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作物学报 ›› 2021, Vol. 47 ›› Issue (10): 1863-1873.doi: 10.3724/SP.J.1006.2021.02088

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

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

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*()   

  1. 中国水稻研究所, 浙江杭州 310006
  • 收稿日期:2020-12-13 接受日期:2021-03-19 出版日期:2021-10-12 网络出版日期:2021-04-13
  • 通讯作者: 高振宇
  • 作者简介:E-mail: 82101186057@caas.cn, Tel: 0571-63370483
  • 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)

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*()   

  1. China National Rice Research Institute, Hangzhou 310006, Zhejiang, China
  • Received:2020-12-13 Accepted:2021-03-19 Published:2021-10-12 Published online:2021-04-13
  • Contact: GAO Zhen-Yu
  • Supported by:
    National Natural Science Foundation of China(32061143039);National Natural Science Foundation of China(31671761)

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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.

Key words: rice, root trait, the longest root length, qLRL4, fine mapping

表1

qLRL4精细定位的InDel标记引物"

分子标记
Marker		 正向引物
Forward primer (5′-3′)		 反向引物
Reverse primer (5′-3′)
IND4-1 TTGGCAGGTAGAGTCCAAAGG TGGCTTAAGAGACGTCCCTAAC
IND4-2 TGCCCTGGAAGTATAAGGATG ATGTCTGCATACCAGAACAAAAG
IND4-3 GCGACCACATAAATACTGTTG AGGTGGGACTATATATTAATGG
IND4-4 AGTTGTTATTCATCGCCATCGG TGATATACCCGAGACCAAAAGTAGC

表2

候选基因实时定量PCR引物"

基因
Gene		 正向序列
Forward primer (5′-3′)		 反向序列
Reverse primer (5′-3′)
LOC_Os04g58870 AATCACTTGAGCAAGCTCTTGG ATGCAAACATGCACAATGCAG
LOC_Os04g58880 AAGAGCTGCGGTCAAAGAGAG ACTCACGCAACTCCGTATCTGG
LOC_Os04g58890 TCGTCGCCGACAGGGTG AGGTCGGTCCCCTCCTCG
LOC_Os04g58900 ACGTATGATTTCCCTGTTGATGTG ACCTCATCTTCCTTCCCAGTAAATC
LOC_Os04g58910 AGAAATGGAAGCCTGTGAACGAC TCATGCTGGCCTCTGCGTC
LOC_Os04g58920 AGCTGTGCGTGGTGGCGC CTGCAAGCAGGGCGAGTTCC
LOC_Os04g58940 AGGCTCTTCGGCTACCTGC ATCAGCTCATCCCCATCACC
LOC_Os04g58960 AGCAGATGACCAATGGTGGG TGGTTGCTGGGTGAGCTAGAAC
Histone H3 GGTCAACTTGTTGATTCCCCTCT AACCGCAAAATCCAAAGAACG

表3

9311和NPB的根系性状"

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)
I 9311 17.3 ± 0.4** 331.38 ± 30.07** 34.23 ± 3.93** 0.36 ± 0.05** 0.32 ± 0.01**
NPB 15.9 ± 0.8 253.08 ± 36.76 27.33 ± 1.65 0.20 ± 0.06 0.25 ± 0.03
II 9311 17.9 ± 0.5** 360.36 ± 31.64** 34.46 ± 0.99** 0.37 ± 0.01** 0.33 ± 0.01**
NPB 15.6 ± 0.6 277.22 ± 28.44 24.44 ± 2.27 0.21 ± 0.02 0.26 ± 0.01

图1

9311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。"

表4

RIL群体的根系性状"

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.

