Scientia Agricultura Sinica ›› 2022, Vol. 55 ›› Issue (24): 4781-4792.doi: 10.3864/j.issn.0578-1752.2022.24.001


Phenotypic Analysis and Gene Cloning of Rice Panicle Apical Abortion Mutant paa21

HE Lei1(),LU Kai1,ZHAO ChunFang1,YAO Shu1,ZHOU LiHui1,ZHAO Ling1,CHEN Tao1,ZHU Zhen1,ZHAO QingYong1,LIANG WenHua1,WANG CaiLin1,ZHU Li2(),ZHANG YaDong1()   

  1. 1Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice/Jiangsu High Quality Rice R&D Center/Nanjing Branch of China National Center for Rice Improvement/Key laboratory of Jiangsu Province for Agrobiology, Nanjing 210014
    2China National Rice Research Institute/State Key Laboratory of Rice Biology, Hangzhou 310006
  • Received:2022-09-27 Accepted:2022-10-24 Online:2022-12-16 Published:2023-01-04
  • Contact: Li ZHU,YaDong ZHANG;;


【Objective】Rice panicle apical abortion affects yield. Identification and cloning of genes related to rice panicle apical abortion can enrich the molecular mechanism of rice panicle development regulation, and provide theoretical basis and genetic resources for rice high-yield molecular design breeding. 【Method】Here, a stably inherited panicle apical abortion 21 (paa21) mutant was screened from EMS mutant library of the japonica rice variety "Wuyunjing 30". Agronomic traits, such as ratio of degraded primary branches, degraded apical spikelets, grains per panicle, plant height, panicle length, and grain yield per plant, were statistically analyzed. Trypan blue and Evans blue staining were used to detect whether programmed cell death occurred in the apical spikelets. H2O2 content in young panicles at different development stages and different panicle parts of WT and paa21 was determined. Genetic analysis was carried out by reciprocal cross of paa21 with indica rice II-32B and 9311 respectively. The F2 population constructed by crossing paa21 with indica rice II-32B was used for gene mapping and cloning. The three-dimensional structure of wild-type and paa21 proteins were predicted using SWISS-MODEL website. The expression levels of ROS response marker genes, programmed cell death related genes and catalase related genes were analyzed by RT-qPCR. 【Result】paa21 produced panicle apical abortion phenotype and the degenerated spikelets were mainly located on the primary branches at the apical panicle. The plant height, grain number per panicle, panicle length and grain yield per plant of paa21 were lower than those of WT. After observing the young panicles at different development stages, we found that the paa21 mutant had a panicle apical abortion phenotype when panicle developed to 12 cm. Trypan blue and Evans blue staining results showed that the apical spikelets of the paa21 mutant had programmed cell death. Stronger DAB staining was observed in the degenerated apical spikelets of paa21 than WT. The results of H2O2 content determination showed that higher level of ROS was accumulated in panicle of paa21 compared with WT. Genetic analysis suggested that paa21 mutant phenotype is controlled by a pair of recessive nuclear genes. The results of map-based cloning showed that a C to T mutation occurred in the second exon of Os02g0673100 in paa21, resulting in the mutation of alanine to valine. This gene encodes an aluminum activated malate transporter, ALMT7. The mutation site was located at the fourth transmembrane helix. SWISS-MODEL prediction results showed that the mutation site did not significantly affect the three-dimensional structure of the mutant protein. The expression level of ROS response marker genes Os01g0826400, Os05g0474800 and Os02g0181300 in paa21 was significantly higher than that in WT when the young spike developed to 10 cm. Compared with WT, the expression level of programmed cell death related genes VPE2 and VPE3 increased significantly in paa21. The expression level of CATA, CATB and CATC which encode catalase in 10 cm young panicle of paa21 was significantly higher than that of WT. The activity of CAT in paa21 10 cm young spikelet was significantly lower than that of WT. 【Conclusion】paa21 accumulate excess ROS in the apical spikelet at late stage of panicle development, resulting in programmed cell death, which eventually leads to the degeneration of the apical spikelet. These results lay a good foundation for further enriching the genetic regulatory network of panicle development.

