Meta-analysis of QTL for Salt Tolerance-related Traits at Seeding Stage in Cotton

doi:10.13304/j.nykjdb.2022.0283

Abstract

Abstract:

To explore the real quantitative trait loci （QTL） controlling salt tolerance at seeding stage in cotton， 194 QTLs for 19 traits from 3 mapping populations were integrated， mapped and QTL meta-analysis by BioMercator V4.2.3 software， which the high-density genetic linkage map of cotton was as a reference. The results showed that a total of 11 meta quantitative trait loci （MQTL） of salt tolerance-related traits at seeding stage were mined by the QTL consensus map in cotton， and each MQTL contained at least 3 original QTLs， which located on 10 chromosomes including A03， A06， A11， A12， A13， D01， D06， D07 and D08. The shortest confidence interval narrowed to 0.92 cM. Candidate gene prediction of MQTL intervals on chromosome A11 showed that 14 candidate genes were associated with salt tolerance at seeding stage in cotton. These results provided a theoretical basis for fine mapping of QTL for salt tolerance-related traits at seeding stage in cotton and molecular selection-assisted breeding.

Key words: cotton, salt tolerance, meta-analysis, MQTL, candidate gene

摘要：

为挖掘控制棉花苗期耐盐的重要数量性状位点（quantitative trait loci， QTL），利用BioMercator V4.2.3软件，以棉花高密度遗传连锁图谱作为参考，对来自3个作图群体涉及19个性状的194个QTLs进行图谱整合、映射以及QTL元分析。结果表明，通过建立棉花苗期耐盐相关性状一致性图谱，共挖掘出11个一致性QTL（meta quantitative trait loci， MQTL）位点，各MQTL至少包含3个原始QTLs，置信区间最短缩小至0.92 cM，分布于A03、A06、A11、A12、A13、D01、D03、D06、D07和D08共10条染色体上。通过对A11染色体上MQTL区间进行候选基因预测，挖掘到14个与棉花苗期耐盐相关的候选基因，为棉花苗期耐盐相关性状精细定位及分子辅助选择育种提供理论依据。

关键词: 棉花, 耐盐, 元分析, 一致性QTL, 候选基因

CLC Number:

S562

Wenjun YANG, Yuting ZHU, Jie ZHANG, Kaixiang XU, Congmin WEI, Quanjia CHEN. Meta-analysis of QTL for Salt Tolerance-related Traits at Seeding Stage in Cotton[J]. Journal of Agricultural Science and Technology, 2023, 25(12): 26-34.

杨文俊, 朱雨婷, 张杰, 徐凯祥, 韦聪敏, 陈全家. 棉花苗期耐盐相关性状QTL元分析[J]. 中国农业科技导报, 2023, 25(12): 26-34.

Figures/Tables 6

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性状 Trait	QTL数量 QTL number	作图群体 Mapping population	群体大小 Population size	群体类型 Population type	置信度 Logarithm of odds	贡献率 R²/%
叶绿素含量 Chlorophyll content	2	CRI-12×AD₃-00	188	F_2：3	2.80	11.60~13.40
	7	TM-1×NM24016	97	RIL	2.54~6.43	11.32~20.54
	10	CCRI35×NH	277	F_2：3	2.56~3.97	0.02~6.84
电导率 Electrical conductivity	14	CCRI35×NH	277	F_2：3	2.51~4.58	0.32~8.29
鲜重 Fresh weight	23	CCRI35×NH	277	F_2：3	2.51~6.05	0.01~9.87
发芽率 Germination rate	6	CCRI35×NH	277	F_2：3	2.54~3.06	0.67~5.78
叶干重 Leaf dry weight	13	CCRI35×NH	277	F_2：3	2.65~4.21	0.66~10.50
叶鲜重 Leaf fresh weight	5	CCRI35×NH	277	F_2：3	2.61~3.25	3.09~4.97
丙二醛含量 Malondialdehyde content	11	CCRI35×NH	277	F_2：3	2.65~5.13	0.09~8.41
株高 Plant height	4	CRI-12×AD₃-00	188	F_2：3	2.80~3.00	7.05~13.30
株高 Plant height	6	TM-1×NM24016	97	RIL	2.59~5.60	11.43~16.54
光合速率 Photosynthetic rate	3	TM-1×NM24016	97	RIL	3.09~4.71	9.43~11.21
根干重 Root dry weight	5	TM-1×NM24016	97	RIL	2.78~4.65	9.54~14.32
根鲜重 Root fresh weight	4	CRI-12×AD₃-00	188	F_2：3	2.90~3.10	5.80~9.58
根鲜重 Root fresh weight	8	TM-1×NM24016	97	RIL	2.55~6.53	11.32~20.43
主根长Root length	4	CRI-12×AD₃-00	188	F_2：3	2.70~2.90	2.50~18.44
相对含水量 Relative water content	11	CCRI35×NH	277	F_2：3	2.58~4.05	0.01~4.13
气孔导度 Stomatal conductance	3	TM-1×NM24016	97	RIL	2.43~3.05	9.43~12.43
地上部干重 Shoot dry weight	8	CRI-12×AD₃-00	188	F_2：3	2.80~3.10	3.54~15.16
地上部干重 Shoot dry weight	6	TM-1×NM24016	97	RIL	3.09~6.99	11.34~15.79
地上部鲜重 Shoot fresh weight	2	CRI-12×AD₃-00	188	F_2：3	2.70~2.90	2.35~3.43
地上部鲜重 Shoot fresh weight	6	TM-1×NM24016	97	RIL	2.90~5.43	7.87~17.32
茎长 Stem length	15	CCRI35×NH	277	F_2：3	2.54~4.26	0.03~7.53
饱和叶重 Saturated leaf weight	15	CCRI35×NH	277	F_2：3	2.53~5.12	0.01~7.60
蒸腾作用 Transpiration	3	TM-1×NM24016	97	RIL	3.08~4.65	9.05~11.45

