棉花重组自交系铃重性状的QTL定位

doi:10.11963/1002-7807.qzyfsl.20190115

摘要/Abstract

摘要：

【目的】铃重是构成棉花产量的基本因子之一。本研究旨在定位铃重QTL（Quantitative trait loci）,为分析铃重遗传组成提供参考。【方法】以中棉所36和海陆渐渗系G2005组配的137个RILs（Recombinant inbred lines）家系为作图群体,利用RAD-seq（Restriction-site associated DNA sequencing）技术及SSR（Simple sequence repeat）标记,构建遗传连锁图谱,并对5个环境下的铃重进行QTL分析。【结果】构建了包含26个连锁群、6 434个标记、总长为 4 071.98 cM、标记间平均距离为0.63 cM的遗传图谱。采用WinQTLCart 2.5软件的复合区间作图法进行QTL定位,共得到32个铃重QTL,分布于15条染色体,单个位点解释的表型变异率为4.46%~15.84%;qBW-A4-1、qBW-A4-2、qBW-A5-2、qBW-D9-1和qBW-D9-2能够在2个环境中检测到,解释5.07%~15.84%的表型变异率。【结论】本研究定位的主效QTL可用于分析铃重遗传机理。

关键词: 棉花; 重组自交系; 铃重; QTL

Abstract:

[Objective] The aim of this study was to explore the quantitative trait locus (QTL) related to the boll weight. [Method] A single seed descended population of 137 recombinant inbred lines (RILs) was developed from the cross of upland cotton (Gossypium hirsutum L.) CCRI 36 and G2005, an introgression inbred line introgressed from G. barbadense. Using restriction-site associated DNA sequencing (RAD-seq), a genetic linkage map composed of 6 434 makers, including 6 295 single nucleotide polymorphisms (SNP) and 139 simple sequence repeat (SSR) markers, was developed from the RILs population. [Result] This map spanned 4 071.98 cM with an average distance of 0.63 cM between adjacent markers. QTL mapping was performed by using boll weight data of five environments through WinQTLCart 2.5 software. Thirty-two QTL, with 4.46%-15.84% explained phenotypic variation related boll weight, were detected and found distributing on 15 chromosomes. qBW-A4-1, qBW-A4-2, qBW-A5-2, qBW-D9-1, and qBW-D9-2 were detected in two environments, which explained 5.07%-15.84% of the phenotypic variation. [Conclusion] Major QTLs detected in this study will provide an important reference for analysis of the genetic mechanism of boll weight.

Key words: cotton; recombinant inbred lines; boll weight; QTL

曲朝阳, 贾晓昀, 马启峰, 王寒涛, 魏恒玲, 范术丽. 棉花重组自交系铃重性状的QTL定位[J]. 棉花学报, 2019, 31(1): 12-22.

Qu Zhaoyang, Jia Xiaoyun, Ma Qifeng, Wang Hantao, Wei Hengling, Fan Shuli. QTL Mapping of Boll Weight Trait Based on Recombinant Inbred Lines in Gossypium hirsutum L.[J]. Cotton Science, 2019, 31(1): 12-22.

0
/ / 推荐

导出引用管理器 EndNote|Reference Manager|ProCite|BibTeX|RefWorks

链接本文: http://journal.cricaas.com.cn/Jweb_mhxb/CN/10.11963/1002-7807.qzyfsl.20190115

http://journal.cricaas.com.cn/Jweb_mhxb/CN/Y2019/V31/I1/12

图/表 6

表1

图1

表 2

表 3

5个环境中检测到的铃重QTLs"

