DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing

References

• Cole CT. Genetic variation in rare and common plants. Annu Rev Ecol Evol Syst. 2003;34: 213–227.
   Web of Science ®Google Scholar
• Hamrick JL. Isozymes and the analysis of genetic structure in plant populations. In: Soltis DE, Soltis PS, Dudley TR, editors. Isozymes in plant biology. Dordrecht: Springer; 1989. p. 87–105.
   Google Scholar
• Kebriyaee D, Kordrostami M, Rezadoost MH, et al. QTL analysis of agronomic traits in rice using SSR and AFLP markers. Not Sci Biol. 2012;4(2):116–123.
   Google Scholar
• Collard BC, Jahufer MZ, Brouwer JB, et al. An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: the basic concepts. Euphytica. 2005;142(1–2):169–196.
   Web of Science ®Google Scholar
• Jiang GL. Molecular markers and marker-assisted breeding in plants. In: Andersen SB, editor. Plant breeding from laboratories to fields. Rijeka: InTech; 2013. p. 45–83.
   Google Scholar
• Eagles HA, Bariana HS, Ogbonnaya FC, et al. Implementation of markers in Australian wheat breeding. Crop Pasture Sci. 2001;52(12):1349–1356.
   Google Scholar
• Karaköy T, Baloch FS, Toklu F, et al. Variation for selected morphological and quality-related traits among 178 faba bean landraces collected from Turkey. Plant Genet Resour. 2014;12(01):5–13.
   Google Scholar
• Bayley DC. Isozymic variation and plant breeders' rights. In: Tanksley SD, Orton TJ, editors. Isozymes in plant genetics and breeding. Amsterdam: Elsevier; 1983. p. 425–440.
   Google Scholar
• Mateu-Andres I, De Paco L. Allozymic differentiation of the Antirrhinum majus and A. siculum species groups. Ann Bot. 2005;95(3):465–473.
   PubMed Web of Science ®Google Scholar
• Mondini L, Noorani A, Pagnotta MA. Assessing plant genetic diversity by molecular tools. Diversity. 2009;1(1):19–35.
   Google Scholar
• Semagn K, Bjørnstad Å, Ndjiondjop MN. An overview of molecular marker methods for plants. Afr J Biotechnol. 2006;(2540):25–68.
   Google Scholar
• Madhumati B. Potential and application of molecular markers techniques for plant genome analysis. Int J Pure App Biosci. 2014;2(1):169–88.
   Google Scholar
• Mullis K, Faloona F, Scharf S, et al. Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harb Symp Quant Biol. 1986;51:263–273.
   PubMedGoogle Scholar
• Joshi M, Deshpande JD. Polymerase chain reaction: methods, principles and application. Int J Biomed Res. 2011;2(1):81–97.
   Google Scholar
• He Q, Marjamäki M, Soini H, et al. Primers are decisive for sensitivity of PCR. Biotechniques. 1994;17(1):82–84.
   PubMed Web of Science ®Google Scholar
• Dieffenbach CW, Lowe TM, Dveksler GS. General concepts for PCR primer design. PCR Methods Appl. 1993;3(3):30–37.
   Google Scholar
• Williams JG, Kubelik AR, Livak KJ, et al. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 1990;18(22):6531–6535.
   PubMed Web of Science ®Google Scholar
• Welsh J, McClelland M. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res. 1990;18(24):7213–7218.
   PubMed Web of Science ®Google Scholar
• Jones CJ, Edwards KJ, Castaglione S, et al. Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories. Mol Breed. 1997;3(5):381–390.
   Web of Science ®Google Scholar
• Wolff K, Schoen ED, Peters-Van Rijn J. Optimizing the generation of random amplified polymorphic DNAs in chrysanthemum. Theor Appl Genet. 1993;86(8):1033–1037.
   PubMed Web of Science ®Google Scholar
• Vos P, Hogers R, Bleeker M, et al. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 1995;23(21):4407–4414.
   PubMed Web of Science ®Google Scholar
• Lynch M, Walsh B. Genetics and analysis of quantitative traits. Sunderland (MA): Sinauer; 1998.
   Google Scholar
• Ridout CJ, Donini P. Use of AFLP in cereals research. Trends Plant Sci. 1999;4(2):76–79.
   PubMed Web of Science ®Google Scholar
• Blears MJ, De Grandis SA, Lee H, et al. Amplified fragment length polymorphism (AFLP): a review of the procedure and its applications. J Ind Microbiol Biotechnol. 1998;21(3):99–114.
   Web of Science ®Google Scholar
• Litt M, Luty JA. A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am J Hum Genet. 1989;44(3):397–401.
   PubMed Web of Science ®Google Scholar
• Tautz D. Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res. 1989;17(16):6463–6471.
   PubMed Web of Science ®Google Scholar
• Schlotteröer C, Amos B, Tautz D. Conservation of polymorphic simple sequence loci in cetacean species. Nature. 1991;354(6348):63–65.
   PubMed Web of Science ®Google Scholar
• Beckmann JS, Weber JL. Survey of human and rat microsatellites. Genomics. 1992;12(4):627–631.
   PubMed Web of Science ®Google Scholar
• Weber JL. Informativeness of human (dC-dA) n·(dG-dT) n polymorphisms. Genomics. 1990;7(4):524–530.
   PubMed Web of Science ®Google Scholar
• Provan J, Powell W, Hollingsworth PM. Chloroplast microsatellites: new tools for studies in plant ecology and evolution. Trends Ecol Evol. 2001;16(3):142–147.
   PubMed Web of Science ®Google Scholar
• Rajendrakumar P, Biswal AK, Balachandran SM, et al. Simple sequence repeats in organellar genomes of rice: frequency and distribution in genic and intergenic regions. Bioinformatics. 2007;23(1):1–4.
   PubMed Web of Science ®Google Scholar
• Morgante M, Hanafey M, Powell W. Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet. 2002;30(2):194–200.
   PubMed Web of Science ®Google Scholar
• Zane L, Bargelloni L, Patarnello T. Strategies for microsatellite isolation: a review. Mol Ecol. 2002;11(1):1–16.
   PubMed Web of Science ®Google Scholar
• Kalia RK, Rai MK, Kalia S, et al. Microsatellite markers: an overview of the recent progress in plants. Euphytica. 2011;177(3):309–334.
   Web of Science ®Google Scholar
• Röder MS, Korzun V, Wendehake K, et al. A microsatellite map of wheat. Genetics. 1998;149(4):2007–2023.
