水稻茎秆细胞壁相关组分含量QTL定位及候选基因分析

doi:10.11983/CBB23100

植物学报 ›› 2023, Vol. 58 ›› Issue (6): 882-892.DOI: 10.11983/CBB23100

水稻茎秆细胞壁相关组分含量QTL定位及候选基因分析

贾绮玮¹^,^†, 钟芊芊¹^,^†, 顾育嘉¹, 陆天麒¹, 李玮¹, 杨帅¹, 朱超宇¹, 胡程翔¹, 李三峰², 王跃星²^,^*(), 饶玉春¹^,^*()

¹浙江师范大学生命科学学院, 金华 321004
²中国水稻研究所, 水稻生物育种全国重点实验室, 杭州 310006

收稿日期:2023-07-28 接受日期:2023-11-02 出版日期:2023-11-01 发布日期:2023-11-27
通讯作者: * E-mail: wangyuexing@caas.cn;ryc@zjnu.cn
作者简介:^† 共同第一作者
基金资助:
浙江省自然科学基金重点项目(LZ23C130003);浙江省大学生科技创新活动计划暨新苗人才计划(2023R404040);浙江省大学生科技创新活动计划暨新苗人才计划(2023R404041)

Mapping of QTL for Cell Wall Related Components in Rice Stem and Analysis of Candidate Genes

Qiwei Jia¹^,^†, Qianqian Zhong¹^,^†, Yujia Gu¹, Tianqi Lu¹, Wei Li¹, Shuai Yang¹, Chaoyu Zhu¹, Chengxiang Hu¹, Sanfeng Li², Yuexing Wang²^,^*(), Yuchun Rao¹^,^*()

¹College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
²National Key Laboratory of Rice Biological Breeding, China National Rice Research Institute, Hangzhou 310006, China

Received:2023-07-28 Accepted:2023-11-02 Online:2023-11-01 Published:2023-11-27
Contact: * E-mail: wangyuexing@caas.cn;ryc@zjnu.cn
About author:^† These authors contributed equally to this paper

摘要/Abstract

摘要： 水稻(Oryza sativa)倒伏是制约其生产的主要因素之一, 而茎秆的机械强度影响水稻抗倒伏能力, 且与茎秆细胞壁相关组分含量密切相关。通过调控水稻茎秆细胞壁相关组分含量提高水稻抗倒伏能力, 是提高水稻产量与品质的有效途径。该研究用籼稻品种华占(O. sativa subsp. indica cv. ‘HZ’)和粳稻品种热研2号(O. sativa subsp. japonica cv. ‘Nekken2’)杂交获得F₁代, 经连续多代自交得到120个重组自交系(RILs)群体, 并以此构建遗传连锁图谱。基于构建的高密度遗传图谱, 对水稻茎秆细胞壁中纤维素、半纤维素和木质素含量相关QTLs进行定位, 结果共检测到4个与纤维素含量相关的QTLs、12个与半纤维素含量相关的QTLs和8个与木质素含量相关的QTLs。对检测到的QTLs区间进行候选基因分析, 共筛选到13个候选基因。利用qRT-PCR检测候选基因的表达水平, 结果表明除LOC_Os02g58590和LOC_Os12g41720外, 其余候选基因的表达量在双亲间均存在显著差异。研究结果为挖掘调控水稻茎秆机械强度的基因, 进而筛选和培育抗倒伏能力强的水稻品种奠定了重要基础。

关键词: 水稻, 茎秆机械强度, QTL定位, 候选基因, 抗倒伏

Abstract: Lodging of rice is one of the main factors reducing rice yield. The mechanical strength of stem affects lodging resistance of rice and is closely related to the content of stem cell wall related components. Improving lodging resistance of rice by regulating the related components in the cell wall of stem is an effective way to improve the yield and quality of rice. In this study, indica rice variety Huazhan (Oryza sativa subsp. indica cv. ‘HZ’) and japonica rice variety Nekken2 (O. sativa subsp. japonica cv. ‘Nekken2’) were crossed to obtain F₁ generation. A total of 120 RILs (recombinant inbred lines) population were obtained by successive multigeneration self-crossing and the genetic linkage map was constructed. Based on the constructed high-density genetic map, the QTLs related to the content of cellulose, hemicellulose, and lignin in the cell wall of rice stem were located and analyzed. The results showed that 4 QTLs related to cellulose, 12 QTLs related to hemicellulose, and 8 QTLs related to lignin. At the same time, candidate genes analyses were conducted on the detected QTLs’ intervals, and a total of 13 candidate genes were screened. The expression levels of candidate genes were detected by qRT-PCR. Except for LOC_Os02g58590 and LOC_Os12g41720, the other candidate genes showed significant differences between parents. The results laid an important foundation for exploring genes that regulate the mechanical strength of rice stems, further screening and breeding rice varieties with strong lodging resistance.

