Welcome to Acta Agronomica Sinica，

Acta Agron Sin ›› 2011, Vol. 37 ›› Issue (02): 224-234.doi: 10.3724/SP.J.1006.2011.00224

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

Assessment of Genetic Diversity in Chinese Sorghum Landraces Using SSR Markers as Compared with Foreign Accessions

ZHANG Han,WANG Jian-Cheng,WANG Dong-Jian,YAO Feng-Xia,XU Jin-Fang,SONG Guo-An,GUAN Yan-An,LI Ru-Yu*   

  1. Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
  • Received:2010-06-01 Revised:2010-09-24 Online:2011-02-12 Published:2010-12-15
  • Contact: LI Ru-Yu, E-mail:li_ruyu@sina.com, Tel: 13606373889

PDF

1453

Cited

18

Abstract: The genetic variation of 184 Chinese sorghum landraces (Sorghum bicolor L.) from a broad geographic area and representing different phenotypes, and 69 representative foreign cultivated sorghum accessions (world sorghum), was assessed using 32 nuclear SSR primer pairs. Overall, lower level of genetic diversity was detected in Chinese sorghum than in world sorghum. The allelic richness (Rs) and Nei’s allele diversity (He) for Chinese sorghum and world sorghum were 9.81 and 0.629, and 11.52 and 0.745, respectively. Fewer unique alleles were detected in Chinese sorghum than in world sorghum. Chinese sorghum had a genetic diversity level lower than accessions from East Africa (He=0.732), North America (He=0.707) and South Asia (He=0.712); and was only comparable to those from South African accessions (He=0.609). Marked differences in level of genetic variation were revealed between Chinese sorghum landraces from 12 provinces, with Rs ranging from 3.64 to 4.88 and He from 0.517 to 0.714. Accessions from Jilin Province exhibited the highest level of genetic diversity among all regions in China, which was comparable to the sorghum in East Africa . The results indicated a strong divergence of Chinese sorghum from world sorghum, but a weak differentiation among Chinese sorghum both on regional and type bases. Principal component analysis (PCA) clearly separated Chinese sorghum from world accessions but could not separate Chinese sorghum into discrete geographical or phenotypic groups. Analysis of molecular variance (AMOVA) indicated that 20.43% of the total genetic variation was attributable to the difference between world and Chinese sorghum and 79.57% occurred among Chinese and world sorghum accessions. For Chinese sorghum, partitioning the total variation revealed that genetic diversity mainly existed among accessions within regions (91.94%) or eco-regions (94.97%) rather than among regions (8.06%) or eco-regions (5.03%). Similarly, a large portion (97.93%) of the total variation was found within types compared to among types (2.07%). Our study supports the view that Chinese sorghum is of African origin. Chinese sorghum may have experienced a long history of natural and human selection when largely isolated from outside world since prehistoric time. Suggestions for sorghum breeding programs were presented in the light of these data.

Key words: Sorghum bicolor, Genetic diversity, Microsatellites, Evolution, Origin

