基于转录组学挖掘与分析NJ9108水稻种子寿命的关键基因

doi:10.16288/j.yczz.24-243

[an error occurred while processing this directive]

Hereditas(Beijing) ›› 2025, Vol. 47 ›› Issue (3): 351-365.doi: 10.16288/j.yczz.24-243

• Research Article • Previous Articles Next Articles

Mining and analysis of key genes related to rice seed longevity in NJ9108 based on transcriptomics

Chaofei Han¹^,²(), Ling Chen⁵, Yuanxiu Wang², Qian Cheng², Sheng Zuo², Huabin Liu⁴(), Chengliang Wang²^,³()

1. College of Life Sciences, China West Normal University, Nanchong 637002, China
2. College of Life Sciences, Anhui Normal University, Wuhu 241001, China
3. State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475000, China
4. College of Life and Health Sciences, Anhui Science and Technology University, Bengbu 233100, China
5. Institute of Advanced Studies, Wuhan University, Wuhan 430072, China

Received:2024-07-11 Revised:2024-11-09 Online:2025-01-16 Published:2025-01-16
Contact: Huabin Liu, Chengliang Wang E-mail:2535022780@qq.com;liuhb@ahstu.edu.cn;clwang@ahnu.edu.cn
Supported by:
National Natural Science Foundation of China(32101646);Key Research and Development Project of Anhui Science and Technology Agency(2023n06020004);China Postdoctoral Science Foundation(348510);Wuhu Science and Technology Bureau Project(2022jc10)

Abstract

Abstract:

Seed longevity is the period over which seeds remain viable and capable of gemination, and is an important trait of seed quality. Longevity changes in seed directly affect the germination rate, seedling morphology, and storage time. Therefore, the identification of seed longevity genes has significant value for cultivating seeds that are storage-resistant and have long lifespan. The study found that NJ9108 seeds are a type of rice that is resistant to aging; Using transcriptomic technology, the annotated genes were subjected to mfuzz fuzzy clustering and divided into 6 subtypes, with a total of 8,384 genes upregulated/downregulated by aging induction. These differentially expressed genes are enriched into biological processes (BP), cellular components (CC), and molecular functions (MF), with 42 genes enriched in phenylpropanoid biosynthesis, 31 genes enriched in sugar signaling, and 42 genes enriched in plant hormone signaling pathways. They are the most important pathways involved in the aging resistance process of NJ9108. qRT-PCR results showed that compared with ZH11, 4CL5, CAD5, PRX3 and PRX86 in the phenylpropanoid biosynthesis pathway were significantly upregulated in NJ9108 after aging; BGLU18, BGLU22 and TPP3 in the sugar signaling pathway were significantly upregulated in NJ9108; RR12 and SAPK5 involved in the plant hormone signaling pathway were significantly upregulated after aging, while IAA12 and IAA20 were significantly downregulated in NJ9108 seeds. The expression trends of these genes are consistent with transcriptomic results, suggesting that these genes regulating rice seed longevity. BGLU18, BGLU22, OsRR12, and TPP3, as the new identified seed longevity genes, can be further studied in the future. Above all, the experimental results provide a theoretical basis for understanding the regulatory network of rice seed longevity and for breeding rice varieties that are resistant to aging.

Key words: seed longevity, transcriptome, plant hormones, sugar signal, phenylpropanoid biosynthesis

Chaofei Han, Ling Chen, Yuanxiu Wang, Qian Cheng, Sheng Zuo, Huabin Liu, Chengliang Wang. Mining and analysis of key genes related to rice seed longevity in NJ9108 based on transcriptomics[J]. Hereditas(Beijing), 2025, 47(3): 351-365.

