基于NCII遗传交配设计的籼稻抽穗期全基因组关联分析

doi:10.3724/SP.J.1006.2023.12079

Abstract

Abstract:

Heading date is jointly regulated by light and temperature resources and gene network, affecting crop yield and regional adaptability of varieties. Identification of significant loci and genes associated with trait variation by genome-wide association analysis (GWAS) is of great significance to analyze the genetic basis of the heading date in rice. In this study, according to the North Carolina design II (NCII), 115 indica rice varieties as the male parents and 5 sterile lines as the female parents had been made test cross, and 575 F₁ test-cross lines were obtained. GWAS was performed on the phenotypic value of the heading date of the male parental varieties (V) and testcross lines (TC), the general combining ability (GCA) of the male parent lines, the special combining ability (SCA), and better parent heterosis (BPH) of testcross lines. (1) A total of 104 significantly associated locus were located and distributed on 12 chromosomes. Of these, 16 significantly associated locus were detected on chromosome 4. There were six, five, fifteen, fifty-seven, and twenty-one significantly associated locus detected in V, GCA, TC, SCA, BPH data sets, respectively. Phenotypic variation analysis of significantly associated sites in these five data sets revealed that the total contribution rate (phenotypic variation explained, PVE) of significantly associated loci to phenotypic variation in V, GCA, TC, SCA, and BPH data sets was 79.57%, 10.51%, 33.35%, 56.42%, and 54.86%, respectively. Twenty-five significantly associated locus were simultaneously detected in two or more than two datasets, that probably was hotspot genomic region of heading date in rice. (2) By comparing all significantly associated locus with the annotation information of the Nipponbare reference genome, five cloned genes related to heading date were found. Among them, three of the five genes within 200 kb from the significantly associated locus detected in this study. Compared with the haplotype combinations in the three genes with the superior haplotype of individual clone gene, we found that the average grain yield per plant of male parental varieties with the haplotype combination SDG724 (Hap. A)_Hd17 (Hap. E)_Ghd7 (Hap. A) was higher and the heading date period was longer. The results indicated that the pyramiding superior haplotype of genes related to heading date would extend the heading date period of conventional rice varieties and improve their yield. However, the situation was different for testcross population, the haplotype combination form of SDG724 (Hap. I)_Hd17 (Hap. K)_Ghd7 (Hap. I) had the superior yield but median heading date period. None superior haplotype pyramiding resulting in high yield or long heading date was found in the testcross lines population, indicating that the genetic basis of heading date of testcross hybrids was more complicated than rice varieties. The combination of genome-wide association analysis and haplotype analysis can utilize the linkage disequilibrium information provided by multiple SNPs, which improves the efficiency of gene detection and facilitates the cultivation of high-yield rice varieties.

Key words: rice, heading date, genome-wide association analysis, haplotype, North Carolina design II

XU Kai, ZHENG Xing-Fei, ZHANG Hong-Yan, HU Zhong-Li, NING Zi-Lan, LI Lan-Zhi. Genome-wide association analysis of indica-rice heading date based on NCII genetic mating design[J].Acta Agronomica Sinica, 2023, 49(1): 86-96.

Figures/Tables 16

Table S1

Information of 115 varieties and 5 sterile lines used in cross experiment"

