Abstract
DNA marker analysis, combined with linkage and quantitative trait locus (QTL) analyses, has drastically changed the scheme of citrus breeding by enabling the marker-assisted selection (MAS) of a promising scion at the early seedling stage. This technique has greatly enhanced breeding efficiency by minimizing the period of trait evaluation at the orchard. It has also provided remarkable achievements for understanding the classification and pedigree of citrus varieties by molecular phylogenetic analysis. In the past decades, valuable DNA markers have been developed from various crosses undertaken for the selection of fruit traits, apomixis, dwarfism and for resistance against pests, stress, or acclimation. Zygotic embryo selection is a basic but important application of MAS for the cross of polyembryonic seed parents. The advent of next-generation sequencing technologies dramatically enhanced the accumulation of genome sequence data. They were used for the development of codominant DNA marker systems (simple sequence repeat: SSR and single nucleotide polymorphism: SNP) that enabled high-throughput genotyping and high-density linkage map construction. Consequently, they also enabled the identification of a gene or genome sequence responsible for a trait by associating the map with the genome sequence. While these advances provided us with the genomic basis for trait selection and the tools to improve breeding, MAS of a complex trait controlled by many genes having a small effect still remained a challenge due to the difficulty in conducting large scale genetic analysis in citrus. Now, two alternative analysis methods based on genome-wide genotype data, genome-wide association study (GWAS) and genomic selection (GS), have become available for identifying QTLs of any trait of interest without the need to cross for predicting the breeding value of offspring. These new methods facilitate the selection of complex traits as well as shed light on the significance of measuring methods, for these methods to become applicable.
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References
Ahmed S, Rattanpal HS, Kumari P, Singh J (2017) Study of genetic variability in citrus fruit crop by molecular markers. Int J Pure Appl Biosci 5:111–128
Aka Kacar Y, Demirel A, Tuzcu O, Yesiloglu T, Ulas M, Yildirim B (2005) Preliminary results on fingerprinting of lemon genotypes tolerant to mal secco disease by RAPD markers. Biol—Sect Cell Mol Biol 60:295–300
Aka Kacar Y, Byrne P, Teixeira da Silva J (2006) Molecular markers in plant tissue culture. In: da Silva JAT (ed) Floriculture, ornamental and plant biotechnology: advances and topical issues, vol II, 1st edn. Global Science Books, pp 444–449
Aleza P, Juárez J, Hernández M, Pina JA, Ollitrault P, Navarro L (2009) Recovery and characterization of a Citrus clementina Hort. ex Tan. “Clemenules” haploid plant selected to establish the reference whole Citrus genome sequence. BMC Plant Biol 9:110. https://doi.org/10.1186/1471-2229-9-110
Aleza P, Juárez J, Cuenca J, Ollitrault P, Navarro L (2010) Recovery of citrus triploid hybrids by embryo rescue and flow cytometry from 2x × 2x sexual hybridisation and its application to extensive breeding programs. Plant Cell Rep 29:1023–1034. https://doi.org/10.1007/s00299-010-0888-7
Asins MJ, Fernández-Ribacoba J, Bernet GP, Gadea J, Cambra M, Gorris MT et al (2012) The position of the major QTL for Citrus tristeza virus resistance is conserved among Citrus grandis, C. aurantium and Poncirus trifoliata. Mol Breed 29:575–587. https://doi.org/10.1007/s11032-011-9574-x
Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA et al (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. In: Fay JC (ed) PLoS One 3:e3376. https://doi.org/10.1371/journal.pone.0003376
Bajgain P, Rouse MN, Anderson JA (2016) Comparing genotyping-by-sequencing and single nucleotide polymorphism chip genotyping for quantitative trait loci mapping in Wheat. Crop Sci 56:232. https://doi.org/10.2135/cropsci2015.06.0389
Balding DJ (2006) A tutorial on statistical methods for population association studies. Nat Rev Genet 7:781–791. https://doi.org/10.1038/nrg1916
Barkley NA, Roose ML, Krueger RR, Federici CT (2006) Assessing genetic diversity and population structure in a citrus germplasm collection utilizing simple sequence repeat markers (SSRs). Theor Appl Genet 112:1519–1531. https://doi.org/10.1007/s00122-006-0255-9
Bassene JB, Berti L, Costantino G, Carcouet E, Kamiri M, Tomi F et al (2009) Inheritance of characters involved in fruit quality in a citrus interspecific allotetraploid somatic hybrid. J Agric Food Chem 57:5065–5070. https://doi.org/10.1021/jf803872f
Bastianel M, Schwarz SF, Coleta Filho H Della, Lin LL, Machado M, Koller OC (1998) Identification of zygotic and nucellar tangerine seedlings (Citrus spp.) using RAPD. Genet Mol Biol 21:123–127. https://doi.org/10.1590/s1415-47571998000100020
Bastianel M, de Oliveira AC, Cristofani M, Filho OG, Freitas-Astúa J, Rodrigues V et al (2006) Inheritance and heritability of resistance to citrus leprosis. Phytopathology 96:1092–1096. https://doi.org/10.1094/phyto-96-1092
Bastianel M, Cristofani-Yaly M, de Oliveira AC, Freitas-Astúa J, Garcia AAF, Resende MDV et al (2009) Quantitative trait loci analysis of citrus leprosis resistance in an interspecific backcross family of (Citrus reticulata Blanco × C. sinensis L. Osbeck) × C. sinensis L. Osb. Euphytica 169:101–111. https://doi.org/10.1007/s10681-009-9950-3
Batley J (eds) (2015) Plant genotyping—methods and protocols [Internet]. Springer New York, New York, NY. https://doi.org/10.1007/978-1-4939-1966-6
Batley J, Barker G, O’Sullivan H, Edwards KJ, Edwards D (2003) Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant Physiol 132:84–91. https://doi.org/10.1104/pp.102.019422.unlike
Bausher MG, Singh ND, Lee S-B, 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. https://doi.org/10.1186/1471-2229-6-21
Bernet GP, Margaix C, Jacas J, Carbonell EA, Asins MJ (2005) Genetic analysis of citrus leafminer susceptibility. Theor Appl Genet 110:1393–1400. https://doi.org/10.1007/s00122-005-1943-6
