Scientia Agricultura Sinica ›› 2020, Vol. 53 ›› Issue (2): 225-238.doi: 10.3864/j.issn.0578-1752.2020.02.001

• Crop Genetics & Breeding·Germplasm Resources·Molecular Genetics • Previous Articles     Next Articles

QTL Mapping for Grain Size Related Traits Based on a High-Density Map in Rice

ZHANG Jian,YANG Jing,WANG Hao,LI DongXiu,YANG GuiLi,HUANG CuiHong,ZHOU DanHua,GUO Tao,CHEN ZhiQiang,WANG Hui()   

  1. South China Agricultural University/National Engineering Research Center of Plant Space Breeding, Guangzhou 510642
  • Received:2019-05-29 Accepted:2019-07-19 Online:2020-01-16 Published:2020-02-17
  • Contact: Hui WANG E-mail:wanghui@scau.edu.cn

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Abstract:

【Objective】Combine QTL mapping for grain size and related traits and screening for candidate genes to lay a good foundation for dissecting genes regulating rice grain size and related traits.【Method】A dwarf mutant CHA-1 screened from the progeny of the indica rice variety Tehuazhan carried by high altitude balloon was hybridized with another mutant H335 selected from the progeny of the indica rice variety Hanghui 7 induced by “Shenzhou 8” spaceflight. A population of 275 recombinant inbred lines (RILs) was structured from CHA-1 ×H335. A high-density genetic map was constructed using genotyping by sequencing (GBS) technology. The RIL population and parents were grown in the experimental base of South China Agricultural University consecutively in the early and late season in 2017. After ripening, rice grain images were scanned, and the grain size and related traits was obtained by SmartGrain software. QTL mapping for rice grain size and related traits was done with QTL IciMapping v 4.0 software based on inclusive composite interval mapping (ICIM).【Result】The constructed high-density genetic map contains 2498 Bin markers ,and all the markers covers 2371.84 cM with an average genetic distance of 0.95 cM/marker. A total of 26 grain-size related QTLs were repeatedly detected on Chr.1, Chr.2, Chr.3, Chr.4, Chr.7 and Chr.9 in the two seasons with single QTL contribution rate ranged from 0.16% to 14.41%. Five QTL clusters (qGS1, qGS2, qGS3-1, qGS3-2, qGS7) were detected on Chr.1, Chr.2, Chr.3, and Chr.7. Among them, qGS1, qGS3-2, and qGS7 have been previously reported. qGS2 and qGS3-1 were novel grain-size related QTLs. qGS2 was repeatedly detected in the same marker interval in the two seasons, and its LOD values in the early and late season were 8.08 and 4.00 with the phenotypic contribution rate 11.38% and 6.67%, respectively. qGS3-1 was detected to be correlated with grain thickness in the two seasons, and its LOD values in the early and late season were 2.94 and 8.59 with the phenotypic contribution rates 4.69% and 14.41%, respectively. Combined with functional annotation and CREP database of gene expression profiles, four candidate grain-size related genes including LOC_Os02g42310, LOC_Os02g42314, LOC_Os02g42370 and LOC_Os02g42380 were screened out in the qGS2 locus. LOC_Os02g42310 encodes a serine carboxypeptidase homologue; LOC_Os02g42314 encodes a ubiquitin-conjugating enzyme; LOC_Os02g42370 encodes a protein kinase domain containing protein; LOC_Os02g42380 encodes a TCP domain containing protein. Three candidate grain-size related genes including LOC_Os03g39020, LOC_Os03g39150 and LOC_Os03g39230 were screened out in the qGS3-1 locus. LOC_Os03g39020 encodes a kinesin motor domain containing protein; LOC_Os03g39150 encodes a protein kinase domain containing protein; LOC_Os03g39230 encodes an OTU-like cysteine protease family protein. Among the genes, LOC_Os02g42314 and LOC_Os03g39020 were highly expressed in the young panicle and endosperm after pollination and recognized as the most possible candidate genes for regulating grain size.【Conclusion】 26 rice grain-size related QTLs were detected. Five QTL clusters (qGS1, qGS2, qGS3-1, qGS3-2, qGS7) were detected on Chr1, Chr.2, Chr.3, and Chr.7, and qGS2 and qGS3-1 were novel QTLs for regulating grain size, and two candidate genes were screened out in this locus.

