QTL mapping and genetic analysis of soluble solids content in the center flesh of muskmelon

doi:10.6048/j.issn.1001-4330.2025.01.021

Xinjiang Agricultural Sciences ›› 2025, Vol. 62 ›› Issue (1): 182-192.DOI: 10.6048/j.issn.1001-4330.2025.01.021

• Plant Protection·Horticultural Special Local Products • Previous Articles Next Articles

QTL mapping and genetic analysis of soluble solids content in the center flesh of muskmelon

FAN Rong¹(), ZHANG Yongbing¹, LI Meihua¹, ZHANG Xuejun¹, YI Hongping¹, LIU Zhao², YANG Yong¹()

1. Center of Hami Melon, Xinjiang Academy of Agricultural Sciences,Urumqi 830091, China
2. Shouguang Sanmu Seed Co.,Ltd,Shouguang Shandong 262700,China

Received:2024-07-17 Online:2025-01-20 Published:2025-03-11
Correspondence author: YANG Yong
Supported by:
Key R & D Project of Xinjiang Uygur Autonomous Region(2022B02002-3);National Natural Science Foundation of China(31860567);China Agriculture Research System of MOF and MARA(CARS-25-G2);Innovation Ability Training Project for Young Sci-Tech Backbone Talents Sponsored by Xinjiang Academy of Agricultural Sciences(xinkq-2022011);Major Science and technology Projects in Xinjiang Uygur Autonomous Region(2022A03004-5);Scientific Research Special Project of Hainan Provincial Academician Innovation Platform(Academician Wu Mingzhu Team Innovation Center);Key Laboratory Project of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables

厚皮甜瓜心部果肉可溶性固形物含量遗传规律分析及QTL定位

范蓉¹(), 张永兵¹, 李寐华¹, 张学军¹, 伊鸿平¹, 刘钊², 杨永¹()

1.新疆农业科学院哈密瓜研究中心,乌鲁木齐 830091
2.山东省寿光市三木种苗有限公司,山东寿光 262700

通讯作者: 杨永
作者简介:范蓉(1995-),女,新疆塔城人,助理研究员,硕士,研究方向为甜瓜遗传分子改良,(E-mail)1029681312@qq.com
基金资助:
新疆维吾尔自治区重点研发项目(2022B02002-3);国家自然科学基金项目(31860567);财政部和农业农村部"国家现代农业产业技术体系资助"(CARS-25-G2);新疆农业科学院青年科技骨干创新能力培养项目(xinkq-2022011);新疆维吾尔自治区重大科技专项(2022A03004-5);海南省院士创新平台科研专项(吴明珠院士团队创新中心);新疆特色果蔬基因组研究与遗传改良重点实验室

Abstract

Abstract:

【Objective】 This study aims to analyze the content of soluble solids in the center flesh of muskmelon by Genetic analysis and QTL mapping in the hope of finding out candidate genes associated with soluble solids in the heart of C. achyum fruits. 【Methods】 Six generations population (P₁, P₂, F₁, B₁, B₂, and F₂) were created using the high-sugar material P₁ and the low-sugar material P₂ as parents. A mixed major gene plus polygene inheritance model was used to analyze soluble solids content in the center flesh of six generations population. Based on the F₂ population, individual plants with higher and lower fruit soluble solids content were selected to construct two pools to locate the soluble solids content of muskmelons by using the BSA method. 【Results】 Muskmelon soluble solids conformed to the E-1 (MX2-ADI-AD) genetic model, with epistatic effects dominating the 2 main gene pairs, followed by dominant and additive effects. Two QTLs were located in chromosome 5 (827066 bp-109953bp) and chromosome 8 (11316600 bp-11729324 bp), with interval sizes of 0.27Mb and 0.41 Mb, respectively, and contained a total of 50 candidate genes. Six candidate genes related to soluble solids content of melon were screened and obtained (MELO3C014619, MELO3C014617, MELO3C014596, MELO3C014594, MELO3C019077 and MELO3C019089). 【Conclusion】 Muskmelon soluble solids conforms to the E-1 (MX2-ADI-AD) genetic model, two QTLs related to soluble solid content of muskmelon are mapped on chromosomes 5 and 8 by BSA method, and six candidate genes related to soluble solid content of muskmelon screened out.