编号 Code	材料名称 Material name	编号 Code	材料名称 Material name	编号 Code	材料名称 Material name
V1	矮仔占 Aizizhan	V41	88B	V81	IRAT109
V2	东秋播 Dongqiubo	V42	湘恢91269 Xianghui 91269	V82	华粳籼74 Huajingxian 74
V3	广秋矮 Guangqiu’ai	V43	陆财号 Lucaihao	V83	紫恢100 Zihui 100
V4	广场矮3784 Guangchang’ai 3784	V44	蜀丰101 Shufeng 101	V84	Varylava
V5	青丰矮 Qingfeng’ai	V45	成都矮3号Chengdu’ai 3	V85	D62B
V6	江二矮 Jiang’er’ai	V46	三颗寸 Sankecun	V86	G46B
V7	青二矮 Qing’er’ai	V47	加巴拉 Jiabala	V87	IR58025B
V8	鸡对伦 Jiduilun	V48	台山糯 Taishannuo	V88	中9B Zhong 9B
V9	阔叶稻 Kuoyedao	V49	桂朝2号 Guichao 2	V89	香5 Xiang 5
V10	叶青仑 Yeqinglun	V50	沪科3号 Huke 3	V90	闷加高2 Menjiagao 2
V11	陆财号 Lucaihao	V51	特青选恢 Teqingxuanhui	V91	鄂香1号 Exiang 1
V12	华南15 Huanan 15	V52	黄丝桂占 Huangsiguizhan	V92	Q198
V13	广场矮 Guangchang’ai 4182	V53	湘晚籼3号 Xiangwanxian 3	V93	黄秀占 Huangxiuzhan
V14	桂阳矮49 Guiyang’ai 49	V54	金优1号 Jinyou 1	V94	蜀恢527 Shuhui 527
V15	朝阳早18 Chaoyangzao 18	V55	成农水晶 Chengnongshuijing	V95	蜀恢288 Shuhui 288
V16	桂朝2号 Guichao 2	V56	墨米Momi	V96	蜀恢707 Shuhui 707
V17	广场13 Guangchang 13	V57	三百粒Sanbaili	V97	龙恢11 Longhui 11
V18	丰青矮 Fengqing’ai	V58	柳沙1号Liusha 1	V98	南恢511 Nanhui 511
V19	青农矮 Qingnong’ai	V59	洞庭晚籼Dongtingwanxian	V99	湘恢529 Xianghui 529
V20	丰矮占1号Feng’aizhan 1	V60	扬稻2号 Yangdao 2	V100	金恢275 Jinhui 275
V21	黄华占 Huanghuazhan	V61	六十早 Liushizao	V101	泸恢5240 Luhui 5240
V22	黄新占 Huangxinzhan	V62	台中籼选2 Taozhongxianxuan 2	V102	明恢2088 Minghui 2088
V23	28占 28 Zhan	V63	南特号 Nantehao	V103	山恢287 Shanhui 287
V24	丰华占 Fenghuazhan	V64	黑督4号 Heidu 4	V104	山恢8281 Shanhui 8281
V25	青六矮 Qingliu’ai	V65	金南特43B Jinnante 43B	V105	R238
V26	丰八占 Fengbazhan	V66	湘早籼7号Xiangzaoxian 7	V106	R727
V27	长丝占 Changsizhan	V67	80B	V107	205R
V28	华丝占 Huasizhan	V68	包协123B Baoxie123B	V108	781R
V29	扬稻2号 Yangdao 2	V69	江农早1号 Jiangnongzao 1	V109	3301R
V30	扬稻六号 Yangdao 6	V70	古154 Gu 154	V110	IR24
V31	特青 Teqing	V71	献改B Xiangai B	V111	IR1544
V32	Sadu-cho	V72	矮沱谷151 Aituogu 151	V112	圭630 Gui 630
V33	山黄占 Shanhuangzhan	V73	闷加丁2 Menjiading 2	V113	辐36-2 Fu 36-2
V34	IR64	V74	解放籼 Jiefangxian	V114	R1318
V35	N22	V75	白壳花螺 Baikehualuo	V115	T9311
V36	矮脚南特 Aijiaonante	V76	柳叶占 Liuyezhan	AS	新安S Xin’an S
V37	广陆矮4号 Guanglu’ai 4	V77	珍汕97 Zhenshan 97	3A	珞红3A Luohong 3A
V38	湘矮早10号 Xiang’aizao 10	V78	明恢63 Minghui 63	Y58S	Y58S
V39	青四矮16B Qingsi’ai 16B	V79	9311	GZ63	广占63S Guangzhan 63S
V40	滇瑞409B Dianrui 409B	V80	南京11 Nanjing 11	PA64	矮培64S Aipei 64S

Table S1

Fig. 1

Fig. 2

Fig. S1

Fig. S2

Fig. S3

Fig. S4

Table S2

Genome-wide association signals of heading date in indica rice"

