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Acta Agronomica Sinica ›› 2021, Vol. 47 ›› Issue (10): 1863-1873.doi: 10.3724/SP.J.1006.2021.02088

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

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 Online:2021-10-12 Published:2021-04-13
  • Contact: GAO Zhen-Yu E-mail:82101186057@caas.cn;gaozhenyu@caas.cn
  • Supported by:
    National Natural Science Foundation of China(32061143039);National Natural Science Foundation of China(31671761)

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

Table 1

Primers 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′)
IND4-1 TTGGCAGGTAGAGTCCAAAGG TGGCTTAAGAGACGTCCCTAAC
IND4-2 TGCCCTGGAAGTATAAGGATG ATGTCTGCATACCAGAACAAAAG
IND4-3 GCGACCACATAAATACTGTTG AGGTGGGACTATATATTAATGG
IND4-4 AGTTGTTATTCATCGCCATCGG TGATATACCCGAGACCAAAAGTAGC

Table 2

Primers 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_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

Table 3

Root 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)
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

Fig. 1

Root morphology of 9311 and NPB cultured in nutrient solution for 21 days NPB: Nipponbare; Bar: 3 cm."

Table 4

Root traits of RIL population"

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

Fig. 2

Frequency 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."

Table 5

Correlation 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 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**

Table 6

SSR 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')
M1-2 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

Fig. 3

Map locations of QTLs for root traits in RIL population Molecular markers for QTLs are listed on the left along each chromosome."

Table 7

QTLs for root traits in the RIL population"

重复
Repeat
性状
Trait
染色体
Chromosome
QTL LOD P
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
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

Fig. 4

Root morphology of 9311 and NIL-qLRL4 cultured in nutrient solution for 21 days Bar: 3 cm."

Table 8

Root 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)
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**

Fig. 5

Fine 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

Candidate genes in the interval of fine mapped qLRL4 and sequence variation resulted in amino acid changes"

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

Fig. 6

Relative 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."

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doi: 10.1007/s11032-015-0425-z
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