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

摘要/Abstract

摘要：

【目的】通过构建高密度SNP遗传图谱，开展棉花多群体产量相关性状的QTL定位，获得稳定性好、精确度高的QTL，为产量性状调控基因的挖掘和有效分子标记的开发提供依据。【方法】以高稳产冀丰1271为母本、优质自交系冀丰173为父本，构建包含200个单株的F₂群体，利用测序基因分型（genotyping by sequencing，GBS）技术开发群体的SNP标记并构建高密度遗传图谱，对F₂、F_2:3、F_2:4群体的衣分、子指和单铃重进行QTL定位，注释主效和稳定QTL位点内的基因并分析基因在不同组织的表达模式，筛选候选基因。【结果】通过简化基因组测序，共获得383.07 Gb数据，包括母本冀丰1271的26.93 Gb、父本冀丰173的27.30 Gb和F₂群体的328.84 Gb，Q30值分别为90.55%、89.95%和95.77%。在F₂群体中开发了1 305 642个SNP标记，其中，用于构建遗传图谱的aa×bb型SNP为410 726个。构建了一张包含16 088个SNP、总图距为4 282.81 cM的高密度遗传图谱，标记间的平均距离为0.27 cM，利用共线性分析证明了图谱具有较高的质量。在3个群体中共定位到108个QTL，包括34个衣分QTL、36个子指QTL和38个单铃重QTL，其中有30个QTL与已报道QTL位置重叠或接近，78个QTL未见报道。发现10个主效QTL、16个稳定QTL，其中有5个主效QTL可在2个或3个群体中被定位到。qLP-A13-4在3个群体中均可被定位到，贡献率达到13.78%；qLP-A13-6在2个群体中被定位到，贡献率达到10.01%；qLP-D10-2在2个群体中被定位到，贡献率达到10.92%；qSI-D10-1在2个群体中被定位到，贡献率达到12.31%；qBW-D5-3在2个群体中被定位到，贡献率达到15.54%。在主效和稳定QTL位点内注释到3 415个基因。通过KEGG和GO分析，注释基因主要参与植物激素信号转导、TCA循环、次生代谢物质和氨基酸生物合成、光合生物的碳固定等通路。利用TM-1和NDM8的转录组数据，发现8个基因在棉花产量相关的纤维、胚珠或种子中具有较高的表达量，可能通过调控纤维或种子的发育，影响衣分或子指，进而影响棉花单铃重和产量。【结论】构建了一张陆地棉种内高密度遗传图谱，定位了108个产量相关QTL，发现5个主效QTL可在多个群体中定位到，鉴定到8个在纤维、胚珠或种子中高效表达的候选基因。

关键词: 陆地棉, 高密度遗传图谱, 产量, QTL定位, 候选基因

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

贾晓昀, 王士杰, 朱继杰, 赵红霞, 李妙, 王国印. 陆地棉高密度遗传图谱的构建及产量相关性状的QTL定位[J]. 中国农业科学, 2023, 56(4): 587-598.

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**