棉花纤维品质相关性状QTL元分析及候选基因鉴定

doi:10.3724/SP.J.1006.2025.44108

作物学报 ›› 2025, Vol. 51 ›› Issue (6): 1445-1466.doi: 10.3724/SP.J.1006.2025.44108

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

棉花纤维品质相关性状QTL元分析及候选基因鉴定

郭栋财(), 吕涛(), 蔡永生, 买吾鲁达·艾合买提, 全家, 曲延英(), 郑凯()

新疆农业大学/新疆作物生物育种重点实验室, 新疆乌鲁木齐 830052

收稿日期:2024-07-05 接受日期:2025-01-23 出版日期:2025-06-12 网络出版日期:2025-02-11
通讯作者: ^*郑凯, E-mail: zhengkai555@126.com;曲延英, E-mail: xjyyq5322@126.com
作者简介:郭栋财, E-mail: 1907821666@qq.com;
吕涛, E-mail: 943308727@qq.com第一联系人：**同等贡献
基金资助:
本研究由国家自然科学基金青年基金项目(32301867);新疆维吾尔自治区重点研发项目(2022B02009-1);“天山英才”培养计划项目(2023TSYCLJ0012);新疆农业大学作物学重点学科发展基金项目(XNCDKY2021016)

Meta-analysis of QTL and identification of candidate genes for fiber quality in cotton

GUO Dong-Cai(), LYU Tao(), CAI Yong-Sheng, MAI WU-LU-DA·AI He-Mai-Ti, CHEN Quan-Jia, QU Yan-Ying(), ZHENG Kai()

Xinjiang Agricultural University / Laboratory of Crop Genetic Improvement and Germplasm Innovation, Urumqi 830052, Xinjiang, China

Received:2024-07-05 Accepted:2025-01-23 Published:2025-06-12 Published online:2025-02-11
Contact: ^*E-mail: zhengkai555@126.com;E-mail: xjyyq5322@126.com
About author:First author contact:**Contributed equally to this work
Supported by:
the National Natural Science Foundation of China Young Scientists Fund(32301867);the Key Research and Development Project of the Xinjiang Uygur Autonomous Region(2022B02009-1);the “Tianshan Talent” Training Program(2023TSYCLJ0012);the Key Discipline Development Fund for Crop Science of Xinjiang Agricultural University(XNCDKY2021016)

摘要/Abstract

摘要：

棉花纤维品质性状是受多基因控制的复杂数量性状, 深入挖掘棉花纤维品质数量性状基因座(quantitative trait loci, QTL)和候选基因对棉花纤维品质遗传改良具有重要意义。本研究利用BioMercator 4.2软件, 以Blenda A等发布的棉花高密度分子标记遗传连锁图谱为参考图谱, 对来自21个独立纤维品质QTL定位研究中的379个控制棉花纤维品质的原始QTL进行图谱整合、映射以及QTL元分析。获得的74个控制棉花纤维品质性状的一致性meta-QTL (meta quantitative trait loci, MQTL), 分布在26条染色体上, 置信区间最小为0.5 cM, 所有MQTL中共包含13,833个基因。通过RNA-seq、GO和KEGG富集分析, 挖掘到32个与棉花纤维品质相关的候选基因。通过qRT-PCR验证发现, 这些基因在棉花纤维发育不同时期差异表达, 推测其可能参与调控棉花纤维发育。本研究为棉花纤维品质性状分子标记辅助选择育种和基因克隆提供理论依据。

关键词: 棉花, 纤维品质, 一致性QTL, 元分析

Abstract:

