小麦茎秆性状的转录组测序及全基因组关联分析

doi:10.3724/SP.J.1006.2024.31076

作物学报 ›› 2024, Vol. 50 ›› Issue (9): 2187-2206.doi: 10.3724/SP.J.1006.2024.31076

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

小麦茎秆性状的转录组测序及全基因组关联分析

禹海龙¹^**(), 吴文雪¹^**(), 裴星旭¹, 刘晓宇¹, 邓跟望², 李西臣², 甄士聪³, 望俊森³, 赵永涛³, 许海霞¹, 程西永¹, 詹克慧¹^,^*()

¹河南农业大学农学院, 河南郑州 450046
²河南华冠种业有限公司, 河南鹿邑 477200
³漯河市农业科学院, 河南漯河 462000

收稿日期:2023-12-01 接受日期:2024-05-21 出版日期:2024-09-12 网络出版日期:2024-06-04
通讯作者: *詹克慧, E-mail: kh486@163.com
作者简介:禹海龙, E-mail: 2444290408@qq.com;
吴文雪, E-mail: 1294464168@qq.com
^**同等贡献
基金资助:
2023年度河南省重点研发专项(231111110700);2022年度河南省重大科技专项(221100110300)

Transcriptome sequencing and genome-wide association study of wheat stem traits

YU Hai-Long¹^**(), WU Wen-Xue¹^**(), PEI Xing-Xu¹, LIU Xiao-Yu¹, DENG Gen-Wang², LI Xi-Chen², ZHEN Shi-Cong³, WANG Jun-Sen³, ZHAO Yong-Tao³, XU Hai-Xia¹, CHENG Xi-Yong¹, ZHAN Ke-Hui¹^,^*()

¹Agronomy College of Henan Agricultural University, Zhengzhou 450046, Henan, China
²Henan Huaguan Seed Industry Co., Ltd., Luyi 477200, Henan, China
³Luohe Academy of Agricultural Sciences, Luohe 46200, Henan, China

Received:2023-12-01 Accepted:2024-05-21 Published:2024-09-12 Published online:2024-06-04
Contact: *E-mail: kh486@163.com
About author:First author contact:^**Contributed equally to this work
Supported by:
Key Research and Development Program of Henan Province in 2023(231111110700);Major Science and Technology Program of Henan Province in 2022(221100110300)

摘要/Abstract

摘要：

小麦的茎秆性状与倒伏紧密相关, 发掘其显著关联的基因位点和候选基因, 为解析小麦茎秆性状的遗传机制和分子标记辅助育种提供依据。本研究以黄淮南部地区的192份小麦品种为材料, 利用小麦660K SNP芯片对7个环境成熟期和4个环境灌浆中期的14个茎秆性状进行了全基因组关联分析(GWAS), 同时利用RNA-seq分析了基部前二节间强度和直径的差异表达基因。结果表明, 所有性状的成熟期与灌浆中期的差异均达到极显著水平。与灌浆中期相比, 成熟期的重心高度增幅较大, 基部第二和第三节间长度增加, 其他性状均降低。GWAS共检测出163个与茎秆性状相关的稳定SNP标记(MTA), 其中45个具有基因或蛋白注释, 与转录组联合分析, 共筛选到3个与小麦茎秆性状相关的候选基因。推测候选基因TraesCS5A02G522100通过合成异戊二酸类化合物调节小麦的光合作用以及通过调节固醇的生成提高细胞膜的稳定性和渗透性, 进而促进茎秆的发育, 改善茎秆性状。候选基因TraesCS1D02G390600直接参与小麦茎秆细胞分裂和器官的形成, 使茎秆变粗, 充实度增加。候选基因TraesCS7A02G481800在小麦中通过参与细胞间的信号传递过程, 调控茎秆的发育、应激响应等过程。这些候选基因通过qRT-PCR验证, 其基因的表达趋势与转录组测序所得结果基本一致。

关键词: 小麦, 茎秆性状, 转录组测序, 全基因组关联分析, 黄淮南部地区

Abstract:

