Skip to main content
SpringerLink
Log in

QTL mapping of mandarin (Citrus reticulata) fruit characters using high-throughput SNP markers

  • Original Article
  • Published:
Tree Genetics & Genomes Aims and scope Submit manuscript

Abstract

Seedlessness, flavor, and color are top priorities for mandarin (Citrus reticulata Blanco) cultivar improvement. Given long juvenility, large tree size, and high breeding cost, marker-assisted selection (MAS) may be an expeditious and economical approach to these challenges. The objectives of this study were to construct high-density mandarin genetic maps and to identify single nucleotide polymorphism (SNP) markers associated with fruit quality traits. Two parental genetic maps were constructed from an F1 population derived from ‘Fortune’ × ‘Murcott’, two mandarin cultivars with distinct fruit characters, using a 1536-SNP Illumina GoldenGate assay. The map for ‘Fortune’ (FOR) consisted of 189 SNPs spanning 681.07 cM and for ‘Murcott’ (MUR) consisted of 106 SNPs spanning 395.25 cM. Alignment of the SNP sequences to the Clementine (Citrus clementina) genome showed highly conserved synteny between the genetic maps and the genome. A total of 48 fruit quality quantitative trait loci (QTLs) were identified, and ten of them stable over two or more samplings were considered as major QTLs. A cluster of QTLs for flavedo color space values L, a, b, and a/b and juice color space values a and a/b were detected in a single genomic region on linkage group 4. Two carotenoid biosynthetic pathway genes, pds1 and ccd4, were found within this QTL interval. Several SNPs were potentially useful in MAS for these fruit characteristics. QTLs were validated in 13 citrus selections, which may be useful in further validation and tentative MAS in mandarin fruit quality improvement.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Albertini M-V, Carcouet E, Pailly O, Gambotti C, Luro F, Berti L (2006) Changes in organic acids and sugars during early stages of development of acidic and acidless citrus fruit. J Agric Food Chem 54(21):8335–8339. doi:10.1021/jf061648j

    Article  CAS  PubMed  Google Scholar 

  • Aldrich J, Cullis CA (1993) RAPD analysis in flax: optimization of yield and reproducibility using Klen Taq 1 DNA polymerase, Chelex 100, and gel purification of genomic DNA. Plant Mol Biol Report 11(2):128–141. doi:10.1007/bf02670471

    Article  CAS  Google Scholar 

  • Aleza P, Cuenca J, Juarez J, Pina JA, Navarro L (2010) ‘Garbi’ mandarin: a new late-maturing triploid hybrid. Hortscience 45(1):139–141

    Google Scholar 

  • Auldridge ME, Block A, Vogel JT, Dabney-Smith C, Mila I, Bouzayen M, Magallanes-Lundback M, DellaPenna D, McCarty DR, Klee HJ (2006a) Characterization of three members of the Arabidopsis carotenoid cleavage dioxygenase family demonstrates the divergent roles of this multifunctional enzyme family. Plant J 45(6):982–993. doi:10.1111/j.1365-313X.2006.02666.x

    Article  CAS  PubMed  Google Scholar 

  • Auldridge ME, McCarty DR, Klee HJ (2006b) Plant carotenoid cleavage oxygenases and their apocarotenoid products. Curr Opin Plant Biol 9(3):315–321. doi:10.1016/j.pbi.2006.03.005

    Article  CAS  PubMed  Google Scholar 

  • Baldwin KL, Jones KG (2013) U.S. Citrus import demand: seasonality and substitution. J Int Food Agric Mark 25(1):24–41. doi:10.1080/08974438.2013.724003

    Google Scholar 

  • Barry G, Gmitter F, Chen C, Roose M, Federici C (2014) Investigating the parentage of ‘Orri’ and ‘Fortune’ mandarin hybrids. Acta Hortic 1065:449–456

