1,638
Views
56
CrossRef citations to date
0
Altmetric
Review Article

Functional molecular markers for crop improvement

, , , &
Pages 917-930 | Received 22 Jul 2014, Accepted 13 May 2015, Published online: 14 Jul 2015

References

  • Abdurakhmonov IY, Abdukarimov A. (2008). Application of association mapping to understanding the genetic diversity of plant germplasm resources. Int J Plant Genomics, 2008, 574927
  • Andersen JR, Lübberstedt T. (2003). Functional markers in plants. Trends Plant Sci, 8, 554–60
  • Andersen JR, Schrag T, Melchinger AE, et al. (2005). Validation of Dwarf8 polymorphisms associated with flowering time in elite European inbred lines of maize (Zea mays L.). Theoret Appl Genet, 111, 206–17
  • Assenov B, Andjelkovic V, Ignjatovic-Micic D, et al. (2013). Identification of SNP mutations in In MYBЕ-1 gene involved in drought stress tolerance in maize. Bulgarian J Agric Sci, 19, 181–5
  • Ayres N, McClung A, Larkin P, et al. (1997). Microsatellites and a single-nucleotide polymorphism differentiate apparentamylose classes in an extended pedigree of US rice germ plasm. Theoret Appl Genet, 94, 773–81
  • Azmach G, Gedil M, Menkir A, Spillane C. (2013). Marker-trait association analysis of functional gene markers for provitamin A levels across diverse tropical yellow maize inbred lines. BMC Plant Biol, 13, 227
  • Bagge M, Xia X, Lübberstedt T. (2007). Functional markers in wheat. Curr Opin Plant Biol, 10, 211–16
  • Batley J, Barker G, O'Sullivan H, et al. (2003). Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant Physiol, 132, 84–91
  • Beales J, Turner A, Griffiths S, et al. (2007). A pseudo-response regulator is misexpressed in the photoperiod insensitive Ppd-D1a mutant of wheat (Triticum aestivum L.). Theoret Appl Genet, 115, 721–33
  • Biruma M. (2013). Development of molecular based tools for resistance breeding of sorghum to Colletotrichum sublineolum. Kampala, Uganda: Makerere University
  • Bollina V, Kumaraswamy GK, Kushalappa AC, et al. (2010). Mass spectrometry – based metabolomics application to identify quantitative resistance-related metabolites in barley against fusarium head blight. Mol Plant Pathol, 11, 769–82
  • Bradbury LM, Henry RJ, Jin Q, et al. (2005). A perfect marker for fragrance genotyping in rice. Mol Breed, 16, 279–83
  • Buetow KH, Edmonson MN, Cassidy AB. (1999). Reliable identification of large numbers of candidate SNPs from public EST data. Nat Genet, 21, 323–5
  • Burch-Smith TM, Anderson JC, Martin GB, Dinesh-Kumar SP. (2004). Applications and advantages of virus – induced gene silencing for gene function studies in plants. Plant J, 39, 734–46
  • Cakir C, Gillespie ME, Scofield SR. (2010). Rapid determination of gene function by virus-induced gene silencing in wheat and barley. Crop Sci, 50, S-77–84
  • Cao A, Xing L, Wang X, et al. (2011). Serine/threonine kinase gene Stpk-V, a key member of powdery mildew resistance gene Pm21, confers powdery mildew resistance in wheat. Proc Natl Acad Sci USA, 108, 7727–32
  • Chai Y, Hao X, Yang X, et al. (2012). Validation of DGAT1-2 polymorphisms associated with oil content and development of functional markers for molecular breeding of high-oil maize. Mol Breed, 29, 939–49
  • Chen YZ, Pang QY, He Y, et al. (2012). Proteomics and metabolomics of Arabidopsis responses to perturbation of glucosinolate biosynthesis. Mol Plant, 5, 1138–50
  • Chen T, Tian M-X, Zhang Y-D, et al. (2010). Development of simple functional markers for low glutelin content gene 1 (Lgc1) in rice (Oryza sativa). Rice Sci, 17, 173–8
  • Chin JH, Gamuyao R, Dalid C, et al. (2011). Developing rice with high yield under phosphorus deficiency: Pup1 sequence to application. Plant Physiol, 156, 1202–16
  • Ching A, Caldwell KS, Jung M, et al. (2002). SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet, 3, 19
  • Chu Z, Yuan M, Yao J, et al. (2006). Promoter mutations of an essential gene for pollen development result in disease resistance in rice. Genes Dev, 20, 1250–5
