Diachronic analysis of genetic diversity in rice landraces under on-farm conservation in Yunnan, China

详细信息    查看全文

• 作者：Di Cui ; Jinmei Li ; Cuifeng Tang ; Xinxiang A…
• 刊名：Theoretical and Applied Genetics
• 出版年：2016
• 出版时间：January 2016
• 年：2016
• 卷：129
• 期：1
• 页码：155-168
• 全文大小：1,016 KB
• 参考文献：Altieri MA, Merrick LC (1987) In situ conservation of crop genetic resources maintenance of traditional farming systems. Econ Bot 41:86–96CrossRef
  Bellon MR, Pham JL, Jackson MT (1997) Genetic conservation: a role for rice farmers. In: Hawkes JG (ed) Plant conservation: the in situ approach. Chapman and Hall, IPGRI, London
  Brown AHD (2000) The genetic structure of crop landraces and the challenge to conserve them in situ on farms. In: Brush SB (ed) Genes in the fields: on–farm conservation of crop diversity. International Plant Genetic Resources Institute (IPGRI), Rome, International Development Research Centre (IDRC), Ottawa and Lewis Publishers, Boca Raton, pp 29–48
  Brush SB (1991) A farmer–based approach to conserving crop germplasm. Econ Bot 45:153–165CrossRef
  Brush SB, Meng E (1998) Farmers’ valuation and conservation of crop genetic resources. Genet Resour Crop Evol 45:139–150CrossRef
  Bandelt HJ, Forster P, Rohl A (1999) Median–joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37–48CrossRef PubMed
  Brown AHD (1978) Isozymes, plant population genetics structure and genetic conservation. Theor Appl Genet 52:145–157CrossRef PubMed
  Caicedo AL, Williamson SH, Hernandez RD et al (2007) Genome–wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genet 3:1745–1756CrossRef PubMed
  Chen JJ, Ding JH, Ouyang YD et al (2008) A triallelic system of S5 is a major regulator of the reproductive barrier and compatibility of indica–japonica hybrids in rice. Proc Natl Acad Sci 105:11436–11441CrossRef PubMed PubMedCentral
  Dai LY, Ye CR, Xu FR et al (1999) Genetic analysis on cold tolerance characteristics of Yunnan rice landrace (Oryza sativa L.) Kunmingxiaobaigu. Chin J Rice Sci 13:73–76
  Doyle JJ, Dickson EE (1987) Preservation of plant samples for DNA restriction endonuclease analysis. Taxon 36:715–722CrossRef
  Deu M, Sagnard F, Chantereau J et al (2010) Spatio–temporal dynamics of genetic diversity in Sorghum bicolor in Niger. Theor Appl Genet 120:1301–1313CrossRef PubMed
  Doi K, Izawa T, Fuse T et al (2004) Ehd1, a B–type response regulator in rice, confers short–day promotion of flowering and controls FT–like gene expression independently of Hd1. Genes Dev 18:926–936CrossRef PubMed PubMedCentral
  Dong SB, Lu BR, Wang YY et al (2010) Preliminary studies on the within-varietal genetic diversity and its maintenance of traditional rice from Yunnan. J Yunnan Agric Univ 25:1–9
  Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620CrossRef PubMed
  Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491PubMed PubMedCentral
  Fu YX, Li WH (1993) Statistical tests of neutrality of mutations. Genetics 133:693–709PubMed PubMedCentral
  Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587PubMed PubMedCentral
  Fu YB, Peterson GW, Richards KW et al (2005) Allelic reduction and genetic shift in the Canadian hard red spring wheat germplasm released from 1845 to 2004. Theor Appl Genet 110:1505–1516CrossRef PubMed
  Glaszmann JC (1987) Isozymes and classification of Asian rice varieties. Theor Appl Genet 74:21–30CrossRef PubMed
  Garris AJ, Tai TH, Coburn J et al (2005) Genetic structure and diversity in Oryza sativa L. Genetics 169:1631–1638CrossRef PubMed PubMedCentral
  Gao LZ (2003) The conservation of Chinese rice biodiversity: genetic erosion, ethnobotany and prospects. Genet Resour Crop Evol 50:17–32CrossRef
