Welcome to Acta Agronomica Sinica,

Acta Agron Sin ›› 2008, Vol. 34 ›› Issue (04): 591-597.doi: 10.3724/SP.J.1006.2008.00591

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Comparative Assessment of SSR Allelic Diversity in Wild and Cultivated Rice in China

ZHANG Xiao-Li12,Guo Hui3,WANG Hai-Gang12,LÜ Jian-Zhen2,YUAN Xiao-Ping2,PENG Suo-Tang1*,WEI Xing-Hua2*   

  1. 1 Shanxi Agricultural University, Taigu 030801, Shanxi; 2 State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, Zhejiang; 3 Guangxi University, Nanning 530004, Guangxi, China
  • Received:2007-07-09 Revised:1900-01-01 Online:2008-04-12 Published:2008-04-12
  • Contact: PENG Suo-Tang,WEI Xing-Hua

Abstract: Forty-eight SSR markers were used to compare genetic diversity in 288 accessions of common wild rice (O. rufipogon Griff.) and cultivated rice (O. sativa L.) in China. There were 505 alleles at the 48 loci investigated. The average number of alleles per locus (Na) was 10.5 with a range from 5 to 20. Total Nei’s genetic diversity index of Nei per locus (He) varied widely from 0.384 (RM409) to 0.905 (RM206) with an average value of 0.731. By comparison of the genetic changes in Na and He, the genetic di-versity of common wild rice was obviously higher than that of cultivated rice. Na and He of cultivated rice was only about 70.2% and 88.2% of common wide rice, respectively. In cultivated rice, Na of landraces and improved varieties were 65.4% and 53.0% of common wild rice respectively, and Na of improved varieties was 81.1% of landraces. Analysis of molecular variance (AMOVA) indicated that 10.3% of the variation was from differences between species. Using locus-by-locus AMOVA procedure, there were 43 loci with significant differentiation. The highest genetic differentiation was 46.3% (RM427) with a range from 0.7% to 46.3%. A cluster analysis showed japonica was the main trend for most of common wild rice in China. In addition, only a few of accessions from Guangdong and Hainan showed tendency towards indica type.

Key words: Common wild rice (O. rufipogon), Cultivated rice (O. sativa), Landrace, Improved variety, Genetic diversity, Analysis of molecular variance