Key words: rice, panicle apical abortion, reactive oxygen species, programmed cell death

Fig. 1

Phenotypic characterization of the paa21 mutant A: Morphology of WT (left) and paa21 (right), Bars=10 cm; B: Panicle of WT (left) and paa21 (right) at heading stage, Bars=2 cm; C: Panicle of WT (left) and paa21 (right) at mature stage, Bars=2 cm; D: Primary branches from one panicle, 1-16 indicate primary branches from the top to the bottom of the panicle in paa21; E: Statistics for normal spikelets and degenerated spikelets correspond to Fig. D; F: Ratio of degenerated primary branches; G: Ratio of degenerated grains per panicle of WT and paa21; H: Quantification of plant height; I: Quantification of grain number per panicle; J: Quantification of panicle length; K: Quantification of grain yield per plant. Error bars mean standard error; ** P≤0.01 by the Student’s t-test. The same as below"

Fig. 2

Developing panicles of WT and paa21 A-F: Developing panicles of WT (left) and paa21 (right). 1 cm (A), 2 cm (B), 5 cm (C), 7 cm (D), 12 cm (E), 17 cm (F). Bars=1 cm"

Fig. 3

Trypan blue and Evans blue staining of apical spikelets in WT and paa21 A: Trypan blue staining; B: Evans blue staining"

Fig. 4

Detection of H2O2 accumulation A: DAB staining of apical spikelets in WT and paa21 panicle; B: H2O2 content in apical spikelets of WT and paa21 at different stages of panicle development, PL; C: H2O2 content in spikelets of different parts of rice panicle, Different letters indicate significantly different values determined using analysis of variance followed by an LSD test for the comparison of means (P<0.05), ap: Apical part, mp: Middle part, bp: Bottom part"

Table 1

Genetic analysis of the paa21"

Crossing combination
Phonotype of F1 plants
F2单株数 Number of F2 plants χ2(3﹕1=3.84)
野生型 Wild type 突变型 Mutant type
paa21×II-32B 野生型Wild type 396 129 0.0514
II-32B×paa21 野生型Wild type 516 182 0.4298
paa21×9311 野生型Wild type 253 81 0.0998
9311×paa21 野生型Wild type 474 164 0.1693

Fig. 5

Map-base cloning of PAA21"

Fig. 6

Amino acid sequence alignment of WT and paa21(A) and predicted 3D structure of WT and paa21 proteins (B, C) M1-M6 represent the transmembrane helices of PAA21 protein, and the red box indicates the mutation site"

Fig. 7

Expression levels of ROS, PCD-related genes, and CAT activity"

