Advances in Genome-Wide Association Study Associated Important Traits in Apple

doi:10.16420/j.issn.0513-353x.2023-0818

Acta Horticulturae Sinica ›› 2024, Vol. 51 ›› Issue (7): 1565-1579.doi: 10.16420/j.issn.0513-353x.2023-0818

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Advances in Genome-Wide Association Study Associated Important Traits in Apple

TIAN Wen¹^,², LI Zichen², WANG Lin², WANG Dajiang², WANG Kun², SUN Simiao², WANG Guangyi², LIU Zhao¹^,², LU Xiang¹^,², FENG Jianrong¹^,^*(), GAO Yuan²^,^*()

¹ Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization，College of Agriculture，Shihezi University，Shihezi，Xinjiang 832000，China
² Key Laboratory of Horticultural Crops Germplasm Resources Utilization，Ministry of Agriculture and Rural Affairs，Research Institute of Pomology，Chinese Academy of Agricultural Sciences，Xingcheng，Liaoning 125100，China

Received:2024-01-27 Revised:2024-05-21 Online:2024-07-25 Published:2024-07-19
Contact: FENG Jianrong, GAO Yuan

Abstract

Abstract:

This paper briefly introduces the basic principles，analysis processes，and advantages of genome-wide association study（GWAS），and focuses on the new progress in the identification of genes related to important traits such as apple phenological period，appearance and internal quality，and resistance to biotic and abiotic stresses in apple. The limitations and prospects of the current research were put forward in order to provide a theoretical basis and reference for breeding breakthrough cultivars of apples.

Key words: apple, genome-wide association study, genetic breeding, advance

TIAN Wen, LI Zichen, WANG Lin, WANG Dajiang, WANG Kun, SUN Simiao, WANG Guangyi, LIU Zhao, LU Xiang, FENG Jianrong, GAO Yuan. Advances in Genome-Wide Association Study Associated Important Traits in Apple[J]. Acta Horticulturae Sinica, 2024, 51(7): 1565-1579.

Figures/Tables 3

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物候期	显著关联的基因、QTL、分子标记或SNP	参考文献
Phenological period	Significantly associated genes，QTL，molecular markers or SNPs	Reference
花期 Flowering period	NAC transcription factor（MD09G1006400），WRKY transcription factor （MD09G1008800），MD09G1009100	Urrestarazu et al.，2017
花期 Flowering period	AX-115409139，AX-115198592，AX-115410038	Jung et al.，2020
成熟期 Ripening period	NAC transcription factor（MD03G1222600，MD03G1222700），NAM/NAC （MD10G1288300，MD10G1299900）	Urrestarazu et al.，2017
	NAC5（MDP0000868419）	McClure et al.，2018
	NAC18.1（MD03G1222600）	Migicovsky et al.，2016；Larsen et al.，2019
	AX-115366114，AX-115350952，AX-115296686	Jung et al.，2020

物候期	显著关联的基因、QTL、分子标记或SNP	参考文献
Phenological period	Significantly associated genes，QTL，molecular markers or SNPs	Reference
花期 Flowering period	NAC transcription factor（MD09G1006400），WRKY transcription factor （MD09G1008800），MD09G1009100	Urrestarazu et al.，2017
花期 Flowering period	AX-115409139，AX-115198592，AX-115410038	Jung et al.，2020
成熟期 Ripening period	NAC transcription factor（MD03G1222600，MD03G1222700），NAM/NAC （MD10G1288300，MD10G1299900）	Urrestarazu et al.，2017
	NAC5（MDP0000868419）	McClure et al.，2018
	NAC18.1（MD03G1222600）	Migicovsky et al.，2016；Larsen et al.，2019
	AX-115366114，AX-115350952，AX-115296686	Jung et al.，2020

