Identification and Fine Mapping of a Gene Related to Pale Green Leaf Phenotype near the Centromere Region in Rice (Oryza sativa)

Abstract

Abstract: A thermo-insensitive pale green leaf mutant (pgl2) was isolated from T-DNA inserted transgenic lines of rice (Oryza sativa L. subsp. japonica cv. Nipponbare). Genetic analysis indicated that the phenotype was caused by a recessive mutation in a single nuclear-encoded gene. To map the PGL2 gene, an F₂ population was constructed by crossing the mutant with Longtefu (Oryza sativa L. subsp. indica). The PGL2 locus was roughly linked to SSR marker RM331 on chromosome 8. To finely map the gene, 14 new InDel markers were developed around the marker, and PGL2 was further mapped to a 2.37 Mb centromeric region. Analysis on chlorophyll contents of leaves showed that there was no obvious difference between the mutant and the wild type in total chlorophyll (Chl) content, while the ratio of Chl a / Chl b in the mutant was only about 1, which was distinctly lower than that in the wild type, suggesting that the PGL2 gene was related to the conversion between Chl a and Chl b. Moreover, the method of primer design around the centromeric region was discussed, which would provide insight into fine mapping of the functional genes in plant centromeres.

Key words: centromere, gene, fine mapping, pale green leaf mutant, chlorophyll a, chlorophyll b, rice

ZHU Li, LIU Wen-zhen, WU Chao, LUAN Wei-jiang, FU Ya-ping, HU Guo-cheng, SI Hua-min, SUN Zong-xiu. Identification and Fine Mapping of a Gene Related to Pale Green Leaf Phenotype near the Centromere Region in Rice (Oryza sativa)[J]. RICE SCIENCE, 2007, 14(3): 172-180 .

