基于高密度遗传图谱的蓖麻种子大小性状QTL定位

doi:10.3724/SP.J.1006.2023.14195

Abstract

Abstract:

The seed size of castor (Ricinus communis L.) directly affects the yield, and there is a great difference in seed size among different castor varieties. It is of great significance to further study the genetic mechanism of castor seed size traits for the development of castor seed industry. In this study, we used monoecious inbred lines SL1 as male parent, pistillate line HCH1 as female parent 1 (Combination 1), and pistillate line HCH3 as female parent 2 (Combination 2) to construct F₂ and BC₁ populations, respectively. Firstly, the correlations between seed size traits were analyzed by phenotypic statistics of the two genetic populations. Secondly, based on the phenotypic data of 150 individual plants in F₂population from Combination 1, a high-density genetic map was constructed using genotyping by whole genome sequencing technology (WGS), and QTL analysis was performed for the seed size traits. Finally, the KEGG pathway enrichment and BLAST comparison were performed to determine the candidate genes in the definite QTL region. The results showed that the correlation between seed traits was different among different combinations and populations, and the correlation between seed length and width was the most significant by the phenotypic analysis. And a total of 18 QTLs were detected for four traits including 2 QTLs for seed length, 5 QTLs for seed width, 4 QTLs for seed thickness, and 7 QTLs for hundred-grain weight, which were distributed on linkage groups 1, 4, 7, 8, 9, and 10, respectively. The LOD values ranged from 3.77 to 7.40, and the contribution of variation rate ranged from 0.71% to 86.20%. Based on these results, six candidate genes (28470.m000435, 29908.m006143, 29848.m004589, 27752.m000045, 29683.m000480, and 29848.m004611) for regulating seed size were screened. This study lays a theoretical foundation for further research on fine mapping and gene cloning, molecular marker-assisted breeding and gene function analysis of castor seed size traits.

Key words: castor, high-density genetic map, seed size, QTL mapping, KEGG, candidate gene

YANG Jun-Fang, WANG Zhou, QIAO Lin-Yi, WANG Ya, ZHAO Yi-Ting, ZHANG Hong-Bin, SHEN DengGao, WANG HongWei, CAO Yue. QTL mapping of seed size traits based on a high-density genetic map in castor[J].Acta Agronomica Sinica, 2023, 49(3): 719-730.

Figures/Tables 9

Table 1

Phenotypic statistical analysis of seed size traits in the two groups of parents and offspring"

群体 Population	性状 Trait		统计量 Number		极小值 Min.		极大值 Max.		均值 Mean		标准差 SD		双侧 Sig.		峰度 Kurtosis	偏度 Skewness
SL1, HCH1	种子长Seed length		2		13.00		16.04		14.52		2.15		0.07		—	—
	种子宽Seed width		2		9.04		9.52		9.28		0.34		0.02		—	—
	种子厚Seed thickness		2		6.40		6.62		6.51		0.16		0.01		—	—
	百粒重100-grain weight		2		29.62		47.20		38.41		12.43		0.14		—	—
B	种子长Seed length		217		13.09		17.22		15.13		0.82		0.00		-0.18	-0.01
	种子宽Seed width		217		8.30		10.04		9.16		0.36		0.00		-0.26	-0.24
	种子厚Seed thickness		217		5.40		7.31		6.39		0.30		0.00		0.28	0.21
	百粒重100-grain weight		217		15.77		52.64		40.13		5.89		0.00		1.42	-0.78
D	种子长Seed length		66		12.73		16.42		14.39		0.69		0.00		0.87	-0.05
	种子宽Seed width		66		8.02		9.84		9.03		0.35		0.00		0.54	-0.57
	种子厚Seed thickness		66		5.70		6.71		6.35		0.21		0.00		0.04	-0.43
	百粒重100-grain weight		66		24.98		43.92		37.09		4.30		0.00		0.42	-0.76
SL1, HCH3	种子长Seed length		2		13.10		16.04		14.57		2.08		0.06		—	—
	种子宽Seed width		2		8.80		9.52		9.16		0.51		0.02		—	—
群体 Population		性状 Trait		统计量 Number	极小值 Min.	极大值 Max.		均值 Mean		标准差 SD		双侧 Sig.		峰度 Kurtosis			偏度 Skewness
		种子厚Seed thickness		2	6.40	6.62		6.51		0.16		0.01		—			—
		百粒重100-grain weight		2	35.02	47.20		41.11		8.61		0.09		—			—
A		种子长Seed length		52	13.16	16.48		14.75		0.63		0.00		0.35			0.03
		种子宽Seed width		52	8.62	10.10		9.31		0.31		0.00		-0.34			-0.15
		种子厚Seed thickness		52	6.00	7.04		6.37		0.24		0.00		-0.06			0.66
		百粒重100-grain weight		52	34.20	48.12		41.16		3.07		0.00		-0.45			-0.10
C		种子长Seed length		41	13.28	15.54		14.41		0.55		0.00		-0.18			-0.14
		种子宽Seed width		41	8.60	9.80		9.15		0.29		0.00		-0.28			0.07
		种子厚Seed thickness		41	5.02	6.60		6.27		0.27		0.00		11.96			2.81
		百粒重100-grain weight		41	30.90	45.64		38.88		3.16		0.00		-0.33			-0.09

