https://doi.org/10.4081/ija.2021.1870

Discovering genetic diversity of Changmaogu, a rice landrace, for conservation and rural development

Vol. 16 No. 3 (2021)
Submitted: 14 March 2021
Accepted: 18 July 2021
Published: 7 September 2021
Changmaogu rice landrace, SSR markers, genetic diversity, conservation strategy, Lama people.
Abstract Views: 871
PDF: 359
HTML: 19
Publisher's note
All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.

Authors

  • Liu He Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission; College of Life and Environmental Sciences, Minzu University of China, China.
  • Yingjie Song Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, China.
  • Xiufang Liu Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission; College of Life and Environmental Sciences, Minzu University of China, China.
  • Qi Kang Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, China.
  • Chunlin Long • long.chunlin@muc.edu.cn https://orcid.org/0000-0002-6573-6049 Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission; College of Life and Environmental Sciences, Minzu University of China; Key Laboratory of Ethnomedicine, Minzu University of China, Ministry of Education, Beijing, China.

Changmaogu is a very rare and endangered rice landrace cultivated in a very limited area by Lama people, a branch of Bai ethnic group in Lanping County, Yunnan, China. No study on this precious landrace had been reported. This study was intended to explore the genetic diversity so as to develop strategy for conserving Changmaogu. The Changmaogu samples were compared with other three varieties (Hejing 16, Nipponbare and Hongxiangmi), using 24 pairs of SSR markers. Among all varieties, Changmaogu showed the richest genetic diversity. Cluster analysis also showed that Changmaogu can be distinguished in the genetic distance of 0.68. These data suggested that landrace is of great significance for the selection of rice varieties under the harsh environment and the acquisition of parents in the breeding work. The high altitude, low temperature and complex microbial community may be the important factors of genetic diversity in Changmaogu. The influence of ‘agriculture-processing-marketing’ mode of landraces should be continuously tracked. The strategy for conservation and sustainable development of Changmaogu was proposed in the present paper.

Highlights
- Changmaogu, a very rare and endangered rice landrace cultivated in a very limited area by Lama people, has more abundant genetic diversity than the three compared cultivars-Hejing 16, Nipponbare and Hongxiangmi, which enables it to adapt to changing environmental conditions, ensures local food supply and agricultural economic development, and makes it an effective supplement to the rice gene pool.
- The result of UPGMA clustering analysis based on genetic distance led to the formation of three clusters, which Changmaogu had further genetic distance compared with hybrid rice Hejing 16 and rice parents Nipponbare, further revealing the utilization potential of Changmaogu in crop breeding.
- The genetic diversity of Changmaogu and Hongxiangmi was compared to reveal the important position of Changmaogu in the protection of landrace, and to explore the potential impact of commercial activities on the genetic diversity of landrace.
- According to the case of Changmaogu, this paper puts forward reasonable and effective strategies for the protection, which can be derived and applied to the protection of other landraces.

Dimensions

Altmetric

PlumX Metrics

Downloads

Download data is not yet available.