Key words: muskmelon; soluble solids; major gene plus polygene; BSA

摘要：

【目的】 研究厚皮甜瓜果实心部可溶性固形物的遗传规律和QTL定位,挖掘厚皮甜瓜果实心部可溶性固形物相关的候选基因。【方法】 以高糖材料P₁和低糖材料P₂为双亲构建六世代分离群体;采用主基因+多基因混合遗传模型研究厚皮甜瓜心部果肉可溶性固形物含量的遗传规律,并基于F₂群体,选取果实可溶性固形物含量极端的单株构建混池,利用BSA方法对甜瓜可溶性固形物含量进行定位。【结果】 甜瓜可溶性固形物符合E-1(MX2-ADI-AD)遗传模型,2对主基因以上位性效应为主,其次为显性效应、加性效应。2个QTL分别在第5号染色体827066 bp-109953 bp和第8号11316600 bp-11729324 bp,区间大小分别为0.27 Mb和0.41 Mb,2个区间内共包含50个候选基因。筛选获得了6个与甜瓜可溶性固形物含量相关的候选基因,分别是MELO3C014619、MELO3C014617、MELO3C014596、MELO3C014594、MELO3C019077、MELO3C019089。【结论】 厚皮甜瓜心部可溶性固形物符合E-1(MX2-ADI-AD)遗传模型,通过BSA方法在5号和8号染色体定位到2个甜瓜可溶性固形物相关QTL,筛选出6个与甜瓜可溶性固形物含量相关的候选基因。

关键词: 厚皮甜瓜, 可溶性固形物, 主基因+多基因, BSA

CLC Number:

S652

FAN Rong, ZHANG Yongbing, LI Meihua, ZHANG Xuejun, YI Hongping, LIU Zhao, YANG Yong. QTL mapping and genetic analysis of soluble solids content in the center flesh of muskmelon[J]. Xinjiang Agricultural Sciences, 2025, 62(1): 182-192.

范蓉, 张永兵, 李寐华, 张学军, 伊鸿平, 刘钊, 杨永. 厚皮甜瓜心部果肉可溶性固形物含量遗传规律分析及QTL定位[J]. 新疆农业科学, 2025, 62(1): 182-192.

Figures/Tables 12

Tab.1 Frequency distribution and average of non-segregating generations of muskmelon heart suger content traits

世代 Generations	次数分布Frequency distribution												平均值 Average(°Brix)
世代 Generations	4	5	6	7	8	9	10	11	12	13	14	15	平均值 Average(°Brix)
P₁									2	6	11	8	14.49±0.89^aA
P₂		3	7	5	2	3							7.34±1.23^dD
F₁				1	2	1	2	10	17	4	2		11.93±1.46^aA
B₁				2			1	1	7	13	24	9	13.68±1.54^bB
B₂	1	3	4	5	5	11	14	11	4				9.48±2.02^cC
F₂		4	7	21	21	30	35	60	101	79	36	4	11.69±2.10^bB

Fig.1 Frequency distribution of soluble solids in the heart of muskmelon in separated generations

Tab.2 Max-likelihood-value and AIC value of the different genetic models

模型代号 Model code	模型 Model	极大似然函数值 Max-likelihood value	AIC值 AIC value
A-1	1MG-AD	-1 215.89	2 439.77
A-2	1MG-A	-1 251.65	2 509.29
A-3	1MG-EAD	-1 250.56	2 507.13
A-4	1MG-NCD	-1 341.19	2 688.38
B-1	2MG-ADI	-1 188.81	2 397.62
B-2	2MG-AD	-1 206.98	2 425.95
B-3	2MG-A	-1 277.68	2 563.36
B-4	2MG-EA	-1 225.30	2 456.59
B-5	2MG-CD	-1 232.31	2 472.61
B-6	2MG-EAD	-1 233.54	2 473.07
C-0	PG-ADI	-1 226.94	2 473.89
C-1	PG-AD	-1 229.72	2 473.43
D-0	MX1-AD-ADI	-1 173.92	2 371.84
D-1	MX1-AD-AD	-1 229.08	2 476.15
D-2	MX1-A-AD	-1 229.68	2 475.35
D-3	MX1-EAD-AD	-1 187.83	2 391.66
D-4	MX1-NCD-AD	-1 229.70	2 475.41
E-0	MX2-ADI-ADI	-1 172.85	2 381.69
E-1	MX2-ADI-AD	-1 169.32	2 368.64
E-2	MX2-AD-AD	-1 229.70	2 481.40
E-3	MX2-A-AD	-1 194.86	2 407.71
E-4	MX2-EA-AD	-1 229.66	2 475.33
E-5	MX2-CD-AD	-1 187.59	2 393.17
E-6	MX2-EAD-AD	-1 229.69	2 475.38

Tab.3 Tests for goodness of fifit model of heart suger traits in different generations

