甜瓜SLAF图谱构建及果实相关性状QTL分析

doi:10.3864/j.issn.0578-1752.2021.19.014

Abstract

Abstract:

【Objective】 Through the QTL mapping and candidate gene analysis of muskmelon (Cucumis melo L.) fruit-related traits, so as to provide a theoretical basis for muskmelon quality breeding, gene mapping and functional verification. 【Method】 The F₁ plant was made cross by 1244 as female parent with thin-skinned melon and M5 with thick-skinned melon as male parent, combined with SFLA sequencing technology to develop molecular tags and construct high-density genetic maps. Based on F_2:3 phenotype data, Mapqtl analysis method was used to detect QTL location. 【Result】 Totally 380 446 Mreads (83.12 Gb) data were obtained, the average Q30 and GC content was 93.59% and 36.87%, respectively; totally 112 844 SLAF tags and 3 274 879 SNPs were obtained; a genetic map contained 12 linkage groups with a total of 10 596 markers were constructed. The genetic map spanned 1 383.88 cM with the average distance was 0.13 cM between markers, and totally 99.92% developed markers were mapped. The gene controling fruit sutures (fst) of melon was located at the end of chromosome 11, between Marker 1993423 (62.18) and Marker 1998820 (63.05), covering 0.72 Mb of the genome, and containing 33 candidate genes. The gene for pericarp pattern (fpp) was located at chromosome 2 between Marker 459584 (90.91) and Marker 459446 (90.91) which covered the genome of 0.08 Mb and contained 5 candidate genes, among them MELO3C026292 (1-deoxy-D-xylulose-5-phosphate reductoisomerase) might be the candidate gene for pericarp pattern. At the same time, QTL locus of pericarp color (fpc) was detected which located between Marker 1229174 (7.14) and Marker 1229973 (7.14) on the chromosome 7, with the contribution rate was 9.9%. One QTL locus of fruit shape (fs) fs9.1 was detected between Marker 1705671 (76.19) and Marker 1705915 (79.23) on chromosome 9 with a contribution rate of 7.6%. Six QTL loci related to single fruit weight (sfw1.1, sfw2.1, sfw2.2, sfw6.1, sfw7.1, sfw10.1) were detected on chromosomes 1, 2, 6, 7, and 10 with the contribution rate were between 3.1% to 17%, and the LOD value were between 3.0 to 5.6. 【Conclusion】The fruit sutures and pericarp pattern genes were located on the chromosomes11 and 2, and then 33 and 5 candidate genes were obtained, respectively; One QTL for pericarp color, one QTL for fruit shape and 6 QTLs for single fruit weight were also detected.

Key words: melon, SLAF sequencing, genetic map construction, fruit related traits, QTL analysis

WANG Ling,CAI Yi,WANG GuiChao,WANG Di,SHENG YunYan. Specific Length Amplified Fragment (SFLA) Sequencing Mapping Construction and QTL Analysis of Fruit Related Traits in Muskmelon[J].Scientia Agricultura Sinica, 2021, 54(19): 4196-4206.

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References 32

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世代 Generation	单株数 Plant number	果面沟表型分离比率 Ratio of fruit sutures	期望比率 Exception ratio	卡方值 χ²	果皮花纹分离比率 Ratio of pericarp pattern	期望比率 Exception ratio	卡方值 χ²
P₁	30	30（有 With）	—	—	0（无 Without）	—	—
P₂	30	0（无 Without）	—	—	30（有 With）	—	—
F₁	30	30（全有 All）	—	—	30（有 With）	—	—
F₂	242	145﹕50 （有﹕无With﹕Without）	3﹕1	0.015	152﹕43 （有﹕无With﹕Without）	3﹕1	0.381
BC₁P₁	150	30（有 With）	—	—	30（有 With）	—	—
BC₁P₂	150	76﹕74 （有﹕无With﹕Without）	1﹕1	0.131	81﹕69 （有﹕无With﹕Without）	1﹕1	0.488

