Evaluation and Validation of Molecular Markers for Fruit Color and Firmness in Multiple Apple Hybrid Progenies

doi:10.16420/j.issn.0513-353x.2026-0240

Acta Horticulturae Sinica ›› 2026, Vol. 53 ›› Issue (7): 1977-1990.doi: 10.16420/j.issn.0513-353x.2026-0240

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

Evaluation and Validation of Molecular Markers for Fruit Color and Firmness in Multiple Apple Hybrid Progenies

ZHANG Xiaoke¹, WANG Jinhong¹, YANG Yazhou², LI Chao², LI Linguang³, HAN Zhenhai¹, WU Ting¹^,^*()

¹ College of Horticulture， China Agricultural University， Beijing 100193， China
² Northwest A & F University， Yangling， Shaanxi 712100， China
³ Shandong Institute of Pomology， Tai’an， Shandong 271000， China

Received:2026-04-23 Revised:2026-06-12 Online:2026-07-25 Published:2026-07-23
Contact: WU Ting

Abstract

Abstract:

In six apple hybrid progenies（‘Honeycrisp’×‘Ruiyang’，‘Mato 1’×‘Gala’，‘Fuji’×‘Pink Lady’，‘Ruiyang’×‘Envy’，‘Fuji’×‘Malus sieversii’，and‘Qinguan’×‘Honeycrisp’），six molecular markers（ERF17，MYB1，ERF4，ACS1，ACO1 and ACS3a866）were validated. The correlation between markers and traits was analyzed by associating genotypes with fruit phenotypes（including peel chlorophyll content，coloration degree，and fruit firmness）. The results showed that the ERF17 marker accurately predicted chlorophyll content in most progenies，but it was not significant in the ‘Mato 1’×‘Gala’progeny. The MYB1 marker achieved a high prediction accuracy of 92.05% for whether the peel is red. ERF4，ACS1，and ACS3a866 showed high accuracy in predicting fruit firmness，but there were interactions among the markers.

Key words: apple, molecular marker, peel degreening, firmness, phenotypic validation, epistasis

ZHANG Xiaoke, WANG Jinhong, YANG Yazhou, LI Chao, LI Linguang, HAN Zhenhai, WU Ting. Evaluation and Validation of Molecular Markers for Fruit Color and Firmness in Multiple Apple Hybrid Progenies[J]. Acta Horticulturae Sinica, 2026, 53(7): 1977-1990.

Figures/Tables 11

References 28

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亲本 Parent	果皮颜色 Peel color	果实硬度 Fruit firmness
"蜜脆"‘Honeycrisp’	鲜红 Bright red	中/高 Medium/high
‘瑞阳’‘Ruiyang’	鲜红或浓红 Bright red or deep red	高 High
‘藤牧1号’‘Mato 1’	鲜红 Bright red	低 Low
‘嘎啦’‘Gala’	淡红 Light red	中/高 Medium/high
‘富士’‘Fuji’	浓红 Deep red	低 Low
‘粉红女士’‘Pink Lady’	鲜红 Bright red	高 High
‘秦冠’‘Qinguan’	暗红或褐红 Dark red or russet red	中 Medium
‘新疆野苹果’‘Malus sieversii’	鲜红或绿 Bright red or green	高 High
‘爱妃’‘Envy’	暗红 Dark red	高 High

亲本 Parent	果皮颜色 Peel color	果实硬度 Fruit firmness
"蜜脆"‘Honeycrisp’	鲜红 Bright red	中/高 Medium/high
‘瑞阳’‘Ruiyang’	鲜红或浓红 Bright red or deep red	高 High
‘藤牧1号’‘Mato 1’	鲜红 Bright red	低 Low
‘嘎啦’‘Gala’	淡红 Light red	中/高 Medium/high
‘富士’‘Fuji’	浓红 Deep red	低 Low
‘粉红女士’‘Pink Lady’	鲜红 Bright red	高 High
‘秦冠’‘Qinguan’	暗红或褐红 Dark red or russet red	中 Medium
‘新疆野苹果’‘Malus sieversii’	鲜红或绿 Bright red or green	高 High
‘爱妃’‘Envy’	暗红 Dark red	高 High

