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水稻苗期根部性状的遗传分析和最长根长QTL qLRL4的精细定位

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田彪,, 丁仕林, 刘朝雷, 阮班普, 姜洪真, 郭锐, 董国军, 胡光莲, 郭龙彪, 钱前, 高振宇,*中国水稻研究所, 浙江杭州 310006

Genetic analysis of seedling root traits and fine mapping of the QTL qLRL4 for the longest root length in rice

TIAN Biao,, DING Shi-Lin, LIU Chao-Lei, RUAN Ban-Pu, JIANG Hong-Zhen, GUO Rui, DONG Guo-Jun, HU Guang-Lian, GUO Long-Biao, QIAN Qian, GAO Zhen-Yu,*China National Rice Research Institute, Hangzhou 310006, Zhejiang, China

通讯作者: *高振宇, E-mail:gaozhenyu@caas.cn, Tel: 0571-63370211

收稿日期:2020-12-13接受日期:2021-03-19网络出版日期:2021-04-13
基金资助:国家自然科学基金项目.32061143039
国家自然科学基金项目.31671761


Corresponding authors: *E-mail:gaozhenyu@caas.cn, Tel: 0571-63370211
Received:2020-12-13Accepted:2021-03-19Published online:2021-04-13
Fund supported: National Natural Science Foundation of China.32061143039
National Natural Science Foundation of China.31671761

作者简介 About authors
E-mail:82101186057@caas.cn,Tel:0571-63370483



摘要
为了解析水培苗期根系相关性状的遗传调控, 以籼稻9311和粳稻日本晴(Nipponbare, NPB)为亲本的148个株系构成的重组自交系群体为材料, 对水稻幼苗根系相关性状开展QTL分析。在2次重复中共检测到26个控制最长根长、总根系长、根表面积、根体积和根直径的QTL, 分布在水稻第1、2、4、7、9、10、11号共7条染色体上, 发现了水稻第2、4、7和10号染色体上的4个QTL簇, 包括第4号染色体上控制最长根长的QTL qLRL4。为了精细定位该QTL, 我们构建了以9311为背景、插入缺失标记IND4-1和IND4-4间来自NPB的近等系NIL-qLRL4。利用NIL-qLRL4和9311构建的F2群体, 最终将qLRL4精细定位在标记IND4-1和IND4-3之间约68.23 kb的区间内并预测了候选基因。此根长QTL的精细定位将有助于水稻根长遗传机理的研究, 为探究水稻根系形态建成的分子机制奠定了基础。
关键词： 水稻;根部性状;最长根长;qLRL4;精细定位

Abstract
In order to analyze the genetic basis of root traits at seedling stage, we performed QTL analysis of root morphology with 148 recombinant inbred lines derived from indica variety 9311 and japonica variety Nipponbare (NPB). In two repetitions, a total of 26 QTLs were detected for the longest root length, total root length, root surface area, root volume, and root diameter, distributed on chromosomes 1, 2, 4, 7, 9, 10, and 11 in rice. Four QTL clusters on chromosomes 2, 4, 7, and 10 were found, including a major QTL qLRL4 controlling the longest root length. To fine mapping of the major QTL, we constructed a near isogenic line NIL-qLRL4 with a segment from NPB between markers IND4-1 and IND4-4 with 9311 background. With a F2 population derived from the NIL-qLRL4 and 9311, we fine mapped the qLRL4 within ~68.23 kb region between markers IND4-1 and IND4-3, where eight candidate genes located. Fine mapping of this QTL for root length will help explore genetic mechanism of root elongation and morphogenesis in rice.
Keywords：rice;root trait;the longest root length;qLRL4;fine mapping


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本文引用格式
田彪, 丁仕林, 刘朝雷, 阮班普, 姜洪真, 郭锐, 董国军, 胡光莲, 郭龙彪, 钱前, 高振宇. 水稻苗期根部性状的遗传分析和最长根长QTL qLRL4的精细定位[J]. 作物学报, 2021, 47(10): 1863-1873 DOI:10.3724/SP.J.1006.2021.02088
TIAN Biao, DING Shi-Lin, LIU Chao-Lei, RUAN Ban-Pu, JIANG Hong-Zhen, GUO Rui, DONG Guo-Jun, HU Guang-Lian, GUO Long-Biao, QIAN Qian, GAO Zhen-Yu. Genetic analysis of seedling root traits and fine mapping of the QTL qLRL4 for the longest root length in rice[J]. Acta Agronomica Sinica, 2021, 47(10): 1863-1873 DOI:10.3724/SP.J.1006.2021.02088