Stem traits in wheat are closely associated with lodging, and the identification of significantly linked gene loci and candidate genes provides a foundation for analyzing the genetic mechanism and molecular marker-assisted breeding of wheat stem traits. In this study, a panel of 192 wheat varieties from the southern Huang-Huai region was utilized to assess 14 stem traits across seven mature stage environments and four mid-filling stage environments. Genome-wide association analysis (GWAS) was conducted using wheat 660K SNP chips, and the differentially expressed genes related to the strength and diameter of the first two basal internodes were analyzed through RNA-seq. The results revealed a substantial difference between the mature stage and the mid-filling stage for all traits. In comparison to the mid-filling stage, the height of the gravity center significantly increased during the mature stage, while the length of the second and third internodes at the base showed an increase, and the other traits exhibited a decrease. GWAS detected a total of 163 stable SNPs (MTA), out of which 45 had gene or protein annotations. Combining GWAS and transcriptome analysis, three candidate genes associated with wheat stem traits were identified. The candidate gene TraesCS5A02G522100 may regulate photosynthesis by synthesizing isoglutaric acid compounds, thereby enhancing cell membrane stability and permeability through sterol production. This regulation, in turn, promotes stem development and improves stem characteristics. The candidate gene TraesCS1D02G390600 is directly involved in cell division and organ formation in the wheat stem, resulting in thicker and fuller stems. The candidate gene TraesCS7A02G481800 plays a role in cell-to-cell signaling, regulation of stem development, and stress response. The expression trends of these candidate genes were consistent with the results of transcriptome sequencing, as validated by qRT-PCR.

Key words: wheat, stem trait, transcriptome sequencing, genome-wide association study, southern Huang-Huai region

禹海龙, 吴文雪, 裴星旭, 刘晓宇, 邓跟望, 李西臣, 甄士聪, 望俊森, 赵永涛, 许海霞, 程西永, 詹克慧. 小麦茎秆性状的转录组测序及全基因组关联分析[J]. 作物学报, 2024, 50(9): 2187-2206.

YU Hai-Long, WU Wen-Xue, PEI Xing-Xu, LIU Xiao-Yu, DENG Gen-Wang, LI Xi-Chen, ZHEN Shi-Cong, WANG Jun-Sen, ZHAO Yong-Tao, XU Hai-Xia, CHENG Xi-Yong, ZHAN Ke-Hui. Transcriptome sequencing and genome-wide association study of wheat stem traits[J]. Acta Agronomica Sinica, 2024, 50(9): 2187-2206.

图/表 24

附表1

供试小麦材料"