    Google Scholar 

  • Bastianel M, Cristofani-Yaly M, de Oliveira AC, Freitas-Astua J, Franco Garcia AA, Vilela de Resende MD, Rodrigues V, Machado MA (2009) Quantitative trait loci analysis of citrus leprosis resistance in an interspecific backcross family of (Citrus reticulata Blanco x C. sinensis L. Osbeck) x C. sinensis L. Osb. Euphytica 169(1):101–111. doi:10.1007/s10681-009-9950-3

    Article  CAS  Google Scholar 

  • Bernet GP, Fernandez-Ribacoba J, Carbonell EA, Asins MJ (2010) Comparative genome-wide segregation analysis and map construction using a reciprocal cross design to facilitate citrus germplasm utilization. Mol Breed 25(4):659–673. doi:10.1007/s11032-009-9363-y

    Article  Google Scholar 

  • Brandi F, Bar E, Mourgues F, Horvath G, Turcsi E, Giuliano G, Liverani A, Tartarini S, Lewinsohn E, Rosati C (2011) Study of ‘Redhaven’ peach and its white-fleshed mutant suggests a key role of CCD4 carotenoid dioxygenase in carotenoid and norisoprenoid volatile metabolism. BMC Plant Biol 11:24–24. doi:10.1186/1471-2229-11-24

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cai Q, Guy CL, Moore GA (1994) Extension of the linkage map in citrus using random amplified polymorphic DNA (RAPD) markers and RFLP mapping of cold-acclimation-responsive loci. Theor Appl Genet 89(5):606–614

    Article  CAS  PubMed  Google Scholar 

  • Campbell R, Ducreux LJM, Morris WL, Morris JA, Suttle JC, Ramsay G, Bryan GJ, Hedley PE, Taylor MA (2010) The metabolic and developmental roles of carotenoid cleavage dioxygenase4 from potato. Plant Physiol 154(2):656–664. doi:10.1104/pp.110.158733

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chamovitz D, Sandmann G, Hirschberg J (1993) Molecular and biochemical-characterization of herbicide-resistant mutants of cyanobacteria reveals that phytoene desaturation is a rate-limiting step in carotenoid biosynthesis. J Biol Chem 268(23):17348–17353

    CAS  PubMed  Google Scholar 

  • Chen C, Gmitter FG (2013) Mining of haplotype-based expressed sequence tag single nucleotide polymorphisms in citrus. BMC Genomics 14(1):746

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen C, Bowman KD, Choi YA, Dang PM, Rao MN, Huang S, Soneji JR, McCollum TG, FG G Jr (2008) EST-SSR genetic maps for Citrus sinensis and Poncirus trifoliata. Tree Genet Genomes 4(1):1–10. doi:10.1007/s11295-007-0083-3

    Article  Google Scholar 

  • Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138(3):963–971

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cristofani M, Machado MA, Grattapaglia D (1999) Genetic linkage maps of citrus sunki Hort. ex. Tan. and Poncirus trifoliata (L.) Raf. and mapping of citrus tristeza virus resistance gene. Euphytica 109(1):25–32. doi:10.1023/a:1003637116745

    Article  CAS  Google Scholar 

  • Dalkilic Z, Timmer LW, Gmitter FG (2005) Linkage of an Alternaria disease resistance gene in mandarin hybrids with RAPD fragments. J Am Soc Hortic Sci 130(2):191–195

    CAS  Google Scholar 

  • Durham RE, Liou PC, Gmitter FG, Moore GA (1992) Linkage of restriction fragment length polymorphisms and isozymes in citrus. Theor Appl Genet 84(1–2):39–48

    CAS  PubMed  Google Scholar 

  • Eduardo I, Pacheco I, Chietera G, Bassi D, Pozzi C, Vecchietti A, Rossini L (2011) QTL analysis of fruit quality traits in two peach intraspecific populations and importance of maturity date pleiotropic effect. Tree Genet Genomes 7(2):323–335. doi:10.1007/s11295-010-0334-6

    Article  Google Scholar 

  • Falchi R, Vendramin E, Zanon L, Scalabrin S, Cipriani G, Verde I, Vizzotto G, Morgante M (2013) Three distinct mutational mechanisms acting on a single gene underpin the origin of yellow flesh in peach. Plant J 76(2):175–187. doi:10.1111/tpj.12283