水稻是人类最主要的粮食作物之一[1], 而根系作为水稻主要的器官, 具有固定水分、吸收养分、合成与分泌激素、酶和有机酸等功能[2]。虽然根系研究与其他性状相比相对薄弱[3], 但是植物学家对根系相关性状已开展了大量遗传研究。徐吉臣等[4]以窄叶青8号和京系17的F1代花培加倍的127个双单倍体(double haploid, DH)群体为材料, 测定了营养液培养条件下亲本及DH株系的最大根长、根干重和根茎干重比, 检测到4个最大根长QTL, 分别位于第2、4、9、10号染色体; 检测到水稻第2号染色体的1个根干重QTL; 根茎干重比共检测到3个QTL, 分别位于第3、5、6号染色体上。滕胜等[5]和胡兴明等[6]也用相同群体进行了根部性状的QTL分析。前者在抽穗期对根系活力进行QTL分析, 在第4号染色体的分子标记RG449和RG809间检测到1个QTL (qRV4)。后者对水稻苗期发根力进行了QTL和上位性分析, 在水稻第3号染色体的C63~CT125之间检测到1个发根力主效QTL; 同时检测到影响水稻发根力的5对上位性效应基因座, 分别位于第2、3、5、6、7、12号染色体上, 其中影响根长和根数的上位性效应各有2对QTL, 有一对QTL同时影响根长和根数。迄今, 国内外科学家已定位了多个水稻根长相关QTL。Mitsuhiro等[7]用粳稻品种Koshihikari和籼稻品种Kasalath杂交和回交得到的38个染色体片段替代系(CSSL)检测生长在5 μmmol L-1或500 μmmol L-1 NH4+中的水稻幼苗根长QTL, 共检测到8个QTL, 分别位于第1、2、4、6、8、11和12号染色体, 并将6号染色体的根长主效QTL qRL6.1精细定位在长臂337 kb区间内。王汝慈等[8]利用协青早B与中恢9308杂交构建的RIL群体在水稻第4号染色体长臂的分子标记RM307与RM1205之间定位到一QTL簇, 控制不同时期的相对根长、相对根冠比、相对根干质量等性状, 其中包括控制水稻根长的主效QTL——qRL4。Obara等[9]以水稻WAB56-104和NERICA7品系的杂交F2群体为材料, 在高NH4+环境下于水稻第1号染色体检测到2个水稻根长相关QTL, 分别命名为qRL1.3- NERICA7和qRL1.4-NERICA7, 其中qRL1.4- NERICA7的定位区间进一步缩小至0.7 Mb。Kitomi等[10]为了鉴定与水稻最大根长相关的基因组区间, 用来自IR64和KinandangPatong间杂交回交得到的26个CSSL进行QTL分析, 得到2个最大根长QTL: 2号染色体的qRO1和6号染色体的qRO2。将qRO1精细定位在SSR标记RM5651和RM6107之间的1.7 Mb区间, 将qRO2定位在SSR标记RM20495和RM3430-1之间884 kb的区间。到目前为止, 科学家已成功克隆了一些控制水稻根系性状的基因[11,12], 如Srt5[13]和OsSPR1[14]基因调控水稻根长, CRL1[15]基因影响冠状根的发生和不定根的形成, ARL1[16]基因影响不定根的形成, WOX11[17]基因促进冠根的起始和伸长, REL2[18]和OsWRKY74[19]基因影响不定根的的数目和长度, SRT6[20]基因抑制初生根的发育, LRT2[21]基因控制侧根发生。为了深入了解水稻根系性状的遗传基础, 我们以9311和日本晴(Nipponbare, NPB)构建的重组自交系(recombinant inbred lines, RIL)群体为材料, 利用水培技术和数量遗传学手段对水稻根系性状相关QTL进行了分析和鉴定。

1 材料与方法

1.1 试验材料

研究采用籼稻品种9311和粳稻品种NPB杂交获得的148个株系构成的RIL群体。我们选择了qLRL4区域具有NPB基因型的RIL与亲本9311回交, 并在插入缺失(InDel)标记IND4-1和IND4-4之间选择目标QTL区域携带NPB纯合等位基因的近等基因系(near isogenic lines, NIL) NIL-qLRL4。

1.2 试验方法

在黑暗条件下, 水稻种子于37°C去离子水中浸泡2 d, 然后转移至漂浮在去离子水上的网格, 培养3 d。将幼苗培养在正常浓度的Kimura B营养液中(pH 5.4), 每3 d更换一次营养液。然后, 将幼苗转移至30°C温室中培养21 d, 用尺子测量5株幼苗的主根长, 然后用i800扫描仪扫描总根长, 用LA-S根分析系统(万深, 中国杭州)进行分析。用亚甲基蓝比色法(Leagene, 中国北京)测定根系活性(总吸收面积和比表面积), 每3株幼苗为1次重复, 3个重复, 总体进行2次重复实验, 记为重复I (Repeat I)和重复II (Repeat II)。

用均匀分布于水稻12条染色体的166个在9311和NPB之间存在多态的SSR和STS标记构建了RIL群体的遗传连锁图谱。使用MultiQTL软件(www. multiqtl.com)对RIL群体采用最大似然区间映射方法进行QTL分析, 根据每个数据集的排列测试(1000个排列, P=0.05)获得LOD阈值。根据McCouch等[22]的方法命名QTL。利用Microsoft Excel软件分析根部形状的表型值与频数分布, 并绘制相关图表; 利用IBM SPSS Statistics 24软件进行显著性差异检验和相关性分析。

通过近等系NIL-qLRL4与9311的杂交和自交, 构建了用于精细定位的830个植株构成的F2群体, 测量了单株根长表型, 在已定位的qLRL4区间内开发了4个InDel标记(表1)检测单株基因型, 用于qLRL4的精细定位。

Table 1
表1
表1qLRL4精细定位的InDel标记引物
Table 1Primers of InDel markers for fine mapping of qLRL4
分子标记
Marker		正向引物
Forward primer (5′-3′)		反向引物
Reverse primer (5′-3′)
IND4-1TTGGCAGGTAGAGTCCAAAGGTGGCTTAAGAGACGTCCCTAAC
IND4-2TGCCCTGGAAGTATAAGGATGATGTCTGCATACCAGAACAAAAG
IND4-3GCGACCACATAAATACTGTTGAGGTGGGACTATATATTAATGG
IND4-4AGTTGTTATTCATCGCCATCGGTGATATACCCGAGACCAAAAGTAGC

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采用Axygen公司的AxyPrep总RNA小量制备试剂盒(AP-MD-MS-RNA-50)提取9311、NPB和NIL-q LRL4的根部RNA并使用TOYOBO公司的cDNA逆转录试剂盒(fsq-101)反转录得到cDNA后, 用候选基因引物和内参Histone H3引物(表2)在ABI7900HT Real-time PCR仪上对样品的候选基因表达量进行相对定量检测。