序号 Serial number	品种 Variety	省份 Province	序号 Serial number	品种 Variety	省份 Province
1	矮丰3号 Aifeng 3	陕西Shaanxi	97	兰考矮早8 Lankaoaizao 8	河南 Henan
2	百农3217 Bainong 3217	河南Henan	98	漯麦4号 Luomai 4	河南 Henan
3	豫麦4号 Yumai 4	河南 Henan	99	郑农17 Zhengnong 17	河南 Henan
4	豫麦18 Yumai 18	河南 Henan	100	洛旱3号 Luohan 3	河南 Henan
5	陕农7859 Shaannong 7859	陕西 Shaanxi	101	濮麦9号 Pumai 9	河南 Henan
6	周麦9号 Zhoumai 9	河南 Henan	102	新麦18 Xinmai 18	河南 Henan
7	兰考86 (79) Lankao 86 (79)	河南 Henan	103	郑麦004 Zhengmai 004	河南 Henan
8	豫麦34 Yumai34	河南 Henan	104	泛麦5号 Fanmai 5	河南 Henan
9	郑优6号Zhengyou 6	河南 Henan	105	西农889 Xinong 889	陕西 Shaanxi
10	陕160 Shaan 160	陕西 Shaanxi	106	小偃81 Xiaoyan 81	北京 Beijing
11	周8425B Zhou 8425B	河南 Henan	107	新麦208 Xinmai 208	河南 Henan
12	新麦9号 Xinmai 9	河南 Henan	108	郑麦366 Zhengmai 366	河南 Henan
13	蒿城8901 Gaocheng 8901	河北 Hebei	109	衡观35 Hengguan 35	河北 Hebei
14	小偃22 Xiaoyan 22	陕西 Shaanxi	110	开麦18 Kaimai 18	河南 Henan
15	豫麦49 Yumai 49	河南 Henan	111	洛麦21 Luomai 21	河南 Henan
16	豫麦51 Yumai 51	河南 Henan	112	濮麦10号 Pumai 10	河南 Henan
17	郑旱 1号 Zhenghan 1	河南 Henan	113	豫农201 Yunong 201	河南 Henan
18	内乡188 Neixiang 188	河南 Henan	114	源育3号 Yuanyu 3	河南 Henan
19	济旱2号 Jihan 2	山东 Shandong	115	百农160 Bainong 160	河南 Henan
20	石4185 Shi 4185	河北 Hebei	116	漯麦8号 Luomai 8	河南 Henan
21	烟农19 Yannong 19	山东 Shandong	117	新麦20 Xinmai 20	河南 Henan
22	郑麦9023 Zhengmai 9023	河南 Henan	118	泛麦11 Fanmai 11	河南 Henan
23	安麦8号 Anmai 8	河南 Henan	119	西农9871 Xinong 9871	陕西 Shaanxi
24	邯6172 Han 6172	河北 Hebei	120	周麦23 Zhoumai 23	河南 Henan
25	周麦16 Zhoumai 16	河南 Henan	121	豫农416 Yunong 416	河南 Henan
26	济麦20 Jimai 20	山东 Shandong	122	豫农982 Yunong 982	河南 Henan
27	太空6号 Taikong 6	河南 Henan	123	兰考198 Lankao 198	河南 Henan
28	偃展4110 Yanzhan 4110	河南 Henan	124	新旱1号 Xinhan 1	河南 Henan
29	豫农9901 Yunong 9901	河南 Henan	125	烟99102 Yan 99102	山东 Shandong
30	众麦1号 Zhongmai 1	河南 Henan	126	亿麦6号 Yimai 6	河南 Henan
31	周麦18 Zhoumai 18	河南 Henan	127	豫教5号 Yujiao 5	河南 Henan
32	周麦19 Zhoumai 19	河南 Henan	128	豫农4023 Yunong 4023	河南 Henan
33	矮抗58 Aikang 58	河南 Henan	129	漯麦18 Luomai 18	河南 Henan
34	豫农949 Yunong 949	河南 Henan	130	郑麦0856 Zhengmai 0856	河南 Henan
35	04中36 04 Zhong 36	河南 Henan	131	郑麦583 Zhengmai 583	河南 Henan
36	鹤麦1号 Hemai 1	河南 Henan	132	周麦26 Zhoumai 26	河南 Henan
37	济麦22 Jimai 22	山东 Shandong	133	百农207 Bainong 207	河南 Henan
38	洛旱6号 Luohan 6	河南 Henan	134	洛麦24 Luomai 24	河南 Henan
39	平安3号 Pingan 3	河南 Henan	135	西农529 Xinong 529	陕西 Shaanxi
40	平安6号 Pingan 6	河南 Henan	136	郑麦101 Zhengmai 101	河南 Henan
41	新麦19 Xinmai 19	河南 Henan	137	博农6号 Bonong 6	河南 Henan
42	偃佃9433 Yandian 9433	河南 Henan	138	存麦5号 Fengdecunmai 5	河南 Henan
43	郑麦9694 Zhengmai 9694	河南 Henan	139	存麦8号 Fengdecunmai 8	河南 Henan
44	豫农202 Yunong 202	河南 Henan	140	华育198 Huayu 198	河南 Henan
45	郑育麦9987 Zhengyumai 9987	河南 Henan	141	淮麦0882 Huaimai 0882	江苏 Jiangsu
46	周麦22 Zhoumai 22	河南 Henan	142	洛麦05159 Luomai 05159	河南 Henan
47	洛新998 Luoxin 998	河南 Henan	143	漯6073 Luo 6073	河南 Henan
48	豫保1号 Yubao 1	河南 Henan	144	秋乐2122 Qiule 2122	河南 Henan
