中国农业科学 ›› 2022, Vol. 55 ›› Issue (1): 12-25.doi: 10.3864/j.issn.0578-1752.2022.01.002
马拴红1(),万炯1,梁瑞清2,张雪海1,邱小倩1,孟淑君1,徐宁坤1,林源1,党昆泰1,王琪月1,赵嘉雯1,丁冬1(),汤继华1()
收稿日期:
2021-07-07
接受日期:
2021-09-03
出版日期:
2022-01-01
发布日期:
2022-01-07
通讯作者:
丁冬,汤继华
作者简介:
马拴红,E-mail: 基金资助:
MA ShuanHong1(),WAN Jiong1,LIANG RuiQing2,ZHANG XueHai1,QIU XiaoQian1,MENG ShuJun1,XU NingKun1,LIN Yuan1,DANG KunTai1,WANG QiYue1,ZHAO JiaWen1,DING Dong1(),TANG JiHua1()
Received:
2021-07-07
Accepted:
2021-09-03
Online:
2022-01-01
Published:
2022-01-07
Contact:
Dong DING,JiHua TANG
摘要:
【目的】生育期相关性状是玉米育种研究的重点之一。作为重要的生育期性状,开花期(抽穗期、吐丝期和散粉期)的提前,可保证玉米充分脱水,适宜机收;也为中国黄淮海地区小麦-玉米一年两熟耕作模式下的小麦播种减轻压力。转录因子是转录水平基因表达调控的重要上游因子,对目标基因发挥转录激活或转录抑制的作用。在全基因组水平上解析转录因子对玉米开花期的调控作用,获得开花期提前且不影响产量的玉米转录因子单倍型组合,进而挖掘优异种质资源,可为培育开花期适宜的玉米育种研究提供基因资源。【方法】使用候选基因关联分析方法,对开花期相关转录因子及显著SNP进行分析;并利用DAP-seq技术捕获了关键转录因子的结合位点和下游基因;随后对转录因子调控的下游基因进行GO分析,探究转录因子通过影响其下游基因对开花期进行调控的基因网络。【结果】玉米开花期3种性状(吐丝期、散粉期、抽穗期)中,与吐丝期和抽穗期性状以及吐丝期和散粉期性状同时关联的转录因子显著SNP均为75个,与抽穗期和散粉期性状同时关联的显著SNP为128个,同时关联到3种表型的显著SNP为58个。表明开花期3种性状可能受相同的转录因子调控。选取含有3个及以上开花期相关显著SNP的转录因子基因,通过DAP-seq,捕获了这些转录因子结合的关键基序及调控的下游基因。转录因子结合的下游基因显著富集于转录因子活性、DNA结合、RNA结合、有机氮化合物的合成代谢过程、与生殖有关的发育过程等;不同的转录因子存在共同调控的下游基因,生育期相关性状关键调控性转录因子为ARF、MYB和NAC。对关键上游转录因子进行单倍型分析,发掘了玉米生育期提前,同时对产量无负向影响的转录因子最优单倍型组合。【结论】运用DAP-seq技术并结合前人研究绘制了全基因组水平上转录因子对生育期相关农艺性状的调控网络,并发掘了既提前玉米生育期又对产量无负向影响的转录因子最优单倍型组合。
马拴红, 万炯, 梁瑞清, 张雪海, 邱小倩, 孟淑君, 徐宁坤, 林源, 党昆泰, 王琪月, 赵嘉雯, 丁冬, 汤继华. 玉米开花期转录因子候选基因的关联分析[J]. 中国农业科学, 2022, 55(1): 12-25.
MA ShuanHong, WAN Jiong, LIANG RuiQing, ZHANG XueHai, QIU XiaoQian, MENG ShuJun, XU NingKun, LIN Yuan, DANG KunTai, WANG QiYue, ZHAO JiaWen, DING Dong, TANG JiHua. Candidate Gene Association Analysis of Maize Transcription Factors in Flowering Time[J]. Scientia Agricultura Sinica, 2022, 55(1): 12-25.
