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作物学报 ›› 2023, Vol. 49 ›› Issue (1): 86-96.doi: 10.3724/SP.J.1006.2023.12079

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

基于NCII遗传交配设计的籼稻抽穗期全基因组关联分析

徐凯1(), 郑兴飞2, 张红燕1, 胡中立3, 宁子岚1, 李兰芝1,*()   

  1. 1湖南农业大学植物保护学院 / 湖南省农业大数据分析与决策工程技术研究中心, 湖南长沙 410128
    2湖北省农业科学院粮食作物研究所, 湖北武汉 430064
    3武汉大学生命科学学院 / 杂交水稻国家重点实验室, 湖北武汉 430072
  • 收稿日期:2021-12-16 接受日期:2022-05-05 出版日期:2023-01-12 网络出版日期:2022-05-23
  • 通讯作者: 李兰芝
  • 作者简介:E-mail: kratix_01279@163.com
  • 基金资助:
    杂交水稻国家重点实验室(湖南杂交水稻研究中心)开放课题项目(2019KF05);杂交水稻国家重点实验室(武汉大学)开放课题项目(KF201912);湖南省教育厅资助科研项目(19A244);湖南省自然科学基金项目(2020JJ4039);湖南省自然科学基金项目(2021JJ30351);湖南省创新型省份建设专项项目(2021NK1011)

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

XU Kai1(), ZHENG Xing-Fei2, ZHANG Hong-Yan1, HU Zhong-Li3, NING Zi-Lan1, LI Lan-Zhi1,*()   

  1. 1Hunan Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-making, College of Plant Protection, Hunan Agricultural University, Changsha 410128, Hunan, China
    2Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crop Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, Hubei, China
    3Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan 430072, Hubei, China
  • Received:2021-12-16 Accepted:2022-05-05 Published:2023-01-12 Published online:2022-05-23
  • Contact: LI Lan-Zhi
  • Supported by:
    Open Project of the State Key Laboratory of Hybrid Rice (Hunan Hybrid Rice Research Center)(2019KF05);State Key Laboratory of Hybrid Rice (Wuhan University)(KF201912);Hunan Provincial Department of Education(19A244);Natural Science Foundation of Hunan Province(2020JJ4039);Natural Science Foundation of Hunan Province(2021JJ30351);Special Funds for Construction of Innovative Provinces in Hunan Province(2021NK1011)

摘要:

抽穗期受光温资源和基因网络的共同调控, 影响作物产量和品种的地域适应性, 通过关联分析鉴定与抽穗期性状相关的显著位点和基因, 对解析抽穗期的遗传基础具有重要意义。本研究按照双因素交叉式遗传设计(North Carolina design II, NCII)将115份籼稻品种作为父本, 5份不育系作为母本, 进行测交, 得到了575个F1代的测交群体。对亲本和F1代抽穗期的表型值、亲本品种群体的一般配合力、F1代群体的特殊配合力和超亲优势值进行全基因组关联分析, (1) 共定位到104个关联位点, 分布在12条染色体上。其中, 第4条染色体上检测到的显著位点最多, 为16个。在亲本的抽穗期表型、一般配合力、F1代的抽穗期表型、特殊配合力、超亲优势值5个数据集中分别检测到6、5、15、57和21个。对这5个数据集中的显著关联位点进行表型变异分析, 发现在亲本抽穗期表型、一般配合力、F1代抽穗期表型、特殊配合力和超亲优势值这5个数据集中的显著关联位点对表型变异的总贡献率(phenotypic variation explained, PVE)分别为79.57%、10.51%、33.35%、56.42%和54.86%。其中, 25个位点在多个数据集中被检测到, 可能为抽穗期相关的热点区域。(2) 通过关联分析得到的显著位点与日本晴参考基因组注释信息比对, 共检测到5个已克隆抽穗期基因, 其中3个基因与显著关联位点的基因组距离小于200 kb, 对这3个基因中的单倍型组合与单个基因的优异单倍型进行比较发现, 亲本品种群体中单倍型组合SDG724 (Hap.A)_Hd17 (Hap. E)_Ghd7 (Hap. A)的对应的水稻单株籽粒产量较高, 抽穗期较长, 该组合中各基因的单倍型对应于单个克隆基因的优异单倍型, 表明优异单倍型的聚合的常规稻, 具有更高的产量和更长的抽穗期。测交子代未见此情形, 测交子代群体中SDG724 (Hap. I)_Hd17 (Hap. K)_Ghd7 (Hap. I)的单倍型组合形式的水稻有适中的抽穗期和较高的产量, 说明测交子代的抽穗期遗传机制较父本(常规水稻品种)复杂。全基因组关联分析和单倍型分析相结合, 能利用到多个SNP提供的连锁不平衡信息, 提高了基因检测效率, 对培育高产的水稻品种具有重要的指导意义。

关键词: 水稻, 抽穗期, 全基因组关联分析, 单倍型, NCII遗传设计

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

附表1

用于测交试验的115份水稻品种及5个不育系材料信息"

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

图1

亲本和测交子代中抽穗期表型值(V和TC)分布 (A): 亲本和测交子代群体表型值分布的箱线图; (B): 测交子代群体抽穗期表型分布柱状图; (C): 父本群体抽穗期表型分布柱状图。"

图2

亲本群体和测交群体的群体结构分析 A: 亲本群体的遗传结构分析; B: 亲本品种群体的K值趋势图; C: 测交群体的遗传结构分析; D: 测交群体的K值趋势图。"

附图1

亲本种群和测交种群的PCA图 a、b、c为亲本群体的2D-PCA图,d为3D-PCA图;e、f、g为测交群体的2D-PCA图,h为3D-PCA图."

附图2

GLM模型的曼哈顿图和分位数图"

附图3

MLM模型的曼哈顿图和分位数图"

附图4

FarmCPU模型的曼哈顿图和分位数图"

附表2

籼稻抽穗期的全基因组关联分析位点"

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

图3

抽穗期Blink模型的曼哈顿图和QQ图 黑色虚竖线代表在多个数据集中定位到的重叠的显著关联位点, 蓝色虚竖线代表多个数据集中距离小于200 kb但非重叠的显著关联位点; 红、蓝、绿色克隆基因代表距离显著位点200 kb以内、200~500 kb、500 kb~1 Mb的抽穗期基因。"

附表3

在多个数据集中检测到的显著关联位点(SALs)"

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

表1

各基因中优异单倍型对应表型"

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

附表4

抽穗期基因SDG724的单倍型分析"

SNP 亲本抽穗期表型V 子代抽穗期表型TC
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

附表5

抽穗期基因SDG724的单倍型对应的抽穗期和产量表型"

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

附表6

抽穗期基因Ghd7的单倍型分析"

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

附表7

抽穗期基因Hd17的单倍型分析"

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

表2

亲本品种群体与测交群体不同基因中单倍型组合对应表型值"

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)
SDG724 Hd17 Ghd7
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
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