植物学报 ›› 2021, Vol. 56 ›› Issue (5): 520-532.DOI: 10.11983/CBB21119
收稿日期:
2021-07-21
接受日期:
2021-09-16
出版日期:
2021-09-01
发布日期:
2021-09-16
通讯作者:
李学勇
作者简介:
* E-mail: lixueyong@caas.cn基金资助:
Jiangyuan Shang, Yan Chun, Xueyong Li*()
Received:
2021-07-21
Accepted:
2021-09-16
Online:
2021-09-01
Published:
2021-09-16
Contact:
Xueyong Li
摘要: 穗型是决定水稻(Oryza sativa)产量的关键因素之一。我们从粳稻品种圣稻808 (SD808)的EMS诱变突变体库中发现4份短穗突变体, 这些突变体的穗长、一级枝梗数、二级枝梗数和穗粒数发生不同程度的降低。基因定位和图位克隆表明, 这些突变体的表型受同一基因控制, 将该基因命名为PAL3 (PANICLE LENGTH3)。PAL3编码一个含12个跨膜结构域的多肽转运蛋白。pal3-1和pal3-2的点突变造成保守区域的氨基酸发生非同义突变; pal3-3的点突变造成第1外显子和内含子拼接错误; pal3-4的点突变造成蛋白翻译提前终止, 导致第12个跨膜域缺失。对PAL3进行单倍型分析, 共鉴定出9个单倍型(Hap1-Hap9), 其中Hap1-Hap3为主要单倍型。Hap1以粳稻为主, Hap2同时包含籼稻和粳稻, Hap3则以籼稻为主。Hap1起源于普通野生稻(O. rufipogon), Hap2和Hap3可能起源于一年生普通野生稻(O. nivara)。统计分析结果表明, Hap3的穗长显著高于Hap1和Hap2, 其具有提高穗长的潜力。该研究揭示了多肽转运蛋白对水稻穗型的重要调控作用, 为水稻穗型改良奠定了理论基础。
尚江源, 淳雁, 李学勇. 水稻穗长基因PAL3的克隆及自然变异分析. 植物学报, 2021, 56(5): 520-532.
Jiangyuan Shang, Yan Chun, Xueyong Li. Map-based Cloning and Natural Variation Analysis of the PAL3 Gene Controlling Panicle Length in Rice. Chinese Bulletin of Botany, 2021, 56(5): 520-532.
Primer name | Forward primer (5′→3′) | Reverse primer (5′→3′) |
---|---|---|
R11-3 | AGAGAGACATCCGGAGACAA | TAAGACGAAAGGTCAAACGT |
R11-5 | GTGCTAACGTTTCGTCTAAC | AATAGCCTTCGGTGGTCTCA |
R11-10 | GTTCGTAATGTGGGCGTCTT | TGGGCACTCTTCTCACACTG |
R11-12 | CAATCTTGCTCTACTAGCTAGTG | GTGGCAACTAACAGATTAGATG |
M1 | GCAGTATATATTCGGCGGCG | GCCGTCGCCATATAGCTG |
M2 | GAGCCTCTCCTACTGTGCTA | AGAGCCCTCAGTTCCTCAAT |
M3 | GCTGACTACAGTAAGATCATGC | AGACAAACGGTCAAACATGT |
M4 | AAGGATCCAAGCTAGCCTCC | CCTGACAGCAAGCGAGAGAT |
M5 | CTTCAGCAAGTGAACTACGA | CCTAAACTAGCACGGATCATAGC |
M6 | TGTGAGGTTTAGGTTCTCGGA | TGAATAGAGATGCGGTCCAAC |
M7 | GGATTCGGCCACTGGTTGTT | GAATGTACTCGGATAAACCC |
表1 定位引物
Table 1 Primers used for mapping
Primer name | Forward primer (5′→3′) | Reverse primer (5′→3′) |
---|---|---|
R11-3 | AGAGAGACATCCGGAGACAA | TAAGACGAAAGGTCAAACGT |
R11-5 | GTGCTAACGTTTCGTCTAAC | AATAGCCTTCGGTGGTCTCA |
R11-10 | GTTCGTAATGTGGGCGTCTT | TGGGCACTCTTCTCACACTG |
R11-12 | CAATCTTGCTCTACTAGCTAGTG | GTGGCAACTAACAGATTAGATG |
M1 | GCAGTATATATTCGGCGGCG | GCCGTCGCCATATAGCTG |
M2 | GAGCCTCTCCTACTGTGCTA | AGAGCCCTCAGTTCCTCAAT |
M3 | GCTGACTACAGTAAGATCATGC | AGACAAACGGTCAAACATGT |
M4 | AAGGATCCAAGCTAGCCTCC | CCTGACAGCAAGCGAGAGAT |
M5 | CTTCAGCAAGTGAACTACGA | CCTAAACTAGCACGGATCATAGC |
M6 | TGTGAGGTTTAGGTTCTCGGA | TGAATAGAGATGCGGTCCAAC |
M7 | GGATTCGGCCACTGGTTGTT | GAATGTACTCGGATAAACCC |
图1 水稻野生型与pal3突变体的表型比较 (A) 野生型与pal3突变体的成熟期株型(Bar=20 cm); (B) 闭合状态下野生型与pal3突变体的穗(Bar=2 cm); (C) 展开状态下野生型与pal3突变体的穗(右) (Bar=2 cm); (D)-(G) 野生型与pal3突变体的穗长(D)、一级枝梗数(E)、二级枝梗数(F)和穗粒数(G)的统计分析。WT: 野生型。图中数据为平均值±标准差(n=20)。**表示在P<0.01水平差异显著(经t检验)。