QTL	环境 Environment	标记区间 Maker interval	位置 Position /cM	LOD	加性效应 Additive effect	贡献率 Phenotypic variation /%
qBW-A3-1	12AY	Marker4598-MGHES66	19.51	3.3	-0.11	5.53
qBW-A3-2	12AY	MGHES66-Marker4593	27.71	3.0	-0.11	5.18
qBW-A4-1	13AY	Marker5055-Marker5072	90.61	5.6	-0.15	9.79
	15AY	Marker5052-Marker5072	90.61	2.6	-0.14	5.07
qBW-A4-2	11AY	Marker5081-Marker5088	104.71	7.4	-0.29	15.83
	12AY	Marker5077-Marker5087	101.91	8.0	-0.20	15.84
qBW-A4-3	12AY	Marker5088-Marker5093	109.61	4.7	-0.15	9.17
qBW-A5-1	11AY	Marker5327-Marker5310	138.91	2.9	-0.14	6.45
qBW-A5-2	11AY	Marker5290-Marker5280	145.31	3.5	-0.15	7.73
	12AY	Marker5290-Marker5280	145.71	3.6	-0.12	6.32
qBW-A7-1	12AY	Marker12294-Marker12303	2.51	6.8	-0.17	12.35
qBW-A7-2	12AY	Marker13237-Marker13262	136.81	4.8	-0.14	8.35
qBW-A9-1	12AY	Marker14917-Marker14853	104.21	2.9	-0.11	5.20
qBW-A9-2	12AY	Marker14860-Marker14853	113.51	2.9	-0.11	5.15
qBW-A10-1	13AY	Marker15678-Marker15699	11.21	2.7	0.10	4.54
qBW-A10-2	15AY	Marker15764-Marker15853	46.71	3.1	0.16	6.13
qBW-A13-1	14AY	Marker18938-Marker18929	137.71	3.3	0.13	5.41
qBW-D1-1	13AY	Marker22291-Marker22481	58.41	4.0	0.17	6.93
qBW-D1-2	13AY	Marker23531-Marker23573	88.41	3.5	-0.20	6.67
qBW-D1-3	13AY	Marker23588-Marker23653	97.21	6.3	-0.24	11.75
qBW-D1-4	15AY	JESPR63-Marker24027	141.91	2.7	-0.14	5.26
qBW-D3-1	15AY	Marker25896-Marker25907	66.01	4.9	-0.23	9.97
qBW-D3-2	15AY	Marker25934-Marker25943	75.51	2.7	-0.20	5.61
qBW-D4-1	14AY	Marker27350-Marker27449	75.21	2.8	-0.13	5.06
qBW-D4-2	14AY	Marker27456-Marker27461	80.91	5.8	-0.18	10.05
qBW-D8-1	11AY	Marker34336-Marker34277	21.61	5.6	-0.20	11.46
qBW-D8-2	13AY	Marker34277-Marker34256	30.31	5.0	-0.15	9.03
qBW-D8-3	11AY	Marker34199-Marker34193	37.61	3.1	0.14	5.98
qBW-D8-4	15AY	Marker33593-Marker33578	135.51	3.1	0.16	5.96
qBW-D9-1	13AY	Marker36042-CGR6771	3.81	4.2	-0.13	7.35
	14AY	Marker36062-NAU3414	2.61	4.0	-0.14	6.73
qBW-D9-2	13AY	CGR6771-Marker36015	12.11	3.9	-0.13	6.78
	14AY	NAU3414-Marker36022	9.31	3.2	-0.13	5.52
qBW-D9-3	13AY	Marker34442-PGML02810	152.11	3.5	-0.12	6.37
qBW-D10-1	12AY	Marker36290-Marker36274	74.91	2.6	-0.10	4.46
qBW-D11-1	14AY	Marker36676-Marker36674	101.31	3.5	-0.13	5.79
qBW-D11-2	14AY	Marker36669-Marker36663	109.01	3.8	-0.14	6.29