49	中育12 Zhongyu 12	河南 Henan	145	未来0818 Weilai 0818	安徽 Anhui
50	洛麦23 Luomai 23	河南 Henan	146	新0208 Xin 0208	河南 Henan
51	汝州0319 Ruzhou 0319	河南 Henan	147	豫农211 Yunong 211	河南 Henan
52	许科1号 Xuke 1	河南 Henan	148	中麦875 Zhongmai 875	北京 Beijing
53	汶农14 Wennong 14	山东 Shandong	149	中育9302 Zhongyu 9302	河南 Henan
54	新麦26 Xinmai 26	河南 Henan	150	中育9307 Zhongyu 9307	河南 Henan
55	存麦1号 Cunmai 1	河南 Henan	151	百农418 Bainong 418	河南 Henan
56	开麦21 Kaimai 21	河南 Henan	152	存麦11 Cunmai 11	河南 Henan
57	平安8号 Pingan 8	河南 Henan	153	泛麦7030 Fanmai 7030	河南 Henan
58	许科316 Xuke 316	河南 Henan	154	泛麦803 Fanmai 803	河南 Henan
59	郑麦7698 Zhengmai 7698	河南 Henan	155	怀川919 Huaichuan 919	河南 Henan
60	周麦27 Zhoumai 27	河南 Henan	156	黄明116 Huangming 116	河南 Henan
61	国麦301 Guomai 301	河南 Henan	157	俊达106 Junda 106	河南 Henan
62	农大1108 Nongda 1108	北京 Beijing	158	洛麦28 Luomai 28	河南 Henan
63	郑麦379 Zhengmai 379	河南 Henan	159	孟麦023 Mengmai 023	河南 Henan
64	周麦24 Zhoumai 24	河南 Henan	160	平安11 Pingan 11	河南 Henan
65	平安9号 Pingan 9	河南 Henan	161	濮麦053 Pumai 053	河南 Henan
66	许科415 Xuke 415	河南 Henan	162	商麦156 Shangmai 156	河南 Henan
67	郑麦103 Zhengmai 103	河南 Henan	163	泰禾麦1号 Taihemai 1	河南 Henan
68	郑育麦043 Zhengyumai 043	河南 Henan	164	亚麦 1号 Yamai 1	河南 Henan
69	存麦10号 Fengdecunmai 10	河南 Henan	165	偃科028 Yanke 028	河南 Henan
70	枣乡158 Zaoxiang 158	河南 Henan	166	偃麦864 Yanmai 864	河南 Henan
71	弘麦118 Hongmai 118	河南 Henan	167	郑麦113 Zhengmai 113	河南 Henan
72	华瑞00712 Huarui 00712	江苏 Jiangsu	168	LS6109 LS 6109	山东 Shandong
73	许麦1242 Xumai 1242	河南 Henan	169	存麦12号 Cunmai 12	河南 Henan
74	郑麦1023 Zhengmai 1023	河南 Henan	170	洛麦31 Luomai 31	河南 Henan
75	郑育麦0519 Zhengyumai 0519	河南 Henan	171	先麦13号 Xianyou 13	河南 Henan
76	小偃6号 Xiaoyan 6	陕西 Shaanxi	172	徐麦0054 Xumai 0054	江苏 Jiangsu
77	良星99 Liangxing 99	山东 Shandong	173	豫农186 Yunong 186	河南 Henan
78	师栾02-1 Shiluan 02-1	河北 Hebei	174	郑品麦8号 Zhengpinmai 8	河南 Henan
79	许科168 Xuke 168	河南 Henan	175	中研麦0708 Zhongyanmai 0708	江苏 Jiangsu
80	豫麦2号 Yumai 2	河南 Henan	176	周麦30 Zhoumai 30	河南 Henan
81	陕优225 Shaanyou 225	陕西 Shaanxi	177	FS059	河南 Henan
82	豫麦14优 Yumai 14 You	河南 Henan	178	国育101 Guoyu 101	河南 Henan
83	豫麦41 Yumai 41	河南 Henan	179	滑育麦118 Huayumai 118	河南 Henan
84	闫麦8911 Yanmai 8911	陕西 Shaanxi	180	济研麦7号 Jiyanmai 7	河南 Henan
85	豫麦47 Yumai 47	河南 Henan	181	浚9917 Jun 9917	河南 Henan
86	豫麦52 Yumai 52	河南 Henan	182	兰考182 Lankao 182	河南 Henan
87	豫麦54 Bainong 64	河南 Henan	183	轮选1298 Lunxuan 1298	河南 Henan
88	周麦13 Zhoumai 13	河南 Henan	184	漯10T07 Luo 10T07	河南 Henan
89	豫麦55 Yumai 55	河南 Henan	185	濮2056 Pu 2056	河南 Henan
90	豫麦58 Yumai 58	河南 Henan	186	瑞泉麦168 Ruiquanmai 168	江苏 Jiangsu
91	豫麦68 Yumai 68	河南 Henan	187	泰农8968 Tainong 8968	山东 Shandong
92	丰优6号 Fengyou 6	河南 Henan	188	囤丰802 Dongfeng 802	河南 Henan
93	淮麦19 Huaimai 19	江苏 Jiangsu	189	温0418 Wen 0418	河南 Henan
94	偃师16 Yanshi 16	河南 Henan	190	温粮1号 Wenliang 1	河南 Henan
95	济南17 Jinan 17	山东 Shandong	191	许科793 Xuke 793	河南 Henan
96	郑麦98 Zhengmai 98	河南 Henan	192	中创805 Zhongchuang 805	河南 Henan