性状 Trait	QTL数量 QTL number	作图群体 Mapping population	群体大小 Population size	群体类型 Population type	置信度 Logarithm of odds	贡献率 R²/%
叶绿素含量 Chlorophyll content	2	CRI-12×AD₃-00	188	F_2：3	2.80	11.60~13.40
	7	TM-1×NM24016	97	RIL	2.54~6.43	11.32~20.54
	10	CCRI35×NH	277	F_2：3	2.56~3.97	0.02~6.84
电导率 Electrical conductivity	14	CCRI35×NH	277	F_2：3	2.51~4.58	0.32~8.29
鲜重 Fresh weight	23	CCRI35×NH	277	F_2：3	2.51~6.05	0.01~9.87
发芽率 Germination rate	6	CCRI35×NH	277	F_2：3	2.54~3.06	0.67~5.78
叶干重 Leaf dry weight	13	CCRI35×NH	277	F_2：3	2.65~4.21	0.66~10.50
叶鲜重 Leaf fresh weight	5	CCRI35×NH	277	F_2：3	2.61~3.25	3.09~4.97
丙二醛含量 Malondialdehyde content	11	CCRI35×NH	277	F_2：3	2.65~5.13	0.09~8.41
株高 Plant height	4	CRI-12×AD₃-00	188	F_2：3	2.80~3.00	7.05~13.30
株高 Plant height	6	TM-1×NM24016	97	RIL	2.59~5.60	11.43~16.54
光合速率 Photosynthetic rate	3	TM-1×NM24016	97	RIL	3.09~4.71	9.43~11.21
根干重 Root dry weight	5	TM-1×NM24016	97	RIL	2.78~4.65	9.54~14.32
根鲜重 Root fresh weight	4	CRI-12×AD₃-00	188	F_2：3	2.90~3.10	5.80~9.58
根鲜重 Root fresh weight	8	TM-1×NM24016	97	RIL	2.55~6.53	11.32~20.43
主根长Root length	4	CRI-12×AD₃-00	188	F_2：3	2.70~2.90	2.50~18.44
相对含水量 Relative water content	11	CCRI35×NH	277	F_2：3	2.58~4.05	0.01~4.13
气孔导度 Stomatal conductance	3	TM-1×NM24016	97	RIL	2.43~3.05	9.43~12.43
地上部干重 Shoot dry weight	8	CRI-12×AD₃-00	188	F_2：3	2.80~3.10	3.54~15.16
地上部干重 Shoot dry weight	6	TM-1×NM24016	97	RIL	3.09~6.99	11.34~15.79
地上部鲜重 Shoot fresh weight	2	CRI-12×AD₃-00	188	F_2：3	2.70~2.90	2.35~3.43
地上部鲜重 Shoot fresh weight	6	TM-1×NM24016	97	RIL	2.90~5.43	7.87~17.32
茎长 Stem length	15	CCRI35×NH	277	F_2：3	2.54~4.26	0.03~7.53
饱和叶重 Saturated leaf weight	15	CCRI35×NH	277	F_2：3	2.53~5.12	0.01~7.60
蒸腾作用 Transpiration	3	TM-1×NM24016	97	RIL	3.08~4.65	9.05~11.45