Figure 1 Comparison of the rice phenotype between wild type and the pal3 mutants (A) Gross morphology of wild type and the pal3 mutants at mature stage (Bar=20 cm); (B) Closed panicle of wild type and the pal3 mutants (Bar=2 cm); (C) Spread panicles of wild type and the pal3 mutants (right) (Bar=2 cm); (D)-(G) Statistic analysis of panicle length (D), primary branch number (E), secondary branch number (F) and grain number per panicle (G) of wild type and the pal3 mutants. WT: Wild type. Data in figure are means±SD (n=20). ** indicate the significant differences at P<0.01 level by Students’t test.
Hybrid combi- nations | Phenotype of F1 | F2 population | χ23:1 | ||
---|---|---|---|---|---|
Wild-type plant number | Mutant-phenotypic plant number | Total number | |||
pal3-1 × WT | WT | 190 | 60 | 250 | 0.13 |
pal3-2 × WT | WT | 196 | 68 | 264 | 0.08 |
pal3-3 × WT | WT | 180 | 63 | 243 | 0.11 |
pal3-4 × WT | WT | 201 | 69 | 270 | 0.04 |
表2 pal3-1、pal3-2、pal3-3和pal3-4水稻突变体的遗传分析
Table 2 Genetic analysis of the pal3-1, pal3-2, pal3-3 and pal3-4 rice mutants
Hybrid combi- nations | Phenotype of F1 | F2 population | χ23:1 | ||
---|---|---|---|---|---|
Wild-type plant number | Mutant-phenotypic plant number | Total number | |||
pal3-1 × WT | WT | 190 | 60 | 250 | 0.13 |
pal3-2 × WT | WT | 196 | 68 | 264 | 0.08 |
pal3-3 × WT | WT | 180 | 63 | 243 | 0.11 |
pal3-4 × WT | WT | 201 | 69 | 270 | 0.04 |
图2 PAL3基因的图位克隆 (A) PAL3基因定位于第11号染色体InDel标记R11-3和R11-5之间; (B), (C) PAL3的精细定位。进一步将PAL3基因定位于M3和M5标记之间, 该区间包含7个开放阅读框(ORFs)。标记下方的数字表示重组个体的数目; (D) PAL3基因的结构示意图及pal3突变体的各突变位点。WT: 野生型
Figure 2 Map-based cloning of the PAL3 gene (A) The PAL3 gene was mapped to a region between InDel markers R11-3 and R11-5 on chromosome 11; (B), (C) Fine-mapping of PAL3. The PAL3 gene was further delimited to the region between markers M3 and M5, which contains seven open reading frames (ORFs). The number of recombinants is indicated beneath the marker positions; (D) Schematic structure of the PAL3 gene and the mutation sites of pal3 mutants. WT: Wild type
Gene ID | Annotation |
---|---|
LOC_Os11g12680 | Expressed protein |
LOC_Os11g12690 | Retrotransposon protein, putative, unclassified, expressed |
LOC_Os11g12700 | Retrotransposon protein, putative, unclassified, expressed |
LOC_Os11g12710 | Retrotransposon protein, putative, unclassified, expressed |
LOC_Os11g12720 | Retrotransposon, putative, centromere-specific |
LOC_Os11g12730 | Transposon protein, putative, CACTA, En/Spm sub-class, expressed |
LOC_Os11g12740 | Peptide transporter PTR2, putative, expressed |
表3 精细定位区间候选基因注释
Table 3 Annotations of candidate genes in the fine-mapping region
