Scientia Agricultura Sinica ›› 2023, Vol. 56 ›› Issue (7): 1260-1274.doi: 10.3864/j.issn.0578-1752.2023.07.005

• SPECIAL FOCUS: PANICLE DEVELOPMENT AND YIELD BREEDING IN RICE • Previous Articles     Next Articles

Map-Based Cloning of the SHORT AND WIDEN GRAIN 1 Gene in Rice (Oryza sativa L.)

ZHU HongHui(), LI YingZi(), GAO YuanZhuo, LIN Hong, WANG ChengYang, YAN ZiYi, PENG HanPing, LI TianYe, XIONG Mao, LI YunFeng()   

  1. Rice Research Institute, Southwest University/Academy of Agricultural Sciences, Southwest University/Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops, Chongqing 400716
  • Received:2022-12-08 Accepted:2023-01-16 Online:2023-04-01 Published:2023-04-03

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Abstract:

【Objective】 Rice yield is composed of effective panicle number per unit area, grains per panicle and grain weight, in which grain weight is mainly determined by grain morphology. Screening and identification of new grain type mutation materials and genes can lay a foundation for molecular design breeding of yield traits. 【Method】 A short and wide grain mutant short and widen grain1 (swg1) was identified in the mutant population of indica rice maintainer line Xida1B(XD1B) induced by ethyl methane sulfonate (EMS). The grain morphology and other agronomic characters were analyzed, and the glume was observed and analyzed by histocytology. Gene mapping was carried out by BSA method, and candidate genes were identified by genetic complementarity experiment. qRT-PCR was used to analyze the expression pattern of the gene and the expression level of other genes related to grain shape and cell development.【Result】 The analysis of agronomic characters showed that the grain length of swg1 mutant was significantly lower and the grain width was significantly higher than that of wild type, showing the phenotype of short and wide grains, and further histological and cytological analysis showed that the shortening of longitudinal cells of glume was the main reason for the shortening of grain length, while the increase of grain width was due to the increase of the number and size of transverse cells of glume at the same time. The results of genetic analysis showed that the mutation was controlled by a recessive single gene, and the candidate gene for SWG1 was determined to be LOC_Os07g42410 by map-based cloning and genetic complementary verification, which encoded a plant-specific transcription factor. qRT-PCR analysis showed that the expression of this gene had no obvious tissue specificity, and its expression is strong in stem, leaf and young panicle. According to the analysis of the expression of known genes related to grain shape, cell cycle and cell expansion, it was found that GS5 and GW8, which positively regulate the number and/or size of glume transverse cells to determine grain width, were significantly up-regulated in the mutants, while GW7/GL7 genes, which positively regulated the number and size of longitudinal cells and negatively regulated the number and size of transverse cells, were significantly down-regulated in the mutants. Some genes related to cell cycle and cell expansion also showed significant differences between mutants and wild types. 【Conclusion】 SWG1 encodes a plant-specific transcription factor, which affects glume cell proliferation and cell expansion by regulating grain shape genes GS5, GW8 and GW7/GL7, thus determining rice grain length and width.

Key words: rice (Oryza sativa L.), grain, development of glumes, gene mapping

Table 1

Primer sequences"