模型 Model	世代 Generation	拟合模型的统计参数Statistic parameter of fifit model
模型 Model	世代 Generation	$U_{1}^{2}$	$U_{2}^{2}$	$U_{3}^{2}$	_nW²	D_n
D-0 MX1-AD-ADI	P₁	0.015 6(0.900 6)	0.032 6(0.856 7)	0.056 7(0.811 7)	0.042 2(0.921 4)	0.104 4(0.900 8)
	F₁	0.300 5(0.583 6)	0.017 5(0.894 7)	2.539 3(0.111 0)	0.243 8(0.201 6)	0.193 4(0.094 3)
	P₂	0.073 8(0.785 8)	0.044 5(0.833 0)	0.043 6(0.834 6)	0.070 9(0.753 4)	0.123 1(0.886 8)
	B₁	1.028 6(0.310 5)	0.114 9(0.734 7)	6.616 5(0.010 1)^*	0.481 1(0.045 5)^*	0.162(0.089 5)
	B₂	0.022 5(0.880 8)	0.147 3(0.701 1)	0.911 3(0.339 8)	0.044 3(0.909 7)	0.068 1(0.933 9)
	F₂	0.155 3(0.693 5)	0.108 0(0.742 4)	0.044 8(0.832 3)	0.097 8(0.607 2)	0.045 9(0.372 5)
E-0 MX2-ADI-ADI	P₁	0.015 6(0.900 5)	0.032 6(0.856 7)	0.056 6(0.812 0)	0.042 2(0.921 3)	0.104 3(0.901 1)
	F₁	0.300 2(0.583 8)	0.017 5(0.894 9)	2.539 4(0.111 0)	0.243 8(0.201 7)	0.193 3(0.094 4)
	P₂	0.073 8(0.785 9)	0.044 4(0.833 1)	0.043 7(0.834 4)	0.070 9(0.753 5)	0.123 0(0.887 0)
	B₁	1.030 0(0.310 2)	0.126 8(0.721 8)	6.282 1(0.012 2)^*	0.469 5(0.048 8)^*	0.161 4(0.091 7)
	B₂	0.003 2(0.954 7)	0.032 2(0.857 6)	0.879 2(0.348 4)	0.069 6(0.760 5)	0.097 2(0.609 1)
	F₂	0.058 9(0.808 2)	0.047 5(0.827 5)	0.004 7(0.945 4)	0.075 8(0.725 7)	0.040 9(0.519 9)
E-1 MX2-ADI-AD	P₁	0.844 6(0.358 1)	1.001 4(0.317 0)	0.196 7(0.657 4)	0.135 4(0.440 5)	0.167 7(0.390 1)
	F₁	0.685 0(0.407 9)	0.185 5(0.666 7)	2.198 9(0.138 1)	0.290 4(0.150 7)	0.209 7(0.055 5)
	P₂	0.275 9(0.599 4)	0.183 2(0.668 6)	0.103 8(0.747 3)	0.099 6(0.597 6)	0.145 3(0.739 3)
	B₁	0.373 7(0.541 0)	1.802 1(0.179 5)	9.012(0.002 7)^*	0.329 5(0.117 7)	0.155 8(0.112 6)
	B₂	0.003 6(0.951 8)	0.100 6(0.751 1)	1.070 3(0.300 9)	0.051 8(0.866 1)	0.079 8(0.825 6)
	F₂	0.213 2(0.644 3)	0.284 9(0.593 5)	0.120 3(0.728 7)	0.095 1(0.621 0)	0.048 8(0.299 0)

Tab.3 Tests for goodness of fifit model of heart suger traits in different generations

