Identification of Candidate Genes for Rice Grain Weight and Shape via QTL Mapping and Omics Analysis

doi:10.7668/hbnxb.20196073

Abstract

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

CLC Number:

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.

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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

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

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

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

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

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