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

doi:10.11983/CBB23100

Abstract

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

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[J]. Chinese Bulletin of Botany, 2023, 58(6): 882-892.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB23100

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

Figures/Tables 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