模型 Model	世代 Generation	拟合模型的统计参数Statistic parameter of fifit model
模型 Model	世代 Generation	$U_{1}^{2}$	$U_{2}^{2}$	$U_{3}^{2}$	_nW²	D_n
D-0 MX1-AD-ADI	P₁	0.015 6(0.900 6)	0.032 6(0.856 7)	0.056 7(0.811 7)	0.042 2(0.921 4)	0.104 4(0.900 8)
	F₁	0.300 5(0.583 6)	0.017 5(0.894 7)	2.539 3(0.111 0)	0.243 8(0.201 6)	0.193 4(0.094 3)
	P₂	0.073 8(0.785 8)	0.044 5(0.833 0)	0.043 6(0.834 6)	0.070 9(0.753 4)	0.123 1(0.886 8)
	B₁	1.028 6(0.310 5)	0.114 9(0.734 7)	6.616 5(0.010 1)^*	0.481 1(0.045 5)^*	0.162(0.089 5)
	B₂	0.022 5(0.880 8)	0.147 3(0.701 1)	0.911 3(0.339 8)	0.044 3(0.909 7)	0.068 1(0.933 9)
	F₂	0.155 3(0.693 5)	0.108 0(0.742 4)	0.044 8(0.832 3)	0.097 8(0.607 2)	0.045 9(0.372 5)
E-0 MX2-ADI-ADI	P₁	0.015 6(0.900 5)	0.032 6(0.856 7)	0.056 6(0.812 0)	0.042 2(0.921 3)	0.104 3(0.901 1)
	F₁	0.300 2(0.583 8)	0.017 5(0.894 9)	2.539 4(0.111 0)	0.243 8(0.201 7)	0.193 3(0.094 4)
	P₂	0.073 8(0.785 9)	0.044 4(0.833 1)	0.043 7(0.834 4)	0.070 9(0.753 5)	0.123 0(0.887 0)
	B₁	1.030 0(0.310 2)	0.126 8(0.721 8)	6.282 1(0.012 2)^*	0.469 5(0.048 8)^*	0.161 4(0.091 7)
	B₂	0.003 2(0.954 7)	0.032 2(0.857 6)	0.879 2(0.348 4)	0.069 6(0.760 5)	0.097 2(0.609 1)
	F₂	0.058 9(0.808 2)	0.047 5(0.827 5)	0.004 7(0.945 4)	0.075 8(0.725 7)	0.040 9(0.519 9)
E-1 MX2-ADI-AD	P₁	0.844 6(0.358 1)	1.001 4(0.317 0)	0.196 7(0.657 4)	0.135 4(0.440 5)	0.167 7(0.390 1)
	F₁	0.685 0(0.407 9)	0.185 5(0.666 7)	2.198 9(0.138 1)	0.290 4(0.150 7)	0.209 7(0.055 5)
	P₂	0.275 9(0.599 4)	0.183 2(0.668 6)	0.103 8(0.747 3)	0.099 6(0.597 6)	0.145 3(0.739 3)
	B₁	0.373 7(0.541 0)	1.802 1(0.179 5)	9.012(0.002 7)^*	0.329 5(0.117 7)	0.155 8(0.112 6)
	B₂	0.003 6(0.951 8)	0.100 6(0.751 1)	1.070 3(0.300 9)	0.051 8(0.866 1)	0.079 8(0.825 6)
	F₂	0.213 2(0.644 3)	0.284 9(0.593 5)	0.120 3(0.728 7)	0.095 1(0.621 0)	0.048 8(0.299 0)

Tab.4 The estimation of genetic parameters of fifit model of melon heart suger resistance traits

一阶遗传参数 1st order parameter	估值Estimate	二阶遗传参数 2nd order parameter	估值Estimate
一阶遗传参数 1st order parameter	E-1	二阶遗传参数 2nd order parameter	B₁	B₂	F₂
m	12.4107	$σ_{m g}^{2}$	0.952 1	2.827 5	3.167 7
d_a	-0.050 7	$σ_{p g}^{2}$	0.19	0	0
d_b	-0.050 7	$h_{m g}^{2}$	39.956 9	69.502 1	71.855 4
h_a	0.953 2	$h_{p g}^{2}$	7.974 8	0.000 2	0.000 2
h_b	-1.419
i	-1.532 9
j_ab	2.358 4
j_ba	-0.013 8
l	1.571
[d]	3.571 5
[h]	-1.651 8

Tab.4 The estimation of genetic parameters of fifit model of melon heart suger resistance traits

一阶遗传参数 1st order parameter	估值Estimate	二阶遗传参数 2nd order parameter	估值Estimate
一阶遗传参数 1st order parameter	E-1	二阶遗传参数 2nd order parameter	B₁	B₂	F₂
m	12.4107	$σ_{m g}^{2}$	0.952 1	2.827 5	3.167 7
d_a	-0.050 7	$σ_{p g}^{2}$	0.19	0	0
d_b	-0.050 7	$h_{m g}^{2}$	39.956 9	69.502 1	71.855 4
h_a	0.953 2	$h_{p g}^{2}$	7.974 8	0.000 2	0.000 2
h_b	-1.419
i	-1.532 9
j_ab	2.358 4
j_ba	-0.013 8
l	1.571
[d]	3.571 5
[h]	-1.651 8