Cotton fiber quality is a complex quantitative trait controlled by multiple genes. Identifying true quantitative trait loci (QTL) and candidate genes associated with fiber quality is critical for the genetic improvement of cotton. In this study, QTL meta-analysis was performed using BioMercator 4.2 software, with a high-density molecular marker genetic linkage map published by Blenda A et al. as the reference. A total of 379 original QTLs related to cotton fiber quality, derived from 21 independent QTL mapping studies, were integrated, mapped, and analyzed. This analysis identified 74 meta-QTLs (MQTLs) associated with cotton fiber quality traits, distributed across 26 chromosomes, with the minimum confidence interval of 0.5 cM. These MQTLs collectively encompassed 13,833 genes. Through RNA-seq analysis combined with GO and KEGG enrichment analysis, 32 candidate genes related to cotton fiber quality were identified. qRT-PCR validation revealed that these genes exhibited differential expression during various stages of fiber development, suggesting their potential roles in regulating fiber growth and quality. This study provides a theoretical basis for molecular marker-assisted breeding and gene cloning for cotton fiber quality.

Key words: cotton, fiber quality, consistency QTL, meta-analysis

郭栋财, 吕涛, 蔡永生, 买吾鲁达·艾合买提, 全家, 曲延英, 郑凯. 棉花纤维品质相关性状QTL元分析及候选基因鉴定[J]. 作物学报, 2025, 51(6): 1445-1466.

GUO Dong-Cai, LYU Tao, CAI Yong-Sheng, MAI WU-LU-DA·AI He-Mai-Ti, CHEN Quan-Jia, QU Yan-Ying, ZHENG Kai. Meta-analysis of QTL and identification of candidate genes for fiber quality in cotton[J]. Acta Agronomica Sinica, 2025, 51(6): 1445-1466.

图/表 11

表1

棉花纤维品质相关性状QTL的文献信息"

亲本组合 Parental combination	群体大小 Population size	群体类型 Population type	QTL数目 QTL number	LOD值 LOD score	贡献率 R² (%)	参考文献 Reference
901-001 × SGK156	250	F₂/F_2:3/F_2:4/F_2:5	11	2.80-6.10	1.08-25.41	[24]
MBI7455 × MBI7358	491	F₂	10	2.35-4.30	2.52-7.89	[25]
中棉所36 × 海1 CCRI 36 × Hai 1	408	BC₅F₃/BC₅F_3:4/BC₅F_3:5	21	2.58-10.80	2.60-11.45	[26]
苏优6167 × 苏棉22号 Suyou 6167 × Sumian 22	348	F₂/F_2:3	11	3.72-31.26	6.76-33.28	[27]
鲁棉研37 × Sealand LMY 37 × Sealand	365	F₂/F_2:3	5	3.81-8.14	3.98-8.09	[28]
中棉所36 × 海1 CCRI 36 × Hai 1	135	BC₁F₁/BC₂F₁/BC₁S₁	21	2.51-4.67	6.62-14.19	[29]
GX1135 × GX100-2	173	F₂/F_2:3/F_2:4	13	2.19-7.46	7.70-14.77	[30]
中棉所36 × 海1 CCRI 36×Hai 1	133	BC₅F₁/BC₅F₂	18	2.58-4.57	6.97-12.93	[31]
中棉所8 × Pima 90-53 CCRI 8 × Pima 90-53	182	BC₃F₅	25	3.05-6.07	1.27-12.45	[32]
中棉所35 × 渝棉1号 CCRI 35 × Yumian 1	180	RIL	48	2.02-3.68	5.00-9.00	[33]
中棉所12 × 中棉所28, 中棉所12 × 湘杂棉2号 CCRI 12 × CCRI 28, CCRI 12 × Xiangzamian 2	262, 260	F₂/F_2:3	13	2.09-16.05	3.97-25.89	[34]
0-153 × sGK9708	250, 196	F₂/F_2:3, RIL	24	2.64-13.49	4.60-27.86	[35]
LY343 × LMY22	209	F₂/F_2:3	11	3.95-14.64	5.29-20.66	[36]
TM-1 × 渝棉1号 TM-1×Yumian 1	228	F₂/F₃	4	2.58-6.53	5.32-19.17	[37]
1138 × NM03102	195	F₂/F_2:3	7	2.73-4.65	6.43-12.64	[38]
中棉所36 × MBI9626 CCRI 36 × MBI9626	152	BC₆F₂/BC₆F_2:3/BC₆F_2:4	7	2.73-3.74	3.67-9.83	[39]
5026 × 李台8号 5026 × Li 8	169	RIL	3	3.02-3.23	6.70-6.80	[40]
中棉所45 × 海1 CCRI 45 × Hai 1	116	BC₄F₁	20	2.54-5.24	7.57-38.39	[41]
鲁棉研22 × R497, 鲁棉研22 × R472 LMY 22 × R497, LMY 22 × R472	544, 541	F₂/F_2:3	9	3.44-8.15	2.84-9.06	[42]
中棉所36 × Hai7124 CCRI 36 × Hai7124	186	F₂/F_2:3	91	2.50-9.50	2.67-51.30	[43]
中棉所8号 × 海岛棉Pima 90-53 CCRI 8 × Haidaomian Pima 90-53	131	BC₁F₂/BC₁F_2:3/BC₁F_2:4	7	2.54-5.64	11.99-42.79	[44]

