基于QTL定位与组学分析挖掘水稻粒质量及粒形候选基因

doi:10.7668/hbnxb.20196073

摘要/Abstract

摘要：

粒质量与粒形是决定水稻产量的关键因素,挖掘相关QTL(基因)对解析籽粒形成机制及指导高产育种具有重要意义。以籼稻昌恢891和粳稻02428构建的BILs群体为材料,利用高密度分子标记遗传图谱,对2个环境下的千粒质量、粒长、粒宽、粒厚和长宽比进行QTL定位研究。结合亲本开花后第5,10,15天的籽粒转录组数据,对QTL区间内的候选基因进行分析。频数分布表明,BILs群体粒质量与粒形呈现数量性状特征,适于QTL定位。在2个环境下,共检测到37个粒质量和粒形相关的QTL,包括海南三亚18个、江西南昌12个,以及两地共同检测到7个。全部QTL分布于水稻第1~5,7,8,11和12号染色体上,其中千粒质量相关7个、粒长相关5个、粒宽相关7个、长宽比相关11个、粒厚相关7个。分析表明,这些QTL的LOD值为2.79~43.10,贡献率为1.36%~46.12%。结合昌恢891和02428开花后第5,10,15天籽粒中差异表达的基因,在37个QTL中共获得28个候选基因,其中,LOC_Os11g10480和LOC_Os11g10100作为重点候选基因,将进行后续深入研究。

关键词: 水稻, 回交重组自交系, 粒形, 千粒质量, QTL

Abstract:

Based on quantitative trait locus(QTL)mapping of grain weight and grain shape-related traits in a backcross inbred line(BIL)population derived from the cross between indica rice variety Changhui 891 and japonica rice variety 02428,this study provided valuable genetic resources for elucidating the genetic basis of grain development and molecular breeding for high yield and quality in rice.A high-density genetic map was used to conduct QTL analysis for thousand-grain weight,grain length,grain width,grain thickness,and length-width ratio under two environments.Transcriptome data of developing grains at 5,10,and 15 days after flowering from both parents were integrated to analyze candidate genes within QTL regions.Frequency distribution indicated that grain weight and shape traits in the BIL population exhibited typical quantitative characteristics,confirming the suitability for QTL mapping.A total of 37 QTLs were detected across both environments,including 18 specific to Hainan(Sanya),12 specific to Jiangxi(Nanchang),and 7 consistently identified in both locations.These QTLs were distributed on chromosomes 1—5,7,8,11,and 12,comprising 7 for thousand grains weight,5 for grain length,7 for grain width,11 for length-width ratio,and 7 for grain thickness.The analysis showed that the LOD values of these QTLs ranged from 2.79 to 43.10,with a contribution rate of 1.36% to 46.12%.By integrating differentially expressed genes from developing grains of both parents at three stages,28 candidate genes were prioritized from the 37 QTL regions.Among these,LOC_Os11g10480 and LOC_Os11g10100 were identified as key candidates for further functional validation.

Key words: Rice, BIL, Grain shape, Thousand-grain weight, QTL

中图分类号:

钟奇, Mvuyeni Nyasulu, 曹国梁, 边建民. 基于QTL定位与组学分析挖掘水稻粒质量及粒形候选基因[J]. 华北农学报, 2026, 41(1): 1-13. doi: 10.7668/hbnxb.20196073.

ZHONG Qi, Mvuyeni Nyasulu, CAO Guoliang, BIAN Jianmin. Identification of Candidate Genes for Rice Grain Weight and Shape via QTL Mapping and Omics Analysis[J]. Acta Agriculturae Boreali-Sinica, 2026, 41(1): 1-13. doi: 10.7668/hbnxb.20196073.