品质类型 Quality type	性状或指标 Trait or indicator			显著关联的基因、QTL、分子标记或SNP		参考文献 Reference
品质类型 Quality type	性状或指标 Trait or indicator			Significantly associated genes，QTL，molecular markers or SNPs		参考文献 Reference
外观品质 Appearance quality	果实大小和形状 Fruit size and shape			fs4.1 (MD04G1027600)，fs15.1 (MD15G1049300)，fs15.2 (MD15G1251500)		Liao et al.，2021
				QTL gwa_w1，QTL gwa_w2		段乃彬，2017
				ERECTA (MD15G1049300)		Chen et al.，2021
				NAP (MD16G1069500)，ABCG25 (MD03G1222900)		Lin et al.，2023
	果皮颜色 Fruit skin color			MDMYB1		Migicovsky et al.，2016，2021；Amyotte et al.，2017；Moriya et al.，2017
				MYB15 (MD13G1213900)，ERF1B (MD13G1213100)，WRKY28 (MD17G1138100)等		Kumar et al.，2022b
				MdMYB133，MD01G1155100，MD01G1200200等		Minamikawa et al.，2021
内在品质 Internal quality	果实质地 Fruit texture	—		FEM_cg_9，FEM_cg_19 (Md-PG1SNP) 等		Di Guardo et al.，2017
		脆度、硬度、多汁 Crispness，firmness and juiciness		MYB6 (MD09G1261200)，MD09G1263800等		Kumar et al.，2022b
		脆度Crisp		S5_11526314，S13_6049060		Amyotte et al.，2017
		汁液Juicy		S13_6049060		Amyotte et al.，2017
		果肉粗细Mealy		S5_11526314，S10_24387143		Amyotte et al.，2017
		硬度Firmness		ERF4		Hu et al.，2020
				NAC18.1(MD03G1222600)		Migicovsky et al.，2016，2021
				gwa_f1		段乃彬，2017
				FAD2 (MD12G1057600)		Lin et al.，2023
				MD07G1071800，MD07G1071900		Chen et al.，2021
				PG1，ACO1		Han et al.，2020
				ERF (MDP0000855671)		McClure et al.，2018
	果皮厚度 Skin thickness			S10_28123441		Amyotte et al.，2017
	果实褐变 Flesh browning	—		CHS (MD02G1218400，MD02G1218500)		Kumar et al.，2022b
		—		MdMYB10 (MDP0000259616)， LAR1 (MDP0000376284)		Kumar et al.，2013
		PPO活性PPO activity		SNP_FB_0600257，RosBREEDSNP_SNP_CA_3097521_Lg16_01116_MAF50_724569_exon1		Kunihisa et al.，2021
		总多酚含量Total polyphenol content		GDsnp00047		Kunihisa et al.，2021
		果汁褐变Juice browning		RosBREEDSNP_SNP_CT_1540624_Lg16_ LAR1_MAF40_1618769_exon2		Kunihisa et al.，2021
		褐变指数 Index number of browning		SNP_FB_0598996，GDsnp00125		Kunihisa et al.，2021
	多酚化合物 Polyphenolic compounds	槲皮苷、绿原酸等 Quercitrin，chlorogenic acid，etc 原花青素Pocyanidin		UGT/F3'H，CCOAMT (MD05G1083900); CAD (MD05G1089900) 等 Myb9-like (MD15G1051400)		McClure et al.，2019 Lin et al.，2023
	可滴定酸 Titratable acidity	—		MDP0000292924 MA1		Kumar et al.，2013 Kumar et al.，2015
				Significantly associated genes，QTL，molecular markers or SNPs
内在品质 Internal quality	有机酸 Organic acid		苹果酸Malic acid	MA1，MdPP2CH MdMYB44 MD14G1135700，MD07G1129000，ILK	Liao et al.，2021 方庭，2018 Chen et al.，2021
	有机酸 Organic acid		柠檬酸Citric acid	MdTDT (MD10G1332900)	Liao et al.，2021
	可溶性固形物Soluble solid content		—	S8_24235959 MD17G1286100,MD05G1300000，MD15G1340300等 SPS3，SPS4，HK1，SUSY1，SUT1	Amyotte et al.，2017 Chen et al.，2021 Han et al.，2020
			葡萄糖Glucose	MdWD40 (MD03G1273100)	Liao et al.，2021
			果糖Fructose	MdFK (MD01G1177300) MD04G1247700，MD17G1149000	Liao et al.，2021 Chen et al.，2021
			蔗糖Sucrose	MdRPM1-like (MD01G1186600)，MdPQLC (MD09G1018900) MD09G1064500	Liao et al.，2021 Chen et al.，2021
			蔗糖；果糖占比/%；蔗糖占比/% Sucrose conyent； Fructose percentage； Sucrose percentage	VIN1 (MDP0000149570)	Larsen et al.，2019
			山梨醇Sorbitol	MdSOT2 (MD10G1079800)	Liao et al.，2021
	香气物质 Aroma compounds		肉豆蔻酸Myristic acid	MD16G1191300	Jiang et al.，2022
			油酸Oleic acid	MD14G1156100，MD16G1261900	Jiang et al.，2022
			亚油酸 Linoleic acid	MdSUP (MD13G1209600)	Jiang et al.，2022
			酯类Esters	MdAAT1 (MDP0000637737) MpAAT1，MdCXE12 (MDP0000445131)， MdCXE4 等 AAT1 (MD02G1013900)	Farneti et al.，2017 Kumar et al.，2015 Larsen et al.，2019
			醇类Alcohols	ADH (MDP0000523942)，MdACS3 (MDP0000247533)等 ADH (MDP0000565848)，MdLOX8b，MdLOX9a	Farneti et al.，2017 Kumar et al.，2015
			醛类Aldehydes	ADH (MDP0000077529)，FB_0442970_L1_PA等	Farneti et al.，2017
			苯丙烯Phenylpropenes	RB_14354679_L5_PA，FB_0086581_L11_PA等	Farneti et al.，2017
			萜烯类Terpenes	MdLOX1e	Kumar et al.，2015
	果肉颜色 Flesh color			MdMYB10，NB-ARC，UGT MdMYB73，MdERF4，MdNAC73等	Chen et al.，2021 Kumar et al.，2022a