[1]Harlan J R, de Wet J M J. A simplified classification of cultivated sorghum. Crop Sci, 1972, 12: 172-176
[2]Grenier C, Deu M, Kresovich S, Bramel-cox P J, Hamon P. Assessment of genetic diversity in three subsets constituted from the ICRISAT sorghum collection using random vs. non-random sampling procedures. B. Using molecular markers. Theor Appl Genet, 2000, 101: 197-202
[3]Li F(李璠), Li J-Y(李敬仪), Lu Y(卢晔), Bai P(白品), Cheng H-F(程华芳). New discovery of the ancient remains of agriculture in the Neolithic site of Dong-Hui hill at Min-Luo county in Gansu. Agric Archaeol (农业考古), 1989, (1): 56-65 (in Chese with English abstract)
[4]Wang F-D(王富德), Liao J-L(廖嘉玲). Origin and domestication of Chinese sorghum. Liaoning Agric Sci (辽宁农业科学), 1981, (4): 23-26 (in Chinese)
[5]Wei S(卫斯). Origin of cultivated sorghum in China. Agric Hist China (中国农史), 1984, (2): 45-50(in Chinese)
[6]Li F(李璠). A brief discussion on the origin and development of the cultivated plants in China. Agric Archaeol (农业考古), 1993, (1): 49-55(in Chinese)
[7]Wang F-D(王富德), Liao J-L(廖嘉玲). Classification of Chinese cultivated sorghum. Liaoning Agric Sci (辽宁农业科学), 1981, (2): 18-22(in Chinese)
[8]Lu Q, Dahlberg J A. Chinese sorghum genetic resources. Econ Bot, 2001, 55: 401-425
[9]Qiao K-D(乔魁多), Wei Z-S(魏振山). Agro-morphological Descriptions of Chinese Sorghum (中国高粱品种志). Beijing: Agricultural Press, 1980 (in Chinese)
[10]Snowden J D. The cultivated races of Sorghum. London: Allard and Son, 1936
[11]de Wet J M J, Huckabay J P. The origin of Sorghum bicolor: II. Distribution and domestication. Evol Int J Org Evo, 1967, 21: 787-802
[12]Wang F-D(王富德), Lu Q-S(卢庆善). An analysis of the pedigrees of the main hybrid sorghum in China. Acta Agron Sin (作物学报), 1985, 11: 9-14 (in Chinese with English abstract)
[13]Li Y, Li C. Genetic contribution of Chinese landraces to the development of sorghum hybrids. Euphytica, 1998, 102: 47-55
[14]Menkir A, Goldsbrough P, Ejeta G. RAPD based assessment of genetic diversity in cultivated races of sorghum. Crop Sci, 1997, 37: 564-569
[15]Li Y, Li C. Phenotypic diversity of sorghum landraces in China. International Conference on Genetic Improvement of Sorghum and Pearl Millet, 1997. pp 659-668
[16]de Oliveira A C, Richter T, Bennetzen J L. Regional and racial specificities in sorghum germplasm assessed with DNA markers. Genome, 1996, 39: 579-587
[17]Deu M, Rattunde F, Chantereau J.A global view of genetic diversity in cultivated sorghum using a core collection. Genome, 2006, 49: 168-280
[18]Aldrich P R, Doebley J. Restriction fragment variation in the nuclear and chloroplast genomes of cultivated and wild Sorghum bicolor. Theor Appl Genet, 1992, 85: 293-302
[19]Deu M, Gonzalez-de-Leon D, Glaszmann J C, Degremont I, Chantereau J, Lanaud C, Hamon P. RFLP diversity in cultivated sorghum in relation to racial differentiation. Theor Appl Genet, 1994, 88: 838-844
[20]Djè Y, Forcioli D, Ater M, Lefèbvre C, Vekemans X. Assessing population genetic structure of sorghum landraces from North-western Morocco using allozyme and microsatellite markers. Theor Appl Genet, 2000, 99: 157-163
[21]Menz M A, Klein R R, Unruh N C, Rooney W R, Klein P E, Mullet J E. Genetic diversity of public inbreds of sorghum determined by mapped AFLP and SSR markers. Crop Sci, 2004, 44: 1236-1244
[22]Folkertsma R H, Frederick H, Rattunde W, Chandra S, Raju G S, Hash C T. The pattern of genetic diversity of Guinea-race Sorghum bicolor (L.) Moench landraces as revealed with SSR markers. Theor Appl Genet, 2005, 111: 399-409
