甘蓝型油菜角果长度和每角粒数基因定位以及角果皮转录组动态分析

doi:10.3724/SP.J.1006.2025.44156

Abstract

Abstract:

Rapeseed (Brassica napus L.) is a major oilseed crop globally, and improving yield remains a primary objective in rapeseed breeding programs. Yield in rapeseed is determined by three main components: siliques per unit area, seeds per silique, and seed weight. Although silique length is not a direct yield component, it influences both seeds per silique and seed weight, and thus indirectly affects yield. In this study, two parental lines with contrasting silique lengths and seeds per silique, YA and Zhongshuang 11, along with their 211 recombinant inbred lines (RILs), were used as experimental materials. The RIL population was genotyped through genome resequencing and grown in two environments: autumn in Changsha and summer in Mingle. Silique length and seeds per silique were measured, and quantitative trait loci (QTL) analysis was conducted. The results identified a major QTL for both silique length and seeds per silique on chromosome A09 in both environments. Comparative RNA-seq analysis of pod walls from the two parents, conducted 3-21 days after flowering, indicated that genes involved in photosynthesis, plant hormone signaling transduction, and secondary metabolite biosynthesis play critical roles in pod wall development. Among the differentially expressed genes, BnaA09.CYP78A9, BnaC08.SCL13, and BnaA04.ARL, which are associated with auxin response and signaling transduction, were identified as candidate genes regulating silique length. These findings provide a foundation for fine mapping and exploring the regulatory mechanisms of genes controlling silique length in rapeseed, which could contribute to yield improvement in breeding programs.

Key words: Brassica napus L, silique length, seeds per silique, quantitative trait location (QTL), transcriptome profiling

WANG Xiao-Lin, LIU Zhong-Song, KANG Lei, YANG Liu. Mapping of silique length and seeds per silique and transcriptome profiling of pod walls in Brassica napus L.[J].Acta Agronomica Sinica, 2025, 51(4): 888-899.

Figures/Tables 12

Table 1

Fig. 1

Table 2

Table S1

Fig. S1

Table 3

Table S2

The candidate genes located within QTL intervals of silique length and seeds per silique in rapeseed (Brassica napus L.)"