Citations

Crossref
Scopus
Google Scholar
Europe PMC
Agriculture Commission on Genetic Resources, 2013. Reviewing the roles of animal genetic resources and options for their conservation. UN Food and Agriculture Organization, Rome, Italy, pp 4-5.
Bellon M, Gotor E, Caracciolo F, 2014. Conserving landraces and improving livelihoods: how to assess the success of on-farm conservation projects? Int. J. Agr. Sustain. 13:167-82. DOI: https://doi.org/10.1080/14735903.2014.986363
Brown A, 1978. Isozymes, plant population genetic structure and genetic conservation. Theor. Appl. Genet. 52:145-57. DOI: https://doi.org/10.1007/BF00282571
Camacho-Villa TC, Maxted N, Scholten M, Ford-Lloyd B, 2005. Defining and identifying crop landraces. Plant Genet. Resour.-C. 3:373-84. DOI: https://doi.org/10.1079/PGR200591
Chen LH, Liang XH, Ke L, 2009. Supporting system for the on-farm conservation of upland rice local species based on villagers’ decision making behaviors, a case study of the Jiangtou Manmi, Jinghong, Yunnan. Yunnan Geograp. Environ. Res. 21:7-15.
Cui D, 2015. Association mapping of stress tolerance in Japonica rice germplasm and diachronic analysis of genetic diversity in rice landraces under on-farm conservation in Yunnan, China. Degree Diss., Chinese Academy of Agricultural Sciences, China. DOI: https://doi.org/10.1007/s00122-015-2617-7
Cui D, Li JM, Tang CF, A XX, Yu TQ, Ma XD, Zhang E, Cao GL, Xu FR, Qiao YL, Dai LY, Han LZ, 2015. Diachronic analysis of genetic diversity in rice landraces under on-farm conservation in Yunnan, China. Theor. Appl. Genet. 129:155-68. DOI: https://doi.org/10.1007/s00122-015-2617-7
Dang XJ, Thi T, Edzesi W, Liang LJ, Liu QM, Liu E, Wang Y, Qiang S, Liu LL, Hong D, 2015. Population genetic structure of Oryza sativa in East and Southeast Asia and the discovery of elite alleles for grain traits. Sci. Rep.-UK. 5:11254. DOI: https://doi.org/10.1038/srep11254
Demissie A, Bjørnstad Å, 1997. Geographical, altitude and agro-ecological differentiation of isozyme and hordein genotypes of landrace barleys from Ethiopia: implications to germplasm conservation. Genet. Resour. Crop Ev. 44:43-55.
Francis CY, Yang RC, Tim B, 2000. POPGENE32 (1.32). Available from: http://www.ualberta.ca/~fyeh/download.htm
Frankel OH, Soule ME, 1982. Conservation and evolution. Cambridge University Press, New York, NY, USA.
Friishansen E, Almekinders C, Boef WD, 2000. Farmers’ management and use of crop genetic diversity in Tanzania. Intermediate Technology Publications, London, UK, pp 66-71.
Hartings H, Berardo N, Mazzinelli G, Valoti P, Verderio A, Motto M, 2008. Assessment of genetic diversity and relationships among maize (Zea mays L.) Italian landraces by morphological traits and AFLP profiling. Theor. Appl. Genet. 117:831-42. DOI: https://doi.org/10.1007/s00122-008-0823-2
He L, Song YJ, Long CL, 2020. Genetic diversity of rice landraces in Yuanyang Hani terraced rice fields under in-situ conservation: research progress. Chin. Agri. Sci. Bull. 36:87-94.
Hu GL, Zhang DL, Pan HQ, Li B, Wu JT, Zhou XY, Zhang QY, Zhou L, Yao GX, Li JZ, Li JJ, Zhang HL, 2011. Fine mapping of the awn gene on chromosome 4 in rice by association and linkage analyses. Chin. Sci. Bull. 56:835-9. DOI: https://doi.org/10.1007/s11434-010-4181-5
Jaggi V, Brindhaa NT, Sahgal M, 2020. Microbial diversity in north western Himalayan agroecosystems: microbial diversity in north western Himalayan agroecosystems: functions and applications. Rhizos. Biol. 135-61. DOI: https://doi.org/10.1007/978-981-15-1902-4_8
Jarvis D, Brown A, Pham Hung C, Collado-Panduro L, Latournerie L, Gyawali S, Tanto T, Mahamadou S, Mar I, Sadiki M, Hue N, Arias-Reyes L, Balma D, Bajracharya J, Castillo F, Rijal D, Belqadi L, Rana R, Saidi S, Hodgkin T, 2008. A global perspective of the richness and evenness of traditional crop-variety diversity maintained by farming community. Proc. Natl. Acad. Sci. U. S. A. 105:5326-31. DOI: https://doi.org/10.1073/pnas.0800607105