Tab.5 Quality statistics of raw data

样本 Sample	原始Reads Raw reads	原始数据量 Raw bases	过滤后Reads Clean reads	过滤后碱基数 Clean bases	有效Reads比 Valid reads (%)	有效数据量比 Valid bases (%)	GC (%)	Q20 (%)	Q30 (%)
HS	38 148 520	11 145 445 500	75 572 218	11 045 883 000	99.05	99.11	36.72	95.56	89.04
LS	37 150 247	11 444 585 400	73 639 220	11 335 832 700	99.11	99.05	37.86	95.56	89.1
P₁	27 381 098	8 214 073 200	54 493 862	8 174 079 300	99.51	99.51	36.39	95.68	89.12
P₂	27 496 523	8 248 618 800	54 723 580	8 208 537 000	99.51	99.51	37.23	95.64	89.13

Tab.6 Matching of quality control data with reference genome

样本 Sample	过滤后Reads Clean reads	比对上数据 Mapping reads	比对率 Mapped (%)	平均测序深度 Mean coverage	1×覆盖度 Coverage≥ 1× (%)	4×覆盖度 Coverage≥ 4× (%)
HS	75 572 218	70 862 228	93.77	24.55	97.8	96.74
LS	73 639 220	69 954 351	95	25.36	97.77	96.67
P₁	54 493 862	52 222 873	95.83	19.52	96.71	95.27
P₂	54 723 580	52 620 862	96.16	19.2	96.86	95.42

Tab.7 Statistics of candidate intervals for 7 different algorithms

染色体编号 Chromosome ID	方法 Methods	关联区间起始位置 Start position of the correlation interval(bp)	关联区间终止位置 End position of the correlation interval(bp)	关联区间大小 Correlation interval size (Mb)
Chr5	Deep Learning	805192	1196476	0.391284
	K value	660399	1099530	0.439131
	ED4	684566	1099550	0.414984
	△SNP index	740823	1187084	0.446261
	SmoothG	738888	1185404	0.446516
	SmoothLOD	827066	1196504	0.369438
	Ridit	735951	1108157	0.372206
Chr8	Deep Learning	11093331	11729324	0.635993
	K value	11115505	11773204	0.657699
	ED4	11316600	14061373	2.744773
	△SNP index	11115505	11773204	0.657699
	SmoothG	11115620	11779123	0.663503
	SmoothLOD	11316350	14061163	2.744813
	Ridit	11164863	11808230	0.643367

Fig.2 QTL mapping of soluble solids content in center flesh of muskmelon based on △SNP index

Fig.3 Candidate gene expression Notes: *indicate significant differences at the 0.05 leve, * *indicate significant differences at the 0.01 level

Tab.8 Functional annotation of 3 candidate genes

基因号 Gene ID	位置 Position	基因方向 Gene orientation	大小 Size (bp)	注释 Annotation	编码区非同义突变 Non synonymous mutation sites in coding regions	启动子区 Promotor Region
MELO3C014622	Chr5:882794-885290	-	2496	丝氨酸/苏氨酸蛋白激酶		2个SNP
MELO3C014621	Chr5:889359-892049	-	2690	含溴结构域的蛋白质		1个Indel
MELO3C014619	Chr5:896637-899328	-	2691	未知	4个SNP	14个SNP,11个Indel
MELO3C014617	Chr5:905878-908840	-	2962	未知	5个SNP	29个SNP,7个Indel
MELO3C014613	Chr5:924958-933054	-	8096	DUF1680结构域蛋白		6个SNP,6个Indel
MELO3C014610	Chr5:953260-954563	-	1303	激酶家族蛋白		6个SNP,6个Indel
MELO3C014596	Chr5:1075795-1079969	+	4174	苹果酸/酮戊二酸转运蛋白	3个SNP	8个SNP,1个Indel
MELO3C014595	Chr5:1085108-1089566	+	4458	MATE外排家族蛋白		10个SNP,1个Indel
MELO3C014594	Chr5:1091412-1093292	+	1880	含五肽重复序列的蛋白质	4个SNP	1个Indel
MELO3C019077	Chr8:11363674-11364042	+	368	液泡融合蛋白CCZ1	2个SNP	22个SNP,5个Indel
MELO3C019082	Chr8:11459977-11463627	+	3650	血清反应因子结合蛋白1		9个SNP,1个Indel
MELO3C019083	Chr8:11498986-11521642	+	22656	微管相关蛋白70-2		21个SNP,4个Indel
MELO3C019087	Chr8:11600872-11603741	+	2869	UDP糖基转移酶超家族蛋白		18个SNP,7个Indel
MELO3C019089	Chr8:11687078-11690459	+	3381	DNA促旋酶亚基B	1个SNP	21个SNP,2个Indel

Fig.4 GO enrichment

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QTL mapping and genetic analysis of soluble solids content in the center flesh of muskmelon

厚皮甜瓜心部果肉可溶性固形物含量遗传规律分析及QTL定位

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