表1
开花期性状相关显著的SNP数目及转录因子统计"
表型 Trait | SNP数量 Number | 转录因子家族 TF families |
---|---|---|
抽穗期 Heading date | 206 | AP2-EREBP、ARF、ARID、AUX/IAA、bHLH、bZIP、C2C2-DOF、C2C2-GATA、C2C2-YABBY、C3H、CCAAT-HAP2、coactivator-p15、DDT、G2-like、GNAT、GRAS、GRF、HB、HSF、LOB、MADS、MYB、MYB-related、NAC、NLP、OFP、Orphans、PHD、PLATZ、Rcd1-like、TCP、TRAF、Trihelix、WRKY |
吐丝期 Silking time | 168 | ABI3VP1、AP2-EREBP、ARF、AUX/IAA、bHLH、bZIP、C2C2-GATA、C2H2、C3H、coactivator-p15、DDT、G2-like、GRAS、GRF、HB、IWS1、MADS、mTERF、MYB、MYB-related、NAC、NLP、Orphans、PHD、Rcd1-like、SNF2、TAZ、WRKY |
散粉期 Pollen shed | 177 | AP2-EREBP、ARF、AUX/IAA、bHLH、bZIP、C2C2-DOF、C2C2-GATA、C2H2、C3H、CCAAT-HAP2、DDT、G2-like、GNAT、GRAS、HB、IWS1、MADS、MYB、MYB-related、NAC、NLP、Orphans、PHD、Rcd1-like、Trihelix、WRKY |
抽穗/吐丝 Heading date/Silking time | 75 | AP2-EREBP、ARF、AUX/IAA、bHLH、bZIP、C2C2-GATA、coactivator-p15、DDT、G2-like、MADS、MYB、NAC、NLP、Orphans、PHD、Rcd1-like、WRKY |
抽穗/散粉 Heading date/Pollen shed | 125 | AP2-EREBP、ARF、bHLH、bZIP、C2C2-DOF、C2C2-GATA、C3H、CCAAT-HAP2、DDT、G2-like、GNAT、HB、MYB、MYB-related、NAC、NLP、Orphans、PHD、Rcd1-like、Trihelix、WRKY |
吐丝/散粉 Silking time/Pollen shed | 75 | AP2-EREBP、ARF、bHLH、bZIP、C2C2-GATA、C2H2、DDT、G2-like、GRAS、IWS1、MYB、NAC、NLP、Orphans、PHD、Rcd1-like、WRKY |
抽穗/吐丝/散粉 Heading date/Silking time/Pollen shed | 58 | AP2-EREBP、ARF、bHLH、bZIP、C2C2-GATA、DDT、G2-like、MYB、NAC、NLP、Orphans、PHD、Rcd1-like、WRKY |
表2
转录因子调控的下游基因"
基因 Gene ID | 功能描述 Description | 上游结合转录因子家族 Upstream binding TF families |
---|---|---|
Zm00001d017660 | 光周期非依赖性早花蛋白 1 Protein PHOTOPERIOD-INDEPENDENT EARLY FLOWERING 1 | NAC/MYB/ARF/HB/C2C2-GATA/C2H2/WRKY/GRF/PLATZ |
Zm00001d034036 | 多梳家族EMBRYONIC FLOWER 2蛋白 Polycomb group protein EMBRYONIC FLOWER 2 | NAC/MYB/ARF |
Zm00001d020364 | 早花蛋白4 Protein EARLY FLOWERING 4 | NAC/MYB/ARF |
Zm00001d047269 | 早花蛋白4 Protein EARLY FLOWERING 4 | NAC/MYB/ARF |
Zm00001d042066 | 糖苷水解酶家族2蛋白 Glycoside hydrolase family 2 protein | bZIP/HB/MYB/ARF |
Zm00001d029378 | LNK1蛋白Protein LNK1 | AP2-EREBP/C2C2-GATA/C2H2/G2-like/MYB/NAC |
Zm00001d035112 | 扩张蛋白A11 Expansin-A11 | AP2-EREBP/C2C2-GATA/C2H2/G2-like/ |
Zm00001d037315 | 含NAC结构域的蛋白质8 NAC domain-containing protein 8 | AP2-EREBP/C2C2-GATA/C2H2/G2-like/ |
Zm00001d048066 | Sec14p样磷脂酰肌醇转移家族蛋白 Sec14p-like phosphatidylinositol transfer family protein | AP2-EREBP/C2C2-GATA/C2H2/G2-like/ARF/NAC |
Zm00001d015082 | 转导家族蛋白/WD-40重复序列家族蛋白 Transducing family protein/WD-40 repeat family protein | WRKY/GRF/PLATZ/NLP/MYB/NAC |
Zm00001d021147 | 蛋白酶体亚单位β-4型 Proteasome subunit beta type-4 | WRKY/GRF/PLATZ/NLP/MYB/NAC/HB |
Zm00001d034832 | 可能的叶绿体酰基激活酶16 Probable acyl-activating enzyme 16 chloroplastic | WRKY/GRF/PLATZ/NLP/MYB |