QTL名称 QTL name	候选基因 Candidate genes ID	拟南芥同源基因 Arabidopsis homolog gene	基因名 Gene name	注释 Functional description	变异类型 Variation type	群体变异类型 Variation type of population
qSL.A06	BnaA06G0062200ZS	AT1G09950	RAS1	对ABA和SALT1的反应 Response to ABA and SALT 1	非同义单核苷酸变异Nonsynonymous SNV	错译突变 Missense
qSL.A06	BnaA06G0068300ZS	AT2G39540	GASA8	赤霉素调节家族蛋白 Gibberellin-regulated family protein	非同义单核苷酸变异和移码突变 Nonsynonymous SNV and frameshift	移码突变 Frameshift
qSL.A09	BnaA09G0545800ZS	AT3G59900	ARGOS	编码生长素调节基因参与器官大小 Encodes auxin-regulated gene involved in organ size	非同义单核苷酸变异和非移码插入 Nonsynonymous SNV and nonframeshift insertion	错译突变 Missense
	BnaA09G0546200ZS	AT3G59940	SKIP20	细胞分裂素反应为阴性 Negative cytokinin response	非移码插入 Nonframeshift insertion	错译突变 Missense
	BnaA09G0550200ZS	AT3G60490	ERF035	ERF/AP2转录因子家族 ERF/AP2 transcription factor family	非同义单核苷酸变异和非移码插入 Nonsynonymous SNV and nonframeshift insertion	错译突变 Missense
	BnaA09G0551600ZS	AT3G60690	SAUR59	ERF/AP2转录因子家族 ERF/AP2 transcription factor family	非移码插入 Nonframeshift insertion	错译突变 Missense
	BnaA09G0553700ZS	AT3G61040	CYP76C7	编码一种具有细胞色素P450结构域的蛋白质 Encodes a protein with cytochrome P450 domain	非同义单核苷酸变异和移码突变 Nonsynonymous SNV and frameshift	错译突变和移码突变 Missense and frameshift
	BnaA09G0558300ZS	AT3G61630	CRF6	CRF蛋白对细胞分裂素的反应 CRF proteins response to cytokinin	非同义单核苷酸变异 Nonsynonymous SNV	错译突变和移码突变 Missense and frameshift
	BnaA09G0559300ZS	AT3G61830	ARF18	生长素反应因子18 Auxin response factor 18	非同义单核苷酸变异和非移码插入 Nonsynonymous SNV and nonframeshift insertion	错译突变和移码突变 Missense and frameshift
	BnaA09G0560100ZS	AT3G61880	CYP78A9	编码一种具有细胞色素P450结构域的单氧酶 Encodes a cytochrome p450 monooxygenase		错译突变 Missense
	BnaA09G0560300ZS	AT3G61900	SAUR33	SAUR样生长素反应蛋白家族 SAUR-like auxin-responsive protein family	非移码插入 Nonframeshift insertion	错译突变 Missense
	BnaA09G0560900ZS	AT3G61970	NGA2	AP2/ B3样转录因子家族蛋白 AP2/B3-like transcriptional factor family protein	非移码插入 Nonframeshift insertion	错译突变 Missense
	BnaA09G0562300ZS	AT3G62100	IAA30	编码Aux/IAA蛋白家族的一个成员 Encodes a member of the Aux/IAA family of proteins	非移码插入 Nonframeshift insertion	错译突变 Missense
qSL.C08	BnaC08G0148600ZS	AT4G17230	SCL13	编码稻草人样蛋白 Encodes a scarecrow-like protein (SCL13)	移码突变和非移码插入 Frameshift deletion and nonframeshift insertion	错译突变 Missense
	BnaC08G0152300ZS	AT4G17490	ERF6	编码ERF子家族的一个成员 Encodes a member of the ERF subfamily	非同义单核苷酸变异Nonsynonymous SNV
	BnaC08G0152400ZS	AT4G17500	ERF1A	编码ERF/AP3转录的一个成员 Encodes a member of the ERF/AP3 transcription	非同义单核苷酸变异 Nonsynonymous SNV	错译突变 Missense
	BnaC08G0154200ZS	AT4G17695	KAN3	同源结构域样超家族蛋白 Homeodomain-like superfamily protein	非同义单核苷酸变异 Nonsynonymous SNV	内含子突变 Intron
	BnaC08G0155100ZS	AT4G17870	PYR1	编码PYR/PYL/RCAR家族蛋白的一个成员 Encodes a member of the PYR/PYL/RCAR family protein	移码突变 Frameshift deletion	移码突变 Frameshift
qSL.A04	BnaA04G0250800ZS	AT2G40260	MYS2	同源结构域样超家族蛋白 Homeodomain-like superfamily protein	移码突变和非移码插入 Frameshift deletion and nonframeshift insertion	移码突变 Frameshift
	BnaA04G0251200ZS	AT2G40200	BHLH51	碱性螺旋-环-螺旋DNA结合超家族蛋白 Basic helix-loop-helix DNA-binding superfamily protein	非同义单核苷酸变异 Nonsynonymous SNV	错译突变 Missense
	BnaA04G0251900ZS	AT2G40116	PLC6	磷酸肌醇特异性磷脂酶C家族蛋白 Phosphoinositide-specific phospholipase C family protein	非同义单核苷酸变异和移码突变 Nonsynonymous SNV and frameshift deletion	错译突变 Missense