    CAS  PubMed  PubMed Central  Google Scholar 

  • Fanciullino A-L, Cercos M, Dhuique-Mayer C, Froelicher Y, Talon M, Ollitrault P, Morillon R (2008) Changes in carotenoid content and biosynthetic gene expression in juice sacs of four orange varieties (Citrus sinensis) differing in flesh fruit color. J Agric Food Chem 56(10):3628–3638. doi:10.1021/jf0732051

    Article  CAS  PubMed  Google Scholar 

  • Fang DQ, Federici CT, Roose ML (1997) Development of molecular markers linked to a gene controlling fruit acidity in citrus. Genome 40(6):841–849

    Article  CAS  PubMed  Google Scholar 

  • Furr JR (1964) New tangerines for the desert. Calif Citrograph 49:266–276

    Google Scholar 

  • Garcia I, Rodgers M, Lenne C, Rolland A, Sailland A, Matringe M (1997) Subcellular localization and purification of a p-hydroxyphenylpyruvate dioxygenase from cultured carrot cells and characterization of the corresponding cDNA. Biochem J 325:761–769

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • García MR, Asins MJ, Carbonell EA (2000) QTL analysis of yield and seed number in citrus. Theor Appl Genet 101(3):487–493

    Article  Google Scholar 

  • Garcia R, Asins MJ, Forner J, Carbonell EA (1999) Genetic analysis of apomixis in citrus and Poncirus by molecular markers. Theor Appl Genet 99(3–4):511–518. doi:10.1007/s001220051264

    Article  CAS  PubMed  Google Scholar 

  • Georgelis N, JW S, EA B (2004) Relationship of tomato fruit sugar concentration with physical and chemical traits and linkage of RAPD markers. J Am Soc Hortic Sci 129(6):839–845

    CAS  Google Scholar 

  • FG Gmitter, Jr., Grosser JW, Castle WS, Moore GA (2007) A comprehensive citrus genetic improvement programme. Citrus Genetics, Breeding and Biotechnology: 9–18. doi:10.1079/9780851990194.0009

  • Gmitter Jr FG, Xiao SY, Huang S, XL H, Garnsey SM, Deng Z (1996) A localized linkage map of the citrus tristeza virus resistance gene region. Theor Appl Genet 92(6):688–695

    Article  CAS  Google Scholar 

  • Gonzalez-Jorge S, Ha S-H, Magallanes-Lundback M, Gilliland LU, Zhou A, Lipka AE, Nguyen Y-N, Angelovici R, Lin H, Cepela J, Little H, Buell CR, Gore MA, DellaPenna D (2013) Carotenoid cleavage dioxygenase4 is a negative regulator of β-carotene content in Arabidopsis seeds. Plant Cell 25(12):4812–4826. doi:10.1105/tpc.113.119677

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Goodner KL, Rouseff RL, Hofsommer HJ (2001) Orange, mandarin, and hybrid classification using multivariate statistics based on carotenoid profiles. J Agric Food Chem 49(3):1146–1150. doi:10.1021/jf000866o

    Article  CAS  PubMed  Google Scholar 

  • Gulsen O, Uzun A, Canan I, Seday U, Canihos E (2010) A new citrus linkage map based on SRAP, SSR, ISSR, POGP, RGA and RAPD markers. Euphytica 173(2):265–277. doi:10.1007/s10681-010-0146-7

    Article  CAS  Google Scholar 

  • Gulsen O, Uzun A, Seday U, Kafa G (2011) QTL analysis and regression model for estimating fruit setting in young citrus trees based on molecular markers. Sci Hortic 130(2):418–424. doi:10.1016/j.scienta.2011.07.010

    Article  CAS  Google Scholar 

  • Hodgson RW (1967) Horticultural varieties of citrus. In: Reuther W, Webber HJ, Batchelor LD (eds) The citrus industry. University of California Division of Agricultural Sciences, Berkeley

