作物杂志, 2024, 40(5): 1-7 doi: 10.16035/j.issn.1001-7283.2024.05.001

遗传育种·种质资源·生物技术

水稻胚乳突变体cse-2的表型分析及基因定位

孙家猛,, 高原, 陈虎, 花芹, 林泉祥, 陈庆全, 李金才, 张海涛,

安徽农业大学农学院,230036,安徽合肥

Phenotypic Analysis and Gene Mapping of Rice Mutant Chalkiness and Shrunken Endosperm-2

Sun Jiameng,, Gao Yuan, Chen Hu, Hua Qin, Lin Quanxiang, Chen Qingquan, Li Jincai, Zhang Haitao,

College of Agronomy, Anhui Agricultural University, Hefei 230036, Anhui, China

通讯作者: 张海涛,研究方向为作物遗传育种,E-mail:43647174@qq.com

收稿日期: 2023-06-24   修回日期: 2023-08-12   网络出版日期: 2023-12-01

基金资助: “十四五”国家重点研发计划(2022YFF1002903)
国家自然科学基金项目(31871603)

Received: 2023-06-24   Revised: 2023-08-12   Online: 2023-12-01

作者简介 About authors

孙家猛,研究方向为作物遗传育种,E-mail:1596038203@qq.com

摘要

淀粉是水稻籽粒中含量最多的大分子物质,其组分及含量对于稻米的各项品质指标均有直接影响。本研究鉴定了1个新的粉质胚乳突变体(chalkiness and shrunken endosperm-2cse-2),分析了突变体的农艺和品质相关性状,并对其开展了基因定位。结果表明,与野生型相比,突变体的株高、穗粒数和结实率等农艺性状以及淀粉含量、淀粉组分比例、淀粉粒形态结构、蛋白质含量、脂肪酸含量等品质性状均发生了显著变化。遗传分析表明,突变性状是由位于4号染色体上的1对隐性核基因控制。序列分析表明,精细定位区间内LOC_Os04g55230/FLO2基因第6064位碱基胞嘧啶(C)突变为胸腺嘧啶(T),形成TAA无义突变。以上结果证明,cse-2是已报道突变体flo2的一个新等位突变体。

关键词: 水稻; 粉质胚乳; 淀粉性质; 基因定位; FLO2

Abstract

Starch is the most abundant macromolecular substance in rice grain, and its composition and content have direct effect on quality indexes of rice. In this paper, agronomic and qualitative traits related to chalkiness and shrunken endosperm-2 (cse-2) were investigated and the candidate gene was mapped. The results showed that the agronomic traits including plant height, grain number per panicle, seed-setting rate, starch content and its components, physicochemical properties, starch grain morphology and structure, protein and fatty acid contents of the mutant had significantly altered. Mapping result showed that mutated phenotype is determined by a pair of nuclear recessive genes locating on chromosome 4. Sequence analysis indicated that a single nucleotide substitution of C-to-T occurred on the 6064th base of LOC_Os04g55230/FLO2, forming a TAA nonsense mutation. Therefore, cse-2 was a new allelic mutant of flo2.

Keywords: Rice; Floury endosperm; Starch property; Gene mapping; FLO2

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本文引用格式

孙家猛, 高原, 陈虎, 花芹, 林泉祥, 陈庆全, 李金才, 张海涛. 水稻胚乳突变体cse-2的表型分析及基因定位. 作物杂志, 2024, 40(5): 1-7 doi:10.16035/j.issn.1001-7283.2024.05.001

Sun Jiameng, Gao Yuan, Chen Hu, Hua Qin, Lin Quanxiang, Chen Qingquan, Li Jincai, Zhang Haitao. Phenotypic Analysis and Gene Mapping of Rice Mutant Chalkiness and Shrunken Endosperm-2. Crops, 2024, 40(5): 1-7 doi:10.16035/j.issn.1001-7283.2024.05.001

