Mapping of Genes Regulating Tomato Fruit Skin Toughness

doi:10.16420/j.issn.0513-353x.2025-0124

Acta Horticulturae Sinica ›› 2025, Vol. 52 ›› Issue (12): 3219-3228.doi: 10.16420/j.issn.0513-353x.2025-0124

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

Mapping of Genes Regulating Tomato Fruit Skin Toughness

QI Yujie¹, ZHAO Shiqi¹, SUN Shuai¹, WANG Haijing¹, CUI Xia¹^,²^,^*(), LI Ren¹^,^*()

¹ State Key Laboratory of Vegetable Biobreeding，Institute of Vegetables and Flowers，Chinese Academy of Agricultural Sciences，Beijing 100081，China
² Zhejiang A & F University，Linan，Zhejiang 311300，China

Received:2025-04-02 Revised:2025-05-08 Online:2025-12-25 Published:2025-12-20
Contact: CUI Xia, LI Ren

Abstract

Abstract:

Fruit firmness is an important quality trait that directly affects the fruit cracking and storability. Skin toughness and compression resistance are key indicators for evaluating fruit firmness. In this study，we found that although processing tomato TS292 and large-fruited tomato TS12 showed no significant difference in compression resistance. However，TS292 fruits exhibited significantly enhanced skin toughness. Histological and metabolomic analyses demonstrated that TS292 possesses a thicker cuticle layer with elevated cutin and wax content in the red fruit pericarp，potentially constituting the primary determinant of its superior skin toughness. To clone key genes regulating fruit skin toughness，we established a recombinant inbred line（RIL）population derived from TS12 × TS292 crosses as a mapping population. Four QTLs control the skin toughness were identified by using Bulked Segregant Analysis（BSA）method. Among these，a major QTL located at the chromosome 7，contributed 30.12% variation of fruit skin toughness. Further genetic analysis narrowed the QTL-FIS3 into a 295 kb region including 16 genes.

Key words: tomato, fruit firmness, skin toughness, cutin, wax

QI Yujie, ZHAO Shiqi, SUN Shuai, WANG Haijing, CUI Xia, LI Ren. Mapping of Genes Regulating Tomato Fruit Skin Toughness[J]. Acta Horticulturae Sinica, 2025, 52(12): 3219-3228.

Figures/Tables 8

References 22

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分子标记 Marker	物理位置/bp Position on SL2.5	引物序列（3′-5′） Primer sequence
M1	59 530 615	GTGAGGAAGATGGTGTGTACTTGGTG
M1	59 530 615	GACGAATATGTGAAAATAGTGATTTC
M2	59 991 416	GACGGAGGAAGTAATTAATG
M2	59 991 416	CGGTGGTGGTAGTGGTGAAACG
M3	60 031 030	GTTCAAATATACTCCTC
M3	60 031 030	GTAGCTTCTATGCTCCTCT
M4	60 309 325	GATAAGAGTCTCAAATTTCTATTGCG
M4	60 309 325	GTTTTTCTTATAGGGCAAGTATGATC
M5	60 326 153	CAAAGGAAGTGAAGCAACTAAGTCA
M5	60 326 153	GGAGATAGCCAACCGCATATGCAAC
M6	60 920 438	GTGGATTTGTCGGCACTGTTGATGG
M6	60 920 438	GAGAATGAAGTATAGTACTTACACTT
M7	61 340 455	CAGTGATAGACGTGAATTCGAAATAGCCG
M7	61 340 455	TGCGACATTGAGATCTGACTATTTCAGAATTC

分子标记 Marker	物理位置/bp Position on SL2.5	引物序列（3′-5′） Primer sequence
M1	59 530 615	GTGAGGAAGATGGTGTGTACTTGGTG
M1	59 530 615	GACGAATATGTGAAAATAGTGATTTC
M2	59 991 416	GACGGAGGAAGTAATTAATG
M2	59 991 416	CGGTGGTGGTAGTGGTGAAACG
M3	60 031 030	GTTCAAATATACTCCTC
M3	60 031 030	GTAGCTTCTATGCTCCTCT
M4	60 309 325	GATAAGAGTCTCAAATTTCTATTGCG
M4	60 309 325	GTTTTTCTTATAGGGCAAGTATGATC
M5	60 326 153	CAAAGGAAGTGAAGCAACTAAGTCA
M5	60 326 153	GGAGATAGCCAACCGCATATGCAAC
M6	60 920 438	GTGGATTTGTCGGCACTGTTGATGG
M6	60 920 438	GAGAATGAAGTATAGTACTTACACTT
M7	61 340 455	CAGTGATAGACGTGAATTCGAAATAGCCG
M7	61 340 455	TGCGACATTGAGATCTGACTATTTCAGAATTC