数据集 DataSet	染色体 Chr.	起始位置 Start	终止位置 End	−log₁₀ (P)最高的位点 Highest association site	P值负对数 −log₁₀ (P)	表型方差解释率 Phenotypic variation explained (%)	克隆基因 Cloned gene
V	3	34355029	34355029	chr03_34355029	7.58	10.46	SNAC1; SPIN1; OsPHY2; OsIDS1; gh1; ZFP182; ZFP15; OsADF3; OsRLCK118
	4	4302632	4302632	chr04_4302632	5.32	24.26	OsEMF2a; ART2; OsCAS
	6	4730505	4730505	chr06_4730505	10.14	8.89	OsPTF1; OsERF71; OsKASI; OsARF16
	9	7869103	7869103	chr09_7869103	6.76	11.15	OsbZIP71; OsMED25; OsEMF2b; SDG724
	10	16080525	16080525	chr10_16080525	6.55	22.07	OsCDC48E; OsABCG25; OsPht1; OsPht1; OsHCI1; OsMTA4
	12	15155333	15155333	chr12_15155333	6.76	2.73	PIOX
GCA	1	33603983	33603983	chr01_33603983	6.86	0.40	OsGH3-1; OsPME1; OsERF3
	2	4065908	4065908	chr02_4065908	5.98	5.44	OsALDH5F1; OsDPK2
	4	20338147	20338147	chr04_20338147	5.19	0.53	OSINV4; GIF1; ACL1; COPT4
	6	4745474	4745474	chr06_4745474	8.93	4.10	OsPTF1; OsERF71; SUS2; OsKASI; OsARF16;
	11	27790672	27790672	chr11_27790672	5.62	0.04	JAmyb; Pikp_2
TC	1	35427407	35427407	chr01_35427407	7.16	5.07	OsWRKY24; OsYSL18; LAX1; OsBAG4; OsAMT2
	2	28380703	28380703	chr02_28380703	7.16	9.44	OsPIE1; 709
	3	2085577	2085577	chr03_2085577	5.39	2.61	RAI1; OsCYP96B4; OsDSS1; sd37; bsh1
	3	14946317	14946317	chr03_14946317	7.71	0.07	OsIRO3
	4	27992334	27992334	chr04_27992334	12.03	3.52	OsHMA5; OsGPX1; cZOGT1; Kala4; OsPIP1; 2; SMG2; OsMKKK10; OsCPK12; es4
	5	16703102	16703102	chr05_16703102	9.5	0.11	YGL1; ygl80; OsEm1; EMP1; OsImp
	6	4745474	4831914	chr06_4831914	13.67	3.29	OsPTF1; OsERF71; RSUS2; RSs1; SUS2; OsKASI; OsARF16
	7	9578963	9578963	chr07_9578963	6.92	0.30	Ghd7
	7	26527050	26562456	chr07_26527050	5.18	0.85	OsLti6a; OsPDK1; Os-eIF6; 1; OsPRMT3; OsHsfB4b
	7	26965963	26965963	chr07_26965963	6.21	0.11	OsbZIP60; qHMS7-ORF1; qHMS7-ORF3; CYP734A5
	10	2918961	2918961	chr10_2918961	7.15	2.75	OsDIL; OsLTP6; OsPRP2; OsPRP1
	11	17832018	17832018	chr11_17832018	5.62	0.91	OsHSD1; OsSOT1; STV11
	12	730797	730797	chr12_730797	5.64	4.08	OsCIPK14
	12	3864512	3864512	chr12_3864512	8.41	0.10	Osmyb2; OsGRX27; OsALDH3H1; OsAPx7; OsAPx6; OsAPx5
	12	11533522	11533522	chr12_11533522	8.44	0.15
SCA	2	2645592	2789913	chr02_2645592	5.82	0.58	OseIF4A; OsMAPK33; OsMPK14; OsMPK3; OsPP18; OsRBCS1; LC2; OsVIL3; YL1; LRK1
	2	4255102	4310130	chr02_4255102	6.38	3.19	OsDPK2; Os4CL3; OsGL1-2
	2	8481676	8481676	chr02_8481676	6.7	1.13	GluD; GluD-1; GluB1; GluB1; RPBF; OsDof3; OsDof-10; OsDof7
	2	29065323	29065323	chr02_29065323	7.06	2.23	OSOTP51; OsABA8ox1
	2	35116043	35133182	chr02_35116043	7.35	0.89	OsABC1-4; OsNDUFA9; flo13; OsIAA10; RTBP1; CYP97A4; OsCBSX3; OsLpa1
	3	23813743	23813743	chr03_23813743	5.75	0.04
	4	18157266	18216943	chr04_18216943	5.31	0.11