Table 2
表2
表2候选基因实时定量PCR引物
Table 2Primers of candidate genes and reference for qRT-PCR
基因
Gene		正向序列
Forward primer (5′-3′)		反向序列
Reverse primer (5′-3′)
LOC_Os04g58870AATCACTTGAGCAAGCTCTTGGATGCAAACATGCACAATGCAG
LOC_Os04g58880AAGAGCTGCGGTCAAAGAGAGACTCACGCAACTCCGTATCTGG
LOC_Os04g58890TCGTCGCCGACAGGGTGAGGTCGGTCCCCTCCTCG
LOC_Os04g58900ACGTATGATTTCCCTGTTGATGTGACCTCATCTTCCTTCCCAGTAAATC
LOC_Os04g58910AGAAATGGAAGCCTGTGAACGACTCATGCTGGCCTCTGCGTC
LOC_Os04g58920AGCTGTGCGTGGTGGCGCCTGCAAGCAGGGCGAGTTCC
LOC_Os04g58940AGGCTCTTCGGCTACCTGCATCAGCTCATCCCCATCACC
LOC_Os04g58960AGCAGATGACCAATGGTGGGTGGTTGCTGGGTGAGCTAGAAC
Histone H3GGTCAACTTGTTGATTCCCCTCTAACCGCAAAATCCAAAGAACG

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2 结果与分析

2.1 9311、NPB及其RIL群体的根系性状

亲本9311和NPB之间的根系形态存在显著差异(表3和图1)。9311的最长根长(the longest root length, LRL)、总根系长(total root length, TRL)、根表面积(root surface area, RSA)、根体积(root volume, RV)和根直径(root diameter, RD)均显著大于NPB。考察9311和NPB构建的RIL群体的最长根长、总根系长、根表面积、根体积和根直径这5个性状, 统计2次重复的平均值, 最长根长为14.8 cm和14.3 cm, 总根系长为296.35 cm和331.61 cm, 根表面积为25.26 cm2和25.62 cm2, 根体积为0.22 cm3和0.26 cm3, 根直径为0.25 mm和0.23 mm。RIL的5个性状与两亲本相比, 最长根长和平均直径均小于两亲本。RIL的平均总根系长、根表面积和根体积介于NPB和9311之间(表4)。在2次重复中, 5个根系性状在RIL群体中均呈连续正态分布(图2), 且大部分呈现出明显的超亲分离, 表明这些性状由多基因控制, 适合进行QTL分析。2次重复之间比较后发现, 重复I和重复II的最长根长、根表面积和根体积的分布范围基本一致。然而, 重复I的总根长和平均直径的变化范围大于重复II。

Table 3
表3
表39311和NPB的根系性状
Table 3Root traits of 9311 and NPB
重复
Repeat		品种
Variety		最长根长
LRL (cm)		总根系长
TRL (cm)		根表面积
RSA (cm2)		根体积
RV (cm3)		根直径
RD (mm)
I931117.3 ± 0.4**331.38 ± 30.07**34.23 ± 3.93**0.36 ± 0.05**0.32 ± 0.01**
NPB15.9 ± 0.8253.08 ± 36.7627.33 ± 1.650.20 ± 0.060.25 ± 0.03
II931117.9 ± 0.5**360.36 ± 31.64**34.46 ± 0.99**0.37 ± 0.01**0.33 ± 0.01**
NPB15.6 ± 0.6277.22 ± 28.4424.44 ± 2.270.21 ± 0.020.26 ± 0.01
NPB: 日本晴; 值表示均值 ± SD; **表示达0.01显著水平差异。LRL: 最长根长; TRL: 总根系长; RSV: 根表面积; RV: 根体积; RD: 根直径。
NPB: Nipponbare; values represent means ± SD; ** indicates significant difference at the 0.01 probability level. LRL: the longest root length; TRL: total root length; RSV: root surface area; RV: root volume; RD: root diameter.

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图1

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图19311和NPB在营养液中培养21 d的根系形态

NPB: 日本晴; 标尺为3 cm。
Fig. 1Root morphology of 9311 and NPB cultured in nutrient solution for 21 days

NPB: Nipponbare; Bar: 3 cm.


Table 4
表4
表4RIL群体的根系性状
Table 4Root traits of RIL population
重复
Repeat		统计参数
Parameter		最长根长
LRL (cm)		总根系长
TRL (cm)		根表面积
RSA (cm2)		根体积
RV (cm3)		根直径
RD (mm)
I均值 Mean14.8296.3525.260.220.25
标准差 SD2.386.907.400.080.04
变幅 Range8.9-24.0132.88-562.929.26-45.120.06-0.450.15-0.34
偏度 Skewness0.500.850.400.31-0.44
峰度 Kurtosis0.900.72-0.09-0.27-0.08
II均值 Mean14.3331.6125.620.260.23
标准差 SD2.957.197.270.080.07
变幅 Range8.9-24.0186.30-481.509.82-45.330.09-0.620.08-0.59
偏度 Skewness0.390.010.390.620.85
峰度 Kurtosis0.240.03-0.081.453.53
LRL: 最长根长; TRL: 总根系长; RSV: 根表面积; RV: 根体积; RD: 根直径。
LRL: the longest root length; TRL: total root length; RSV: root surface area; RV: root volume; RD: root diameter.

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图2

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图2在2次重复中9311和NPB构建的RIL群体5个根系性状的频数分布

NPB: 日本晴; 倒三角指示亲本的平均值; LRL: 最长根长; TRL: 总根系长; RSV: 根表面积; RV: 根体积; RD: 根直径。
Fig. 2Frequency distribution of five root traits in the RIL population from 9311 and NPB in two repetitions

NPB: Nipponbare; the inverted triangle indicates the average value of the parent. LRL: the longest root length; TRL: total root length; RSV: root surface area; RV: root volume; RD: root diameter.