   PubMed Web of Science ®Google Scholar
• Navascues M, Emerson BC. Chloroplast microsatellites: measures of genetic diversity and the effect of homoplasy. Mol Ecol. 2005;14(5):1333–1341.
   PubMed Web of Science ®Google Scholar
• Ebert D, Peakall RO. Chloroplast simple sequence repeats (cpSSRs): technical resources and recommendations for expanding cpSSR discovery and applications to a wide array of plant species. Mol Ecol Resour. 2009;9(3):673–690.
   PubMed Web of Science ®Google Scholar
• Liu Y, Xue JY, Wang B, et al. The mitochondrial genomes of the early land plants Treubia lacunosa and Anomodon rugelii: dynamic and conservative evolution. PLoS One. 2011;6(10):e25836.
   PubMed Web of Science ®Google Scholar
• Zhang DX, Hewitt GM. Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects. Mol Ecol. 2003;12(3):563–584.
   PubMed Web of Science ®Google Scholar
• Wu KS, Jones R, Danneberger L, Scolnik PA. Detection of microsatellite polymorphisms without cloning. Nucleic Acids Res. 1994;22(15):3257–3258.
   PubMed Web of Science ®Google Scholar
• Salazar JA, Rasouli M, Moghaddam RF, et al. Low-cost strategies for development of molecular markers linked to agronomic traits in Prunus. Agric Sci. 2014;5(05):430–439.
   Google Scholar
• Li G, Quiros CF. 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. 2001;103(2–3):455–461.
   Web of Science ®Google Scholar
• Uzun A, Yesiloglu T, Aka-Kacar Y, et al. Genetic diversity and relationships within citrus and related genera based on sequence related amplified polymorphism markers (SRAPs). Sci Hort. 2009;121(3):306–312.
   Web of Science ®Google Scholar
• Zietkiewicz E, Rafalski A, Labuda D. Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics. 1994;20(2):176–183.
   PubMed Web of Science ®Google Scholar
• Gupta M, Chyi YS, Romero-Severson J, et al. Amplification of DNA markers from evolutionarily diverse genomes using single primers of simple-sequence repeats. Theor Appl Genet. 1994;89(7–8):998–1006.
   PubMed Web of Science ®Google Scholar
• Fang DQ, Roose ML. Identification of closely related citrus cultivars with inter-simple sequence repeat markers. Theor Appl Genet. 1997;95(3):408–417.
   Web of Science ®Google Scholar
• Moreno S, Martín JP, Ortiz JM. Inter-simple sequence repeats PCR for characterization of closely related grapevine germplasm. Euphytica. 1998;101(1):117–25.
   Web of Science ®Google Scholar
• Tsumura Y, Ohba K, Strauss SH. Diversity and inheritance of inter-simple sequence repeat polymorphisms in Douglas-fir (Pseudotsuga menziesii) and sugi (Cryptomeria japonica). Theor Appl Genet. 1996;92(1):40–45.
   PubMed Web of Science ®Google Scholar
• Ng WL, Tan SG. Inter-simple sequence repeat (ISSR) markers: are we doing it right? ASM Sci J. 2015;9:30–39.
   Google Scholar
• Chatterjee SN, Vijayan K, Roy GC, et al. ISSR profiling of genetic variability in the ecotypes of Antheraea mylitta Drury, the tropical tasar silkworm. Russ J Genet. 2004; 40(2):152–159.
   Web of Science ®Google Scholar
• Kar PK, Vijayan K, Mohandas TP, et al. Genetic variability and genetic structure of wild and semi-domestic populations of tasar silkworm (Antheraea mylitta) ecorace Daba as revealed through ISSR markers. Genetica. 2005;125(2–3):173–183.
   PubMed Web of Science ®Google Scholar
• Finnegan DJ. Eukaryotic transposable elements and genome evolution. Trends Genet. 1989; 5:103–107.
   PubMed Web of Science ®Google Scholar
• Grzebelus D. Transposon insertion polymorphism as a new source of molecular markers. J Fruit Ornam Plant Res. 2006;14(Suppl 1):21–29.
   Google Scholar
• Kumar A, Bennetzen JL. Plant retrotransposons. Annu Rev Genet. 1999;33(1):479–532.
   PubMedGoogle Scholar
• Kalendar R, Vicient CM, Peleg O, et al. Large retrotransposon derivatives: abundant, conserved but nonautonomous retroelements of barley and related genomes. Genetics. 2004;166(3):1437–1450.
   PubMed Web of Science ®Google Scholar
• Shirasu K, Schulman AH, Lahaye T, et al. A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion. Genome Res. 2000;10(7):908–915.
   PubMed Web of Science ®Google Scholar
• Pearce SR, Pich U, Harrison G, et al. TheTy1-copia group retrotransposons of Allium cepa are distributed throughout the chromosomes but are enriched in the terminal heterochromatin. Chromosome Res. 1996;4(5):357–364.
   PubMed Web of Science ®Google Scholar
• Voytas DF, Boeke JD. Ty1 and Ty5 of Saccharomyces cerevisiae. In: Craigie R, Gellert M, Lambowitz A editors. Mobile DNA II American Society of Microbiology. Washington (DC): ASM Press; 2002. p. 631–662.
   Google Scholar
• Roy NS, Choi JY, Lee SI, et al. Marker utility of transposable elements for plant genetics, breeding, and ecology: a review. Genes Genom. 2015;37(2):141–151.
   Web of Science ®Google Scholar
• Schulman AH, Wicker T. A field guide to transposable elements. In: Fedoroff NV, editor. Vol. 2, Plant transposons and genome dynamics in evolution. Oxford, Wiley-Blackwell; 2013. p. 15–40.
   Google Scholar
• Kalendar R, Flavell AJ, Ellis TH, et al. Analysis of plant diversity with retrotransposon-based molecular markers. Heredity. 2011;106(4):520–530.
   PubMed Web of Science ®Google Scholar
• Kalendar R, Grob T, Regina M, et al. IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Theor Appl Genet. 1999;98(5):704–711.
   Web of Science ®Google Scholar
• Poczai P, Varga I, Laos M, et al. Advances in plant gene-targeted and functional markers: a review. Plant Methods. 2013;9(1):6.
   PubMedGoogle Scholar
• Kalendar R, Schulman AH. IRAP and REMAP for retrotransposon-based genotyping and fingerprinting. Nat Protoc. 2006;1(5):2478–2484.