Key words: rice, RIL population, high-density genetic map, grain size, grain shape, QTL mapping, candidate gene

Table 1

Performance of grain size traits in CHA-1/H335 RIL population and parents under two seasons"

性状
Trait		 季节
Season		 亲本Parents
重组自交系RIL
CHA-1 H335 均值+标准差
Mean±SD		 变幅
Range		 变异系数
CV (%)		 峰度
Kurtosis		 偏度
Skewness
粒长
GL(mm)		 2017E 8.59 9.15* 9.33±0.44 7.41—10.47 4.71 1.13 -0.27
2017L 8.83 9.71* 9.89±0.61 7.54—12.08 6.13 3.13 0.33
粒宽
GW(mm)		 2017E 1.92 2.27** 2.46±0.12 2.11—3.04 4.88 1.57 0.31
2017L 2.14 2.47** 2.50±0.16 2.12—3.27 6.34 2.55 0.84
粒厚
GT(mm)		 2017E 1.74 1.92** 1.88±0.05 1.74—2.02 3.17 0.12 -0.15
2017L 1.68 1.89** 1.89±0.06 1.71—2.07 3.42 -0.05 -0.16
长宽比
GLWR		 2017E 4.4 4.03** 3.82±0.25 2.68—4.55 6.54 3.49 -0.82
2017L 4.13 3.94** 3.99±0.27 2.33—4.85 6.89 6.93 -1.53
籽粒圆度
CS		 2017E 0.43 0.46* 0.48±0.03 0.41—0.62 6.25 5.94 1.32
2017L 0.44 0.46* 0.46±0.03 0.38—0.65 5.99 12.46 2.42
籽粒周长
PL(mm)		 2017E 19.58 20.86** 21.50±0.96 17.72—23.83 4.47 0.52 -0.09
2017L 20.35 22.58** 22.84±1.33 18.18—27.83 5.81 2.75 0.53
籽粒截面积
AS(mm2)		 2017E 13.59 16.04** 17.79±1.28 14.30—21.09 7.19 -0.01 0.08
2017L 14.64 18.75** 19.11±1.96 14.70—28.93 10.25 5.17 1.45
千粒重
TGW(g)		 2017E 15.29 22.25** 21.87±1.96 15.50—32.00 8.95 2.78 0.41
2017L 16.02 24.13** 23.02±2.24 14.86—28.50 9.73 0.46 -0.12

Fig. 1

CHA-1/H335 parents and RILs grain size differences a: Grain size differences between CHA-1 and H335; b: Grain size differences between RILs"

Fig. 2

Distribution of grain size traits for CHA-1/H335 RIL population and parents E: Early season; L: Late season"

Table 2

Correlationship analysis on grain size traits in CHA-1/H335 recombinant inbred lines"

性状
Traits		 粒长
GL		 粒宽
GW		 粒厚
GT		 谷粒截面积
AS		 谷粒周长
PL		 长宽比
GLWR		 谷粒圆度
CS		 千粒重
TGW
粒长GL 0.293** 0.291** 0.825* * 0.991** 0.577** -0.586** 0.448**
粒宽GW 0.062 0.555** 0.724** 0.385** -0.598** 0.555** 0.488**
粒厚GT 0.256** 0.368** 0.475** 0.339** -0.237** 0.193** 0.749**
谷粒截面积AS 0.739** 0.686 ** 0.428** 0.875** 0.045 -0.043 0.559**
谷粒周长PL 0.987** 0.188** 0.295** 0.819 ** 0.490** -0.510** 0.490**
长宽比GLWR 0.651** -0.709** -0.107 -0.01 0.548 ** -0.967** -0.059
谷粒圆度CS -0.674** 0.656 ** 0.087 -0.02 -0.583** -0.974** 0.012
千粒重TGW 0.498** 0.377 ** 0.666** 0.616 ** 0.536 ** 0.043 -0.063

Table 3

Description on basic characteristics of linkage map"

连锁群编号
Linkage group ID		 总标记数
Total marker		 总图距
Total distance (cM)		 平均图距
Average distance (cM)		 最大Gap
Max gap (cM)		 Gap ＜5 cM
(%)
Chr.1 251 219.89 0.88 2.85 100.00
Chr.2 316 196.26 0.62 6.69 99.37
Chr.3 313 217.40 0.70 5.54 99.68
Chr.4 309 207.84 0.67 11.89 99.68
Chr.5 138 238.62 1.74 6.83 99.27
Chr.6 212 202.72 0.96 10.02 99.05
Chr.7 156 171.16 1.10 5.17 99.35
Chr.8 141 111.26 0.79 5.77 99.29
Chr.9 192 181.65 0.95 4.07 100.00
Chr.10 185 326.27 1.77 25.61 98.37
Chr.11 140 89.95 0.65 1.82 100.00
Chr.12 145 208.82 1.45 3.24 100.00
总计Total 2498 2371.84 0.95 25.61 99.51