成分 Ingredient	绿熟果实 Mature green fruit		红熟果实 Red fruit
成分 Ingredient	TS292	TS12	TS292	TS12
十六烷 Hexadecane	3.08 ± 0.28 a	3.09 ± 0.73 a	3.41 ± 0.79 a	3.07 ± 0.08 a
9-十八烯酰胺 9-Octadecylamide	4.86 ± 1.75 ab	3.64 ± 0.09 ab	2.35 ± 1.95 b	6.53 ± 1.87 a
16-羟基十六烷 16-OH hexadecanoic	26.17 ± 2.22 a	26.23 ± 6.07 a	21.04 ± 10.23 a	25.99 ± 1.75 a
十六烷二酸 Hexadecanedioic acid	4.84 ± 0.95 b	2.09 ± 0.87 c	6.92 ± 0.41 a	4.45 ± 0.14 b
十六碳-7-烯酸 Hexadec-7-enoate	3.80 ± 1.88 ab	5.17 ± 1.23 a	2.83 ± 0.06 ab	2.45 ± 0.12 b
7-甲基-Z-十四烯-1-醇 7-Methyl-Z-tetradene-1-ol	3.60 ± 0.38 a	4.02 ± 0.74 a	2.84 ± 1.18 a	2.76 ± 0.26 a
10-羟基十六烷酸 10-OH hexadecanoic	324.13 ± 39.36 b	305.78 ± 17.68 b	481.46 ± 68.36 a	325.07 ± 73.82 b
9,10-二羟基十八烷酸 9,10-DiOH octadecanoic	22.04 ± 0.57 a	21.56 ± 2.00 a	39.25 ± 1.02 b	30.33 ± 0.29 b
(Z)-十八碳-9-烯酸（Z）-9-Octadecenoic acid	14.10 ± 3.86 b	10.05 ± 3.20 b	43.24 ± 18.88 a	18.07 ± 1.06 b
11-环戊基十一酸 11-Cyclopentylundecanoic	30.87 ± 1.26 bc	21.02 ± 2.11 c	46.47 ± 0.61 a	42.64 ± 3.10 ab
Z,Z,Z-4,6,9-十九碳三烯 Z,Z,Z-4,6,9-Nonadecatriene	3.41 ± 0.12 b	3.34 ± 0.52 b	5.46 ± 0.30 a	4.87 ± 0.47 a
9,12-二羟基十八烷酸 9,12-DiOH octadecanoic	3.30 ± 0.27 b	3.37 ± 0.60 b	5.32 ± 0.19 a	4.55 ± 0.43 a
顺式-3-辛基环氧辛酸 cis-3-Octyl epoxycapic acid	3.96 ± 0.64 bc	3.21 ± 0.07 c	5.91 ± 0.10 a	4.64 ± 0.35 b
合计 Total	448.17	412.56	666.51	475.4

成分 Ingredient	绿熟果实 Mature green fruit		红熟果实 Red fruit
成分 Ingredient	TS292	TS12	TS292	TS12
十六烷 Hexadecane	3.08 ± 0.28 a	3.09 ± 0.73 a	3.41 ± 0.79 a	3.07 ± 0.08 a
9-十八烯酰胺 9-Octadecylamide	4.86 ± 1.75 ab	3.64 ± 0.09 ab	2.35 ± 1.95 b	6.53 ± 1.87 a
16-羟基十六烷 16-OH hexadecanoic	26.17 ± 2.22 a	26.23 ± 6.07 a	21.04 ± 10.23 a	25.99 ± 1.75 a
十六烷二酸 Hexadecanedioic acid	4.84 ± 0.95 b	2.09 ± 0.87 c	6.92 ± 0.41 a	4.45 ± 0.14 b
十六碳-7-烯酸 Hexadec-7-enoate	3.80 ± 1.88 ab	5.17 ± 1.23 a	2.83 ± 0.06 ab	2.45 ± 0.12 b
7-甲基-Z-十四烯-1-醇 7-Methyl-Z-tetradene-1-ol	3.60 ± 0.38 a	4.02 ± 0.74 a	2.84 ± 1.18 a	2.76 ± 0.26 a
10-羟基十六烷酸 10-OH hexadecanoic	324.13 ± 39.36 b	305.78 ± 17.68 b	481.46 ± 68.36 a	325.07 ± 73.82 b
9,10-二羟基十八烷酸 9,10-DiOH octadecanoic	22.04 ± 0.57 a	21.56 ± 2.00 a	39.25 ± 1.02 b	30.33 ± 0.29 b
(Z)-十八碳-9-烯酸（Z）-9-Octadecenoic acid	14.10 ± 3.86 b	10.05 ± 3.20 b	43.24 ± 18.88 a	18.07 ± 1.06 b
11-环戊基十一酸 11-Cyclopentylundecanoic	30.87 ± 1.26 bc	21.02 ± 2.11 c	46.47 ± 0.61 a	42.64 ± 3.10 ab
Z,Z,Z-4,6,9-十九碳三烯 Z,Z,Z-4,6,9-Nonadecatriene	3.41 ± 0.12 b	3.34 ± 0.52 b	5.46 ± 0.30 a	4.87 ± 0.47 a
9,12-二羟基十八烷酸 9,12-DiOH octadecanoic	3.30 ± 0.27 b	3.37 ± 0.60 b	5.32 ± 0.19 a	4.55 ± 0.43 a
顺式-3-辛基环氧辛酸 cis-3-Octyl epoxycapic acid	3.96 ± 0.64 bc	3.21 ± 0.07 c	5.91 ± 0.10 a	4.64 ± 0.35 b
合计 Total	448.17	412.56	666.51	475.4