   PubMed Web of Science ®Google Scholar
• Fan F, Cui B, Zhang T, et al. LTR-retrotransposon activation, IRAP marker development and its potential in genetic diversity assessment of masson pine (Pinus massoniana). Tree Genet Genomes. 2014;10(1):213–222.
   Web of Science ®Google Scholar
• Flavell AJ, Knox MR, Pearce SR, et al. Retrotransposon-based insertion polymorphisms (RBIP) for high throughput marker analysis. Plant J. 1998;16(5):643–650.
   PubMed Web of Science ®Google Scholar
• Agarwal M, Shrivastava N, Padh H. Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep. 2008;27(4):617–631.
   PubMed Web of Science ®Google Scholar
• Jing R, Bolshakov V, Flavell AJ. The tagged microarray marker (TAM) method for high-throughput detection of single nucleotide and indel polymorphisms. Nat Protoc. 2007;2(1):168–177.
   PubMed Web of Science ®Google Scholar
• Kalendar R, Antonius K, Smýkal P, et al. iPBS: a universal method for DNA fingerprinting and retrotransposon isolation. Theor Appl Genet. 2010;121(8):1419–1430.
   PubMed Web of Science ®Google Scholar
• Baloch FS, Alsaleh A, de Miera LE, et al. DNA based iPBS-retrotransposon markers for investigating the population structure of pea (Pisum sativum) germplasm from Turkey. Biochem Syst Ecol. 2015;61:244–252.
   Web of Science ®Google Scholar
• Maeda M, Uryu N, Murayama N, et al. A simple and rapid method for HLA-DP genotyping by digestion of PCR-amplified DNA with allele-specific restriction endonucleases. Hum Immunol. 1990;27(2):111–121.
   PubMed Web of Science ®Google Scholar
• Jarvis P, Lister C, Szabo V, et al. Integration of CAPS markers into the RFLP map generated using recombinant inbred lines of Arabidopsis thaliana. Plant Mol Biol. 1994;24(4):685–687.
   PubMed Web of Science ®Google Scholar
• Michaels SD, Amasino RM. A robust method for detecting single-nucleotide changes as polymorphic markers by PCR. Plant J. 1998;14(3):381–385.
   PubMed Web of Science ®Google Scholar
• Spaniolas S, May ST, Bennett MJ, et al. Authentication of coffee by means of PCR-RFLP analysis and lab-on-a-chip capillary electrophoresis. J Agric Food Chem. 2006;54(20):7466–7470.
   PubMed Web of Science ®Google Scholar
• Weiland JJ, Yu MH. A cleaved amplified polymorphic sequence (CAPS) marker associated with root-knot nematode resistance in sugarbeet. Crop Sci. 2003;43(5):1814–188.
   Web of Science ®Google Scholar
• Paran I, Michelmore RW. Development of reliable PCR-based markers linked to downy mildew resistance genes in lettuce. Theor Appl Genet. 1993;85(8):985–993.
   PubMed Web of Science ®Google Scholar
• Yang L, Fu S, Khan A, et al. Molecular cloning and development of RAPD-SCAR markers for Dimocarpus longan variety authentication. Springer Plus. 2013;2:501.
   PubMed Web of Science ®Google Scholar
• Bhagyawant SS. RAPD-SCAR markers: an interface tool for authentication of traits. J Biosci Med. 2016;4:1–9.
   Google Scholar
• Kiran U, Khan S, Mirza KJ, et al. SCAR markers: a potential tool for authentication of herbal drugs. Fitoterapia. 2010;81(8):969–976.
   PubMed Web of Science ®Google Scholar
• Franca LT, Carrilho E, Kist TB. A review of DNA sequencing techniques. Q Rev Biophys. 2002;35(2):169–200.
   PubMed Web of Science ®Google Scholar
• Davey JW, Hohenlohe PA, Etter PD, et al. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet. 2011;12(7):499–510.
   PubMed Web of Science ®Google Scholar
• Heather JM, Chain B. The sequence of sequencers: the history of sequencing DNA. Genomics. 2016;107(1):1–8.
   PubMed Web of Science ®Google Scholar
• Sanger F, Coulson AR. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol. 1975;94(3):441–448.
   PubMed Web of Science ®Google Scholar
• Englund PT. Analysis of nucleotide sequences at 3′termini of duplex deoxyribonucleic acid with the use of the T4 deoxyribonucleic acid polymerase. J Biol Chem. 1971;246(10):3269–3276.
   PubMed Web of Science ®Google Scholar
• Englund PT. The 3′-terminal nucleotide sequences of T7 DNA. J Mol Biol. 1972;66(2):209–224.
   PubMed Web of Science ®Google Scholar
• Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci. 1977;74(12):5463–5467.
   PubMed Web of Science ®Google Scholar
• Hyman ED. A new method of sequencing DNA. Anal Biochem. 1988;174(2):423–436.
   PubMed Web of Science ®Google Scholar
• Ronaghi M. Pyrosequencing sheds light on DNA sequencing. Genome Res. 2001;11(1):3–11.
   PubMed Web of Science ®Google Scholar
• Gharizadeh B, Herman ZS, Eason RG, et al. Large-scale Pyrosequencing of synthetic DNA: a comparison with results from Sanger dideoxy sequencing. Electrophoresis. 2006;27(15):3042–3047.
   PubMed Web of Science ®Google Scholar
• Ronaghi M, Karamohamed S, Pettersson B, et al. Real-time DNA sequencing using detection of pyrophosphate release. Anal Biochem. 1996;242(1):84–89.
   PubMed Web of Science ®Google Scholar
• Ronaghi M, Uhlén M, Nyren P. A sequencing method based on real-time pyrophosphate. Science. 1998;281(5375):363–365.
   PubMed Web of Science ®Google Scholar
• Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol. 2008;26(10):1135–1145.
   PubMed Web of Science ®Google Scholar
• Bentley DR, Balasubramanian S, Swerdlow HP, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008;456(7218):53–59.
   PubMed Web of Science ®Google Scholar
• Thudi M, Li Y, Jackson SA, et al. Current state-of-art of sequencing technologies for plant genomics research. Brief Funct Genomics. 2012;11(1):3–11.
   PubMed Web of Science ®Google Scholar
• Rothberg JM, Hinz W, Rearick TM, et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature. 2011;475(7356):348–352.
