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Acta Agronomica Sinica ›› 2020, Vol. 46 ›› Issue (11): 1734-1742.doi: 10.3724/SP.J.1006.2020.02009

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

Genetic analysis and fine mapping of a sheathed panicle mutant sui2 in rice (Oryza sativa L.)

SUN Qi1(), ZHAO Zhi-Chao2(), ZHANG Jin-Hui2, ZHANG Feng2, CHENG Zhi-Jun2,*(), ZOU De-Tang1,*()   

  1. 1 Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
    2 Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
  • Received:2020-02-14 Accepted:2020-06-02 Online:2020-11-12 Published:2020-06-22
  • Contact: Zhi-Jun CHENG,De-Tang ZOU E-mail:517596634@qq.com;zhaozhichao@caas.cn;chengzhijun@caas.cn;zoudtneau@126.com
  • Supported by:
    This study was supported by the National Natural Science Foundation of China(31871603)

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Abstract:

The elongation and development of rice uppermost internode plays an important role in plant architecture development. In general, the sheathed panicle phenomenon in rice sterility line is caused by the elongation and development hindrance of the uppermost internode. The study on molecular mechanisms underlying sheathed panicle would be helpful for improving plant architecture in sterility line. At the present study, we reported the study on a sheathed panicle mutant, named sui2, originated from a tissue-culture progeny. Its uppermost internode severely shortened, resulted in its pancleen closed by flag leaf sheath, without significantly length alternation at other internodes. The cytological analysis demonstrated that the shorten of the uppermost internode is caused by insufficient elongation of the parenchyma cells. Genetic analysis of the progeny derived from the cross-combination of sui2 and IRAT129 revealed that sui2 is a single gene dominant mutant. Linkage analysis to 608 normal individuals from F2 generation showed that SUI2 was located in a 110 kb region delimited by InDel marks S4-14.1 and S4-14.2 on the end of chromosome 4 long arm. The annotated genes on this region did not display any difference in genomic sequence, while the expression level of LOC_Os04g39430, encoding a cytochrome P450 protein and an allele of D11, increased by 264 times expression amount in mutant. Analysis of qRT-PCR for several crucial genes on BR (brasssinolide) signaling pathway showed that in mutant the expression level of all these genes increased, indicating that genes in BR signaling pathway may be involved in the regulation to the elongation and development of uppermost internode.

Key words: rice, sheathed panicle, fine mapping, SUI2, BR signaling pathway

Table 1

Newly developed polymorphic InDel and SNP primers used in fine mapping"

标记
Marker		 正向引物
Forward primer (5′-3′)		 反向引物
Reverse primer (5′-3′)
S4-13 CGACGATATCCGTGCATCACC ACGATTGCATCTGCGTCACACC
S4-14 AGTGATGCACTTCTGTTTGTCC GGTCCTCTTGTTCAAGTCAAACC
S4-14.1 AGAAGACGACGACTTGGACA TAGACGACCTGGGTTCGAAG
S4-14.2 AAATTCCACATGCCAATTCC ATTGAGGCTCGATCCATGAC
S4-14.3 CTTTTGCGAGGGGTCTCATA CATGGGGCTTTTGCACTAAT
S4-14.4 GCCACAAACTCCCAGCTAAC GTGGAGACTGGAGAGGTGGA
S4-15 ACCTTTTCTTGGCTTGAGGG GCTTTTGCTACTTTTGGGGG

Table 2

Primers used for qRT-PCR"

引物名
Primer name		 正向引物
Forward primer (5′-3′)		 反向引物
Reverse primer (5′-3′)
LOC_Os04g39360 TGATCTCGATGGCGATCACC GCTCCTCGCAGTAGACCATC
LOC_Os04g39380 CTAATTCATCGCCACGTACAAACG TGATCACCGGCTATCAACAGAAAC
LOC_Os04g39410 CGATTGCCATGAGTTCACCAAGC TGGCGTCTCGGACCACAATTTC
LOC_Os04g39420 GCGGGTATACGCAGGTTTATGC ACTCGTTGAAGATGGCCACAGC
LOC_Os04g39430 TGAGGTTCCTCAGTCCTCATGC AAACACCCTCCCATACCTGGAG
LOC_Os04g39440 TGTGTCACACTGCCACTTACCC TGGAGCAACTACGTTTCAGTCAGC
LOC_Os04g39444 CCAAGATGAAGCTCGTCAGGTTTC AGTCTTCAAGTGGGTGTTCATGC
LOC_Os04g39450 GGCCTTCTATGCATCTCTGAGC TGATGGAGTTGCTGCCATCTTC
LOC_Os04g39470 AGCTCACGAATCACATGGTGTAGC ATGTGGATCATGGCGTGCTTCG
LOC_Os04g39489 TCCTCTTGGAAATTCAGGACACAC GGACGCCTTCTTCATCGTCTTG
BRD1 ATTATGATCCATTCCTGTACCCTG TCTTCCTCCCATCTGTATTGAGT
BRD2 TCAAGGCCACACAGGGTGAATC GCACAGCCACAGTGGATAAACCTC
DWARF4 GATGGGCTCTGAAACAATCTAACCTT TCCCCTCTTAGCCTTTGTCTCCTT
BAK1 ACTCTGGTCAATCCGTGCACTTG AGTGCAGCATTCCCAAGATCAAC
BRI1 TCGTTGGCTCAGTTCTTGGAGAG TCTCTTGGCTAGAACAAGAAGTGC
BU1 CGACGACGAAGCTGCTGAAGGA AGGAGGCTGCGGATGATCTCG
LIC1 CTGCACCACTTGCTGCCCCTAC TGTTCCCAACAGATTCCTCAAACATC
TUD1 GTCCGCCTCATCCGCATACTC CGCACCGATGCTAACAATCAAAC
BZR1 CGTTCCGGCACCCCTTCTTC TGGCGTCACCCTCCCCTTGT
Ubiquitin AACCAGCTGAGGCCCAAGA ACGATTGATTTAACCAGTCCATGA