Figures/Tables 7

Table 1

Fig. 1

Fig. 2

Fig. 3

Fig. 4

Fig. 5

Fig. 6

References 27

[1]	Leprince O, Pellizzaro A, Berriri S, Buitink J. Late seed maturation: drying without dying. J Exp Bot, 2017, 68(4): 827-841. doi: 10.1093/jxb/erw363 pmid: 28391329
[2]	Xue F, Qu CL, Wang RL, Li H. Progress on the fever and moldy of paddy during storage. Sci Technol Food Ind, 2017, 38(12): 338-341.
	薛飞, 渠琛玲, 王若兰, 李慧. 稻谷储藏过程中发热霉变研究进展. 食品工业科技, 2017, 38(12): 338-341.
[3]	Zinsmeister J, Leprince O, Buitink J. Molecular and environmental factors regulating seed longevity. Biochem J, 2020, 477(2): 305-323. doi: 10.1042/BCJ20190165 pmid: 31967650
[4]	Sano N, Rajjou L, North HM, Debeaujon I, Marion-Poll A, Seo M. Staying alive: molecular aspects of seed longevity. Plant Cell Physiol, 2016, 57(4): 660-674. doi: 10.1093/pcp/pcv186 pmid: 26637538
[5]	Li T, Zhang YM, Wang D, Liu Y, Dirk LMA, Goodman J, Downie AB, Wang JM, Wang GY, Zhao TY. Regulation of seed vigor by manipulation of raffinose family oligosaccharides in maize and Arabidopsis thaliana. Mol Plant, 2017, 10(12): 1540-1555.
[6]	Pirredda M, Fañanás-Pueyo I, Oñate-Sánchez L, Mira S. Seed longevity and ageing: a review on physiological and genetic factors with an emphasis on hormonal regulation. Plants (Basel), 2023, 13(1): 41.
[7]	Chen DF, Li YL, Fang T, Shi XL, Chen XW. Specific roles of tocopherols and tocotrienols in seed longevity and germination tolerance to abiotic stress in transgenic rice. Plant Sci, 2016, 244: 31-39. doi: 10.1016/j.plantsci.2015.12.005 pmid: 26810451
[8]	He WP, Wang R, Zhang Q, Fan MX, Lyu YY, Chen S, Chen DF, Chen XW. E3 ligase ATL5 positively regulates seed longevity by mediating the degradation of ABT1 in Arabidopsis. New Phyto, 2023, 239(5): 1754-1770.
[9]	Wang CL, Chen S, Dong YP, Ren RJ, Chen DF, Chen XW. Chloroplastic Os3BGlu6 contributes significantly to cellular ABA pools and impacts drought tolerance and photosynthesis in rice. New Phytol, 2020, 226(4): 1042-1054. doi: 10.1111/nph.16416 pmid: 31917861
[10]	Gupta R, Min CW, Choet JH, Jung JY, Jeon JS, Kim YJ, Kim JK, Kim ST. Integrated "-omics" analysis highlights the role of brassinosteroid signaling and antioxidant machinery underlying improved rice seed longevity during artificial aging treatment. Plant Physiol Biochem, 2024, 206: 108308.
[11]	Fenollosa G, Jené L, Munné-Bosch S. A rapid and sensitive method to assess seed longevity through accelerated aging in an invasive plant species. Plant Methods, 2020, 16: 64. doi: 10.1186/s13007-020-00607-3 pmid: 32411273
[12]	Liu FZ, Li NN, Yu YY, Chen W, Yu SB, He HZ. Insights into the regulation of rice seed storability by seed tissue- specific transcriptomic and metabolic profiling. Plants (Basel), 2022, 11(12): 1570.
[13]	Ren RJ, Wang P, Wang LN, Su JP, Sun LJ, Sun Y, Chen DF, Chen XW. Os4BGlu14, a monolignol β-Glucosidase, negatively affects seed longevity by influencing primary metabolism in rice. Plant Mol Biol, 2020, 104(4-5): 513-527.
[14]	MacGregor DR, Kendall SL, Florance H, Fedi F, Moore K, Paszkiewicz K, Smirnoff N, Penfield S. Seed production temperature regulation of primary dormancy occurs through control of seed coat phenylpropanoid metabolism. New Phytol, 2015, 205(2): 642-652. doi: 10.1111/nph.13090 pmid: 25412428
[15]	Liang MX, Davis E, Gardner D, Cai XN, Wu YG. Involvement of AtLAC15 in lignin synthesis in seeds and in root elongation of Arabidopsis. Planta, 2006, 224(5): 1185-1196.
[16]	Prasad CTM, Kodde J, Angenent GC, Hay FR, McNally KL, Groot SPC. Identification of the rice Rc gene as a main regulator of seed survival under dry storage conditions. Plant Cell Environ, 2023, 46(6): 1962-1980.
[17]	徐亮, 包维楷, 何永华. 种子贮藏物质变化及其贮藏生理. 种子, 2003, (5): 60-63.
[18]	Huang ZB, Ying JF, Peng LL, Sun S, Huang CW, Li C, Wang ZF, He YQ. A genome-wide association study reveals that the cytochrome b5 involved in seed reserve mobilization during seed germination in rice. Theor Appl Genet, 2021, 134(12): 4067-4076. doi: 10.1007/s00122-021-03948-2 pmid: 34546380
[19]	Lee KH, Piao HL, Kim HY, Choi SM, Jiang F, Hartung W, Hwang I, Kwak JM, Lee IJ, Hwang I. Activation of glucosidase via stress-induced polymerization rapidly increases active pools of abscisic acid. Cell, 2006, 126(6): 1109-1120. doi: 10.1016/j.cell.2006.07.034 pmid: 16990135
[20]	Kretzschmar T, Pelayo MA, Trijatmiko KR, Gabunada LFM, Alam R, Jimenez R, Mendioro MS, Slamet-Loedin IH, Sreenivasulu N, Bailey-Serres J, Ismail AM, Mackill DJ, Septiningsih EM. A trehalose-6-phosphate phosphatase enhances anaerobic germination tolerance in rice. Nat Plants, 2015, 1: 15124. doi: 10.1038/nplants.2015.124 pmid: 27250677
[21]	Pellizzaro A, Neveu M, Lalanne D, Vu BL, Kanno Y, Seo M, Leprince O, Buitink J. A role for auxin signaling in the acquisition of longevity during seed maturation. New Phytol, 2019, 225(1): 284-296.
[22]	Wei YS, Peng QL, Huang YA, Chen YR, Zhao-Cheng YF, Xi XY. Advance in research on mechanism of plant seed senescence. Acta Agric Boreali-Occident Sin, 2024, 33(5): 775-786.
	魏永胜, 彭琪朗, 黄滢奥, 陈彦如, 赵程亚菲, 郗欣悦. 植物种子衰老机制研究进展. 西北农业学报, 2024, 33(5): 775-786.
[23]	Yuan ZY, Fan K, Wang YT, Tian L, Zhang CP, Sun WQ, He HZ, Yu SB. OsGRETCHENHAGEN3-2 modulates rice seed storability via accumulation of abscisic acid and protective substances. Plant Physiol, 2021, 186(1): 469-482. doi: 10.1093/plphys/kiab059 pmid: 33570603
[24]	He YQ, Zhao J, Yang B, Sun S, Peng LL, Wang ZF. Indole-3-acetate beta-glucosyltransferase OsIAGLU regulates seed vigour through mediating crosstalk between auxin and abscisic acid in rice. Plant Biotechnol J, 2020, 18(9): 1933-1945. doi: 10.1111/pbi.13353 pmid: 32012429
[25]	Xu MR, Huang LY, Zhang F, Zhu LH, Zhou YL, Li ZK. Genome-wide phylogenetic analysis of stress-activated protein kinase genes in rice (OsSAPKs) and expression profiling in response to Xanthomonas oryzae pv. oryzicola infection. Plant Mol Biol Rep, 2013, 31(4): 877-885.
[26]	Kobayashi Y, Yamamoto S, Minami H, Kagaya Y, Hattori T. Differential activation of the rice sucrose nonfermenting1- related protein kinase2 family by hyperosmotic stress and abscisic acid. Plant Cell, 2004, 16(5): 1163-1177. doi: 10.1105/tpc.019943 pmid: 15084714
[27]	Siadat SA, Moosavi SA, Sharafizadeh M. Alleviate seed ageing effects in silybum marianum by application of hormone seed priming. Not Sci Biol, 2015, 7(3): 316-321.