	BnaA04G0256400ZS	AT2G39310	JAL22	Jacalin类凝集素 22 Jacalin-related lectin 22	移码突变和非移码插入 Frameshift deletion and nonframeshift insertion	错译突变和移码突变 Missense and frameshift
	BnaA04G0257000ZS	AT2G40330	PYL6	编码PYR/PYL/RCAR家族蛋白的一个成员 Encodes a member of the PYR/PYL/RCAR family protein	非同义单核苷酸变异 Nonsynonymous SNV
	BnaA04G0257100ZS	AT2G40340	DREB2C	编码ERF亚家族转录的一个成员 Encodes a member of the ERF subfamily transcription	非同义单核苷酸变异 Nonsynonymous SNV	错译突变 Missense
	BnaA04G0261800ZS	AT5G42440	MDH9	蛋白激酶超家族蛋白 Protein kinase superfamily protein	非同义单核苷酸变异 Nonsynonymous SNV	错译突变Missense
	BnaA04G0263900ZS	AT2G41310	ARR8	参与细胞分裂素介导的信号传导 Involve in cytokinin-mediated signalling	非同义单核苷酸变异 Nonsynonymous SNV	错译突变 Missense
	BnaA04G0265500ZS	AT2G41510	CKX1	类似于细胞分裂素氧化酶/脱氢酶 Similar to cytokinin oxidase/dehydrogenase	非同义单核苷酸变异和移码突变 Nonsynonymous SNV and frameshift deletion	错译突变和框内缺失 Missense and inframe_deletion
	BnaA04G0267400ZS	AT4G13770	CYP83A1	编码细胞色素p450，在生长素稳态中起作用 Encodes CYP450, has a role in auxin homeostasis.	非同义单核苷酸变异和移码突变 Nonsynonymous SNV and frameshift deletion	错译突变 Missense
	BnaA04G0267500ZS	AT1G58260	CYP79C2	细胞色素p450的CYP79C亚家族成员 Member of CYP79C subfamily of cytochrome p450s.	非同义单核苷酸变异和移码突变 Nonsynonymous SNV and frameshift deletion	错译突变移码突变 Missense and frameshift deletion
	BnaA04G0272500ZS	AT2G42870	PAR1	作为生长素应答基因的转录抑制因子 Transcriptional repressor of auxin-responsive genes	非同义单核苷酸变异 Nonsynonymous SNV	错译突变 Missense
	BnaA04G0280200ZS	AT2G44080	ARL	由芸薹素内酯上调 Upregulated by brassinosteroid.	非同义单核苷酸变异 Nonsynonymous SNV
	BnaA04G0280600ZS	AT5G18090	NGA2	AP2/ B3样转录因子家族蛋白 AP2/B3-like transcriptional factor family protein	非同义单核苷酸变异 Nonsynonymous SNV	错译突变 Missense
qSPS.A02	BnaA02G0199900ZS	AT1G72430	SAUR78	SAUR样生长素反应蛋白家族 SAUR-like auxin-responsive protein family	非同义单核苷酸变异 Nonsynonymous SNV	-
	BnaA02G0196600ZS	AT1G71960	ABCG25	涉及脱落酸运输 Involve abscisic acid transport	非同义单核苷酸变异和移码突变 Nonsynonymous SNV and frameshift deletion	错译突变 Missense
	BnaA02G0179200ZS	AT1G69120	AP1	SRF转录因子 SRF transcription factors	非移码插入 Nonframeshift insertion	错译突变 Missense
	BnaA02G0192900ZS	AT1G71130	ERF070	编码ERF子家族的一个成员 Encodes a member of the ERF subfamily	非同义单核苷酸变异和移码突变 Nonsynonymous SNV and frameshift deletion	错译突变和框内缺失 Missense and inframe_insertion
qSPS.A06	BnaA06G0135100ZS	AT1G19350	BZR2	编码芸薹素内酯信号蛋白 Encodes BR signalling protein	非移码插入 Nonframeshift insertion	错译突变 Missense
	BnaA06G0138000ZS	AT2G39670	--	自由基SAM超家族蛋白 Radical SAM superfamily protein	非同义单核苷酸变异 Nonsynonymous SNV	错译突变和移码突变 Missense and frameshift
	BnaA06G0138600ZS	AT1G19770	PUP14	与PUP1相关的蛋白家族成员 Member of a family of proteins related to PUP1	非同义单核苷酸变异 Nonsynonymous SNV	错译突变和移码突变 Missense and frameshift
	BnaA06G0138900ZS	AT1G19770	PUP14	与PUP1相关的蛋白家族成员 Member of a family of proteins related to PUP1	非同义单核苷酸变异和移码突变 Nonsynonymous SNV and frameshift deletion	错译突变移码突变 Missense and frameshift
	BnaA06G0144000ZS	AT1G20470	SAUR60	SAUR样生长素反应蛋白家族 SAUR-like auxin-responsive protein family	非同义单核苷酸变异 Nonsynonymous SNV	错译突变和框内缺失 Missense and inframe_insertion
	BnaA06G0147700ZS	AT1G20925	PILS1	生长素外排载体家族蛋白 Auxin efflux carrier family protein	非同义单核苷酸变异 Nonsynonymous SNV	错译突变 Missense
qSPS.A09	BnaA09G0568300ZS	AT3G63010	GID1B	具有GA结合活性，对GA4有较高亲和力 Has GA-binding activity, showing higher affinity to GA4	非同义单核苷酸变异Nonsynonymous SNV	错译突变 Missense
qSPS.A09	BnaA09G0568800ZS	AT3G63110	IPT3	对细胞分裂素合成酶进行编码 Encodes cytokinin synthase involved	非同义单核苷酸变异Nonsynonymous SNV	错译突变 Missense

