陆地棉高密度遗传图谱的构建及产量相关性状的QTL定位

doi:10.3864/j.issn.0578-1752.2023.04.001

Abstract

Abstract:

【Objective】By constructing a high-density SNP genetic map, QTL mapping for cotton yield related traits of multiple populations was carried out to obtain stable and accurate QTL. It will provide references for the excavation of yield trait regulatory genes and the development of effective molecular markers. 【Method】Jifeng 1271 with high and stable yield and Jifeng173 with super fiber quality were used to construct an F₂ population composing of 200 plants. A high-density SNP genetic map was constructed by GBS (Genotyping by sequencing), and QTL mapping was carried out for lint percentage, seed index and boll weight of F₂, F_2:3 and F_2:4 populations. Genes in major and stable QTL were annotated, and the expression patterns in different tissues were analyzed for candidate genes selection. 【Result】A total of 383.07 Gb data was obtained by GBS, including 26.93 Gb for the maternal cultivar Jifeng 1271, 27.30 Gb for the paternal inbred line Jifeng 173 and 328.84 Gb for the 200 F₂ plants, and Q30 scores were 90.55%, 89.95% and 95.77%, respectively. And 1 305 642 SNP markers were developed in the F₂population, including 410 726 aa×bb type SNP that were used for genetic map construction. A high-density genetic map containing 16 088 SNP and spanning 4 282.81 cM was constructed, and the average genetic distance between adjacent SNP was 0.27 cM. Collinearity analysis proved high quality of the genetic map. A total of 108 yield related QTL were mapped, including 34 lint percentage QTL, 36 seed index QTL and 38 boll weight QTL. 30 QTL overlapped with or were close to the published QTL, and the other 78 QTL were new. 10 major QTL and 16 stable QTL were found, and 5 major QTL could be mapped in 2 or 3 populations. qLP-A13-4 could be mapped in 3 populations, and the R² reached 13.78%. qLP-A13-6 could be mapped in 2 populations, and the R² reached 10.01%. qLP-D10-2 could be mapped in 2 populations, and the R² reached 10.92%. qSI-D10-1 could be mapped in 2 populations and the R² reached 12.31%. qBW-D5-3 could be mapped in 2 populations and the R² reached 15.54%. A total of 3 415 genes were annotated in these major and stable QTL. By KEGG and GO analysis, the annotated genes are mainly involved in plant hormone signal transduction, TCA cycle, biosynthesis of secondary metabolites and amino acids, carbon fixation in photosynthetic organisms. Using the transcriptome data of TM-1 and NDM8, 8 genes were highly expressed in fiber, ovule or seed, which may be important candidate genes for boll weight and yield by regulating lint percentage or seed index. 【Conclusion】An intra-specific high-density genetic map was constructed for upland cotton. 108 yield related QTL were mapped, 5 major QTL could be mapped in at least 2 populations, and 8 candidate genes with high expression level in fiber, ovule or seed were identified.

Key words: Upland cotton, high density genetic map, yield, QTL mapping, candidate gene

JIA XiaoYun, WANG ShiJie, ZHU JiJie, ZHAO HongXia, LI Miao, WANG GuoYin. Construction of A High-Density Genetic Map and QTL Mapping for Yield Related Traits in Upland Cotton[J].Scientia Agricultura Sinica, 2023, 56(4): 587-598.

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材料 Material	测序数据量 Sequence data (Gb)	GC含量 GC content (%)	平均Q30值 Average Q30 (%)	比对率 Mapped ratio (%)	平均深度 Average depth (×)	覆盖度 Coverage (5×) (%)
冀丰1271 Jifeng1271	26.93	34.98	90.55	99.64	9.58	86.45
冀丰173 Jifeng173	27.30	35.96	89.95	99.47	9.69	84.28
F₂群体 F₂ population	328.84	41.44	95.77	99.69	0.70	4.17

标记类型 Marker type	SNP数量 No. of SNP
aa×bb	410726
ab×cc	159
ab×cd	0
cc×ab	47
ef×eg	340
hk×hk	325126
lm×ll	162538
nn×np	406706
总计Total	1305642

连锁群 Linkage group	SNP数量 No. of SNP	长度 Distance (cM)	平均距离 Average distance (cM)	大于5 cM的Gap数量 No. of gaps>5 cM	最大Gap Largest gap (cM)	相关系数 Correlation coefficient
A1	1724	160.35	0.09	0	1.98	-1.00
A2	246	167.21	0.68	3	8.22	-1.00
A3	921	158.58	0.17	1	8.07	-1.00
A4	756	173.12	0.23	1	9.12	-1.00
A5	734	161.56	0.22	0	2.77	-1.00
A6	288	171.10	0.60	1	7.47	-1.00
A7	747	154.62	0.21	0	1.99	-1.00
A8	569	172.90	0.30	0	3.08	-1.00
A9	1130	169.12	0.15	0	3.82	-1.00
A10	545	159.40	0.29	0	3.61	-1.00
A11	499	167.66	0.34	0	3.01	-1.00
A12	259	171.19	0.66	3	17.82	-1.00
A13	828	164.37	0.20	1	5.82	-1.00
D1	320	179.92	0.56	1	5.69	-1.00
D2	459	151.62	0.33	1	6.31	-1.00
D3	39	157.33	4.14	10	19.75	-1.00
D4	131	176.25	1.36	5	10.71	-1.00
D5	1746	172.23	0.10	0	0.80	-1.00
D6	610	151.84	0.25	0	4.58	-1.00
D7	419	175.99	0.42	0	4.46	-1.00
D8	312	150.41	0.48	2	14.97	-1.00
D9	512	178.40	0.35	1	9.43	-1.00
D10	1201	152.77	0.13	0	1.13	-1.00
D11	429	164.12	0.38	1	7.20	-1.00
D12	473	170.61	0.36	1	5.60	-1.00
D13	191	150.12	0.79	1	8.46	-1.00
总计Total	16088	4282.81	0.27	33	19.75

群体与性状 Population and trait	F₂			F_2:3			F_2:4
群体与性状 Population and trait	衣分 LP (%)	子指 SI (g)	单铃重 BW (g)	衣分 LP (%)	子指 SI (g)	单铃重 BW (g)	衣分 LP (%)	子指 SI (g)	单铃重 BW (g)
冀丰1271 Jifeng 1271	41.10**	11.00*	6.40**	41.98*	10.75**	6.35**	40.78**	11.20*	6.13**
冀丰173 Jifeng173	38.70	10.30	4.90	40.66	9.60	5.04	38.41	10.70	4.79
最大值Maximun	45.31	12.00	8.83	45.53	11.90	6.66	43.88	12.90	6.39
最小值Minimun	37.60	7.90	4.37	37.64	8.00	4.23	34.76	8.80	4.62
平均值Average	40.59	9.90	5.68	41.63	10.09	5.57	39.15	11.05	5.45
偏度Skewness	0.02	-0.37	0.02	-0.22	-0.23	-0.05	0.05	0.05	0.02
峰度Kurtosis	-0.20	0.85	0.79	0.60	0.53	0.42	0.79	-0.15	-0.29
变异系数CV (%)	3.73	7.62	16.24	3.03	6.05	7.21	3.74	6.74	6.87

性状 Trait	F₂		F_2:3		F_2:4
性状 Trait	子指SI	单铃重BW	子指SI	单铃重BW	子指SI	单铃重BW
衣分LP	-0.33**	0.08	-0.31**	0.04	-0.36**	0.09
子指SI	1	0.34**	1	0.51**	1	0.56**

Construction of A High-Density Genetic Map and QTL Mapping for Yield Related Traits in Upland Cotton

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