Evaluation of Cold Tolerance of 90 Apple Cultivars and Genome Wide Association Analysis

doi:10.16420/j.issn.0513-353x.2022-0052

Acta Horticulturae Sinica ›› 2023, Vol. 50 ›› Issue (5): 921-932.doi: 10.16420/j.issn.0513-353x.2022-0052

• Genetic & Breeding·Germplasm Resources·Molecular Biology • Next Articles

Evaluation of Cold Tolerance of 90 Apple Cultivars and Genome Wide Association Analysis

KAN Zhiyong, ZHANG Dehui(), LI Zhongxing, YU Sisi, QIAN Qian, FAN Tianle, LI Xuewei, MA Fengwang, GUAN Qingmei()

State Key Laboratory of Crop Stress Biology for Arid Areas，College of Horticulture，Northwest A & F University，Yangling，Shannxi 712100，China

Received:2022-11-01 Revised:2023-02-21 Online:2023-05-25 Published:2023-05-31
Contact: ZHANG Dehui, GUAN Qingmei E-mail:tsu.zhangdehui@163.com;qguan@nwsuaf.edu.cn

Abstract

Abstract:

In this study，ninety apple cultivars were used as experimental materials to evaluate cold tolerance by a relative electrical conductivity test. Genome-wide association analysis was conducted on 1 247 162 SNPs detected in apple accessions by genome resequencing technology，and candidate genes significantly associated with cold tolerance were selected. Three cultivars with the strongest cold tolerance were identified，and their relative electrical conductivity was all less than 40%，which were‘Jinhong’，‘Ederbostdorf’and‘Haralson’. Based on the association analysis using 1 247 162 high-quality SNPs and index of relative electrical conductivity characterizing cold tolerance，five significant correlated loci related to cold tolerance were identified，which were distributed on chromosome 4，15，and 16，respectively. Three candidate genes TIF3B1（MD04G1241100），COR47（MD15G1003900），and MD16G1069900 closely related to cold stress tolerance were identified.

Key words: apple, cold resistance, genome-wide association analysis

CLC Number:

S661.1

KAN Zhiyong, ZHANG Dehui, LI Zhongxing, YU Sisi, QIAN Qian, FAN Tianle, LI Xuewei, MA Fengwang, GUAN Qingmei. Evaluation of Cold Tolerance of 90 Apple Cultivars and Genome Wide Association Analysis[J]. Acta Horticulturae Sinica, 2023, 50(5): 921-932.