水稻是三大主粮作物之一,我国水稻播种面积常年保持在3000万hm2,产量约2亿t[1]。淀粉是胚乳中含量最多的物质,其含量、组成成分及所占比例均会影响水稻的产量和品质。淀粉的合成是由多种酶共同参与的有序而复杂的生理生化过程,其中主要涉及的酶有5种,分别是ADP-葡萄糖焦磷酸化酶(ADP-glucose pyrophosphorylase,AGPase)、可溶性淀粉合成酶(soluble starch synthase,SSS)、分支酶(branching enzyme,BE)、脱分支酶(debranching enzyme,DBE)以及颗粒结合淀粉酶(granule- bound starch synthase,GBSS)[2-3],以上酶功能的缺失均可能导致一系列异常水稻胚乳的产生。例如,AGPase由2个小亚基(small subunits,SSU)和4个大亚基(large subunits,LSU)构成,OsAGPL2负责编码AGPase的1个亚基,其发生突变会导致AGPase功能受损进而使胚乳产生皱缩表型[4]OsSSIIIa/Flo5编码淀粉合成酶IIIa(SSIIIa)蛋白,该基因突变致使SSIIIa功能异常,胚乳产生心白表型[5];淀粉分支酶(SBE)参与支链淀粉合成以及分支短链的形成,其功能缺陷时,导致支链淀粉链长变长、胚乳出现垩白和籽粒皱缩[6];异淀粉酶1(isoamylase 1,ISA 1)是一种DBE,当其失去原有的催化功能时,胚乳淀粉粒形成会受到阻碍,进而引起胚乳皱缩[7]

间接影响淀粉合成相关酶的功能也会形成异常胚乳。例如,FLO6编码一个含有CBM48结构域的蛋白,与淀粉结合,并通过与SSIVb及GBSS相互作用调节淀粉合成,突变体flo6中的胚乳具有粉质不透明的表型,且胚乳内淀粉含量明显减少[8-9]FLO8编码UDP-葡萄糖焦磷酸化酶(UDP- glucose pyrophosphorylase 1,Ugp1),该基因突变使Ugp1活性降低,进而影响大部分淀粉合成酶的活性,导致胚乳粉质不透明、总淀粉和支链淀粉的含量降低、脂质含量升高、支链淀粉结构改变[10]FLO2编码的蛋白含有3个可以介导蛋白质互作的四肽重复基序(TPR)结构域,在水稻胚乳发育过程中,FLO2蛋白可以调节一些与贮藏淀粉及贮藏蛋白合成有关基因的表达以及应对高温胁迫[11-13],在水稻突变体flo2中,籽粒明显皱缩,胚乳粉质不透明,直链淀粉含量降低,支链淀粉结构改变[11]

此外,与胚乳线粒体、造粉体和糊粉层发育、碳氮代谢、养分吸收转运相关的基因突变也会导致胚乳异常。基因FLO13负责编码线粒体复合体I附属亚基OsNDUFA9,其突变体的线粒体复合体I组装异常,导致线粒体结构改变、功能受损,使籽粒内干物质积累下降、复合淀粉粒排列疏松、胚乳粉质不透明[14]FLO10Fse5FLO18分别与线粒体NADH脱氢酶复合体I的3个亚基基因nad1、nad4nad5的mRNA加工有关[15-17]FLO18负责nad5的5ʹ末端剪切,FLO10Fse5分别负责nad1nad4的第一内含子的反式剪切,它们的突变都会导致线粒体形态结构发生变化,胚乳表型异常。此外,FLO10对水稻糊粉层的发育也有影响。OsROS1与DNA去甲基化有关,其突变使DNA高甲基化以及可能与糊粉层发育有关的转录因子RISBZ1RPBF表达受抑制,最终导致糊粉层的细胞层数增加,引起胚乳不透明、淀粉和直链淀粉含量减少、脂质和蛋白质含量提升[18]FLO7影响造粉体发育及外围胚乳淀粉合成的功能,在突变体flo7中,外围胚乳呈现出粉质不透明的表型、胚乳内复合淀粉粒排列松散、淀粉组分及结构发生改变[19]OsPPDKB编码丙酮酸磷酸双激酶(PPDKB),该基因与碳代谢有关,其突变体flo4籽粒不仅具有心白的表型,且胚乳中淀粉含量明显减少,脂肪酸含量升高[20]OsBT1编码的蛋白与腺苷二磷酸葡萄糖(ADP-glucose,ADPglc)转运有关,其突变体由于OsBT1功能受损而使得在合成淀粉时ADPG供应不足,最终胚乳异常,总淀粉及直链淀粉的含量降低[21]FLO19编码一个质体定位的丙酮酸脱氢酶复合物E1的亚基α1(ptPDC-E1-α1),该酶参与内半乳糖的生物合成,在突变体flo19中由于半乳糖合成减少而使造粉体发育异常、淀粉合成减少、复合淀粉颗粒形状异常、胚乳粉质不透明[22]