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 25:659–673. https://doi.org/10.1007/s11032-009-9363-y
Bink MCAM, Jansen J, Madduri M, Voorrips RE, Durel CE, Kouassi AB et al (2014) Bayesian QTL analyses using pedigreed families of an outcrossing species, with application to fruit firmness in apple. Theor Appl Genet 127:1073–1090. https://doi.org/10.1007/s00122-014-2281-3
Biswas MK, Xu Q, Deng X (2010) Utility of RAPD, ISSR, IRAP and REMAP markers for the genetic analysis of Citrus spp. Sci Hortic (Amsterdam) 124:254–261. https://doi.org/10.1016/j.scienta.2009.12.013
Biswas MK, Chen P, Amar MH, Deng X (2015) Novel polymorphic EST-based microsatellite marker isolation and characterization from Poncirus trifoliata (Rutaceae). Front Agric Sci Eng 2:60. https://doi.org/10.15302/J-FASE-2015048
Botha A-M, Venter E, van der Vyver C, Kunert KJ, Bornman CH (2004) Development and application of molecular DNA markers in Africa: a South African view. South African J Bot 70:152–166. https://doi.org/10.1016/S0254-6299(15)30276-3
Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331
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 89:606–614. https://doi.org/10.1007/BF00222455
Carbonell-Caballero J, Alonso R, Ibañez V, Terol J, Talon M, Dopazo J (2015) A phylogenetic analysis of 34 chloroplast genomes elucidates the relationships between wild and domestic species within the genus Citrus. Mol Biol Evol 32:2015–2035. https://doi.org/10.1093/molbev/msv082
Carlos de Oliveira A, Novac Garcia A, Cristofani M, Machado MA (2002) Identification of citrus hybrids through the combination of leaf apex morphology and SSR markers. Euphytica 128:397–403. https://doi.org/10.1023/a:1021223309212
Carlos de Oliveira A, Bastianel M, Cristofani-Yaly M, Morais do Amaral A, 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 48:219–231. http://www.ncbi.nlm.nih.gov/pubmed/17666774
Chen C, Zhou P, Choi YA, Huang S, Gmitter FG (2006) Mining and characterizing microsatellites from citrus ESTs. Theor Appl Genet 112:1248–1257. https://doi.org/10.1007/s00122-006-0226-1
Chen C, Bowman KD, Choi YA, Dang PM, Rao MN, Huang S et al (2008) EST-SSR genetic maps for Citrus sinensis and Poncirus trifoliata. Tree Genet Genomes 4:1–10. https://doi.org/10.1007/s11295-007-0083-3
Chen C, Grosser JW, Ćalović M, Serrano P, Pasquali G, Gmitter J et al (2008) Verification of mandarin and pummelo somatic hybrids by expressed sequence tag—simple sequence repeat marker analysis 133:794–800
Chen C, Lyon MT, O’Malley D, Federici CT, Gmitter J, Grosser JW et al (2008c) Origin and frequency of 2n gametes in Citrus sinensis × Poncirus trifoliata and their reciprocal crosses. Plant Sci 174:1–8. https://doi.org/10.1016/j.plantsci.2007.08.005
Chen B, Cole JW, Grond-Ginsbach C (2017) Departure from Hardy Weinberg equilibrium and genotyping error. Front Genet 8:167. https://doi.org/10.3389/fgene.2017.00167
Cheng F, Roose M (1995) Origin and inheritance of dwarfing by the citrus rootstock Poncirus trifoliata “Flying Dragon.” J Am Soc Hortic Sci 120:286–291. http://journal.ashspublications.org/content/120/2/286.short
Choi YA, Chen C, Huang S, Gmitter FGJ (2005) Quantitative trait linkage (QTL) mapping for resistance to citrus canker within Citrus. In: The 2nd international Canker/Huanlongbin workshop. Orland, FL, USA, p P10
Close TJ, Wanamaker S, Roose ML, Lyon M (2007) HarvEST. Methods Mol Biol 406:161–177. http://www.ncbi.nlm.nih.gov/pubmed/18287692
Cloutier S, Landry BS (1994) Molecular markers applied to plant tissue culture. Vitr Cell Dev Biol—Plant 30:32–39. https://doi.org/10.1007/BF02632117
Coletta Filho HD, Machado MA, Targon MLPN, Moreira MCPQDG, Pompeu J Jr (1998) Analysis of the genetic diversity among mandarins (Citrus spp.) using RAPD markers. Euphytica 102:133–139. https://doi.org/10.1023/a:1018300900275
Combrink NK, Labuschagne MT, Bijzet Z (2013) Variation of fruit size and shape in Kiyomi tangor families. Sci Hortic (Amsterdam). Elsevier B.V. 162:357–364. https://doi.org/10.1016/j.scienta.2013.08.010
Combrink NK, Bijzet Z, Sippel AD, Booyse M, Labuschagne MT (2015) Genotypic variation of rind colour in citrus tangor Kiyomi families. Acta Hortic 1065:439–448. https://doi.org/10.17660/actahortic.2015.1065.54
Corazza-Nunes MJ, Machado MA, Nunes WMC, Cristofani M, Targon MLPN (2002) Assessment of genetic variability in grapefruits (Citrus paradisi Macf.) and pummelos (C. maxima (Burm.) Merr.) using RAPD and SSR markers. Euphytica 126:169–176. https://doi.org/10.1023/a:1016332030738
Costa F (2015) MetaQTL analysis provides a compendium of genomic loci controlling fruit quality traits in apple. Tree Genet Genomes 11:1–11. https://doi.org/10.1007/s11295-014-0819-9
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 109:25–32. https://doi.org/10.1023/a:1003637116745
Cuenca J, Aleza P, Vicent A, Brunel D, Ollitrault P, Navarro L (2013) Genetically based location from triploid populations and gene ontology of a 3.3-Mb genome region linked to Alternaria brown spot resistance in citrus reveal clusters of resistance genes. PLoS One 8:1–18. https://doi.org/10.1371/journal.pone.0076755
Cuenca J, Aleza P, Garcia-Lor A, Ollitrault P, Navarro L (2016) Fine mapping for identification of citrus Alternaria brown spot candidate resistance genes and development of new SNP markers for marker-assisted selection. Front Plant Sci 7:1–13. https://doi.org/10.3389/fpls.2016.01948
Curk F, Ancillo G, Ollitrault F, Perrier X, Jacquemoud-Collet JP, Garcia-Lor A et al (2015) Nuclear species-diagnostic SNP markers mined from 454 amplicon sequencing reveal admixture genomic structure of modern Citrus varieties. PLoS ONE 10:1–25. https://doi.org/10.1371/journal.pone.0125628
Curk F, Ollitrault F, Garcia-Lor A, Luro F, Navarro L, Ollitrault P (2016) Phylogenetic origin of limes and lemons revealed by cytoplasmic and nuclear markers. Ann Bot 117:565–583. https://doi.org/10.1093/aob/mcw005