Jarvis D, Hodgkin T, Brown A, Tuxill J, Lopez-Noriega I, Smale M, Sthapit B, 2016. Crop Genetic Diversity in the Field and on the Farm. Yale University Press., New Haven & London, UK.
Khan G, Shikari A, Vaishnavi R, Najeeb S, Padder BA, Bhat Z, Parray G, Bhat M, Kumar R, Singh N, 2018. Marker-assisted introgression of three dominant blast resistance genes into an aromatic rice cultivar Mushk Budji. Sci. Rep.-UK. 8:4091. DOI: https://doi.org/10.1038/s41598-018-22246-4
Kobayashi A, Ebana K, Fukuoka S, Nagamine T, 2006. Microsatellite markers revealed the genetic diversity of an old Japanese rice landrace ‘Echizen’. Genet. Resour. Crop Ev. 53:499-506. DOI: https://doi.org/10.1007/s10722-004-2029-z
Li C, Zhang Y, Ying K, Liang XL, Han B, 2004. Sequence variations of simple sequence repeats on chromosome-4 in two subspecies of the Asian cultivated rice. Theor. Appl. Genet. 108:392-400. DOI: https://doi.org/10.1007/s00122-003-1457-z
Li YJ, 2010. A study on the advancement of hybrid rice technology in China (1964～2010). Degree Diss., Nanjing Agricultural University, China.
Li YL, Long CL, Kato KJ, Yang CY, Sato K, 2011. Indigenous knowledge and traditional conservation of hulless barley (Hordeum vulgare) germplasm resources in the Tibetan communities of Shangri-la, Yunnan, SW China. Genet. Resour. Crop Ev. 58:645-55. DOI: https://doi.org/10.1007/s10722-010-9604-2
Long CL, 2016. Can commercialization save rare landraces in small ethnic communities? in The 7th International Crop Science Congress (7th ICSC) China, Beijing, China.
Lopes M, El-Basyoni I, Baenziger P, Singh S, Royo C, Ozbek K, Aktas H, Özer E, Ozdemir F, Manickavelu A, Ban T, Vikram P, 2015. Exploiting genetic diversity from landraces in wheat breeding for adaptation to climate change. J. Exp. Bot. 66:3477-86. DOI: https://doi.org/10.1093/jxb/erv122
Luo BS, Liu B, Zhang HZ, Zhang HK, Li X, Ma LJ, Wang YZ, Bai YJ, Zhang XB, Li JQ, Yang J, Long CL, 2019. Wild edible plants collected by Hani from terraced rice paddy agroecosystem in Honghe Prefecture, Yunnan, China. J. Ethnobiol. Ethnomed. 15:56. DOI: https://doi.org/10.1186/s13002-019-0336-x
Mitchell M. 2011. GeneMarker® HID: a reliable software tool for the analysis of forensic STR data. J. Forensic Sci. 56:29-35. DOI: https://doi.org/10.1111/j.1556-4029.2010.01565.x
Morgante M, Olivieri AM, 1993. PCR-amplified microsatellites as markers in plant genetics. Plant J. 3:175-82. DOI: https://doi.org/10.1111/j.1365-313X.1993.tb00020.x
Nagy S, Poczai P, Cernák I, Gorji AM, Hegedűs G, Taller J, 2012. PIC Calc: an online program to calculate polymorphic information content for molecular genetic studies. Biochem. Genet. 50:670-2. DOI: https://doi.org/10.1007/s10528-012-9509-1
Pagnotta MA, Impiglia A, Tanzarella OA, Nachit MM, Porceddu E, 2005. Genetic variation of the durum wheat landrace Haurani from different agro-ecological regions. Genet. Resour. Crop Ev. 51:863-9. DOI: https://doi.org/10.1007/s10722-005-0775-1
Pusadee T, Jamjod S, Chiang Y, Rerkasem B, Schaal B, 2009. Genetic structure and isolation by distance in a landrace of Thai rice. Proc. Natl. Acad. Sci. U. S. A. 106:13880-5. DOI: https://doi.org/10.1073/pnas.0906720106
Schlötterer C, Amos W, Tautz D, 1991. Conservation of polymorphic simple sequence loci in Cetacean species. Nature. 354:63-5. DOI: https://doi.org/10.1038/354063a0
Song YJ, Qiong F, Jarvis D, Bai K, Liu DM, Feng JC, Long CL, 2019. Network analysis of seed flow, a traditional method for conserving tartary buckwheat (Fagopyrum tataricum) landraces in Liangshan, Southwest China. Sustain.-Basel. 11:4263. DOI: https://doi.org/10.3390/su11164263
Sponenberg DP, 2014. Genetic resources and their conservation. In: The Genetics of the Horse (eds Bowling AT, Ruvinsky A). CABI Publishing, Wallingford, Oxfordshire, UK, pp 392-3.