[23]Powell W, Machray G C, Provan J. Polymorphism revealed by single sequence repeats. Trends Plant Sci, 1996, 1: 215-222
[24]Brown S M, Hopkins M S, Mitchell S E, Senior M L, Wang T Y, Duncan R R, Gonzalez-candelas F, Kresovich S. Multiple methods for the identification of polymorphic simple sequence repeats (SSRs) in sorghum
[Sorghum bicolor (L.) Moench]. Theor Appl Genet, 1996, 93: 190-198
[25]Kong L, Dong J, Hart G E. Characteristics, linkage-map positions, and allelic differentiation of Sorghum bicolor (L.) Moench DNA simple sequence repeats (SSRs). Theor Appl Genet, 2000, 101: 438-448
[26]Bhattramakki D, Dong J, Chhabra A K, Hart G E.An integrated SSR and RFLP linkage map of Sorghum bicolor (L.) Moench. Genome, 2000, 43: 988-1002
[27]Schloss S J, Mitchell S E, White G M, Kukatla R, Bowers J E, Paterson A H, Kresovich S. Characterization of RFLP probe sequences for gene discovery and SSR development in Sorghum bicolor (L.) Moench. Theor Appl Genet, 2002, 105: 912-920
[28]Djè Y, Heuertz M, Lefèbvre C, Vekemans X. Assessment of genetic diversity within and among germplasm accessions in cultivated sorghum using microsatellite markers. Theor Appl Genet, 2000, 100: 918-925
[29]Casa A M, Mitchell S E, Hamblin M T, Sun H, Bowers J E, Paterson A H, Aquadro C F, Krosovich S .Diversity and selection in sorghum: simultaneous analysis using simple sequence repeats. Theor Appl Genet, 2005, 111: 23-30
[30]Ghebru B, Schmidt R J, Bennetzen J L. Genetic diversity of Eritrean sorghum landraces assessed with simple sequence repeat (SSR) markers. Theor Appl Genet, 2002, 105: 229-236
[31]Abu Assar A H, Uptmoor R, Abdelmula A A, Salih M, Ordon F, Friedt W. Genetic variation in sorghum germplasm from Sudan, ICRISAT and USA assessed by simple sequence repeats (SSRs). Crop Sci, 2005, 45: 1636-1644
[32]Li R, Zhang H, Zhou X, Guan Y, Yao F, Song G, Wang J, Zhang C. Genetic diversity in Chinese sorghum landraces revealed by chloroplast simple sequence repeats. Genetic Resources Crop Evolution, 2010, 57: 1-15
[33]Doyle J J, Doyle J L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull, 1987, 19: 11-15
[34]Sambrook J, Fritsch E F, Maniatis T. Molecular cloning. New York: Cold Spring Harbor Laboratory Press, 1989
[35]Menz M A, Klein R R, Mullet J E, Obert J A, Unruh N C, Klein P E. A high-density genetic map of Sorghum bicolor (L.) Moench based on 2926 AFLP, RFLP and SSR markers. Plant Mol Biol, 2002, 48: 483-492
[36]Panaud O, Chen X, McCouch S R. Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol Gen Genet, 1996, 252: 597-607
[37]Excoffier, Laval L G, Schneider S. Arlequin Ver. 3.0: An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 2005, 1: 47-50
[38]Nei M. Molecular Evolutionary Genetics. New York: Columbia University Press, 1987
[39]Goudet J. FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). Available from http://www.unil.ch/izea/softwares/ fstat.html, 2001
[40]Liu K, Muse S V. PowerMarker: Intergrated analysis environment for genetic marker data. Bioinformatics, 2005, 21: 2128-2129
[41]Dice L R. Measures of the amount of ecological associations between species. Ecology, 1945, 26: 297-302
[42]Rohlf FJ. NTSYS-pc version 2.10 t. Applied Biostatistics. SSPS, Chicago, 2001
[43]Nei M, Li M H. Mathematical model for studying genetic variation in terms of restriction endonuclease. Proc Natl Acad Sci USA, 1979, 76: 5269-5273
[44]de Wet J M J, Harlan J R. The origin and domestication of Sorghum bicolor. Econ Bot, 1971, 25: 128-131