附表1

表1

表2

表3

图1

表4

表5

小麦茎秆性状候选基因及其功能注释"

性状 Trait	SNP	染色体 Chr.	位置 Position	基因 Gene	基因注释或编码蛋白 Gene annotation or coding proteins
ZJ1	AX-109898312	5B	476634277	TraesCS5B02G290700	Bin/amphiphysin/Rvs (BAR) domain
ZJ1	AX-109937796	1B	579938080	TraesCS1B02G349500	Casein kinase substrate phosphoprotein PP28
ZJ1	AX-111004440	1B	579937443	TraesCS1B02G349500	Casein kinase substrate phosphoprotein PP28
ZJ1	AX-108857434	1B	579938129	TraesCS1B02G349500	Casein kinase substrate phosphoprotein PP28
ZJ1	AX-111044868	1B	579001042	TraesCS1A02G335700	S-adenosylmethionine-dependent methyltransferases
ZJ1	AX-111044868	1B	579001042	TraesCS1A02G335700	Dimerization domain
ZJ1	AX-109056066	3B	244985330	TraesCS3B02G208800	Superfamily II DNA and RNA helicase
ZJ1	AX-109056066	3B	244985330	TraesCS3B02G208800	Protein of unknown function (DUF3615)
ZJ1	AX-94792426	7B	291529	TraesCS7B02G001300	DEUBAD domain found in nuclear factor related to kappa-B-binding protein (NFRKB) and similar proteins
ZJ2	AX-94619650	7A	12198370	TraesCS7D02G026300	Catalytic domain of the serine/threonine kinase, with no Lysine (WNK) kinase
ZJ2	AX-94619650	7A	12198370	TraesCS7D02G026300	Oxidative-stress-responsive kinase 1 C-terminal domain
ZJ2	AX-95136011	7A	5078210	TraesCS7D02G030200	The adenylation domain of non-ribosomal peptide synthetases (NRPS)
ZJ2	AX-109481330	6A	52789093	TraesCS7A02G069800	NB-ARC domain
ZJ2	AX-109022590	3A	10953753	TraesCS3A02G017100	Protein kinases, catalytic domain
ZJ2	AX-109342218	3A	10953642	TraesCS3A02G017100	Protein kinases, catalytic domain
ZJ2	AX-95136011	7A	5078210	TraesCS7D02G030200	Outer membrane protein assembly factor Bam B, contains PQQ-like beta-propeller repeat
ZJ2	AX-111678795	3A	10955264	TraesCS3A02G017100	Protein kinases, catalytic domain
ZJ3	AX-111557672	7A	674103879	TraesCS7A02G481800	Syntaxin
ZJ3	AX-111557672	7A	674103879	TraesCS7A02G481800	SNARE motif
CD1	AX-94610974	5B	6654327	TraesCS5B02G005100	Ubiquitin-conjugating enzyme
CD2	AX-86164054	3D	596915235	TraesCS3D02G512400	Aph-1 protein
CD2	AX-95684045	5A	656936217	TraesCS3D02G145000	WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor
CD2	AX-95252850	5B	712972538	TraesCS5B02G572600	ABC transporter G family member
CD2	AX-95252850	5B	712972538	TraesCS5B02G572600	Herpes virus major outer envelope glycoprotein (BLLF1)
CD2	AX-86164054	3D	596915235	TraesCS3A02G505100	Aph-1 protein
CD2	AX-94635034	6B	47860783	TraesCS6B02G071100	P-loop containing nucleoside triphosphate hydrolases
CD2	AX-94635034	6B	47860783	TraesCS6B02G071100	Chromosome segregation ATPase
CD3	AX-95654430	5D	562652154	TraesCS7B02G000400	MAEBL
CD3	AX-95654430	5D	562652154	TraesCS7B02G000400	Type III pyridoxal 5-phosphate (PLP)-dependent enzymes
CD3	AX-109357138	1A	577840649	TraesCS1A02G422100	Asparagine synthase