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 Mean 14.8 296.35 25.26 0.22 0.25
标准差 SD 2.3 86.90 7.40 0.08 0.04
变幅 Range 8.9-24.0 132.88-562.92 9.26-45.12 0.06-0.45 0.15-0.34
偏度 Skewness 0.50 0.85 0.40 0.31 -0.44
峰度 Kurtosis 0.90 0.72 -0.09 -0.27 -0.08
II 均值 Mean 14.3 331.61 25.62 0.26 0.23
标准差 SD 2.9 57.19 7.27 0.08 0.07
变幅 Range 8.9-24.0 186.30-481.50 9.82-45.33 0.09-0.62 0.08-0.59
偏度 Skewness 0.39 0.01 0.39 0.62 0.85
峰度 Kurtosis 0.24 0.03 -0.08 1.45 3.53

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。"

表5

RIL群体根系性状间的相关系数"

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 TRL 0.359**
根表面积 RSA 0.399** 0.946**
根体积 RV 0.365** 0.859** 0.975**
根直径 RD 0.011 0.408** 0.571** 0.671**
II 总根系长 TRL 0.041
根表面积 RSA 0.030 0.684**
根体积 RV 0.043 0.749** 0.831**
根直径 RD 0.084 0.799** 0.737** 0.914**

表6

QTL定位的SSR和STS标记引物"

分子标记
Marker		 正向引物
Forward primer (5'-3')		 反向引物
Reverse primer (5'-3')
M1-2 ACAATTTGGAGCAAGAAAGA CTTGTCGCAGTACAGTTTTG
M1-4 AACATCGAGAATGTGAATCC TGCTGATTCGTATAGCTTTG
M1-16 AGAGAGCTGTACCAAAGCTG TACATCATATGCCACCAAAC
分子标记
Marker		 正向引物
Forward primer (5'-3')		 反向引物
Reverse primer (5'-3')
M1-18 CCTAAATGACAAAGTTTGGG TGTTTGGACTTAGAAATCTCG
M1-19 TTTCCATGGCTATTGCTAAC ATCTTGGGGATCATGAATTG
M1-20 TGCATTTATGCATCTACTGG TCACTGCATTTGCAAGTTAC
M1-21 AAGATGATGAGGTTCATTGG TATACGACGTGGCTGTATCA
M1-22 GATGTCACTTTAGCGGTAGC AAAATTTTCTTTCTCGAGGG
M2-10 TGCTGCTTCTGTCCAGTGAG GGATCATAACAAGTGCCTCG
M2-13 ACAAGGAAATCCAAAGCTG CTTCTTCAAAAATTGACGGT
M2-14 GTAGCAGAAACCAATGCTC ATTCGCGATAAATATGGACT
M4-10 AAAGAAGAAGATGAGTCCCC AGACATATTCCCGTCTGTTG
M4-13 AATTGGAGCTAGTAGTTGGCT AGCGAAGTAAACAAGAGCTG
M7-1 TATGTCCTTAGCATGGAAGACC CGTTGTTGATCATCTGGTACG
M7-3 GTCCATGCATCCATCTCTAG ACGGAAGGAATACGTCTGTA
M9-7 GATTAATTAAGGAAAAAGTTACACA TTTAAGAAACACAGTCCATAACA
M9-10 CTCGTTTATTACCTACAGTACC CTACCTCCTTTCTAGACCGATA
M10-4 TTTGTACTGTGAGTGCCAAG AACACCCAAACTTGTGAAAC
M10-7 AATGGTGCATATTTAATGGG ATTGTTTGTTTCCTTGTTGG
M11-2 TTGTCAGGAACAACCTTAGC ACCGAGCCTAGCAACTTAG
M11-6 CGCTTGAAAGGACTCCAGAC CCATCTACTCACCAAACGTTCC
M11-9 CGGCATGTCATGGACTACG CAGGAAATCTGTAACCAGAGG
M11-11 TGAACCCTGCTCTTCTGAGTC AAAGAAGATATGAAGGCACCG
M11-13 TGCTTGATCTGTGTTCGTCC TAGCAGCACCAGCATGAAAG

图3

RIL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。"

表7

RIL群体的根系性状QTL"