  • Clark TG, Andrew T, Cooper GM, et al. (2007). Functional constraint and small insertions and deletions in the ENCODE regions of the human genome. Genome Biol, 8, R180
  • Clark RM, Wagler TN, Quijada P, Doebley J. (2006). A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture. Nat Genet, 38, 594–7
  • Collard BC, Vera Cruz CM, McNally KL, et al. (2008). Rice molecular breeding laboratories in the genomics era: current status and future considerations. Int J Plant Genomics, 2008, 524847
  • Degenkolbe T, Do PT, Kopka J, et al. (2013). Identification of drought tolerance markers in a diverse population of rice cultivars by expression and metabolite profiling. PLoS One, 8, e63637
  • Dhlamini Z, Spillane C, Moss J, et al. (2005). Status of research and application of crop biotechnologies in developing countries: preliminary assessment. Rome: FAO
  • Domon E, Yanagisawa T, Saito A, Takeda K. (2004). Single nucleotide polymorphism genotyping of the barley waxy gene by polymerase chain reaction with confronting two-pair primers. Plant Breed, 123, 225–8
  • Dong C-H, Ma Z-Y, Xia X-C, et al. (2012). Allelic variation at the TaZds-A1 locus on wheat chromosome 2A and development of a functional marker in common wheat. J Integr Agric, 11, 1067–74
  • Duez P, Kumps A, Mardens Y. (1996). GC-MS profiling of urinary organic acids evaluated as a quantitative method. Clin Chem, 42, 1609–15
  • Edae EA, Byrne PF, Manmathan H, et al. (2013). Association mapping and nucleotide sequence variation in five drought tolerance candidate genes in spring wheat. Plant Genome, 6, 1–13
  • Ellis M, Spielmeyer W, Gale K, et al. (2002). “Perfect” markers for the Rht-B1b and Rht-D1b dwarfing genes in wheat. Theoret Appl Genet, 105, 1038–42
  • Estoup A, Tailliez C, Cornuet J-M, Solignac M. (1995). Size homoplasy and mutational processes of interrupted microsatellites in two bee species, Apis mellifera and Bombus terrestris (Apidae). Mol Biol Evol, 12, 1074–84
  • Fan C, Yu S, Wang C, Xing Y. (2009). A causal C – a mutation in the second exon of GS3 highly associated with rice grain length and validated as a functional marker. Theoret Appl Genet, 118, 465–72
  • Farooq S, Azam F. (2002). Molecular markers in plant breeding-lll: practical applications and difficulties encountered. Pakistan J Biol Sci, 5, 1148–54
  • Fiume E, Christou P, Gianì S, Breviario D. (2004). Introns are key regulatory elements of rice tubulin expression. Planta, 218, 693–703
  • Fleury D, Whitford R. (2014). Crop breeding: methods and protocols. New York: Humana Press, 1145
  • Forster B, Ellis R, Thomas W, et al. (2000). The development and application of molecular markers for abiotic stress tolerance in barley. J Exp Bot, 51, 19–27
  • Fu D, Szucs P, Yan L, et al. (2005). Large deletions within the first intron in VRN-1 are associated with spring growth habit in barley and wheat. Mol Genet Genomics, 273, 54–65
  • Garcia M, Mather DE. (2014). From genes to markers: exploiting gene sequence information to develop tools for plant breeding. Methods Mol Biol,1145, 21–36
  • Garg B, Lata C, Prasad M. (2012). A study of the role of gene TaMYB2 and an associated SNP in dehydration tolerance in common wheat. Mol Biol Rep, 39, 10865–71
  • Gaut BS, Clegg M. (1993). Nucleotide polymorphism in the Adh1 locus of pearl millet (Pennisetum glaucum) (Poaceae). Genetics, 135, 1091–7
  • Geng H, Xia X, Zhang L, et al. (2012). Development of functional markers for a lipoxygenase gene on chromosome 4BS in common wheat. Crop Sci,52, 568–76
  • Godfray HCJ, Beddington JR, Crute IR, et al. (2010). Food security: the challenge of feeding 9 billion people. Science,327, 812–18
  • Godge MR, Purkayastha A, Dasgupta I, Kumar PP. (2008). RETRACTED ARTICLE: Virus-induced gene silencing for functional analysis of selected genes. Plant Cell Rep,27, 209–19