http://www.hbnxb.net/CN/Y2026/V41/I1/1

图/表 12

表1 实时定量PCR引物

Tab.1 Primers used for qRT-PCR

序号 No.	基因 Gene	正向引物(5'—3') Forward primer(5'—3')	反向引物(5'—3') Reverse primer(5'—3')
1	LOC_Os08g10430	GGTGGAGATGTTGCCTCACA	TCTCGACACGGATGTGTTGG
2	LOC_Os04g14190	GCCGTTGACATGAGGAAGGA	TCTTATCTTCGCGGCTGTCG
3	LOC_Os01g04070	GGATAGGGGCCCACAAGAAC	GCAAGTCCACGAGATCACCA
4	LOC_Os01g04040	CAAGGGCAACACTGAGACCA	CACAGGGTGAGTCTTGACGA
5	LOC_Os01g71930	GGCATCTCCCTCATCGAGTCCA	GACAGCTCGCCGATCTCTTTGG
6	LOC_Os03g14280	TGACTGAAGCTGCACAACGA	TGACCATATCCCCAGGAGCA
7	LOC_Os02g36400	CATCCCTTTTCGGGAGCAGT	AACTCATGGGCATCCTGGTG
8	LOC_Os04g40630	CGCTGTGCAGTCATTTCAAGGG	GCTGCTGCTGTACCTCGCC
9	LOC_Os11g09418	CTCCTTCCTGCCAGCGCAC	CGGTTTGGAACTCGAGCTCATCA
10	LOC_Os03g14280	AGGTGGCTTCTGGGGAGAAG	TTGAGCAGCGTAATTCCATTAGC
11	LOC_Os04g40900	TGCGGTTGACCTCACCTGCA	GCTTGTCCTTGCGGAGAGCA
12	LOC_Os11g10480	CTCTTCACCTCGCTCTGCCACA	GGCACACTCCTTGCACTCCCC
13	LOC_Os11g10100	TCAGGTCTGGCATGACAAGGGAC	TCATACGCACATTGGATGGGTT
14	LOC_Os11g09590	CACTGCATCTGGATGCCATAAC	GCAGAAGCACGCAGTTCTCAG
15	LOC_Os11g09329	AGCCAAGGATACACTCAAGCTCC	CTCCCGAACATTTAAATCTGGCT
16	OsActin	CTTCATAGGAATGGAAGCTGCGGGTA	CGACCACCTTGATCTTCATGCTGCTA

表2 BILs群体及其亲本昌恢891和02428的性状表现

Tab.2 Traits of BILs population and parents Changhui 891 and 02428

性状 Trait	环境 Environment	亲本 Parents		回交重组自交系 BILs
性状 Trait	环境 Environment	02428	昌恢891 Changhui 891	均值±标准差 Mean±s	偏度 Skewness	峰度 Kurtosis	变幅 Ranges
千粒质量/g	E1	27.96±2.30a	24.84±0.70b	25.78±2.85	0.12	-0.43	18.82~32.52
Thousand grains weight	E2	25.62±2.12a	23.66±1.12b	22.19±3.11	0.61	0.54	15.83~31.13
粒长/mm	E1	6.84±0.70b	9.22±0.55a	7.10±0.71	1.36	2.06	5.82~9.69
Grain length	E2	6.76±0.67b	9.26±0.18a	6.99±0.74	1.67	2.83	5.84~9.41
粒厚/mm	E1	2.38±0.14a	1.89±0.42b	2.22±0.16	-0.17	-0.44	1.85~2.60
Grain thickness	E2	2.35±0.17a	1.87±0.23b	2.15±0.15	-0.15	-0.64	1.84~2.44
长宽比	E1	1.77±0.24b	3.83±0.16a	2.11±0.40	1.65	3.38	1.58~3.79
Length-width ratio	E2	1.85±0.30b	3.77±0.76a	2.23±0.40	1.62	2.82	1.78~3.87
粒宽/mm	E1	3.87±0.22a	2.42±0.39b	3.44±0.31	-0.48	-0.16	2.51~4.04
Grain width	E2	3.65±0.17a	2.46±0.27b	3.19±0.28	-0.37	-0.36	2.44~3.75

图1 昌恢891和02428的性状表现 A.成熟亲本植株表型,比例尺=15 cm;B、C.昌恢891和02428的成熟水稻籽粒,比例尺=2 mm。

Fig.1 Traits of Changhui 891 and 02428 A.Phenotype of mature parent plant,scale bar=15 cm;B,C.Mature rice grains of Changhui 891 and 02428,scale bar=2 mm.

图2 BILs群体在E1、E2环境中的粒形表型值分布

Fig.2 Distributions of grain shape in the BILs population in environments E1 and E2

图3 BILs群体粒质量和粒形相关性分析 GL.粒长;GW.粒宽;LWR.长宽比;GT.粒厚;TGW.千粒质量。^**.极显著相关(P<0.01)。图4同。

Fig.3 Correlation analysis between grain weight and grain shape in BILs population GL.Grain length;GW.Grain width;LWR.Length-width ratio;GT.Grain thickness;TGW.Thousand grains weight.^**.Highly significant correlation(P<0.01).The same as Fig.4.