表1

图1

表2

棉花纤维品质相关性状QTL元分析结果"

编号 Number	染色体 Chr.	原始性状 Original trait	QTL 数目 QTL number	位置 Position (cM)	置信区间 Confidence interval (cM)	侧翼标记 Flanking marker	MQTL的物理距离 Physical length of MQTL (Mb)
MQTL1	A01	FL, FS	3	26.63	13.12-40.14	NAU3254-NAU2741	108.53-113.32
MQTL2	A01	FL, FS, FM	5	42.57	39.27-45.87	NAU2095-NAU5163	108.21-111.37
MQTL3	A01	FL, FS, FM	5	46.03	43.94-48.12	NAU2741-NAU3433	105.90-108.53
MQTL4	A01	FL, FS	3	55.88	53.91-57.85	NAU3433-BNL3886	60.38-105.90
MQTL5	A01	FS, FU	2	66.00	57.87-74.13	BNL3886-TMB0062	17.45-60.32
MQTL6	A02	FL, FU	4	37.82	37.68-37.96	HAU2690-HAU1155	96.37-97.39
MQTL7	A03	FL, FM	2	12.40	0.00-28.42	NAU5289-HAU2127	102.24-103.78
MQTL8	A03	FL, FS, FM, FU, FE	13	52.10	49.97-54.23	CIR245-NAU1248	93.53-97.33
MQTL9	A03	FL, FS, FM, FU, FE	13	56.43	52.47-60.39	NAU1068-BNL4034	89.61-95.44
MQTL10	A03	FL, FS, FM, FU, FE	16	61.25	58.02-64.48	BNL4034-Gh129	85.30-89.61
MQTL11	A03	FL, FS, FM, FU, FE	14	77.28	69.66-84.90	BNL3398-TMB1898	142.58-74.88
MQTL12	A04	FL, FM, FU, FE	5	40.96	40.32-41.60	MUSS396-Gh124	11.64-20.54
MQTL13	A05	FS, FU	2	11.98	1.08-22.88	MUSS219-Gh260	96.96-101.83
MQTL14	A05	FS, FM, FU, FE	5	30.83	27.51-34.15	CIR185-JESPR065	92.00-95.32
MQTL15	A05	FS, FM, FE	5	36.43	29.16-43.70	JESPR065-TMB1314	87.66-92.00
MQTL16	A05	FL, FS, FM, FU, FE	17	73.93	72.8-75.06	JESPR241-BNL0542	28.38-30.52
MQTL17	A06	FL, FM, FU	4	73.84	66.9-80.78	Gh185-TMB2504	105.25-112.36
MQTL18	A06	FL, FM, FU	4	87.65	78.64-96.66	BNL2691-JESPR163	53.58-108.95
MQTL19	A07	FL, FS, FM, FU, FE	17	53.16	48.63-57.69	NAU5439-DPL0852	85.35-88.45
MQTL20	A07	FL, FS, FM, FU	7	76.17	73.13-79.21	HAU1780-NAU1362	21.54-29.31
MQTL21	A08	FL, FS, FM	3	45.47	31.85-59.09	NAU1017-BNL3556	112.23-116.31
MQTL22	A09	FL, FM, FE	4	14.23	6.35-22.11	BNL1707-CIR079	5.76-10.40
MQTL23	A09	FM, FU, FE	5	31.15	24.12-38.18	BNL0686-DPL0618	1.17-9.41