Key words: Oryza sativa, mechanical strength of stem, QTL mapping, candidate genes, lodging-resistant

贾绮玮, 钟芊芊, 顾育嘉, 陆天麒, 李玮, 杨帅, 朱超宇, 胡程翔, 李三峰, 王跃星, 饶玉春. 水稻茎秆细胞壁相关组分含量QTL定位及候选基因分析. 植物学报, 2023, 58(6): 882-892.

Qiwei Jia, Qianqian Zhong, Yujia Gu, Tianqi Lu, Wei Li, Shuai Yang, Chaoyu Zhu, Chengxiang Hu, Sanfeng Li, Yuexing Wang, Yuchun Rao. Mapping of QTL for Cell Wall Related Components in Rice Stem and Analysis of Candidate Genes. Chinese Bulletin of Botany, 2023, 58(6): 882-892.

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链接本文: https://www.chinbullbotany.com/CN/10.11983/CBB23100

https://www.chinbullbotany.com/CN/Y2023/V58/I6/882

图/表 7

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Primer name	Sequence (5′-3′)	Tm (°C)	Length (bp)	Size (bp)
LOC_Os01g04930-F-qrt	GAGGGGGAACTGGTTCATGG	60.00	20	164
LOC_Os01g04930-R-qrt	CGAGGTCCCTGAAGTGGTTC	60.00	20	164
LOC_Os01g08440-F-qrt	AGCAACGACCTCTTCAAGCA	59.90	20	178
LOC_Os01g08440-R-qrt	TCCTCAGCACCCACAAGAAC	59.90	20	178
LOC_Os01g09850-F-qrt	CTCCTCCTACCAGCAACGTG	60.10	20	180
LOC_Os01g09850-R-qrt	GACCCAAGAAGTCCCTGGTG	60.00	20	180
LOC_Os02g56460-F-qrt	CTGCTGGAGCGACTACGAAT	59.90	20	182
LOC_Os02g56460-R-qrt	CGTGGTTGGTGCTGAAGTTG	60.00	20	182
LOC_Os02g58480-F-qrt	ACCGTCGGACTACCTCAAGA	60.00	20	187
LOC_Os02g58480-R-qrt	GTCGGTCAGCTTGGAAGACA	60.00	20	187
LOC_Os02g58590-F-qrt	GCCTCGCACAAGCAGAAAAA	60.00	20	183
LOC_Os02g58590-R-qrt	AGGTCTGCACGCTCCTTTTT	60.00	20	183
LOC_Os04g52280-F-qrt	GGATGAGGGTGACGGTGATC	59.90	20	179
LOC_Os04g52280-R-qrt	TGCCAGGTAAGAGTGCATGG	60.00	20	179
LOC_Os08g14760-F-qrt	AATACCAGTCGCCTTCGTGG	60.10	20	186
LOC_Os08g14760-R-qrt	AGATGTTGCAGCTGCTTCCT	60.00	20	186
LOC_Os11g04400-F-qrt	CAGTGCACCCATGGAGGATT	60.00	20	183
LOC_Os11g04400-R-qrt	TTCTCCAACATCTCGCCGAC	60.10	20	183
LOC_Os12g29300-F-qrt	GTCTTCTTCGACTGCACCGA	60.00	20	155
LOC_Os12g29300-R-qrt	TCTTCTCCGAGTAGGCGACA	60.00	20	155
LOC_Os12g36890-F-qrt	CTTCACCTCCGTGTTCCTCC	60.00	20	162
LOC_Os12g36890-R-qrt	CCGGACCACTTGATCTCGAG	59.90	20	162
LOC_Os12g41720-F-qrt	CAACTACGTCCGCATCCAGG	60.80	20	163
LOC_Os12g41720-R-qrt	CCGGTTTGACTTCTCCGACA	60.00	20	163
LOC_Os12g41780-F-qrt	TTCACTGGCATCCCGAAGTC	60.00	20	187
LOC_Os12g41780-R-qrt	CAATGCCTGATCTTCGCAGC	60.00	20	187