表3 利用BILs群体定位到的粒质量与粒形QTL

Tab.3 QTLs for grain weight and grain shape detected by BILs population

性状 Trait	位点 QTL	区间 Marker interval	染色体 Chr.	E1			E2
性状 Trait	位点 QTL	区间 Marker interval	染色体 Chr.	贡献率/% PVE	LOD LOD	加性效应 Add	贡献率/% PVE	LOD LOD	加性效应 Add
粒厚	qGT2	bin2-201~bin2-202	2	10.27	3.34	0.04
Grain thickness	qGT4.1	bin4-156~bin4-157	4	13.72	4.47	0.07
	qGT4.2	bin4-269~bin4-270	4	13.86	4.58	0.04	8.16	2.79	0.03
	qGT4.3	bin4-274~bin4-275	4				26.18	7.11	0.07
	qGT5.1	bin5-39~bin5-40	5				19.20	5.47	0.07
	qGT5.2	bin5-56~bin5-57	5	20.01	6.37	0.06
	qGT8	bin8-130~bin8-131	8	8.89	3.05	0.04
粒宽	qGW2.1	bin2-28~bin2-29	2	12.34	5.53	0.09
Grain width	qGW2.2	bin2-201~bin2-202	2	22.55	9.09	0.11	13.83	3.34	0.06
	qGW3	bin3-57~bin3-58	3	12.49	5.55	0.08
	qGW4.1	bin4-153~bin4-154	4	10.14	4.64	0.10
	qGW4.2	bin4-156~bin4-157	4				22.44	6.23	0.13
	qGW4.3	bin4-269~bin4-270	4				13.19	3.80	0.06
	qGW5	bin5-56~bin5-57	5	18.76	7.95	0.11	20.22	5.68	0.09
长宽比	qLWR2	bin2-145~bin2-146	2	1.36	4.62	-0.07
Length-width	qLWR3.1	bin3-206~bin3-207	3	3.37	10.75	-0.08
ratio	qLWR3.2	bin3-212~bin3-213	3				4.97	7.10	-0.07
	qLWR4.1	bin4-65~bin4-66	4	30.96	43.10	0.34
	qLWR4.2	bin4-198~bin4-199	4	27.71	40.43	0.33
	qLWR4.3	bin4-274~bin4-275	4				3.37	5.16	-0.06
	qLWR5	bin5-50~bin5-51	5	4.45	13.46	-0.10	10.61	13.61	-0.11
	qLWR8.1	bin8-57~bin8-58	8				10.55	13.61	0.12
	qLWR8.2	bin8-59~bin8-60	8	5.02	14.60	0.10
	qLWR8.3	bin8-72~bin8-73	8	14.00	28.74	-0.20	23.98	23.89	-0.18
	qLWR11	bin11-64~bin11-65	11				22.98	22.93	0.29
粒长	qGL1.1	bin1-15~bin1-16	1	15.52	5.37	0.17
Grain length	qGL1.2	bin1-320~bin1-321	1	16.82	5.76	0.18
	qGL3	bin3-229~bin3-230	3	22.45	7.65	-0.19
	qGL11	bin11-37~bin11-38	11				46.12	17.26	-0.60
	qGL12	bin12-248~bin12-249	12	8.68	3.27	0.11	11.22	5.51	0.16
千粒质量	qTGW1.1	bin1-71~bin1-72	1				6.17	4.40	-2.46
Thousand-grain	qTGW1.2	bin1-139~bin1-140	1	25.13	10.92	-3.11
weight	qTGW2	bin2-267~bin2-268	2	12.10	5.87	1.09	7.61	5.73	1.11
	qTGW3	bin3-94~bin3-95	3	7.86	4.00	0.87
	qTGW4	bin4-194~bin4-195	4				38.58	20.47	-5.78
	qTGW7	bin7-22~bin7-23	7	7.53	3.86	-0.85
	qTGW8	bin8-25~bin8-26	8				6.29	4.46	1.19