Curtolo M, Cristofani-Yaly M, Gazaffi R, Takita MA, Figueira A, Machado MA (2017) QTL mapping for fruit quality in Citrus using DArTseq markers. BMC Genom 18:289. https://doi.org/10.1186/s12864-017-3629-2
Curtolo M, Soratto TAT, Gazaffi R, Takita MA, Machado MA, Cristofani-Yaly M (2018) High-density linkage maps for Citrus sunki and Poncirus trifoliata using DArTseq markers. Tree Genet Genomes 14. https://doi.org/10.1007/s11295-017-1218-9
Dalkilic Z, Timmer LW, Gmitter FG Jr (2005) Linkage of an Alternaria disease resistance gene in mandarin hybrids with RAPD fragments. J Am Soc Hortic Sci 130:191–195. isi:000227632500007
de Oliveira RP, Cristofani M, Machado MA (2005) Integrated genetic map of citrus based on RAPD markers. Fruits 60:187–193. https://doi.org/10.1051/fruits:2005025
De Simone M, Russo MP, Puleo G, Marsan PA, Lorenzoni C, Marocco A et al (1998) Construction of genetic maps for Citrus aurantium and C. latipes based on AFLP, RAPD and RFLP markers. Fruits 53:383–390
De Oliveira RP, Cristofani M, Machado MA (2004) Genetic linkage maps of “Pêra” sweet orange and “Cravo” mandarin with RAPD markers. Pesqui Agropecuária Bras 39:159–165. https://doi.org/10.1590/S0100-204X2004000200009
Deng ZN, Gentile A, Nicolosi E, Domina F, Vardi A, Tribulato E (1995) Identification of in vivo and in vitro lemon mutants by RAPD markers. J Hortic Sci 70:117–125. https://doi.org/10.1080/14620316.1995.11515281
Deng Z, Huang S, Xiao S, Gmitter FG (1997) Development and characterization of SCAR markers linked to the citrus tristeza virus resistance gene from Poncirus trifoliata. Genome 704:697–704
Deng Z, Huang S, Ling P, Yu C, Tao Q, Chen C et al (2001) Fine genetic mapping and BAC contig development for the citrus tristeza virus resistance gene locus in Poncirus trifoliata (Raf.). Mol Genet Genomics 265:739–747. https://doi.org/10.1007/s004380100471
Durham RE, Liou PC, Gmitter FG, Moore GA (1992) Linkage of restriction fragment length polymorphisms and isozymes in Citrus. Theor Appl Genet 84:39–48. https://doi.org/10.1007/BF00223979
Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES et al (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6:e19379. https://doi.org/10.1371/journal.pone.0019379
Fang DQ, Roose ML (1997) Identification of closely related citrus cultivars with inter-simple sequence repeat markers. Theor Appl Genet 95:408–417. https://doi.org/10.1007/s001220050577
Fang DQ, Federici CT, Roose ML (1997) Development of molecular markers linked to a gene controlling fruit acidity in citrus. Genome 40:841–849. https://doi.org/10.1139/g97-809
Fang D, Krueger RR, Roose ML (1998) Phylogenetic relationships among selected Citrus germplasm accessions revealed by inter-simple sequence repeat (ISSR) markers. J Am Soc Hortic Sci 123:612–617
Fang D, Federici C, Roose M (1998) A high-resolution linkage map of the citrus tristeza virus resistance gene region in Poncirus trifoliata (L.) Raf Genetics 150:883–890. http://www.genetics.org/content/150/2/883.short
Federici CT, Fang DQ, Scora RW, Roose ML (1998) Phylogenetic relationships within the genus Citrus (Rutaceae) and related genera as revealed by RFLP and RAPD analysis. Theor Appl Genet 96:812–822. https://doi.org/10.1007/s001220050807
Ferrante SP, Lucretti S, Reale S, De Patrizio A, Abbate L, Tusa N et al (2010) Assessment of the origin of new citrus tetraploid hybrids (2n = 4x) by means of SSR markers and PCR based dosage effects. Euphytica 173:223–233. https://doi.org/10.1007/s10681-009-0093-3
Ferreira A, da Silva MF, Silva LDCE, Cruz CD (2006) Estimating the effects of population size and type on the accuracy of genetic maps. Genet Mol Biol 29:187–192. https://doi.org/10.1590/S1415-47572006000100033
Freeman T, Robbertse PJ (2003) Internal quality of ‘Valencia’ orange fruit as influenced by tree fruit position and winter girdling. South African J Plant Soil 20:199–202. https://doi.org/10.1080/02571862.2003.10634935
Froelicher Y, Bassene JB, Jedidi-Neji E, Dambier D, Morillon R, Bernardini G et al (2007) Induced parthenogenesis in mandarin for haploid production: induction procedures and genetic analysis of plantlets. Plant Cell Rep 26:937–944. https://doi.org/10.1007/s00299-007-0314-y
Froelicher Y, Dambier D, Bassene JB, Costantino G, Lotfy S, Didout C et al (2008) Characterization of microsatellite markers in mandarin orange (Citrus reticulata Blanco). Mol Ecol Resour 8:119–122. https://doi.org/10.1111/j.1471-8286.2007.01893.x
Fu Y-B, Cheng B, Peterson GW (2014) Genetic diversity analysis of yellow mustard (Sinapis alba L.) germplasm based on genotyping by sequencing. Genet Resour Crop Evol 61:579–594. https://doi.org/10.1007/s10722-013-0058-1
Fujii H, Ogata T, Shimada T, Endo T, Iketani H, Shimizu T et al (2013) Minimal Marker: an algorithm and computer program for the identification of minimal sets of discriminating DNA markers for efficient variety identification. J Bioinform Comput Biol 11:1250022. https://doi.org/10.1142/S0219720012500229
García R, Asíns MJ, Forner J, Carbonell EA (1999) Genetic analysis of apomixis in Citrus and Poncirus by molecular markers. Theor Appl Genet 99:511–518. https://doi.org/10.1007/s001220051264
García MR, Asíns MJ, Carbonell EA (2000) QTL analysis of yield and seed number in Citrus. Theor Appl Genet 101:487–493. https://doi.org/10.1007/s001220051507
Gmitter FG, 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 92:688–695. https://doi.org/10.1007/BF00226090
Gmitter FG, Chen C, Machado MA, Souza AA, Ollitrault P, Froehlicher Y et al (2012) Citrus genomics. Tree Genet Genomes 8:611–626. https://doi.org/10.1007/s11295-012-0499-2
Goffinet B, Gerber S (2000) Quantitative trait loci: a meta-analysis. Genetics 155:463–473. http://www.genetics.org/content/155/1/463.short
Gois IB, Borém A, Cristofani-Yaly M, De Resende MDV, Azevedo CF, Bastianel M et al (2016) Genome wide selection in citrus breeding. Genet Mol Res 15:1–14. https://doi.org/10.4238/gmr15048863
Goodwin W, Linacre A, Hadi S (2011) An introduction to forensic genetics, vol 2. John Wiley & Sons