引物名称
Primer name		 正向序列
Forward sequence (5′-3′)		 反向序列
Reverse sequences (5′-3′)		 用途
Purpose
RM234 TTCAGCCAAGAACAGAACAGTGG CTTCTCTTCATCCTCCTCCTTGG 定位
Mapping
RM21934 GCAGCAGTGTTGTACTGTTCTTCG GGGAGGGCTTACTCTGTATCAGG
RM21968 GTCATCGACATCCAGCTTCAAGG TCGACTCCATTATCGGATGTGC
RM21979 ACGCCGCGAGATAGTTATCAACC GAGCACGGTGTTGTAGGAGACG
ACTIN TGGCATCTCTCAGCACATTCC TGCACAATGGATGGGTCAGA qRT-PCR
qSWG1 TGCGTGATAGCCTAGAACGAAG CTGGAATCAGCACTCCTGGATG
qOsEXPB2 TCGTCTACACCAACGACTGG CATGAACGGGTACTGGTTGG
qOsEXPB3 TTCTCGTCGATGACCTCCTG AGGGTGGTTGACGCATCTTA
qOsEXPB4 GTCGGTCTGTGTTGCGATTTG CCTCCATTTCCCACACAGCTT
qOsEXPB5 AAGGCTGTGGCTTGATTGACA TTAGGCCCAATTTTGCTATTTTG
qOsEXPB7 ACGGTGATCATCACGGACAT TCGAAGTGGTACAGCGACACT
qOsEXPB10 TGACCAACTACAACGTGGTCCC GCCAGTGTATGTTTTGCCGAAG
qCycA1;1 CTTTCGGTTGACGAGACGATGT CGCTGCAAGGAACCTAGAACTG
qCycA2;1 AATATTGAGCGAAACAGGGACAG AGGAAGCACACATTTGAGGATTT
qCycA3;2 AGGTTGTCAAGATGGAGAGCGA CGCTTTTTGTCTTCCTGGCA
qCycB1;1 CACTCTCAAGCACCACACTGGA ACAACCCTCAGCTTGCTCTCAG
qCycB2;1 CGCTTGCAGCAACCGAGTA CATCCATCAGCTCAAACTTGTGAT
qCycB2;2 CTCAAGGCTGCACAATCTGACA GCATTGACGGCTGGAATTTG
qGS5 CATTCCATGCAAATGCCAGTGGAC CAGCCCTGCTTTGATGAGCTTG
qGW2 CAGCAGCGCATTCCCAGTTTTC GTGGTCAGCCGAGCACTCTC
qGL3.1 TCACAACTCCCAGGATAGG TTTGTCTCGCTCGCTCAT
qGW8 AGGAGTTTGATGAGGCCAAG GCGTGTAGTATGGGCTCTCC
qGL6 TCTGCTTGACATGTGACAGGA GAGGATGTTGGAGAGGTCGC
qGL7 CCCCTAGCATCGACACCAAG CGGGTTCCAGCACTCCTCT
qTGW2 CCCGGAAACTGTCTCATCAC GAACTGAGCCCTCATCTTGG
qTGW6 TTGAACTTGCAAAAGGCAGA CGGTTCCCCTAATGCAGAT
qGS2 ACCACTCTCTTTACCCTGCT CGGGTTCCAGCACTCCTCT
qGS3 CATCGGAGAAGCGAAGTCAT TTGAGGTTGAAGGAGGAGGA

Fig. 1

Phenotypic identification and agronomic traits statistics in the wild type and swg1 mutant A: Comparison of plant types between wild type and mutant at mature stage; B: Comparison of spike type between wild type and mutant at maturity; C: Grain of wild type and mutant; D: Rice of wild type and mutant; E: Panicle length; F: No. of primary branches; G: Grains per panicle; H: No. of secondary branches; I: 1000 grain weight; J: 1000 rice weight; K: Grain length; L: Grain width; M: Grain length-width ratio; N: Rice length; O: Rice width; P: Rice length-width ratio. *: Significant difference at P<0.05; **: Significant difference at P<0.01. The same as below"

Fig. 2

Histocytology analysis of wild-type and swg1 mutant glumes A: The epidermis of wild-type glume under scanning electron microscope, Bar=4 mm; B: The epidermis of lemma of wild type under scanning electron microscope, Bar=400 μm; C: Paraffin section of cross section of wild-type spikelets, Bar=2 mm; D: Partly paraffin section and cell type labeling on the cross section of wild-type spikelets; E: The epidermis of mutant glume under scanning electron microscope, Bar=4 mm; F: The epidermis of lemma of mutant under scanning electron microscope, Bar=400 μm; G: Paraffin section of cross section of mutant spikelets, Bar=2 mm; H: Partly paraffin section and cell type labeling on the cross section of mutant spikelets; I: Statistics of the number of outer epidermal cells in lemma longitudinal direction; J: Statistics of the length of outer epidermal cells in lemma longitudinal direction; K: Statistics of the number of outer epidermal cells in lemma transverse direction; L: Statistics of the width of outer epidermal cells in lemma transverse direction; M: Statistics of the number of inner epidermal cells in lemma transverse direction; N: Statistics of the number of inner epidermal cells in lemma transverse direction; O: Statistics of the number of sclerenchyma cells in lemma transverse direction; P: Statistics of the area of sclerenchyma cells in lemma transverse direction. LE: Lemma; OEP: Outer epidemics; SC: Sclerenchyma cells; PA: Parenchyma cells; IEP: Inner epidermal cells"