2.2 RIL群体各根系性状间的相关性分析

将RIL群体各根系性状进行相关性分析发现(表5), 在重复I中, 最长根长与总根系长、根表面积、根体积均呈显著正相关, 相关系数为0.359’0.399, 与根直径没有显著相关性。总根系长与根表面积和根体积的相关系数为0.946和0.859, 远大于与最长根长和根直径的0.359和0.408。同样, 根表面积与根体积间具有显著相关性。总的来说, 这5个性状, 最长根长与根直径没有显著的相关性, 其他性状之间都存在显著正相关。而在重复II中, 最长根长与其他4个性状间均无明显相关性, 其他性状相互之间都存在显著正相关。

Table 5
表5
表5RIL群体根系性状间的相关系数
Table 5Correlation coefficients among root traits of RIL population
重复
Repeat		性状
Trait		最长根长
LRL (cm)		总根系长
TRL (cm)		根表面积
RSA (cm2)		根体积
RV (cm3)
I总根系长 TRL0.359**
根表面积 RSA0.399**0.946**
根体积 RV0.365**0.859**0.975**
根直径 RD0.0110.408**0.571**0.671**
II总根系长 TRL0.041
根表面积 RSA0.0300.684**
根体积 RV0.0430.749**0.831**
根直径 RD0.0840.799**0.737**0.914**
** 表示0.01显著水平相关。LRL: 最长根长; TRL: 总根系长; RSV: 根表面积; RV: 根体积; RD: 根直径。
** indicates significant difference at the 0.01 probability level. LRL: the longest root length; TRL: total root length; RSV: root surface area; RV: root volume; RD: root diameter.

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2.3 RIL群体根系性状的QTL分析

利用一些SSR和STS标记引物进行QTL定位(表6), 然后对9311和NPB构建的RIL群体的最长根长、总根系长、根表面积、根体积和根直径这5个性状进行QTL分析(图3和表7)。重复I共检测到15个QTL, 分布在水稻第1、2、4、7、10和11染色体上。控制最长根长的QTL有3个, 分布在第1、4和10号染色体, 变异贡献率幅度为4.8%’10.3%。其中, 贡献率超过5%的位点有2个: qLRL1和qLRL10, 贡献率分别为10.3%和6.3%, 前者效应来自NPB, 后者效应来自9311。我们检测到控制总根系长的QTL 4个, 分布在水稻第1、2、7和11号染色体上, LOD值为2.92’8.47。这些QTL的表型变异贡献率均超过5%, 幅度为7.8%’42.5%。qTRL1的效应来自NPB, 其余3个QTL的效应来自9311。控制根表面积的QTL有3个, 分布于水稻第2、7和11号染色体, 3个QTL的表型变异贡献率均超过5%。控制根体积的QTL有4个, 分布于水稻第2、7、10和11号染色体, 贡献率(除qRV10外)都超过5%。控制根直径的QTL有2个, 分布在水稻第1和4号染色体, 这2个QTL的贡献率均超过5%。qRD1的效应来自9311, qRD4的效应来自NPB。

Table 6
表6
表6QTL定位的SSR和STS标记引物
Table 6SSR and STS primers of markers for QTL mapping
分子标记
Marker		正向引物
Forward primer (5'-3')		反向引物
Reverse primer (5'-3')
M1-2ACAATTTGGAGCAAGAAAGACTTGTCGCAGTACAGTTTTG
M1-4AACATCGAGAATGTGAATCCTGCTGATTCGTATAGCTTTG
M1-16AGAGAGCTGTACCAAAGCTGTACATCATATGCCACCAAAC
分子标记
Marker		正向引物
Forward primer (5'-3')		反向引物
Reverse primer (5'-3')
M1-18CCTAAATGACAAAGTTTGGGTGTTTGGACTTAGAAATCTCG
M1-19TTTCCATGGCTATTGCTAACATCTTGGGGATCATGAATTG
M1-20TGCATTTATGCATCTACTGGTCACTGCATTTGCAAGTTAC
M1-21AAGATGATGAGGTTCATTGGTATACGACGTGGCTGTATCA
M1-22GATGTCACTTTAGCGGTAGCAAAATTTTCTTTCTCGAGGG
M2-10TGCTGCTTCTGTCCAGTGAGGGATCATAACAAGTGCCTCG
M2-13ACAAGGAAATCCAAAGCTGCTTCTTCAAAAATTGACGGT
M2-14GTAGCAGAAACCAATGCTCATTCGCGATAAATATGGACT
M4-10AAAGAAGAAGATGAGTCCCCAGACATATTCCCGTCTGTTG
M4-13AATTGGAGCTAGTAGTTGGCTAGCGAAGTAAACAAGAGCTG
M7-1TATGTCCTTAGCATGGAAGACCCGTTGTTGATCATCTGGTACG
M7-3GTCCATGCATCCATCTCTAGACGGAAGGAATACGTCTGTA
M9-7GATTAATTAAGGAAAAAGTTACACATTTAAGAAACACAGTCCATAACA
M9-10CTCGTTTATTACCTACAGTACCCTACCTCCTTTCTAGACCGATA
M10-4TTTGTACTGTGAGTGCCAAGAACACCCAAACTTGTGAAAC
M10-7AATGGTGCATATTTAATGGGATTGTTTGTTTCCTTGTTGG
M11-2TTGTCAGGAACAACCTTAGCACCGAGCCTAGCAACTTAG
M11-6CGCTTGAAAGGACTCCAGACCCATCTACTCACCAAACGTTCC
M11-9CGGCATGTCATGGACTACGCAGGAAATCTGTAACCAGAGG
M11-11TGAACCCTGCTCTTCTGAGTCAAAGAAGATATGAAGGCACCG
M11-13TGCTTGATCTGTGTTCGTCCTAGCAGCACCAGCATGAAAG

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图3

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图3RIL群体根系性状QTL的遗传图谱位置

每条染色体的左边列出为分子标记。
Fig. 3Map locations of QTLs for root traits in RIL population

Molecular markers for QTLs are listed on the left along each chromosome.