表 3

图2

表4

参考文献 36

[1]	汤建. 棉花花铃期影响铃重的因素及提高技术[J]. 现代农业科技, 2014(7): 67-68.
	Tang Jian. The factors that affect the weight of the boll and the enhancement technique in cotton during flowing and boll formation stage[J]. Modern Agricultural Science and Technology, 2014(7): 67-68.
[2]	董合忠, 毛树春, 张旺锋,等. 棉花优化成铃栽培理论及其新发展[J]. 中国农业科学, 2014, 47(3): 441-445.
	Dong Hezhong, Mao Shuchun, Zhang Wangfeng, et al. On boll-setting optimization theory for cotton cultivation and its new development[J]. Scientia Agricultura Sinica, 2014, 47(3): 441-445.
[3]	Fedak G. Molecular aids for integration of alien chromatin through wide crosses[J]. Genome, 1999, 42(42): 584-591. doi: 10.1139/g99-046
[4]	邓琳, 余小刚, 姜朵,等. 棉花分子育种研究进展[J]. 山东农业科学, 2017, 49(5): 144-150.
	Deng Lin, Yu Xiaogang, Jiang Duo, et al. Research progress of cotton molecular breeding[J]. Shandong Agricultural Sciences, 2017, 49(5): 144-150.
[5]	Wang Yonghong, Xue Yongbiao, Li Jiayang. Towards molecular breeding and improvement of rice in China[J]. Trends in Plant Science, 2005, 10(12): 610-614. pmid: 16290216
[6]	程式华, 庄杰云, 曹立勇,等. 超级杂交稻分子育种研究[J]. 中国水稻科学, 2004, 18(5): 377-383.
	Cheng Shihua, Zhuang Jieyun, Cao Liyong, et al. Molecular breeding for super rice hybrids[J]. Chinese Journal of Rice Science, 2004, 18(5): 377-383.
[7]	李成奇, 郭旺珍, 马晓玲,等. 陆地棉衣分差异群体产量及产量构成因素的QTL标记和定位[J]. 棉花学报, 2008, 20(3): 163-169.
	Li Chengqi, Guo Wangzhen, Ma Xiaoling,et al. Tagging and mapping of QTL for yield and its components in upland cotton(Gossypium hirsutum L.) population with varied lint percentage[J]. Cotton Science, 2008, 20(3): 163-169.
[8]	王婷. 陆地棉铃重相关性状的QTL定位分析[D]. 南京: 南京农业大学, 2013.
	Wang Ting. QTL mapping for traits related to boll weight in upland cotton (Gossypium hirsutum L.)[D]. Nanjing: Nanjing Agricultural University, 2013.
[9]	Wu Jiaxiang, Gutierrez O A, Jenkins J N, et al. Quantitative analysis and QTL mapping for agronomic and fiber traits in an RI population of upland cotton[J]. Euphytica, 2009, 165(2): 231-245. doi: 10.1007/s10681-008-9748-8
[10]	Wang Baohua, Guo Wangzhen, Zhu Xiefeng, et al. QTL mapping of yield and yield components for elite hybrid derived-RILs in upland cotton[J]. Journal of Genetics and Genomics, 2007, 34(1): 35-45. pmid: 17469776
[11]	Zhang Shuwen, Feng Liuchun, Xing Luting,et al. New QTLs for lint percentage and boll weight mined in introgression lines from two feral landraces into Gossypium hirsutum acc TM-1[J]. Plant Breeding, 2016, 135(1): 90-101. doi: 10.1111/pbr.2016.135.issue-1
[12]	Fan Liping, Wang Liping, Wang Xinyi, et al. A high-density genetic map of extra-long staple cotton (Gossypium barbadense) constructed using genotyping-by sequencing based single nucleotide polymorphic markers and identification of fiber traits-related QTL in a recombinant inbred line population[J]. BMC Genomics, 2018, 19: 489. https://doi.org/10.1186/s12864-018-4890-8. doi: 10.1186/s12864-018-4890-8 pmid: 29940861
[13]	Yu Jiwen, Zhang Ke, Li Shuaiyang, et al. Mapping quantitative trait loci for lint yield and fiber quality across environments in a Gossypium hirsutum×Gossypium barbadense backcross inbred line population[J]. Theoretical and Applied Genetics, 2013, 126(1): 275-287. doi: 10.1007/s00122-012-1980-x pmid: 23064252
[14]	Zhang Zhen, Shang Haihong, Shi Yuzhen, et al. Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to quantitative trait loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.)[J]. BMC Plant Biology, 2016, 16(1): 79. https://doi.org/10.1186/s12870-016-0741-4. doi: https://doi.org/10.1186/s12870-016-0741-4
[15]	杨继龙. 利用RILs进行棉花早熟和纤维品质性状的QTL定位研究[D]. 武汉: 华中农业大学, 2013.
	Yang Jilong. QTL location of earliness and fiber quality in cotton using RILs[D]. Wuhan: Huazhong Agricultural University, 2013.
[16]	Paterson A H, Brubaker C L, Wendel J F. A rapid method for extraction of cotton (Gossypium spp.) genomic DNA suitable for RFLP or PCR analysis[J]. Plant Molecular Biology Reporter, 1993, 11(2): 122-127. doi: 10.1007/BF02670470
[17]	Willing E M, Hoffmann M, Klein J D,et al. Paired-end RAD-seq for de novo assembly and marker design without available reference[J]. Bioinformatics, 2011, 27(16): 2187-2193. doi: 10.1093/bioinformatics/btr346
[18]	Miller M R, Dunham J P, Amores A,et al. Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers[J]. Genome Research, 2007, 17(2): 240-248. doi: 10.1101/gr.5681207
