棉花功能基因图位克隆的研究进展

doi:10.3864/j.issn.0578-1752.2023.23.006

中国农业科学 ›› 2023, Vol. 56 ›› Issue (23): 4635-4647.doi: 10.3864/j.issn.0578-1752.2023.23.006

所属专题：专题——棉花纤维发育

棉花功能基因图位克隆的研究进展

臧新山¹^,²^,⁴(), 王康文¹^,³(), 张先亮¹^,², 王雪平¹, 王军¹, 梁雨¹, 裴小雨¹, 任翔¹^,², 吕宇龙¹^,², 高宇¹, 王星星¹, 彭云玲³(), 马雄风¹^,²^,³^,⁴()

¹ 中国农业科学院棉花研究所/棉花生物学国家重点实验室/农业农村部棉花生物学与遗传育种重点实验室，河南安阳 455000
² 中国农业科学院西部农业研究中心，新疆昌吉 831100
³ 甘肃农业大学农学院/甘肃省干旱生境作物学重点实验室/甘肃省作物遗传改良与种质创新重点实验室，兰州 730070
⁴ 郑州大学农学院，郑州 450001

收稿日期:2023-02-08 接受日期:2023-04-17 出版日期:2023-12-04 发布日期:2023-12-04
通信作者:
彭云玲，E-mail：pengyunlingpyl@163.com。
马雄风，E-mail：maxf_caas@163.com
联系方式: 臧新山，E-mail：zangxinshan@163.com。王康文，E-mail：wangkangwen@126.com。臧新山和王康文为同等贡献作者。
基金资助:
国家棉花产业技术体系(CARS-15-07); 新疆维吾尔自治区重点研发任务专项(2022B02052-2); 新疆维吾尔自治区天山英才计划(2021); 昌吉回族自治州科技重大专项(2021Z01-01)

Research Advances of Map-Based Cloning Genes in Cotton

ZANG XinShan¹^,²^,⁴(), WANG KangWen¹^,³(), ZHANG XianLiang¹^,², WANG XuePing¹, WANG Jun¹, LIANG Yu¹, PEI XiaoYu¹, REN Xiang¹^,², LÜ YuLong¹^,², GAO Yu¹, WANG XingXing¹, PENG YunLing³(), MA XiongFeng¹^,²^,³^,⁴()

¹ Institute of Cotton Research of Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology/Key Laboratory of Biological and Genetic Breeding of Cotton, Ministry of Agriculture and Rural Affairs, Anyang 455000, Henan
² Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, Xinjiang
³ College of Agronomy, Gansu Agricultural University/Gansu Provincial Key Lab of Arid Land Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070
⁴ School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001

Received:2023-02-08 Accepted:2023-04-17 Published:2023-12-04 Online:2023-12-04

摘要/Abstract

摘要：

图位克隆是鉴定特定表型变异遗传基础的经典有效策略。棉花功能基因图位克隆，对育种工作者创新利用种质资源、培育和定向设计新品种、提高育种效率有重要指导作用。近年来，随着雷蒙德氏棉、亚洲棉、陆地棉和海岛棉等基因组测序的完成和不断完善，基因的物理位置信息已知，省去了筛选基因组文库和构建候选区段物理图谱的过程，棉花功能基因图位克隆研究进入快速发展期。2016年，利用正向遗传学方法首次图位克隆了陆地棉显性无腺体Gl₂^e（GoPGF），目前已有20个质量性状基因和5个数量性状基因通过图位克隆策略鉴定。本文从基因符号、名称、染色体定位、候选基因等方面系统综述棉花纤维、腺体、蜜腺、叶型、株型、植株颜色、育性等性状相关图位克隆基因；并从图位克隆作图群体和集团分离分析法测序（bulked segregate analysis-sequencing，BSA-seq）应用等方面系统综述图位克隆策略。随着基因组测序技术的升级、测序成本的降低、BSA-seq等新方法的应用，图位克隆发展更加快速准确。利用转基因和基因组编辑技术对基因功能开展全面系统的鉴定评价，将为棉花分子设计育种提供理论基础和基因资源，加快棉花遗传改良进程。

关键词: 棉花, 图位克隆, 分子标记, 作图群体, BSA-seq

Abstract:

Map-based cloning is a classical and effective method to identify candidate genes for specific phenotypic variants. Map-based cloning of functional genes plays important roles in the innovative utilization of germplasm resources, molecular design breeding and improving breeding efficiency. In recent years, the whole-genome sequencing of Gossypium raimondii, Gossypium arboreum, Gossypium hirsutum, and Gossypium barbadense has been completed and improved. Map-based cloning has entered into a crucial period. In 2016, the dominant glandless gene Gl₂^e (GoPGF) was the first map-based cloning gene in cotton. So far, 20 qualitative traits genes and 5 quantitative traits genes have been identified by map-based cloning technology. In this paper, research progress was systematically reviewed in fiber, gland, nectary, leaf type, plant architecture, plant color, and fertility in terms of gene symbols, names, chromosomal positioning, and candidate genes. Moreover, map-based cloning strategies were systematically reviewed in mapping populations and bulked segregate analysis-sequencing (BSA-seq). With the reduction of sequencing cost and utilization of BSA-seq, it is believed that more and more genes will be cloned by map-based cloning technology. In addition, transformation and genome editing have been successfully used to evaluate the function of the candidate gene in the target interval. It is believed that map-based cloning could provide a theoretical basis and genetic resources for molecular design breeding in cotton.

Key words: cotton, map-based cloning, molecular marker, mapping population, BSA-seq

臧新山, 王康文, 张先亮, 王雪平, 王军, 梁雨, 裴小雨, 任翔, 吕宇龙, 高宇, 王星星, 彭云玲, 马雄风. 棉花功能基因图位克隆的研究进展[J]. 中国农业科学, 2023, 56(23): 4635-4647.

ZANG XinShan, WANG KangWen, ZHANG XianLiang, WANG XuePing, WANG Jun, LIANG Yu, PEI XiaoYu, REN Xiang, LÜ YuLong, GAO Yu, WANG XingXing, PENG YunLing, MA XiongFeng. Research Advances of Map-Based Cloning Genes in Cotton[J]. Scientia Agricultura Sinica, 2023, 56(23): 4635-4647.

图/表 3

表1

表2

表3

棉花图位克隆的作图群体"