Table 7
表7
表7RIL群体的根系性状QTL
Table 7QTLs for root traits in the RIL population
重复
Repeat		性状
Trait		染色体
Chromosome		QTLLODP值
P-value		分子标记
Marker		遗传位置
Genetic position (cM)		贡献率
PEV (%)		加性效应
Additive effect
I最长根长 LRL1qLRL12.300.01M1-16-M1-19173.3-188.010.3-1.48
4qLRL42.380.01M4-10-M4-13161.1-190.64.81.47
10qLRL102.330.01M10-4-M10-715.2-43.46.31.16
总根系长 TRL1qTRL14.620.01M1-20-M1-22224.4-256.042.5-102.52
2qTRL212.920.01M2-10-M2-13153.9-178.117.064.91
7qTRL75.840.01M7-1-M7-30.0-18.69.147.36
11qTRL118.470.01M11-11-M11-13126.5-136.07.843.95
根表面积 RSA2qRSA24.590.01M2-10-M2-13153.9-178.115.75.67
7qRSA73.600.01M7-2-M7-418.6-62.217.76.03
11qRSA113.190.01M11-9-M11-1392.0-136.07.13.81
根体积 RV2qRV23.490.01M2-10-M2-13153.9-178.111.30.05
7qRV73.270.01M7-2-M7-418.6-62.215.90.06
10qRV102.370.01M10-4-M10-715.2-43.44.60.03
11qRV113.770.01M11-2-M11-624.1-41.29.40.05
根直径 RD1qRD14.380.01M1-2-M1-415.1-49.38.70.02
4qRD44.040.01M4-10-M4-13161.1-190.626.3-0.04
II最长根长 LRL4qLRL42.030.04M4-10-M4-13161.1-190.68.31.99
总根系长 TRL1qTRL113.530.01M1-18-M1-21185.0-254.822.1-53.10
重复
Repeat		性状
Trait		染色体
Chromosome		QTLLODP 值
P-value		分子标记
Marker		遗传位置
Genetic position (cM)		贡献率
PEV (%)		加性效应
Additive effect
7qTRL716.840.01M7-2-M7-418.6-62.218.648.80
9qTRL910.290.01M9-7-M9-1086.2-97.611.7-38.67
11qTRL116.950.01M11-9-M11-1392.0-136.024.756.19
根表面积RSA2qRSA24.610.01M2-10-M2-14153.9-192.015.616.63
7qRSA73.640.01M7-2-M7-418.6-62.217.917.84
11qRSA113.360.01M11-9-M11-1392.0-136.07.411.48
根体积RV10qRV102.000.04M10-4-M10-715.2-43.46.50.03
根直径 RD4qRD43.100.01M4-10-M4-13161.1-190.69.4-0.04
11qRD112.830.01M11-4-M11-729.0-60.28.10.04
LRL: 最长根长; TRL: 总根系长; RSV: 根表面积; RV: 根体积; RD: 根直径。
LRL: the longest root length; TRL: total root length; RSV: root surface area; RV: root volume; RD: root diameter.

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重复II共检测到11个QTL, 分布在第1、2、4、7、9、10和11号染色体上。我们只在4号染色体上发现了一个控制最长根长的QTL, 贡献率为8.3%, 加性效应来自于9311。控制总根长的QTL有4个, 分布在水稻第1、7、9和11号染色体上, LOD值为6.95’16.84。这些QTL的表型变异贡献率均超过5%, 幅度为11.7%’24.7%。qTRL7和qTRL9的效应来自NPB, 其余2个QTL的效应来自9311。控制根表面积的QTL有3个, 分布于水稻第2、7和11号染色体, 3个QTL的表型变异贡献率均超过5%。控制根体积的QTL有1个, 在10号染色体上。控制根直径的QTL有2个, 分布在水稻第4和11号染色体, 这2个QTL的贡献率均超过5%。其中, qRD4的效应来自NPB, qRD11的效应来自9311。

对2个重复进行分析发现, 有5个控制相同性状的QTL在同一位置被重复检测到。包括4号染色体上的qLRL4和qRD4, 7号染色体上的qRSA7, 10号染色体上的qRV10和11号染色体上的qRSA11。qLRL4、qRSA7、qRV10和qRSA11这4个QTL的效应在2个重复中均来自9311, 说明RIL的最长根长、根表面积和根体积的正效应来自9311等位型。qRD4的效应在2个重复中来自NPB, 说明RIL根直径受NPB等位型的正调控。综合2个重复鉴定的QTL来看, 在7条染色体上共分布有4个QTL簇, 分别位于水稻第2、4、7和10号染色体, 只有4号染色体上检测到的最长根长和根直径相关QTL, 在2次重复中定位的染色体相同位置。因此, 我们对QTL qLRL4开展精细定位。

2.4 最长根长QTL qLRL4的精细定位和候选基因确定

位于水稻第4号染色体的QTL qLRL4是控制最长根长的QTL。9311背景下InDel标记IND4-1和IND4-4间约158 kb来自NPB的近等系NIL-qLRL4与9311相比, 最长根长缩短, 根直径略微变大, 总吸收面积和活跃吸收面积减少, 其他性状基本无变化(图4和表8)。利用近等系NIL-qLRL4和9311构建的大规模F2群体, 结合个体的InDel标记基因型和根长表型, 我们进一步精细定位这一最长根长QTL qLRL4, 最终将其定位于标记IND4-1和IND4-3之间约68.23 kb的物理距离内(图5和表1)。依据水稻基因组注释数据库(http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/), 该区间包含了8个候选基因, 其中有7个基因存在引起氨基酸改变的单核苷酸多态(SNP)或InDel (表9)。qRT-PCR检测8个候选基因相对表达量(图6), 在NPB和NIL-qLRL4中, 基因LOC_Os04g58890、LOC_Os04g58920和LOC_ Os04g58940的相对表达量较9311极显著上升; 而基因LOC_ Os04g58870的相对表达量极显著下降。其他4个基因除LOC_Os04g58960的相对表达量在NPB中极显著上升外, LOC_Os04g58880、LOC_ Os04g58900和LOC_Os04g58910的相对表达量在NPB 或NIL-qLRL4中与9311间无显著差异。

图4

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图49311和NIL-qLRL4在营养液中培养21 d的根系形态

标尺为3 cm。
Fig. 4Root morphology of 9311 and NIL-qLRL4 cultured in nutrient solution for 21 days

Bar: 3 cm.