品质类型 Quality type	性状或指标 Trait or indicator			显著关联的基因、QTL、分子标记或SNP		参考文献 Reference
品质类型 Quality type	性状或指标 Trait or indicator			Significantly associated genes，QTL，molecular markers or SNPs		参考文献 Reference
外观品质 Appearance quality	果实大小和形状 Fruit size and shape			fs4.1 (MD04G1027600)，fs15.1 (MD15G1049300)，fs15.2 (MD15G1251500)		Liao et al.，2021
				QTL gwa_w1，QTL gwa_w2		段乃彬，2017
				ERECTA (MD15G1049300)		Chen et al.，2021
				NAP (MD16G1069500)，ABCG25 (MD03G1222900)		Lin et al.，2023
	果皮颜色 Fruit skin color			MDMYB1		Migicovsky et al.，2016，2021；Amyotte et al.，2017；Moriya et al.，2017
				MYB15 (MD13G1213900)，ERF1B (MD13G1213100)，WRKY28 (MD17G1138100)等		Kumar et al.，2022b
				MdMYB133，MD01G1155100，MD01G1200200等		Minamikawa et al.，2021
内在品质 Internal quality	果实质地 Fruit texture	—		FEM_cg_9，FEM_cg_19 (Md-PG1SNP) 等		Di Guardo et al.，2017
		脆度、硬度、多汁 Crispness，firmness and juiciness		MYB6 (MD09G1261200)，MD09G1263800等		Kumar et al.，2022b
		脆度Crisp		S5_11526314，S13_6049060		Amyotte et al.，2017
		汁液Juicy		S13_6049060		Amyotte et al.，2017
		果肉粗细Mealy		S5_11526314，S10_24387143		Amyotte et al.，2017
		硬度Firmness		ERF4		Hu et al.，2020
				NAC18.1(MD03G1222600)		Migicovsky et al.，2016，2021
				gwa_f1		段乃彬，2017
				FAD2 (MD12G1057600)		Lin et al.，2023
				MD07G1071800，MD07G1071900		Chen et al.，2021
				PG1，ACO1		Han et al.，2020
				ERF (MDP0000855671)		McClure et al.，2018
	果皮厚度 Skin thickness			S10_28123441		Amyotte et al.，2017
	果实褐变 Flesh browning	—		CHS (MD02G1218400，MD02G1218500)		Kumar et al.，2022b
		—		MdMYB10 (MDP0000259616)， LAR1 (MDP0000376284)		Kumar et al.，2013
		PPO活性PPO activity		SNP_FB_0600257，RosBREEDSNP_SNP_CA_3097521_Lg16_01116_MAF50_724569_exon1		Kunihisa et al.，2021
		总多酚含量Total polyphenol content		GDsnp00047		Kunihisa et al.，2021
		果汁褐变Juice browning		RosBREEDSNP_SNP_CT_1540624_Lg16_ LAR1_MAF40_1618769_exon2		Kunihisa et al.，2021
		褐变指数 Index number of browning		SNP_FB_0598996，GDsnp00125		Kunihisa et al.，2021
	多酚化合物 Polyphenolic compounds	槲皮苷、绿原酸等 Quercitrin，chlorogenic acid，etc 原花青素Pocyanidin		UGT/F3'H，CCOAMT (MD05G1083900); CAD (MD05G1089900) 等 Myb9-like (MD15G1051400)		McClure et al.，2019 Lin et al.，2023
	可滴定酸 Titratable acidity	—		MDP0000292924 MA1		Kumar et al.，2013 Kumar et al.，2015
				Significantly associated genes，QTL，molecular markers or SNPs
内在品质 Internal quality	有机酸 Organic acid		苹果酸Malic acid	MA1，MdPP2CH MdMYB44 MD14G1135700，MD07G1129000，ILK	Liao et al.，2021 方庭，2018 Chen et al.，2021
	有机酸 Organic acid		柠檬酸Citric acid	MdTDT (MD10G1332900)	Liao et al.，2021
	可溶性固形物Soluble solid content		—	S8_24235959 MD17G1286100,MD05G1300000，MD15G1340300等 SPS3，SPS4，HK1，SUSY1，SUT1	Amyotte et al.，2017 Chen et al.，2021 Han et al.，2020
			葡萄糖Glucose	MdWD40 (MD03G1273100)	Liao et al.，2021
			果糖Fructose	MdFK (MD01G1177300) MD04G1247700，MD17G1149000	Liao et al.，2021 Chen et al.，2021
			蔗糖Sucrose	MdRPM1-like (MD01G1186600)，MdPQLC (MD09G1018900) MD09G1064500	Liao et al.，2021 Chen et al.，2021
			蔗糖；果糖占比/%；蔗糖占比/% Sucrose conyent； Fructose percentage； Sucrose percentage	VIN1 (MDP0000149570)	Larsen et al.，2019
			山梨醇Sorbitol	MdSOT2 (MD10G1079800)	Liao et al.，2021
	香气物质 Aroma compounds		肉豆蔻酸Myristic acid	MD16G1191300	Jiang et al.，2022
			油酸Oleic acid	MD14G1156100，MD16G1261900	Jiang et al.，2022
			亚油酸 Linoleic acid	MdSUP (MD13G1209600)	Jiang et al.，2022
			酯类Esters	MdAAT1 (MDP0000637737) MpAAT1，MdCXE12 (MDP0000445131)， MdCXE4 等 AAT1 (MD02G1013900)	Farneti et al.，2017 Kumar et al.，2015 Larsen et al.，2019
			醇类Alcohols	ADH (MDP0000523942)，MdACS3 (MDP0000247533)等 ADH (MDP0000565848)，MdLOX8b，MdLOX9a	Farneti et al.，2017 Kumar et al.，2015
			醛类Aldehydes	ADH (MDP0000077529)，FB_0442970_L1_PA等	Farneti et al.，2017
			苯丙烯Phenylpropenes	RB_14354679_L5_PA，FB_0086581_L11_PA等	Farneti et al.，2017
			萜烯类Terpenes	MdLOX1e	Kumar et al.，2015
	果肉颜色 Flesh color			MdMYB10，NB-ARC，UGT MdMYB73，MdERF4，MdNAC73等	Chen et al.，2021 Kumar et al.，2022a