表3 利用BILs群体定位到的粒质量与粒形QTL

Tab.3 QTLs for grain weight and grain shape detected by BILs population

性状 Trait	位点 QTL	区间 Marker interval	染色体 Chr.	E1			E2
性状 Trait	位点 QTL	区间 Marker interval	染色体 Chr.	贡献率/% PVE	LOD LOD	加性效应 Add	贡献率/% PVE	LOD LOD	加性效应 Add
粒厚	qGT2	bin2-201~bin2-202	2	10.27	3.34	0.04
Grain thickness	qGT4.1	bin4-156~bin4-157	4	13.72	4.47	0.07
	qGT4.2	bin4-269~bin4-270	4	13.86	4.58	0.04	8.16	2.79	0.03
	qGT4.3	bin4-274~bin4-275	4				26.18	7.11	0.07
	qGT5.1	bin5-39~bin5-40	5				19.20	5.47	0.07
	qGT5.2	bin5-56~bin5-57	5	20.01	6.37	0.06
	qGT8	bin8-130~bin8-131	8	8.89	3.05	0.04
粒宽	qGW2.1	bin2-28~bin2-29	2	12.34	5.53	0.09
Grain width	qGW2.2	bin2-201~bin2-202	2	22.55	9.09	0.11	13.83	3.34	0.06
	qGW3	bin3-57~bin3-58	3	12.49	5.55	0.08
	qGW4.1	bin4-153~bin4-154	4	10.14	4.64	0.10
	qGW4.2	bin4-156~bin4-157	4				22.44	6.23	0.13
	qGW4.3	bin4-269~bin4-270	4				13.19	3.80	0.06
	qGW5	bin5-56~bin5-57	5	18.76	7.95	0.11	20.22	5.68	0.09
长宽比	qLWR2	bin2-145~bin2-146	2	1.36	4.62	-0.07
Length-width	qLWR3.1	bin3-206~bin3-207	3	3.37	10.75	-0.08
ratio	qLWR3.2	bin3-212~bin3-213	3				4.97	7.10	-0.07
	qLWR4.1	bin4-65~bin4-66	4	30.96	43.10	0.34
	qLWR4.2	bin4-198~bin4-199	4	27.71	40.43	0.33
	qLWR4.3	bin4-274~bin4-275	4				3.37	5.16	-0.06
	qLWR5	bin5-50~bin5-51	5	4.45	13.46	-0.10	10.61	13.61	-0.11
	qLWR8.1	bin8-57~bin8-58	8				10.55	13.61	0.12
	qLWR8.2	bin8-59~bin8-60	8	5.02	14.60	0.10
	qLWR8.3	bin8-72~bin8-73	8	14.00	28.74	-0.20	23.98	23.89	-0.18
	qLWR11	bin11-64~bin11-65	11				22.98	22.93	0.29
粒长	qGL1.1	bin1-15~bin1-16	1	15.52	5.37	0.17
Grain length	qGL1.2	bin1-320~bin1-321	1	16.82	5.76	0.18
	qGL3	bin3-229~bin3-230	3	22.45	7.65	-0.19
	qGL11	bin11-37~bin11-38	11				46.12	17.26	-0.60
	qGL12	bin12-248~bin12-249	12	8.68	3.27	0.11	11.22	5.51	0.16
千粒质量	qTGW1.1	bin1-71~bin1-72	1				6.17	4.40	-2.46
Thousand-grain	qTGW1.2	bin1-139~bin1-140	1	25.13	10.92	-3.11
weight	qTGW2	bin2-267~bin2-268	2	12.10	5.87	1.09	7.61	5.73	1.11
	qTGW3	bin3-94~bin3-95	3	7.86	4.00	0.87
	qTGW4	bin4-194~bin4-195	4				38.58	20.47	-5.78
	qTGW7	bin7-22~bin7-23	7	7.53	3.86	-0.85
	qTGW8	bin8-25~bin8-26	8				6.29	4.46	1.19

图4 水稻粒质量与粒形QTL在染色体上的分布

Fig.4 Distribution of QTLs for rice grain weight and grain shape on chromosomes

图5 DEGs分析与qRT-PCR验证 A.E1环境下DEGs的上调和下调分析;B.E2环境下DEGs的上调和下调分析C.E1和E2环境下的转录组DEGs分析;D.使用RNA-Seq和qRT-PCR比较10个转录本的Log₂(Fold Change)。

Fig.5 DEGs analysis and qRT-PCR verification A.Analysis of up-regulation and down-regulation of DEGs in E1 environment;B.Analysis of up-regulation and down-regulation of DEGs in E2 environment;C.Transcriptome DEGs analysis in E1 and E2 environments;D.Comparison of the Log₂(Fold Change)of 10 transcripts using RNA-Seq and qRT-PCR.