[1] XING Y, ZHANG Q. Genetic and molecular bases of rice yield. Annual Review of Plant Biology, 2010, 61: 421-442.
doi: 10.1146/annurev-arplant-042809-112209 pmid: 20192739
[2] TEO Z W N, SONG S, WANG Y Q, LIU J, YU H. New insights into the regulation of inflorescence architecture. Trends in Plant Science, 2014, 19(3): 158-165.
doi: 10.1016/j.tplants.2013.11.001 pmid: 24315403
[3] IKEDA-KAWAKATSU K, YASUNO N, OIKAWA T, IIDA S, NAGATO Y, MAEKAWA M, KYOZUKA J. Expression level of ABERRANT PANICLE ORGANIZATION1 determines rice inflorescence form through control of cell proliferation in the meristem. Plant Physiology, 2009, 150(2): 736-747.
doi: 10.1104/pp.109.136739
[4] IKEDA K, ITO M, NAGASAWA N, KYOZUKA J, NAGATO Y. Rice ABERRANT PANICLE ORGANIZATION 1, encoding an F-box protein, regulates meristem fate. The Plant Journal, 2007, 51(6): 1030-1040.
doi: 10.1111/j.1365-313X.2007.03200.x
[5] IKEDA K, NAGASAWA N, NAGATO Y. ABERRANT PANICLE ORGANIZATION 1 temporally regulates meristem identity in rice. Developmental Biology, 2005, 282(2): 349-360.
doi: 10.1016/j.ydbio.2005.03.016
[6] LI M, TANG D, WANG K, WU X, LU L, YU H, GU M, YAN C, CHENG Z. Mutations in the F-box gene LARGER PANICLE improve the panicle architecture and enhance the grain yield in rice. Plant Biotechnology Journal, 2011, 9(9): 1002-1013.
doi: 10.1111/j.1467-7652.2011.00610.x
[7] HUANG X, QIAN Q, LIU Z, SUN H, HE S, LUO D, XIA G, CHU C, LI J, FU X. Natural variation at the DEP1 locus enhances grain yield in rice. Nature Genetics, 2009, 41(4): 494-497.
doi: 10.1038/ng.352
[8] KOMATSU M, MAEKAWA M, SHIMAMOTO K, KYOZUKA J. The LAX1 and FRIZZY PANICLE 2 genes determine the inflorescence architecture of rice by controlling rachis-branch and spikelet development. Developmental Biology, 2001, 231(2): 364-373.
doi: 10.1006/dbio.2000.9988
[9] WANG H, TANG S, ZHI H, XING L, ZHANG H, TANG C, WANG E, ZHAO M, JIA G, FENG B, DIAO X. The boron transporter SiBOR1 functions in cell wall integrity, cellular homeostasis, and panicle development in foxtail millet. The Crop Journal, 2022, 10(2): 342-353.
doi: 10.1016/j.cj.2021.05.002
[10] PEI Y, DENG Y, ZHANG H, ZHANG Z, LIU J, CHEN Z, CAI D, LI K, DU Y, ZANG J, XIN P, CHU J, CHEN Y, ZHAO L, LIU J, CHEN H. EAR APICAL DEGENERATION1 regulates maize ear development by maintaining malate supply for apical inflorescence. The Plant Cell, 2022, 34(6): 2222-2241.
doi: 10.1093/plcell/koac093 pmid: 35294020
[11] BAI J, ZHU X, WANG Q, ZHANG J, CHEN H, DONG G, ZHU L, ZHENG H, XIE Q, NIAN J, CHEN F, FU Y, QIAN Q, ZUO J. Rice TUTOU1 encodes a suppressor of cAMP receptor-like protein that is important for actin organization and panicle development. Plant Physiology, 2015, 169(2): 1179-1191.
doi: 10.1104/pp.15.00229
[12] 陈惠哲, 朱德峰, 林贤青, 张玉屏. 穗肥施氮量对两优培九枝梗及颖花分化和退化的影响. 浙江农业学报, 2008, 20(3): 181-185.
CHEN H Z, ZHU D F, LIN X Q, ZHANG Y P. Effect of nitrogen levels in spike stage on differentiation and degeneration of branches and spikelet of hybrid rice cultivar Liangyoupeijiu. Acta Agriculturae Zhejiangensis, 2008, 20(3): 181-185. (in Chinese)