[45]de Wet J M J. Systematic and evolution of Sorghum sect. Sorghum (Gramineae). Am J Bot, 1978, 65: 477-484
[46]Aldrich P R, Doebley J, Scherts K F, Stec A. Patterns of allozyme variation in cultivated and wild Sorghum bicolor. Theor Appl Genet, 1992, 85: 451-460
[47]Garris A J, Tai T H, Coburn J, Kresovich S, McCouch S. Genetic structure and diversity in Oryza sativa L. Genetics, 2005, 169: 1631-1638
[48]Ayana A, Bryngelsson T, Bekele E. Genetic variation of Ethiopian and Eritrean sorghum (Sorghum bicolor ssp. Verticiliflorum (L.) Monech) germplasm assessed by random amplified polymorphic DNA (RAPD). Genet Resour Crop Evol, 2000, 47: 471-482
[49]Djè Y, Ater M, Lefèbvre C, Vekemans X. Pattern of morphological and allozyme variation in sorghum landraces of Northwest Morocco. Genet Resour Crop Evol, 1998, 45: 541-548
[50]Doggett H. Sorghum, 2nd edn. London: Longman, 1988
[51]Harlan J R, Stemler A B L. Races of Sorghum in Africa. In: Harlan J R, de Wet J M J, Stemler ABL eds. Origins of African Plant Domestication. The Hague: Mouton Press, 1976
[52]Chen W (陈文明). Agricultural Archaeology in China (农业考古). Beijing: Cultural Relics Publishing House, 2002 (in Chinese)
[53]Mann J A, Kimber C T, Miller F R. The origin and early cultivation of sorghum in Africa. Texas Agricultural & Mechanical Station Bulletin No. 1454, Texas Agricultural & Mechanical University, College Station, Tex., USA. 1983. pp 1-21
[54]Harlan J R. The Living Fields, Our Agricultural Heritage. Cambridge: Cambridge University Press, 1995
[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] JIN Min-Shan, QU Rui-Fang, LI Hong-Ying, HAN Yan-Qing, MA Fang-Fang, HAN Yuan-Huai, XING Guo-Fang. Identification of sugar transporter gene family SiSTPs in foxtail millet and its participation in stress response [J]. Acta Agronomica Sinica, 2022, 48(4): 825-839.
[3] JIN Rong, JIANG Wei, LIU Ming, ZHAO Peng, ZHANG Qiang-Qiang, LI Tie-Xin, WANG Dan-Feng, FAN Wen-Jing, ZHANG Ai-Jun, TANG Zhong-Hou. Genome-wide characterization and expression analysis of Dof family genes in sweetpotato [J]. Acta Agronomica Sinica, 2022, 48(3): 608-623.
[4] 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.
[5] ZHAO Jia-Jia, QIAO Ling, WU Bang-Bang, GE Chuan, QIAO Lin-Yi, ZHANG Shu-Wei, YAN Su-Xian, ZHENG Xing-Wei, ZHENG Jun. Seedling root characteristics and drought resistance of wheat in Shanxi province [J]. Acta Agronomica Sinica, 2021, 47(4): 714-727.
[6] 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.
[7] 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.
[8] 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.
[9] 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.
[10] 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.
[11] 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.
[12] 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.
[13] 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.
[14] WANG Yan-Hua,XIE Ling,YANG Bo,CAO Yan-Ru,LI Jia-Na. Flowering genes in oilseed rape: identification, characterization, evolutionary and expression analysis [J]. Acta Agronomica Sinica, 2019, 45(8): 1137-1145.
[15] Hong-Ju JIAN,Bo YANG,Yang-Yang LI,Hong YANG,Lie-Zhao LIU,Xin-Fu XU,Jia-Na LI. Identification and expression analysis of PEBP gene family in oilseed rape [J]. Acta Agronomica Sinica, 2019, 45(3): 354-364.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
No Suggested Reading articles found!
Add: No. 80 Xueyuan South Rd, Beijing 100081, P. R. China E-mail: zwxb301@caas.cn
Supported by Beijing Magtech Co.Ltd