    Google Scholar 

  • Ikoma Y, Komatsu A, Kita M, Ogawa K, Omura M, Yano M, Moriguchi T (2001) Expression of a phytoene synthase gene and characteristic carotenoid accumulation during citrus fruit development. Physiol Plant 111(2):232–238. doi:10.1034/j.1399-3054.2001.1110215.x

    Article  CAS  Google Scholar 

  • Jansen RC, Stam P (1994) High-resolution of quantitative traits into multiple loci via interval mapping. Genetics 136(4):1447–1455

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jarrell DC, Roose ML, Traugh SN, Kupper RS (1992) A genetic map of citrus based on the segregation of isozymes and RFLPs in an intergeneric cross. Theor Appl Genet 84(1–2):49–56

    CAS  PubMed  Google Scholar 

  • Kato M, Ikoma Y, Matsumoto H, Sugiura M, Hyodo H, Yano M (2004) Accumulation of carotenoids and expression of carotenoid biosynthetic genes during maturation in citrus fruit. Plant Physiol 134(2):824–837. doi:10.1104/pp.103.031104

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kijas JMH, MR T, Fowler JCS, Roose ML (1997) Integration of trinucleotide microsatellites into a linkage map of citrus. Theor Appl Genet 94(5):701–706. doi:10.1007/s001220050468

    Article  CAS  Google Scholar 

  • Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121(1):185–199

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lee HS (2001) Characterization of carotenoids in juice of red navel orange (Cara cara). J Agric Food Chem 49(5):2563–2568. doi:10.1021/jf001313g

    Article  CAS  PubMed  Google Scholar 

  • Lee HS, Castle WS (2001) Seasonal changes of carotenoid pigments and color in Hamlin, Earlygold, and Budd blood orange juices. J Agric Food Chem 49(2):877–882. doi:10.1021/jf000654r

    Article  CAS  PubMed  Google Scholar 

  • Ling P, Duncan LW, Deng Z, Dunn D, Hu X, Huang S, Gmitter Jr FG (2000) Inheritance of citrus nematode resistance and its linkage with molecular markers. Theor Appl Genet 100(7):1010–1017

    Article  CAS  Google Scholar 

  • Liu Q, Xu J, Liu Y, Zhao X, Deng X, Guo L, Gu J (2007) A novel bud mutation that confers abnormal patterns of lycopene accumulation in sweet orange fruit (Citrus sinensis L. Osbeck). J Exp Bot 58(15–16):4161–4171. doi:10.1093/jxb/erm273

    Article  CAS  PubMed  Google Scholar 

  • Ma BQ, Zhao S, BH W, Wang DM, Peng Q, Owiti A, Fang T, Liao L, Ogutu C, Korban SS, Li SH, Han YP (2016) Construction of a high density linkage map and its application in the identification of QTLs for soluble sugar and organic acid components in apple. Tree Genet Genomes 12(1):10. doi:10.1007/s11295-015-0959-6

    Article  Google Scholar 

  • Matsumoto H, Ikoma Y, Kato M, Kuniga T, Nakajima N, Yoshida T (2007) Quantification of carotenoids in citrus fruit by LC-MS and comparison of patterns of seasonal changes for carotenoids among citrus varieties. J Agric Food Chem 55(6):2356–2368. doi:10.1021/jf062629c

    Article  CAS  PubMed  Google Scholar 

  • Miyazaki T, Plotto A, Goodner K, FG G Jr (2011) Distribution of aroma volatile compounds in tangerine hybrids and proposed inheritance. J Sci Food Agric 91(3):449–460. doi:10.1002/jsfa.4205

    Article  CAS  PubMed  Google Scholar 

  • Norris SR, Barrette TR, DellaPenna D (1995) Genetic dissection of carotenoid synthesis in Arabidopsis defines plastoquinone as an essential component of phytoene desaturation. Plant Cell 7(12):2139–2149

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Norris SR, Shen XH, DellaPenna D (1998) Complementation of the Arabidopsis pds1 mutation with the gene encoding p-hydroxyphenylpyruvate dioxygenase. Plant Physiol 117(4):1317–1323. doi:10.1104/pp.117.4.1317