样品名称 Sample ID	序列数 Total reads	碱基数 Total base	测序质量≥30 的碱基数所占百分数 Q30 (%)	G、C 所占总碱基的百分数 GC (%)
1244	38911978	11653958274	92.31	37.01
M5	31878110	9548013962	92.67	36.72
F₂ 群体 F₂ population	2692579	538400027	95.81	36.88
对照 Control	1188503	237656096	96.33	40.87
总量 Total	380446747	83117975446	93.59	36.87

样本 Sample	比对序列数占比 Mapped (%)	测序序列比对参考基因组占比 Properly_mapped (%)	SNP数量 SNP Number	杂合SNP数量 Number of Heter-SNP	纯合SNP数量 Number of Homo-SNP	杂合率 Heter ratio (%)
1244	97.39	90.44	2 250 862	282 705	1 968 157	12.55
MS5	96.56	89.08	1 489 767	146 401	1 343 366	9.82
F₂	97.97	92.50	806 865	60 289	211 029	22.19

染色体 LG	标记数 Number of markers	Gap<5 cM比值 Gap<5 cM ration (%)	秩相关系数 Spearman	最大Gap Max Gap (cM)	总图距 Total distance (cM)	平均图距 Average distance (cM)
1	1267	100.00	0.987	1.74	110.2	0.09
2	504	99.80	0.994	9.33	98.74	0.2
3	1363	100.00	0.989	4.97	111.19	0.08
4	901	100.00	0.995	1.83	138.63	0.15
5	875	100.00	0.992	2.18	94.2	0.11
6	1070	100.00	0.963	3.57	125.08	0.12
7	300	99.00	0.995	6.84	112.25	0.37
8	1104	100.00	0.984	1.83	127.49	0.12
9	649	99.69	0.996	7.98	96.19	0.15
10	591	100.00	0.965	3.05	135.64	0.23
11	1579	100.00	0.982	2.17	137.24	0.09
12	393	99.74	0.996	10.75	97.03	0.25
共计 Total	10596	99.85	0.986	10.75	1383.88	0.13

性状 Traits	QTL位点 QTL position	LOD值LOD threshold	染色体Group ID	起始位点 Start (cM）	基因组位置 Position	结束位点 End (cM)	基因组位置Position	峰值 Max LOD	加性效应ADD	显性效应DOM	贡献率 PVE (%)	候选基因数Candidate gene number
果型指数 Fruit shape (fs)	fs9.1	3.0	9	Marker 1705671 (76.19)	23034060	Marker 1705915 (79.23)	23259152	5.91	0.19	0.05	7.6	23
单果重 Single fruit weight (sfw)	sfw1.1	3.0	1	Marker 297654 (91.06)	34295745	Marker 298408 (91.49)	34435727	3.3	-28.38	-22.21	8.3	17
	sfw2.1	3.0	2	Marker 316077 (18.35)	1626517	Marker 316123 (18.35)	1635504	3.0	17.81	-8.88	3.1	1
	sfw2.2	3.0	2	Marker 414271 (60.38)	18344184	Marker 413648 (60.82)	18881371	5.6	-45.10	-13.59	17.0	15
	sfw6.1	3.0	6	Marker 1186096 (74.87)	30841187	Marker 1186721 (74.89)	38291645	4.2	-21.93	34.30	10.2	354
	sfw7.1	3.0	7	Marker 1254170 (34.54)	4758046	Marker 1255749 (34.97)	7547788	3.2	-25.56	8.55	5.9	113
	sfw10.1	3.0	10	Marker 1718615 (3.05)	485913	Marker 1718692 (3.48)	504601	3.1	-30.64	-14.42	8.3	2
果面沟 Fruit sutures (fst)	fst	—	11	Marker 1993423 (62.18)	20408304	Marker 1998820 (63.05)	21129670	18.3	-0.42	-0.284		33
果皮花纹 Fuit pericarp pattern (fpp)	fpp	—	2	Marker 459584 (90.91)	26112655	Marker 459446 (90.91)	26189137	7.7	0.309	0.087		5
果皮底色 Fruit pericarp color (pc)	fpc	3.0	7	Marker1229174 (7.14)	709451	Marker1229973 (7.14)	892244	4.7	-0.444	-0.09	9.9	15

Specific Length Amplified Fragment (SFLA) Sequencing Mapping Construction and QTL Analysis of Fruit Related Traits in Muskmelon

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