Primer name	Sequence (5′-3′)	Tm (°C)	Length (bp)	Size (bp)
LOC_Os01g04930-F-qrt	GAGGGGGAACTGGTTCATGG	60.00	20	164
LOC_Os01g04930-R-qrt	CGAGGTCCCTGAAGTGGTTC	60.00	20	164
LOC_Os01g08440-F-qrt	AGCAACGACCTCTTCAAGCA	59.90	20	178
LOC_Os01g08440-R-qrt	TCCTCAGCACCCACAAGAAC	59.90	20	178
LOC_Os01g09850-F-qrt	CTCCTCCTACCAGCAACGTG	60.10	20	180
LOC_Os01g09850-R-qrt	GACCCAAGAAGTCCCTGGTG	60.00	20	180
LOC_Os02g56460-F-qrt	CTGCTGGAGCGACTACGAAT	59.90	20	182
LOC_Os02g56460-R-qrt	CGTGGTTGGTGCTGAAGTTG	60.00	20	182
LOC_Os02g58480-F-qrt	ACCGTCGGACTACCTCAAGA	60.00	20	187
LOC_Os02g58480-R-qrt	GTCGGTCAGCTTGGAAGACA	60.00	20	187
LOC_Os02g58590-F-qrt	GCCTCGCACAAGCAGAAAAA	60.00	20	183
LOC_Os02g58590-R-qrt	AGGTCTGCACGCTCCTTTTT	60.00	20	183
LOC_Os04g52280-F-qrt	GGATGAGGGTGACGGTGATC	59.90	20	179
LOC_Os04g52280-R-qrt	TGCCAGGTAAGAGTGCATGG	60.00	20	179
LOC_Os08g14760-F-qrt	AATACCAGTCGCCTTCGTGG	60.10	20	186
LOC_Os08g14760-R-qrt	AGATGTTGCAGCTGCTTCCT	60.00	20	186
LOC_Os11g04400-F-qrt	CAGTGCACCCATGGAGGATT	60.00	20	183
LOC_Os11g04400-R-qrt	TTCTCCAACATCTCGCCGAC	60.10	20	183
LOC_Os12g29300-F-qrt	GTCTTCTTCGACTGCACCGA	60.00	20	155
LOC_Os12g29300-R-qrt	TCTTCTCCGAGTAGGCGACA	60.00	20	155
LOC_Os12g36890-F-qrt	CTTCACCTCCGTGTTCCTCC	60.00	20	162
LOC_Os12g36890-R-qrt	CCGGACCACTTGATCTCGAG	59.90	20	162
LOC_Os12g41720-F-qrt	CAACTACGTCCGCATCCAGG	60.80	20	163
LOC_Os12g41720-R-qrt	CCGGTTTGACTTCTCCGACA	60.00	20	163
LOC_Os12g41780-F-qrt	TTCACTGGCATCCCGAAGTC	60.00	20	187
LOC_Os12g41780-R-qrt	CAATGCCTGATCTTCGCAGC	60.00	20	187

Year	Cell wall component	QTL	Chromosome	Physical distance (bp)	Position of support (cM)	Likelihood of odd (LOD)
2020	Cellulose	qCel202	2	35381094-35599368	151.67-152.60	3.48
		qCel204	4	29276416-29507404	125.50-126.49	2.82
	Hemicellulose	qHem201	1	2070966-6568005	8.88-28.16	5.02
		qHem203	3	29806859-30321190	127.77-129.99	2.53
		qHem208	8	4587694-8917564	19.67-38.23	3.48
		qHem2012-1	12	15484322-15779533	66.38-67.64	2.94
		qHem2012-2	12	22426037-27516985	96.13-117.95	5.52
	Lignin	qLig202	2	33583953-35902152	143.97-153.90	3.03
		qLig204-1	4	27558155-28380156	118.13-121.66	3.19
		qLig204-2	4	31066903-31212801	133.18-133.80	3.25
		qLig2011	11	1449031-5404218	6.21-23.17	3.46
		qLig2012-1	12	24319945-24511904	104.25-105.66	3.45
		qLig2012-2	12	27434341-27516085	117.60-117.95	2.60
2021	Cellulose	qCel211	1	2192312-2834929	9.39-12.15	3.34
		qCel2112	12	25510919-27516085	109.35-117.95	3.94
	Hemicellulose	qHem211	1	5699636-6152981	24.43-26.37	3.34
		qHem213-1	3	8841716-8989609	37.90-38.53	2.55
		qHem213-2	3	20915784-21229182	89.66-91.00	3.07
		qHem214	4	2647701-5256057	11.34-22.53	3.81
		qHem218	8	1430252-1451568	6.13-6.22	2.50
		qHem2112-1	12	7276559-7573232	31.19-32.46	2.55
		qHem2112-2	12	17268215-18172857	74.02-77.90	3.40
	Lignin	qLig215-1	5	327464-853216	1.40-3.65	2.90
		qLig215-2	5	25519701-27453301	109.39-117.68	3.35