Metrics

Comments

www.chinagene.cn
备案号：京ICP备09063187号

基因ID	正向引物(5′→3′)	反向引物(5′→3′)
Os08g0448000	GCCGTCGTCCCAATGAAG	GTAGAACACCACCTGCTTTGC
Os08g0270400	GCAGGAGCACTGGAGATGA	ATCTCGTGCCCAGGAACAA
Os01g0962700	CGTCAAACTGGCCGGTG	GCGTCGAGGTTGAGCTTG
Os06g0547400	CAATGGATGTGACGGCTCG	CCCACCCAGCAGGTTGAC
Os04g0513900	GGCGTTCGAAACTCCGTG	AAAGTGGGCATCGCTGTTG
Os05g0366600	TACAGGGACAAGTACCAGGCTA	CCAGTATCCAACCGACCATG
Os08g0473600	GCATCTTCTACGACCATGTGTTC	CACCTTGCCGTCGATCATG
Os09g0457600	AGTACCCTGCATTTTCTACGACC	CGTCATACCGTGTCCCAATC
Os07g0624600	CGACTGGATGGAGAAGCACC	CCGCCTCTCTCATTTCGTCG
Os09g0397300	AGGCTGAAGAGAGATGCAGAATG	GGCCCTTGCTTACACCCTG
Os03g0633800	CCATGTTCGTCTGCTTCTCC	GCTGGTGAACATGTCGAAAG
Os06g0166500	AATGGGCAACAAGAGGAGG	GCCCATCCTCTTGGTTAGTG
Os01g0764800	CACCGAGTTCCTCACCAGC	CCTGGCACGTACAAGTTCATG
Os04g0691100	TCTCGCGCATCATGTCCG	CCCATGCTGATGCGCTTG
Os08g0377200	CGCCATAACGTCCGAGTG	GGTGATTTCTTCACTTCCATGAG
Os04g0604300	CCACCTGCTACTTCATGTCGG	CCCGTCCACCAGCACAAG