图6 DEGs的GO富集统计 A.E1环境下DEGs的GO富集统计:1.生物过程;2.蛋白质磷酸化;3.转录调控,DNA模板;4.防御反应;5.转录,DNA模板;6.氧化还原过程;7.信号转导;8.蛋白质泛素化;9.缺水响应;10.损伤响应;11.类黄酮生物合成过程;12.跨膜受体蛋白酪氨酸激酶信号通路;13.多细胞生物发育;14.冷响应;15.脱落酸响应;16.盐胁迫响应;17.转运;18.类黄酮葡萄糖醛酸化;19.蛋白水解;20.细胞壁组织;21.次生代谢物生物合成过程;22.光刺激响应;23.镉离子响应;24.植物-过敏性响应;25.SCF-依赖的蛋白酶体泛素-依赖性蛋白质分解代谢过程;26.细胞核;27.质膜;28.膜的整合组分;29.细胞质;30.叶绿体;31.胞外区域;32.细胞溶质;33.线粒体;34.膜;35.高尔基体;36.胞间连丝;37.细胞壁;38.液泡;39.内质网;40.液泡膜;41.分子功能;42.蛋白质结合;43.ATP结合;44.蛋白质丝氨酸/苏氨酸激酶活性;45.转录因子活性,序列特异性DNA结合;46.DNA结合;47.金属离子结合;48.激酶活性;49.锌离子结合;50.ADP结合。B.E2环境下DEGs的GO富集统计:1.生物过程;2.蛋白质磷酸化;3.防御反应;4.转录调控,DNA模板;5.氧化还原过程;6.转录,DNA模板;7.类黄酮生物合成过程;8.类黄酮葡萄糖醛酸化;9.信号转导;10.脱落酸响应;11.蛋白质泛素化;12.次生代谢物生物合成过程;13.损伤响应;14.盐胁迫响应;15.光刺激响应;16.冷响应;17.SCF-依赖的蛋白酶体泛素-依赖性蛋白质分解代谢过程;18.转运;19.细胞壁组织;20.跨膜受体蛋白酪氨酸激酶信号通路;21.多细胞生物发育;22.缺水响应;23.脱落酸激活的信号通路;24.蛋白水解;25.谷胱甘肽代谢过程;26.细胞核;27.质膜;28.膜的整合组分;29.细胞质;30.叶绿体;31.胞外区域;32.线粒体;33.细胞溶质;34.膜;35.高尔基体;36.胞间连丝;37.细胞壁;38.细胞内膜结合细胞器;39.叶绿体类囊体膜;40.叶绿体基质;41.分子功能;42.蛋白质结合;43.ATP结合;44.蛋白质丝氨酸/苏氨酸激酶活性;45.DNA结合;46.转录因子活性,序列特异性DNA结合;47.金属离子结合;48.锌离子结合;49.激酶活性;50.泛素-蛋白质转移酶活性。