Year	Cell wall component	QTL	Chromosome	Physical distance (bp)	Position of support (cM)	Likelihood of odd (LOD)
2020	Cellulose	qCel202	2	35381094-35599368	151.67-152.60	3.48
		qCel204	4	29276416-29507404	125.50-126.49	2.82
	Hemicellulose	qHem201	1	2070966-6568005	8.88-28.16	5.02
		qHem203	3	29806859-30321190	127.77-129.99	2.53
		qHem208	8	4587694-8917564	19.67-38.23	3.48
		qHem2012-1	12	15484322-15779533	66.38-67.64	2.94
		qHem2012-2	12	22426037-27516985	96.13-117.95	5.52
	Lignin	qLig202	2	33583953-35902152	143.97-153.90	3.03
		qLig204-1	4	27558155-28380156	118.13-121.66	3.19
		qLig204-2	4	31066903-31212801	133.18-133.80	3.25
		qLig2011	11	1449031-5404218	6.21-23.17	3.46
		qLig2012-1	12	24319945-24511904	104.25-105.66	3.45
		qLig2012-2	12	27434341-27516085	117.60-117.95	2.60
2021	Cellulose	qCel211	1	2192312-2834929	9.39-12.15	3.34
		qCel2112	12	25510919-27516085	109.35-117.95	3.94
	Hemicellulose	qHem211	1	5699636-6152981	24.43-26.37	3.34
		qHem213-1	3	8841716-8989609	37.90-38.53	2.55
		qHem213-2	3	20915784-21229182	89.66-91.00	3.07
		qHem214	4	2647701-5256057	11.34-22.53	3.81
		qHem218	8	1430252-1451568	6.13-6.22	2.50
		qHem2112-1	12	7276559-7573232	31.19-32.46	2.55
		qHem2112-2	12	17268215-18172857	74.02-77.90	3.40
	Lignin	qLig215-1	5	327464-853216	1.40-3.65	2.90
		qLig215-2	5	25519701-27453301	109.39-117.68	3.35

Gene ID	Chromosome	Function	Cloned or not
LOC_Os01g04930	1	MYB transcription factor	Not cloned
LOC_Os01g08440	1	UDP glucoside transferase	Not cloned
LOC_Os01g09850	1	C2H2-type zinc finger transcription factor	Cloned (Huang et al., 2018)
LOC_Os02g56460	2	Cinnamyl CoA reductase	Cloned (Kawasaki et al., 2006)
LOC_Os02g58480	2	Sucrose synthase	Not cloned
LOC_Os02g58590	2	N-acetylglucosaminyltransferase I	Cloned (Fanata et al., 2013)
LOC_Os04g52280	4	Cinnamyl alcohol dehydrogenase	Cloned (Li et al., 2009b)
LOC_Os08g14760	8	4-coumarate:coenzyme A ligase	Cloned (Gu et al., 2011)
LOC_Os11g04400	11	GRAS family transcription factor	Not cloned
LOC_Os12g29300	12	CESA10-cellulase synthesis	Not cloned
LOC_Os12g36890	12	Cellulose synthase-like	Cloned (Hu et al., 2010)
LOC_Os12g41720	12	Patatin-related phospholipase A	Not cloned
LOC_Os12g41780	12	Glycosyltransferase	Not cloned

水稻茎秆细胞壁相关组分含量QTL定位及候选基因分析

Mapping of QTL for Cell Wall Related Components in Rice Stem and Analysis of Candidate Genes

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