本研究以一个来源于ZH11的粉质胚乳突变体cse-2为试验材料,通过对其农艺性状、籽粒表型和胚乳淀粉粒形态、胚乳组分含量、基因定位及测序验证等研究,发现突变体cse-2flo2的1个新等位突变体。

1 材料与方法

1.1 试验材料

突变体cse-2源于粳稻品种ZH11(Oryza sativa L. ssp. japonica cv. Zhonghua 11)的组织培养突变体。突变体与籼稻品种IRAT129杂交获得F2定位群体,用于遗传分析及精细定位。以上材料于2021-2022年种植于安徽农业大学大杨镇基地,田间管理与大田生产一致。

1.2 测定指标与方法

1.2.1 农艺性状和遗传分析

成熟植株用于株高、分蘖数、节间长度、穗长、有效穗数、穗粒数、结实率等农艺性状的调查,利用t检验方法比较数据间差异性,用SPSS 20软件进行统计分析,用Excel软件进行数据处理并作图。

F1和F2代植株种子完全成熟后收获并脱壳,将糙米置于医用观片灯上观察胚乳透明情况,分析cse-2的遗传方式。

1.2.2 显微镜观察

用刀片横切突变体和野生型的籽粒,在体视镜下观察拍照。籽粒横切面经E1010型离子溅射仪(日立,日本)喷金镀膜处理后,利用S-4800型高分辨率扫描电子显微镜(日立,日本)观察并拍照[23]

1.2.3 籽粒成分及含量

糙米碾磨成粉后,用100目筛过筛后置于烘箱中35 ℃烘干。用A1481-1植物淀粉含量试剂盒(南京建成生物工程研究所)测定总淀粉含量;依据NY 147―88[24]测定直链淀粉含量。采用DA7200型近红外快速分析仪(Perten,美国)测定胚乳中的蛋白质含量、脂肪酸含量、淀粉的胶稠度及碱消值等[25-27];采用蒽酮比色法测定胚乳中所含的可溶性糖含量[28]。所有试验均进行3次生物学重复。

1.2.4 胚乳淀粉糊化温度

精米过100目筛后置于烘箱中35 ℃烘干备用。称取2.00 mg米粉样品,使用Pyris DSC 8000型差示扫描热量仪(DSC,Perten,美国)测定淀粉糊化温度以及糊化过程中的焓变[29]。所有试验均进行3次生物学重复。

1.3 突变基因定位及表达分析

采用图位克隆的方法对突变基因进行精细定位。提取F2叶片DNA[30],利用分布于水稻12条染色体上的79对具有多态性的分子标记对目的基因进行初步连锁分析。初步连锁后,利用 https://www.gramene.org网站下载籼稻(Oryza sativa L. ssp. indica)和粳稻(Oryza sativa L. ssp. japonica)基因组,并用NCBI网站(blast.ncbi.nlm.nih.gov/Blast. cgi)比较基因组片段序列,寻找具有SNP或Indel的位点,然后通过Primer3Plus(www.primer3plus.com)设计定位引物。由生工生物工程(上海)股份有限公司和擎科生物工程(南京)股份有限公司代为完成引物的合成以及候选基因的测序分析。