Zm00001d037377 | 姐妹染色单体结合蛋白PDS5同源物A Sister chromatid cohesion protein PDS5 homolog A | WRKY/GRF/PLATZ/NLP/MYB/NAC |
Zm00001d039518 | 真核起始因子3 Eukaryotic initiation factor3 | WRKY/GRF/PLATZ/NLP/NAC/bZIP/HB/ARF |
Zm00001d014895 | 推测的跨膜蛋白保守区(DUF2404) Putative integral membrane protein conserved region (DUF2404) | C2H2/G2-like/WRKY/GRFARF/NAC/MYB/HB |
Zm00001d029329 | 多嘧啶结合束蛋白同源物1 Polypyrimidine tract-binding protein homolog 1 | C2H2/G2-like/WRKY/GRFNAC/MYB |
Zm00001d043093 | MOR1蛋白 Protein MOR1 | C2H2/G2-like/WRKY/GRFARF/NAC/MYB/HB |
Zm00001d044566 | 胼胝质合酶7 Callose synthase 7 | C2H2/G2-like/WRKY/GRFNAC/MYB |
表3
关键转录因子不同单倍型组合对应的产量和开花期表型"
单倍型组合 Haplotype combination | 表型值 Phenotypic value | 份数 Number | 表型值 Phenotypic value | 份数 Number | 表型值 Phenotypic value | 份数 Number | |||
---|---|---|---|---|---|---|---|---|---|
单穗产量 Yield per ear | 抽穗期 Heading date | 单穗产量 Yield per ear | 吐丝期 Silking time | 单穗产量 Yield per ear | 散粉期 Pollen shed | ||||
A1 | 41.66 | 62.29 | 28 | 40.27 | 67.40 | 22 | 41.66 | 65.30 | 28 |
B1 | 41.45 | 63.97 | 27 | - | 69.11 | - | 41.45 | 66.79 | 27 |
C1 | 42.76 | 63.35 | 27 | 44.29 | 68.58 | 10 | 42.43 | 66.29 | 27 |
A2 | 45.21 | 67.55 | 424 | 45.21 | 72.43 | 414 | 45.14 | 70.41 | 424 |
B2 | 45.22 | 67.48 | 425 | - | 72.34 | - | 45.22 | 70.34 | 425 |
C2 | 45.17 | 67.54 | 424 | 45.16 | 72.38 | 424 | 45.20 | 70.39 | 424 |
A2B2 | 45.30 | 67.64 | 410 | - | - | - | 45.23 | 70.51 | 409 |
A2C2 | 45.30 | 67.73 | 402 | 45.29 | 72.47 | 414 | 45.23 | 70.58 | 401 |
B2C2 | 45.37 | 67.74 | 398 | - | - | - | 45.37 | 70.59 | 398 |
A2B2C2 | 45.12 | 67.81 | 389 | - | - | - | 45.30 | 70.67 | 388 |
A1B1 | 40.20 | 62.77 | 13 | - | - | - | 40.20 | 65.56 | 13 |
A1C1 | 39.89 | 61.92 | 9 | 41.85 | 66.49 | 4 | 40.44 | 64.22 | 9 |
A1B2 | 42.93 | 63.29 | 15 | - | - | - | 44.30 | 67.05 | 11 |
A1C2 | 42.50 | 63.58 | 19 | 39.28 | 67.24 | 15 | 43.74 | 67.05 | 14 |
A2B1 | 42.61 | 65.09 | 14 | - | - | - | 42.61 | 67.93 | 14 |
A2C1 | 44.28 | 64.06 | 18 | 45.69 | 69.70 | 5 | 44.23 | 67.12 | 17 |
B1C1 | 39.88 | 63.38 | 4 | 38.68 | 65.65 | 5 | |||
B1C2 | 41.72 | 64.07 | 23 | 42.08 | 67.05 | 22 | |||
B2C1 | 43.28 | 63.34 | 23 | 43.28 | 66.25 | 23 | |||
A1B1C1 | 40.20 | 63.76 | 3 | - | - | - | 38.62 | 65.24 | 4 |
A1B2C1 | 39.73 | 60.99 | 6 | - | - | - | 39.73 | 63.53 | 6 |
A1B2C2 | 45.06 | 64.82 | 9 | - | - | - | 45.06 | 67.79 | 9 |
A1B1C2 | 40.20 | 62.47 | 10 | - | - | - | 40.90 | 65.71 | 9 |
A2B1C2 | - | - | - | - | - | - | 42.90 | 67.98 | 13 |
A2B2C1 | - | - | - | - | - | - | 44.61 | 67.20 | 17 |
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