Mining and analysis of key genes related to rice seed longevity in NJ9108 based on transcriptomics

RichHTML

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

Figures/Tables 7

References 27

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	Min Chen, Na Han, Yu Miao, Yujun Qiang, Wen Zhang, Pengbo Liu, Qiyong Liu, Dongmei Li. Differential transcriptome profiling of Bartonella spp. influenced by the species divergence factors [J]. Hereditas(Beijing), 2025, 47(3): 366-381.
[2]	Heng Wei, Tianpeng Liu, Jihong He, Kongjun Dong, Ruiyu Ren, Lei Zhang, Yawei Li, Ziyi Hao, Tianyu Yang. Genome-wide identification of GRF transcription factors and their expression profile in stem meristem of broomcorn millet (Panicum miliaceum L.) [J]. Hereditas(Beijing), 2024, 46(3): 242-255.
[3]	Xin Wen, Jin Mei, Meiyu Qian, Yidan Jiang, Juan Wang, Shibo Xu, Cuizhe Wang, Jun Zhang. Screening and analysis of GULP1 downstream target genes based on transcriptomic sequencing [J]. Hereditas(Beijing), 2024, 46(10): 860-870.
[4]	Yan Guo, Lele Yang, Huayu Qi. Transcriptome analysis of mouse male germline stem cells reveals characteristics of mature spermatogonial stem cells [J]. Hereditas(Beijing), 2022, 44(7): 591-608.
[5]	Min Cao, Tongda Xu. The molecular mechanism of apical hook development in dicot plant [J]. Hereditas(Beijing), 2021, 43(8): 723-736.
[6]	Hongbo Luo, Pengbo Cao, Gangqiao Zhou. Prognostic and predictive value of a DNA methylation-driven transcriptional signature in hepatocellular carcinoma [J]. Hereditas(Beijing), 2020, 42(8): 775-787.
[7]	Tianpei Shi,Li Zhang. Application of whole transcriptomics in animal husbandry [J]. Hereditas(Beijing), 2019, 41(3): 193-205.
[8]	Gaohua Zhang, Shutao Yu, He Wang, Xuda Wang. Transcriptome profiling of high oleic peanut under low temperatureduring germination [J]. Hereditas(Beijing), 2019, 41(11): 1050-1059.
[9]	Lan Ren,Rudan Xiao,Qian Zhang,Xiaomin Lou,Zhaojun Zhang,Xiangdong Fang. Synergistic regulation of the erythroid differentiation of K562 cells by KLF1 and KLF9 [J]. Hereditas(Beijing), 2018, 40(11): 998-1006.
[10]	Yajun Liu,Feng Zhang,Hongde Liu,Xiao Sun. The application of next-generation sequencing techniques in studying transcriptional regulation in embryonic stem cells [J]. Hereditas(Beijing), 2017, 39(8): 717-725.
[11]	Kai Wei,Lei Ma. Concept development of housekeeping genes in the high-throughput sequencing era [J]. Hereditas(Beijing), 2017, 39(2): 127-134.
[12]	Guangqi Li, Congjiao Sun, Guiqin Wu, Fengying Shi, Aiqiao Liu, Hao Sun, Ning Yang. Transcriptome sequencing identifies potential regulatory genes involved in chicken eggshell brownness [J]. Hereditas(Beijing), 2017, 39(11): 1102-1111.
[13]	Yongming Liu, Ling Zhang, Tao Qiu, Zhuofan Zhao, Moju Cao. Research progress on mechanisms of male sterility in plants based on high-throughput RNA sequencing [J]. Hereditas(Beijing), 2016, 38(8): 677-687.
[14]	Xiao Zhang, Guifang Jia. RNA epigenetic modification: N⁶-methyladenosine [J]. HEREDITAS(Beijing), 2016, 38(4): 275-288.
[15]	Shuaiqi Zhu, Yifu Gong, Yuqing Hang, Hao Liu, Heyu Wang. Transcriptome analysis of Dunaliella viridis [J]. HEREDITAS(Beijing), 2015, 37(8): 828-836.