MQTL24	A09	FM, FU, FE	6	37.44	34.97-39.91	NAU3101-DPL0854	7.55-10.79
MQTL25	A09	FL, FM, FU, FE	6	44.40	42.44-46.36	NAU4021-NAU2832	42.52-50.44
MQTL26	A09	FL, FS, FM, FU, FE	8	49.12	45.49-52.75	NAU2832-TMB2920	50.44-51.32
MQTL27	A09	FS, FM, FU, FE	7	65.03	43.96-86.10	MUSS432-MUCS426	45.76-68.19
MQTL28	A10	FS, FM, FE	5	39.45	32.53-46.37	CIR305-NAU2991	103.64-105.66
MQTL29	A10	FS, FU, FE	3	56.00	54.69-57.31	NAU4008-BNL2960	99.86-100.53
MQTL30	A11	FL, FS, FE	8	34.25	11.78-56.72	MUSS123-NAU3695	1.19-7.83
MQTL31	A11	FL, FS, FM, FE	9	100.83	94.53-107.13	NAU3657-NAU2651	17.43-18.19
MQTL32	A12	FS	2	9.22	5.26-13.18	DPL0469-HAU2486	0.94-1.70
MQTL33	A12	FL, FU, FE	4	38.69	33.36-44.02	BNL3261-CIR167	6.67-8.01
MQTL34	A12	FL, FS, FE	9	50.09	47.84-52.34	DPL0742-HAU1434	75.56-77.44
MQTL35	A12	FL, FS, FU, FE	6	57.52	56.15-58.89	BNL0391-NAU5419	79.41-85.05
MQTL36	A13	FS, FM, FE	4	44.11	41.37-46.85	MUCS404-BNL1495	5.29-6.22
MQTL37	A13	FM, FE	3	54.68	53.05-56.31	DPL0763-CIR096	10.47-14.62
MQTL38	D02	FL, FS, FM, FU, FE	25	18.73	14.78-22.68	NAU2960-CIR084	65.89-66.71
MQTL39	D02	FL, FS, FM, FU, FE	26	39.24	36.94-41.54	NAU5465-NAU4022	62.96-64.01
MQTL40	D02	FL, FS, FM, FU, FE	20	75.51	71.88-79.14	Gh067-MUCS105	26.35-28.22
MQTL41	D01	FL, FM, FU, FE	11	47.55	43.29-51.81	NAU2343-NAU2823	57.98-60.89
MQTL42	D01	FL, FS, FE	8	90.84	89.88-91.80	BNL4095-HAU1427	14.62-14.66
MQTL43	D07	FL, FS, FM, FU, FE	13	35.38	32.09-38.67	NAU3608-HAU1555	48.18-54.56
MQTL44	D07	FL, FS, FM, FU, FE	13	55.73	54.47-56.99	JESPR228-NAU5061	21.37-24.66
MQTL45	D03	FL, FM, FU	10	45.03	39.74-50.32	HAU0880-NAU3805	3.24-4.20
MQTL46	D03	FL, FM, FU, FE	15	50.31	49.07-51.55	BNL2706-BNL3590	28.73-31.95
MQTL47	D03	FL, FM, FU, FE	9	65.82	55.65-75.99	BNL3590-BNL3371	31.96-41.76
MQTL48	D13	FL, FS, FM, FU, FE	14	29.39	26.35-32.43	HAU2497-NAU2697	3.89-3.90
MQTL49	D13	FL, FS, FM, FU, FE	13	39.30	36.04-42.56	NAU3203-Gh678	4.67-13.06