Table 1

Fig. 1

Fig. 2

Table 2

Table 3

Fig. 3

Table 4

Fig. 4

Table 5

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性状 Trait	种子长 Seed length	种子宽 Seed width	种子厚 Seed thickness	百粒重 100-grain weight
种子长Seed length		0.621^** B	0.610^** B	0.583^** B
		0.650^** D	0.521^** D	0.297^* D
种子宽Seed width	0.386^* C		0.505^** B	0.558^** B
	0.551^** A		0.381^** D	0.323^** D
种子厚Seed thickness	0.127 C	-0.028 C		0.445^** B
	0.359^** A	0.465^** A		0.117 D
百粒重100-grain weight	0.560^** C	0.453^** C	0.411^* C
	0.086 A	0.108 A	0.006 A

连锁群 Linkage	标记数目 Marker number	遗传距离 Length (cM)	平均距离 Average length (cM)	最大间隙 Maximum gap
LG1	1949	1171.78	0.60	61.01
LG2	970	458.32	0.47	9.05
LG3	659	397.43	0.60	20.54
LG4	626	349.77	0.56	9.40
LG5	497	281.76	0.57	6.46
LG6	246	134.67	0.55	23.25
LG7	243	196.25	0.81	24.37
LG8	182	120.87	0.66	25.15
LG9	242	170.22	0.70	12.33
LG10	99	73.96	0.75	4.53
平均Average	571	335.50	0.59	—
总计Total	5713	3355.03	—	—

性状 Trait	染色体 Chr.	QTL	位置 Position (cM)	LOD值 LOD value	加性效应Additive effect	显性效应Dominant effect	贡献率 R²(%)	99%置信区间 99% confidence interval
SL	1	qSL1	11.21	4.06	0.06	0.00	3.67	7.8-12.9
SL	7	qSL7	97.81	7.40	-0.02	0.00	22.16	91.2-98.9
SW	4	qSW4	169.31	3.87	0.10	-0.03	77.60	163.2-170.1
SW	7	qSW7-1	10.91	4.82	-0.05	-0.02	8.74	3.6-13.9
SW	7	qSW7-2	115.51	3.77	-0.04	0.01	11.59	107.0-119.6
SW	8	qSW8-1	96.01	4.60	-0.13	0.04	80.40	92.2-96.7
SW	8	qSW8-2	107.01	3.90	0.13	0.04	70.21	106.1-107.7
ST	4	qST4	85.51	3.87	-0.04	-0.01	23.75	83.9-88.3
ST	8	qST8-1	93.21	4.67	-0.05	0.01	86.20	90.9-96.0
ST	8	qST8-2	107.51	3.94	0.09	0.01	80.55	106.7-108.7
ST	10	qST10	71.11	5.26	-0.01	-0.01	0.71	67.5-73.0
HGW	1	qHGW1-1	3.31	4.11	-1.57	0.20	75.55	3.0-5.2
HGW	1	qHGW1-2	223.21	5.34	-1.70	0.08	30.79	223.1-236.5
HGW	1	qHGW1-3	397.91	4.30	-1.88	0.15	75.55	396.9-398.7
HGW	7	qHGW7-1	29.41	4.21	-0.27	-0.04	9.44	26.7-36.0
HGW	7	qHGW7-2	84.51	4.35	-0.26	0.13	16.60	84.1-86.2
HGW	7	qHGW7-3	97.81	4.88	-0.27	0.16	19.68	92.1-98.9
HGW	9	qHGW9	149.41	4.76	-0.23	0.26	20.05	138.2-157.3

性状位点 Trait locus	染色体位置Scaffords	物理位置 Physical position (bp)	所在基因ID Gene ID	拟南芥基因 Arabidopsis gene	描述 Description
qSL7, qHGW7-3, qHGW7-2	29,848	962,738, 961,557, 961,387	29848.t000167: 29848.m004611	AT4G32190.1	参与淀粉起始的蛋白质 Protein involved in starch initiation
qST4	29,908	169,970	29908.t000194: 29908.m006143	AT1G01720.1	具有NAC结构域的转录激活家族 Belongs to a large family of putative transcriptional activators with NAC domain.
qST8-1	29,683	197,190	29683.t000018: 29683.m000480	AT2G17030.1	编码SKP1/ASK互作蛋白 Encodes a SKP1/ASK-interacting protein
qHGW1-2	27,752	2,960	27752.t000001: 27752.m000045	AT3G07870.1	F-BOX 92蛋白 F-BOX protein 92
qHGW7-3, qSL7	29,848	849,320	29848.t000145: 29848.m004589	AT1G80490.2	与在胚胎发生过程中介导生长素依赖的转录抑制密切相关 It is closely related to Topless (TPL), which mediates auxin-dependent transcriptional repression during embryogenesis
qHGW9	28,470	118,469	28470.t000014: 28470.m000435	AT5G04010	F-box家族蛋白 F-box family protein

QTL mapping of seed size traits based on a high-density genetic map in castor

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