Table 8
表8
表89311和NIL-qLRL4的根系性状和活性
Table 8Root traits and vitality of 9311 and NIL-qLRL4
品种/品系
Variety/Line		最长根长
Longest root length (cm)		总根系长
Total root length (cm)		根表面积
Root surface area (cm2)		根体积
Root volume (cm3)		根直径
Root diameter (mm)		总吸收面积
Total absorbing area (m2)		比表面积
Specific surface area (cm2 cm-3)
931117.3 ± 0.4331.38 ± 30.0734.23 ± 3.930.36 ± 0.050.32 ± 0.010.636 ± 0.0324243.3 ± 210.2
NIL-qLRL414.6 ± 0.1**340.40 ± 19.9134.44 ± 3.150.36 ± 0.040.35 ± 0.020.535 ± 0.023**3566.9 ± 150.3**
**表示达0.01显著水平差异。
** indicates significant difference at the 0.01 probability level.

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图5

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图5qLRL4的精细定位

qLRL4被缩小到标记IND4-1和IND4-3之间的68.23 kb区间内。图例的黑色条块代表9311基因型, 白色条块代表NPB基因型。NPB: 日本晴。最长根长表示为均值±标准差。*和**分别表示0.05和0.01显著水平差异。LRL: 最长根长。
Fig. 5Fine mapping of qLRL4

qLRL4 was narrowed down to a 68.23 kb interval defined by markers IND4-2 and IND4-3. Black box represents 9311 genotype, and white box represents NPB genotype. NPB: Nipponbare. Values represent means ± SD. * and ** indicate significant difference at the 0.05 and 0.01 probability levels compared with NIL-qLRL4, respectively. LRL: the longest root length.


Table 9
表9
表9qLRL4精细定位区间的候选基因和候选基因中引起氨基酸改变的序列变化
Table 9Candidate genes in the interval of fine mapped qLRL4 and sequence variation resulted in amino acid changes
基因 Gene注释 AnnotationSNPINDELNPB9311CDS
LOC_Os04g58870exo70 exocyst complex subunit, putative, expressed40GT487
TC514
AG632
TG1529
LOC_Os04g58880exo70 exocyst complex subunit, putative, expressed10AG1279
LOC_Os04g58890Expressed protein10TG416
LOC_Os04g58900Hydrolase, NUDIX family, domain containing protein, expressed10CT142
LOC_Os04g58910Receptor protein kinase TMK1 precursor, putative, expressed31GT223
AG1630
AG1909
+TCC014
LOC_Os04g58920U-box domain-containing protein, putative, expressed10GT338
LOC_Os04g58940Expressed protein0000
LOC_Os04g58960Regulator of chromosome condensation, putative, expressed30TG1148
CT1116
CT2582
SNP和InDel为引起氨基酸改变的SNP数目和InDel数目。字母为改变的碱基, 数字为CDS上的位点。
SNP and InDel represent the number of SNPs and InDels that cause amino acid changes. The letters are changed bases and the numbers are positions on the CDS.

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图6

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图6候选基因的相对表达量

相对表达量数据为平均数±标准差, n = 3。**表示与9311比较达到0.01的差异显著水平。
Fig. 6Relative expression level of candidate genes

Data represent means ± SD of three biological replicates. ** indicates significant difference at the 0.01 probability level compared with 9311.


3 讨论

在QTL分析中, 同一染色体区间存在多个QTL控制多个根系性状, 这可能是一因多效的作用。姜树坤等[23]以笹锦和北陆129杂交衍生的重组自交系群体为材料, 对水稻移栽后的新生根相关性状进行研究, 共检测到10个QTL, 分别控制根平均直径、总根长、平均根表面积、平均根长和根数等性状。并且对第11号染色体的分子标记C477和G320B之间的新主效QTL——同时控制根长、根表面积和根数的QTL qRL11.1、qRSA11和qRN11.1进行了验证。这些QTL簇体现了QTL的一因多效作用。由于一因多效QTL/基因的存在, 在开展水稻分子育种时, 我们可以考虑选择单个QTL/基因同时改良多个性状。徐晓明等[24]以超级稻协优9308衍生的重组自交系与轮回亲本中恢9308回交多代群体为材料, 采用琼脂无土栽培技术开展了水稻根长主效QTL qRL4的精细定位, 最终将其定位在水稻第4号染色体分子标记RM5687与InDel149之间约624.6 kb的范围内。我们定位的qLRL4是控制最长根长的新QTL, 其位置与报道的qRL4在4号染色体上的位置并不相同, 这可能是所用亲本和群体不同所致。幼苗期根的生长为作物获取水和营养物质提供了保障[25]。近等系NIL-qLRL4在发芽后根的生长受到抑制, 根的总吸收面积和活跃吸收面积相对9311也显著减小(图4和表8)。Raffaele等[26,27]在拟南芥中研究发现, 具有较大根分生组织的突变体往往根较长, 而根分生组织的大小受生长素和细胞分裂素的共同调节。水稻中已克隆了一些与根发育相关的基因, 例如CRL1基因调控不定根的数目[15], REL2基因调控不定根的数目与长短[18], OsCKI1基因调控侧根和不定根的数量[28], SOR1通过根系与乙烯的特异性反应来影响根的生长发育[29]。调控水稻根长的基因也有报道, Rf1a/Rf-1/Rf5基因影响水稻主根长短[30]; Srt5基因通过外源性蔗糖、葡萄糖和果糖的调控影响水稻根系的长短[13]; OsSPR1基因通过影响根细胞的长短与数目影响水稻根系的长短[14]; SRT6基因影响水稻苗期根长与直径的作用可能与ABA的感知或信号传导有关[20]。我们的研究最终将最长根长QTL qLRL4精细定位到约68.23 kb的区间内, 依据基因注释发现该区间包含8个候选基因, 其中有7个基因存在引起氨基酸改变的SNP或InDel, 包括编码水解酶、受体蛋白激酶和染色质结构调节因子的基因。根部转录水平的表达分析显示, 4个候选基因的相对表达量在NIL-qLRL4或NPB与9311之间存在显著差异。因此, 这4个基因作为qLRL4候选基因的可能性更大。当然, 候选基因的最终确定还有待进一步基因克隆和功能验证。

