Genetic diversity of Poncirus and phylogenetic relationships with its relatives revealed by SSR and SNP/InDel markers

详细信息    查看全文

• 作者：Shiping Zhu ; Fusheng Wang ; Wanxia Shen ; Dong Jiang…
• 关键词：Trifoliate orange ; Rootstock ; Genetic diversity ; Molecular marker
• 刊名：Acta Physiologiae Plantarum
• 出版年：2015
• 出版时间：July 2015
• 年：2015
• 卷：37
• 期：7
• 全文大小：869 KB
• 参考文献：Bañuls J, Dolores Serna M, Legaz F, Talon M, Primo-Millo E (1997) Growth and gas exchange parameters of citrus plants stressed with different salts. J Plant Physiol 150:194–199CrossRef
  Bausher MG, Singh ND, Lee SB, Jansen RK, Daniell H (2006) The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var ‘Ridge Pineapple’: organization and phylogenetic relationships to other angiosperms. BMC Plant Biol 6(21):1–11
  Bowman KD, Albrecht U, Mccollum G (2008) Comparison of three new citrus rootstocks from USDA: US-802, US-812, US-897. In: Proceedings International Society of Citriculture, pp 198–199
  Chen QY (1987) Some new Poncirus germplasms. Hortic Confer Sichuan 8:1–8 (in Chinese)
  Chen J, Shen WX, Zhu SP, Lu ZM, Zhao XC (2015) Investigation and analysis of phenophase of trifoliate oranges. South China Fruits 44(2):5–9 (in Chinese)
  Cheng FSZ, Roose M (1995) Origin and inheritance of dwarfing by the citrus rootstock Poncirus trifoliata `Flying Dragon’. J Amer Soc Hortic Sci 120(2):286–291
  Fang DQ, Roose ML, Krueger RR, Federici CT (1997) Fingerprinting trifoliate orange germplasm accessions with isozymes, RFLPs, and inter-simple sequence repeat markers. Theor Appl Genet 95:211–219CrossRef
  Forner JB, Forner-Giner A, Alcaide A (2003) New hybrid citrus rootstocks released in Spain. Hortscience 38(4):629–630
  Frankham R, Ballou JD, Briscoe DA (2002) Introduction to conservation genetics. Cambridge University Press, Cambridge, pp 29–62CrossRef
  Garcia-Lor Luro F, Navarro L, Ollitrault F (2012) Comparative use of InDel and SSR markers in deciphering the interspecific structure of cultivated citrus genetic diversity: a perspective for genetic for association studies. Mol Genet Genomics 287:77–94PubMed CrossRef
  Garcia-Lor A, Curk F, Snoussi-Trifa H, Morillon R, Ancillo G, Luro F, Navarro L, Ollitrault P (2013) A nuclear phylogenetic analysis: SNPs, indels and SSRs deliver new insights into the relationships in the ‘true citrus fruit trees’ group (Citrinae, Rutaceae) and the origin of cultivated species. Ann Bot 111:1–19PubMedCentral PubMed CrossRef
  Gmitter FG Jr, Xiao SY, Huang S, Hu XL, Garnsey SM, Deng Z (1996) A localized linkage map of the citrus tristeza virus resistance gene region. Theor Appl Genet 92:688–695PubMed CrossRef
  Golein B, Bigonah M, Azadvar M, Golmohammadi M (2012) Analysis of genetic relationship between ‘Bakraee’ (Citrus sp.) and some known citrus genotypes through SSR and PCR-RFLP markers. Sci Hortic 148:147–153CrossRef
  Gong GZ, Hong QB, Peng ZC, Jiang D, Xiang SQ (2008) Genetic diversity of Poncirus and its phylogenetic relationships with relatives as revealed by nuclear and chloroplast SSR. Acta Hortic Sin 35(12):1742–1750
  Guo TC, Chen QY, Ye YM, Du YX (1996) The germplasm of Poncirus trifoliata (L.) Raf. South China Fruit 25(3):8–10 (In Chinese)
  Hardy S, Donovan N, Barkley PB (2008) Citrus exocortis. Primefact 772:1–3
  Kim IJ, Ko KC, Kim CS, Chung WI (2001) Isolation and characterization of cDNAs encoding β-carotene hydroxylase in citrus. Plant Sci 161:1005–1010CrossRef
  Liang SQ, Wang XZ, Wan TX (1999) The biological characters of Early Poncirus and the performances using as rootstock. Zhejiang Citrus 16(3):2–4 (In Chinese)
  Liu SR, Li WY, Long D, Hu CG, Zhang JZ (2013) Development and characterization of genomic and expressed SSRs in citrus by genome-wide analysis. PLoS ONE 8(10):1–10
  Marshall TC, Slate J, Kruuk LEB, Pemberton JM (1998) Statistical confidence for likelihood-based paternity inference in natural populations. Mol Ecol 7:639–655PubMed CrossRef
  Maya MA, Rabbani MG, Mahboob MG, Matsubara Y (2012) Assessment of genetic relationship among 15 citrus fruit using RAPD. Asian J Biotech 4(1):31–37CrossRef
  O’Bannon JH (1977) Resistance in citrus rootstocks to Radopholus similes and Tylenchulus semipenetrans (Nematoda). Proc Inter Soc Citric 2:544–549
  Ollitrault P, Terol J, Garcia-Lor A, Bérard A, Chauveau A, Froelicher Y, Belzile C, Morillon R, Navarro L, Brunel D, Talon M (2012) SNP mining in C. clementina BAC end sequences; transferability in the Citrus genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping. BMC Genom 13:13–32CrossRef
  Pang XM, Deng XX, Hu CG (2003) Construction of AFLP fingerprint of 36 Poncirus accessions. Acta Hortic Sin 30(4):394–398 (in Chinese)
  Pang XM, Hu CG, Deng XX (2007) Phylogenetic relationships within citrus and its related genera as inferred from AFLP markers. Genet Resour Crop Evol 54:429–436CrossRef
  Rohlf FJ (1998) NTSYS-pc Numerical taxonomy and multivariate analysis system, Version 2.00. Exeter Software Publications, Setauket, New York, p 31
  Siviero A, Cristofani M, Furtando EL, Garcia AAF, Coelho ASG, Machado MA (2006) Identification of QTLs associated with citrus resistance to Phytophthora gummosis. J Appl Genet 47(1):23–28PubMed CrossRef
  Swingle WT, Reece PC (1967) The botany of Citrus and its wild relatives. In: Reuther W, Webber HJ, Batchelor LD (eds) The citrus industry. University of California Press, Berkeley, pp 190–430
  Sykes SR (2011) Chloride and sodium excluding capacities of citrus rootstock germplasm introduced to Australia from the People’s Republic of China. Sci Hortic 128(4):443–449CrossRef
  Varshney RK, Chabane K, Hendre PS, Aggarwal RK, Graner A (2007) Comparative assessment of EST-SSR, EST-SNP and AFLP markers for evaluation of genetic diversity and conservation of genetic resources using wild, cultivated and elite barleys. Plant Sci 173:638–649CrossRef
  Wang FS, Jiang D (2010) Studies on genetic background of important germplasm resources among citrus based on cpSSR and EST-SSR marker. Acta Hortic Sin Cssr 37(3):465–474 (in Chinese)
  Wei ZX (2010) SNP markers screening and application in genetic polymorphism of citrus. Master’s thesis of Southwest University, Chongqing
  Wu XE, Fan MT, Gao J, Li WX, Long WH, Xu MH (2003) Studies on the RAPD analysis and taxonomic relationships of trifoliate orange, fuming trifoliate orange and citrange. J Yunnan Agri Uni 18(3):277–280 (in Chinese)
  Wu B, Yang RT, Zhu SP, Zhong Y, Jiang B, Zeng JW, Zhong GY (2012) Genotyping single nucleotide polymorphisms in mandarin cultivars using high resolution melting analysis. Acta Hortic Sin 39(4):777–782 (in Chinese)
  Young RH (1977) The effect of rootstock on citrus cold hardiness. Proc Inter Soc Citric 2:518–522
  Zhao XY, He XH (1997) Different responses of 8 Poncirus trifoliata to sweet orange ‘Yellow-ring disease’ grafted on Poncirus rootstocks. South China Fruit 26(4):9–10 (in Chinese)
  Zhu SP, Chen J, Ma YY, Yan ST, Zhong GY (2013a) Advances in the Studies on Citrus Rootstock Evaluation and Application. Acta Hortic Sin 40(9):1669–1678 (in Chinese)
  Zhu SP, Jiang D, Hong QB, Gong GZ, Liu XF, Zhao XC (2013b) Advances in citrus rootstock breeding. South China Fruit 42(2):30–34 (in Chinese)
  Zhu SP, Wu B, Ma YY, Chen J, Zhong GY (2013c) Obtaining citrus hybrids by in vitro culture of embryos from mature seeds and early identification of hybrid seedlings by allele-specific PCR. Sci Hortic 161:300–305CrossRef
  Zhu SP, Wang J, Ye JL, Zhu AD, Guo WW, Deng XX (2014) Isolation and characterization of LEAFY COTYLEDON 1-LIKE gene related to embryogenic competence in Citrus sinensis. Plant Cell Tiss Organ Cult 119:1–13CrossRef
  