Goto S, Yoshioka T, Ohta S, Kita M, Hamada H, Shimizu T (2016) Segregation and heritability of male sterility in populations derived from progeny of Satsuma mandarin. In: Fang DD (ed) PLoS One 11:e0162408. https://doi.org/10.1371/journal.pone.0162408
Goto S, Yoshioka T, Ohta S, Kita M, Hamada H, Shimizu T (2018) QTL mapping of male sterility and transmission pattern in progeny of Satsuma mandarin. PloS one 13(7)
Grattapaglia D, Sederoff R (1994) Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers. Genetics 137:1121–1137. http://www.genetics.org/content/137/4/1121.short
Gregory TR (2004) Insertion-deletion biases and the evolution of genome size. Gene 324:15–34. https://doi.org/10.1016/j.gene.2003.09.030
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 173:265–277. https://doi.org/10.1007/s10681-010-0146-7
Guo F, Yu H, Tang Z, Jiang X, Wang L, Wang X et al (2015) Construction of a SNP-based high-density genetic map for pummelo using RAD sequencing. Tree Genet Genomes 11:2. https://doi.org/10.1007/s11295-014-0831-0
Hall D, Tegström C, Ingvarsson PK (2010) Using association mapping to dissect the genetic basis of complex traits in plants. Briefings Funct Genomics Proteomics 9:157–165. https://doi.org/10.1093/bfgp/elp048
He J, Zhao X, Laroche A, Lu Z-X, Liu H, Li Z (2014) Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Front Plant Sci 5:1–8. https://doi.org/10.3389/fpls.2014.00484
Holla KMS, Khan JA, Sowjanya MS, Shashidhar HE (2014) Monomorphic molecular markers are as informative as polymorphic molecular markers. Indian J Genet Plant Breed 74:596. https://doi.org/10.5958/0975-6906.2014.00896.7
Hong Q, Gong G, Peng Z, Xiang S, Jiang D, Tiangang L (2008) A consensus map constructed with SSR and EST-SSR markers using progeny population from sweet orange tangor. In: Deng X, Xu J, Lin S (eds) Proceedings of the 11th International Society of Citriculture. China Agricultural Press, Wuhan, China, pp 1:284–288
Hoskins R, Phan A, Naeemuddin M, Mapa F, Ruddy D, Ryan J et al (2001) Single nucleotide polymorphism markers for genetic mapping in Drosophila melanogaster. Genome Res 11:1100–1113. https://doi.org/10.1101/gr.178001.4
Hussain W, Baenziger PS, Belamkar V, Guttieri MJ, Venegas JP, Easterly A et al (2017) Genotyping-by-Sequencing derived high-density linkage map and its application to QTL mapping of flag leaf traits in bread wheat. Sci Rep. Springer US 7:16394. https://doi.org/10.1038/s41598-017-16006-z
Imai A, Yoshioka T, Hayashi T (2017) Quantitative trait locus (QTL) analysis of fruit-quality traits for mandarin breeding in Japan. Tree Genet Genomes 13:79. https://doi.org/10.1007/s11295-017-1162-8
Imai A, Nonaka K, Kuniga T, Yoshioka T, Hayashi T (2018) Genome-wide association mapping of fruit-quality traits using genotyping-by-sequencing approach in citrus landraces, modern cultivars, and breeding lines in Japan. Tree Genet Genomes 14:24. https://doi.org/10.1007/s11295-018-1238-0
Iwata H, Minamikawa MF, Kajiya-Kanegae H, Ishimori M, Hayashi T (2016) Genomics-assisted breeding in fruit trees. Breed Sci 66:100–115. https://doi.org/10.1270/jsbbs.66.100
Jackson SA, Iwata A, Lee S-H, Schmutz J, Shoemaker R (2011) Sequencing crop genomes: approaches and applications. New Phytol 191:915–925. https://doi.org/10.1111/j.1469-8137.2011.03804.x
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 84:49–56. https://doi.org/10.1007/BF00223980
Jiang D, Guang-Yan Z, Hong Q-B (2006) Analysis of microsatellites in Citrus unigenes. Acta Genet Sin 33:345–353. https://doi.org/10.1016/S0379-4172(06)60060-7
Jiang D, Ye Q, Wang F, Cao L (2010) The mining of citrus EST-SNP and its application in cultivar discrimination. Agric Sci China 9:179–190. https://doi.org/10.1016/S1671-2927(09)60082-1
Jones AG, Ardren WR (2003) Methods of parentage analysis in natural populations. Mol Ecol 12:2511–2523. https://doi.org/10.1046/j.1365-294X.2003.01928.x
Kacar Y, Uzun A, Polat I, Yesiloglu T, Yilmaz B, Gulsen O et al (2013) Molecular characterization and genetic diversity analysis of mandarin genotypes by SSR and SRAP markers. J Food Agric Environ 11:516–521
Kage U, Kumar A, Dhokane D, Karre S, Kushalappa AC (2016) Functional molecular markers for crop improvement. Crit Rev Biotechnol 36:917–930. https://doi.org/10.3109/07388551.2015.1062743
Kalia RK, Rai MK, Kalia S, Singh R, Dhawan AK (2011) Microsatellite markers: an overview of the recent progress in plants. Euphytica 177:309–334. https://doi.org/10.1007/s10681-010-0286-9
Kaminuma E, Fujisawa T, Tanizawa Y, Sakamoto N, Kurata N, Shimizu T et al (2013) H2DB: a heritability database across multiple species by annotating trait-associated genomic loci. Nucleic Acids Res 41:D880–D884. https://doi.org/10.1093/nar/gks1216
Kepiro JL, Roose ML (2007) Nucellar embryony. In: Khan IA (ed) Citrus genetics, breeding and biotechnology. CABI, CAB International, Nosworthy Way Wallingford, pp 141–149
Kepiro JL, Roose ML (2009) AFLP markers closely linked to a major gene essential for nucellar embryony (apomixis) in Citrus maxima × Poncirus trifoliata. Tree Genet Genomes 6:1–11. https://doi.org/10.1007/s11295-009-0223-z
Khalid S, Malik AU, Saleem BA, Khan AS, Khalid MS, Amin M (2012) Tree age and canopy position affect rind quality, fruit quality and rind nutrient content of “Kinnow” mandarin (Citrus nobilis Lour × Citrus deliciosa Tenora). Sci Hortic (Amsterdam). Elsevier B.V. 135:137–144. https://doi.org/10.1016/j.scienta.2011.12.010
Kijas JM, Fowler JC, Thomas MR (1995) An evaluation of sequence tagged microsatellite site markers for genetic analysis within Citrus and related species. Genome 38:349–355. http://www.nrcresearchpress.com/doi/pdf/10.1139/g95-045
Kijas JMH, Thomas MR, Fowler JCS, Roose ML (1997) Integration of trinucleotide microsatellites into a linkage map of Citrus. Theor Appl Genet 94:701–706. https://doi.org/10.1007/s001220050468
Kilian A, Wenzl P, Huttner E, Carling J, Xia L, Blois H et al (2012) Diversity arrays technology: a generic genome profiling technology on open platforms. In: Bonin FP (ed) Data production and analysis in population genomics. Humana Press, Totowa, NJ, pp 67–89. https://doi.org/10.1007/978-1-61779-870-2_5