Table 4

QTLs for grain size-related traits of recombinant inbred lines under two seasons"

性状
Trait		 季别
Season		 QTL 染色体
Chr.		 位置
Position (cM)		 标记区间
Marker interval		 LOD
 贡献率
PVE (%)		 加性效应
Add.
粒长 GL 2017E qGL1 1 81 Block391— Block433 2.70 4.13 0.89
qGL2-1 2 112 Block3789— Block3802 6.57 10.37 1.38
2017L qGL2-2 2 135 Block3934—Block3940 96.99 11.07 10.47
qGL2-3 2 139 Block3954— Block3957 86.71 8.87 -9.38
qGL9 9 151 Block15927— Block15938 3.45 0.16 -1.26
粒宽 GW 2017E qGW3-2 3 204 Block6009—Block6012 3.92 6.50 0.32
2017L qGW3-1 3 36 Block5332— Block5419 2.94 5.29 0.35
谷粒截面积 AS 2017E qAS2-2 2 112 Block3789— Block3802 6.57 11.36 40.48
qAS3 3 34 Block5273— Block5280 2.86 4.87 26.75
2017L qAS2-1 2 111 Block3794— Block3802 4.00 7.08 47.52
谷粒周长 PL 2017E qPL1 1 81 Block391—Block433 3.33 4.50 2.08
qPL2-2 2 112 Block3789— Block3802 8.08 11.38 3.27
2017L qPL2-1 2 111 Block3794— Block3802 4.07 6.67 3.30
qPL9 9 137 Block15834— Block15856 3.22 5.25 -2.93
长宽比 GLWR 2017E qGLWR3 3 203 Block6004— Block6012 2.53 4.22 -0.05
2017L qGLWR7 7 164 Block12538— Block12681 2.85 4.81 0.06
谷粒圆度 CS 2017L qCS7 7 164 Block12538—Block12681 2.69 4.58 -0.01
粒厚 GT 2017E qGT3-1 3 37 Block5421- Block5424 3.06 4.69 0.01
qGT3-2 3 216 Block6268— Block6282 4.68 7.27 0.01
qGT4-2 4 135 Block7726— Block7769 3.16 4.88 0.01
qGT7 7 166 Block12689— Block12716 4.16 6.42 -0.01
2017L qGT3-1 3 37 Block5421— Block5424 8.59 14.41 0.02
qGT4-1 4 13 Block6302—Block6677 3.23 5.21 0.01
千粒重 TGW 2017E qTGW2-2 2 133 Block3892— Block3931 4.35 6.75 0.50
2017L qTGW2-1 2 128 Block3805— Block3823 5.72 9.92 0.62
qTGW4 4 33 Block6738— Block6765 2.73 4.62 0.42

Fig. 3

Distribution of detected QTLs related to grain size traits on high-density genetic map GL: Grain length; GW: Grain width; GT: Grain thickness; GLWR: Length-to-width ratio of grain; CS: Circularity; AS: Area size of grain; PL: Perimeter length of grain; TGW: 1000-grain-weight; E: Early season; L: Late season"

Table 5

QTL clusters associated with grain size traits detected in this study"

QTL簇
QTL cluster		 染色体
Chr.		 标记区间
Marker interval		 物理区间
Physical interval (bp)		 相关性状
Involved trait		 LOD 贡献率
PVE (%)		 报道QTL
QTL reported
qGS1 1 Block391—Block433 9107381—10916140 GL、PL 2.70—3.33 4.13—4.50 YGL8[28]
qGS2 2 Block3789—Block3802 25385152—25530071 GL、AS、PL 4.00—8.08 6.67—11.38
qGS3-1 3 Block5421—Bloc5424 21695710—21786126 GW、GT 2.94—8.59 4.69—14.41
qGS3-2 3 Block6004—Block6012 31084034—31304364 GW、GLWR 2.53—3.92 4.22—6.50 qST3[29]
qGS7 7 Block12538—Block12716 24107455—28343282 GT、GLWR、CS 2.69—4.16 4.58—6.42 GL7; GW7[4]

Fig. 4

Annotation and expression profiling of genes in qGS2 and qGS3-1 locus The expression level of each sample is printed as deep blue representing the lowest value to deep red representing the highest value in the heat map. The gene names are followed closely by their annotation information"

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