Monitoring the Expression Profiles of Cereal Crops Seedlings by Using Rice cDNA Microarray

Abstract

Abstract:

Through exploiting the high homology of cereal crop genes, membranous cDNA microarrays containing 3 311 unique rice transcripts (including 1 639 endosperm-derived transcripts and 1 672 mature stem-derived transcripts) were used for monitoring the expression profiles of 1-leaf stage seedlings of 4 cereal crop species: rice, maize, sorghum and barley. After hybridizing with [α-³³P] labeled probes, 73.6 % of the arrayed genes generated reliable signals in all of the four cereal crops. Further analysis revealed that among the arrayed genes, a higher percentage of the endosperm-derived transcripts (86.6 %) expressed than that of the mature stem-derived genes (60.9 %), indicating that most of the endosperm expressed genes functioned in young seedlings while considerable amount of mature stem tissue expressed genes did not express. These results also inferred that some genes might function only at certain developmental stages. By comparing the obtained profiles, 84 genes were identified constantly expressed in all the four cereal crops. Many housekeeping genes, such as polyubiquitin, ubiquitin conjugating enzyme and ribosomal proteins were included in this catalogue. The experiment also identified 14 rice seedling specifically expressed genes, including 3 biotic and abiotic stress induced genes and 1 apoptosis suppressor encoding gene Bax inhibitor-1. This investigation provided invaluable information for comparative genomics of gramineae members.

Key words: rice, cereal crops, cDNA microarray, expression profile

SUN Liang-xian, DONG Hai-tao, LI De-bao. Monitoring the Expression Profiles of Cereal Crops Seedlings by Using Rice cDNA Microarray[J]. RICE SCIENCE.

References

1 Kellogg E A. Relationships of cereal crops and other grasses. Proc Natl Acad Sci, USA, 1998, 95 (5): 2005–2010.

2 Gale M D, Devos K M. Plant comparative genetics after 10 years. Science, 1998, 282(23): 656–659.

3 Chandler V L, Wessler S. A grasses collective model genetic system. Plant Physiol, 2001, 125: 1155–1156 .

4 Freeling M. Grasses as a single genetic system reassessment. Plant Physiol, 2001, 125:1191–1197.

5 Goff S A, Ricke D, Lan T H, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange B M, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun W L, Chen L, Cooper B, Park S, Wood T C, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller R M, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science, 2002, 296: 92–100.

6 Sun L X, Dong H T, Li D B. Monitoring the expression pattern of some metabolic important genes in germinating rice(Oryza sativa) by using cDNA microarray. Chinese J Rice Sci, 2002, 16 (4): 299–303. (in Chinese with English abstract)

7 Sambrook J, Fritsch E F, Maniatis T M. Molecular Clone: A laboratory manual. 2^nd ed. New York: Cold Spring Harbor Laboratory Press, 1989. 7–52.

8 Richmond T, Somerville S. Chasing the dream: plant est microarray. Curr Opn Plant Biol, 2000, 3: 108–116.

9 Springob K, Lukacœ R, Ernwein C, Matern U. Specificities of functionally expressed chalcone and acridone synthases from Ruta graveolens. Eur J Biochem, 2000, 267: 6552–6559.

10 Leister D, Kurth J, Laurie D A, Yano M, Sasaki T, Devos K. Rapid reorganization of resistance gene homologues in cereal genomes. Proc Natl Acad Sci, USA, 1998, 95: 370–375.

11 Yamada M K, Jin L, Yoshinaga K, Hirata A, Uchimiya H. Mammalian Bax-induced plant cell death can be down-regulated by overexpression of Arabidopsis Bax Inhibitor-1 (AtBI-1). Proc Natl Acad Sci, USA, 2001, 98: 12295–12300.

12 Lee M H, Min M K, Lee Y J, Jin J B, Shin D H, Kim D H, Lee K H. ADP-ribosylation factor 1 of Arabidopsis plays a critical role in intracellular trafficking and maintenance of endoplasmic reticulum morphology in Arabidopsis. Plant Physiol, 2002, 129(4): 1507–1520.

13 Hu H, Zhang Q, Ochi K. Activation of antibiotic biosynthesis by specified mutations in the rpoB gene (encoding the RNA polymerase beta subunit) of Streptomyces lividans. J Bacteriol, 2002 , 184 (14): 3984–3991.

14 Komatsu K, Zhu S, Fushimi H, Qui T K, Cai S, Kadota S. Phylogenetic analysis based on 18S rRNA gene and matK gene sequences of Panax vietnamensis and five related species. Planta Med, 2001, 67 (5): 461–465.

15 Zamore P D, Green M R. Identification, purification, and biochemical characterization of U2 small nuclear ribonucleoprotein auxiliary factor. Proc Natl Acad Sci, USA, 1989, 86 (23): 9243–927I.

16 Velculescu V E, Zhang L, Zhou W, Vogelstein J, Munira A, Kinzler K W. Characterization of the teast transcriptome. Cell, 1997, 88: 243–251.