2 结果与分析

2.1 农艺性状及籽粒表型

与野生型ZH11相比,突变体的株高、主茎穗长、第3及第4节间长分别显著减少9.1%、10.9%、22.6%、29.7%;二次枝梗数减少19.3%,穗粒数减少13.5%,结实率减少10.2%;胚乳呈粉质不透明的外观,未脱壳籽粒的粒长和粒宽无显著差异,但粒厚下降16.7%,cse-2的糙米萎缩(图1表1)。扫描电镜(图2)显示,突变体cse-2胚乳中的淀粉粒填充不紧实,淀粉粒间的空隙明显,形态呈大小不一松散的球体外观。

图1

图1   野生型(ZH11)与突变体(cse-2)的表型比较

株高(a)、籽粒(b~e)。比例尺为10 cm(a)、1 cm(b~d)和1 mm(e)。

Fig.1   Comparison of phenotypes between wild type (ZH11) and mutant (cse-2)

Plant height (a) and grain (b-e). Bars=10 cm (a), 1 cm (b-d) and1 mm (e).


表1   野生型(ZH11)与突变体(cse-2)农艺性状比较

Table 1  Comparison of agronomic traits between wild type (ZH11) and mutant (cse-2)

农艺性状Agronomic traitZH11cse-2
株高Plant height (cm)104.05±0.5694.55±1.18**
主茎穗长Main panicle length (cm)23.80±0.4621.22±0.51**
第1节间长
The first internode length (cm)
42.20±0.66
40.21±0.75
第2节间长
The second internode length (cm)
19.16±0.64
18.57±0.40
第3节间长
The third internode length (cm)
13.68±0.56
10.55±0.56**
第4节间长
The fourth internode length (cm)
7.35±0.14
5.24±0.17**
有效分蘖数Effective tiller number20.75±2.4724.85±2.56
一次枝梗数Primary branch number13.88±0.4013.83±1.01
二次枝梗数Secondary branch number44.00±1.4035.50±1.76**
穗粒数Grain number per panicle221.85±6.84191.90±6.11**
结实率Seed-setting rate (%)89.84±0.1380.58±0.19**
粒长Grain length (mm)7.68±0.067.67±0.09
粒宽Grain width (mm)3.51±0.013.49±0.02
粒厚Grain thickness (mm)2.35±0.032.04±0.02**
千粒重1000-kernel weight (g)25.63±0.4019.16±0.17**

**”表示在P < 0.01水平上有极显著差异,下同。

**”indicates extremely significant difference at P < 0.01 level, the same below.

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图2

图2   野生型(ZH11)与突变体(cse-2)籽粒横截面扫描电镜图片

Fig.2   SEM images of grain cross section of wild type (ZH11) and mutant (cse-2)


2.2 突变体cse-2的遗传分析

突变体cse-2和籼稻IRAT129杂交后,F1胚乳均为正常表型,F2的胚乳表型发生了分离,其中籽粒胚乳表型正常的有191株,籽粒胚乳表型异常的有72株。经χ2检验符合孟德尔3:1分离比(χ2=0.67<χ20.05,1=3.84),表明突变体cse-2的表型是由1对隐性核基因控制。

2.3 籽粒理化性质分析

与野生型相比,突变体的总淀粉及直链淀粉含量分别极显著减少了22.4%和46.7%,而突变体蛋白质、脂肪酸及可溶性糖含量分别极显著增加了14.3%、78.4%、168.0%(图3)。

图3

图3   野生型(ZH11)和突变体(cse-2)籽粒成分含量对比

“**”表示在P < 0.01水平上有极显著差异。

Fig.3   Comparison of grain component contents of wild type (ZH11) and mutant (cse-2)

“**”indicates extremely significant difference at P < 0.01 level.