[1] XIAO Ying-Ni, YU Yong-Tao, XIE Li-Hua, QI Xi-Tao, LI Chun-Yan, WEN Tian-Xiang, LI Gao-Ke, HU Jian-Guang. Genetic diversity analysis of Chinese fresh corn hybrids using SNP Chips [J]. Acta Agronomica Sinica, 2022, 48(6): 1301-1311.
[2] WANG Yan-Yan, WANG Jun, LIU Guo-Xiang, ZHONG Qiu, ZHANG Hua-Shu, LUO Zheng-Zhen, CHEN Zhi-Hua, DAI Pei-Gang, TONG Ying, LI Yuan, JIANG Xun, ZHANG Xing-Wei, YANG Ai-Guo. Construction of SSR fingerprint database and genetic diversity analysis of cigar germplasm resources [J]. Acta Agronomica Sinica, 2021, 47(7): 1259-1274.
[3] LIU Shao-Rong, YANG Yang, TIAN Hong-Li, YI Hong-Mei, WANG Lu, KANG Ding-Ming, FANG Ya-Ming, REN Jie, JIANG Bin, GE Jian-Rong, CHENG Guang-Lei, WANG Feng-Ge. Genetic diversity analysis of silage corn varieties based on agronomic and quality traits and SSR markers [J]. Acta Agronomica Sinica, 2021, 47(12): 2362-2370.
[4] ZHAO Xu-Yang, YAO Fang-Jie, LONG Li, WANG Yu-Qi, KANG Hou-Yang, JIANG Yun-Feng, LI Wei, DENG Mei, LI Hao, CHEN Guo-Yue. Evaluation of resistance to stripe rust and molecular detection of resistance genes of 93 wheat landraces from the Qinghai-Tibet spring and winter wheat zones [J]. Acta Agronomica Sinica, 2021, 47(10): 2053-2063.
[5] SUN Qian, ZOU Mei-Ling, ZHANG Chen-Ji, JIANG Si-Rong, Eder Jorge de Oliveira, ZHANG Sheng-Kui, XIA Zhi-Qiang, WANG Wen-Quan, LI You-Zhi. Genetic diversity and population structure analysis by SNP and InDel markers of cassava in Brazil [J]. Acta Agronomica Sinica, 2021, 47(1): 42-49.
[6] Meng-Liang ZHAO,Li-Hui WANG,Yan-Jing REN,Xue-Mei SUN,Zhi-Qiang HOU,Shi-Peng YANG,Li LI,Qi-Wen ZHONG. Genetic diversity of phenotypic traits in 257 Jerusalem artichoke accessions [J]. Acta Agronomica Sinica, 2020, 46(5): 712-724.
[7] YAN Cai-Xia,WANG Juan,ZHANG Hao,LI Chun-Juan,SONG Xiu-Xia,SUN Quan-Xi,YUAN Cui-Ling,ZHAO Xiao-Bo,SHAN Shi-Hua. Developing the key germplasm of Chinese peanut landraces based on phenotypic traits [J]. Acta Agronomica Sinica, 2020, 46(4): 520-531.
[8] Hong-Yan ZHANG,Tao YANG,Rong LIU,Fang JIN,Li-Ke ZHANG,Hai-Tian YU,Jin-Guo HU,Feng YANG,Dong WANG,Yu-Hua HE,Xu-Xiao ZONG. Assessment of genetic diversity by using EST-SSR markers in Lupinus [J]. Acta Agronomica Sinica, 2020, 46(3): 330-340.
[9] MA Yan-Ming, FENG Zhi-Yu, WANG Wei, ZHANG Sheng-Jun, GUO Ying, NI Zhong-Fu, LIU Jie. Genetic diversity analysis of winter wheat landraces and modern bred varieties in Xinjiang based on agronomic traits [J]. Acta Agronomica Sinica, 2020, 46(12): 1997-2007.
[10] MA Yan-Ming, LOU Hong-Yao, CHEN Zhao-Yan, XIAO Jing, XU Lin, NI Zhong-Fu, LIU Jie. Genetic diversity assessment of winter wheat landraces and cultivars in Xinjiang via SNP array analysis [J]. Acta Agronomica Sinica, 2020, 46(10): 1539-1556.
[11] LIU Yi-Ke,ZHU Zhan-Wang,CHEN Ling,ZOU Juan,TONG Han-Wen,ZHU Guang,HE Wei-Jie,ZHANG Yu-Qing,GAO Chun-Bao. Revealing the genetic diversity of wheat varieties (lines) in China based on SNP markers [J]. Acta Agronomica Sinica, 2020, 46(02): 307-314.
[12] YE Wei-Jun,CHEN Sheng-Nan,YANG Yong,ZHANG Li-Ya,TIAN Dong-Feng,ZHANG Lei,ZHOU Bin. Development of SSR markers and genetic diversity analysis in mung bean [J]. Acta Agronomica Sinica, 2019, 45(8): 1176-1188.
[13] Mi WU,Nian WANG,Chao SHEN,Cong HUANG,Tian-Wang WEN,Zhong-Xu LIN. Development and evaluation of InDel markers in cotton based on whole-genome re-sequencing data [J]. Acta Agronomica Sinica, 2019, 45(2): 196-203.
[14] Yuan LU,Wei-Da AI,Qing HAN,Yi-Fa WANG,Hong-Yang LI,Yu-Ji QU,Biao SHI,Xue-Fang SHEN. Genetic diversity and population structure analysis by SSR markers in waxy maize [J]. Acta Agronomica Sinica, 2019, 45(2): 214-224.
[15] BAI Yan-Ming,LI Long,WANG Hui-Yan,LIU Yu-Ping,WANG Jing-Yi,MAO Xin-Guo,CHANG Xiao-Ping,SUN Dai-Zhen,JING Rui-Lian. Genetic diversity assessment in derivative offspring of Mazhamai and Xiaobaimai wheat [J]. Acta Agronomica Sinica, 2019, 45(10): 1468-1477.
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed   
No Suggested Reading articles found!