标记名称 Marker name	等位基因 Alleles	SNP或InDel SNP or InDel	基因变异位点 Genetic variation locus	引物序列（5′-3′） Primer sequence
ACS3a866	GG GT TT	SNP	启动子区-866位点G/T The G/T polymorphism at the-866 site in the promoter region	F：CTTCCAGATTACTCCTCAAGCTTTA R：AGTCTCTTTCTATTTGTCTTTATGTAGTTTC
ERF4	CC CG GG	SNP	EAR结构域SNP（C→G），导致氨基酸改变SNP（C→G）in the EAR domain，leading to an amino acid change	F：CTCGCATCTTTCTCCAAGCAGC R：CCGGAAAGAAAGAAAAGCGGTGATC
MYB1	1/1 1/2 1/3	SNP/InDel	启动子区多态性，等位基因与红色果皮相关A promoter region polymer- phism where the allele is associated with red pericarp	F：CCTGAACACGTGGGAACCGGCCCGTTGGTAAC R：GTGAAGGTTGTCTTTATTAGTGACGTG
ERF17	8S/8S 8S/6S	Indel	ERF17蛋白中丝氨酸重复数（3S/6S/ 8S）差异Differences in the number of serine repeats （3S/6S/8S）in the ERF17 protein	F：CTTTCACTGCATGTCAAACCACTTC R：CTCTAGAAATTCCAGAGGAAAGACTC
ACS1	1/1 1/2 2/2	InDel	启动子区有一个长度为166 bp转座子插入There is a 166 bp transposon insertion in the promoter region	F：AGAGAGATGCCATTTTTGTTCGTAC R：CCTACAAACTTGCGTGGGGATTATAAGTGT
ACO1	1/2	SNP/InDel	ACO1启动子区的SNP1229以及一个与InDel62连锁的SNP769的变异Variations of SNP1229 and SNP769，which is linked to InDel62，in the ACO1 promoter region	F：TCCCCCCAATGCACCACTCCA R：GATTCCTTGGCCTTCATAGCTTC

标记名称 Marker name	等位基因 Alleles	SNP或InDel SNP or InDel	基因变异位点 Genetic variation locus	引物序列（5′-3′） Primer sequence
ACS3a866	GG GT TT	SNP	启动子区-866位点G/T The G/T polymorphism at the-866 site in the promoter region	F：CTTCCAGATTACTCCTCAAGCTTTA R：AGTCTCTTTCTATTTGTCTTTATGTAGTTTC
ERF4	CC CG GG	SNP	EAR结构域SNP（C→G），导致氨基酸改变SNP（C→G）in the EAR domain，leading to an amino acid change	F：CTCGCATCTTTCTCCAAGCAGC R：CCGGAAAGAAAGAAAAGCGGTGATC
MYB1	1/1 1/2 1/3	SNP/InDel	启动子区多态性，等位基因与红色果皮相关A promoter region polymer- phism where the allele is associated with red pericarp	F：CCTGAACACGTGGGAACCGGCCCGTTGGTAAC R：GTGAAGGTTGTCTTTATTAGTGACGTG
ERF17	8S/8S 8S/6S	Indel	ERF17蛋白中丝氨酸重复数（3S/6S/ 8S）差异Differences in the number of serine repeats （3S/6S/8S）in the ERF17 protein	F：CTTTCACTGCATGTCAAACCACTTC R：CTCTAGAAATTCCAGAGGAAAGACTC
ACS1	1/1 1/2 2/2	InDel	启动子区有一个长度为166 bp转座子插入There is a 166 bp transposon insertion in the promoter region	F：AGAGAGATGCCATTTTTGTTCGTAC R：CCTACAAACTTGCGTGGGGATTATAAGTGT
ACO1	1/2	SNP/InDel	ACO1启动子区的SNP1229以及一个与InDel62连锁的SNP769的变异Variations of SNP1229 and SNP769，which is linked to InDel62，in the ACO1 promoter region	F：TCCCCCCAATGCACCACTCCA R：GATTCCTTGGCCTTCATAGCTTC