References

1 Lin X, Bevan M, Murphy G, Harris B, Parnell L D, McCombie W R, Martienssen R A, Marra M, Preuss D. Genetic definition and sequence analysis of Arabidopsis centromeres. Science, 1999, 286: 2468-2474.
2 Heslop-Harrison J S, Murata M, Ogura Y, Schwarzacher T, Motoyoshi F. Polymorphisms and genomic organization of repetitive DNA from centromeric regions of Arabidopsis chromosomes. Plant Cell, 1999, 11: 31-42.
3 Kumekawa N, Hosouchi T, Tsuruoka H, Kotani H. The size and sequence organization of the centromeric region of Arabidopisis thaliana chromosome 4. DNA Res, 2001, 8: 285-290.
4 Cheng Z, Dong F, Langdon T, Ouyang S, Buell C R, Gu M, Blattner F R, Jiang J. Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell, 2002, 14:1691-1704.
5 Nagaki K, Cheng Z, Ouyang S, Talbert P B, Kim M, Jones K M, Henikoff S, Buell C R, Jiang J. Sequencing of a rice centromere uncovers active genes. Nat Genet, 2004, 36:138-145.
6 Wu J, Yamagata H, Hayashi-Tsugane M, Hijishita S, Fujisawa M, Shibata M, Ito Y, Nakamura M, Sakaguchi M, Yoshihara R, Kobayashi H, Ito K, Karasawa W, Yamamoto M, Saji S, Katagiri S, Kanamori H, Namiki N, Katayose Y, Matsumoto T, Sasaki T. Composition and structure of the centromeric region of rice chromosome 8. Plant Cell, 2004, 16: 967-976.
7 Zhang Y, Huang Y, Zhang L, Li Y, Lu T, Lu Y, Feng Q, Zhao Q, Cheng Z, Xue Y, Wing R A, Han B. Structural features of the rice chromosome 4 centromere. Nucl Acids Res, 2004, 32: 2023-2030.
8 Ananiev E V, Phillips R L, Rines H W. Chromosome- specific molecular organization of maize (Zea mays L.) centromeric regions. Proc Natl Acad Sci, USA, 1998, 95: 13073-13078.
9 Jin W, Melo J R, Nagaki K, Talbert P B, Henikoff S, Dawe R K, Jiang J. Maize centromeres: Organization and functional adaptation in the genetic background of oat. Plant Cell, 2004, 16: 571-581.
10 Sun X, Wahlstrom J, Karpen G. Molecular structure of a functional Drosophila centromere. Cell, 1997, 91: 1007-1009.
11 Sun X, Le H D, Wahlstrom J M, Karpen G H. Sequence analysis of a functional Drosophila centromere. Genome Res, 2003, 13: 182-194.
12 Schueler M G, Higgins A W, Rudd M K, Gustashaw K, Willard H F. Genomic and genetic definition of a functional human centromere. Science, 2001, 294: 109-115.
13 Rudd M K, Schueler M G, Willard H F. Sequence organization and functional annotation of human centromeres. Cold Spring Harb Symp Quant Biol, 2003, 68: 141-149.
14 Martinez-Zapater J M, Estelle M A, Somerville C R. A high repeated sequence in Arabidopsis thaliana. Mol Gen Genet, 1986, 204(3): 417-423.
15 Waye J S, Willard H F. Nucleotide sequence heterogeneity of alpha satellite repetitive DNA: A survey of alphoid sequences from different human chromosomes. Nucl Acids Res, 1987, 15: 7549-7569.
16 Nagaki K, Neumann P, Zhang D, Ouyang S, Buell C R, Cheng Z, Jiang J. Structure, divergence, and distribution of the CRR centromeric retrotransposon family in rice. Mol Biol Evol, 2005, 22(4): 845-855.
17 Kumar A, Bennetzen J L. Plant retrotransposons. Annu Rev Genet, 1999, 33: 479-532.
18 Choo K H, Vissel B, Nagy A, Earle E, Kalitsis P. A survey of the genomic distribution of alpha-satellite DNA on all the human chromosomes, and derivation of a new consensus sequence. Nucl Acids Res, 1991, 19: 1179-1182.
19 Kaszas E, Birchler J A. Misdivision analysis of centromere structure in maize. EMBO J, 1996, 15: 5246-5255.
20 Hosouchi T, Kumekawa N, Tsuruoka H, Kotani H. Physical map-based sizes of the centromeric regions of Arabidopsis thaliana chromosomes 1, 2, and 3. DNA Res, 2002, 9: 117-121.
21 Ma J X, Jackson S A. Retrotransposon accumulation and satellite amplification mediated by segmental duplication facilitate centromere expansion in rice. Genome Res, 2006, 16: 251-259.
22 Yan H H, Jiang J M. Rice as a model for centromere and heterochromatin research. Chrom Res, 2007, 15: 77-84.
23 Huq E，Al-Sady B，Hudson M，Kim C, Apel K，Quail P H. PHYTOCHROME-INTERACTING FACTOR 1 is a critical bHLH regulator of chlorophyll biosynthesis. Science, 2004, 305: 1937-1941.
24 Nakanishi H，Nozue H，Suzuki K，Kaneko Y, Taguchi G, Hayashida N. Characterization of the Arabidopsis thaliana mutant pcb2 which accumulates divinyl chlorophylls. Plant Cell Physiol, 2005, 46(3): 467-473.
25 Nagata N，Tanaka R，Satoh S，Tanaka A. Identification of a vinyl reductase gene for chlorophyll synthesis in Arabidopsis thaliana and implications for the evolution of prochlorococcus species. Plant Cell, 2005, 17: 233-240.
26 Frick G, Su Q, Apel K, Armstrong G A. An Arabidopsis porB porC double mutant lacking light-dependent NADPH: Protochlorophyllide oxidoreductases B and C is highly chlorophyll-deficient and developmentally arrested. Plant J, 2003, 35: 141-153.