Table S2

Fig. 2

Fig. 3

Table S3

Fig. 4

Fig. 5

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性状 Trait	环境 Environment	亲本 Parents		重组自交系群体 RIL population
性状 Trait	环境 Environment	YA	中双11号 ZS11	均值±标准差 Mean ± SD	变幅 Range	变异系数 CV (%)	遗传力 H²	t检验 t test
角果长度 SL (mm)	长沙CS	65.83±2.71	79.86±1.93^**a	71.61±13.30	48.84-101.30	18.57	0.85	111.98^**b
角果长度 SL (mm)	民乐ML	117.26±2.70	106.11±1.00^**a	89.59±20.70	51.02-153.40	23.16	0.85	111.98^**b
每角粒数 SPS	长沙CS	23.10±0.51	24.96±0.70^**a	22.29±2.32	14.50-29.98	10.41	0.67	611.13^**b
每角粒数 SPS	民乐ML	29.12±0.19	30.54±0.21^**a	28.27±2.63	21.81-35.80	9.30	0.67	611.13^**b

性状Trait	环境Environment	角果长度Silique length
每角粒数	长沙Changsha	0.17
Seeds per silique	民乐Minle	0.35^*

染色体 Chr.	长度 Length (bp)	SNP数量 No. SNPs	InDel数量 No. InDels	SNP密度 SNP density (No. kb^-1)	InDel密度 InDel density (No. kb^-1)
A01	38,004,428	408,118	148,331	10.74	3.90
A02	35,943,954	378,213	139,136	10.52	3.87
A03	44,868,710	471,360	180,809	10.51	4.03
A04	25,679,024	331,446	113,166	12.91	4.41
A05	45,991,561	448,337	145,210	9.75	3.16
A06	48,704,706	515,232	171,757	10.58	3.53
A07	32,302,721	376,703	135,121	11.66	4.18
A08	28,329,074	270,930	90,883	9.56	3.21
A09	65,862,748	674,712	227,786	10.24	3.46
A10	26,592,803	304,512	103,703	11.45	3.90
C01	57,880,920	559,868	161,997	9.67	2.80
C02	65,293,782	616,357	172,192	9.44	2.64
C03	79,061,710	758,738	241,922	9.60	3.06
C04	71,179,181	684,885	196,442	9.62	2.76
C05	59,550,008	468,231	141,037	7.86	2.37
C06	52,512,057	444,081	139,948	8.46	2.67
C07	60,986,212	481,327	147,925	7.89	2.43
C08	53,660,391	432,875	145,004	8.07	2.70
C09	68,416,614	545,825	171,533	7.98	2.51
Whole	960,820,604	9,171,750	2,973,902	9.82	3.24

性状 Trait	环境 Environment	QTL名称 QTL name	染色体 Chromosome	遗传位置 Position (cM)	阈值 LOD	表型解释率 R² (%)	置信区间 Confidence interval (cM)
角果长度 Silique length	长沙Changsha	qSL.A06	A06	26.28	5.44	5.00	22.32-28.13
		qSL.A09-1	A09	91.82	33.48	43.60	91.82-91.82
		qSL.C08	C08	6.20	4.14	3.80	5.54-6.94
	民乐Minle	qSL.A04	A04	61.70	3.74	2.00	59.42-64.98
	民乐Minle	qSL.A09-2	A09	87.76	40.77	57.60	87.76-91.82
每角粒数 Seeds per silique	长沙Changsha	qSPS.A02	A02	38.75	2.89	5.41	35.22-39.27
	民乐Minle	qSPS.A06	A06	45.64	4.94	8.40	43.64-45.89
	民乐Minle	qSPS.A09	A09	95.36	6.11	10.60	93.65-95.36

基因名称 Gene name	染色体上位置 Chromosomal Position	基因结构 Gene structure	基因变化 insertion/deletion Variation	氨基酸变化 Variation in amino acid residue	YA	中双11 Zhongshuang 11
BnaA09.CYP78A9	57,359,135	转座子Transposon	C/CTA	I/L	1\|1	0/0
BnaA04.ARL	24,561,360	外显子Exon	C/CCTT	-/L	1\|1	0/0
BnaA04.ARL	24,561,376	外显子Exon	C/CTTA	-/S	1\|1	0/0
BnaC08.SCL13	25,560,026	外显子Exon	C/A	I/M	1\|1	0/0
BnaC08.SCL13	25,560,032	外显子Exon	G/T	V/M	1\|1	0/0
BnaC08.SCL13	25,560,035	外显子Exon	G/A	T/S	1\|1	0/0
BnaC08.SCL13	25,560,683	外显子Exon	A/G	M/C	1\|1	0/0
BnaC08.SCL13	25,560,686	外显子Exon	T/A	E/K	1\|1	0/0
BnaC08.SCL13	25,561,346	内含子Intron	TAAA/ TAAAAA	-/R	1\|1	0/0

Mapping of silique length and seeds per silique and transcriptome profiling of pod walls in Brassica napus L.

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