群体名称 Progeny	基因型 Genotype	株数 Number of plants	叶绿素含量/ (mg · g^-1 FW) Chlorophyll content
‘蜜脆’×‘瑞阳’ ‘Honeycrisp’×‘Ruiyang’	ERF17-8S/8S	65	0.1189 ± 0.0652
‘蜜脆’×‘瑞阳’ ‘Honeycrisp’×‘Ruiyang’	ERF17-8S/6S	75	0.1281 ± 0.0587
‘富士’×‘粉红女士’ ‘Fuji’×‘Pink Lady’	ERF17-8S/8S	56	0.2114 ± 0.1186
‘富士’×‘粉红女士’ ‘Fuji’×‘Pink Lady’	ERF17-8S/6S	52	0.2278 ± 0.1058
‘瑞阳’×‘爱妃’ ‘Ruiyang’×‘Envy’	ERF17-8S/8S	70	0.1336 ± 0.0385
‘瑞阳’×‘爱妃’ ‘Ruiyang’×‘Envy’	ERF17-8S/6S	71	0.1487 ± 0.0412^*
‘藤牧1号’×‘嘎啦’ ‘Mato 1’×‘Gala’	ERF17-8S/8S	28	0.0874 ± 0.0576
‘藤牧1号’×‘嘎啦’ ‘Mato 1’×‘Gala’	ERF17-8S/6S	34	0.0810 ± 0.0526
‘富士’×‘新疆野苹果’ ‘Fuji’× Malus sieversii	ERF17-8S/8S	45	0.0214 ± 0.0085
‘富士’×‘新疆野苹果’ ‘Fuji’× Malus sieversii	ERF17-8S/6S	32	0.0270 ± 0.0102^*

Evaluation and Validation of Molecular Markers for Fruit Color and Firmness in Multiple Apple Hybrid Progenies

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群体名称 Progeny	携带MYB1-1等位基因株数 No. of plants carrying MYB1-1 allele	红色果皮株数 No. of red peel plants	非红色果皮株数 No. of non-red peel plants	准确率/% Accuracy
‘蜜脆’×‘瑞阳’‘Honeycrisp’×‘Ruiyang’	151	143	8	94.70
‘富士’×‘粉红女士’‘Fuji’×‘Pink Lady’	107	104	3	97.20
‘藤牧1号’×‘嘎啦’‘Mato 1’×‘Gala’	60	57	3	95.00
‘秦冠’×‘蜜脆’‘Qinguan’×‘Honeycrisp’	98	84	14	85.71
‘富士’× 新疆野苹果‘Fuji’× Malus sieversii	105	92	13	87.62

分子标记 Marker	基因型 Genotype	株数 Number of plants	硬度/（kg · cm^-2） Firmness
ERF4	CC	157	10.47 ± 2.80 a
	CG	203	10.05 ± 2.44 a
	GG	73	8.86 ± 1.92 b
ACS1	1/1	77	9.41 ± 2.18 b
	1/2	212	9.96 ± 2.37 ab
	2/2	145	10.36 ± 2.56 a
ACS3a866	GG	236	10.58 ± 2.45 a
	GT	171	9.41 ± 2.31 b
	TT	26	8.64 ± 2.18 b

ERF4			株数 Number of plants	硬度/（kg · cm^-2） Firmness
CC	1/1	GG	10	10.44 ± 1.55
	1/1	GT	18	9.76 ± 1.35^*
	1/2	GG	58	10.99 ± 1.77
	1/2	GT	17	8.25 ± 1.54^*
	2/2	GG	30	11.38 ± 1.67
	2/2	GT	17	10.47 ± 1.45^*
CG	1/1	GG	9	9.66 ± 1.35
	1/1	GT	18	9.82 ± 1.44
	1/2	GG	57	10.46 ± 1.67
	1/2	GT	43	9.50 ± 1.55^*
	2/2	GG	45	10.71 ± 1.76
	2/2	GT	26	9.67 ± 1.54^*
GG	1/2	GG	16	8.94 ± 1.23
	1/2	GT	13	8.82 ± 1.13^*
	2/2	GG	6	10.97 ± 1.35
	2/2	GT	11	9.31 ± 1.22^*

ACS1			株数 Number of plants	硬度/（kg · cm^-2） Firmness
1/1	GG	CC	10	10.44 ± 1.55
	GG	CG	9	9.66 ± 1.35
	GT	CC	18	9.76 ± 1.35
	GT	CG	18	9.82 ± 1.44
1/2	GG	CC	58	10.99 ± 1.77 a
		CG	57	10.46 ± 1.67 a
		GG	16	8.94 ± 1.23 b
	GT	CC	17	8.25 ± 1.54 b
		CG	43	9.50 ± 1.55 a
		GG	13	8.82 ± 1.13 b
2/2	GG	CC	30	11.38 ± 1.67 a
		CG	45	10.71 ± 1.76 a
		GG	6	10.97 ± 1.35 a
	GT	CC	17	10.47 ± 1.55 a
		CG	26	9.67 ± 1.54 a
		GG	11	9.31 ± 1.22 a

