录因子MYC4 Transcription factor MYC4
GB_D11G1084	D11:9109215-9209215	-
GB_D11G1085	D11:9109215-9209215	CBL相互作用的丝氨酸残基或蛋白CBL-interacting serine
GB_D11G1086	D11:9109215-9209215	-
GB_D11G1087	D11:9109215-9209215	异质性核核糖核蛋白Q Heterogeneous nuclear ribonucleoprotein Q
GB_D11G1088	D11:9109215-9209215	IQ结构域蛋白1 Protein IQ-DOMAIN 1
GB_D11G1089	D11:9109215-9209215	含NAC结构域的蛋白43 NAC domain-containing protein 43
GB_D11G2706	D11:54169214-54269214	囊泡相关蛋白2-2 Vesicle-associated protein 2-2
GB_D11G2707	D11:54169214-54269214	钠离子Sodium
GB_D11G2708	D11:54169214-54269214	-
GB_D11G2709	D11:54169214-54269214	E3泛素-蛋白连接酶类RING1 E3 ubiquitin-protein ligase RING1-like
GB_D12G1060	D12:30671261-30771261	质膜型ATP酶9 ATPase 9, plasma membrane-type
GB_D12G1061	D12:30671261-30771261	蛋白CAJ1 Protein CAJ1

Table 4

Fig. 8

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时期 Stage	地点 Environment	年份 Year	最小值 Min	最大值 Max	均值±标准差 Mean±SD	偏度 Skewness	峰度 Kurtosis	变异系数 CV (%)
蕾期 BU	南疆 South Xinjiang	2023	26.97	55.57	38.62±3.93	0.111	-0.117	10.18
	南疆 South Xinjiang	2024	25.97	56.66	43.13±4.94	-0.076	-0.309	11.46
	北疆 North Xinjiang	2023	32.70	69.83	50.06±5.07	-0.077	0.092	10.14
	北疆 North Xinjiang	2024	24.27	53.60	40.28±4.11	0.049	-0.029	10.20
花期 FL	南疆 South Xinjiang	2023	31.56	56.33	44.23±3.28	0.212	0.44	7.42
	南疆 South Xinjiang	2024	30.25	62.12	48.44±3.88	-0.327	0.561	8.01
	北疆 North Xinjiang	2023	32.47	73.13	51.29±5.06	-0.073	0.459	9.86
	北疆 North Xinjiang	2024	36.23	65.20	53.03±4.43	-0.265	0.203	8.35
铃期 BO	南疆 South Xinjiang	2023	35.68	58.87	46.73±2.89	0.076	0.335	6.19
	南疆 South Xinjiang	2024	32.92	66.47	52.25±4.15	-0.544	0.832	7.93
	北疆 North Xinjiang	2023	30.80	88.43	52.45±5.61	-0.017	0.99	10.69
	北疆 North Xinjiang	2024	40.20	65.13	54.99±3.79	-0.137	-0.168	6.90

Genome-Wide Association Analysis and Prediction of Candidate Genes for Chlorophyll Content in Gossypium barbadense

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基因Gene	引物序列Primer sequence (5′-3′)
GB_A05G0097	F: CCATCATTGCGTTCCCTCA R: CCACTTCAATGCGTTGCTCTT
GB_A05G0093	F: AGGAGATTGGATGGATTTATGG R: CGAAGCACTTGGTTCAGACGA
GB_A05G0094	F: CTCCAAAGGGACCTAAGCG R: TTGTCATCTTCGGCTGCTTC
GB_D05G0108	F: AGGCGGAGACTTCAAGAGCA R: GAAAGCAAACCACCACAACAG
GB_D05G0111	F: TTCATCTGCGATAGTGCCAAGT R: CGTGAGCCTGACCACCATAA
GB_D09G0241	F: ATTCTTTTATCGGCACTGGG R: TTCGCACATGCACTTCCTC
GB_D11G2706	F: AGGAACTGGCGCTGTTGAG R: CACTGCATGATTGTTGCTGGA
GB_A05G0104	F: CTATCAAGCCAATGGTCGTCA R: CAAGGTAGCCAAAGAAATCACG
GB_A05G2753	F: GGTTGATAGAAGGGAGGCTGAG R: TGTTGATTGCTGGCGGTGT
GB_A06G1512	F: TGCCAACATCAGTCGAAGAA R: CCAAACTCGCCTCCAAATAC
GB_D09G0837	F: GCACTCAGTCCTCTGCTTTCTC R: TGCCACCAACCATGATTTCT

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