基因符号 Gene symbol	群体 Populations	群体类型 Population type	群体大小 Population size	群体大小（总和） Population size (Sum)	连锁的分子标记 Linked molecular markers	物理距离 Physical distance (kb)	参考文献 Reference
Gl₂^e	TM-1(腺体Glanded)×Hai-1(无腺体Glandless)	F₂	1599	2197	w7954 Gl₂^e w5383	43	[12]
	TM-1 (腺体Glanded)×N1(无腺体Glandless)	F₂	244
	TM-1 (腺体Glanded)×N7(无腺体Glandless)	F₂	354
	CCRI12(腺体Glanded)×Dgl-CCRI12(无腺体Glandless)	F₂	1225	4530	CS2 Gl₂^e CS4	15	[18]
	CCRI12(腺体Glanded)×Dgl-CCRI12(无腺体Glandless)	F₂	1051
	L7(腺体Glanded)×Dgl-L7(无腺体Glandless)	F₂	2254
N₁	N₁(光籽突变体Naked seed mutant)×Xinhai 16 (正常种子Normal seed)	F₂	232	2012	H5532 N₁ H5536	49	[14]
	N₁(光籽突变体Naked seed mutant)×Junhai 1(正常种子Normal seed)	F₂	408
	N₁(光籽突变体Naked seed mutant)×CSIL158(正常种子Normal seed)	F₂	1372
L₂^o	RIL034(鸡脚叶Okra leaf)×Yumian1(正常叶Normal leaf)	F₂	1873	2360	SWU07749 L₂^o SWU07354	12	[22]
	RIL090(鸡脚叶Okra leaf)×Jinnong08(正常叶Normal leaf)	F₂	310
	陆地棉品系 Gossypium hirsutum accessions	自然群体 Natural population	177
	TM-1(正常叶Normal leaf)×IL-15-5-1(鸡脚叶Okra leaf)	F₂	770	1278	JESPR152 L₂^o NAU3040	183	[23]
	TM-1(正常叶Normal leaf)×IL-15-5-1(鸡脚叶Okra leaf)	F₂	508	1278	JESPR152 L₂^o NAU3040	183	[23]
_L-D₁	NC05AZ21(鸡脚叶Okra leaf)×NC11-2100 (正常叶Normal leaf)	F₂	1027	1565	N.A.	52	[24]
_L-D₁	异源四倍体棉花品系 Tetraploid cotton accessions	自然群体 Natural population	538	1565	N.A.	52	[24]
v₁	[TM-1(正常Normal)×T582(芽黄Virescent)]×T582(芽黄Virescent)	BC₁	412	2576	K5499 v₁ K5846	44	[28]
	TM-1(正常Normal)×T582(芽黄Virescent)	F₂	2164	2576	K5499 v₁ K5846	44	[28]
	TM-1(正常Normal)×CCRI60(芽黄Virescent)	F₂	1132	4232	D10M-180 v₁ D10BIN45	84.1	[29]
	TM-1(正常Normal)×CCRI60(芽黄Virescent)	F₂	3100	4232	D10M-180 v₁ D10BIN45	84.1	[29]
Li₁	DP5690NIL(短纤维Short fiber)×DP5690(正常纤维 Normal fiber)	F₂	2567	4319	N.A.	N.A.	[15]
	DP5690NIL(短纤维Short fiber)×DP5690(正常纤维 Normal fiber)	F₃	426
	DP5690NIL(短纤维Short fiber)×DP5690(正常纤维 Normal fiber)	F₃	470
	DP5690NIL(短纤维Short fiber)×DP5690(正常纤维 Normal fiber)	F₃	670
	陆地棉品种 Gossypium hirsutum cultivars	自然群体 Natural population	186
Li₃	XZ142FLM (无绒无絮种子Lintless-fuzzless seed)×n2NSM (无绒种子Fuzzless seed)	F₂	4662	9330	W1644 Li₃ W1650	79.8	[16]
Li₃	XZ142FLM (无绒无絮种子Lintless-fuzzless seed)×n2NSM (无绒种子Fuzzless seed)	BC₁	4668	9330	W1644 Li₃ W1650	79.8	[16]
Ghlmm	Ghlmm(病变模拟突变体Lesion mimic mutant)×TM-1(正常植株Normal plant)	F₂	763	763	NAU7928 Ghlmm S2393	371	[34]
ne1/ ne2	MD90ne(无蜜腺 Nectariless line)×TM-1(有蜜腺 Nectary line)	F₂	1021	6477	K9201 ne2 K5116	467	[21]
	MD90ne(无蜜腺Nectariless line)×TM-1(有蜜腺Nectary line)	F₂	1972
	MD90ne(无蜜腺Nectariless line)×TM-1(有蜜腺 Nectary line)	F₂	2240
	MD90ne(无蜜腺Nectariless line)×TM-1(有蜜腺 Nectary line)	BC₁	539		K5997 ne2 K9224	156
	MD90ne(无蜜腺Nectariless line)×TM-1(有蜜腺 Nectary line)	BC₁	715		K5997 ne2 K9224	156
Cl₁	TM-1(正常植株Normal plant)×Xinhai 25(从生铃Clustered boll)	F₂	998	2079	K4918 Cl₁ K583	390	[25]
	T582(从生铃Clustered boll)×TM-1(正常植株Normal plant) ；[TM-1(正常植株Normal plant)×T582(从生铃Clustered boll)]×T582(从生铃Clustered boll)	F₂/BC₁	852
	海岛棉品种 Gossypium barbadense cultivars	自然群体 Natural population	229
	CCRI35(正常植株Normal plant)×Hai170(从生铃Cluster fruiting)	F₂	310	5163	SWU07707 Cl SWU08487	69	[26]