4 结论

利用籼稻9311和粳稻日本晴为亲本的RIL群体对水稻苗期根系相关性状开展QTL分析, 共检测到26个控制最长根长、总根系长、根表面积、根体积和根直径的QTL, 发现水稻第2、4、7和10号染色体上的4个QTL簇, 包括第4号染色体上控制最长根长的QTL qLRL4。精细定位将qLRL4定位于InDel标记IND4-1和IND4-3之间约68.23 kb的区间, 包含了8个候选基因。其中7个基因在亲本间有引起氨基酸改变的SNP或InDel, 4个基因在近等基因系NIL-qLRL4和9311之间的转录水平相对表达量上存在显著差异。此最长根长QTL的精细定位为水稻根系发育相关基因的克隆奠定了基础。

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章怡兰, 林雪, 吴仪, 李梦佳, 张晟婕, 路梅, 饶玉春, 王跃星. 水稻根系遗传育种研究进展
植物学报, 2020, 55:382-393.
DOI [本文引用: 1]
根系作为水稻(Oryza sativa)植株的重要组成部分, 在水稻生长发育过程中发挥多种作用, 包括植物的固定、水分和营养物质的获取以及氨基酸和激素的生物合成等, 其形态结构和生理功能与水稻产量和稻米品质以及抗性等密切相关。目前, 通过遗传及生化等诸多手段, 已挖掘到较多水稻根系QTLs与控制基因。该文综述了水稻根系QTL和基因的研究进展, 并对未来根系研究进行展望, 以期为进一步克隆水稻根系基因和完善水稻理想株型模型提供参考。
Zhang Y L, Lin X, Wu Y, Li M J, Zhang S J, Lu M, Rao Y C, Wang Y X. Research progress on rice root genetics and breeding
Chin Bull Bot, 2020, 55:382-393 (in Chinese with English abstract).
[本文引用: 1]

梁永书, 周军杰, 南文斌, 段东东, 张汉马. 水稻根系研究进展
植物学报, 2016, 51:98-106.
[本文引用: 1]

Liang Y S, Zhou J J, Nan W B, Duan D D, Zhang H M. Research progress of rice root system
Chin Bull Bot, 2016, 51:98-106 (in Chinese with English abstract).
[本文引用: 1]

Yao S G, Mushika J, Taketa S, Ichii M. The short root mutation srt5 defines a sugar-mediated root growth in rice(Oryza sativa L.)
Plant Sci, 2004, 167:49-54.
DOIURL [本文引用: 2]

Jia L, Zhang B, Mao C. OsCYT-INV1 for alkaline/neutral invertase is involved in root cell development and reproductivity in rice (Oryza sativa L.)
Planta, 2008, 228:51-59.
DOIURL [本文引用: 2]

Inukai Y, Sakamoto T, Ueguchitanka M. Crown rootless1, which is essential for crown root formation in rice, is a target of an auxin response factor in auxin signaling
Plant Cell, 2005, 17:1387-1396.
DOIURL [本文引用: 2]

Liu H, Wang S, Yu X, Yu J, He X, Zhang S, Shou H, Wu P. ARL1, a LOB-domain protein required for adventitious root formation in rice
Plant J, 2005, 43:47-56.
DOIURL [本文引用: 1]

Zhao Y, Hu Y F, Dai M G, Huang L M, Zhou D Y. The WUSCHEL-related homeobox gene WOX11 is required to activate shoot-borne crown root development in rice
Plant Cell, 2009, 21:736-748.
DOIPMID [本文引用: 1]
In rice (Oryza sativa), the shoot-borne crown roots are the major root type and are initiated at lower stem nodes as part of normal plant development. However, the regulatory mechanism of crown root development is poorly understood. In this work, we show that a WUSCHEL-related Homeobox (WOX) gene, WOX11, is involved in the activation of crown root emergence and growth. WOX11 was found to be expressed in emerging crown roots and later in cell division regions of the root meristem. The expression could be induced by exogenous auxin or cytokinin. Loss-of-function mutation or downregulation of the gene reduced the number and the growth rate of crown roots, whereas overexpression of the gene induced precocious crown root growth and dramatically increased the root biomass by producing crown roots at the upper stem nodes and the base of florets. The expressions of auxin- and cytokinin-responsive genes were affected in WOX11 overexpression and RNA interference transgenic plants. Further analysis showed that WOX11 directly repressed RR2, a type-A cytokinin-responsive regulator gene that was found to be expressed in crown root primordia. The results suggest that WOX11 may be an integrator of auxin and cytokinin signaling that feeds into RR2 to regulate cell proliferation during crown root development.

