Scientia Agricultura Sinica ›› 2021, Vol. 54 ›› Issue (12): 2487-2498.doi: 10.3864/j.issn.0578-1752.2021.12.001

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

Gene Mapping and Candidate Gene Analysis of Grain Width Mutant gw87 in Rice

ZHANG XiangYu(),GUO Jia,WANG San,CHEN CongPing,SUN ChangHui,DENG XiaoJian,WANG PingRong()   

  1. Rice Research Institute, Sichuan Agricultural University, Chengdu 611130
  • Received:2020-11-18 Accepted:2021-01-15 Online:2021-06-16 Published:2021-06-24
  • Contact: PingRong WANG E-mail:964670742@qq.com;prwang@sicau.edu.cn

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Abstract:

【Objective】Phenotypic identification, genetic analysis, gene mapping and candidate gene analysis of grain width mutant gw87 (grain width87) were performed in rice, so as to lay a good foundation for further understanding molecular mechanism and utilization potentiality of this gene regulating rice grain size.【Method】Through ethyl methanesulfonate mutagenesis, we isolated gw87 mutant showing significant increase of grain width and 1000-grain weight from indica restorer line material 676R. To identify phenotypic and physiological characteristics of the mutant, we performed observation of phenotypes, investigation of agronomic traits, sensitivity analysis of exogenous brassinolide (BL), determination of chlorophyll contents and photosynthetic parameters by using gw87 and its wild type. To analyze its genetic behavior, we investigated F1 phenotypes and F2 segregation of the crossing combination between gw87 and its wild-type parent 676R. To find candidate gene of gw87, we conducted high-throughput sequencing and MutMap analysis of 30 mutant plants from the F2 population of gw87×676R, and molecular mapping using the F2 population crossing gw87 and japonica cultivar Nipponbare. Meanwhile, we confirmed the candidate gene by sequencing its DNA and cDNA sequences. In addition, we detected expression levels of brassinolide synthesis pathway genes OsDWARF4, D11 and D2 using qRT-PCR analysis.【Result】Compared with the wild-type parent 676R, the gw87 mutant showed significant reduction of productive panicle number per plant, main panicle length and seed setting rate, but significant increase of grain width and 1000-grain weight. Meanwhile, the mutant displayed decreased plant height and shortened internodes, in which the first internode was distorted and its length is shortened the most. Besides, leaf length of gw87 was decreased but the width was increased. Sensitivity assays of exogenous BL suggested that the sensitivity of gw87 seedlings to exogenous BL was reduced. Determination of photosynthetic pigments and photosynthetic parameters showed that chlorophyll content and net photosynthetic rate were decreased. Genetic analysis revealed that the mutant phenotype of gw87 was governed by a single recessive nuclear gene. High-throughput sequencing and MutMap analysis suggested that the gw87 locus was located in the middle of chromosome 5, and only one base mutation causing amino acid change of the encoded protein occurred in this chromosome region. Molecular marker linkage analysis demonstrated that the gw87 gene was mapped to a 101 kb genomic region between InDel markers X2 and X3. The MutMap and molecular mapping revealed that the candidate gene was LOC_Os05g32270 that encodes a transcription factor containing the AP2/EREBP DNA-binding domain. Subsequently, we confirmed the candidate gene by sequencing its DNA and cDNA. In the gw87 mutant, a single nucleotide G-to-A substitution occurred at position 1041 in its DNA sequence, and the 76-bp intron sequence adjacent to this mutated nucleotide was spliced into exon in its cDNA, which caused shift of the reading frame and then premature termination of the protein translation. In addition, qRT-PCR analysis showed that the expression of BR synthetic genes were significantly up-regulated in gw87, indicating that BR signal was weakened in the mutant.【Conclusion】gw87 is a new allelic mutant of smos1, shb, rla1, and ngr5. However, unlike these mutants, gw87 exhibited significant increase of grain width and 1000-grain weight relative to its wild type. The reason for the differentiation could be that different mutation sites in the LOC_Os05g32270 gene, resulting in different functional activities of the encoded protein.