[13] 王亚梁, 张玉屏, 朱德峰, 向镜, 武辉, 陈惠哲, 张义凯. 水稻穗分化期高温胁迫对颖花退化及籽粒充实的影响. 作物学报, 2016, 42(9): 1402-1410.
doi: 10.3724/SP.J.1006.2016.01402
WANG Y L, ZHANG Y P, ZHU D F, XIANG J, WU H, CHEN H Z, ZHANG Y K. Effect of heat stress on spikelet degeneration and grain filling at panicle initiation period of rice. Acta Agronomica Sinica, 2016, 42(9): 1402-1410. (in Chinese)
doi: 10.3724/SP.J.1006.2016.01402
[14] 张兴元, 罗胜, 王敏, 丛楠, 赵志超, 程治军. 与SP1互作的水稻穗顶部退化基因qPAA3的精细定位. 中国农业科学, 2015, 48(12): 2287-2295.
ZHANG X Y, LUO S, WANG M, CONG N, ZHAO Z C, CHENG Z J. Fine mapping of rice panicle apical abortion gene qPAA3interacting with SP1. Scientia Agricultura Sinica, 2015, 48(12): 2287-2295. (in Chinese)
[15] TAN C J, SUN Y J, XU H S, YU S B. Identification of quantitative trait locus and epistatic interaction for degenerated spikelets on the top of panicle in rice. Plant Breeding, 2011, 130(2): 177-184.
doi: 10.1111/j.1439-0523.2010.01770.x
[16] 徐华山, 孙永建, 周红菊, 余四斌. 构建水稻优良恢复系背景的重叠片段代换系及其效应分析. 作物学报, 2007, 33(6): 979-986.
XU H S, SUN Y J, ZHOU H J, YU S B. Development and characterization of contiguous segment substitution lines with background of an elite restorer line. Acta Agronomica Sinica, 2007, 33(6): 979-986. (in Chinese)
[17] CHENG Z J, MAO B G, GAO S W, ZHANG L, WANG J L, LEI C L, ZHANG X, WU F Q, GUO X P, WAN J M. Fine mapping of qPAA8, a gene controlling panicle apical development in rice. Journal of Integrative Plant Biology, 2011, 53(9): 710-718.
[18] HENG Y, WU C, LONG Y, LUO S, MA J, CHEN J, LIU J, ZHANG H, REN Y, WANG M, TAN J, ZHU S, WANG J, LEI C, ZHANG X, GUO X, WANG H, CHENG Z, WAN J. OsALMT7 maintains panicle size and grain yield in rice by mediating malate transport. The Plant Cell, 2018, 30(4): 889-906.
doi: 10.1105/tpc.17.00998 pmid: 29610210
[19] ZAFAR S A, PATIL S B, UZAIR M, FANG J, ZHAO J, GUO T, YUAN S, UZAIR M, LUO Q, SHI J, SCHREIBER L, LI X. DPS1) encodes a cystathionine β-synthase domain containing protein required for anther cuticle and panicle development in rice. New Phytologist, 2020, 225(1): 356-375.
doi: 10.1111/nph.16133
[20] PENG Y B, HOU F X, BAI Q, XU P Z, LIAO Y X, ZHANG H Y, GU C J, DENG X S, WU T K, CHEN X Q, ALI A, WU X J. Rice calcineurin b-like protein-interacting protein kinase 31 (OsCIPK31) is involved in the development of panicle apical spikelets. Frontiers in Plant Science, 2018, 9.
[21] 王中豪. 水稻钙氢离子交换蛋白基因CAX1a的图位克隆和功能分析[D]. 北京: 中国农业科学院, 2021.
WANG Z H. Map-based cloning and functional analysis of the Ca2+/H+ exchanger gene CAX1a in rice[D]. Beijing: Chinese Academy of Agricultural Sciences, 2021. (in Chinese)
[22] LOOR G, KONDAPALLI J, SCHRIEWER J M, CHANDEL N S, VANDEN HOEK T L, SCHUMACKER P T. Menadione triggers cell death through ROS-dependent mechanisms involving PARP activation without requiring apoptosis. Free Radical Biology and Medicine, 2010, 49(12): 1925-1936.
doi: 10.1016/j.freeradbiomed.2010.09.021 pmid: 20937380