	CCRI35(正常植株Normal plant)×Hai170(从生铃Cluster fruiting)	F₂	2341
	Duan063(正常植株Normal plant)×Pima-S6(从生铃Cluster fruiting)	F₂	184
	Yumian1(正常植株Normal plant)×Chaozao3(从生铃Cluster fruiting)	F₂	2236
	海岛棉品系 Sea island cotton accessions	自然群体 Natural population	92
Lc₁	T586(棕色纤维Dark-brown fiber)×Yumian No. 1(正常纤维Normal fiber)	RIL population (F_2:7)	270	1968	TT2-1A Lc₁ TT2-3A	67	[17]
Lc₁	T586(棕色纤维Dark-brown fiber)×Yumian No. 1(正常纤维Normal fiber)	F₂	1698	1968	TT2-1A Lc₁ TT2-3A	67	[17]
Le₄	[TM-1(正常植株Normal plant)×R4-4(杂交致死植株Lethality plant)]×TM-1(正常植株Normal plant)	BC₁	2013	2013	K1805 Le₄ W8424	267	[31]
R1	T586(红色植株Red plant)×Yumian 1 (正常植株Normal plant)	RIL	270	270	S5 R1 S6	136	[30]
ob1	TM-1(正常植株Normal plant)×CS-B18(柱头外露Open bud)	F₂	4333	6137	M6058 ob1 M25377	400	[27]
ob1	TM-1(正常植株Normal plant)×(TM-1(正常植株Normal plant)×CS-B18(柱头外露Open bud))	BC₁	1804	6137	M6058 ob1 M25377	400	[27]
R3	LR(红花Red flowers)×LW(白花White flowers) LR(红花Red flowers)×LW(白花White flowers) LR(红花Red flowers)×LW(白花White flowers)	F₂ F₂ F₂	351 1191 136	1678	A07-0594 R3 A07-0592	33.2	[35]
Ms	NanNong6(雄性不育系Male-sterile line)×GangZa8 (可育品种Fertile cultivar)	F₂	485	1962	T1 Ms5 T5 T1 Ms6 T5	212	[32]
	NanNong6 (雄性不育系Male-sterile line)×GangZa8 (可育品种Fertile cultivar)	F₂	913
	NanNong6 (雄性不育系Male-sterile line)×GangZa8 (可育品种Fertile cultivar)	F₂	563
GhNsp	1355A(雄性不育系Male-sterile line)×E22 (可育品种Fertile cultivar)	F₂	64	1904	flanked by D02-2919	103	[33]
GhNsp	1355A (雄性不育系Male-sterile line)×1355B (可育系 Fertile line)	NIL	1840	1904	flanked by D02-2919	103	[33]
GbBM	HaiR(花瓣基斑Spotted petal)×P30B (无花瓣基斑Nonspotted petal)	F₂	120	5780	CMB5 GbBM CMB7	298	[36]
GbBM	HaiR(花瓣基斑Spotted petal)×P30B (无花瓣基斑Nonspotted petal)	F₂	5660	5780	CMB5 GbBM CMB7	298	[36]
EFN	GA0028(无蜜腺Nectariless)×GA0028(花外蜜腺Nectary)	F₂	96	2481	H1893 EFN H8099	96.6	[20]
EFN	GA0028(无蜜腺Nectariless)×GA0028(花外蜜腺Nectary)	F₂	2385	2481	H1893 EFN H8099	96.6	[20]
qFS-D3-1	RIL168(高纤维强度Fine fiber strength)×86-1(低纤维强度Low fiber strength)	F₂	747	1864	K5219 qFS- D3-1 K5221	930	[37]
	RIL98(高纤维强度Fine fiber strength)×86-1(低纤维强度Low fiber strength)	F₂	355
	RIL120(高纤维强度Fine fiber strength)×86-1(低纤维强度Low fiber strength)	F₂	417
	RIL143(高纤维强度Fine fiber strength)×86-1(低纤维强度Low fiber strength)	F₂	345
qFL-c10-1	DJ61(高纤维长度Fine fiber length)×Jimian5(低纤维强度Low-fiber length)	F₂	1081	1081	SNP-294 qFL- c10-1A10-29	96.5	[38]
qBWT-c12	Emian22高铃重High boll weight×BS41(低铃重Lowered boll weight)	F₂	311	3841	AD-A12_07 qBWT-c12 AD-FM_44	180	[39]
	Emian22 (高铃重High boll weight)×BS41(低铃重Lowered boll weight)	F₂	795
	Emian22 (高铃重High boll weight)×BS41(低铃重Lowered boll weight)	F₃	2289
	Emian22 (高铃重High boll weight)×BS41(低铃重Lowered boll weight)	F₄	446
qVW-Bp2-1	CSIL SuVR043(高黄萎病抗性Highly verticillium wilt resistant)×Sumian 8(易感黄萎病susceptible to verticillium wilt)	F₂	176	176	cgr6409 qVW- Bp2-1 ZHX37	254	[40]
qVW-Bp2-2	CSIL SuVR043(高黄萎病抗性Highly verticillium wilt resistant)×Sumian 8(易感黄萎病susceptible to verticillium wilt)	F₂	176	176	ZHX57 qVW- Bp2-2 ZHX70	140	[40]