[1]	Prathap V, Suresh KUMAR, Nand Lal MEENA, Chirag MAHESHWARI, Monika DALAL, Aruna TYAGI. Phosphorus Starvation Tolerance in Rice Through a Combined Physiological, Biochemical and Proteome Analysis [J]. Rice Science, 2023, 30(6): 8-.
[2]	Serena REGGI, Elisabetta ONELLI, Alessandra MOSCATELLI, Nadia STROPPA, Matteo Dell’ANNO, Kiril PERFANOV, Luciana ROSSI. Seed-Specific Expression of Apolipoprotein A-I_Milano Dimer in Rice Engineered Lines [J]. Rice Science, 2023, 30(6): 6-.
[3]	Sundus ZAFAR, XU Jianlong. Recent Advances to Enhance Nutritional Quality of Rice [J]. Rice Science, 2023, 30(6): 4-.
[4]	Kankunlanach KHAMPUANG, Nanthana CHAIWONG, Atilla YAZICI, Baris DEMIRER, Ismail CAKMAK, Chanakan PROM-U-THAI. Effect of Sulfur Fertilization on Productivity and Grain Zinc Yield of Rice Grown under Low and Adequate Soil Zinc Applications [J]. Rice Science, 2023, 30(6): 9-.
[5]	FAN Fengfeng, CAI Meng, LUO Xiong, LIU Manman, YUAN Huanran, CHENG Mingxing, Ayaz AHMAD, LI Nengwu, LI Shaoqing. Novel QTLs from Wild Rice Oryza longistaminata Confer Rice Strong Tolerance to High Temperature at Seedling Stage [J]. Rice Science, 2023, 30(6): 14-.
[6]	LIN Shaodan, YAO Yue, LI Jiayi, LI Xiaobin, MA Jie, WENG Haiyong, CHENG Zuxin, YE Dapeng. Application of UAV-Based Imaging and Deep Learning in Assessment of Rice Blast Resistance [J]. Rice Science, 2023, 30(6): 10-.
[7]	Md. Forshed DEWAN, Md. AHIDUZZAMAN, Md. Nahidul ISLAM, Habibul Bari SHOZIB. Potential Benefits of Bioactive Compounds of Traditional Rice Grown in South and South-East Asia: A Review [J]. Rice Science, 2023, 30(6): 5-.
[8]	Raja CHAKRABORTY, Pratap KALITA, Saikat SEN. Phenolic Profile, Antioxidant, Antihyperlipidemic and Cardiac Risk Preventive Effect of Chakhao Poireiton (A Pigmented Black Rice) in High-Fat High-Sugar induced Rats [J]. Rice Science, 2023, 30(6): 11-.
[9]	LI Qianlong, FENG Qi, WANG Heqin, KANG Yunhai, ZHANG Conghe, DU Ming, ZHANG Yunhu, WANG Hui, CHEN Jinjie, HAN Bin, FANG Yu, WANG Ahong. Genome-Wide Dissection of Quan 9311A Breeding Process and Application Advantages [J]. Rice Science, 2023, 30(6): 7-.
[10]	JI Dongling, XIAO Wenhui, SUN Zhiwei, LIU Lijun, GU Junfei, ZHANG Hao, Tom Matthew HARRISON, LIU Ke, WANG Zhiqin, WANG Weilu, YANG Jianchang. Translocation and Distribution of Carbon-Nitrogen in Relation to Rice Yield and Grain Quality as Affected by High Temperature at Early Panicle Initiation Stage [J]. Rice Science, 2023, 30(6): 12-.
[11]	Nazaratul Ashifa Abdullah Salim, Norlida Mat Daud, Julieta Griboff, Abdul Rahim Harun. Elemental Assessments in Paddy Soil for Geographical Traceability of Rice from Peninsular Malaysia [J]. Rice Science, 2023, 30(5): 486-498.
[12]	Monica Ruffini Castiglione, Stefania Bottega, Carlo Sorce, Carmelina SpanÒ. Effects of Zinc Oxide Particles with Different Sizes on Root Development in Oryza sativa [J]. Rice Science, 2023, 30(5): 449-458.
[13]	Tan Jingyi, Zhang Xiaobo, Shang Huihui, Li Panpan, Wang Zhonghao, Liao Xinwei, Xu Xia, Yang Shihua, Gong Junyi, Wu Jianli. ORYZA SATIVA SPOTTED-LEAF 41 (OsSPL41) Negatively Regulates Plant Immunity in Rice [J]. Rice Science, 2023, 30(5): 426-436.
[14]	Ammara Latif, Sun Ying, Pu Cuixia, Noman Ali. Rice Curled Its Leaves Either Adaxially or Abaxially to Combat Drought Stress [J]. Rice Science, 2023, 30(5): 405-416.
[15]	Liu Qiao, Qiu Linlin, Hua Yangguang, Li Jing, Pang Bo, Zhai Yufeng, Wang Dekai. LHD3 Encoding a J-Domain Protein Controls Heading Date in Rice [J]. Rice Science, 2023, 30(5): 437-448.