棉花60K功能位点基因芯片的制备及应用

doi:10.3724/SP.J.1006.2025.44146

Abstract

Abstract:

Cotton is the leading source of natural textile fiber and an important source of oil. However, functional locus gene chips, which can significantly improve the accuracy of breeding value assessments and breeding efficiency, remain underutilized in cotton research. In this study, we developed a 60K functional locus gene chip for cotton, leveraging high-throughput sequencing datasets, including Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq), Chromatin Immunoprecipitation sequencing (ChIP-seq) and High-throughput Chromosome Conformation Capture (Hi-C) data from diverse cotton varieties. Compared to existing cotton gene chips, this newly developed chip incorporates a higher number of functionally annotated loci with genetic variations derived from multi-dimensional data, offering richer insights into gene function. Using this gene chip in a genome-wide association study (GWAS) of cotton fiber quality traits, we identified 40 significant single nucleotide polymorphisms (SNPs) linked to fiber quality. These include twenty-five SNPs associated with fiber elongation rate (FE), five with fiber micronaire value (FM), two with fiber strength (FS), four with fiber length (FL), and four with fiber uniformity (FU). The 60K functional locus gene chip provides a powerful tool for the evaluation of cotton germplasm resources, genetic mapping, and genome-wide selection breeding. This advancement holds great promise for accelerating genomic breeding efforts, ultimately driving improvements in cotton production and quality.

Key words: cotton breeding, gene chip, cotton 60K functional locus gene chip, genome-wide association analysis, domestication selection

WANG Ya-Wen, QI Zheng-Yang, YOU Jia-Qi, NIE Xin-Hui, CAO Juan, YANG Xi-Yan, TU Li-Li, ZHANG Xian-Long, WANG Mao-Jun. Preparation of cotton 60K functional locus gene chip and its application to genetic research[J].Acta Agronomica Sinica, 2025, 51(5): 1178-1188.

Figures/Tables 12

Table S1

Cotton accessions used in this study"