CD3	AX-86171374	5A	657181133	TraesCS5A02G486000	Pectinase
CD3	AX-94479513	5B	646672158	TraesCS5A02G486100	Calmodulin-binding protein like
CD3	AX-110417422	5A	656939720	TraesCS3A02G192500	Piezo non-specific cation channel, R-Ras-binding domain
CD3	AX-111518838	5A	682932836	TraesCS4D02G347500	Per1 family
CD3	AX-111518838	5A	682932836	TraesCS4B02G353500	Per1 family
CD3	AX-111594865	5A	683342266	TraesCS5A02G522100	Hydroxymethyl glutaryl-CoA synthase
CD3	AX-111594865	5A	683342266	TraesCS5A02G522100	The largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain
CD3	AX-111450784	1A	32769697	TraesCS5D02G498900	RNA polymerase Rpb1, domain 6
CD3	AX-111450784	1A	32769697	TraesCS5D02G498900	Herpes virus major outer envelope glycoprotein (BLLF1)
CD3	AX-111450784	1A	32769697	TraesCS5D02G498900	Transcriptional regulator ICP4
CD3	AX-111215929	3B	771392394	TraesCS3B02G530200	Plant-specific B3-DNA binding domain
CD3	AX-108956666	3B	771392207	TraesCS3B02G530200	Plant-specific B3-DNA binding domain
CD3	AX-111518838	5A	682932836	TraesCS5A02G521800	Per1-like family
CD3	AX-94516717	5B	662851468	TraesCS5B02G495000	Protein of unknown function (DUF1298)
CS1	AX-110994869	7B	6179850	TraesCS7A02G112000	2-oxoglutarate dehydrogenase E2 component
CS1	AX-110994869	7B	6179850	TraesCS5A02G521800	Per1 family
CS1	AX-94806548	5A	321932077	TraesCS5A02G146000	Pimeloyl-ACP methyl ester carboxylesterase
CS1	AX-110911707	5A	536985712	TraesCS5A02G327200	5'-3' exonuclease [replication, recombination and repair]
CS2	AX-110562242	4A	5813275	TraesCS4A02G009700	Transferase family
CS2	AX-111738737	5A	126641162	TraesCS5D02G103800	Arabidopsis aldehyde double bond reductase and leukotriene B4 12-hydroxydehydrogenase
CS2	AX-95174598	1D	462052343	TraesCS1D02G390600	Protein phosphatase 2A regulatory B subunit (B56 family)
CS2	AX-111463970	3B	513813668	TraesCS3B02G319000	ABC transporter G family member
ZD2	AX-94968843	7A	31875912	TraesCS7A02G063700	SPX domain of proteins found in plants and germ cells
ZD2	AX-94968843	7A	31875912	TraesCS7A02G063700	Major facilitator superfamily
ZG	AX-94618164	5B	646668297	TraesCS5B02G473000	DNA polymerase III subunit gamma/tau
ZG	AX-110978768	3B	771340138	TraesCS4B02G149600	Major facilitator superfamily
ZG	AX-111664693	5D	528617621	TraesCS5D02G498900	Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II)
ZG	AX-111664693	5D	528617621	TraesCS5D02G498900	Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain;
ZG	AX-110610464	5A	656864665	TraesCS5D02G499000	RNA polymerase Rpb1, domain 6
ZG	AX-110610464	5A	656864665	TraesCS5D02G499000	Herpes virus major outer envelope glycoprotein (BLLF1)
ZG	AX-94989341	6B	30276993	TraesCS6B02G050900	Protein kinases, catalytic domain
ZG	AX-94518282	1A	593287088	TraesCS1A02G445500	Arginine protein