	4	18903071	18907437	chr04_18903071	6.46	2.19	OsExo70‐F3
	4	19647607	19647607	chr04_19647607	6.36	0.30	OsAFB2; OsJAZ5; OsTIFY9; LAX2; Gnp4; OsClpC1; OsRap2.6; pi21
	4	19894988	20618276	chr04_19931704	8.65	0.66	pi21; OsHAK1; OsClpD2; OSINV4; GIF1; OsCIN2; ACL1; COPT4
	4	20879608	21022879	chr04_20890026	7.76	1.05	Asr4; ASR6; OsASR2
	4	22158990	22189682	chr04_22164037	5.6	0.33	OsRR1; OsFRO1; OsAP37; OSZEP1
	4	23386304	23437449	chr04_23386304	5.86	2.07	MOF; OsGASR2; d11; CYP724B1; CPB1; sg4; cl4; OsMYB80; OsMYB103
	4	23998714	23998714	chr04_23998714	7.28	1.17	Rf17; RMS; CRC1; OsPIMT2; OsWS1; WSL3
	4	24214858	24214858	chr04_24214858	5.03	0.03	OsPIMT2; OsWS1; WSL3; OsRAD21-2
	4	27009473	27236519	chr04_27058044	9.28	0.10	Glup3; OsVPE1; OsALDH3B1; OsLCBK2; Oshox22; OsYSL16; SDG703; OsERF1
	4	35115325	35115325	chr04_35115325	6.27	2.23	OsBSK3; OsCAF1B
	5	2264054	2450291	chr05_2284407	8.17	0.68	OsSAMS1; OsPti1a; OsLti6b; ddOs32; APG; OsMYB2P-1; OsMPK14; OsGH3-6; OsPPKL2; PTB1; OsVIL4
	5	3049063	3158516	chr05_3111450	6.4	1.22	OsGRX15; OsTIR1; APIP6; SRS3; OsKinesin-13A; sar1; Chalk5
	5	3511793	3814100	chr05_3607357	7.21	1.99	Chalk5; GS5; OsZIP6
	5	17826917	17826917	chr05_17826917	5.04	0.87	OsBiP3; RH1; OsFTIP7; OsRLCK185
	5	18633931	18854859	chr05_18633931	5.66	0.90	OsBC1L4; OsNADK3; SMOS1; shb; RLA1
	5	20101785	20464861	chr05_20101785	7.02	0.91	TCD5; OsbZIP39; OsPCS1; TCM5; SERF1; OsCc1
	5	21819212	23047221	chr05_22813721	6.34	1.09	OsAUX1; OsCOI1b; SH5; OsP5CS; OsP5CS1; OsALDH18B1; Osrboh4; OsAMT2; 1; OsPDC1; OsZIP5
	5	23534940	23549991	chr05_23545588	6.84	1.22	OsAMTR1; OsSTN8; EUI1; i-sd-1(t)
	5	23946757	23946757	chr05_23946757	5.85	3.93	OsDMI3; Osmyb5; SDG728; SDG728; OsCML9; OsCam2
	6	2160801	2160801	chr06_2160801	5.12	0.02	dp1; DDF1; OsENOD93a; Hd17; Ef7; OsELF3; OsELF3-1; OsELF3.1; Hd-q; OsPRMT10; SPDT
	6	21268145	21268145	chr06_21268145	5.23	0.56
	6	25011887	25011887	chr06_25011887	5.46	0.86	OsARID3; OsbZIP50; OsbZIP74; TGW6; SPP
	6	25716036	25716036	chr06_25716036	5.46	0.86	OsPSK
	6	26086130	26086130	chr06_26086130	5.35	0.52	DCM1; OsSAL1; OVP1; OsVP1
	6	26870826	26894242	chr06_26884987	6.32	1.35	OsRpoTp; OsGL1-3; Os4CL4
	6	27148504	27148504	chr06_27148504	6.32	0.38	OsGRX18; OsPIN2; OsPLS1; OsbZIP52; RISBZ5
	7	7918837	7918837	chr07_7918837	5.29	0.11	OsAPL4; OsAGPL4
	7	8181872	8485133	chr07_8181872	5.29	0.76	OsAPL4; OsAGPL4; LLB; pls3; OsMTS1
	7	9129150	9129150	chr07_9129150	5.32	0.15	OsNRAMP1; Ghd7
	7	10123301	10123301	chr07_10123301	5.32	0.24
	7	26337284	26337284	chr07_26337284	7.73	2.36	RNP29; OsRH36; OsLti6a; OsPDK1
	7	27649737	27670134	chr07_27649737	5.09	1.25	NTRC; SPIN6; Fd-GOGAT1; lc7; ABC1; spl23
	8	6184657	6293033	chr08_6184657	5.76	0.73	OsHAK12; SPL29; UAP1; OsZIP4