差示扫描热量仪检测结果(表2)表明,突变体淀粉在糊化时的热特性与野生型间均存在极显著变化,其中突变体淀粉的糊化起始温度、峰值温度、终止温度分别下降4.7、4.1、2.5 ℃,糊化过程中吸收的热量显著减少10.8%。近红外快速分析仪测定的胶稠度以及碱消值均与野生型有极显著差异,其中突变体的碱消值极显著下降5.0%,而胶稠度极显著上升23.4%。以上结果表明,突变体淀粉的理化性质发生了明显变化。

表2   野生型(ZH11)与突变体(cse-2)大米理化性质比较

Table 2  Comparison of the rice phypical and chemical properties between wild type (ZH11) and mutant (cse-2)

材料
Material
起始温度
To (℃)
峰值温度
TP (℃)
结束温度
TC (℃)
焓变
H (J/g)
碱消值
Alkali consumption value
胶稠度
Gel consistency (mm)
ZH1166.90±0.5572.20±0.3776.10±0.276.50±0.228.10±0.3756.40±0.18
cse-262.20±0.31**68.10±0.48**73.60±0.17**5.80±0.11**7.70±0.48**69.60±0.15**

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2.4 CSE-2基因的精细定位及表达特性

初定位将目标基因定位于第4条染色体长臂端标记s4-1 ~ s4-2。在该区间内继续设计分子标记,利用1378个极端隐性单株群体把目的基因最后定位在s4-6 ~ s4-4约50 kb区间内。基于粳稻品种日本晴参考基因组注释信息发现,在精细定位区间内存在6个预测基因,其中包括1个已克隆的控制胚乳发育的基因LOC_Os04g55230/FLO2。进一步测序发现LOC_Os04g55230/FLO2第6064位碱基胞嘧啶(C)突变为胸腺嘧啶(T),使mRNA的1483~ 1485位由CAA突变为TAA,导致无义突变和蛋白翻译提前终止(图4图5)。

图4

图4   CSE-2基因的精细定位

a~d:横线上方为定位所用的分子标记,横线下方为交换单株数,浅蓝色箭头表示候选基因;e:候选基因CSE-2结构图,浅蓝色框代表外显子,其中间空白部分代表内含子,红色箭头分别表示起始密码子、终止密码子、突变位点,黑线框内容表示突变位点;f:目的基因反向测序峰图,红线框内为突变位点;g:部分蛋白质序列比对,无义突变引起的氨基酸缺失。

Fig.4   Fine mapping of CSE-2 gene

a-d: the numbers above and beneath the bold lines represent the molecular markers and recombinants, respectively, and the light blue arrow represent the candidate gene; e: the structure diagram of candidate gene CSE-2, the light blue box represent the exon, the blank part represent the intron, the red arrows represent the start codon, stop codon and mutation site, respectively, and the content in the black box represent the mutation; f: target gene reverse sequencing peak map, with mutated sites in the red line box; g: partial protein sequence alignment near the none-sense mutation site.


图5

图5   野生型(ZH11)与突变体(cse-2)中FLO2蛋白质序列比对

红色箭头表示cse-2突变体内FLO2突变形成终止密码子的位点。

Fig.5   Sequence alignment of FLO2 protein between wild type (ZH11) and mutant (cse-2)

Red arrow indicates the site that the stop codon occurred of FLO2 in the cse-2 mutant.