Figures/Tables 8

References 56

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名称 Name	电导率/% Electrical conductivity	名称 Name	电导率/% Electrical conductivity	名称 Name	电导率/% Electrical conductivity
金红Jinhong	34.43 ± 1.59	瑞丹Judaine	48.29 ± 3.16	A35	53.82 ± 3.23
埃德尔博斯多夫Edelborsdorfer	38.98 ± 1.62	Seromine	48.39 ± 1.91	北海道9号Hokkaido 9	54.78 ± 2.54
赫拉森Haralson	39.60 ± 2.26	瑞星Judestar	48.50 ± 3.86	凯密欧Cameo	55.00 ± 3.84
C32	41.19 ± 3.33	昂林Korin	49.00 ± 1.30	荷斯坦Holstein	55.52 ± 5.54
15	43.23 ± 3.43	王林Orin	49.21 ± 3.19	N1	55.52 ± 2.08
夕阳Sundowner	43.40 ± 0.38	Challenger	49.27 ± 5.12	信浓红CinanoRed	55.85 ± 3.76
蜜脆Honeycrisp	43.41 ± 0.30	弘前富士Hirosakifuji	49.36 ± 4.56	Kiku	55.85 ± 3.98
C10	43.85 ± 3.58	早红1号Early Red One	49.42 ± 2.96	玫瑰光芒Rosy Glow	55.98 ± 2.08
Ruby Mac	43.97 ± 3.63	美味Ambrosia	49.47 ± 0.49	皮诺娃Pinova	56.18 ± 2.37
Halerstadter Jungfermapfe	44.17 ± 2.98	Northfield Beauty	49.62 ± 3.39	凉香的季节Ryoka No Kisetsu	56.29 ± 3.42
Redcord	44.35 ± 1.60	Juliana	49.72 ± 3.99	皇家嘎拉Royal Gala	56.35 ± 4.72
福拉瑞娜Florina	44.37 ± 0.63	阿莱特Arlet	49.91 ± 1.45	AC	56.36 ± 1.52
魔笛Modi	44.57 ± 2.02	N7	49.95 ± 3.25	JA	56.62 ± 1.34
红勋1号Hongxun 1	44.58 ± 3.21	秋光Qiuguang	50.09 ± 0.78	千秋Senshu	56.95 ± 1.21
Yellow Transparent	44.69 ± 4.72	寒富Hanfu	50.41 ± 3.95	富士2001 Fuji 2001	57.04 ± 2.81
Chenago Strawberry	44.70 ± 2.34	Reinders	50.80 ± 3.23	鲁宾斯Rubens	57.19 ± 1.50
甘红Ganhong	45.15 ± 1.96	小国光Ralls	51.03 ± 2.92	坎兹Kanzi	57.26 ± 3.55
署红James Grieve	45.58 ± 1.62	茜Akane	51.09 ± 4.86	Gloster69	57.31 ± 1.34
晨雾Morning Mist	45.70 ± 1.69	秦阳Qinyang	51.21 ± 2.62	T22	57.33 ± 3.22
丽嘎啦 Regal Gala	46.45 ± 3.55	Goldgeld55544	51.26 ± 4.14	Chanterler	57.64 ± 1.10
1	46.50 ± 0.77	Maririi Red	51.27 ± 3.91	Su	58.38 ± 2.78
瑞林Jude-line	46.78 ± 5.88	NJ-90	51.92 ± 3.79	红盖露 Gale Gala	59.12 ± 3.90
信浓甜Cinano Sweet	47.30 ± 1.70	K296	52.62 ± 3.88	平成Heisei	59.43 ± 4.01
千秋Senshu	47.39 ± 1.60	Roho3615	53.04 ± 0.96	斯派克Spike	60.03 ± 4.67
Pound Sweet	47.98 ± 2.09	Fujiko	53.15 ± 2.80	粉金Pinkgold	60.26 ± 0.91
威廉姆斯女士Lady Williams	48.08 ± 1.90	秦冠Qinguan	53.21 ± 1.95	太平洋玫瑰Pacific Rose	60.81 ± 2.03
花嫁Wealthy	48.17 ± 3.44	凉香Ryoka	53.29 ± 4.36	红露Hongro	61.00 ± 2.96
N9	48.19 ± 4.83	阿丽亚娜Ariane	53.53 ± 1.21	大都Daitron	63.03 ± 0.32
长富2号 Nagafu 2	48.22 ± 0.80	Idared	53.68 ± 3.42	布瑞本Braeburn	64.61 ± 5.66
N2	48.25 ± 1.86	C25	53.81 ± 2.59	津轻Tsugaru	65.16 ± 5.71