栽培棉 Cultivars of G. hirsutum L.
序号 No.	材料名称 Accession name	序号 No.	材料名称 Accession name	序号 No.	材料名称 Accession name
S5	鄂棉11 Emian 11	S130	源棉10 Yuanmian 10	S255	邯7860 Han 7860
S7	Mei87-22	S133	39-38	S274	新陆中48 Xinluzhong 48
S9	晋棉17 Jinmian 17	S137	466	S275	晋棉21 Jinmian 21
S10	中植棉2 Zhongzhimian 2	S139	斯字棉4 Stoneville 4	S279	n2
S11	苏棉11 Sumian 11	148	C-450-555	280	新陆早39 Xinluzao 39
S12	泗棉3 Simian 3	S151	P09	S297	SCK321
S17	岱红岱 Daihongdai	S152	Beiersinuo	S298	光叶大籽Guangyedazimian
S18	豫棉8 Yumian 8	S154	鄂棉21 Emian 21	S300	LL
S21	斯字棉2B Stoneville 2B	S160	Zhangyang 1	S307	皖棉17 Wanmian 17
S25	鄂光棉 Eguangmian	S161	新陆中32 Xinluzhong 32	S310	黑山棉1 Heishanmian 1
S27	Nantongbian 3	S162	辽96-103 Liao 96-103	S322	晋棉29 Jinmian 29
S32	新陆中1 Xinluzhong 1	S163	陕棉1 Shaanmian 1	S323	HMJ wu
S40	陕2786 Shaan 2786	S169	敦煌77-116 Dunhuang 77-116	S324	邯109 Han 109
S42	农大94-7 Nongda 94-7	S174	大铃棉69 Dalingmian 69	S335	HC03
S44	辽金棉5 Liaojinmian 5	S176	K1543	S336	豫棉19 Yumian 19
S48	Duangguozhi 8-9	S177	新陆中75 Xinluzhong75	S337	Bawangbian
S51	陕3619 Shaan 3619	S182	晋棉20 Jinmian 20	S340	盐棉1 Yanmian 1
S52	Dunn18	S189	塔什干2 Tashigan 2	S350	华棉4 Huamian 4
S60	鄂抗棉33 Ekangmian 33	S192	晋棉13 Jinmian 13	S401	新陆中68 Xinluzhong 68
S71	豫棉5 Yumian 5	S194	Gailiangkezimian	S402	陕棉9 Shaanmian 9
S79	川7327 Chuan 7327	S198	P24	S403	岱字棉14 Deltapine cotton 14
S90	新陆早36 Xinluzao36	S204	Hopical 130263	S404	豫棉14 Yumian 14
S93	科遗181 Keyi 181	S205	鲁棉研32 Lumianyan 32	S405	苏联8908 Sulian 8908
S97	鄂抗棉7 Ekangmian 7	S208	罗甸铁籽Luodiantiezi	S406	源棉5 Yuanmian 5
S99	苏抗191 Sukang 191	S209	宾川373 Binchuan 373	S407	宁棉1 Ningmian 1
S102	中棉所19 Zhongmiansuo 19	S216	苏棉20 Sumian 20	S408	鄂抗棉33 Ekangmian 33
S107	豫棉15 Yumian 15	S217	晋棉26 Jinmian 26	S409	石远321 Shiyuan 321
S109	Pengzeyahuang	S221	HC01	S410	471guangzi
S110	益棉8 Yimian 8	S222	中25 Zhong 25	S411	商丘24 Shangqiu 24
S111	川棉98 Chuanmian 98	S224	中棉所45 Zhongmiansuo 45	S412	新陆中48 Xinluzao 48
S113	Gz Nn	S225	华东6 Huadong 6	S413	渤棉2 Bomian 2
S116	中棉所32 Zhongmiansuo 32	S235	Lixiandatao	S414	Dunn18
S117	源棉8 Yuanmian8	S244	13P041	S415	新陆早31 Xinluzao31
S121	晋棉2 Jinmian 2	S253	沙农6 Shanong 6	S416	陆长丰 Luchangfeng
半野生棉 Semi-wild accessions of G. hirsutum L.
序号 No.	材料名称 Accession name	序号 No.	材料名称 Accession name	序号 No.	材料名称 Accession name
S1387	尖斑棉1103 Jianbanmian 1103	S1419	莫利尔194 Molier 194	S1559	雷奇蒙地281 Leiqimengdi 281
S1388	尖斑棉1108K Jianbanmian 1108K	S1421	莫利尔255 Molier 255	S1560	雷奇蒙地461 Leiqimengdi 461
S1390	尖斑棉144 Jianbanmian 144	S1423	帕默尔1045A Pamoer 1045A	S1561	玛利加郎特1259 Malijialangte 1259
S1393	尖斑棉488 Jianbanmian 488	S1424	帕默尔11 Pamoer 11	S1563	玛利加郎特2304C Malijialangte 2304C
S1395	尖斑棉94 Jianbanmian 94	S1430	尤卡坦1039A Youkatan 1039A	S1564	玛利加郎特246 Malijialangte 246
S1397	阔叶棉177 Kuoyemian 177	S1431	尤卡坦1046 Youkatan 1046	S1565	玛利加郎特368 Malijialangte 368
S1399	阔叶棉21 Kuoyemian 21	S1432	尤卡坦1236 Youkatan 1236	S1566	玛利加郎特883A Malijialangte 883A
S1400	阔叶棉221 Kuoyemian 221	S1434	尤卡坦2094 Youkatan 2094	S1567	玛利加郎特904 Malijialangte 904
S1402	阔叶棉482 Kuoyemian 482	S1539	尖斑棉1103 Jianbanmian 1103	S1568	莫利尔131X Molier131X
S1403	雷奇蒙地1102 Leiqimengdi 1102	S1540	尖斑棉1108K Jianbanmian 1108K	S1569	莫利尔133 Molier 133
S1404	雷奇蒙地145 Leiqimengdi 145	S1541	尖斑棉114 Jianbanmian 114	S1571	莫利尔194 Molier 194
S1407	雷奇蒙地281 Leiqimengdi 281	S1542	尖斑棉144 Jianbanmian 144	S1573	莫利尔255 Molier 255
S1411	玛利加郎特2304C Malijialangte 2304C	S1544	尖斑棉27 Jianbanmian 27	S1575	帕默尔1045A Pamoer 1045A
S1413	玛利加郎特368 Malijialangte 368	S1545	尖斑棉488 Jianbanmian 488	S1576	帕默尔11 Pamoer 11
S1414	玛利加郎特883A Malijialangte 883A	S1547	尖斑棉94 Jianbanmian 94	S1582	尤卡坦1039A Youkatan 1039A
S1415	玛利加郎特904 Malijialangte 904	S1552	阔叶棉221 Kuoyemian 221	S1583	尤卡坦1046 Youkatan 1046
S1416	莫利尔131X Molier 131X	S1554	阔叶棉482 Kuoyemian 482	S1584	尤卡坦1236 Youkatan 1236
S1417	莫利尔133 Molier 133	S1555	雷奇蒙地1102 Leiqimengdi 1102	S1586	尤卡坦2094B Youkatan 2094B
S1418	莫利尔137X Molier 137X	S1556	雷奇蒙地145 Leiqimengdi 145	S1587	尤卡坦2094D Youkatan 2094D

Table S1

Table S2

Result of principal component analysis and the corresponding semi-wild accessions of G. hirsutum L. of each category"