   PubMed Web of Science ®Google Scholar
• Deschamps S, Llaca V, May GD. Genotyping-by-sequencing in plants. Biology. 2012;1(3):460–483.
   PubMedGoogle Scholar
• Metzker ML. Sequencing technologies—the next generation. Nat Rev Genet. 2010;11(1):31–46.
   PubMed Web of Science ®Google Scholar
• Elshire RJ, Glaubitz JC, Sun Q, et al. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PloS one. 2011;6(5):e19379.
   PubMed Web of Science ®Google Scholar
• Mardis ER. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet. 2008;9:387–402.
   PubMed Web of Science ®Google Scholar
• Poland JA, Rife TW. Genotyping-by-sequencing for plant breeding and genetics. Plant Genome. 2012;5(3):92–102.
   Web of Science ®Google Scholar
• Beissinger TM, Hirsch CN, Sekhon RS, et al. Marker density and read depth for genotyping populations using genotyping-by-sequencing. Genetics. 2013;193(4):1073–1081.
   PubMed Web of Science ®Google Scholar
• Xu Y. Molecular plant breeding. Wallingford: CABI; 2010.
   Google Scholar
• Sobrino B, Brión M, Carracedo A. SNPs in forensic genetics: a review on SNP typing methodologies. Forensic Sci Int. 2005;154(2):181–194.
   PubMed Web of Science ®Google Scholar
• Jaccoud D, Peng K, Feinstein D, et al. Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Res. 2001;29(4):E25.
   PubMed Web of Science ®Google Scholar
• Wenzl P, Carling J, Kudrna D, et al. Diversity Arrays Technology (DArT) for whole-genome profiling of barley. Proc Natl Acad Sci U S A. 2004;101(26):9915–9920.
   PubMed Web of Science ®Google Scholar
• Huttner E, Wenzl P, Akbari M, et al. Diversity arrays technology: a novel tool for harnessing the genetic potential of orphan crops. In: Serageldin I, Persley GJ, editors. Discovery to delivery: BioVision Alexandria 2004; Proceedings of the 2004 Conference of the World Biological Forum; 2004 Apr 3–6; Alexandria, Egypt. Wallingford: CABI; 2005. p. 145–155.
   Google Scholar
• Slatkin M. Gene flow and the geographic structure of natural populations. Science. 1987;236:787–793.
   PubMed Web of Science ®Google Scholar
• Wei C, Wang L, Yang Y, et al. Identification of an S5n allele in Oryza rufipogon Griff. and its effect on embryo sac fertility. Chinese Sci Bull. 2010;55(13):1255–1262.
   Google Scholar
• Tong J, Li Y, Yang Y, et al. Molecular evolution of rice S5n allele and functional comparison among different sequences. Chinese Sci Bull. 2011;56(19):2016–2024.
   Google Scholar
• Peng H, Shahid MQ, Li YH, et al. Molecular evolution of S5 locus and large differences in its coding region revealed insignificant effect on indica× japonica embryo sac fertility. Plant Syst Evol. 2015;301(2):639–655.
   Web of Science ®Google Scholar
• Wang Y, Ghouri F, Shahid MQ, et al. The genetic diversity and population structure of wild soybean evaluated by chloroplast and nuclear gene sequences. Biochem Syst Ecol. 2017;71:170–178.
   Web of Science ®Google Scholar
• Dong W, Liu J, Yu J, et al. Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding. PLoS One. 2012;7(4):e35071.
   PubMed Web of Science ®Google Scholar
• Wang Y, Shahid MQ, Baloch FS. Phylogeographical studies of Glycine soja: implicating the refugium during the quaternary glacial period and large-scale expansion after the last glacial maximum. Turk J Agric For. 2016;40(6):825–838.
   Web of Science ®Google Scholar
• Comings DE, MacMurray JP. Molecular heterosis: a review. Mol Gen Metab. 2000;71(1):19–31.
   PubMed Web of Science ®Google Scholar
• Martin JM, Talbert LE, Lanning SP, et al. Hybrid performance in wheat as related to parental diversity. Crop Sci. 1995;35(1):104–108.
   Web of Science ®Google Scholar
• Betran FJ, Ribaut JM, Beck D, et al. Genetic diversity, specific combining ability, and heterosis in tropical maize under stress and nonstress environments. Crop Sci. 2003;43(3):797–806.
   Web of Science ®Google Scholar
• Yu CY, Hu SW, Zhao HX, et al. Genetic distances revealed by morphological characters, isozymes, proteins and RAPD markers and their relationships with hybrid performance in oilseed rape (Brassica napus L.). Theor Appl Genet. 2005;110(3):511–518.
   PubMed Web of Science ®Google Scholar
• Wu JW, Hu CY, Shahid MQ, et al. Analysis on genetic diversification and heterosis in autotetraploid rice. Springer Plus. 2013;2(1):439.
   PubMedGoogle Scholar
• Xie F, He Z, Esguerra MQ, et al. Determination of heterotic groups for tropical Indica hybrid rice germplasm. Theor Appl Genet. 2014;127(2):407–417.
   Web of Science ®Google Scholar
• Guo H, Mendrikahy JN, Xie L, et al. Transcriptome analysis of neo-tetraploid rice reveals specific differential gene expressions associated with fertility and heterosis. Sci Rep. 2017;7:40139.
   PubMed Web of Science ®Google Scholar
• Li X, Shahid MQ, Xia J, et al. Analysis of small RNAs revealed differential expressions during pollen and embryo sac development in autotetraploid rice. BMC Genomics. 2017;18(1):129.
   PubMedGoogle Scholar
• Kasha KJ, Maluszynski M. Production of doubled haploids in crop plants. An introduction. In: Maluszynski M, Kasha KJ, Forster BP, Szarejko I, editors. Doubled haploid production in crop plants. Dordrecht: Springer; 2003. p. 1–4.
   Google Scholar
• Khush GS, Virmani SS. Haploids in plant breeding. In: Jain SM, Sopory SK, Veilleux RE, editors. In vitro haploid production in higher plants. Current plant science and biotechnology in agriculture. Dordrecht: Springer; 1996. p. 11–33.
   Google Scholar
• Künzel G, Korzun L, Meister A. Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints. Genetics. 2000;154(1):397–412.
   PubMed Web of Science ®Google Scholar
• Belicuas PR, Guimarães CT, Paiva LV, et al. Androgenetic haploids and SSR markers as tools for the development of tropical maize hybrids. Euphytica. 2007;156(1–2):95–102.