Kolpakov R, Bana G, Kucherov G (2003) mreps: efficient and flexible detection of tandem repeats in DNA. Nucleic Acids Res 31:3672–3678. https://doi.org/10.1093/nar/gkg617
Kotoda N, Matsuo S, Honda I, Yano K, Shimizu T (2015) Isolation and functional analysis of two Gibberellin 20-oxidase genes from Satsuma mandarin (Citrus unshiu Marc.). Hortic J 85:128–140. https://doi.org/10.2503/hortj.mi-085
Li G, Quiros CF (2001) Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theor Appl Genet 103:455–461. https://doi.org/10.1007/s001220100570
Liang G, Xiong G, Guo Q, He Q, Li X (2007) AFLP analysis and taxonomy of Citrus. Acta Hortic 760:137–142. https://doi.org/10.17660/ActaHortic.2007.760.17
Ling P, Yu C, Deng Z, Chen C, Huang S, Wendell MK et al (1999) Citrus genome mapping with AFLP markers. In: Plant and Animal Genome XIII Conference. San Diego, CA, USA, p P189
Ling P, Duncan LW, Deng Z, Dunn D, Hu X, Huang S et al (2000) Inheritance of citrus nematode resistance and its linkage with molecular markers. Theor Appl Genet 100:1010–1017. https://doi.org/10.1007/s001220051382
Liou P-C (1990) A molecular study of the citrus genome through restriction fragment length polymorphism and isozyme mapping [Internet]. The University of Florida. https://archive.org/details/molecularstudyof00liou
Liou PC, Gmitter FG, Moore GA (1996) Characterization of the citrus genome through analysis of restriction fragment length polymorphism. Theor Appl Genet 92:425–435
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:e75149. https://doi.org/10.1371/journal.pone.0075149
Luro F, Laigret F, Bové JM, Ollitrault P (1994) Application of random amplified polymorphic DNA (R.A.P.D.) to Citrus genetics and taxonomy. In: Tribulato E, Gentile A (eds) Proceedings of the 7th International Citrus Congress 1:225–228. http://agritrop.cirad.fr/464648/
Luro F, Laigret F, Bove JM, Ollitrault P (1995) DNA amplified fingerprinting, a useful tool for determination of genetic origin and diversity analysis in Citrus. HortScience 30:1063–1067
Luro F, Laigret F, Lorieux M, Ollitrault P (1996) Citrus genome mapping with molecular markers: two maps obtained by segregation analysis of progeny of one intergeneric cross. In: International Citrus Congress, vol 2. Sun City, South Africa, pp 862–866. http://agritrop.cirad.fr/390226/
Luro F, Rist D, Ollitrault P (2001) Evaluation of genetic relationships in citrus genus by means of sequence tagged microsatellites. Acta Hortic 237–242. https://doi.org/10.17660/actahortic.2001.546.27
Luro F, Maddy F, Jacquemond C, Froelicher Y, Morillon R, Rist D et al (2004) Identification and evaluation of diplogyny in Clementine (Citrus clementina) for use in breeding. Acta Hortic 841–848. https://doi.org/10.17660/actahortic.2004.663.152
Luro F, Costantino G, Billot C, Froelicher Y, Morillon R, Ollitrault P et al (2007) Genetic maps of clementine mandarin and intergeneric hybrid clementine X poncirus using genomic and EST microsatellite markers. In: Plant and Animal Genomes XVth. San Diego, CA, USA, p 487. http://www.intl-pag.org/15/abstracts/PAG15_Late_487.html
Luro FL, Costantino G, Terol J, Argout X, Allario T, Wincker P et al (2008) Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping. BMC Genomics 9:287 [pii]. https://doi.org/10.1186/1471-2164-9-287
Lyon MP (2008) A genomic genetic map of the common sweet orange and Poncirus trifoliata. Ph.D. thesis, University of California, Riverside [Internet]. http://www.worldcat.org/title/genomic-genetic-map-of-the-common-sweet-orange-and-poncirus-trifoliata/oclc/269016514
Lyon MT, Federici CT, Kacar Y, Chen C, O’Malley D, Chaparro JX et al (2007) SSR-based linkage maps for sweet orange and trifoliate orange. In: Plant and Animal Genomes XIV, p 480
Ma X, Gong G, Peng Z, Xue ZH, Hong Q (2012) Development of SSR markers from citrus BAC end sequences and their integration into linkage map. Acta Bot Boreali-Occidentalia Sin 32: 1112–1117
Machado MA, Coletta Filho HD, Targon MLPN, Pompeu J (1996) Genetic relationship of Mediterranean mandarins (Citrus deliciosa Tenore) using RAPD markers. Euphytica 92:321–326. http://dx.doi.org/10.1007/BF00037115
Machado MA, Cristofani M, Amaral AM Do, de Oliveira AC (2005) Genética, melhoramento e biotecnologia de citros. In: De Mattos Júnior D, De Negri JD, Pio RM, Pompeu Júnior J (eds) Citros. Campinas, IAC, Fundag, pp 221–277
Machado MA, Cristofani-Yaly M, Bastianel M (2011) Breeding, genetic and genomic of citrus for disease resistance. Rev Bras Frutic 33:158–172. https://doi.org/10.1590/S0100-29452011000500019
Mammadov J, Aggarwal R, Buyyarapu R, Kumpatla S (2012) SNP markers and their impact on plant breeding. Int J Plant Genomics 2012:1–11. https://doi.org/10.1155/2012/728398
Marak CK, Laskar MA (2010) Analysis of phenetic relationship between Citrus indica Tanaka and a few commercially important citrus species by ISSR markers. Sci Hortic (Amsterdam). Elsevier B.V. 124:345–348. https://doi.org/10.1016/j.scienta.2010.01.014
Meuwissen T (2003) Genomic selection: the future of marker assisted selection and animal breeding. In: Lanteri S (ed) Marker assisted selection: a fast track to increase genetic gain in plant and animal breeding? Electronic forum on biotechnology in food and agriculture, pp 54–59
Meuwissen THE, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819–1829. http://www.genetics.org/content/157/4/1819.abstract
Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci U S A. 88:9828–9832. http://www.ncbi.nlm.nih.gov/pubmed/1682921
Minamikawa MF, Nonaka K, Kaminuma E, Kajiya-Kanegae H, Onogi A, Goto S et al (2017) Genome-wide association study and genomic prediction in citrus: potential of genomics-assisted breeding for fruit quality traits. Sci Rep. Springer US 7:4721. https://doi.org/10.1038/s41598-017-05100-x
Miyazaki T, Plotto A, Goodner K, Gmitter FG (2011) Distribution of aroma volatile compounds in tangerine hybrids and proposed inheritance. J Sci Food Agric 91:449–460. https://doi.org/10.1002/jsfa.4205