Gene ID | Annotation |
---|---|
LOC_Os11g12680 | Expressed protein |
LOC_Os11g12690 | Retrotransposon protein, putative, unclassified, expressed |
LOC_Os11g12700 | Retrotransposon protein, putative, unclassified, expressed |
LOC_Os11g12710 | Retrotransposon protein, putative, unclassified, expressed |
LOC_Os11g12720 | Retrotransposon, putative, centromere-specific |
LOC_Os11g12730 | Transposon protein, putative, CACTA, En/Spm sub-class, expressed |
LOC_Os11g12740 | Peptide transporter PTR2, putative, expressed |
图3 PAL3跨膜域及系统发育分析 (A) PAL3的12个跨膜域及pal3-1、pal3-2和pal3-4突变体的突变位点; (B) PAL3及其同源蛋白的系统发育分析。系统发育树采用MEGA X软件, bootstrap重复1 000次, 最大似然距离法构建。
Figure 3 Transmembrane regions and phylogenetic analysis of PAL3 (A) 12 transmembrane domains of PAL3 and the mutation sites of the pal3-1, pal3-2 and pal3-4 mutants; (B) Phylogenetic analysis of PAL3 and its homologs. The phylogenetic analysis was carried out by MEGA X with 1 000 bootstrap replicates and was constructed using the distance method with maximum likelihood.
Species | Locus ID | Gene name |
---|---|---|
Rice | LOC_Os11g12740 | PAL3/SP1 |
LOC_Os07g01070 | OsPTR1 | |
LOC_Os12g44100 | OsPTR2 | |
LOC_Os10g33210 | OsPTR3 | |
LOC_Os07g41250 | OsPTR4 | |
LOC_Os04g50940 | OsPTR5 | |
LOC_Os04g50950 | OsPTR6 | |
LOC_Os01g04950 | OsPTR7 | |
LOC_Os03g51050 | OsPTR8 | |
LOC_Os06g49250 | OsPTR9 | |
LOC_Os03g13274 | OsNTR1.1 | |
LOC_Os10g40600 | OsNRT1.1B | |
LOC_Os01g54515 | OsNPF4.5 | |
Arabidopsis | At1g12110 | AtNRT1.1 |
At5g62680 | AtNRT1.10 | |
At1g52190 | AtNRT1.11 | |
At1g33440 | AtNRT1.13 | |
At1g59740 | AtNRT1.14 | |
At1g72120 | AtNRT1.15 | |
At1g72125 | AtNRT1.16 | |
At1g69850 | AtNRT1.2 | |
At3g21670 | AtNRT1.3 | |
At2g26690 | AtNRT1.4 | |
At1g32450 | AtNRT1.5 | |
At1g27080 | AtNRT1.6 | |
At1g69870 | AtNRT1.7 | |
At4g21680 | AtNRT1.8 | |
At1g18880 | AtNRT1.9 | |
At3g54140 | AtPTR1 | |
At2g02040 | AtPTR2/AtNTR1 | |
At5g46050 | AtPTR3 | |
At2g02020 | AtPTR4 | |
At5g01180 | AtPTR5 | |
At1g62200 | AtPTR6 | |
At1g27040 | AIT2 | |
At3g25260 | AIT3 | |
At3g25280 | AIT4 | |
At3g47960 | GTR1 | |
At3g45650 | NAXT1 | |
At1g68570 | Nitr |
表4 PAL3及其同源家族基因的基因号和名称
Table 4 Locus ID and gene name of PAL3 and its homologs
Species | Locus ID | Gene name |
---|---|---|
Rice | LOC_Os11g12740 | PAL3/SP1 |
LOC_Os07g01070 | OsPTR1 | |
LOC_Os12g44100 | OsPTR2 | |
LOC_Os10g33210 | OsPTR3 | |
LOC_Os07g41250 | OsPTR4 | |
LOC_Os04g50940 | OsPTR5 | |
LOC_Os04g50950 | OsPTR6 | |
LOC_Os01g04950 | OsPTR7 | |
LOC_Os03g51050 | OsPTR8 | |
LOC_Os06g49250 | OsPTR9 | |
LOC_Os03g13274 | OsNTR1.1 | |
LOC_Os10g40600 | OsNRT1.1B | |
LOC_Os01g54515 | OsNPF4.5 | |
Arabidopsis | At1g12110 | AtNRT1.1 |
At5g62680 | AtNRT1.10 | |
At1g52190 | AtNRT1.11 | |