   Web of Science ®Google Scholar
• Melchinger AE, Winter M, Mi X, et al. Controlling misclassification rates in identification of haploid seeds from induction crosses in maize with high-oil inducers. Crop Sci. 2015;55(3):1076–1086.
   Web of Science ®Google Scholar
• Tang F, Tao Y, Zhao T, et al. In vitro production of haploid and doubled haploid plants from pollinated ovaries of maize (Zea mays). Plant Cell Tissue Organ Cult. 2006;84(2):233–237.
   Web of Science ®Google Scholar
• Shahid MQ, Chen FY, Li HY, et al. Double-neutral genes, and, for pollen fertility in rice to overcome× hybrid sterility. Crop Sci. 2013;53(1):164–176.
   Web of Science ®Google Scholar
• Wu J, Shahid MQ, Chen L, et al. Polyploidy enhances F1 pollen sterility loci interactions that increase meiosis abnormalities and pollen sterility in autotetraploid rice. Plant Physiol. 2015;169(4):2700–2717.
   PubMed Web of Science ®Google Scholar
• Nawaz MA, Baloch FS, Rehman HM, et al. Development of a competent and trouble free DNA isolation protocol for downstream genetic analysis in glycine species. Turk J Agri Food Sci Tech. 2016;4(8):700–705.
   Google Scholar
• Nawaz MA, Sadia B, Awan FS, et al. 2013. Genetic diversity in hyper glucose oxidase producing Aspergillus niger UAF mutants by using molecular markers. Int J Agric Biol. 2013;15(2):362–366.
   Web of Science ®Google Scholar
• Nawaz MA, Yang SH, Rehman HM, et al. Genetic diversity and population structure of Korean wild soybean (Glycine soja Sieb. and Zucc.) inferred from microsatellite markers. Biochem Syst Ecol. 2017;71:87–96.
   Web of Science ®Google Scholar
• Nawaz MA, Rehman HM, Baloch FS, et al. Genome and transcriptome-wide analysis of cellulose synthase gene superfamily in soybean. J Plant Physiol. 2017;215:163–175.
   PubMed Web of Science ®Google Scholar
• Liu W, Shahid MQ, Bai L, et al. Evaluation of genetic diversity and development of a core collection of wild rice (Oryza rufipogon Griff.) populations in China. PloS One. 2015;10(12):e0145990.
   PubMed Web of Science ®Google Scholar
• Wang Y, Shahid MQ, Ghouri F, et al. Evaluation of the geographical pattern of genetic diversity of glycine soja and glycine max based on four single copy nuclear gene loci: for conservation of soybean germplasm. Biochem Syst Ecol. 2015;62:229–235.
   Web of Science ®Google Scholar
• Tiwari JK, Singh BP, Gopal J, et al. Molecular characterization of the Indian Andigena potato core collection using microsatellite markers. Afr J Biotechnol. 2013;12(10).1025–1033.
   Google Scholar
• Naeem M, Ghouri F, Shahid MQ, et al. Genetic diversity in mutated and non-mutated rice varieties. Genet Mol Res. 2015;14(4):17109–17123.
   PubMed Web of Science ®Google Scholar
• Baloch FS, Alsaleh A, Shahid MQ, et al. A whole genome DArTseq and SNP analysis for genetic diversity assessment in durum wheat from Central Fertile Crescent. PloS One. 2017;12(1):e0167821.
   PubMed Web of Science ®Google Scholar
• Simmonds NW. Introgression and incorporation. Strategies for the use of crop genetic resources. Biol Rev. 1993;68(4):539–562.
   Web of Science ®Google Scholar
• Wang YH, Liu SJ, Ji SL, et al. Fine mapping and marker-assisted selection (MAS) of a low glutelin content gene in rice. Cell Res. 2005;15(8):622–630.
   PubMed Web of Science ®Google Scholar
• You-Xin Y, Yan-Hong L, Jing-Fei T. Wide-compatibility gene exploited by functional molecular markers and its effect on fertility of intersubspecific rice hybrids. Crop Sci. 2012;52(2):669–675.
   Web of Science ®Google Scholar
• Angaji SA. QTL mapping: a few key points. Int J Appl Res Nat Prod. 2009;2(2):1–3.
   Google Scholar
• Paterson AH. Making genetic maps. In: Paterson AH, editor. Genome mapping in plants. Austin (TX): R.G. Landes Company; 1996. p. 23–39.
   Google Scholar
• Mohan M, Nair S, Bhagwat A, et al. Genome mapping, molecular markers and marker-assisted selection in crop plants. Mol Breed. 1997;3(2):87–103.
   Web of Science ®Google Scholar
• Dhingani RM, Umrania VV, Tomar RS, et al. Introduction to QTL mapping in plants. Ann Plant Sci. 2015;4(04):1072–1079.
   Google Scholar
• Bernardo A, Wang S, Amand PS, et al. Using next generation sequencing for multiplexed trait-linked markers in wheat. PloS One. 2015;10(12):e0143890.
   PubMed Web of Science ®Google Scholar
• Risch N. Genetic linkage: interpreting LOD scores. Science. 1992;255(5046):803–805.
   PubMed Web of Science ®Google Scholar
• Tanksley SD. Mapping polygenes. Annu Rev Genet. 1993;27(1):205–233.
   PubMed Web of Science ®Google Scholar
• Lander ES, Botstein D. Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics. 1989;121(1):185–199.
   PubMed Web of Science ®Google Scholar
• Silva LD, Wang S, Zeng ZB. Composite interval mapping and multiple interval mapping: procedures and guidelines for using Windows QTL cartographer. Methods Mol Biol. 2012;871:75–119.
   PubMedGoogle Scholar
• Broman KW, Wu H, Sen Ś, et al. R/qtl: QTL mapping in experimental crosses. Bioinformatics. 2003;19(7):889–890.
   PubMed Web of Science ®Google Scholar
• Yang J, Hu C, Hu H, et al. QTLNetwork: mapping and visualizing genetic architecture of complex traits in experimental populations. Bioinformatics. 2008;24(5):721–723.
   PubMed Web of Science ®Google Scholar
• Utz HF, Melchinger AE. PLABQTL: a program for composite interval mapping of QTL. J Quant Trait Loci. 1996;2(1):1–5.
   Google Scholar
• Nelson JC. QGENE: software for marker-based genomic analysis and breeding. Mol Breed. 1997;3(3):239–245.
   Web of Science ®Google Scholar
• Voorrips RE. MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered. 2002;93(1):77–78.