Fig.6 GO enrichment statistics of DEGs A.GO enrichment statistics of DEGs in E1 environment:1.Biological process;2.Protein phosphorylation;3.Regulation of transcription,DNA-templated;4.Defense response;5.Transcription,DNA-templated;6.Oxidation-reduction process;7.Signal transduction;8.Protein ubiquitination;9.Response to water deprivation;10.Response to wounding;11.Flavonoid biosynthetic process;12.Transmembrane receptor protein tyrosine kinase signaling pathway;13.Multicellular organism development;14.Response to cold;15.Response to abscisic acid;16.Response to salt stress;17.Transport;18.Flavonoid glucuronidation;19.Proteolysis;20.Cell wall organization;21.Secondary metabolite biosynthetic process;22.Response to light stimulus;23.Response to cadmium ion;24.Plant-type hypersensitive response;25.SCF-dependent proteasomal ubiquitin-dependent protein catabolic process;26.Nucleus;27.Plasma membrane;28.Integral component of membrane;29.Cytoplasm;30.Chloroplast;31.Extracellular region;32.Cytosol;33.Mitochondrion;34.Membrane;35.Golgi apparatus;36.Plasmodesma;37.Cell wall;38.Vacuole;39.Endoplasmic reticulum;40.Vacuolar membrane;41.Molecular function;42.Protein binding;43.ATP binding;44.Protein serine/threonine kinase activity;45.Transcription factor activity,sequence-specific DNA binding;46.DNA binding;47.Metal ion binding;48.Kinase activity;49.Zinc ion binding;50.ADP binding.B.GO enrichment statistics of DEGs in E2 environment:1.Biological process;2.Protein phosphorylation;3.Defense response;4.Regulation of transcription,DNA-templated;5.Oxidation-reduction process;6.Transcription,DNA-templated;7.Flavonoid biosynthetic process;8.Flavonoid glucuronidation;9.Signal transduction;10.Response to abscisic acid;11.Protein ubiquitination;12.Secondary metabolite biosynthetic process;13.Response to wounding;14.Response to salt stress;15.Response to light stimulus;16.Response to cold;17.SCF-dependent proteasomal ubiquitin-dependent protein catabolic process;18.Transport;19.Cell wall organization;20.Transmembrane receptor protein tyrosine kinase signaling pathway;21.Multicellular organism development;22.Response to water deprivation;23.Abscisic acid-activated signaling pathway;24.Proteolysis;25.Glutathione metabolic process;26.Nucleus;27.Plasma membrane;28.Integral component of membrane;29.Cytoplasm;30.Chloroplast;31.Extracellular region;32.Mitochondrion;33.Cytosol;34.Membrane;35.Golgi apparatus;36.Plasmodesma;37.Cell wall;38.Intracellular membrane-bounded organelle;39.Chloroplast thylakoid membrane;40.Chloroplast stroma;41.Molecular function;42.Protein binding;43.ATP binding;44.Protein serine/threonine kinase activity;45.DNA binding;46.Transcription factor activity,sequence-specific DNA binding;47.Metal ion binding;48.Zinc ion binding;49.Kinase activity;50.Ubiquitin-protein transferase activity.

图7 DEGs的KEGG富集统计 A.E1环境下DEGs的KEGG富集统计:1.色氨酸代谢;2.牛磺酸和次牛磺酸代谢;3.植物-病原体相互作用;4.苯丙氨酸代谢;5.其他类型的O-聚糖;6.核苷酸切除修复;7.甘氨酸、丝氨酸和苏氨酸代谢;8.果糖和甘露糖代谢;9.二萜类生物合成;10.半胱氨酸和甲硫氨酸代谢;11.类胡萝卜素生物合成;12.碳代谢;13.光合生物中的碳固定;14.油菜素内酯生物合成;15.β-丙氨酸代谢;16.抗坏血酸和醛糖酸代谢;17.氨基糖和核苷酸糖代谢;18.α-亚麻酸代谢;19.丙氨酸、天冬氨酸和谷氨酸代谢;20.ABC运输载体。B.E2环境下DEGs的KEGG富集统计:1.玉米素生物合成;2.植物-病原体相互作用;3.光合作用天线蛋白;4.苯丙烷类生物合成;5.苯丙氨酸代谢;6.错配修复;7.同源重组;8.鞘脂生物合成-乳糖系列和新乳糖系列;9.半乳糖代谢;10.果糖和甘露糖代谢;11.类黄酮生物合成;12.黄酮和黄酮醇的生物合成;13.DNA复制;14.咖啡因代谢;15.油菜素内酯生物合成;16.苯并恶嗪类;17.花青素生物合成;18.氨基糖和核苷酸糖代谢;19.丙氨酸、天冬氨酸和谷氨酸代谢;20.ABC运输载体。