名称 Name	电导率/% Electrical conductivity	名称 Name	电导率/% Electrical conductivity	名称 Name	电导率/% Electrical conductivity
金红Jinhong	34.43 ± 1.59	瑞丹Judaine	48.29 ± 3.16	A35	53.82 ± 3.23
埃德尔博斯多夫Edelborsdorfer	38.98 ± 1.62	Seromine	48.39 ± 1.91	北海道9号Hokkaido 9	54.78 ± 2.54
赫拉森Haralson	39.60 ± 2.26	瑞星Judestar	48.50 ± 3.86	凯密欧Cameo	55.00 ± 3.84
C32	41.19 ± 3.33	昂林Korin	49.00 ± 1.30	荷斯坦Holstein	55.52 ± 5.54
15	43.23 ± 3.43	王林Orin	49.21 ± 3.19	N1	55.52 ± 2.08
夕阳Sundowner	43.40 ± 0.38	Challenger	49.27 ± 5.12	信浓红CinanoRed	55.85 ± 3.76
蜜脆Honeycrisp	43.41 ± 0.30	弘前富士Hirosakifuji	49.36 ± 4.56	Kiku	55.85 ± 3.98
C10	43.85 ± 3.58	早红1号Early Red One	49.42 ± 2.96	玫瑰光芒Rosy Glow	55.98 ± 2.08
Ruby Mac	43.97 ± 3.63	美味Ambrosia	49.47 ± 0.49	皮诺娃Pinova	56.18 ± 2.37
Halerstadter Jungfermapfe	44.17 ± 2.98	Northfield Beauty	49.62 ± 3.39	凉香的季节Ryoka No Kisetsu	56.29 ± 3.42
Redcord	44.35 ± 1.60	Juliana	49.72 ± 3.99	皇家嘎拉Royal Gala	56.35 ± 4.72
福拉瑞娜Florina	44.37 ± 0.63	阿莱特Arlet	49.91 ± 1.45	AC	56.36 ± 1.52
魔笛Modi	44.57 ± 2.02	N7	49.95 ± 3.25	JA	56.62 ± 1.34
红勋1号Hongxun 1	44.58 ± 3.21	秋光Qiuguang	50.09 ± 0.78	千秋Senshu	56.95 ± 1.21
Yellow Transparent	44.69 ± 4.72	寒富Hanfu	50.41 ± 3.95	富士2001 Fuji 2001	57.04 ± 2.81
Chenago Strawberry	44.70 ± 2.34	Reinders	50.80 ± 3.23	鲁宾斯Rubens	57.19 ± 1.50
甘红Ganhong	45.15 ± 1.96	小国光Ralls	51.03 ± 2.92	坎兹Kanzi	57.26 ± 3.55
署红James Grieve	45.58 ± 1.62	茜Akane	51.09 ± 4.86	Gloster69	57.31 ± 1.34
晨雾Morning Mist	45.70 ± 1.69	秦阳Qinyang	51.21 ± 2.62	T22	57.33 ± 3.22
丽嘎啦 Regal Gala	46.45 ± 3.55	Goldgeld55544	51.26 ± 4.14	Chanterler	57.64 ± 1.10
1	46.50 ± 0.77	Maririi Red	51.27 ± 3.91	Su	58.38 ± 2.78
瑞林Jude-line	46.78 ± 5.88	NJ-90	51.92 ± 3.79	红盖露 Gale Gala	59.12 ± 3.90
信浓甜Cinano Sweet	47.30 ± 1.70	K296	52.62 ± 3.88	平成Heisei	59.43 ± 4.01
千秋Senshu	47.39 ± 1.60	Roho3615	53.04 ± 0.96	斯派克Spike	60.03 ± 4.67
Pound Sweet	47.98 ± 2.09	Fujiko	53.15 ± 2.80	粉金Pinkgold	60.26 ± 0.91
威廉姆斯女士Lady Williams	48.08 ± 1.90	秦冠Qinguan	53.21 ± 1.95	太平洋玫瑰Pacific Rose	60.81 ± 2.03
花嫁Wealthy	48.17 ± 3.44	凉香Ryoka	53.29 ± 4.36	红露Hongro	61.00 ± 2.96
N9	48.19 ± 4.83	阿丽亚娜Ariane	53.53 ± 1.21	大都Daitron	63.03 ± 0.32
长富2号 Nagafu 2	48.22 ± 0.80	Idared	53.68 ± 3.42	布瑞本Braeburn	64.61 ± 5.66
N2	48.25 ± 1.86	C25	53.81 ± 2.59	津轻Tsugaru	65.16 ± 5.71

引物名称 Primer name	正向引物（5′-3′） Forward primer	反向引物（5′-3′） Reverse primer
MD04G1241100	CAAAGAGAGGACTCATGGATACAAG	GTCCAGAAAGTGCGTTTGTAGAAC
MD15G1003900	AAGACTGAGGAGGTTCCAGTTGG	CTTCTCTTTCTCCTTGATGTCCTTG
MD16G1069900	GCTACATAGCATGAGGGACATGTTG	TCAAGCTCTGCCATGTTATCCAC

引物名称 Primer name	正向引物（5′-3′） Forward primer	反向引物（5′-3′） Reverse primer
MD04G1241100	CAAAGAGAGGACTCATGGATACAAG	GTCCAGAAAGTGCGTTTGTAGAAC
MD15G1003900	AAGACTGAGGAGGTTCCAGTTGG	CTTCTCTTTCTCCTTGATGTCCTTG
MD16G1069900	GCTACATAGCATGAGGGACATGTTG	TCAAGCTCTGCCATGTTATCCAC

染色体 Chromosome	SNP位置/bp SNP position	基因型 Genotype	SNP注释 SNP annotation	P值 P value
Chr04	31 829 140	G/A	外显子区域Exonic	3.26E-06
	31 821 706	G/A	内含子Intronic	7.21E-06
Chr15	238 509	T/C	外显子区域Exonic	5.47E-06
	7 277 652	T/C	外显子区域Exonic	8.57E-06
Chr16	4 918 081	A/G	基因间Intergenic	4.22E-06

Evaluation of Cold Tolerance of 90 Apple Cultivars and Genome Wide Association Analysis

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