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ohmiya A, Kishimoto S, Aida R, Yoshioka S, Sumitomo K (2006) Carotenoid cleavage dioxygenase (CmCCD4a) contributes to white color formation in chrysanthemum petals. Plant Physiol 142(3):1193–1201. doi:10.1104/pp.106.087130

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • de Oliveira AC, Bastianel M, Cristofani-Yaly M, do Amara AM, Machado MA (2007) Development of genetic maps of the citrus varieties ‘Murcott’ tangor and ‘Pera’ sweet orange by using fluorescent AFLP markers. J Appl Genet 48(3):219–231

    Article  Google Scholar 

  • Oliveira RPD, Cristofani M, Machado MA (2002) Genetic mapping for citrus variegated chlorosis resistance. Laranja 23(1):247–261

    Google Scholar 

  • Ollitrault P, Terol J, Chen C, Federici CT, Lotfy S, Hippolyte I, Ollitrault F, Berard A, Chauveau A, Cuenca J, Costantino G, Kacar Y, Mu L, Garcia-Lor A, Froelicher Y, Aleza P, Boland A, Billot C, Navarro L, Luro F, Roose ML, Gmitter FG, Talon M, Brunel D (2012a) A reference genetic map of C. clementina Hort. ex Tan.; citrus evolution inferences from comparative mapping. BMC Genomics 13. doi:10.1186/1471-2164-13-593

  • Ollitrault P, Terol J, Garcia-Lor A, Berard A, Chauveau A, Froelicher Y, Belzile C, Morillon R, Navarro L, Brunel D, Talon M (2012b) SNP mining in C. clementina BAC end sequences; transferability in the citrus genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping. BMC Genomics 13. doi:10.1186/1471-2164-13-13

  • Raga V, Bernet GP, Carbonell EA, Asins MJ (2012) Segregation and linkage analyses in two complex populations derived from the citrus rootstock Cleopatra mandarin. Inheritance of seed reproductive traits. Tree Genet Genomes 8(5):1061–1071. doi:10.1007/s11295-012-0486-7

    Article  Google Scholar 

  • Ritter E, Gebhardt C, Salamini F (1990) Estimation of recombination frequencies and construction of RFLP linkage maps in plants from crosses between heterozygous parents. Genetics 125(3):645–654

    CAS  PubMed  PubMed Central  Google Scholar 

  • Roose ML, Feng D, Cheng FS, Tayyar RI, Federici CT, Kupper RS (2000) Mapping the citrus genome. Acta Hortic 535:25–32

    Article  CAS  Google Scholar 

  • Ruiz C, Asins MJ (2003) Comparison between Poncirus and citrus genetic linkage maps. Theor Appl Genet 106(5):826–836. doi:10.1007/s00122-002-1095-x

    CAS  PubMed  Google Scholar 

  • Sahin-Cevik M, Moore GA (2012) Quantitative trait loci analysis of morphological traits in citrus. Plant Biotechnol Rep 6(1):47–57. doi:10.1007/s11816-011-0194-z

    Article  Google Scholar 

  • Sankar AA, Moore GA (2001) Evaluation of inter-simple sequence repeat analysis for mapping in citrus and extension of the genetic linkage map. Theor Appl Genet 102(2–3):206–214. doi:10.1007/s001220051637

    Article  CAS  Google Scholar 

  • Shapiro SS, Wilk MB (1965) An analysis of variance test for normality (complete samples). Biometrika 52:591–611. doi:10.2307/2333709

    Article  Google Scholar 

  • Sinclair WB (1984) The biochemistry and physiology of the lemon and other citrus fruits. University of California Division of Agriculture and Natural Resources, Riverside, CA

    Google Scholar 

  • Sleper DA, Poehlman JM (2006) Breeding field crops . vol Ed. 5. Blackwell Publishing, Oxford, UK

    Google Scholar 

  • Socquet-Juglard D, Christen D, Devenes G, Gessler C, Duffy B, Patocchi A (2013) Mapping architectural, phenological, and fruit quality QTLs in apricot. Plant Mol Biol Report 31(2):387–397. doi:10.1007/s11105-012-0511-x