表5

表6

表7

附表2

图2

图3

图4

图5

图6

图7

图8

图9

图10

图11

图12

图13

图14

图15

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基因Gene	上游引物Forward primer (5'-3')	下游引物Reverse primer (5'-3')
TraesCS1D02G390600	AGCGAGACTCCCTCAAGA	TGTCACGCAGTATGTCAACT
TraesCS5A02G522100	GCCATTTTCAATCGTCG	GTCATACAGGGGCTTCG
TraesCS3B02G485000	ATCAGCCTTCTTGGTGC	CTGGGTAGATTTTGTTTGC
TraesCS6B02G466600	CCTTGGGTTGCCAGATA	AAGAGGGACGCTACTAAATT
TraesCS5B02G038600	CAGCATCCGTCGCAAAC	CCCCATCCAAAGTCCGT
TraesCS1A02G422100	AGATGAAGGCGTTGAGTG	ATGGACAGTGCCAAGGTA
内参基因β-actin	GTGTCGCACCAGAGGATCAT	CGCTGGCATACAAGGACAGA

性状 Trait	均值 Mean	范围 Range	变异系数 CV (%)	P值 P-value			遗传力 h_B²(%)
性状 Trait	均值 Mean	范围 Range	变异系数 CV (%)	环境间 Environment (E)	品种间 Variety (V)	品种×环境 V× E	遗传力 h_B²(%)
株高ZG (cm)	81.31	58.67-128.35	9.69	0	0	2.02E-41	97.65
重心高度ZX (cm)	59.61	44.25-90.58	8.65	1.00E-298	0	2.55E-42	96.69
基部第一节间长度CD1 (cm)	6.48	2.45-14.85	25.31	1.50E-117	1.31E-51	2.97E-07	89.11
基部第二节间长度CD2 (cm)	9.37	5.09-23.04	16.76	3.72E-93	0	4.74E-40	86.15
基部第三节间长度CD3 (cm)	11.29	7.10-24.20	18.32	9.70E-126	0	2.06E-56	89.87
基部第一节间直径ZJ1 (mm)	4.09	2.68-5.79	10.67	8.50E-156	1.23E-50	1.72E-05	96.43
基部第二节间直径ZJ2 (mm)	4.35	3.10-5.96	9.14	8.50E-237	8.80E-154	9.98E-37	98.09
基部第三节间直径ZJ3 (mm)	4.39	3.08-5.90	9.35	3.50E-276	2.60E-148	1.03E-30	98.53
基部第一节间强度ZD1 (N)	12.10	4.33-35.59	29.67	3.10E-192	3.55E-55	5.17E-16	93.86
基部第二节间强度ZD2 (N)	8.90	2.43-22.57	26.16	1.70E-193	9.90E-103	2.27E-22	93.92
基部第三节间强度ZD3 (N)	8.25	2.95-28.35	27.92	3.20E-201	1.90E-133	3.34E-25	94.21
基部第一节间充实度CS1 (g cm^-1)	2.20E-02	5.00E-03-4.40E-02	24.46	2.30E-09	1.00E-03	5.25E-08	63.27
基部第二节间充实度CS2 (g cm^-1)	1.50E-02	5.00E-03-3.60E-02	22.94	4.08E-61	2.58E-12	5.74E-06	89.24
基部第三节间充实度CS3 (g cm^-1)	1.30E-02	4.00E-03-3.20E-02	21.94	1.24E-15	5.87E-08	3.00E-03	65.22

性状 Trait	灌浆中期Mid-filling stage			成熟期Mature stage			P值 P-value	相关系数 Correlation coefficient
性状 Trait	均值 Mean	范围 Range	变异系数 CV (%)	均值 Mean	范围 Range	变异系数 CV (%)	P值 P-value	相关系数 Correlation coefficient
ZG (cm)	84.75	64.85-132.80	9.38	83.31	66.25-126.00	8.47	2.66E-118	0.96^**
ZX (cm)	48.44	35.50-71.35	9.26	60.04	48.80-83.40	7.80	3.68E-70	0.91^**
CD1 (cm)	6.98	2.89-15.13	22.50	6.97	2.60-14.85	23.48	2.60E-24	0.83^**
CD2 (cm)	9.39	5.30-20.76	16.99	9.49	5.73-23.04	17.09	2.43E-27	0.94^**
CD3 (cm)	11.20	6.59-24.40	19.15	11.33	7.16-24.20	19.16	1.71E-10	0.91^**
ZJ1 (mm)	4.06	2.64-5.78	9.65	3.93	2.68-5.29	8.58	1.59E-56	0.83^**
ZJ2 (mm)	4.31	3.02-5.65	8.19	4.20	3.23-5.50	8.07	7.26E-64	0.88^**
ZJ3 (mm)	4.39	3.01-5.99	8.54	4.23	3.08-5.45	8.41	3.82E-53	0.86^**
ZD1 (N)	13.52	5.87-33.96	26.86	11.01	5.44-23.06	27.56	5.58E-30	0.64^**
ZD2 (N)	10.38	4.90-20.93	23.60	8.04	2.43-17.30	23.87	2.73E-37	0.71^**
ZD3 (N)	9.36	3.95-21.77	24.14	7.60	2.95-18.46	27.82	1.15E-37	0.76^**
CS1 (g cm^-1)	2.60E-02	5.00E-03-5.40E-02	28.68	2.20E-02	5.00E-03-4.40E-02	25.23	2.00E-06	0.33^**
CS2 (g cm^-1)	2.10E-02	4.00E-03-4.70E-02	25.39	1.40E-02	5.00E-03-3.60E-02	22.43	5.62E-11	0.51^**
CS3 (g cm^-1)	2.00E-02	4.00E-03-4.30E-02	26.16	1.30E-02	6.00E-03-2.60E-02	20.60	1.31E-09	0.44^**