   PubMed Web of Science ®Google Scholar
• George ML, Prasanna BM, Rathore RS, et al. Identification of QTLs conferring resistance to downy mildews of maize in Asia. Theor Appl Genet. 2003;107(3):544–551.
   PubMed Web of Science ®Google Scholar
• Haley CS, Andersson LE. Linkage mapping of quantitative trait loci in plants and animals. In: Dear PH, editor. Genome mapping: a practical approach. Oxford: IRL Press; 1997. p. 49–71.
   Google Scholar
• Hackett CA. Statistical methods for QTL mapping in cereals. Plant Mol Biol. 2002;48(5–6):585–599.
   PubMed Web of Science ®Google Scholar
• Ogbonnaya FC, Subrahmanyam NC, Moullet O, et al. Diagnostic DNA markers for cereal cyst nematode resistance in bread wheat. Crop Pasture Sci. 2001;52(12):1367–1374.
   Google Scholar
• Lukowitz W, Gillmor CS, Scheible WR. Positional cloning in Arabidopsis. Why it feels good to have a genome initiative working for you. Plant Physiol. 2000;123(3):795–806.
   PubMed Web of Science ®Google Scholar
• Salvi S, Tuberosa R. To clone or not to clone plant QTLs: present and future challenges. Trends Plant Sci. 2005;10(6):297–304.
   PubMed Web of Science ®Google Scholar
• Gallavotti A, Whipple CJ. Positional cloning in maize (Zea mays subsp. mays, Poaceae). Appl Plant Sci. 2015;3(1):1400092.
   Web of Science ®Google Scholar
• Ochman H, Gerber AS, Hartl DL. Genetic applications of an inverse polymerase chain reaction. Genetics. 1988;120(3):621–623.
   PubMed Web of Science ®Google Scholar
• Arnold C, Hodgson IJ. Vectorette PCR: a novel approach to genomic walking. Genome Res. 1991;1(1):39–42.
   Google Scholar
• Rishi AS, Nelson ND, Goyal A. Genome walking of large fragments: an improved method. J Biotechnol. 2004;111(1):9–15.
   PubMed Web of Science ®Google Scholar
• Young ND, Kumar L, Menancio-Hautea D, et al. RFLP mapping of a major bruchid resistance gene in mungbean (Vigna radiata, L. Wilczek). Theor Appl Genet. 1992;84(7-8):839–844.
   PubMed Web of Science ®Google Scholar
• Price AH. Believe it or not, QTLs are accurate ! Trends Plant Sci. 2006;11(5):213–216.
   PubMed Web of Science ®Google Scholar
• Neale DB, Savolainen O. Association genetics of complex traits in conifers. Trends Plant Sci. 2004;9(7):325–330.
   PubMed Web of Science ®Google Scholar
• Lübberstedt T, Zein I, Andersen JR, et al. Development and application of functional markers in maize. Euphytica. 2005;146(1):101–108.
   Web of Science ®Google Scholar
• Jannink JL, Walsh B. Association mapping in plant populations. In: Kang MS, editor. Quantitative genetics, genomics and plant breeding. Oxford: CAB International; 2002. p. 59–68.
   Google Scholar
• Zhang P, Zhong K, Shahid MQ, et al. Association analysis in rice: from application to utilization. Front Plant Sci. 2016;7:1202.
   PubMed Web of Science ®Google Scholar
• Zhang P, Zhong K, Tong H, et al. Association mapping for aluminum tolerance in a core collection of rice landraces. Front Plant Sci. 2016:7:1415.
   PubMed Web of Science ®Google Scholar
• Kraakman AT, Martinez F, Mussiraliev B, et al. Linkage disequilibrium mapping of morphological, resistance, and other agronomically relevant traits in modern spring barley cultivars. Mol Breed. 2006;17(1):41–58.
   Web of Science ®Google Scholar
• Holland JB. Genetic architecture of complex traits in plants. Curr Opin Plant Biol. 2007;10(2):156–161.
   PubMed Web of Science ®Google Scholar
• Gupta PK, Rustgi S, Kulwal PL. Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol Biol. 2005;57(4):461–485.
   PubMed Web of Science ®Google Scholar
• Goldstein DB, Weale ME. Population genomics: linkage disequilibrium holds the key. Curr Biol. 2001;11(14):576–579.
   Web of Science ®Google Scholar
• Mackay I, Powell W. Methods for linkage disequilibrium mapping in crops. Trends Plant Sci. 2007;12(2):57–63.
   PubMed Web of Science ®Google Scholar
• Abdurakhmonov IY, Abdukarimov A. Application of association mapping to understanding the genetic diversity of plant germplasm resources. Int J Plant Genomics. 2008;2008:574927.
   PubMedGoogle Scholar
• Abecasis GR, Cookson WO. Gold – graphical overview of linkage disequilibrium. Bioinformatics. 2000;16(2):182–183.
   PubMed Web of Science ®Google Scholar
• Bradbury PJ, Zhang Z, Kroon DE, et al. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics. 2007;23(19):2633–2635.
   PubMed Web of Science ®Google Scholar
• Sehgal D, Singh R, Rajpal VR. Quantitative trait loci mapping in plants: concepts and approaches. In: Rajpal V, Rao S, Raina S, editors. Vol. 2, Molecular breeding for sustainable crop improvement. Cham: Springer International; 2016. p. 31–59. (Sustainable development and biodiversity; Vol. 11).
   Google Scholar
• Tabor HK, Risch NJ, Myers RM. Candidate-gene approaches for studying complex genetic traits: practical considerations. Nat Rev Genet. 2002;3(5):391–397.
   PubMed Web of Science ®Google Scholar
• Mackay TF. The genetic architecture of quantitative traits. Annu Rev Genet. 2001;35(1):303–339.
   PubMed Web of Science ®Google Scholar
• Whitt SR, Buckler ES. Using natural allelic diversity to evaluate gene function. Plant Func Genomics. 2003;236:123–139.
   Google Scholar
• Lau WC, Rafii MY, Ismail MR, et al. Review of functional markers for improving cooking, eating, and the nutritional qualities of rice. Front Plant Sci. 2015;6:832.
   PubMed Web of Science ®Google Scholar
• Atwell S, Huang YS, Vilhjálmsson BJ, et al. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature. 2010;465(7298):627–631.