    Article  CAS  Google Scholar 

  • Sooriyapathirana SS, Khan A, Sebolt AM, Wang D, Bushakra JM, Lin-Wang K, Allan AC, Gardiner SE, Chagne D, Iezzoni AF (2010) QTL analysis and candidate gene mapping for skin and flesh color in sweet cherry fruit (Prunus avium L.). Tree Genet Genomes 6(6):821–832. doi:10.1007/s11295-010-0294-x

    Article  Google Scholar 

  • Sugiyama A, Omura M, Matsumoto H, Shimada T, Fujii H, Endo T, Shimizu T, Nesumi H, Ikoma Y (2011) Quantitative trait loci (QTL) analysis of carotenoid content in citrus fruit. J Jpn Soc Hortic Sci 80(2):136–144

    Article  Google Scholar 

  • Sugiyama A, Omura M, Shimoda T, Fujii H, Endo T, Shimizu T, Nesumi H, Nonaka K, Ikoma Y (2014) Expression quantitative trait loci analysis of carotenoid metabolism-related genes in citrus. J Jpn Soc Hortic Sci 83(1):32–43

    Article  CAS  Google Scholar 

  • Tietel Z, Plotto A, Fallik E, Lewinsohn E, Porat R (2011) Taste and aroma of fresh and stored mandarins. J Sci Food Agric 91(1):14–23. doi:10.1002/jsfa.4146

    Article  CAS  PubMed  Google Scholar 

  • Tozlu I, Guy CL, Moore GA (1999a) QTL analysis of morphological traits in an intergeneric BC1 progeny of Citrus and Poncirus under saline and non-saline environments. Genome 42(5):1020–1029

    Article  CAS  Google Scholar 

  • Tozlu I, Guy CL, Moore GA (1999b) QTL analysis of Na and Cl-accumulation related traits in an intergeneric BC1 progeny of citrus and Poncirus under saline and nonsaline environments. Genome 42(4):692–705

    Article  CAS  Google Scholar 

  • Van Ooijen JW (2006) JoinMap 4: software for the calculation of genetic linkage maps in experimental populations. Kyazma BV, Wageningen, Netherlands

  • Van Ooijen JW (2011a) MapQTL 6: software for the mapping of quantitative trait loci in experimental populations of diploid species. Wageningen, The Netherlands

    Google Scholar 

  • Van Ooijen JW (2011b) Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species. Genet Res 93(5):343–349. doi:10.1017/s0016672311000279

    Article  CAS  Google Scholar 

  • Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93(1):77–78. doi:10.1093/jhered/93.1.77

    Article  CAS  PubMed  Google Scholar 

  • Weber CA, Moore GA, Deng Z, Gmitter FG (2003) Mapping freeze tolerance quantitative trait loci in a Citrus grandis × Poncirus trifoliata F1 pseudo-testcross using molecular markers. J Am Soc Hortic Sci 128(4):508–514

    CAS  Google Scholar 

  • Wei X, Chen C, Yu Q, Gady A, Yu Y, Liang G, Gmitter Jr FG (2014) Novel expression patterns of carotenoid pathway-related genes in citrus leaves and maturing fruits. Tree Genetics & Genomes: 1–10

  • Wheaton TA (1997) Alternate bearing of citrus in Florida. Citrus flowering and fruiting short course. Lake Alfred: University of Florida, Citrus Research and Education Center: 87–92

  • Wu GA, Prochnik S, Jenkins J, Salse J, Hellsten U, Murat F, Perrier X, Ruiz M, Scalabrin S, Terol J, Takita MA, Labadie K, Poulain J, Couloux A, Jabbari K, Cattonaro F, Del Fabbro C, Pinosio S, Zuccolo A, Chapman J, Grimwood J, Tadeo FR, Estornell LH, Munoz-Sanz JV, Ibanez V, Herrero-Ortega A, Aleza P, Perez-Perez J, Ramon D, Brunel D, Luro F, Chen C, Farmerie WG, Desany B, Kodira C, Mohiuddin M, Harkins T, Fredrikson K, Burns P, Lomsadze A, Borodovsky M, Reforgiato G, Freitas-Astua J, Quetier F, Navarro L, Roose M, Wincker P, Schmutz J, Morgante M, Machado MA, Talon M, Jaillon O, Ollitrault P, Gmitter F, Rokhsar D (2014) Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nat Biotechnol 32(7):656–662