Fig.7 KEGG enrichment statistics of DEGs A.KEGG enrichment statistics of DEGs in E1 environment:1.Tryptophan metabolism;2.Taurine and hypotaurine metabolism;3.Plant-pathogen interaction;4.Phenylalanine metabolism;5.Other types of O-glycan;6.Nucleotide excision repair;7.Glycine,serine and threonine metabolism;8.Fructose and mannose metabolism;9.Diterpenoid biosynthesis;10.Cysteine and methionine metabolism;11.Carotenoid biosynthesis;12.Carbon metabolism;13.Carbon fixation in photosynthetic organisms;14.Brassinosteroid biosynthesis;15.Beta-alanine metabolism;16.Ascorbate and aldarate metabolism;17.Amino sugar and nucleotide sugar metabolism;18.Alpha-linolenic acid metabolism;19.Alanine,aspartate and glutamate metabolism;20.ABC transporters.B.KEGG enrichment statistics of DEGs in E2 environment:1.Zeatin biosynthesis;2.Plant-pathogen interaction;3.Photosynthesis-antenna proteins;4.Phenylpropanoid biosynthesis;5.Phenylalanine metabolism;6.Mismatch repair;7.Homologous recombination;8.Glycosphingolipid biosynthesis-lacto and neolacto series;9.Galactose metabolism;10.Fructose and mannose metabolism;11.Flavonoid biosynthesis;12.Flavone and flavonol biosynthesis;13.DNA replication;14.Caffeine metabolism;15.Brassinosteroid biosynthesis;16.Benzoxazinoid;17.Anthocyanin biosynthesis;18.Amino sugar and nucleotide sugar metabolism;19.Alanine,aspartate and glutamate metabolism;20.ABC transporters.

表4 28个候选基因分析

Tab.4 Analysis of 28 candidate genes

基因 Gene	注释 Annotation	上调/下调 Up-regulation/ Down-regulation	数量性状位点 QTL
LOC_Os11g09864	推测表达wali7	下调	qGL11
LOC_Os11g09460	表达蛋白	上调
LOC_Os11g09690	表达含OsFBX410-F-box结构域的蛋白质	下调
LOC_Os11g09850	表达蛋白	下调
LOC_Os11g09710	表达蛋白	下调
LOC_Os11g10480	推测表达脱氢酶	下调
LOC_Os11g10100	表达STE_MEKK_ste11_MAP3K.3-STE激酶,包括来自酵母的sterile 7、sterile 11和sterile 20的同源物	下调
LOC_Os11g09590	表达含OsFBX404-F-box结构域的蛋白质	下调
LOC_Os11g09329	表达含VHS和GAT结构域的蛋白质	上调
LOC_Os11g09820	表达蛋白	上调
LOC_Os11g09360	表达含OsFBX398-F-box结构域的蛋白质	上调
LOC_Os01g04070	推测表达黄萎病抗性蛋白	上调	qGL1.1
LOC_Os01g04040	推测表达BBTI11-Bowman-Birk型麸皮胰蛋白酶抑制剂前体	下调
LOC_Os04g14140	表达蛋白	上调	qLWR4.1
LOC_Os04g14190	表达TRAF型锌指家族蛋白	下调
LOC_Os04g40900	推测表达外切酶	下调	qLWR4.2
LOC_Os04g41000	表达蛋白	上调
LOC_Os08g10250	推测表达SHR5受体样激酶	下调	qLWR8.1
LOC_Os08g10300	推测表达SHR5受体样激酶	下调
LOC_Os01g34610	表达蛋白	下调	qTGW1.2
LOC_Os01g34660	表达含RNA酶P Rpr2/Rpp21亚基结构域的蛋白质	上调
LOC_Os01g71930	表达糖基水解酶家族17蛋白	上调	qGL1.2
LOC_Os02g05199	表达蛋白	上调	qGW2.1
LOC_Os03g14290	表达蛋白	下调	qGW3
LOC_Os05g08910	表达蛋白	上调	qGT5.2
LOC_Os08g10430	推测表达NBS-LRR抗病蛋白	上调	qLWR8.2
LOC_Os11g19149	表达蛋白	上调	qLWR11
LOC_Os04g56700	推测表达柚皮素、2-酮戊二酸3-双加氧酶	上调	qLWR4.3、qGT4.3

图8 候选基因分析 A.QTL区间内基因与转录组DEGs分析;B.候选基因在亲本开花后第5,10,15天后籽粒转录组中的表达量分析;C.候选基因在亲本开花后第5,10,15天后籽粒中的qRT-PCR分析。数字5,10,15分别代表开花后第5,10,15天。

Fig.8 Candidate genes analysis A.Analysis of genes in the QTLs interval and DEGs of transcriptomes;B.Analysis of the expression levels of candidate genes in the transcriptome of seeds after 5,10,and 15 days of parental flowering;C.qRT-PCR analysis of candidate genes in the seeds after 5,10,and 15 days of parental flowering.The numbers 5,10,and 15 represent the 5th,10th,and 15th days after flowering,respectively.

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