Sudhir K, Glen S, Li M, Christina K, Koichiro T, 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35:1547-9. DOI: https://doi.org/10.1093/molbev/msy096
Virk D, Singh DN, Prasad SC, Gangwar JS, Witcombe J, 2003. Collaborative and consultative participatory plant breeding of rice for the rainfed uplands of eastern India. Euphytica. 132:95-108. DOI: https://doi.org/10.1023/A:1024674422343
Virk D, Witcombe J, 2007. Trade-offs between on-farm varietal diversity and highly client-oriented breeding - A case study of upland rice in India. Genet. Resour. Crop Ev. 54:823-35. DOI: https://doi.org/10.1007/s10722-006-9158-5
Wang XQ, Pang YL, Zhang J, Wu ZC, Chen K, Ali J, Ye GY, Xu JL, Li ZK, 2017. Genome-wide and gene-based association mapping for rice eating and cooking characteristics and protein content. Sci. Rep.-UK. 7:17203. DOI: https://doi.org/10.1038/s41598-017-17347-5
Wang YJ, Wang YL, Sun XD, Caiji ZM, Yang JB, Cui D, Cao GL, Ma XD, Han B, Xue DY, 2016. Influence of ethnic traditional cultures on genetic diversity of rice landraces under on-farm conservation in southwest China. J. Ethnobiol. Ethnomed. 12:51. DOI: https://doi.org/10.1186/s13002-016-0120-0
Williams J, Kubelik A, Livak K, Rafalski J, Tingey S, 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 18:6531-5. DOI: https://doi.org/10.1093/nar/18.22.6531
Xiang JT, 2012. An environmental anthropology study of red-rice of the Hani Yich piople in Langdi, Honghe County, Yunnan Province, China. Degree Diss., Yunnan University, China.
Yang GP, Maroof S, Xu C, Zhang Q, Biyashev R, 1994. Comparative analysis of microsatellite DNA polymorphism in landraces and cultivars of rice. Mol. Gen. Genet. 245:187-94. DOI: https://doi.org/10.1007/BF00283266
Yang JB, Wang YC, Wang D, Guo L, 2018. Application of traditional knowledge of Hani people in biodiversity conservation. Sustain.-Basel. 10:4555. DOI: https://doi.org/10.3390/su10124555
Yang YH, Bai KY, Devra J, Long CL, 2019. Xishuangbanna cucumber landraces and associated traditional knowledge. Biodiv. Sci. 27:743-8. DOI: https://doi.org/10.17520/biods.2019108
Zeng YW, Li ZC, Yang ZY, Wang XK, Shen SQ, Zhang HL, Chen YM, 2000. Law and center of diversity of main characters of indigenous rice (Oryza sativa L.) in Yunnan. J. Huazhong Agri. Univ. 511-7.
Zeng YW, Wang JJ, Yang ZY, Shen SQ, Wu LH, Chen XY, Meng JG, 2001. The diversity and sustainable development of crop genetic resources in the Lancang River Valley. Genet. Resour. Crop Ev. 48:297-306.
Zeng YW, Zhang HL, Li ZC, Shen SQ, Wen GS, 2007. Evaluation of genetic diversity of rice landraces (Oryza sativa L.) in Yunnan, China. Breeding Sci. 57:91-9. DOI: https://doi.org/10.1270/jsbbs.57.91
Zhang HL, Sun JL, Wang MX, Liao DQ, Zeng YW, Shen SQ, Yu P, Mu P, Wang XK, Li ZC, 2007. Genetic structure and phylogeography of rice landraces in Yunnan, China, revealed by SSR. Genome. 50:72-83. DOI: https://doi.org/10.1139/g06-130
Zhang YY, 2005. The analysis of genetic diversity for indica local rice from different place of China. Degree Diss., Chinese Academy of Agricultural Sciences, China.
Zhu MY, Wang YY, Zhu YY, Lu BR, 2004. Estimating genetic diversity of rice landraces from Yunnan by SSR assay and its implication for conservation. Acta Bot. Sin. 46:12.

How to Cite

He, L., Song, Y., Liu, X., Kang, Q., & Long, C. (2021). Discovering genetic diversity of Changmaogu, a rice landrace, for conservation and rural development. Italian Journal of Agronomy, 16(3). https://doi.org/10.4081/ija.2021.1870
Copyright (c) 2021 The Author(s) Creative Commons License

This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.

PAGEPress has chosen to apply the Creative Commons Attribution NonCommercial 4.0 International License (CC BY-NC 4.0) to all manuscripts to be published.