序号 No.	材料名称 Accession name	所属类群 Category	序号 No.	材料名称 Accession name	所属类群 Category	序号 No.	材料名称 Accession name	所属类群 Category
S1561	玛利加郎特1259 Malijialangte1259	Cluster 4	S1411	玛利加郎特2304C Malijialangte 2304C	Cluster 1	S1402	阔叶棉482 Kuoyemian 482	Cluster 1
S1414	玛利加郎特883A Malijialangte 883A	Cluster 4	S1566	玛利加郎特883A Malijialangte 883A	Cluster 1	S1552	阔叶棉221 Kuoyemian 221	Cluster 1
S1563	玛利加郎特2304C Malijialangte 2304C	Cluster 4	S1430	尤卡坦1039A Youkatan 1039A	Cluster 1	S1413	玛利加郎特368 Malijialangte 368	Cluster 1
S1587	尤卡坦2094D Youkatan 2094D	Cluster 4	S1582	尤卡坦1039A Youkatan 1039A	Cluster 1	S1564	玛利加郎特246 Malijialangte 246	Cluster 1
S1418	莫利尔137X Molier 137X	Cluster 4	S1434	尤卡坦2094 Youkatan 2094	Cluster 1	S1423	帕默尔1045A Pamoer 1045A	Cluster 3
S1567	玛利加郎特904 Malijialangte 904	Cluster 4	S1586	尤卡坦2094B Youkatan 2094B	Cluster 1	S1575	帕默尔1045A Pamoer 1045A	Cluster 3
S1547	尖斑棉94 Jianbanmian 94	Cluster 2	S1416	莫利尔131X Molier 131X	Cluster 1	S1388	尖斑棉1108K Jianbanmian 1108K	Cluster 3
S1545	尖斑棉488 Jianbanmian 488	Cluster 2	S1569	莫利尔133 Molier 133	Cluster 1	S1539	尖斑棉1103 Jianbanmian 1103	Cluster 3
S1540	尖斑棉1108K Jianbanmian 1108K	Cluster 2	S1417	莫利尔133 Molier 133	Cluster 1	S1565	玛利加郎特368 Malijialangte 368	Cluster 3
S1554	阔叶棉482 Kuoyemian 482	Cluster 2	S1568	莫利尔131X Molier 131X	Cluster 1	S1395	尖斑棉94 Jianbanmian 94	Cluster 3
S1431	尤卡坦1046 Youkatan 1046	Cluster 2	S1559	雷奇蒙地281 Leiqimengdi 281	Cluster 1	S1403	雷奇蒙地1102 Leiqimengdi 1102	Cluster 3
S1583	尤卡坦1046 Youkatan 1046	Cluster 2	S1432	尤卡坦1236 Youkatan 1236	Cluster 1	S1421	莫利尔255 Molier 255	Cluster 3
S1399	阔叶棉21 Kuoyemian 21	Cluster 2	S1584	尤卡坦1236 Youkatan 1236	Cluster 1	S1573	莫利尔255 Molier 255	Cluster 3
S1390	尖斑棉144 Jianbanmian 144	Cluster 2	S1419	莫利尔194 Molier 194	Cluster 1	S1393	尖斑棉488 Jianbanmian 488	Cluster 3
S1397	阔叶棉177 Kuoyemian 177	Cluster 2	S1571	莫利尔194 Molier 194	Cluster 1	S1404	雷奇蒙地145 Leiqimengdi 145	Cluster 3
S1556	雷奇蒙地145 Leiqimengdi 145	Cluster 2	S1424	帕默尔11 Pamoer 11	Cluster 1	S1387	尖斑棉1103 Jianbanmian 1103	Cluster 3
S1541	尖斑棉114 Jianbanmian 114	Cluster 2	S1576	帕默尔11 Pamoer 11	Cluster 1	S1544	尖斑棉27 Jianbanmian 27	Cluster 3
S1542	尖斑棉144 Jianbanmian 144	Cluster 2	S1407	雷奇蒙地281 Leiqimengdi 281	Cluster 1	S1400	阔叶棉221 Kuoyemian 221	Cluster 3
S1415	玛利加郎特904 Malijialangte 904	Cluster 1	S1560	雷奇蒙地461 Leiqimengdi 461	Cluster 1	S1555	雷奇蒙地1102 Leiqimengdi 1102	Cluster 3

Table S2

Table 1

Table 2

Fig. 1

Fig. 2

Fig. 3

Fig. 4

Fig. 5

Fig. 6

Table 3

Table 4

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试验数据 Experimental data	组织 Tissue	峰值 Peak number
H3K27ac	下胚轴 Hypocotyl	39,663
H3K27ac	子叶 Cotyledon	37,635
H3K4me3	胚珠 Ovule	53,993
H3K4me3	胚根 Radicle	42,671
H3K4me3	下胚轴 Hypocotyl	40,116
H3K4me3	叶片 Leaf	59,619
ATAC	子叶, 胚珠, 胚根, 下胚轴, 叶片 Cotyledon, ovule, radicle, hypocotyl, leaf	219,379