	8	7502244	7502244	chr08_7502244	5.76	0.36	OsVIL1; OsDPK1; zl16; OsHAD1
	8	9334312	9354921	chr08_9354921	7.8	1.41
	8	15462160	15462160	chr08_15462160	5.66	3.11	OsBRL3; HDA705
	8	20967437	20988336	chr08_20981726	5.25	0.17	GF14c; 14-3-3; OsMYB106; ONAC106
	10	1520673	1520673	chr10_1520673	6.73	0.03	OsSNDP1; OsADF
	10	15824748	15824748	chr10_15824748	6.07	0.09
	10	16100848	16100848	chr10_16100848	7.25	0.20	OsPht1; 8; OsPT8; OsHCI1
	10	16334199	16334199	chr10_16334199	5.53	0.24	Osgrp-2
	10	22283651	22283651	chr10_22283651	6.51	0.92	MYBS3; OsHox1; REL2; CycP4; 1; CYCU4; 1; OsSAPK3; REK; OsCBL1; OsHUB2; FRRP1; OsCAO2
	10	23018816	23183833	chr10_23018816	6.96	0.16	OsMYC2; OsITPK5; JMJ706; OsSRO1a; OsCSLD1; rth-2; OsDUR3
	11	1762018	1762018	chr11_1762018	5.66	0.12	OsCML2; OsCPK25
	11	10572420	10572420	chr11_10572420	5.36	0.10
	11	22419901	22419901	chr11_22419901	5.66	0.52	BGL11(t)
	11	27487132	27487132	chr11_27487132	5.02	2.32	OsGPAT3; OsJAMyb
	11	28800508	28800508	chr11_28800508	5.02	1.27	DHD1; CycD7; 1; WDL1
	12	14124949	14125467	chr12_14124949	7.3	3.19	OsNCED2
	12	16519849	16519849	chr12_16519849	5.31	0.98	DEC
BPH	1	33223657	34531439	chr01_34042495	7.89	1.68	OsKTN80c; Pish; OsGH3.1; LC1; OsPME1; OsERF3; OsAP37; CycB1; 1; OsLRR1; OsCML1; OsCam3; OsCaM61; SDG709; OsGAmyb; MYBGA; OsNAC4; ONAC068
	2	24241454	24241454	chr02_24241454	5.01	7.46	du3; OsCBP20; OsNST1; BC14; BBM2; LP2
	2	28453213	28453213	chr02_28453213	5.07	5.16	OsPIE1; 709
	2	28881879	28881879	chr02_28881879	5.33	5.16	AOX1c; OsPUT1; OsBRXL1; OsGRF4; GS2; GL2; PT2; LGS1; OSOTP51; OsABA8ox1
	2	29687730	29687730	chr02_29687730	5.72	1.27	Os4CL2; AOX1c; OsPUT1; OsBRXL1; OsGRF4; GS2; OSOTP51; OsABA8ox1; ADL1; OsDEK1; OsGAP1; OsFAD2-1; Ghd2; DTH2
	3	4911745	4911745	chr03_4911745	5.46	5.40	OsRab6a; OsDSR4; pRINO1; OsINO1-1
	3	13598822	13598822	chr03_13598822	5.04	5.80	OsDIS1; VLN2
	4	4804275	4804275	chr04_4804275	5.7	4.53	ETR2; OS-ETR2
	4	5307896	5307896	chr04_5307896	5.33	0.83	OsCPS4; OsCyc1; CYP99A3; OsMAS; OsDTS2; OsKSL4; KS4; CYP99A2
	5	16703102	16703102	chr05_16703102	5.96	0.11	YGL1; ygl80; OsEm1; EMP1; OsImp
	6	17983222	17983222	chr06_17983222	7.23	0.24
	11	3977659	3977659	chr11_3977659	15.42	5.24
	11	10747918	10763678	chr11_10747918	5.13	1.20	BBM1
	12	3970723	3970723	chr12_3970723	5.44	1.91	Osmyb2; OsGRX27; OsALDH3H1; OsAPx7; OsAPx6; OsAPx5
	12	10735585	10735585	chr12_10735585	5.73	0.67	Pita; Pi-4a; MIR
	12	11432955	11432955	chr12_11432955	5.47	0.62	OsRBCS3; OsRBCS5; OsRBCS4
	12	11767635	11767635	chr12_11767635	5.47	0.62
	12	12314314	12314314	chr12_12314314	6.04	1.27
	12	13772007	13772007	chr12_13772007	5.47	0.62
	12	14602287	14602287	chr12_14602287	11.49	4.68
	12	24447076	24447076	chr12_24447076	5.11	0.37	CycD5