Miyazaki T, Plotto A, Baldwin EA, Reyes-De-Corcuera JI, Gmitter FG (2012) Aroma characterization of tangerine hybrids by gas-chromatography-olfactometry and sensory evaluation. J Sci Food Agric 92:727–735. https://doi.org/10.1002/jsfa.4663
Nageswara Rao M, Soneji JR, Chen C, Huang S, Gmitter FG (2007) Characterization of zygotic and nucellar seedlings from sour orange-like citrus rootstock candidates using RAPD and EST-SSR markers. Tree Genet Genomes 4:113–124. https://doi.org/10.1007/s11295-007-0092-2
Nakano M, Shimizu T, Kuniga T, Nesumi H, Omura M (2008) Mapping and haplotyping of the flanking region of the polyembryony locus in Citrus unshiu Marcow. J Japanese Soc Hortic Sci 77:109–114. https://doi.org/10.2503/jjshs1.77.109
Nakano M, Shimada T, Endo T, Fujii H, Nesumi H, Kita M et al (2012) Characterization of genomic sequence showing strong association with polyembryony among diverse Citrus species and cultivars, and its synteny with Vitis and Populus. Plant Sci 183:131–142. https://doi.org/10.1016/j.plantsci.2011.08.002
Nasu S, Suzuki J, Ohta R, Hasegawa K, Yui R, Kitazawa N et al (2002) Search for and analysis of single nucleotide polymorphisms (SNPs) in rice (Oryza sativa, Oryza rufipogon) and establishment of SNP markers. DNA Res 9:163–171. https://doi.org/10.1093/dnares/9.5.163
Nicolosi E, Deng ZN, Gentile A, La Malfa S, Continella G, Tribulato E (2000) Citrus phylogeny and genetic origin of important species as investigated by molecular markers. Theor Appl Genet 100:1155–1166. https://doi.org/10.1007/s001220051419
Novelli VM, Takita MA, Machado MA (2004) Identification and analysis of single nucleotide polymorphisms (SNPs) in citrus. Euphytica 138:227–237. https://doi.org/10.1023/B:EUPH.0000047086.47988.82
Novelli VM, Cristofani M, Souza AA, Machado MA (2006) Development and characterization of polymorphic microsatellite markers for the sweet orange (Citrus sinensis L. Osbeck). Genet Mol Biol 29:90–96. https://doi.org/10.1590/s1415-47572006000100018
Oddou-Muratorio S, Vendramin GG, Buiteveld J, Fady B (2009) Population estimators or progeny tests: what is the best method to assess null allele frequencies at SSR loci? Conserv Genet 10:1343–1347. https://doi.org/10.1007/s10592-008-9648-4
Ohta S, Yano K, Kurita Y, Kita M, Shimizu T, Nesumi H (2013) A sample preparation method for direct and non-direct PCR in woody plants. J Japanese Soc Hortic Sci 82:14–21. https://doi.org/10.2503/jjshs1.82.14
Ohta S, Endo T, Shimada T, Fujii H, Shimizu T, Kita M et al (2015) Construction of genetic linkage map and graphical genotyping of pseudo-backcrossed F2 (BC ’2) progeny to introduce a CTV resistance from Poncirus trifoliata (L.) Raf. into Citrus by introgression breeding. Tree Genet Genomes 11:797. https://doi.org/10.1007/s11295-014-0797-y
Ollitrault P, Lotfy S, Costantino G, T. Federici C, Mu L, Chen C et al (2008) International effort toward a SSR-based linkage map for C. clementina [Internet]. In: 11th International Citrus Congress, International Society of Citriculture. Wuhan, China. http://agritrop.cirad.fr/548797/
Ollitrault F, Terol J, Pina JA, Navarro L, Talon M, Ollitrault P (2010) Development of SSR markers from Citrus clementina (Rutaceae) BAC end sequences and interspecific transferability in Citrus. Am J Bot 97:e124–e129. https://doi.org/10.3732/ajb.1000280
Ollitrault P, Terol J, Chen C, Federici CT, Lotfy S, Hippolyte I et al (2012a) A reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping. BMC Genom 13:593. https://doi.org/10.1186/1471-2164-13-593
Ollitrault P, Terol J, Garcia-Lor A, Bérard A, Chauveau A, Froelicher Y et al (2012b) SNP mining in C. clementina BAC end sequences; transferability in the Citrus genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping. BMC Genomics 13:13. https://doi.org/10.1186/1471-2164-13-13
Omura M, Shimada T (2016) Citrus breeding, genetics and genomics in Japan. Breed Sci 66:3–17. https://doi.org/10.1270/jsbbs.66.3
Omura M, Ueda T, Kita M, Komatsu A, Takanokura Y, Shimada T et al (2000) EST mapping of Citrus. In: Davies FS (ed) Proceedings of the International Society of Citriculture. Orland, FL, USA, pp 71–74
Oraguzie NC, Rikkerink EHA, Gardiner SE, De Silva HN (2007) Association mapping in plants [Internet]. In: Oraguzie NC, Rikkerink EHA, Gardiner SE, De Silva HN (eds). Springer New York, New York, NY. https://doi.org/10.1007/978-0-387-36011-9
Palmieri DA, Novelli VM, Bastianel M, Cristofani-Yaly M, Astúa-Monge G, Carlos EF et al (2007) Frequency and distribution of microsatellites from ESTs of citrus. Genet Mol Biol 30:1009–1018. https://doi.org/10.1590/S1415-47572007000500029
Pang XM, Hu CG, Deng XX (2007) Phylogenetic relationships within Citrus and its related genera as inferred from AFLP markers. Genet Resour Crop Evol 54:429–436. https://doi.org/10.1007/s10722-006-0005-5
Parida SK, Kalia SK, Kaul S, Dalal V, Hemaprabha G, Selvi A et al (2009) Informative genomic microsatellite markers for efficient genotyping applications in sugarcane. Theor Appl Genet 118:327–338. https://doi.org/10.1007/s00122-008-0902-4
Pessina D, Gentili R, Barcaccia G, Nicolè S, Rossi G, Barbesti S et al (2011) DNA content, morphometric and molecular marker analyses of Citrus limonimedica, C. limon and C. medica for the determination of their variability and genetic relationships within the genus Citrus. Sci Hortic (Amsterdam). Elsevier B.V. 129:663–673. https://doi.org/10.1016/j.scienta.2011.05.012
Poland JA, Rife TW (2012) Genotyping-by-sequencing for plant breeding and genetics. Plant Genome J 5:92. https://doi.org/10.3835/plantgenome2012.05.0005
Polat I, Kacar YA, Yesiloglu T, Uzun A, Tuzcu O, Gulsen O et al (2012) Molecular characterization of sour orange (Citrus aurantium) accessions and their relatives using SSR and SRAP markers. Genet Mol Res 11:3267–3276. http://dx.doi.org/10.4238/2012.September.12.10
Pompanon F, Bonin A, Bellemain E, Taberlet P (2005) Genotyping errors: causes, consequences and solutions. Nat Rev Genet 6:846–847. https://doi.org/10.1038/nrg1707
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 8:1061–1071. https://doi.org/10.1007/s11295-012-0486-7