Table 2

Genetic analysis of short and widen grain characters in swg1 mutant"

杂交组合
Crossing combination		 正常表型
Normal phenotype		 突变表型
Mutant phenotype		 总和
Summation		 卡方值
（χ20.05=3.84）
56S/swg1 308 95 403 0.438

Fig. 3

Linkage map of SWG1 gene on rice chromosome 7 A: Fine positioning of SWG1; B: 18 open reading frames within the mapping interval; C: Gene structure of SWG1. Ser: Serine; Pro: Proline; Arg: Arginine"

Table 3

Annotated genes in the mapping region"

序号Number 基因名称 Locus name 基因注释 Gene annotation
1 LOC_Os07g42390 含有DUF581结构域的蛋白，表达DUF581 domain containing protein, expressed
2 LOC_Os07g42395 DNA定向RNA聚合酶II亚基RPB9，推测，表达
DNA-directed RNA polymerase II subunit RPB9, putative, expressed
3 LOC_Os07g42400 转座子蛋白，推测，未分类，表达Transposon protein, putative, unclassified, expressed
4 LOC_Os07g42410 转录因子Transcription factor
5 LOC_Os07g42420 3-氧酰基合酶，推测，表达3-oxoacyl-synthase, putative, expressed
6 LOC_Os07g42430 表达蛋白质Expressed protein
7 LOC_Os07g42440 乙醇酸氧化酶Glycolate oxidase
8 LOC_Os07g42450 核糖体蛋白S2，推测，表达Ribosomal protein S2, putative, expressed
9 LOC_Os07g42460 转座子蛋白，推测，未分类，表达Transposon protein, putative, unclassified, expressed
10 LOC_Os07g42470 表达蛋白质Expressed protein
11 LOC_Os07g42490 水稻蔗糖合酶Sucrose synthase in rice
12 LOC_Os07g42500 FYVE锌指结构域蛋白，表达FYVE zinc finger domain containing protein, expressed
13 LOC_Os07g42510 含有AP2结构域的蛋白，表达AP2 domain containing protein, expressed
14 LOC_Os07g42520 客观的，推测，表达Dirigent, putative, expressed
15 LOC_Os07g42530 转座子蛋白，推测，未分类，表达Transposon protein, putative, unclassified, expressed
16 LOC_Os07g42540 转座子蛋白，推测，Pong亚类Transposon protein, putative, Pong sub-class
17 LOC_Os07g42550 表达蛋白质Expressed protein
18 LOC_Os07g42560 表达蛋白质Expressed protein

Fig. 4

Results of complementary vector construction and genetic transformation experiment A: Schematic representation of the vector pCAMBIA1300-SWG1; B: Electropherograms of positive results of seven transgenic plants; C: Sequencing peak of the F2-R2 fragment; D-F: Spike types of wild-type, mutant and complementary plants, Bar=1 cm; G: Ten grain length of wild-type, mutant and complementary plants; H: Ten grain width of wild-type, mutant and complementary plants"

Fig. 5

Expression of SWG1 gene by qRT-PCR in wild type"

Fig. 6

qRT-PCR expression of genes related to grain shape and cell development in wild-type and swg1 mutant A: Transcriptional levels in wild type and mutant of grain type-related genes; B: Transcriptional levels in wild type and mutant of cell cycle-related genes; C: Transcriptional levels in wild type and mutant of cell expansion-related genes"

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