   PubMed Web of Science ®Google Scholar
• Zargar SM, Raatz B, Sonah H, et al. Recent advances in molecular marker techniques: insight into QTL mapping, GWAS and genomic selection in plants. JCSB. 2015;18(5):293–308.
   Google Scholar
• Hindorff LA, Sethupathy P, Junkins HA, et al. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci. 2009;106(23):9362–9367.
   PubMed Web of Science ®Google Scholar
• Jia P, Zhao Z. Network-assisted analysis to prioritize GWAS results: principles, methods and perspectives. Hum Genet. 2014;133(2):125–138.
   PubMed Web of Science ®Google Scholar
• Yu J, Holland JB, McMullen MD, et al. Genetic design and statistical power of nested association mapping in maize. Genetics. 2008;178(1):539–551.
   PubMed Web of Science ®Google Scholar
• McMullen MD, Kresovich S, Villeda HS, et al. Genetic properties of the maize nested association mapping population. Science. 2009;325(5941):737–740.
   PubMed Web of Science ®Google Scholar
• Cavanagh C, Morell M, Mackay I, et al. From mutations to MAGIC: resources for gene discovery, validation and delivery in crop plants. Curr Opin Plant Biol. 2008;11(2):215–221.
   PubMed Web of Science ®Google Scholar
• Darvasi A, Soller M. Advanced intercross lines, an experimental population for fine genetic mapping. Genetics. 1995;141(3):1199–1207.
   PubMed Web of Science ®Google Scholar
• Bandillo N, Raghavan C, Muyco PA, et al. Multi-parent advanced generation inter-cross (MAGIC) populations in rice: progress and potential for genetics research and breeding. Rice. 2013;6(1):11.
   PubMedGoogle Scholar
• Francia E, Tacconi G, Crosatti C, et al. Marker assisted selection in crop plants. Plant Cell Tiss Org. 2005;82(3):317–342.
   Web of Science ®Google Scholar
• Holland JB. Implementation of molecular markers for quantitative traits in breeding programs—challenges and opportunities. In: New directions for a diverse planet; Proceedings of the 4th International Crop Science Congress; 2004 Sep 26–Oct 1; Brisbane, Australia. Gosford: Regional Institute; 2004. Available from: www.cropscience.org.au/icsc2004
   Google Scholar
• Charcosset A. Marker-assisted introgression of quantitative trait loci. Genetics. 1997; 147(3):1469–1485.
   PubMed Web of Science ®Google Scholar
• Hospital F. Selection in backcross programmes. Philos Trans Biol Sci. 2005:1503–1511.
   PubMed Web of Science ®Google Scholar
• Collard BC, Mackill DJ. Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philos Trans R Soc B. 2008;363(1491):557–572.
   PubMed Web of Science ®Google Scholar
• Bernardo R, Charcosset A. Usefulness of gene information in marker-assisted recurrent selection: a simulation appraisal. Crop Sci. 2006;46(2):614–621.
   Web of Science ®Google Scholar
• Eathington SR, Crosbie TM, Edwards MD, et al. Molecular markers in a commercial breeding program. Crop Sci. 2007;47(Suppl 3):S154–S163.
   Google Scholar
• Luo Y, Sangha JS, Wang S, et al. Marker-assisted breeding of Xa4, Xa21 and Xa27 in the restorer lines of hybrid rice for broad-spectrum and enhanced disease resistance to bacterial blight. Mol Breed. 2012;30(4):1601–1610.
   Web of Science ®Google Scholar
• Gupta PK, Langridge P, Mir RR. Marker-assisted wheat breeding: present status and future possibilities. Mol Breed. 2010;26(2):145–161.
   Web of Science ®Google Scholar
• Ye G, Smith KF. Marker-assisted gene pyramiding for inbred line development: basic principles and practical guidelines. Int J Plant Breed. 2008;2(1):1–10.
   Google Scholar
• Andersen JR, Lübberstedt T. Functional markers in plants. Trends Plant Sci. 2003;8(11):554–560.
   PubMed Web of Science ®Google Scholar
• Xu Y, McCouch SR, Zhang Q. How can we use genomics to improve cereals with rice as a reference genome? Plant Mol Biol. 2005;59(1):7–26.
   PubMed Web of Science ®Google Scholar
• Liu Y, He Z, Appels R, et al. Functional markers in wheat: current status and future prospects. Theor Appl Genet. 2012;125(1):1–10.
   PubMed Web of Science ®Google Scholar
• Zhang X, Yang S, Zhou Y, et al. Distribution of the Rht-B1b, Rht-D1b and Rht8 reduced height genes in autumn-sown Chinese wheats detected by molecular markers. Euphytica. 2006;152(1):109–116.
   Web of Science ®Google Scholar
• Andeden E, Yediay F, Baloch F, et al. Distribution of vernalization and photoperiod genes (Vrn-A1, Vrn-B1, Vrn-D1, Vrn-B3, Ppd-D1) in Turkish bread wheat cultivars and landraces. Cereal Res Commun. 2011;39(3):352–364.
   Web of Science ®Google Scholar
• Shaaf S, Sharma R, Baloch FS, et al. The grain Hardness locus characterized in a diverse wheat panel (Triticum aestivum L.) adapted to the central part of the Fertile Crescent: genetic diversity, haplotype structure, and phylogeny. Mol Genet Genomics. 2015;291(3):1259–1275.
   Web of Science ®Google Scholar
• Anuradha K, Agarwal S, Rao YV, et al. Mapping QTLs and candidate genes for iron and zinc concentrations in unpolished rice of Madhukar× Swarna RILs. Gene. 2012;508(2):233–240.
   PubMed Web of Science ®Google Scholar
• McCallum CM, Comai L, Greene EA, et al. Targeting induced local lesions in genomes (TILLING) for plant functional genomics. Plant Physiol. 2000;123(2):439–442.
   PubMed Web of Science ®Google Scholar
• Kurowska M, Daszkowska-Golec A, Gruszka D, et al. TILLING – a shortcut in functional genomics. J Appl Genet. 2011;52(4):371–390.
   PubMed Web of Science ®Google Scholar
• Comai L, Henikoff S. TILLING: practical single-nucleotide mutation discovery. Plant J. 2006;45(4):684–694.
   PubMed Web of Science ®Google Scholar
• Gupta B, Saha J, Sengupta A, et al. Recent advances on virus induced gene silencing (VIGS): plant functional genomics. J Plant Biochem Physiol. 2013:1:e116.