胁迫类型 Stress type	抗逆性状 Stress resistance trait	显著关联的基因、QTL、分子标记或SNP	参考文献 Reference
胁迫类型 Stress type	抗逆性状 Stress resistance trait	Significantly associated genes，QTL，molecular markers or SNPs	参考文献 Reference
生物胁迫 Biotic stress	斑点落叶病 Apple leaf spot	MD05G1054300，MD05G1054400，MD05G1054500等	储宝华等，2022
	火疫病 Fire blight	MdSNPui06011，MdSNPui08421，MdSNPui01364等	Khan et al.，2013
	火疫病 Fire blight	GBS_35513256，GBS_35346100，GBS_35346084等	Thapa et al.，2021
	黑星病 Apple scab	MDP0000432882，MDP0000213589，MDP0000088815等	McClure et al.，2018
	褐斑病 Apple marssonina blotch	LOC103442381，LOC103443382，LOC103425912等	Noh et al.，2020
非生物胁迫 Abiotic stress	耐寒性 Cold resistance	TIF3B1 (MD04G1241100)，COR47 (MD15G1003900)等	坎智勇等，2023
	耐热性 Heat resistance	FLOWERING LOCUS C-LIKE，INDUCER OF C-REPEAT BINDING FACTOR EXPRESSION 1，MITOCHONDRIAL PHOSPHATE TRANSPORTER	Chen et al.，2022
	抗旱性 Drought resistance	MdSHN1，MdLTP4，MdWSD1等	Cao et al.，2021
	抗旱性 Drought resistance	CCT1，WSD1，MdMYB94	姜丽娟，2022

Advances in Genome-Wide Association Study Associated Important Traits in Apple

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