  Hammera K, Gladisa Th, Diederichsen A (2003) In situ and on-farm management of plant genetic resources. Eur J Agron 19:509–517CrossRef
  Hall TA (1999) Bioedit: a user–friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98
  Hudson RR, Kaplan NL (1985) Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111:147–164PubMed PubMedCentral
  Holsinger KE, Weir BS (2009) Genetics in geographically structured populations: defining, estimating and interpreting F(ST). Nat Rev Genet 10:639–650CrossRef PubMed PubMedCentral
  Harlan JR (1975) Crops and man. American Society of Agronomy, Madison
  Londo JP, Chiang YC, Hung KH et al (2006) Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. Proc Natl Acad Sci 103:9578–9583CrossRef PubMed PubMedCentral
  Liu XZ, Zhao MF, He YQ et al (2007) Breeding and blast resistance identification of Lijiangxintuanheigu nearnisogenic pyramid lines. Acta Agron Sin 33:20–24
  Li ZM, Zheng XM, Ge S (2011a) Genetic diversity and domestication history of African rice (Oryza glaberrima) as inferred from multiple gene sequences. Theor Appl Genet 123:21–31CrossRef PubMed
  Li YB, Fan CC, Xing YZ et al (2011b) Natural variation in GS5 plays an important role in regulating grain size and yield in rice. Nat Genet 43:1266–1269CrossRef PubMed
  Maxted N, Guarino L, Myer L et al (2002) Towards a methodology for on–farm conservation of plant genetic resources. Genet Resour Crop Evol 49:31–46CrossRef
  Mao HL, Sun SY, Yao JL et al (2010) Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. Proc Natl Acad Sci 107:19579–19584CrossRef PubMed PubMedCentral
  Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York
  Pusadee T, Jamjod S, Chiang YC et al (2009) Genetic structure and isolation by distance in a landrace of Thai rice. Proc Natl Acad Sci 106:13880–13885CrossRef PubMed PubMedCentral
  Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMed PubMedCentral
  Parzies HK, Spoor W, Ennos RA (2004) Inferring seed exchange between farmers from population genetic structure of barley landrace Arabi Aswad from Northern Syria. Genet Resour Crop Evol 51:471–478CrossRef
  Rozas J (2009) DNA sequence polymorphism analysis using DnaSP. Methods Mol Biol 537:337–350CrossRef PubMed
  Second G (1982) Origin of the genetic diversity of cultivated rice (Oryza spp.): study of polymorphism scored at 40 isoezyme loci. Jpn J Genet 57:25–57CrossRef
  Sirabanchongkran A, Yimyam N, Boonma W et al (2004) Varietal turnover and seed exchange: implications for conservation of rice genetic diversity on-farm. Int Rice Res Notes 29(2):18–19
  Shang JJ, Tao Y, Chen XW et al (2009) Identification of a new rice blast resistance gene, Pid3, by genomewide comparison of paired nucleotide-binding site–leucine-rich repeat genes and their pseudogene alleles between the two sequenced rice genomes. Genetics 182:1303–1311CrossRef PubMed PubMedCentral
  Sun JC, Cao GL, Jing Ma et al (2012) Comparative genetic structure within single–origin pairs of rice (Oryza sativa L.) landraces from in situ and ex situ conservation programs in Yunnan of China using microsatellite markers. Genet Resour Crop Evol 59:1611–1623CrossRef
  Thompson JD, Gibson TJ, Plewniak F et al (1997) The CLUSTALX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882CrossRef PubMed PubMedCentral
  Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595PubMed PubMedCentral
  Tsegaye B, Berg T (2007) Genetic erosion of Ethiopian tetraploid wheat landraces in Eastern Shewa, Central Ethiopia. Genet Resour Crop Evol 54:715–726CrossRef