Key words: rice (Oryza sativa L.), grain, 1000-grain weight, brassinosteroid, AP2-type transcription factor

Table 1

The primers for qRT-PCR"

基因 Gene 正向引物 Forward primers (5′-3′) 反向引物 Reverse primers (5′-3′)
OsDWARF4 TCGTCGGCGAGACGTTCG GGTAGCTGCACTCGAACA
D11 TTGGTGAGACGCTGAGGT CACAGGACACTATGGTGGG
D2 GGAATTTATTGTCGGCCTCA CTCGCCATCTTCTTCTTGG
Actin1 CCCCCATGCTATCCTTCGT GGCCGTTGTGGTGAATGACT

Fig. 1

Plant phenotypes of gw87 mutant and its wild type (WT) A, B and D: Plants at seedling stage, tillering stage and grain-filling stage, respectively; C: Leaf angle at grain-filling stage. Bar=5 cm"

Table 2

Comparison of major agronomic traits between gw87 and its wild-type parent 676R"

性状Trait 676R (WT) gw87 比WT增减 Compared with CK (%)
株高 Plant height (cm) 118.0±1.9 80.2±1.7 -32.0**
单株有效穗 No. of productive panicles per plant 5.8±0.4 4.9±0.2 -15.5*
主穗穗长 Length of main panicle (cm) 27.5±1.0 18.6±1.2 -32.4**
主穗一次枝梗数 No. of primary branches per main panicle 14.8±0.5 16.7±1.0 12.8*
主穗二次枝梗数 No. of secondary branches per main panicle 42.5±1.1 30.5±1.0 -28.2**
主穗着粒数 Total No. of grains per main panicle 214.6±2.5 216.8±5.1 1.0
结实率Seed setting rate (%) 83.9±0.4 67.3±2.0 -16.6**
千粒重1000-grain weight (g) 37.4±0.2 41.9±0.2 12.0**

Fig. 2

Panicles, stems and grains of gw87 mutant and its wild type (WT) A: Panicles and internodes of WT (left) and gw87 (right) (P indicates panicle, Ⅰ-Ⅵ indicate the first to the sixth internodes from the top), Bar=5 cm; B: Length of panicles and internode; C and D: Grains of WT and gw87, Bar=1 cm; E and F: Length and width of grains, respectively; * and ** indicate significant difference at P<0.05 and P<0.01, respectively. The same as below"

Fig. 3

Leaf comparison of gw87 mutant and its wild type (WT) A, B and C: Morphology, length and width of the third fully expanding leaf at seeding stage; D, E and F: Morphology, length and width of the flag leaf at heading stage. Bar=3 cm"

Fig. 4

Responses of gw87 mutant and its wild type (WT) to exogenous BL A, B and G: Change of root length under presence or absence of 0.001 μmol·L-1 exogenous BL in the dark; C, D and H: Change of coleoptile length under presence or absence of 1 μmol·L-1 exogenous BL under light; E, F and I: Change of leaf angle under different concentrations of exogenous BL. Bar=1 cm"

Table 3

Pigment contents in leaves of the gw87 mutant and wild-type 676R"

材料 Material 叶绿素a Chl a 叶绿素b Chl b 总叶绿素 Total Chl Chla/Chlb 类胡萝卜素 Caro
676R(WT) 2.18±0.15 0.49±0.04 2.67±0.19 4.38±0.05 0.46±0.04
gw87 2.54±0.15 0.61±0.05 3.16±0.19 4.18±0.12 0.51±0.03
与WT相比Compared to WT (%) 16.5* 24.5* 18.4* -4.6 10.9

Table 4

Determination of leaf photosynthetic parameters of the gw87 mutant and wild-type 676R"

材料
Material		 净光合速率Pn
Net photosynthetic rate (μmol·m-2.s-1)		 蒸腾速率Tr
Transpiration rate (μmol·m-2.s-1)		 气孔导度Gs
Stomatal conductance to water vapor (μmol·m-2.s-1)		 胞间CO2浓度Ci
Intercellular CO2 concentration (μmol·m-2.s-1)
676R(WT) 21.65±2.91 4.52±0.36 0.29±0.04 225.04±29.92
gw87 23.16±2.32 4.84±0.22 0.26±0.02 198.56±26.79
与WT相比Compared with WT (%) 7.0 7.1 -10.3 -11.8