Rai M (2006) Refinement of the Citrus tristeza virus resistance gene (Ctv) positional map in Poncirus trifoliata and generation of transgenic grapefruit (Citrus paradisi) plant lines with candidate resistance genes in this region. Plant Mol Biol 61:399–414. https://doi.org/10.1007/s11103-006-0018-7
Raman H, Raman R, Kilian A, Detering F, Carling J, Coombes N et al (2014) Genome-wide delineation of natural variation for pod shatter resistance in Brassica napus. PLoS One 9. https://doi.org/10.1371/journal.pone.0101673
Rauf S, Iqbal Z, Shahzad M (2013) Genetic improvement of Citrus for disease resistance. Arch Phytopathol Plant Prot 46:2051–2061. https://doi.org/10.1080/03235408.2013.783982
Roose ML, Feng D, Cheng FS, Tayyar RI, Federici CT, Kupper RS (2000) Mapping the Citrus genome. Acta Hortic 25–32. https://doi.org/10.17660/actahortic.2000.535.1
Rouseff R, Gmitter F, Grosser J (1994) Citrus breeding and flavour. In: Piggott JR, Paterson A (eds) Understanding natural flavors. Springer US, pp 113–127. https://doi.org/10.1007/978-1-4615-2143-3
Ruiz C, Asins M (2003) Comparison between Poncirus and Citrus genetic linkage maps. Theor Appl Genet 106:826–836. https://doi.org/10.1007/s00122-002-1095-x
Ruiz C, Breto MP, Asíns MJ (2000) A quick methodology to identify sexual seedlings in citrus breeding programs using SSR markers. Euphytica 112:89–94. https://doi.org/10.1023/A:1003992719598
Salazar JA, Pacheco I, Shinya P, Zapata P, Silva C, Aradhya M et al (2017) Genotyping by sequencing for SNP-based linkage analysis and identification of QTLs linked to fruit quality traits in Japanese plum (Prunus salicina Lindl.). Front Plant Sci 8:476. https://doi.org/10.3389/fpls.2017.00476
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 102:206–214. https://doi.org/10.1007/s001220051637
Sansaloni C, Petroli C, Jaccoud D, Carling J, Detering F, Grattapaglia D et al (2011) Diversity Arrays Technology (DArT) and next-generation sequencing combined: genome-wide, high throughput, highly informative genotyping for molecular breeding of Eucalyptus. BMC Proc 5:P54. https://doi.org/10.1186/1753-6561-5-S7-P54
Schlötterer C (2004) Opinion: the evolution of molecular markers—just a matter of fashion? Nat Rev Genet 5:63–69. https://doi.org/10.1038/nrg1249
Shahsavar A, Izadpanah K, Tafazoli E, Tabatabaei BES (2007) Characterization of citrus germplasm including unknown variants by inter-simple sequence repeat (ISSR) markers. Sci Hortic (Amsterdam) 112:310–314. https://doi.org/10.1016/j.scienta.2006.12.039
Shan X, Blake TK, Talbert LE (1999) Conversion of AFLP markers to sequence-specific PCR markers in barley and wheat. Theor Appl Genet 98:1072–1078. https://doi.org/10.1007/s001220051169
Shimada T, Fujii H, Endo T, Ueda T, Sugiyama A, Nakano M et al (2014) Construction of a citrus framework genetic map anchored by 708 gene-based markers. Tree Genet Genomes 10:1001–1013. https://doi.org/10.1007/s11295-014-0738-9
Shimizu T, Kitajima A, Nonaka K, Yoshioka T, Ohta S, Goto S et al (2016a) Hybrid origins of citrus varieties inferred from DNA marker analysis of nuclear and organelle genomes. PLoS ONE 11:e0166969. https://doi.org/10.1371/journal.pone.0166969
Shimizu T, Kaminuma E, Nonaka K, Yoshioka T, Goto S, Matsumoto T et al (2016b) A genomic approach to selecting robust and versatile SNP sets from next-generation sequencing data for genome-wide association study in citrus cultivars. Acta Hortic 1135:23–32. https://doi.org/10.17660/actahortic.2016.1135.4
Shimizu T, Tanizawa Y, Mochizuki T, Nagasaki H, Yoshioka T, Toyoda A et al (2017) Draft sequencing of the heterozygous diploid genome of Satsuma (Citrus unshiu Marc.) using a hybrid assembly approach. Front Genet 8:180. https://doi.org/10.3389/fgene.2017.00180
Siviero A, Cristofani M, Furtado EL, Garcia AAF, Coelho ASG, Machado MA (2006) Identification of QTLs associated with citrus resistance to Phytophthora gummosis. J Appl Genet 47:23–28. https://doi.org/10.1007/BF03194595
Soto-Cerda BJ, Cloutier S (2012) Association mapping in plant genomes. In: Caliskan M (ed) Genetic diversity in plants. InTech Europe, Rijeka, Croatia, pp 29–54. https://doi.org/10.5772/33005
Spaniolas S, May ST, Bennett MJ, Tucker GA (2006) Authentication of coffee by means of PCR-RFLP analysis and Lab-on-a-chip capillary electrophoresis. J Agric Food Chem 54:7466–7470. https://doi.org/10.1021/jf061164n
Sugiyama A, Ikoma Y, Fujii H, Shimada T, Endo T, Shimizu T et al (2010) Structure and expression levels of alleles of Citrus zeaxanthin epoxidase genes. J Japanese Soc Hortic Sci 79:263–274. https://doi.org/10.2503/jjshs1.79.263
Sugiyama A, Omura M, Shimada T, Fujii H, Endo T, Shimizu T et al (2014) Expression quantitative trait loci analysis of carotenoid metabolism-related genes in citrus. J Japanese Soc Hortic Sci 83:32–43. https://doi.org/10.2503/jjshs1.CH-054
Tautz D (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res 17:6463–6471. https://doi.org/10.1093/nar/17.16.6463
Terol J, Conesa A, Colmenero JM, Cercos M, Tadeo F, Agustí J et al (2007) Analysis of 13000 unique citrus clusters associated with fruit quality, production and salinity tolerance. BMC Genom 8:31. https://doi.org/10.1186/1471-2164-8-31
Terol J, Naranjo MA, Ollitrault P, Talon M (2008) Development of genomic resources for Citrus clementina: characterization of three deep-coverage BAC libraries and analysis of 46,000 BAC end sequences. BMC Genet 9:423. https://doi.org/10.1186/1471-2164-9-423
Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ES (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28:286–289. https://doi.org/10.1038/90135
Thudi M, Bohra A, Nayak SN, Varghese N, Shah TM, Penmetsa RV et al (2011) Novel SSR markers from BAC-end sequences, DArT arrays and a comprehensive genetic map with 1,291 marker loci for Chickpea (Cicer arietinum L.). In: Hansson B (ed) PLoS One 6: e27275. https://doi.org/10.1371/journal.pone.0027275
Torres AM, Mau-Lastovicka T, Williams TE, Soost RK (1985) Segregation distortion and linkage of Citrus and Poncirus isozyme genes. J Hered 76:289–294. https://doi.org/10.1093/oxfordjournals.jhered.a110094