Table S2

Fig. 3

Table S3

Table 1

Table S4

The haplotype analysis for gene SDG724 of heading date"

SNP	亲本抽穗期表型V								子代抽穗期表型TC
SNP	Hap.A	Hap.B	Hap.C	Hap.D	Hap.E	Hap.F	Hap.G	Hap.H	Hap.I	Hap.J	Hap.K	Hap.L	Hap.M	Hap.N	Hap.O	Hap.P	Hap.Q
chr09_8039256	CC	CC	TT	TT	TT	TT	TT	TT	CC	CC	CT	CT	CT	CT	CT	CT	CT
chr09_8039344	GG	GG	AA	AA	GG	GG	GG	GG	GG	GG	AG	AG	GG	GG	GG	GG	GG
chr09_8039349	CC	CC	AA	AA	AA	AA	AA	AA	CC	CC	AC	AC	AC	AC	AC	AC	CC
chr09_8039459	CC	CC	CC	CC	AA	AA	AA	CC	CC	CC	CC	CC	AC	AC	AC	CC	CC
chr09_8039498	AA	AA	TT	TT	TT	TT	TT	TT	AA	AA	AT	AT	AT	AT	AT	AT	AA
chr09_8039637	CC	CC	GG	GG	GG	GG	GG	GG	CC	CC	CG	CG	CG	CG	CG	CG	CG
chr09_8040762	AA	AA	GG	GG	GG	GG	GG	GG	AA	AA	AG	AG	AG	AG	AG	AG	AG
chr09_8040844	CC	CC	GG	GG	GG	GG	GG	GG	CC	CC	CG	CG	CG	CG	CG	CG	CC
chr09_8041219	CC	CC	GG	GG	GG	GG	GG	GG	CC	CC	CG	CG	CG	CG	CG	CG	CC
chr09_8041764	TT	TT	AA	AA	AA	AA	AA	AA	TT	TT	AT	AT	AT	AT	AT	AT	TT
chr09_8042022	CC	CC	TT	TT	CC	CC	CC	CC	CC	CC	CT	CT	CC	CC	CC	CC	CC
chr09_8042255	AA	AA	AA	GG	GG	GG	GG	GG	AA	AA	AA	AG	AG	AG	AG	AG	AA
chr09_8042778	AA	AA	GG	GG	GG	GG	GG	GG	AA	AA	AG	AG	AG	AG	AG	AG	AA
chr09_8042789	TT	TT	CC	CC	TT	TT	TT	TT	TT	TT	CT	CT	TT	TT	TT	TT	TT
chr09_8043742	TT	TT	GG	GG	GG	GG	GG	GG	TT	TT	GT	GT	GT	GT	GT	GT	TT
chr09_8043997	GG	GG	GG	GG	AA	AA	GG	GG	GG	GG	GG	GG	AG	AG	GG	GG	GG
chr09_8044399	GG	GG	CC	CC	CC	CC	CC	CC	GG	GG	CG	CG	CG	CG	CG	CG	GG
chr09_8044407	TT	TT	CC	CC	CC	CC	CC	CC	TT	TT	CT	CT	CT	CT	CT	CT	TT
chr09_8044747	AA	AA	GG	GG	GG	GG	GG	GG	AA	AA	AG	AG	AG	AG	AG	AG	AA
chr09_8044939	CC	CC	TT	TT	CC	CC	CC	TT	CC	CC	CT	CT	CC	CC	CC	CT	CC
chr09_8044997	TT	TT	CC	CC	TT	TT	TT	TT	TT	TT	CT	CT	TT	TT	TT	TT	TT
chr09_8045096	CC	CC	TT	TT	CC	TT	TT	TT	CC	CC	CT	CT	CC	CT	CT	CT	CC
chr09_8045337	AA	AA	CC	CC	CC	CC	CC	CC	AA	AA	AC	AC	AC	AC	AC	AC	AA
chr09_8045404	TT	TT	CC	CC	CC	CC	CC	CC	TT	TT	CT	CT	CT	CT	CT	CT	TT
chr09_8045607	TT	TT	CC	CC	CC	CC	CC	CC	TT	TT	CT	CT	CT	CT	CT	CT	CT
chr09_8045608	GG	GG	AA	AA	AA	AA	AA	AA	GG	GG	AG	AG	AG	AG	AG	AG	GG
chr09_8045752	TT	TT	TT	TT	GG	GG	GG	TT	TT	TT	TT	TT	GT	GT	GT	TT	TT
chr09_8045837	GG	GG	AA	AA	AA	AA	AA	AA	GG	GG	AG	AG	AG	AG	AG	AG	GG
chr09_8045891	CC	CC	CC	CC	TT	TT	TT	CC	CC	CC	CC	CC	CT	CT	CT	CC	CC
chr09_8046082	AA	AA	GG	GG	GG	GG	GG	GG	AA	AA	AG	AG	AG	AG	AG	AG	AG
chr09_8046222	GG	GG	AA	AA	AA	AA	AA	AA	GG	GG	AG	AG	AG	AG	AG	AG	GG
chr09_8046390	TT	TT	AA	AA	TT	TT	TT	TT	TT	TT	AT	AT	TT	TT	TT	TT	TT
chr09_8046463	AA	AA	AA	AA	GG	GG	GG	AA	AA	AA	AA	AA	AG	AG	AG	AA	AA
chr09_8046722	AA	GG	GG	GG	GG	GG	GG	GG	AA	AG	AG	AG	AG	AG	AG	AG	AA

Table S4

Table S5

Table S6

Table S7

Table 2

References 36

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数据集 Data set	基因 Gene name	优异单倍型 Superior haplotype	抽穗期 Heading days (d)	产量 Yield (g)
V	SDG724	Hap. A	93.07±7.06	29.68±11.05
	Hd17	Hap. E	93.51±6.41	30.18±10.11
	Ghd7	Hap. A	93.96±6.26	30.15±9.05
TC	SDG724	Hap. I	93.00±6.68	42.73±13.54
	Hd17	Hap. P	93.49±6.44	43.38±13.49
	Ghd7	Hap. H	90.09±7.21	43.81±12.86