Yang S Q, Li W Q, Miao H, Gan P F, Qiao L, Chang Y L, Shi C H, Chen K M. REL2, a gene encoding an unknown function protein which contains DUF630 and DUF632 domains controls leaf rolling in rice
Rice, 2016, 9:1-14.
DOIURL [本文引用: 2]

Dai X Y, Wang Y Y, Zhang W H. OsWRKY74, a WRKY transcription factor, modulates tolerance to phosphate starvation in rice
J Exp Bot, 2016, 67:947-960.
DOIURL [本文引用: 1]

Ao S G, Shin T, Masahiko I. Isolation and characterization of an abscisic acid-insensitive mutation that affects specifically primary root elongation in rice (Oryza sativa L.)
Plant Sci, 2003, 164:971-978.
DOIURL [本文引用: 2]

Jing H W, Yang X L, Zhang J, Liu X H, Zheng H K, Dong G J, Nian J Q, Feng J, Xia B, Qian Q, Li J Y, Zuo J R. Peptidyl-prolyl isomerization targets rice Aux/IAAs for proteasomal degradation during auxin signaling
Nat Commun, 2015, 6:7395.
DOIURL [本文引用: 1]

McCouch S, Cho Y, Yano M, Paul E, Blinstrub M, Morishima H, Kinoshita T. Report on QTL nomenclature
Rice Genet Newsl, 1997, 14:11-131.
[本文引用: 1]

姜树坤, 张凤鸣, 白良明, 孙世臣, 王彤彤, 丁国华, 姜辉, 张喜娟. 水稻移栽后新生根系相关性状的QTL分析
中国水稻科学, 2014, 6:598-604.
[本文引用: 1]

Jiang S K, Zhang F M, Bai L M, Sun S C, Wang T T, Ding G H, Jiang H, Zhang X J. QTL analysis of the related traits of new roots after transplanting rice
Chin J Rice Sci, 2014, 6:598-604 (in Chinese with English abstract).
[本文引用: 1]

徐晓明, 张迎信, 王会民, 任翠, 王汝慈, 沈希宏, 占小登, 吴玮勋, 程式华, 曹立勇. 一个水稻根长QTL qRL4的分离鉴定
中国水稻科学, 2016, 30:363-370.
[本文引用: 1]

Xu X M, Zhang Y X, Wang H M, Ren C, Wang R C, Shen X H, Zhan X D, Wu W X, Cheng S H, Cao L Y. Isolation and identification of a QTL qRL4 of rice root length
Chin J Rice Sci, 2016, 30:363-370 (in Chinese with English abstract).
[本文引用: 1]

Rogers E D, Benfey P N. Regulation of plant root system architecture: implications for crop advancement
Curr Opin Biotechnol, 2015, 32:93-98.
DOIURL [本文引用: 1]

Raffaele D I, Francisco S L, Emanuele S. Cytokinins determine Arabidopsis root-meristem size by controlling cell differentiation
Curr Biol, 2007, 17:678-682.
PMID [本文引用: 1]
Plant postembryonic development takes place in the meristems, where stem cells self-renew and produce daughter cells that differentiate and give rise to different organ structures. For the maintenance of meristems, the rate of differentiation of daughter cells must equal the generation of new cells: How this is achieved is a central question in plant development. In the Arabidopsis root meristem, stem cells surround a small group of organizing cells, the quiescent center. Together they form a stem cell niche [1, 2], whose position and activity depends on the combinatorial action of two sets of genes - PLETHORA1 (PLT1) and PLETHORA2 (PLT2)[3, 4] and SCARECROW (SCR) and SHORTROOT (SHR)[2] - as well as on polar auxin transport. In contrast, the mechanisms controlling meristematic cell differentiation remain unclear. Here, we report that cytokinins control the rate of meristematic cell differentiation and thus determine root-meristem size via a two-component receptor histidine kinase-transcription factor signaling pathway. Analysis of the root meristems of cytokinin mutants, spatial cytokinin depletion, and exogenous cytokinin application indicates that cytokinins act in a restricted region of the root meristem, where they antagonize a non-cell-autonomous cell-division signal, and we provide evidence that this signal is auxin.

Raffaele D I, Kinu N, Laila M. A genetic framework for the control of cell division and differentiation in the root meristem
Science, 2008, 322:1380-1384.
DOIPMID [本文引用: 1]
Plant growth and development are sustained by meristems. Meristem activity is controlled by auxin and cytokinin, two hormones whose interactions in determining a specific developmental output are still poorly understood. By means of a comprehensive genetic and molecular analysis in Arabidopsis, we show that a primary cytokinin-response transcription factor, ARR1, activates the gene SHY2/IAA3 (SHY2), a repressor of auxin signaling that negatively regulates the PIN auxin transport facilitator genes: thereby, cytokinin causes auxin redistribution, prompting cell differentiation. Conversely, auxin mediates degradation of the SHY2 protein, sustaining PIN activities and cell division. Thus, the cell differentiation and division balance necessary for controlling root meristem size and root growth is the result of the interaction between cytokinin and auxin through a simple regulatory circuit converging on the SHY2 gene.

Liu W, Xu Z H, Luo D. Roles of OsCKI1, a rice casein kinase I, in root development and plant hormone sensitivity
Plant J, 2003, 36:189-202.
DOIURL [本文引用: 1]

Chen H, Ma B, Zhou Y, He S J, Tang S Y, Lu X, Xie Q, Chen S Y, Zhang J S. E3 ubiquitin ligase SOR1 regulates ethylene response in rice root by modulating stability of Aux/IAA protein
Proc Natl Acad Sci USA, 2018, 115:4513-4518.
DOIURL [本文引用: 1]

Zhang H G, Zhang L J, Si H, Ge Y S, Liang G H, Gu M H, Tang S Z. Rf5 is able to partially restore fertility to Honglian-type cytoplasmic male sterile japonica rice(Oryza sativa) lines
Mol Breed, 2016, 36:1-10.
DOIURL [本文引用: 1]

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