[19]	Liu Dongyuan, Ma Chouxian, Hong Weiguo,et al. Construction and analysis of high-density linkage map using high-throughput sequencing data[J]. PLoS One, 2014, 9(6): e98855. https://doi.org/10.1371/journal.pone.0098855. doi: https://doi.org/10.1371/journal.pone.0098855
[20]	Zeng Zhaobang. Precision mapping of quantitative trait loci[J]. Genetics, 1994, 136(4): 1457-1468. pmid: 8013918
[21]	McCouch S R, Chen Xiuli, Panaud O, et al. Microsatellite marker development, mapping and applications in rice genetics and breeding[J]. Plant Molecular Biology, 1997, 35(1/2): 89-99. doi: 10.1023/A:1005711431474
[22]	Zhang Tianzhen, Hu Yan, Jiang Wenkai,et al. Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement[J]. Nature Biotechnology, 2015, 33(5): 531-537. doi: 10.1038/nbt.3207 pmid: 25893781
[23]	贾晓昀. 陆地棉种内高密度遗传图谱构建及重要农艺性状QTL定位[D]. 杨凌: 西北农林科技大学, 2017.
	Jia Xiaoyun. Inter-specific high-density genetic map construction and major agronomic traits QTL mapping for upland cotton (Gossypium hirsutum L.)[D]. Yangling: Northwest A&F University, 2017.
[24]	Jia Xiaoyun, Pang Chaoyou, Wei Hengling, et al. High-density linkage map construction and QTL analysis for earliness-related traits in Gossypium hirsutum L.[J]. BMC Genomics, 2016, 17 (1): 909. https://doi.org/ 10.1186/s12864-016-3269-y. doi: https://doi.org/ 10.1186/s12864-016-3269-y pmid: 27835938
[25]	Wang Hantao, Jin Xin, Zhang Beibei, et al. Enrichment of an intraspecific genetic map of upland cotton by developing markers using parental RAD sequencing[J]. DNA Research, 2015, 22(2): 147-160. doi: 10.1093/dnares/dsu047 pmid: 25656006
[26]	Wang Hantao, Huang Cong, Guo Huanle, et al. QTL mapping for fiber and yield traits in upland cotton under multiple environments[J]. PLoS One, 2015, 10(6): e130742. https://doi.org/10.1371/journal.pone.0130742. doi: https://doi.org/10.1371/journal.pone.0130742
[27]	徐云碧. 分子植物育种[M]. 北京: 科学出版社, 2014: 132.
	Xu Yunbi. Molecular Plant Breeding[M]. Beijing: Science Press, 2014: 132.
[28]	郑巨云, George O, Khan M K R,等. 毛棉苗期抗旱性状的QTL定位[J]. 棉花学报, 2017, 29(1): 29-39. doi: https://doi.org/10.11963/issn.1002-7807.201701004
	Zheng Juyun, George O, Khan M K R, et al. Mapping QTLs for traits related to drought tolerance at the seedling stage in an inter-specific[J]. Cotton Science, 2017, 29(1): 29-39. https://doi.org/10.11963/issn.1002-7807.201701004 doi: https://doi.org/10.11963/issn.1002-7807.201701004
[29]	Nielsen R, Paul J S, Albrechtsen A, et al. Genotype and SNP calling from next-generation sequencing data[J]. Nature Reviews Genetics, 2011, 12(6): 443-451. doi: 10.1038/nrg2986 pmid: 21587300
[30]	Lorenzo B, Sergio L, Ezio P, et al. Identification of SNP and SSR markers in eggplant using RAD tag sequencing[J]. BMC Genomics, 2011, 12(1): 1-9. doi: 10.1186/1471-2164-12-1
[31]	Blenda A, Fang D D, Rami J F, et al. A high density consensus genetic map of tetraploid cotton that integrates multiple component maps through molecular marker redundancy check[J]. PLoS One, 2012, 7(9): e45739. https://doi.org/ 10.1371/journal.pone.0045739. doi: https://doi.org/ 10.1371/journal.pone.0045739
[32]	Liang Zhao, Lü Yuanda, Cai Caiping, et al. Toward allotetraploid cotton genome assembly: integration of a high-density molecular genetic linkage map with DNA sequence information[J]. BMC Genomics, 2012, 13(1): 539. https://doi.org/10.1186/1471-2164-13-539. doi: https://doi.org/10.1186/1471-2164-13-539
[33]	Tanksley S D, Nelson J C. Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines[J]. Theoretical and Applied Genetics, 1996, 92(2): 191-203. doi: 10.1007/BF00223376 pmid: 24166168
[34]	Jiang Chunxiao, Wright R J, El-Zik K M, et al. Polyploid formation created unique avenues for response to selection in Gossypium (cotton)[J]. Proceedings of the National Academy of Sciences of the United States of America, 1998, 95(8): 4419-4424. pmid: 9539752
[35]	Yu Jing, Kohel R J, Smith C W. The construction of a tetraploid cotton genome wide comprehensive reference map[J]. Genomics, 2010, 95(4): 230-240. doi: 10.1016/j.ygeno.2010.02.001 pmid: 20171271
[36]	Wang Kai, Song Xianliang, Han Zhiguo, et al. Complete assignment of the chromosomes of Gossypium hirsutum L. by translocation and fluorescence in situ hybridization mapping[J]. Theoretical and Applied Genetics, 2006, 113(1): 73-80. pmid: 16609860

