High-Density Genetic Map Construction and QTL Mapping of Fruit Acidity in the Cerasus humilis

doi:10.16420/j.issn.0513-353x.2025-0105

Acta Horticulturae Sinica ›› 2026, Vol. 53 ›› Issue (4): 1113-1124.doi: 10.16420/j.issn.0513-353x.2025-0105

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

High-Density Genetic Map Construction and QTL Mapping of Fruit Acidity in the Cerasus humilis

GUO Caizhen¹^,², WANG Pengfei¹, MU Xiaopeng¹, ZHANG Jiancheng¹, DU Junjie¹^,^*()

¹ College of Horticulture，Shanxi Agricultural University，Taigu，Shanxi 030801，China
² Department of Biological and Food Engineering，Lyuliang University，Lyuliang，Shanxi 033000，China

Received:2025-04-17 Revised:2025-12-11 Online:2026-04-25 Published:2026-04-20
Contact: DU Junjie

Abstract

Abstract:

In this study，whole-genome resequencing was performed on Cerasus humilis cultivars‘Nongda 4'and‘DS-1'and their 208 F₁ progeny in this study to construct the first high-density genetic linkage map of the C. humilis，and trait loci for fruit acidity were located by QTL mapping. The fruit titratable acid content of the‘Nongda 4'×‘DS-1'hybrid population showed a continuous normal distribution for two consecutive years，which was a quantitative trait controlled by multiple genes. The genetic map contained eight linked groups and 5 371 single-nucleotide polymorphism markers. The total genetic distance was 1 321.5 cM，with an average distance of 0.26 cM between markers. QTL mapping was performed based on titratable acid content in fruits. A total of 13 QTLs related to the titratable acid content of the fruits were identified，with a phenotypic variation contribution rate from 7.1% to 13.1%. Based on these results and transcriptome analysis，one structural gene（VHA-e1，linkage group LG3）and two transcription factors（MYB44 and bHLH148，LG1）significantly related to fruit acidity were screened.

Key words: Cerasus humilis, fruit acidity, re-sequencing, genetic map, quantitative trait locus mapping

GUO Caizhen, WANG Pengfei, MU Xiaopeng, ZHANG Jiancheng, DU Junjie. High-Density Genetic Map Construction and QTL Mapping of Fruit Acidity in the Cerasus humilis[J]. Acta Horticulturae Sinica, 2026, 53(4): 1113-1124.

Figures/Tables 12

References 42

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遗传参数Genetic parameter	2021	2022
母本/% Female	2.06 ± 0.03	2.13 ± 0.01
父本/% Male	0.90 ± 0.03	0.91 ± 0.03
F₁株数 F₁ Number	139	196
子代平均值/% Progeny mean	1.82	1.58
变异范围/% Progenies distribution	0.82 ~ 2.96	0.84 ~ 2.80
变异系数/% CV	25.74	25.22
超低亲率/% Ultra-low parent	1.44	2.04
超高亲率/% Ultra-high parent	30.94	10.72
遗传传递力/% Ta	122.88	104.40
广义遗传力/% H²	99.70	99.73
年份间相关系数Correlation coefficient	0.66（P < 0.01）

遗传参数Genetic parameter	2021	2022
母本/% Female	2.06 ± 0.03	2.13 ± 0.01
父本/% Male	0.90 ± 0.03	0.91 ± 0.03
F₁株数 F₁ Number	139	196
子代平均值/% Progeny mean	1.82	1.58
变异范围/% Progenies distribution	0.82 ~ 2.96	0.84 ~ 2.80
变异系数/% CV	25.74	25.22
超低亲率/% Ultra-low parent	1.44	2.04
超高亲率/% Ultra-high parent	30.94	10.72
遗传传递力/% Ta	122.88	104.40
广义遗传力/% H²	99.70	99.73
年份间相关系数Correlation coefficient	0.66（P < 0.01）

样本 Sample	Clean Reads总数 Total clean reads	Clean Bases总数/Gb Total clean bases	Q30/%	GC/%
农大4号Nongda 4	35 128 984	5.21	91.16	42.13
DS-1	36 044 564	5.17	89.58	40.24
F₁子代 F₁ Progenies	1 839 622 152	261.89	89.29	39.61
合计Total	1 910 795 700	272.27	90.01	40.66

样本 Sample	Clean Reads总数 Total clean reads	Clean Bases总数/Gb Total clean bases	Q30/%	GC/%
农大4号Nongda 4	35 128 984	5.21	91.16	42.13
DS-1	36 044 564	5.17	89.58	40.24
F₁子代 F₁ Progenies	1 839 622 152	261.89	89.29	39.61
合计Total	1 910 795 700	272.27	90.01	40.66

名称 Sample	Clean 序列 Clean reads	Clean reads比对率/% Mapped-rate	平均测序深度/× Ave-depth	覆盖5×的碱基比 Cov_ratio_5×
农大4号 Nongda 4	35 128 984	92.71	20.33	79.66
DS-1	3 604 456	93.21	20.04	80.90
F₁均值F₁mean	8 844 337	94.00	4.96	33.94

High-Density Genetic Map Construction and QTL Mapping of Fruit Acidity in the Cerasus humilis

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连锁群 Linkage group	SNP数量 SNP number	总图距/cM Total distance	平均图距/cM Average distance	最大Gap/cM Max Gap	Gaps < 5 cM/%
LG1	828	162.43	0.20	8.82	99.88
LG2	655	197.41	0.30	12.52	99.08
LG3	962	147.40	0.15	4.60	100.00
LG4	446	153.86	0.34	7.67	99.78
LG5	826	173.45	0.21	8.94	99.64
LG6	558	158.51	0.28	7.43	99.82
LG7	504	159.51	0.32	5.12	99.80
LG8	592	168.93	0.29	7.64	99.15
总计 Total	5 371	1 321.50	—	—	—
平均 Average	671	165	0.26	7.84	99.64