Table 5

Segregation of F2 population from the cross between gw87 mutant and its wild-type parent 676R"

F2组合
Combination		 总株数
Total No. of plants		 正常植株
No. of normal plants		 矮秆宽粒植株
No. of plants with dwarf and wide grain		 理论比
Expected ratio		 χ2
gw87×676R 800 622 178 3﹕1 3.08

Table 6

MutMap results of the gw87 gene, and InDel and SSR makers developed for fine mapping of gw87"

标记名称
SNP and marker name		 物理位置
Physical location (bp)		 SNP指数
SNP Index		 注释基因及碱基突变位点,或分子标记引物序列
Annotated gene and its nucleotide mutation site, or marker primers
SNP01 9834287 0.956 LOC_Os05g17170 downstream, G2464A
SNP02 10490240 0.920 LOC_Os05g18240 downstream, G1713A
SNP03 11888797 0.909 LOC_Os05g20290 upstream, -2662G>A
SNP04 12878107 1 LOC_Os05g22680 downstream,79G>A
SNP05 13399064 0.962 Intergenic_region, LOC_Os05g23430-LOC_Os05g23440,13399064C>T
SNP06 13926842 0.960 LOC_Os05g24140 upstream,-1434C>T
SNP07 13966225 0.958 LOC_Os05g24190 upstream,-3398C>T
SNP08 14365938 0.906 LOC_Os05g24790 upstream,-2425C>T
SNP09 14647328 0.913 LOC_Os05g25240,synonymous,93C>T|p.Cys31Cys
SNP10 14908086 0.960 LOC_Os05g25640 upstream_gene, -3616G>A
X1 18307365 F: TATAGCCAGGATGAGAAG, R: CTGCTGTGGATCATCTTG
X2 18753900 F: GTACCCATCATAGCAAGA, R: AATAGGGTTGGAAGAATG
SNP11 18813290 1 LOC_Os05g32270, splice_donor_variant&intron_variant,1040+1G>A
X3 18854840 F: CTATTTGCTATCGGACAC, R: ATTACTCTTTGGGTTTGG
SNP12 18932427 1 LOC_Os05g32430 downstream,117G>A
X4 18932825 F: CGGCAACAAGAGGAGGAT, R: ACAGCAATGTCCGCAACGGTTTACA
RM163 19251955 F: ATCCATGTGCGCCTTTATGAGGA, R: CGCTACCTCCTTCACTTACTAGT

Fig. 5

Gene mapping and candidate gene analysis of gw87 mutant A: The gw87 locus was mapped to a region between SSR marker RM163 and InDel marker X1 on chromosome 5; B: The locus was narrowed down to a 101-kb genomic region between InDel markers X2 and X3; C: The 101 kb region contains 15 putative genes; D: A single nucleotide G-to-A substitution occurred at position 1041 in candidate gene LOC_Os05g32270 in the gw87 mutant, which was indicated with an arrow. Due to the point mutation, 76 bp of intron sequences were spliced into exons in the cDNA sequence of LOC_Os05g32270 in the mutant. The sequences of extron and intron are shown in upper and lower case, respectively; E: Amplification of LOC_Os05g3227 cDNA containing the specific sequence of 76 bp intron in gw87. M: DL5000 DNA Marker"

Fig. 6

Expression analysis of the genes for BR biosynthesis in gw87 mutant and its wild type (WT) A: The relative transcript levels of OsDWARF4, D11 and D2 in gw87 and its wild type at seedling stage. The transcript level of each gene in wild type was defined as 1, and that in gw87 mutant was calculated accordingly. B: The relative transcript levels of OsDWARF4, D11 and D2 in gw87 and its wild type without or with 100 nmol·L-1 BL treatment for 3 h. Total RNAs were extracted from 0.5 cm of the lamina joints of the first intact leaf"

Fig. 7

Comparison of mutation sites among smos1, shb, rla1, ngr5 and gw87 mutants"

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