Fig. 1

Phenotypic comparison between wild type and mutant sui2 A: Phenotypes of WT (left) and sui2 (right) plants at rippen period; B: Phenotype comparison of the sheathed panicle of WT (left) and sui2 (right) at the maturation period; C: Comparison of internodes between WT (left) and sui2 (right), from left to right is the uppermost internode, penultimate internode, antepenult internode, fourth internode from top down; D, E: Transverse sections of the first internode of WT (D) and sui2 (E); F: Longitudinal sections of the uppermost internode of wild type and sui2; G, H: The leaf angles between the last and penultimate leaf in the WT (G) and sui2 (H) at the seedling stage. Scale bars: (A) 15 cm; (B) 5 cm; (C) 5 cm; (D, E) 200 μm; (F) 50 μm."

Table 3

Comparison of agronomic traits between wild type Kitaake and mutant sui2"

农艺性状Agronomic trait Kitaake sui2 P
株高Plant height (cm) 63.73±2.55 43.08±3.79 *P < 0.05
分蘖数Tiller number 14.40±2.01 25.00±3.43 **P < 0.01
每穗粒数Number of spikelets per panicle 42.75±8.70 27.10±3.41 **P < 0.01
千粒重1000-grain weight (g) 4.415±0.02 4.852±0.06 **P < 0.01
结实率Seed setting rate (%) 0.969±0.05 0.837±0.08 **P < 0.01
粒长Seed length (mm) 7.06±0.33 8.10±0.22 **P < 0.01
粒宽Seed weight (mm) 3.26±0.10 3.47±0.12 **P < 0.01
粒厚Seed thickness (mm) 2.20±0.07 2.14±0.07 **P < 0.01
剑叶宽Flag leaf length (cm) 1.10±0.08 0.90±0.08 **P < 0.01
倒一节间长Length of the uppermost internode (cm) 29.61±3.27 14.68±2.57 **P < 0.01

Fig. 2

Comparisons of cell size and number of the parenchyma cells in the uppermost internode between wild type and sui2 A: Comparisons of the length and width of stem parenchyma cells from longitudinal sections of the uppermost internode in wild type and sui2; B: comparison of cell numbers of the radius in the transverse sections of the uppermost internode in wild type and sui2. * represents significantly different at P < 0.05; ** represents significantly different at P < 0.01."

Fig. 3

Schematic diagram of map-based cloning on the candidate gene SUI2 A: Rough mapping of the gene SUI2 flanked by two markers S4-14 and S4-15; B: SUI2 was fine mapped to a 110 kb interval delimited by two markers S4-14.1 and S4-14.2 region; C: 14 ORFs and 2 transposons within the fine-mapped fragment. The molecular markers used in linkage analysis were indicated above the bold lines, and the umbers beneath the bold lines represented the recombinants identified by the corresponding markers."

Table 4

Gene annotations in the mapping interval"

基因名称
Locus name		 基因注释
Gene annotation
LOC_Os04g39360 Heavy metal transport/detoxification protein, putative, expressed
LOC_Os04g39370 Heavy metal associated domain containing protein, expressed
LOC_Os04g39380 Heavy metal transport/detoxification protein, putative, expressed
LOC_Os04g39390 Retrotransposon protein, putative, unclassified, expressed
LOC_Os04g39400 Retrotransposon protein, putative, unclassified, expressed
LOC_Os04g39410 Pentatricopeptide, putative, expressed
LOC_Os04g39420 6-phosphofructokinase 2, putative, expressed
LOC_Os04g39430 D11; cytochrome P450; small grain 4; clustered spikelets 4
LOC_Os04g39440 Ras-related protein, putative, expressed
LOC_Os04g39444 LSM domain containing protein, expressed
LOC_Os04g39450 Expressed protein
LOC_Os04g39460 NBS-LRR type disease resistance protein, putative, expressed
LOC_Os04g39470 Transcription factor with an MYB domain
LOC_Os04g39489 Amino acid transporter, putative, expressed
LOC_Os04g39510 Expressed protein
LOC_Os04g39520 ZOS4-08-C2H2 zinc finger protein, expressed

Fig. 4

Expression level of candidate genes by qRT-PCR"

Fig. 5

SUI2 expression levels of the different tissues in WT and sui2 mutant"

Fig. 6

Expression levels of BR-related genes in WT and sui2 A: Relative expression levels of the genes related to BR biosynthesis in WT and sui2 culms. B: Relative expression levels of the genes related to BR signaling in the young WT and sui2 young culms. * represents significantly different at P < 0.05; ** represents significantly different at P < 0.01."

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