27 Benedetti C E，Arruda P. Altering the expression of the chlorophyllase gene ATHCOR1 in transgenic Arabidopsis caused changes in the chlorophyll-to-chlorophyllide ratio. Plant Physiol, 2002, 128: 1255-1263.
28 Rzeznicka K, Walker C J, Westergren T，Kannangara C G, Wettstein D, Merchant S, Gough S P, Hansson M. Xantha-l encodes a membrane subunit of the aerobic Mg-protoporphyrin IX monomethyl ester cyclase involved in chlorophyll biosynthesis. Proc Natl Acad Sci, USA, 2005, 102(16): 5886-5891.
29 Jung K H, Hur J, Ryu C H, Choi Y, Chung Y Y, Miyao A, Hirochika H, An G. Characterization of a rice chlorophyll- deficient mutant using the T-DNA gene-trap system. Plant Cell Physiol, 2003, 44(5): 463-472.
30 Zhang H, Li J, Yoo J H, Yoo S C, Cho S H, Koh H J, Seo H S, Paek N C. Rice Chlorina-1 and Chlorina-9 encode ChlD and ChlI subunits of Mg-chelatase, a key enzyme for chlorophyll synthesis and chloroplast development. Plant Mol Biol, 2006, 62: 325-337.
31 Lee S, Kim J H, Yoo E S, Lee C H, Hirochika H，An G. Differential regulation of chlorophyll a oxygenase genes in rice. Plant Mol Biol, 2005, 57: 805-818.
32 Zhu Z G, Xiao H, Fu Y P, Hu G C, Yu Y H, Si H M, Zhang J L, Sun Z X. Construction of transgenic rice populations by inserting the maize transponson Ac/Ds and genetic analysis for several mutants. Chinese J Biotech, 2001, 17(3): 288-292. (in Chinese with English abstract)
33 Chuong P V, Omura T. Studies on the chlorosis expressed under low temperature conditions in rice Oryza sativa L. Bull Inst Trop Agric, 1982, 5: 1-58.
34 Shu Q Y, Liu G F, Xia Y W. Temperature-sensitive leaf color mutant in rice (Oryza sativa L.). Acta Agric Nucl Sin, 1996, 10(1): 6-10. (in Chinese with English abstract)
35 Cui H R, Xia Y W, Gao M W. Effects of temperature on leaf color and chlorophyll biosynthesis of rice mutant w1. Acta Agric Nucl Sin, 2001, 15 (5): 269-273. (in Chinese with English abstract)
36 Shao J R, Zhu X M, Xie R, Ren Z L, Sun J S. Alteration of protein and amino acid components and rubisco activity in leaves of thermo-sensitive mutant line of rice during induced of green and yellow banding. Acta Biol Exp Sin, 2004, 37(3): 183-188. (in Chinese with English abstract)
37 Arnon D I. Copper enzymes in isolated chloroplasts: Polyphenoloxidase in Beta vulgaris. Plant Physiol, 1949, 24: 1-15.
38 Lu Y J, Zheng K L. A simple method for isolation of rice DNA. Chinese J Rice Sci, 1992, 6(1): 47-48. (in Chinese)
39 Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): Frequency, length, variation, transposon associations, and genetic marker potential. Genome Res, 2001, 11: 1441-1452.
40 McCouch S R, Teytelman L, Xu Y B, Lobos K B, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L. Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res, 2002, 9: 199-207.
41 Wu J, Maehara T, Shimokawa T, Yamamoto S, Harada C, Takazaki Y, Ono N, Mukai Y, Koike K, Yazaki J, Fujii F, Shomura A, Ando T, Kono I, Waki K, Yamamoto K, Yano M, Matsumoto T, Sasaki T. A comprehensive rice transcript map containing 6591 expressed sequence tag sites. Plant Cell, 2002, 14: 525–535.
42 Yan H H, Jin W W, Nagaki K, Tian S L, Ouyang S, Buell C R, Talbert P B, Henikoff S, Jiang J M. Transcription and histone modifications in the recombination-free region spanning a rice centromere. Plant Cell, 2005, 17: 3227-3238.
43 Eckhardt U, Grimm B, Hörtensteiner S. Recent advances in chlorophyll biosynthesis and breakdown in higher plants. Plant Mol Biol, 2004, 56: 1-14.
44 Grossman A R, Lohr M, Im C S. Chlamydomonas reinhardtii in the landscape of pigments. Annu Rev Genet, 2004, 38: 119-173.

[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]	XIA Xiaodong, ZHANG Xiaobo, WANG Zhonghao, CHENG Benyi, Sun Huifeng, XU Xia, GONG Junyi, YANG Shihua, WU Jianli, SHI Yongfeng, XU Rugen. Mapping and Functional Analysis of LE Gene in a Lethal Etiolated Rice Mutant at Seedling Stage [J]. Rice Science, 2023, 30(6): 13-.
[7]	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-.
[8]	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-.
[9]	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-.
[10]	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-.
[11]	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-.
[12]	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.
[13]	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.
[14]	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.
[15]	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.