环境 Environment	G2005 /g	CCRI 36 /g	重组自交系 RILs population
环境 Environment	G2005 /g	CCRI 36 /g	最小值 Minimum /g	最大值 Maximum /g	平均值 Average /g	方差 Variance	偏度 Skewness	峰度 Kurtosis
2011AY	3.87^*	3.13	2.43	5.52	4.15	0.26	-0.33	0.59
2012AY	4.86^**	3.96	2.84	5.81	4.48	0.22	-0.23	0.82
2013AY	5.67^*	5.17	3.84	6.07	5.01	0.22	-0.17	-0.07
2014AY	6.01^**	4.67	3.28	6.41	5.25	0.28	-0.76	1.03
2015AY	5.25^*	4.37	2.87	6.22	4.68	0.36	-0.33	-0.06

染色体 Chromosomes	总标记数 No. of markers	SNP 标记数 No. of SNP makers	SSR 标记数 No. of SSR markers	图距 Distance /cM	平均间距 Average interval /cM	最大间距 Maximum interval /cM
A1	190	184	6	133.20	0.70	10.61
A2	218	216	2	163.92	0.76	7.25
A3	218	212	6	136.23	0.63	4.38
A4	169	169	0	160.85	0.95	7.19
A5	325	325	0	152.42	0.47	4.41
A6	411	399	12	147.89	0.36	7.19
A7	305	305	0	152.55	0.50	4.38
A8	386	386	0	175.59	0.45	6.65
A9	281	261	20	196.04	0.70	9.15
A10	258	258	0	146.32	0.57	4.89
A11	357	349	8	174.97	0.49	9.69
A12	157	154	3	160.88	1.03	15.37
A13	325	318	7	147.25	0.45	5.76
A 亚组 A subgenome	3 600	3 536	64	2 048.11	0.57	15.37
D1	257	240	17	152.01	0.59	9.25
D2	268	258	10	177.07	0.66	9.31
D3	179	179	0	143.18	0.80	6.65
D4	178	178	0	98.98	0.56	11.19
D5	252	241	11	190.57	0.76	13.70
D6	258	241	17	143.48	0.56	13.76
D7	208	208	0	157.77	0.76	5.48
D8	257	257	0	143.18	0.56	5.30
D9	201	189	12	153.85	0.77	10.32
D10	198	193	5	155.65	0.79	18.24
D11	112	109	3	174.54	1.57	8.07
D12	229	229	0	167.80	0.73	13.15
D13	237	237	0	165.79	0.70	10.72
D 亚组 D subgenome	2 834	2 759	75	2 023.87	0.71	18.24
总计 Total	6 434	6 295	139	4 071.98	0.63	18.24