Optimization of a Reaction System of Sequence Related Amplified Polymorphism and Segregation of Polymorphic Loci in an F2 Population of Rice

Abstract

Abstract: An effective PCR protocol for detecting the sequence related amplified polymorphism (SRAP) in rice was developed. One hundred and ten pairs of SRAP primers were used for segregation analysis in an F2 population derived from a cross between Shennong 606 and Lijiangxintuanheigu. Among the 110 primer pairs, 35 pairs generated 143 polymorphic bands with an average of 4.09 polymorphic bands per primer pair, and 24 pairs (16.78%) showed the genetic distortion (P<0.05). Of the 24 primer pairs, 12 pairs deviated toward the male parent Shennong 606 and 11 pairs toward the female parent Lijiangxintuanheigu, only one toward heterozygote. It was found that the segregation distortion might be caused by the joint gametic and zygotic effects.

Key words: rice, sequence related amplification polymorphism, amplified protocol, segregation distortion

JIANG Shu-kun, ZHONG Ming, ZHANG Xi-juan, ZHANG Li, XU Zheng-jin. Optimization of a Reaction System of Sequence Related Amplified Polymorphism and Segregation of Polymorphic Loci in an F2 Population of Rice[J]. RICE SCIENCE, 2008, 15(2): 95-100 .

References

1 Li G, Quiros C F. Sequence related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction and its application to mapping and gene tagging in Brassica. Theor Appl Genet, 2001, 103: 455–461.
2 Lin Z X, Zhang X L, Nie Y C, He D H, Wu M Q. Construction of a genetic linkage map for cotton based on SRAP. Chinese Sci Bull, 2003, 48(19): 2063–2067. (in Chinese with English abstract)
3 Qian W C, Zhang G H, Chen F X, Han Y K, Chen D F, Du S L. Characteristics of SRAP marker in detecting polymorphism of cucumber genome. Hereditas (Beijing), 2006, 28(11): 1435–1439. (in Chinese with English abstract)
4 Riza A, Li G, Quresh Z. Genetic diversity of oilseed Brassica napu inbred lines based on sequence related amplified polymorphism and its relation to hybrid performance. Plant Breeding, 2001, 20(5): 411–415.
5 Ferriol M, Pico B, Nuez F. Genetic diversity of a germplasm collection of Cucurbita pepo using SRAP and AFLP marker. Theor Appl Genet, 2003, 107(2): 271–282.
6 Ren Y, Wang D Y, Zhang Y D. Optimization of SRAP-PCR in hot pepper (Capsicum annuum L.). Mol Plant Breeding, 2004, 5(2): 689–693. (in Chinese with English abstract)
7 Jiang S K, Zhong M, Xu Z J, Zhang L, Ma H, Liu S X. Classification of rice cultivars with RAPD molecular markers. J Shenyang Agric Univ, 2006, 37(4): 639–641. (in Chinese with English abstract)
8 Pham J L, Glaszmann J C, Sano R. Isozyme markers in rice: Genetic analysis and linkage relationships. Genome, 1990, 33: 348–359.
9 Tan J, Xue Q Z. Mapping by molecular markers showing segregation distortion. Hereditas (Beijing), 2004, 26(3): 356–358. (in Chinese with English abstract)
10 Zhang D S, Chen S Y, Hui D W, Zhuang B C. Segregation distortion of RFLP markers in F2 population of cultivated/ semi-wild soybean and the causal analysis. Acta Genet Sin, 1997, 24 (4): 362–367. (in Chinese with English abstract)
11 Xu Y, Zhu L, Xiao J, Huang N, McCouch S R. Chromosomal regions associated with segregation distortion of molecular markers in F2, backcross, double haploid, and recombinant inbred populations in rice (Oryza sativa L.). Mol Gen Genet, 1997, 253: 535–545.
12 Matsushita S, Iseki T, Fukuta Y. Characterization of segregation distortion chromosome 3 induced in wide hybridization between indica and japonica type rice varieties. Euphytica, 2003, 134: 27–32.
13 Konishi T, Yano Y, Abe K. Geographic distribution of alleles at the Ga2 locus for segregation distortion in barley. Theor Appl Genet, 1992, 85: 419–422.
14 Xu Y B, Shen Z T, Chen Y. Distorted segregation of RFLP markers and their distribution on chromosomes in an indica/japonica F2 population of rice. Acta Bot Sci, 1995, 37 (2): 91–96. (in Chinese with English abstract)
15 Harushima Y, Kurata N, Yano M. Detection of segregation distortions in an indica-japonica rice cross using a high- resolution molecular map. Theor Appl Genet, 1996, 92: 145–150.
16 Kinishita T. Report of the committee on gene symbolization, nomenclature and linkage group. Rice Genet Newsl, 1991, 8: 2–37.
17 Kinishita T. Report of the committee on gene symbolization, nomenclature and linkage group. Rice Genet Newsl, 1993, 10: 7–39.
18 Liu F, Wu X L, Chen S Y. Segregation distortion of molecular markers in recombinant inbred populations in soybean (G. max). Acta Genet Sin, 2000, 27(10): 883–887. (in Chinese with English abstract)

[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.