重复
Repeat		 性状
Trait		 染色体
Chromosome		 QTL LOD P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 LRL 1 qLRL1 2.30 0.01 M1-16-M1-19 173.3-188.0 10.3 -1.48
4 qLRL4 2.38 0.01 M4-10-M4-13 161.1-190.6 4.8 1.47
10 qLRL10 2.33 0.01 M10-4-M10-7 15.2-43.4 6.3 1.16
总根系长 TRL 1 qTRL1 4.62 0.01 M1-20-M1-22 224.4-256.0 42.5 -102.52
2 qTRL2 12.92 0.01 M2-10-M2-13 153.9-178.1 17.0 64.91
7 qTRL7 5.84 0.01 M7-1-M7-3 0.0-18.6 9.1 47.36
11 qTRL11 8.47 0.01 M11-11-M11-13 126.5-136.0 7.8 43.95
根表面积 RSA 2 qRSA2 4.59 0.01 M2-10-M2-13 153.9-178.1 15.7 5.67
7 qRSA7 3.60 0.01 M7-2-M7-4 18.6-62.2 17.7 6.03
11 qRSA11 3.19 0.01 M11-9-M11-13 92.0-136.0 7.1 3.81
根体积 RV 2 qRV2 3.49 0.01 M2-10-M2-13 153.9-178.1 11.3 0.05
7 qRV7 3.27 0.01 M7-2-M7-4 18.6-62.2 15.9 0.06
10 qRV10 2.37 0.01 M10-4-M10-7 15.2-43.4 4.6 0.03
11 qRV11 3.77 0.01 M11-2-M11-6 24.1-41.2 9.4 0.05
根直径 RD 1 qRD1 4.38 0.01 M1-2-M1-4 15.1-49.3 8.7 0.02
4 qRD4 4.04 0.01 M4-10-M4-13 161.1-190.6 26.3 -0.04
II 最长根长 LRL 4 qLRL4 2.03 0.04 M4-10-M4-13 161.1-190.6 8.3 1.99
总根系长 TRL 1 qTRL1 13.53 0.01 M1-18-M1-21 185.0-254.8 22.1 -53.10
重复
Repeat		 性状
Trait		 染色体
Chromosome		 QTL LOD P 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
7 qTRL7 16.84 0.01 M7-2-M7-4 18.6-62.2 18.6 48.80
9 qTRL9 10.29 0.01 M9-7-M9-10 86.2-97.6 11.7 -38.67
11 qTRL11 6.95 0.01 M11-9-M11-13 92.0-136.0 24.7 56.19
根表面积RSA 2 qRSA2 4.61 0.01 M2-10-M2-14 153.9-192.0 15.6 16.63
7 qRSA7 3.64 0.01 M7-2-M7-4 18.6-62.2 17.9 17.84
11 qRSA11 3.36 0.01 M11-9-M11-13 92.0-136.0 7.4 11.48
根体积RV 10 qRV10 2.00 0.04 M10-4-M10-7 15.2-43.4 6.5 0.03
根直径 RD 4 qRD4 3.10 0.01 M4-10-M4-13 161.1-190.6 9.4 -0.04
11 qRD11 2.83 0.01 M11-4-M11-7 29.0-60.2 8.1 0.04

图4

9311和NIL-qLRL4在营养液中培养21 d的根系形态 标尺为3 cm。"

表8

9311和NIL-qLRL4的根系性状和活性"

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)
9311 17.3 ± 0.4 331.38 ± 30.07 34.23 ± 3.93 0.36 ± 0.05 0.32 ± 0.01 0.636 ± 0.032 4243.3 ± 210.2
NIL-qLRL4 14.6 ± 0.1** 340.40 ± 19.91 34.44 ± 3.15 0.36 ± 0.04 0.35 ± 0.02 0.535 ± 0.023** 3566.9 ± 150.3**

图5

qLRL4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。"

表9

qLRL4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"

基因 Gene 注释 Annotation SNP INDEL NPB 9311 CDS
LOC_Os04g58870 exo70 exocyst complex subunit, putative, expressed 4 0 G T 487
T C 514
A G 632
T G 1529
LOC_Os04g58880 exo70 exocyst complex subunit, putative, expressed 1 0 A G 1279
LOC_Os04g58890 Expressed protein 1 0 T G 416
LOC_Os04g58900 Hydrolase, NUDIX family, domain containing protein, expressed 1 0 C T 142
LOC_Os04g58910 Receptor protein kinase TMK1 precursor, putative, expressed 3 1 G T 223
A G 1630
A G 1909
+TCC 0 14
LOC_Os04g58920 U-box domain-containing protein, putative, expressed 1 0 G T 338
LOC_Os04g58940 Expressed protein 0 0 0 0
LOC_Os04g58960 Regulator of chromosome condensation, putative, expressed 3 0 T G 1148
C T 1116
C T 2582

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。"

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