变异种类 Variation category	权重分数 Weighting score	变异种类 Variation category	权重分数 Weighting score
下游区间 Downstream	1	未知类型 Unknown	1
基因间区 Intergenic	1	上游区间 Upstream	1
内含子区 Intronic	1	上下游区间 Upstream, downstream	1
非同义变异 Nonsynonymous SNV	2	3'非翻译区 3' untranslated regions (UTR3)	4
剪接位点区域 Splicing	5	5'非翻译区 5' untranslated regions (UTR5)	4
终止密码子获得 Stopgain	4	5'和3'非翻译区 5' untranslated regions (UTR5); 3' untranslated regions (UTR3)	4
终止密码子丢失 Stoploss	4	染色质开放区/染色质免疫共沉淀ATAC/ChIP	3
同义变异 Synonymous SNV	3	GWAS和eQTL位点 GWAS-associated and eQTL loci	30

性状 Trait	SNP位点 SNP loci	染色体 Chromosome	物理位置 Position (bp)	P值 P-value
纤维伸长率 Fiber elongation rate	A06_30632495	A06	30,632,495	1.93E-05
	A06_29826691	A06	29,826,691	2.72E-05
	A06_29886743	A06	29,886,743	2.72E-05
	A06_29911584	A06	29,911,584	2.72E-05
	A06_29998092	A06	29,998,092	2.72E-05
	A06_30075108	A06	30,075,108	2.72E-05
	A06_30090240	A06	30,090,240	2.72E-05
	A06_30183612	A06	30,183,612	2.72E-05
	A06_30360014	A06	30,360,014	2.72E-05
	A06_30395423	A06	30,395,423	2.72E-05
	A06_30481656	A06	30,481,656	2.72E-05
	A06_30521701	A06	30,521,701	2.72E-05
	A06_30540961	A06	30,540,961	2.72E-05
	A06_30729030	A06	30,729,030	2.72E-05
	A06_30804606	A06	30,804,606	2.72E-05
	A06_30822647	A06	30,822,647	2.72E-05
	A06_30882123	A06	30,882,123	2.72E-05
	A06_31067102	A06	31,067,102	2.72E-05
	A06_31179803	A06	31,179,803	2.72E-05
	A06_31422198	A06	31,422,198	2.72E-05
	A06_31452632	A06	31,452,632	2.72E-05
	A06_31542493	A06	31,542,493	2.72E-05
	A06_34928645	A06	34,928,645	2.72E-05
	A06_35040024	A06	35,040,024	2.72E-05
	A06_30414712	A06	30,414,712	9.08E-05
马克隆值 Fiber micronaire value	A06_114669594	A06	114,669,594	3.05E-05
	D12_54915368	D12	54,915,368	3.65E-05
	D11_58293439	D11	58,293,439	4.67E-05
	D11_58625039	D11	58,625,039	4.67E-05
	A06_114526277	A06	114,526,277	5.84E-05
纤维强度 Fiber strength	A10_69492454	A10	69,492,454	2.43E-05
纤维强度 Fiber strength	D07_58335177	D07	58,335,177	4.74E-05
纤维长度 Fiber length	A11_19546832	A11	19,546,832	1.32E-05
	A11_19343086	A11	19,343,086	1.96E-05
	A07_1121676	A07	1,121,676	4.18E-05
	A10_69492454	A10	69,492,454	5.73E-05
纤维整齐度 Fiber uniformity	D09_810409	D09	810,409	4.85E-06
	A05_21431509	A05	21,431,509	4.37E-05
	D11_28341684	D11	28,341,684	4.60E-05
	A06_30632495	A06	30,632,495	6.19E-05

SNP位点 SNP loci	性状 Trait	基因型频率Genotype frequency				FST值 Fixation index	遗传多样性比率 Genetic diversity ratio (π_w/π_c)
SNP位点 SNP loci	性状 Trait	栽培棉 Cultivars of G. hirsutum L.		半野生棉 Semi-wild accessions of G. hirsutum L.		FST值 Fixation index	遗传多样性比率 Genetic diversity ratio (π_w/π_c)
A06_29826691	纤维伸长率 Fiber elongation rate	A: 0.942	G: 0.058	A: 0.421	G: 0.579	0.627	3.958
A06_30632495	纤维伸长率, 纤维整齐度 Fiber elongation rate, fiber uniformity	A: 0.964	G: 0.036	A: 0.628	G: 0.372	0.365	6.829
D11_28341684	纤维整齐度 Fiber uniformity	C: 0.919	T: 0.081	C: 0.143	T: 0.857	0.773	1.643

Preparation of cotton 60K functional locus gene chip and its application to genetic research

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