[23] MITTLER R. ROS are good. Trends in Plant Science, 2017, 22(1): 11-19.
doi: S1360-1385(16)30112-1 pmid: 27666517
[24] LI Z, MO W, JIA L, XU Y C, TANG W, YANG W, GUO Y L, LIN R. Rice FLUORESCENT1 is involved in the Regulation of Chlorophyll. Plant Cell Physiology, 2019, 60(19): 2307-2318.
doi: 10.1093/pcp/pcz129
[25] SU T, WANG P, LI H, ZHAO Y, LU Y, DAI P, REN T, WANG X, LI X, SHAO Q, ZHAO D, ZHAO Y, MA C. The Arabidopsis catalase triple mutant reveals important roles of catalases and peroxisome- derived signaling in plant development. Journal of Integrative Plant Biology, 2018, 60(7): 591-607.
doi: 10.1111/jipb.12649
[26] DENG M, BIAN H, XIE Y, KIM Y, WANG W, LIN E, ZENG Z, GUO F, PAN J, HAN N, WANG J, QIAN Q, ZHU M. Bcl-2 suppresses hydrogen peroxide-induced programmed cell death via OsVPE2 and OsVPE3, but not via OsVPE1 and OsVPE4, in rice. The FEBS Journal, 2011, 278(24): 4797-4810.
doi: 10.1111/j.1742-4658.2011.08380.x
[27] LU W Y, DENG M J, GUO F, WANG M Q, ZENG Z H, HAN N, YANG Y N, ZHU M Y, BIAN H W. Suppression of OsVPE3 enhances salt tolerance by attenuating vacuole rupture during programmed cell death and affects stomata development in rice. Rice, 2016, 9.
[28] DAI D, ZHANG H, HE L, CHEN J, DU C, LIANG M, ZHANG M, WANG H, MA L. Panicle apical abortion 7 regulates panicle development in rice (Oryza sativa L.). International Journal of Molecular Sciences, 2022, 23(16): 9487.
doi: 10.3390/ijms23169487
[29] HU P, TAN Y Q, WEN Y, FANG Y X, WANG Y Y, WU H, WANG J G, WU K X, CHAI B Z, ZHU L, ZHANG G H, GAO Z Y, REN D Y, ZENG D L, SHEN L, XUE D W, QIAN Q, HU J. LMPA regulates lesion mimic leaf and panicle development through ROS-induced PCD in rice. Frontiers in Plant Science, 2022, 13.
[30] YANG F, XIONG M, HUANG M, LI Z, WANG Z, ZHU H, CHEN R, LU L, CHENG Q, WANG Y, TANG J, ZHUANG H, LI Y. Panicle apical abortion 3 controls panicle development and seed size in rice. Rice, 2021, 14(1): 68.
doi: 10.1186/s12284-021-00509-5 pmid: 34264425
[31] WANG Q L, SUN A Z, CHEN S T, CHEN L S, GUO F Q. SPL6 represses signalling outputs of ER stress in control of panicle cell death in rice. Nature Plants, 2018, 4(5): 280-288.
doi: 10.1038/s41477-018-0131-z
[32] ALI A, XU P, RIAZ A, WU X. Current advances in molecular mechanisms and physiological basis of panicle degeneration in rice. International Journal of Molecular Sciences, 2019, 20(7): 1613.
doi: 10.3390/ijms20071613
[33] 彭永彬. 水稻穗顶退化突变体paa1019paa74的基因克隆与功能分析[D]. 成都: 四川农业大学, 2018.
PENG Y B. Cloning and functional charactization of panicle apical abortion 1019 and panicle apical abortion 74 in rice[D]. Chengdu: Sichuan Agriculture University, 2018. (in Chinese)
[34] WASZCZAK C, CARMODY M, KANGASJÄRVI J. Reactive oxygen species in plant signaling. Annual Review of Plant Biology, 2018, 69(1): 209-236.
doi: 10.1146/annurev-arplant-042817-040322
[35] MHAMDI A, VAN BREUSEGEM F. Reactive oxygen species in plant development. Development, 2018, 145(15).
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