编号 Code	染色体 Chromosome	原始性状（数量） Original trait（amount）	AIC值 AIC value	位置 Position/cM	置信区间 Confidence interval/cM	图距 Map distance/cM	侧翼标记 Flanking marker
MQTL1	A03	EC， SFW（2）	46.26	203.90	198.84~208.97	10.13	mk11960~mk2075
MQTL2	A06	SFW（3）， SL， SLW（2）	46.26	34.55	34.00~35.11	1.11	mk4998_A06~mk5000_A06
MQTL3	A11	PH， SFW， SL	40.90	36.19	35.52~36.86	1.34	DPL0209（b）~mk7803_A11
MQTL4	A12	EC， FW， SL	95.89	128.66	125.17~132.17	7.03	MON_CGR5815~mk9166_A12
MQTL5	A13	GR， MDA， RWC	95.89	113.94	109.27~118.61	9.34	mk10274_A13~HAU3159
MQTL6	D01	FW（2）， SLW	54.64	111.16	109.00~113.32	4.32	mk10917_D01~mk10911_D01
MQTL7	D01	FW（2）， SLW（2）	54.64	139.25	135.85~142.65	6.80	mk10884_D01~mk10753_D01
MQTL8	D03	LDW， LFW（2）， SLW（2）	185.41	219.66	217.89~221.41	3.53	mk12142_D03~mk12152_D03
MQTL9	D06	LDW（2）， LFW， SL， SLW	31.16	136.04	129.70~142.39	12.69	mk13562_D09~mk13549_D09
MQTL10	D07	CHL（2）， RFW	64.74	31.89	31.43~32.35	0.92	MUSB0921~mk14878_D07
MQTL11	D08	FW（3）. SLW	55.18	268.62	263.66~273.59	9.93	MulMa514_D08~MulMa185-m

编号 Code	染色体 Chromosome	原始性状（数量） Original trait（amount）	AIC值 AIC value	位置 Position/cM	置信区间 Confidence interval/cM	图距 Map distance/cM	侧翼标记 Flanking marker
MQTL1	A03	EC， SFW（2）	46.26	203.90	198.84~208.97	10.13	mk11960~mk2075
MQTL2	A06	SFW（3）， SL， SLW（2）	46.26	34.55	34.00~35.11	1.11	mk4998_A06~mk5000_A06
MQTL3	A11	PH， SFW， SL	40.90	36.19	35.52~36.86	1.34	DPL0209（b）~mk7803_A11
MQTL4	A12	EC， FW， SL	95.89	128.66	125.17~132.17	7.03	MON_CGR5815~mk9166_A12
MQTL5	A13	GR， MDA， RWC	95.89	113.94	109.27~118.61	9.34	mk10274_A13~HAU3159
MQTL6	D01	FW（2）， SLW	54.64	111.16	109.00~113.32	4.32	mk10917_D01~mk10911_D01
MQTL7	D01	FW（2）， SLW（2）	54.64	139.25	135.85~142.65	6.80	mk10884_D01~mk10753_D01
MQTL8	D03	LDW， LFW（2）， SLW（2）	185.41	219.66	217.89~221.41	3.53	mk12142_D03~mk12152_D03
MQTL9	D06	LDW（2）， LFW， SL， SLW	31.16	136.04	129.70~142.39	12.69	mk13562_D09~mk13549_D09
MQTL10	D07	CHL（2）， RFW	64.74	31.89	31.43~32.35	0.92	MUSB0921~mk14878_D07
MQTL11	D08	FW（3）. SLW	55.18	268.62	263.66~273.59	9.93	MulMa514_D08~MulMa185-m

MQTL	基因序列号Gene ID		注释信息Annotation information
MQTL	棉花 Gossypium hirsutum	拟南芥 Arabidopsis thaliana	注释信息Annotation information
MQTL3	Ghi_A11G02286	AT5G61790	钙离子结合、碳水化合物结合 Calcium ion binding， carbohydrate binding
	Ghi_A11G02291	AT5G07350	mRNA分解代谢过程 mRNA catabolic process
	Ghi_A11G02376	AT1G74920	乙醛脱氢酶（NAD⁺）活性、甜菜碱醛脱氢酶活性 Aldehyde dehydrogenase （NAD⁺） activity， betaine-aldehyde dehydrogenase activity
	Ghi_A11G02386	AT3G51370	金属离子结合 Metal ion binding
	Ghi_A11G02401	AT1G19910	质子转运ATPase活性 Proton-transporting ATPase activity
	Ghi_A11G02416	AT4G36130	mRNA结合 mRNA binding
	Ghi_A11G02421	AT1G19835	微管聚合、毛状体形态发生 Microtubule polymerization， brichome morphogenesis
	Ghi_A11G02456	AT2G17820	磷酸酯酶传感器激酶活性、组氨酸磷酸转移激酶活性、渗透传感器活性 Phosphorelay sensor kinase activity， histidine phosphotransfer kinase activity， osmosensor activity
	Ghi_A11G02496	AT2G18170	MAP激酶活性、丝氨酸/苏氨酸激酶活性、ATP结合 MAP kinase activity， protein serine/threonine kinase activity， ATP binding
	Ghi_A11G02546	AT4G36740	DNA结合转录因子活性 DNA-binding transcription factor activity
	Ghi_A11G02611	AT5G66960	苏氨酸类内肽酶活性 Serine-type endopeptidase activity
	Ghi_A11G02631	AT5G66880	蛋白激酶活性、ATP结合、丝氨酸激酶活性 Protein kinase activity， ATP binding， protein serine kinase activity
	Ghi_A11G02636	AT4G37180	DNA结合转录因子活性、基因表达的负调控 DNA-binding transcription factor activity， negative regulation of gene expression
	Ghi_A11G02641	AT5G66850	MAP激酶激酶激酶活性 MAP kinase kinase kinase activity