   Google Scholar
• Lu R, Malcuit I, Moffett P, et al. High throughput virus-induced gene silencing implicates heat shock protein 90 in plant disease resistance. Embo J. 2003;22(21):5690–5699.
   PubMed Web of Science ®Google Scholar
• Braae A, Thompson CE, Morgan K. Comparison of custom designed KASP and TaqMan genotyping assays for a rare genetic variant identified through resequencing GWAS loci. Available from: www.lgcgroup.com
   Google Scholar
• Kumpatla SP, Abdurakhmonov IY, Mammadov JA, et al. Genomics-assisted plant breeding in the 21st century: technological advances and progress. Rijeka: InTech; 2012.
   Google Scholar
• Rasheed A, Wen W, Gao F, et al. Development and validation of KASP assays for genes underpinning key economic traits in bread wheat. Theor Appl Genet. 2016;129(10):1843–1860.
   PubMed Web of Science ®Google Scholar
• Meuwissen TH, Hayes BJ, Goddard ME. Prediction of total genetic value using genome-wide dense marker maps. Genetics. 2001;157(4):1819–1829.
   PubMed Web of Science ®Google Scholar
• Newell MA, Jannink JL. Genomic selection in plant breeding. In: Fleury D, Whitford R, editors. Crop breeding: methods and protocols. New York (NY): Humana Press; 2014. p. 117–130. (Methods in Molecular Biology; Vol. 1145).
   Google Scholar
• Goddard ME, Hayes BJ. Genomic selection. J Anim Breed Genet. 2007;124(6):323–330.
   PubMed Web of Science ®Google Scholar
• Ingvarsson PK, Street NR. Association genetics of complex traits in plants. New Phytol. 2011;189(4):909–922.
   PubMed Web of Science ®Google Scholar
• Lorenz AJ, Chao S, Asoro FG, et al. Chapter 2: genomic selection in plant breeding: knowledge and prospects. In: Sparks DL, editor. Vol. 110, Advances in agronomy. San Diego (CA): Academic Press; 2011; p. 77–123.
   Google Scholar
• Furbank RT, Tester M. Phenomics – technologies to relieve the phenotyping bottleneck. Trends Plant Sci. 2011;16(12):635–644.
   PubMed Web of Science ®Google Scholar
• Finkel E. With ‘phenomics,’ plant scientists hope to shift breeding into overdrive. Science. 2009;325(5939):380–381.
   PubMed Web of Science ®Google Scholar
• Spalding EP, Miller ND. Image analysis is driving a renaissance in growth measurement. Curr Opin Plant Biol. 2013;16(1):100–104.
   PubMed Web of Science ®Google Scholar
• Montes JM, Technow F, Dhillon BS, et al. High-throughput non-destructive biomass determination during early plant development in maize under field conditions. Field Crop Res. 2011;121(2):268–273.
   Web of Science ®Google Scholar
• Spindel JE, Begum H, Akdemir D, et al. Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement. Heredity. 2016;116;395–408.
   PubMed Web of Science ®Google Scholar
• Feng Z, Zhang B, Ding W, et al. Efficient genome editing in plants using a CRISPR/Cas system. Cell Res. 2013;23(10):1229–1232.
   PubMed Web of Science ®Google Scholar
• Hsu PD, Scott DA, Weinstein JA, et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol. 2013;31(9):827–832.
   PubMed Web of Science ®Google Scholar
• Lozano-Juste J, Cutler SR. Plant genome engineering in full bloom. Trends Plant Sci. 2014;19(5):284–287.
   PubMed Web of Science ®Google Scholar
• Qi LS, Larson MH, Gilbert LA, et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 2013;152(5):1173–1183.
   PubMed Web of Science ®Google Scholar
• Jinek M, East A, Cheng A et al. RNA-programmed genome editing in human cells. Elife. 2013;2:e00471.
   PubMed Web of Science ®Google Scholar
• Makarova KS, Haft DH, Barrangou R et al. Evolution and classification of the CRISPR–Cas systems. Nat Rev Microbiol. 2011;9(6):467–477.
   PubMed Web of Science ®Google Scholar
• Shan Q, Wang Y, Li J, et al. Targeted genome modification of crop plants using a CRISPR-Cas system. Nat Biotechnol. 2013;31(8):686–688.
   PubMed Web of Science ®Google Scholar
• Ali Z, Abul-faraj A, Piatek M, et al. Activity and specificity of TRV-mediated gene editing in plants. Plant Signal Behav. 2015;10:e1044191.
   PubMed Web of Science ®Google Scholar
• Svitashev S, Young JK, Schwartz C, et al. Targeted mutagenesis, precise gene editing, and site-specific gene insertion in maize using Cas9 and guide RNA. Plant Physiol. 2015;169(2):931–945.
   PubMed Web of Science ®Google Scholar
• Ma X, Zhang Q, Zhu Q et al. A robust CRISPR/Cas9 system for convenient, high-efficiency multiplex genome editing in monocot and dicot plants. Mol Plant. 2015;8(8):1274–1284.
   PubMed Web of Science ®Google Scholar
• Garneau JE, Dupuis ME, Villion M, et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature. 2010;468(7320):67–71.
   PubMed Web of Science ®Google Scholar
• Karvelis T, Gasiunas G, Miksys A et al. crRNA and tracrRNA guide Cas9-mediated DNA interference in Streptococcus thermophilus. RNA Biol. 2013;10(5):841–851.
   PubMed Web of Science ®Google Scholar
• Marraffini LA, Sontheimer EJ. CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat Rev Genet. 2010;11(3):181–190.
   PubMed Web of Science ®Google Scholar
• Xu Y, Crouch JH. Marker-assisted selection in plant breeding: from publications to practice. Crop Sci. 2008;48(2):391–407.
   Web of Science ®Google Scholar
• Baloch FS, Alsaleh A, Andeden et al. High levels of segregation distortion in the molecular linkage map of bread wheat representing the West Asia and North Africa region. Turk J Agric For 2016;40(3):352–364.
   Web of Science ®Google Scholar
• Baloch FS, Derya M, Andeden EE, et al. Inter-primer binding site retrotransposon and inter-simple sequence repeat diversity among wild Lens species. Biochem Syst Ecol. 2015;58:162–168.
   Web of Science ®Google Scholar
• Andeden EE, Baloch FS, et al. Development, characterization and mapping of microsatellite markers for lentil (Lens culinaris Medik.). Plant Breed. 2015;134(5):589–598.
   Web of Science ®Google Scholar