At1g33440 | AtNRT1.13 | |
At1g59740 | AtNRT1.14 | |
At1g72120 | AtNRT1.15 | |
At1g72125 | AtNRT1.16 | |
At1g69850 | AtNRT1.2 | |
At3g21670 | AtNRT1.3 | |
At2g26690 | AtNRT1.4 | |
At1g32450 | AtNRT1.5 | |
At1g27080 | AtNRT1.6 | |
At1g69870 | AtNRT1.7 | |
At4g21680 | AtNRT1.8 | |
At1g18880 | AtNRT1.9 | |
At3g54140 | AtPTR1 | |
At2g02040 | AtPTR2/AtNTR1 | |
At5g46050 | AtPTR3 | |
At2g02020 | AtPTR4 | |
At5g01180 | AtPTR5 | |
At1g62200 | AtPTR6 | |
At1g27040 | AIT2 | |
At3g25260 | AIT3 | |
At3g25280 | AIT4 | |
At3g47960 | GTR1 | |
At3g45650 | NAXT1 | |
At1g68570 | Nitr |
图4 PAL3及其同源蛋白序列比对 黑色背景表示所有氨基酸序列都高度同源, 灰色部分表示部分氨基酸序列同源, 白色部分表示氨基酸序列完全不同源。*依次为pal3-1、pal3-2和pal3-4突变体的突变位点; △为Hap1和Hap3的差异位点。
Figure 4 Sequences alignment of PAL3 and its homologs The black background represent that all amino acid sequences are homologous. The gray part represent that some of the amino acid sequences are homologous. The white part represent that the amino acid sequences are completely different. * indicate the mutation sites of the pal3-1, pal3-2 and pal3-4 mutants in turn; △: The variation sites between Hap1 and Hap3.
图5 PAL3基因的单倍型分析 (A) PAL3基因结构及各单倍型变异所在位置; (B) PAL3在栽培稻中的单倍型。单倍型数据通过水稻分子育种整合组学知识库(MBKbase) (Peng et al., 2020)分析而来, 共包含2 187个栽培稻品种, 分析时去除了内含子变异、杂合变异和同义变异(-: 碱基对缺失); (C) Hap1和Hap3差异位点的保守性分析(Δ: Hap1和Hap3的差异位点)。
Figure 5 Haplotype analysis of PAL3 (A) Structure of PAL3 gene and the location of haplotypes; (B) Haplotypes of PAL3 in the cultivated rice. Haplotype data were analyzed by Rice Molecular Breeding Knowledgebase (MBKbase) (Peng et al., 2020), including 2 187 cultivated rice varieties. Variations on intron, heterozygous variations and synonymous variations were removed during analysis (-: The deletion of base pair); (C) Sequence alignment around the variation sites between Hap1 and hap3 (Δ: The variation sites between Hap1 and Hap3).
图6 PAL3在野生稻中的单倍型 野生稻单倍型数据来源于禾本科基因组数据库(Gramene)和水稻相关物种基因组数据库(Rice Relatives-GD) (Mao et al., 2019)。*: D475和G476缺失; ●: 无数据
Figure 6 Haplotype of PAL3 in the wild rice Haplotype data of wild rice were from Gramene and Rice Relatives-GD (Mao et al., 2019). *: D475 and G476 deletion; ●: No datum
图7 PAL3基因Hap1、Hap2和Hap3的亚种组成及穗型分析 (A) Hap1、Hap2和Hap3的亚种构成; (B) Hap1、Hap2和Hap3的穗长比较; (C) Hap1、Hap2和Hap3的穗长统计。不同小写字母表示差异显著(P<0.05)。
Figure 7 Subspecies composition and panicle phenotype analysis of Hap1, Hap2 and Hap3 of the PAL3 gene (A) Subspecies composition of Hap1, Hap2 and Hap3; (B) Comparison of panicle length among Hap1, Hap2 and Hap3; (C) Statistic of panicle length of Hap1, Hap2 and Hap3. Different lowercase letters indicate significant differences (P<0.05).
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