ERF4			株数 Number of plants	硬度/（kg · cm^-2） Firmness
CC	GG	1/1	10	10.44 ± 1.55 a
		1/2	58	10.99 ± 1.77 a
		2/2	30	11.38 ± 1.67 a
	GT	1/1	18	9.76 ± 1.35 a
		1/2	17	8.25 ± 1.54 b
		2/2	17	10.47 ± 1.45 a
CG	GG	1/1	9	9.66 ± 1.35 a
		1/2	57	10.46 ± 1.67 a
		2/2	45	10.71 ± 1.76 a
	GT	1/1	18	9.82 ± 1.44 a
		1/2	43	9.50 ± 1.55 a
		2/2	26	9.67 ± 1.54 a
GG	GG	1/2	16	8.94 ± 1.23
	GG	2/2	6	10.97 ± 1.35^*
	GT	1/2	13	8.82 ± 1.13
	GT	2/2	11	9.31 ± 1.22

标记 Marker	群体名称 Progeny	基因型 Genotype	株数 Number of plants	硬度/（kg · cm^-2） Firmness
ERF4	‘蜜脆’×‘瑞阳’ ‘Honeycrisp’×‘Ruiyang’	CC	48	9.72 ± 3.04 a
		CG	58	9.18 ± 2.64 a
		GG	35	8.38 ± 2.05 a
	‘富士’×‘粉红女士’ ‘Fuji’×‘Pink Lady’	CC	35	11.86 ± 3.13^*
	‘富士’×‘粉红女士’ ‘Fuji’×‘Pink Lady’	CG	38	10.59 ± 2.62
	‘富士’×‘新疆野苹果’ ‘Fuji’×‘Malus sieversii’	CC	6	11.10 ± 2.50 a
		CG	28	10.84 ± 2.18 a
		GG	18	9.31 ± 1.67 b
	‘秦冠’×‘蜜脆’ ‘Qinguan’×‘Honeycrisp’	CC	30	11.16 ± 2.30 a
		CG	24	10.68 ± 2.08 a
		GG	4	10.06 ± 1.67 a
	‘藤牧1号’×‘嘎啦’ ‘Mato 1’×‘Gala’	CC	20	8.35 ± 1.86 a
		CG	15	8.55 ± 1.67 a
		GG	3	8.77 ± 1.28 a
	‘瑞阳’×‘爱妃’ ‘Ruiyang’×‘Envy’	CC	18	10.69 ± 2.63 a
		CG	40	10.84 ± 2.40 a
		GG	13	9.51 ± 1.92 b
ACS1	‘蜜脆’×‘瑞阳’ ‘Honeycrisp’×‘Ruiyang’	1/1	20	7.81 ± 1.92 c
		1/2	50	8.78 ± 2.24 b
		2/2	38	9.73 ± 2.43 a
	‘富士’×‘粉红女士’ ‘Fuji’×‘Pink Lady’	1/1	4	12.28 ± 1.60 a
		1/2	35	11.10 ± 2.56 a
		2/2	30	10.68 ± 2.31 a
	‘藤牧1号’×‘嘎啦’ ‘Mato 1’×‘Gala’	1/1	4	8.67 ± 1.28 a
		1/2	28	8.36 ± 1.67 a
		2/2	20	9.00 ± 1.48 a
	‘秦冠’×‘蜜脆’ ‘Qinguan’×‘Honeycrisp’	1/1	30	10.21 ± 1.99 a
		1/2	42	11.09 ± 2.18 a
		2/2	8	9.95 ± 1.61 a
	‘瑞阳’×‘爱妃’ ‘Ruiyang’× Envy’	1/1	19	9.51 ± 2.08 b
		1/2	57	10.15 ± 2.31 ab
		2/2	49	11.00 ± 2.50 a
ACS3a866	‘蜜脆’×‘瑞阳’ ‘Honeycrisp’×‘Ruiyang’	GG	60	9.19 ± 2.30 a
		GT	70	9.00 ± 2.18 a
		TT	22	8.80 ± 1.99 a
	‘瑞阳’×‘爱妃’ ‘Ruiyang’×‘Envy’	GG	94	10.85 ± 2.56^*
	‘瑞阳’×‘爱妃’ ‘Ruiyang’×‘Envy’	GT	50	10.15 ± 2.31
	‘秦冠’×‘蜜脆’ ‘Qinguan’×‘Honeycrisp’	GG	51	10.68 ± 2.24 a
		GT	35	10.78 ± 2.08 a
		TT	4	11.11 ± 1.86 a
	‘藤牧1号’×‘嘎啦’ ‘Mato 1’×‘Gala’	GG	31	8.53 ± 1.67
	‘藤牧1号’×‘嘎啦’ ‘Mato 1’×‘Gala’	GT	16	8.54 ± 1.54

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