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 42:1020–1029. https://doi.org/10.1139/g99-035
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 42:692–705. https://doi.org/10.1139/g99-003
Uddin MS, Cheng Q (2015). Recent application of biotechniques for the improvement of mango research. In: Applied plant genomics and biotechnology. Woodhead Publishing, Oxford, pp 195–212. https://doi.org/10.1016/b978-0-08-100068-7.00012-4
Ueno I, Iwamasa M, Nishiura M (1967) Embryo number of various varieties of Citrus and it’s relatives. Bull Hort Res Sta Japan, Ser B 7:11–21
Utsuno H, Minaguchi K (2004) Influence of template DNA degradation on the genotyping of SNPs and STR polymorphisms from forensic materials by PCR. Bull Tokyo Dent Coll 45:33–46. http://www.ncbi.nlm.nih.gov/pubmed/15346882
Uzun A, Yesiloglu T, Aka-Kacar Y, Tuzcu O, Gulsen O (2009a) Genetic diversity and relationships within Citrus and related genera based on sequence related amplified polymorphism markers (SRAPs). Sci Hortic (Amsterdam) 121:306–312. https://doi.org/10.1016/j.scienta.2009.02.018
Uzun A, Gulsen O, Kafa G, Seday U (2009b) Field performance and molecular diversification of lemon selections. Sci Hortic (Amsterdam) 120:473–478. https://doi.org/10.1016/j.scienta.2008.12.003
Uzun A, Gulsen O, Yesiloglu T, Aka-Kacar Y, Tuzcu O (2010) Distinguishing grapefruit and pummelo accessions using ISSR markers. Czech J Genet Plant Breed 46:170–177
van Nocker S, Gardiner SE (2014) Breeding better cultivars, faster: applications of new technologies for the rapid deployment of superior horticultural tree crops. Hortic Res 1:14022. https://doi.org/10.1038/hortres.2014.22
Varshney A, Mohapatra T, Sharma RP (2004) Molecular mapping and marker assisted selection of traits for crop improvement. In: Srivastava PS, Narula A, Srivastava S (eds) Plant biotechnology and molecular markers. Springer Netherlands, Dordrecht, pp 289–330. https://doi.org/10.1007/1-4020-3213-7_20
Verreynne JS, Rabe E, Theron KI (2004) Effect of bearing position on fruit quality of mandarin types. South African J Plant Soil 21:1–7. https://doi.org/10.1080/02571862.2004.10635014
Veyrieras J-B, Goffinet B, Charcosset A (2007) MetaQTL: a package of new computational methods for the meta-analysis of QTL mapping experiments. BMC Bioinform 8:49. https://doi.org/10.1186/1471-2105-8-49
Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M et al (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414. https://doi.org/10.1093/nar/23.21.4407
Wang X, Xu Y, Zhang S, Cao L, Huang Y, Cheng J et al (2017) Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction. Nat Genet 49:765–772. https://doi.org/10.1038/ng.3839
Weber CA, Moore GA, Deng Z, Gmitter FG (2003) Mapping freeze tolerance quantitative trait loci in a Citrus grandis x Poncirus trifoliata F-1 pseudo-testcross using molecular markers. J Am Soc Hortic Sci 128:508–514
Williams LM, Ma X, Boyko AR, Bustamante CD, Oleksiak MF (2010) SNP identification, verification, and utility for population genetics in a non-model genus. BMC Genet 11:32. https://doi.org/10.1186/1471-2156-11-32
Wu GA, Prochnik S, Jenkins J, Salse J, Hellsten U, Murat F et al (2014) Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nat Biotechnol. Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved 32:656–662. https://doi.org/10.1038/nbt.2906
Xiong M, Jin L (1999) Comparison of the power and accuracy of biallelic and microsatellite markers in population-based gene-mapping methods. Am J Hum Genet 64:629–640. https://doi.org/10.1086/302231
Xu Q, Chen L-L, Ruan X, Chen D, Zhu A, Chen C et al (2013) The draft genome of sweet orange (Citrus sinensis). Nat Genet. Nature Publishing Group 45:59–66. https://doi.org/10.1038/ng.2472
Yang Z, Ye X, Molina J, Roose ML, Mirkov TE (2003) Sequence analysis of a 282-kilobase region surrounding the citrus Tristeza virus resistance gene (Ctv) locus in Poncirus trifoliata L. Raf. Plant Physiol 131:482–492. https://doi.org/10.1104/pp.011262
Yang X, Li H, Liang M, Xu Q, Chai L, Deng X (2015) Genetic diversity and phylogenetic relationships of citron (Citrus medica L.) and its relatives in southwest China. Tree Genet Genomes 11:129. https://doi.org/10.1007/s11295-015-0955-x
Yu Y, Chen C, Gmitter FG (2016) QTL mapping of mandarin (Citrus reticulata) fruit characters using high-throughput SNP markers. Tree Genet Genomes 12:77. https://doi.org/10.1007/s11295-016-1034-7
Yu Y, Bai J, Chen C, Plotto A, Yu Q, Baldwin EA et al (2017) Identification of QTLs controlling aroma volatiles using a ‘Fortune’ x ‘Murcott’ (Citrus reticulata) population. BMC Genom 18:646. https://doi.org/10.1186/s12864-017-4043-5
Zane L, Bargelloni L, Patarnello T (2002) Strategies for microsatellite isolation: a review. Mol Ecol 11:1–16. https://doi.org/10.1046/j.0962-1083.2001.01418.x
Zhang Z, Gerstein M (2003) Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. Nucleic Acids Res 31:5338–5348. http://www.ncbi.nlm.nih.gov/pubmed/12954770
Zhang H, Xie Y, Liu C, Chen S, Hu S, Xie Z et al (2017) Comprehensive comparative analysis of volatile compounds in citrus fruits of different species. Food Chem 230:316–326. https://doi.org/10.1016/j.foodchem.2017.03.040
Zhou G, Jian J, Wang P, Li C, Tao Y, Li X et al (2008) Construction of an ultra-high density consensus genetic map, and enhancement of the physical map from genome sequencing in Lupinus angustifolius. Theor Appl Genet. Springer Berlin Heidelberg 131:209–223. https://doi.org/10.1007/s00122-017-2997-y
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The authors thank Emma Tacken, Ph.D., from Edanz Group (www.edanzediting.com/ac) for editing a draft of this manuscript.
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Shimizu, T., Aka Kacar, Y., Cristofani-Yaly, M., Curtolo, M., Machado, M.A. (2020). Markers, Maps, and Marker-Assisted Selection. In: Gentile, A., La Malfa, S., Deng, Z. (eds) The Citrus Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-030-15308-3_7
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