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xu CJ, Fraser PD, Wang W-J, Bramley PM (2006) Differences in the carotenoid content of ordinary citrus and lycopene-accumulating mutants. J Agric Food Chem 54(15):5474–5481. doi:10.1021/jf060702t

    Article  CAS  PubMed  Google Scholar 

  • Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136(4):1457–1468

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

This work was partly funded by New Varieties Development & Management Corporation, Citrus Research and Development Foundation, and the University of Florida Plant Molecular Breeding Initiative. The authors thank Yanzi Zhang, Marjorie Wendell, Xu Wei, Qibin Yu, and Misty Holt for technical assistance, as well as Sanghamitra Das for help with editing and Harry Klee for critical reading of the manuscript.

Author information

Authors and Affiliations

  1. Citrus Research and Education Center, University of Florida, Lake Alfred, FL, 33850, USA

    Yuan Yu & Frederick G. Gmitter Jr.

  2. Southeastern Fruit and Tree Nut Research Laboratory, ARS, USDA, Byron, GA, 31008, USA

    Chunxian Chen

Authors
  1. Yuan Yu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Chunxian Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Frederick G. Gmitter Jr.
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Frederick G. Gmitter Jr..

Ethics declarations

Conflict of interest

The authors declare that they have no conflicts of interest.

Author’s contributions

FGG and CC conceived and designed the study; the mapping population was developed within the breeding program of FGG. YY carried out the work, analyzed the data, and wrote the manuscript. CC developed the GoldenGate array and read SNP genotyping data. CC and FGG critically read and revised the manuscript. All authors read and approved the final manuscript.

Data archiving statement

The SNPs, genetic maps, and QTL data reported in this manuscript will be made publicly available through the Citrus Genome Database (www.citrusgenomedb.org).

Additional information

Communicated by W.-W. Guo

Electronic supplementary material

ESM 1

Frequency distributions of mandarin quality traits for the F1 population in three samplings (January and February in 2012 and February in 2013). (PPTX 90 kb)

ESM 2

Phenotypic variation of 15 fruit quality traits evaluated in ‘Fortune’, ‘Murcott’ and the F1 population in four samplings (January and February in 2012 and 2013). (XLSX 15 kb)

ESM 3

Phenotypic correlations among 15 fruit quality traits measured in the ‘Fortune’ x ‘Murcott’ F1 progeny in four samplings (January and February in 2012 and 2013). (XLSX 13 kb)

ESM 4

Two-factor (Genotype, sampling date) ANOVA for mandarin fruit quality traits in four samplings (January and February in 2012 and 2013). Fruit diameter (FD), fruit weight (FW), juice percentage (JP), seed number (SD), soluble solids content (SSC), titratable acidity (TA), SSC over TA ratio (ST), flavedo color space value L (FCL), a (FCA), b (FCB), a over b ratio (FCAB), juice color space value L (JCL), a (JCA), b (JCB), a over b ratio (JCAB). (XLSX 11 kb)

ESM 5

SNP-based markers and genetic position on the linkage groups. The maternal parent is ‘Fortune’ (FOR), and the paternal parent is ‘Murcott’ (MUR). (XLSX 67 kb)

ESM 6

Validation of QTLs in the 13 citrus selections. (XLSX 11 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Yu, Y., Chen, C. & Gmitter, F.G. QTL mapping of mandarin (Citrus reticulata) fruit characters using high-throughput SNP markers. Tree Genetics & Genomes 12, 77 (2016). https://doi.org/10.1007/s11295-016-1034-7

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s11295-016-1034-7

Keywords

Search

Navigation