MQTL50	D13	FL, FS, FM, FU, FE	14	61.66	55.65-67.67	NAU3211-DPL0807	36.96-47.47
MQTL51	D05	FE	3	38.98	29.93-48.03	JESPR023-BNL1706	47.10-56.76
MQTL52	D05	FL, FS, FM, FU, FE	13	75.70	66.66-84.74	NAU0986-TMB1282	24.28-29.20
MQTL53	D05	FL, FS, FM, FU, FE	10	86.01	77.06-94.96	NAU4042-DPL0071	21.02-26.95
MQTL54	D10	FL, FS, FM, FU	5	37.97	21.51-54.43	NAU2139-NAU1280	58.15-62.56
MQTL55	D10	FL, FS, FM	5	67.83	64.43-71.23	DPL0026-BNL0169	54.87-56.50
MQTL56	D11	FL, FS, FM, FU	11	78.88	78.11-79.65	BNL1034-DPL0062	5.81-6.88
MQTL57	D04	FS, FM,FU, FE	5	47.74	36.75-58.73	NAU3591-TMB1919	7.37-40.77
MQTL58	D09	FM, FU, FE	4	37.26	31.08-43.44	HAU2382-MUSS300	118.32-5.93
MQTL59	D09	FL, FS, FM, FU, FE	13	51.28	37.16-65.40	HAU2893-NAU6323	22.91-34.72
MQTL60	D09	FL, FS, FM, FU, FE	17	68.45	64.96-71.94	BNL3823-TMB2943	22.91-29.65
MQTL61	D09	FL, FS, FM, FU, FE	17	80.75	78.85-82.65	NAU5350-BNL3031	32.83-33.44
MQTL62	D08	FL, FM, FU, FE	8	32.17	24.44-39.90	DPL0353-JESPR308	63.37-65.27
MQTL63	D08	FL, FS, FM, FU	16	51.53	46.32-56.74	NAU2306-DPL0461	59.84-61.66
MQTL64	D08	FL, FS, FM, FU	14	60.37	57.33-63.41	DPL0461-NAU0478	57.76-59.84
MQTL65	D08	FL, FS, FM, FU	14	66.90	64.47-69.33	NAU0478-NAU4099	57.32-57.76
MQTL66	D08	FS, FU, FE	5	79.51	76.98-82.04	NAU1197-BNL2616	50.79-51.85
MQTL67	D06	FL, FS, FM, FE	7	26.60	9.17-44.03	HAU1324-DPL0282	59.81-62.03
MQTL68	D06	FL, FS, FM, FU, FE	20	59.55	56.92-62.18	NAU1277-NAU2397	55.43-55.56
MQTL69	D06	FL, FS, FM, FU, FE	16	67.10	58.97-75.23	NAU0928-Gh371	44.28-55.55
MQTL70	D06	FL, FS, FM, FU, FE	9	82.72	70.40-95.04	NAU2717-BNL3190	7.21-18.47
MQTL71	D12	FL, FS, FM, FU, FE	10	33.31	29.45-37.17	BNL2578-NAU1274	3.33-4.12
MQTL72	D12	FL, FS, FM, FU, FE	12	43.37	41.51-45.23	JESPR295-NAU1119	6.00-6.40
MQTL73	D12	FL, FS, FM, FU, FE	12	49.62	44.68-54.56	NAU1039-NAU2857	6.09-8.23
MQTL74	D12	FL, FS, FM, FU, FE	11	62.68	57.30-68.06	BNL3510-BNL1669	21.35-31.49