  Wright SI, Gaut BS (2005) Molecular population genetics and the search for adaptive evolution in plants. Mol Biol Evol 22:506–519CrossRef PubMed
  Wei X, Qiao WH, Chen YT et al (2012) Domestication and geographic origin of Oryza sativa in China: insights from multilocus analysis of nucleotide variation of O. sativa and O. rufipogon. Mol Ecol 21:5073–5087CrossRef PubMed
  Watterson GA (1975) On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7:256–276CrossRef PubMed
  Xu FR, Zhang EL, Dong C et al (2010a) Comparison of phenotypic traits of rice landraces, grown in two different periods in Hani’s terraced fields in Yuanyang County, Yunnan. Biodiversity Science 18:365–372CrossRef
  Xu FR, Tang CF, Yu TQ et al (2010b) Diversity of paddy rice varieties from Yuanyang Hani’s terraced fields in Yunnan, China. Acta Ecologica Sinica 30:3346–3357
  Xu FR, Dong C, Yang WY et al (2011) Comparison of genetic diversity of rice landraces planted in two periods in Hani’s terraced fields in Yuanyang County, Yunnan province, China using microsatellite markers. Chin J Rice Sci 25:38l–386
  Yan HM, Dong C, Zhang EL et al (2012) Analysis of genetic variation in rice paddy landraces across 30 years as revealed by microsatellite DNA markers. Hereditas 34:87–94CrossRef PubMed
  Zhou YH (1988) Regionalization of rice cropping in Yunnan. In: Min SK, Wu XZ (eds) Regionalization of rice cropping in China. Zhejiang Science, and Technology Pubublication, Hangzhou, pp 104–108
  Zeng YW, Wang JJ, Yang ZY et al (2001) The diversity and sustainable devolopment of crop genetic resources in the Lancang River Valley. Genet Resour Crop Evol 48:297–306CrossRef
  Zhu YY, Chen HR, Fan JH et al (2003) The use of rice variety diversity for rice blast control. Sci Agric Sin 36:521–527
  Zhang HL, Sun JL, Wang MX et al (2006) Genetic structure and phylogeography of rice landraces in Yunnan, China, revealed by SSR. Genome 50:72–83
  Zeng YW, Zhang HL, Li ZC et al (2007) Evaluation of genetic diversity of rice landraces (Oryza sativa L.) in Yunnan, China. Breed Sci 57:91–99CrossRef
  Zeng YW, Shen SQ, Li ZC et al (2003) Ecogeographic and genetic diversity based on morphological characters of indigenous rice (Oryza sativa L.) in Yunnan, China. Genet Resour Crop Evol 50:567–577CrossRef
  Zhu QH, Zheng XM, Luo JC et al (2007) Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice. Mol Biol Evol 24:875–888CrossRef PubMed
  Zheng XM, Ge S (2010) Ecological divergence in the presence of gene flow in two closely related Oryza species (Oryza rufipogon and O. nivara). Mol Ecol 19:2439–2454CrossRef PubMed
  
• 作者单位：Di Cui (1)
  Jinmei Li (1)
  Cuifeng Tang (2)
  Xinxiang A (2)
  Tengqiong Yu (2)
  Xiaoding Ma (1)
  Enlai Zhang (2)
  Guilan Cao (1)
  Furong Xu (2)
  Yongli Qiao (1)
  Luyuan Dai (2)
  Longzhi Han (1)
  
  1. Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Crop Germplasm Resources and Utilization, The National Key Facility for Crop Gene Resources and Genetic Improvement, Ministry of Agriculture, No.12 Zhongguancun Nandajie, Beijing, 100081, China
  2. Institute of Biotech and Germplasm Resources, Yunnan Academy of Agricultural Sciences, No.9 Xueyunlu, Kunming, 650205, Yunnan, China
  
• 刊物主题：Plant Breeding/Biotechnology; Plant Genetics & Genomics; Agriculture; Plant Biochemistry; Biochemistry, general; Biotechnology;
• 出版者：Springer Berlin Heidelberg
• ISSN：1432-2242

文摘

Key message Diachronic analysis showed no significant changes in the level of genetic diversity occurred over the past 27 years’ domestication, which indicated genetic diversity was successfully maintained under on-farm conservation.