年份 Year	连锁群 Linkage group	位点 QTL	置信区间/ cM Confidence interval	包含标记数 Mark number	LOD	贡献率/% Phenotypic variation explained（PVE）
2021	LG1	21TA-1	67.863	1	3.35	10.5
	LG1	21TA-2	77.669	1	3.72	11.6
	LG6	21TA-3	44.269 ~ 47.515	6	3.68 ~ 4.17	10.9 ~ 13.1
	LG7	21TA-4	68.627 ~ 69.023	2	3.29 ~ 3.52	10.3 ~ 11.0
	LG7	21TA-5	69.610 ~ 69.699	1	3.60	11.0
2022	LG1	22TA-1	71.508 ~ 71.509	2	4.57 ~ 4.60	10.3 ~ 10.4
	LG1	22TA-2	75.915 ~ 75.929	4	3.42 ~ 3.60	7.8 ~ 8.2
	LG1	22TA-3	85.683 ~ 85.949	4	3.88 ~ 4.86	8.8 ~ 11.0
	LG1	22TA-4	91.371 ~ 91.417	2	3.75 ~ 3.86	8.6 ~ 8.8
	LG1	22TA-5	106.103 ~ 106.335	3	3.76 ~ 5.18	8.6 ~ 11.6
	LG2	22TA-6	99.136 ~ 99.197	2	3.64 ~ 3.82	8.3 ~ 8.7
	LG2	22TA-7	134.655 ~ 134.665	2	3.13 ~ 3.31	7.2 ~ 7.6
	LG3	22TA-8	67.600 ~ 67.883	4	3.07 ~ 3.13	7.1 ~ 7.2

基因ID Gene ID	位置 Location	注释 Annotation
ouLi_002143	Chr01:21547678-21553051	丙酮酸脱氢酶E1亚基Pyruvate dehydrogenase E1 component subunit
ouLi_002975	Chr01:27180756-27193970	铝激活苹果酸转运蛋白Aluminum-activated malate transporter（ALMT9）
ouLi_004592	Chr01:36585973-36587431	V型质子ATP酶c''1亚基V-type proton ATPase subunit c''1（VHA-c''1）
ouLi_003613	Chr01:30704188-30710433	V型质子ATP酶a3亚基V-type proton ATPase subunit a3（VHA-a3）
ouLi_004286	Chr01:34805791-3498913	NADP依赖型苹果酸酶NADP-dependent malic enzyme（ME1）
ouLi_005250	Chr01:41036263-41042630	磷酸烯醇式丙酮酸羧激酶Phosphoenolpyruvate carboxykinase（PEPCK）
ouLi_005370	Chr01:42084592-42085645	V型质子ATP酶G1亚基V-type proton ATPase subunit G1（VHA-G1）
ouLi_000951	Chr01:7754069-7757303	丙酮酸脱氢酶激酶Pyruvate dehydrogenase kinase（PDK）
ouLi_002922	Chr01:26894035-26900595	磷酸烯醇式丙酮酸羧化酶4 Phosphoenolpyruvate carboxylase 4（PEPC4）
ouLi_002547	Chr01:24612635-24617562	丙酮酸脱氢酶E1亚基Pyruvate dehydrogenase E1 component subunit
ouLi_006462	Chr02:3493489-3498913	V型质子ATP酶E2亚基V-type proton ATPase subunit E2（VHA-E2）
ouLi_007563	Chr02:10814886-10815511	琥珀酸脱氢酶Succinate dehydrogenase（SDH2-3）
ouLi_007908	Chr02:16373753-16377457	琥珀酸脱氢酶Succinate dehydrogenase（SDH6）
ouLi_006283	Chr02:2636998-2641289	焦磷酸驱动液泡膜质子泵Pyrophosphate-energized vacuolar membrane proton pump（AVP1）
ouLi_007013	Chr02:6659085-6661164	V型质子ATP酶G亚基V-type proton ATPase subunit G（VHA-G）
ouLi_007032	Chr02:6777034-6779884	NAD依赖型异柠檬酸脱氢酶Isocitrate dehydrogenase [NAD]（IDH5）
ouLi_007280	Chr02:8350333-8353503	磷酸烯醇式丙酮酸羧激酶Phosphoenolpyruvate carboxykinase（PEPCK）
ouLi_007281	Chr02:8357959-8363295	磷酸烯醇式丙酮酸羧激酶Phosphoenolpyruvate carboxykinase（PEPCK）
ouLi_007562	Chr02:10809841-10814853	琥珀酸脱氢酶Succinate dehydrogenase（SDH2-3）
ouLi_009926	Chr03:9029672-9035094	琥珀酰辅酶A连接酶succinate-CoA ligase
ouLi_010115	Chr03:11715042-11717715	V型质子ATP酶e1亚基V-type proton ATPase subunit e1（VHA-e1）
ouLi_010174	Chr03:12276025-12278623	NAD依赖型异柠檬酸脱氢酶Isocitrate dehydrogenase [NAD]（IDH1）

基因 Gene	可滴定酸含量 Titrable acid content	苹果酸含量 Malic acid content
VHA-e1	0.83^**	0.53^**
MYB44	0.69^**	0.80^**
bHLH148	0.56^**	0.68^**

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