表3

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性状 Trait	基因符号 Gene symbol	名称 Name	染色体定位 Chromosome location	候选基因 Candidate gene	参考文献 Reference
纤维 Fiber	N₁	光籽 Naked seed	A12	GhMML3_A12 (Gh_A12G185500)	[14]
	Li₁	李氏无纤维 Ligon lintless	D04	GhACT_LI1 (Gh_D04G101800)	[15]
	Li₃	李氏无纤维 Ligon lintless	D12	GhMML4_D12 (Gh_D12G181300)	[16]
	Lc₁	棕色纤维 Brown lint	A07	GhTT2-3A (Gh_A07G020100)	[17]
腺体 Gland	Gl₂^e	有无腺体植株 Glandless and glanded plant	A12	GoPGF (Gh_A12G265100)	[12]
	Gl₂^e	有无腺体植株 Glandless and glanded plant	A12	MYC (Gh_A12G265100)	[18]
	gl₁	无腺体棉铃 Glandless boll	D08	GoSPGF (Gh_D08G192900)	[19]
蜜腺 Nectary	EFN	花外蜜腺 Extrafloral nectary	A12	GaNEC1 (Ga12G1409)	[20]
	ne₁	无蜜腺 Nectariless	A12	GhNe₁ (Gh_A12G165500)	[21]
	ne₂	无蜜腺 Nectariless	D12	GhNe₂ (Gh_D12G163600)	[21]
叶型 Leaf type	L₂^o	鸡脚叶 Okra leaf	D01	GhOKRA (Gh_D01G231000)	[22]
	L₂^o			GhOKRA-Dt (Gh_D01G231000)	[23]
	_L-D₁			GhLMI1-D1b (Gh_D01G230600)	[24]
株型 Plant architecture	Cl₁	丛生铃/零式果枝 Clustered boll / Cluster fruiting	D07	GbAF (Gh_D07G116400)	[25]
	Cl₁	丛生铃/零式果枝 Clustered boll / Cluster fruiting	A08	GoCEN-Dt (Gh_D07G116400)	[26]
	ob₁	柱头外漏 Open bud	D13	GhMML10_Dt (Gh_D13G085500)	[27]
植株颜色 Plant color	v₁	芽黄 Virescent	D10	GhCHLI (Gh_D10G031700)	[28]
	v₁	芽黄 Virescent	D10	GhCHLI (Gh_D10G031700)	[29]
	R₁	红株 Red plant	D07	GhPAP1D/RLC1 (Gh_D07G083600)	[30]
育性 Fertility	Le₄	致死基因 Lethality gene	D11	CC-NBS-LRR (Gh_D11G325500)	[31]
	Ms	不育基因 Male-sterile	A12	Ms5 (Gh_A12G129100)	[32]
	Ms	不育基因 Male-sterile	D12	Ms6 (Gh_D12G129300)	[32]
	GhNsp	败育恢复基因 No spine pollen	D02	GhNSP (Gh_D02G264700)	[33]
其他性状 Other traits	Ghlmm	类病变突变体 Lesion mimic mutant	D05	GhLMMD (Gh_D05G236600)	[34]
	R₃	红色花瓣 Red petal	A07	GhTT19 (Gh_A07G079800)	[35]
	GbBM	花瓣基斑 Beauty mark	A07	GbBM (Gbar_A07G008330)	[36]

性状 Trait	基因符号 Gene symbol	名称 Name	染色体定位 Chromosome location	候选基因 Candidate gene	参考文献 Reference
纤维 Fiber	qFS-D3-1	纤维强度 Fiber strength	D03	GHUBX (Gh_D03G097900)	[37]
纤维 Fiber	qFL-c10-1	纤维长度 Fiber length	A10	GhFL10 (Ghir_A10G022020)	[38]
铃重 Boll weight	qBWT-c12	铃重 Boll weight	A12	GhBRH1_A12 (Gh_A12G124400)	[39]
黄萎病 Verticillium wilt	qVW-Bp2-1	黄萎病 Verticillium wilt	D04	GbTMEM214 (GOBAR_DD35466)	[40]
黄萎病 Verticillium wilt	qVWBp2-2	黄萎病 Verticillium wilt	D04	GbCYP450 (GOBAR_DD30825)	[40]

棉花功能基因图位克隆的研究进展

Research Advances of Map-Based Cloning Genes in Cotton

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