• 作者单位：Shiping Zhu (1) (2)
  Fusheng Wang (1)
  Wanxia Shen (1)
  Dong Jiang (1) (2)
  Qibin Hong (1) (2)
  Xiaochun Zhao (1) (2)
  
  1. Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Xiema, Beibei, Chongqing, 400712, People’s Republic of China
  2. National Citrus Engineering Research Center, Xiema, Beibei, Chongqing, 400712, People’s Republic of China
  
• 刊物主题：Plant Physiology; Plant Genetics & Genomics; Plant Biochemistry; Plant Pathology; Plant Anatomy/Development; Agriculture;
• 出版者：Springer Berlin Heidelberg
• ISSN：1861-1664

文摘

The polymorphic markers of nuclear SSR (simple sequence repeat), SNP (single nucleotide polymorphism)/InDel (insertion–deletion length polymorphism), and cpSSR (chloroplast SSR) were used to evaluate the genetic diversity of 52 trifoliate oranges and their relatives. The two genomic DNA-based markers produced high values of PIC (polymorphic information content) at 0.45 for SNP/InDel and 0.32 for nuclear SSR, indicating that there is a large diversity of genetic variation within the trifoliate oranges. Three UPGMA (unweighted pair-group method with arithmetic means) dendrograms were generated based on the results of three marker systems. At 0.76 of coefficient, all of Poncirus accessions were clustered into one group, except the 74-1 Early Poncirus, one of the three precocious trifoliate oranges, which was placed separately into another group by nuclear SSR. At a higher coefficient, the trifoliate oranges were discriminated into 4, 6 and 6 groups by nuclear SSR (0.86), SNP/InDel (0.95), and cpSSR (0.95), respectively. The results revealed that three precocious trifoliate oranges were originated from different sources. Hubei Early Poncirus and Beibei Early Poncirus were the asexual mutants of different trifoliate oranges, and 74-1 was probably a sexual hybrid. The present study also indicated that ‘Zhiwenzhou,’ a diploid chimera of trifoliate orange and Satsuma is more closely related to Satsuma rather than to trifoliate orange, which is in concordance with the results of morphological observation.