表2

图2

图3

图4

表3

棉花纤维品质相关性状MQTL区间内候选基因"

基因序列号 Gene ID	拟南芥同源基因 Homologous genes in Arabidopsis thaliana	注释信息 Annotation information	棉花相关研究文献 Cotton related research reports literature
Gbar_A05G037160	AT5G39670	可能是钙结合蛋白CML45 Probable calcium-binding protein CML45	[45]
Gbar_A09G014540	AT2G36026	转录抑制因子OFP6 Transcription repressor OFP6	[46-47]
Gbar_D04G012030	AT2G36950	重金属相关异戊二烯化植物蛋白6 Heavy metal-associated isoprenylated plant protein 6
Gbar_D05G026610	AT2G14900	一种富含半胱氨酸的抗菌肽 Snakin-1
Gbar_D06G016480	AT1G61800	葡萄糖-6-磷酸/磷酸转运体2 Glucose-6-phosphate/phosphate translocator 2
Gbar_D09G001430	AT5G39670	可能是钙结合蛋白CML45 Probable calcium-binding protein CML45	[45,48]
Gbar_D13G006970	AT1G69850	NRT1/ PTR蛋白家族 Protein NRT1/ PTR FAMILY
Gbar_A01G009900	AT1G20450	脱水蛋白ERD10 Dehydrin ERD10
Gbar_A01G014270	AT1G23090	可能的硫酸盐转运体3.3 Probable sulfate transporter 3.3
Gbar_A01G016110	AT4G38770	富含脯氨酸的蛋白质2 Proline-rich protein 2
Gbar_A05G035190	AT5G05960	可能是非特异性脂质转移蛋白2 Probable non-specific lipid-transfer protein 2
Gbar_A06G016660	AT5G47550	半胱氨酸蛋白酶抑制剂5 Cysteine proteinase inhibitor 5
Gbar_A12G003760	AT4G38670	肌动蛋白解聚因子5 Actin-depolymerizing factor 5	[49]
Gbar_D01G020370	AT2G41290	蛋白质类缩糖醇合酶2 Protein STRICTOSIDINE SYNTHASE-LIKE 2
Gbar_D03G011950	AT4G24910	不规则木质部15 Protein IRREGULAR XYLEM 15	[50]
Gbar_D05G023780	AT4G08300	相关蛋白At4g08300 WAT1-related protein At4g08300
Gbar_D08G020390	AT5G23860	微管蛋白-9链 Tubulin beta-9 chain
Gbar_D08G020540	AT5G44340	微管蛋白-1链 Tubulin beta-1 chain
Gbar_D08G020920	AT3G07590	小核糖核蛋白SmD1b Small nuclear ribonucleoprotein SmD1b
Gbar_D09G001560	AT5G15230	赤霉素调节蛋白4 Gibberellin-regulated protein 4	[51-52]
Gbar_D03G011120	AT5G51190	乙烯应答转录因子ERF105 Ethylene-responsive transcription factor ERF105	[53-54]
Gbar_D05G035740	AT3G15210	乙烯应答转录因子4 Ethylene-responsive transcription factor 4	[53-54]
Gbar_A01G014360	AT1G23190	葡萄糖磷酸变位酶, 胞质 Phosphoglucomutase, cytoplasmic
Gbar_A05G040040	AT4G39490	烷烃羟化酶MAH1 Alkane hydroxylase MAH1
Gbar_D04G009400	AT2G41970	可能是蛋白激酶At2g41970 Probable protein kinase At2g41970
Gbar_A11G006280	AT1G06280	含LOB结构域的蛋白2 LOB domain-containing protein 2	[55]
Gbar_A05G041330	AT1G24430	维诺任碱合酶 Vinorine synthase
Gbar_A06G018130	AT5G04530	3-酮酰基辅酶a合成酶19 3-ketoacyl-CoA synthase 19	[56-57]
Gbar_A10G022590	AT2G39420	咖啡酰莽草酸酯酶 Caffeoylshikimate esterase
Gbar_D01G021770	AT2G36460	果糖-二磷酸醛缩酶6, 胞质 Fructose-bisphosphate aldolase 6, cytosolic
Gbar_D04G006470	AT1G75270	谷胱甘肽S-转移酶DHAR2 Glutathione S-transferase DHAR2	[58]
Gbar_D07G015210	AT3G61640	阿拉伯半乳聚糖肽20 Arabinogalactan peptide 20

表3

图5

图6

附图1

图7

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棉花纤维品质相关性状QTL元分析及候选基因鉴定

Meta-analysis of QTL and identification of candidate genes for fiber quality in cotton

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