数据集 Dataset	单倍型 Haplotype	抽穗期 hd (mean±sd, d)	产量 yield (mean±sd, g)	数量 Count
V	Hap.A	93.07±7.06	29.67±11.01	48
	Hap.B	80.5±NA	47.21±NA	1
	Hap.C	98±9.19	29.51±11.45	2
	Hap.D	89.26±8.49	27.93±8.99	37
	Hap.E	92.5±NA	18.36±NA	1
	Hap.F	93.62±5.12	28.59±10.24	17
	Hap.G	85.25±15.91	37.25±20	2
	Hap.H	89.12±4.46	37.07±20.21	4
TC	Hap.I	92.81±6.98	42.72±14.07	224
	Hap.J	87.7±10.37	33.4±4.38	5
	Hap.K	88.15±16.29	36.11±10.99	10
	Hap.L	91.76±9.51	41.83±12.97	158
	Hap.M	95.9±4.16	56.53±17.87	5
	Hap.N	90.38±10.54	39.53±13.1	74
	Hap.O	94.31±5.5	58.29±21.91	8
	Hap.P	86.94±9.7	33.4±14.23	17
	Hap.Q	98.5±3.67	43.86±17.47	5

数据集 Data set	单倍型Haplotype			个数 No.	亲本抽穗期 HD.V (d)	子代抽穗期 HD.TC (d)	一般配合力 GCA	特殊配合力 SCA	超亲优势值 BPH	亲本产量 YD.V (g)	子代产量 YD.TC (g)
数据集 Data set	SDG724	Hd17	Ghd7	个数 No.	亲本抽穗期 HD.V (d)	子代抽穗期 HD.TC (d)	一般配合力 GCA	特殊配合力 SCA	超亲优势值 BPH	亲本产量 YD.V (g)	子代产量 YD.TC (g)
V	Hap.A	Hap.E	Hap.A	23	94.30	93.59	2.09	-0.06	1.12	31.97	41.88
	Hap.A	HapA	Hap.A	9	92.22	92.92	1.41	0.06	0.08	28.68	37.21
	Hap.D	HapA	Hap.A	12	94.21	94.94	3.43	-0.13	1.91	29.88	40.68
	Hap.D	Hap.B	Hap.C	5	86.80	88.78	-2.73	-0.25	0.08	22.52	44.59
	Hap.A	HapA	Hap.C	13	90.31	90.27	-1.24	-0.04	0.68	25.92	47.03
	Hap.D	HapA	Hap.C	12	86.71	88.54	-3.10	0.12	1.08	29.76	41.98
	Hap.F	HapA	Hap.C	11	93.32	90.83	-2.32	1.34	-1.26	32.15	39.79
TC	Hap.I	Hap.P	Hap.D	20	93.43	95.73	2.24	-0.33	3.26	31.12	40.48
	Hap.L	Hap.G	Hap.E	24	94.21	94.09	3.43	-0.33	1.23	29.88	39.46
	Hap.I	Hap.K	Hap.E	45	94.14	93.59	2.25	0.37	0.76	32.09	42.10
	Hap.I	Hap.K	Hap.F	27	91.24	93.93	1.15	0.50	0.84	28.93	43.61
	Hap.L	Hap.K	Hap.F	28	90.55	94.19	1.98	0.05	2.79	31.55	40.46
	Hap.I	Hap.P	Hap.F	43	94.01	92.58	1.94	-0.80	1.44	31.54	43.33
	Hap.I	Hap.G	Hap.H	26	90.31	90.37	-1.24	0.62	-0.54	25.92	45.75
	Hap.L	Hap.G	Hap.H	22	84.41	90.09	-3.35	2.45	2.13	29.88	44.01
	Hap.I	Hap.K	Hap.I	23	89.85	90.83	0.20	-0.77	1.02	25.68	48.86

Genome-wide association analysis of indica-rice heading date based on NCII genetic mating design

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SAL	数据集 DataSet	染色体 Chromosome	起始位置 Start	终止位置 End	关联到阈值水平最高的位点 Highest Association Site	P值负对数 −log₁₀ (P)
SAL1	V	6	4730505	4730505	chr06_4730505	10.14061526
	V	10	16080525	16080525	chr10_16080525	6.545290071
	GCA	1	33603983	33603983	chr01_33603983	6.85737051
	GCA	2	4065908	4065908	chr02_4065908	5.976967
	GCA	4	20338147	20338147	chr04_20338147	5.185557
	GCA	6	4745474	4745474	chr06_4745474	8.926052
	TC	2	28380703	28380703	chr02_28380703	7.163092
	TC	5	16703102	16703102	chr05_16703102	6.499328302
	TC	7	26527050	26562456	chr07_26527050	5.176122719
	TC	12	3864512	3864512	chr12_3864512	8.410424
	TC	12	11533522	11533522	chr12_11533522	8.43912
	SCA	2	29065323	29065323	chr02_29065323	7.064964096
	SCA	11	10572420	10572420	chr11_10572420	5.360353371
SAL2	TC	6	4745474	4831914	chr06_4831914	13.66548
	SCA	10	16100848	16100848	chr10_16100848	7.247927987
	BPH	1	33223657	34531439	chr01_34042495	7.888104243
	SCA	2	4255102	4310130	chr02_4255102	6.381851153
	SCA	4	19894988	20618276	chr04_19931704	8.646770265
	TC	6	4745474	4831914	chr06_4831914	13.66548
	BPH	2	28453213	28453213	chr02_28453213	5.07193869
	BPH	5	16703102	16703102	chr05_16703102	5.960448446
	SCA	7	26337284	26337284	chr07_26337284	7.734907569
	BPH	12	3970723	3970723	chr12_3970723	5.436513114
	BPH	12	11432955	11432955	chr12_11432955	5.470334349
	BPH	2	28881879	28881879	chr02_28881879	5.326320712
	BPH	11	10747918	10763678	chr11_10747918	5.125963338