染色体Chromosome	物理位置/bp Postion on SL2.50	SNP指数 ΔSNP-index	表型变异贡献率/% PVE	长度/bp length
SL2.50ch07	59 991 671 ~ 60 990 579	0.501089	30.12	998 908
SL2.50ch09	9 731 112 ~ 9 957 832	0.58164	17.03	226 720
SL2.50ch09	32 049 034 ~ 32 184 175	0.53399	17.02	135 141
SL2.50ch09	47 052 310 ~ 47 360 989	0.456416	13.15	308 679
SL2.50ch09	55 337 072 ~ 57 388 709	0.604067	1.99	2 051 637

Mapping of Genes Regulating Tomato Fruit Skin Toughness

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基因编号 Gene ID	变异位置 Change position	在果实中表达 Expression in fruit		基因注释 Annotation
Solyc07g049680	编码区，启动子，内含子，非翻译区 CDS，promoter，intron，UTR	是Yes		凝缩蛋白复合体亚基2 Condensin complex subunit 2
Solyc07g049690	启动子，内含子，非翻译区 Promoter，intron，UTR	是Yes		氢过氧化物裂解酶 Hydroperoxide lyase
Solyc07g049700	编码区，启动子 CDS，promoter	是Yes		抗病蛋白 Disease resistance protein
Solyc07g049710	启动子，内含子 Promoter，intron	是Yes		ATP酶亚基e1 ATPase subunit e1
Solyc07g049720	启动子，内含子，非翻译区 Promoter，intron，UTR	是Yes		光系统Ⅱ的10 kD多肽前体 10 kD polypeptide precursor of photosystem 2
Solyc07g049730	启动子，内含子，非翻译区 Promoter，intron，UTR	是Yes		预测的跨膜蛋白 Transmembrane protein，putative
Solyc07g049740	启动子，内含子，非翻译区 Promoter，intron，UTR	是Yes		脂质A二糖合酶 Lipid-A-disaccharide synthase
Solyc07g049750	启动子，内含子，非翻译区 Promoter，intron，UTR	是Yes		牙本质涎磷蛋白样蛋白 Dentin sialophosphoprotein-like protein
Solyc07g049760	启动子，内含子，非翻译区 Promoter，intron，UTR		否No	CCR4-NOT转录复合物亚基 CCR4-NOT transcription complex subunit 9-like
Solyc07g049770	编码区，启动子，内含子，非翻译区 CDS，promoter，intron，UTR		否No	细胞分化，Rcd1样蛋白 Cell differentiation，Rcd1-like protein
Solyc07g049780	编码区，启动子，内含子，非翻译区 CDS，promoter，intron，UTR		是Yes	细胞分化，Rcd1样蛋白 Cell differentiation，Rcd1-like protein
Solyc07g049790	编码区，启动子，内含子，非翻译区 CDS，promoter，intron，UTR		否No	细胞分化，Rcd1样蛋白 Cell differentiation，Rcd1-like protein
Solyc07g049800	CDS，promoter，intron，UTR 编码区，启动子，内含子，非翻译区		是Yes	细胞分化，Rcd1样蛋白 Cell differentiation，Rcd1-like protein
Solyc07g051800	编码区，启动子，内含子，非翻译区 CDS，promoter，intron，UTR		否No	未知蛋白 Unknown protein
Solyc07g051810	编码区，启动子，内含子，非翻译区 CDS，promoter，intron，UTR		否No	细胞分化，Rcd1样蛋白 Cell differentiation，Rcd1-like protein
Solyc07g051820	编码区，启动子，内含子，非翻译区 CDS，promoter，intron，UTR		是Yes	纤维素合酶 Cellulose synthase

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