性状 Trait	MTA数 MTA	稳定的MTA数 Stable MTA	稳定的位点数 Stable loci	log₁₀ (P)范围 log₁₀ (P) range	贡献率范围 Range for R² (%)
ZG	345	30	8	4.00-7.18	4.30-19.46
ZX	280	29	9	4.00-7.20	6.72-15.95
CD1	218	4	3	4.00-5.07	8.66-11.82
CD2	241	5	4	4.00-5.50	8.59-12.94
CD3	784	43	11	4.00-7.16	7.33-13.39
ZJ1	187	13	7	4.00-5.35	4.27-12.85
ZJ2	168	14	8	4.00-5.82	5.45-16.31
ZJ3	241	9	6	4.00-5.95	5.86-10.54
ZD1	179	0	0	4.00-5.88	6.28-10.37
ZD2	172	5	2	4.00-5.25	5.35-8.36
ZD3	86	0	0	4.00-5.15	6.39-9.72
CS1	522	1	1	4.00-9.59	3.41-13.50
CS2	1198	10	8	4.00-12.91	6.64-11.81
CS3	169	0	0	4.01-6.29	6.32-17.63

品种 Variety	灌浆中期Mid-filling stage		成熟期Mature stage
品种 Variety	ZD1/N	ZD2/N	ZD1/N	ZD2/N
LKAZ8	19.83±2.5 A	13.73±1.73 A	19.72±2.53 A	15.12±2.22 A
THM1	14.97±1.79 B	13.21±1.83 A	13.16±1.60 B	10.91±0.84 B
ZM18	15.69±2.08 B	11.06±1.38 B	13.74±1.80 B	9.73±1.13 BC
LM21	10.77±0.82 C	7.94±0.82 C	10.31±1.34 C	8.58±1.12 CD
JN17	10.50±1.64 C	7.68±0.97 C	9.02±1.37 C	7.36±1.28 DE
XY81	9.35±1.66 C	6.66±1.43 C	8.02±1.38 C	6.03±1.01 E

小麦茎秆性状的转录组测序及全基因组关联分析

Transcriptome sequencing and genome-wide association study of wheat stem traits

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品种 Variety	灌浆中期Mid-filling stage		成熟期Mature stage
品种 Variety	ZJ1	ZJ2	ZJ1	ZJ2
LKAZ8	5.44±0.17 A	5.44±0.10 A	5.43±0.28 A	5.50±0.23 A
PA6	4.04±0.15 BC	4.61±0.10 B	4.42±0.15 B	4.66±0.10 B
BN418	4.30±0.08 B	4.41±0.21 B	4.41±0.24 B	4.73±0.34 B
ZM26	3.35±0.11 D	4.01±0.07 C	3.75±0.16 C	3.95±0.16 C
JN17	3.87±0.16 C	3.50±0.15 D	3.44±0.16 D	3.58±0.16 D
XY81	3.35±0.13 D	3.50±0.15 D	3.38±0.16 D	3.53±0.14 D

样品Sample	Clean Reads	Clean Bases (Gb)	Clean Q20 (%)	Clean Q30 (%)
JC-1	61398958	9.13	99.08	96.08
JC-2	71622432	10.64	99.15	96.39
JC-3	63550980	9.45	99.09	96.11
JQ-1	79999678	11.83	99.21	96.67
JQ-2	71797632	10.66	99.10	96.20
JQ-3	82731740	12.25	99.18	96.57
JR-1	72941814	10.83	99.15	96.38
JR-2	74865844	11.11	99.14	96.36
JR-3	65958148	9.80	99.12	96.28
JX-1	81739280	12.10	99.20	96.60
JX-2	69896536	10.37	99.13	96.31
JX-3	65331538	9.70	99.11	96.23
TJC-1	70710204	10.51	99.19	96.54
TJC-2	70541826	10.49	99.13	96.29
TJC-3	69786280	10.35	99.15	96.42
TJQ-1	83117982	12.32	99.18	96.59
TJQ-2	69221538	10.29	99.10	96.24
TJQ-3	81843308	12.15	99.15	96.43
TJR-1	67457962	10.03	99.10	96.17
TJR-2	67630680	10.05	99.10	96.22
TJR-3	77556940	11.51	99.19	96.57
TJX-1	64582230	9.67	98.92	95.40
TJX-2	72268944	10.82	98.98	95.73
TJX-3	56040790	8.39	98.90	95.26

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