数据集 DataSet	单倍型 Haplotype	chr07_9152479	chr07_9152659	chr07_9154485	chr07_9154489	抽穗期 hd (mean±sd, d)	产量 yield (mean±sd, g)	数量 Count
V	Hap.A	CC	CC	GG	GG	93.96±6.16	29.09±9.91	57
	Hap.B	GG	CC	GG	GG	87.3±9	29.88 ± 12.85	5
	Hap.C	GG	TT	TT	CC	89.31±8.24	29.67±11.75	50
TC	Hap.D	CC	CC	GG	GG	95.7±6.75	42.4±11.44	48
	Hap.E	CG	CC	GG	GG	93.38±6.7	39.94±12.84	118
	Hap.F	CG	CT	GT	CG	93.46±8.4	41.16±15.06	143
	Hap.G	GG	CC	GG	GG	85.64±15.42	43.47±23.5	11
	Hap.H	GG	CT	GT	CG	89.37±8.82	43.59±12.83	102
	Hap.I	GG	TT	TT	CC	88.85±10.05	42.96±14.85	84

数据集 DataSet	单倍型 Haplotype	chr06_2234168	chr06_2234700	chr06_2234735	chr06_2235191	chr06_2235522	chr06_2236645	chr06_2237266	chr06_2237521	chr06_2238002	chr06_2238193	chr06_2238719	chr06_2239035	抽穗期 hd (mean±sd, d)	产量 yield (mean±sd, g)	数量 Count
V	Hap.A	GG	CC	GG	GG	CC	AA	AA	GG	AA	CC	AA	GG	91.11±8	29.52±11.32	63
	Hap.B	GG	CC	GG	GG	CC	AA	TT	GG	AA	CC	AA	GG	89.29±7.72	24.97±7.54	7
	Hap.C	GG	CC	GG	GG	CC	GG	AA	AA	GG	GG	AA	GG	87.25±8.96	20.01±2.59	4
	Hap.D	TT	TT	AA	AA	TT	AA	AA	AA	GG	CC	GG	GG	80.5±NA	47.21±NA	1
	Hap.E	TT	TT	AA	AA	TT	GG	AA	AA	GG	GG	GG	TT	93.52±6.41	30.18±10.11	33
	Hap.F	TT	TT	AA	GG	TT	GG	AA	AA	GG	GG	GG	TT	94.25±7.46	33.28±12.46	4
TC	Hap.G	GG	CC	GG	GG	CC	AA	AA	GG	AA	CC	AA	GG	90.2±8.93	40.86±12.86	121
	Hap.H	GG	CC	GG	GG	CC	AA	AT	GG	AA	CC	AA	GG	85.73±14.37	46.25±12.64	13
	Hap.I	GG	CC	GG	GG	CC	AG	AA	AG	AG	CG	AA	GG	89.75±10.38	34.52±14.33	8
	Hap.J	GT	CT	AG	AG	CT	AA	AA	AG	AG	CC	AG	GG	98.75±2.47	29.9±3.04	2
	Hap.K	GT	CT	AG	AG	CT	AG	AA	AG	AG	CG	AG	GT	92.22±8.69	42.1±14.82	223
	Hap.L	GT	CT	AG	AG	CT	AG	AT	AG	AG	CG	AG	GT	89.38±8.37	41.91±14.6	21
	Hap.M	GT	CT	AG	AG	CT	GG	AA	AA	GG	GG	AG	GT	100.89±12.14	33.86±11.89	9
	Hap.N	GT	CT	AG	GG	CT	AG	AA	AG	AG	CG	AG	GT	95.29±6.96	50.74±17.13	7
	Hap.O	TT	TT	AA	AA	TT	AG	AA	AA	GG	CG	GG	GT	80.33±2.89	35.73±3.66	3
	Hap.P	TT	TT	AA	AA	TT	GG	AA	AA	GG	GG	GG	TT	93.49±6.44	43.34±13.59	88
	Hap.Q	TT	TT	AA	AG	TT	GG	AA	AA	GG	GG	GG	TT	97.41±4.81	39.72±11.23	11

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