3 讨论

基因LOC-Os04g55230曾被报道并命名为FLO2[11],目前已有多个flo2的等位突变体被报道,She等[11]通过诱变得到8个突变位点位于第11(2个突变位点)、14(3个突变位点一样)、21外显子以及第14和21内含子的剪切位点上flo2的等位突变体;Qiao等[31]借助诱变手段获得了3个flo2等位突变体,其突变位点分别位于第1、14(2个)外显子上;Wu等[32]通过诱变获得了3个flo2的等位突变体,其突变位点分别位于第9、11内含子的3′ 剪切位点以及第19外显子;邱家静[33]通过60Co辐射诱变得到9个flo2的等位突变体,其突变位点分别位于第13、14(2个)、16和17内含子剪切位点以及第6、10(编码区1431位点突变)、11、21外显子处。本研究鉴定了一个具有粉质皱缩胚乳的水稻突变体cse-2,是由基因LOC-Os04g55230第6064位碱基C突变成T引起无义突变导致的,该突变位点与以往发现的FLO2突变位点不同,故cse-2FLO2的一个新等位基因,突变体是flo2的一个新等位突变体。FLO2蛋白含有介导蛋白互作的TPR结构域及一个功能不明确的CLU结构域,由于cse-2中该基因的无义突变,使翻译的蛋白只含有N端的CLU结构域。一些参与多肽运输、控制分蘖及花粉育性有关的蛋白质同样含有TPR结构域[34-35],这表明FLO2除影响贮藏淀粉及贮藏蛋白的合成外,可能还具有其他生理功能,对于cse-2的研究将为TPR结构域的功能研究提供基因资源。

cse-2的胚乳外围表型正常,而中心部分粉质不透明,这与She等[11]、Qiao等[31]、邱家静[33]报道的表型类似,与Wu等[32]报道的3个暗胚突变体不同。此外,而本研究中的cse-2的粒长比野生型明显降低,这与邱家静[33]报道的同为第10外显子的等位突变体M227的糙米粒长表型不同。突变体cse-2的株高、主茎穗长、穗粒数和结实率等均有显著变化,而突变体flo2在这些农艺性状方面与野生型并无差异,这可能是由于2种突变体内FLO2蛋白序列不同引起的。cse-2胚乳中总淀粉和直链淀粉含量明显降低,蛋白质、脂肪酸以及可溶性糖含量却极显著升高,这表明由于淀粉合成途径受阻,而对多种初级和次级代谢产物的产生影响,导致脂肪酸等中间产物合成积累增加。此外,有报道[36]指出,CSE-2在拟南芥中的同源基因AtFLO2的突变引起脂质合成有关基因的表达水平降低,进而导致胚乳内脂肪酸含量下降,这一结果与cse-2中的情况相反,表明CSE-2及其同源基因在不同物种中对合成脂肪酸的影响机制可能有所不同。cse-2胚乳与报道过的胚乳突变体w24[4]、flo5[6]fse5[18]flo6[10]osagpl2-3[37]等均为胚乳中心粉质不透明。但这些突变体籽粒内的淀粉粒形态相似,osagpl2-3的淀粉粒虽然大小不一但形状也一致[37],而cse-2内部的淀粉粒大小不一且形态多样。

由于cse-2胚乳中淀粉的热特性、糊化时的焓变、胶稠度、碱消值与野生型均存在极显著差异,表明基因CSE-2的突变改变了淀粉的理化性质。有研究[38]指出,直链淀粉和支链淀粉比例会影响淀粉的糊化温度,在cse-2的胚乳淀粉中直链淀粉所占的比例极显著降低,并且淀粉的糊化温度和糊化焓变也明显下降,这表明cse-2淀粉的热特性发生变化的原因是淀粉组分含量的变化。糊化温度的降低可以减少米饭蒸煮的时间和用水量[39],而较低含量的直链淀粉可以使米饭更柔软,根据本研究的结果,cse-2可尝试通过育种途径,创制特异种质,用于水稻蒸煮品质的改良。

4 结论

cse-2胚乳具有粉质不透明的表型、胚乳内的淀粉粒排列松散、淀粉粒外形异常,并且在株高、穗粒数、结实率等农艺性状方面与野生型存在显著差异。此外,突变体的淀粉含量显著低于野生型,蛋白质、脂肪酸以及可溶性糖的含量高于野生型。在理化性质上,突变体淀粉的热特性指数显著低于野生型,表明突变体淀粉更易糊化。遗传分析表明该性状受1对核隐性基因控制,图位克隆以及测序结果表明,基因LOC_Os04g55230的一个碱基替换导致该突变性状,该基因曾被报道为FLO2,故突变体cse-2flo2的一个新的等位突变体。

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