  • Gopaul S, Farrell K, Abbott F. (2000). Gas chromatography/negative ion chemical ionization mass spectrometry and liquid chromatography/electrospray ionization tandem mass spectrometry quantitative profiling of N-acetylcysteine conjugates of valproic acid in urine: application in drug metabolism studies in humans. J Mass Spectrom, 35, 698–704
  • Goymer P. (2007). Synonymous mutations break their silence. Nat Rev Genet, 8, 92
  • Gregory TR. (2004). Insertion–deletion biases and the evolution of genome size. Gene, 324, 15–34
  • Gunnaiah R, Kushalappa AC, Duggavathi R, et al. (2012). Integrated metabolo-proteomic approach to decipher the mechanisms by which wheat QTL (Fhb1) contributes to resistance against Fusarium graminearum. PLoS One, 7, e40695
  • Hayashi K, Hashimoto N, Daigen M, Ashikawa I. (2004). Development of PCR-based SNP markers for rice blast resistance genes at the Piz locus. Theoret Appl Genet, 108, 1212–20
  • Hayashi K, Yasuda N, Fujita Y, et al. (2010). Identification of the blast resistance gene Pit in rice cultivars using functional markers. Theoret Appl Genet, 121, 1357–67
  • He X, Zhang Y, He Z, et al. (2008). Characterization of phytoene synthase 1 gene (Psy1) located on common wheat chromosome 7A and development of a functional marker. Theoret Appl Genet, 116, 213–21
  • He X, He Z, Zhang L, et al. (2007). Allelic variation of polyphenol oxidase (PPO) genes located on chromosomes 2A and 2D and development of functional markers for the PPO genes in common wheat. Theoret Appl Genet, 115, 47–58
  • He C, Holme J, Anthony J. (2014). SNP genotyping: the KASP assay. Methods Mol Biol, 1145, 75–86
  • Ikemura T. (1982). Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes: differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs. J Mol Biol, 158, 573–97
  • Ikemura T. (1985). Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol, 2, 13–34
  • Iyer-Pascuzzi AS, McCouch SR. (2007). Functional markers for xa5-mediated resistance in rice (Oryza sativa, L.). Mol Breed, 19, 291–6
  • Jena K, Mackill D. (2008). Molecular markers and their use in marker-assisted selection in rice. Crop Sci, 48, 1266–76
  • Ji Q, Lu J, Chao Q, et al. (2010). Two sequence alterations, a 136 bp InDel and an A/C polymorphic site, in the S5 locus are associated with spikelet fertility of indica-japonica hybrid in rice. J Genet Genomics, 37, 57–68
  • Jia Y, Redus M, Wang Z, Rutger JN. (2004). Development of a SNLP marker from the Pi-ta blast resistance gene by tri-primer PCR. Euphytica, 138, 97–105
  • Jiang Q, Hou J, Hao C, et al. (2011). The wheat (T. aestivum) sucrose synthase 2 gene (TaSus2) active in endosperm development is associated with yield traits. Funct Integr Genomics, 11, 49–61
  • Jiang D, Ye Q-L, Wang F-S, Cao L. (2010). The mining of citrus EST-SNP and its application in cultivar discrimination. Agric Sci China, 9, 179–90
  • Jin Q, Waters D, Cordeiro GM, et al. (2003). A single nucleotide polymorphism (SNP) marker linked to the fragrance gene in rice (Oryza sativa L.). Plant Sci, 165, 359–64
  • Jones JD, Witek K, Verweij W, et al. (2014). Elevating crop disease resistance with cloned genes. Phil Trans R Soc B Biol Sci, 369, 20130087
  • Jones E, Chu W-C, Ayele M, et al. (2009). Development of single nucleotide polymorphism (SNP) markers for use in commercial maize (Zea mays L.) germplasm. Mol Breed, 24, 165–76
  • Kaur S, Cogan NO, Stephens A, et al. (2013). EST-SNP discovery and dense genetic mapping in lentil (Lens culinaris Medik.) enable candidate gene selection for boron tolerance. Theoret Appl Genet, 127, 703–13
  • Khoo K. (2014). Temperature Switch PCR (TSP): a gel-based molecular marker technique for investigating single nucleotide polymorphisms. Methods Mol Biol, 1145, 37–46
  • Kim M, Van K, Lestari P, et al. (2005). SNP identification and SNAP marker development for a GmNARK gene controlling supernodulation in soybean. Theoret Appl Genet, 110, 1003–10
  • Kushalappa AC, Gunnaiah R. (2013). Metabolo-proteomics to discover plant biotic stress resistance genes. Trends Plant Sci, 18, 522–31
  • Lagudah ES, Krattinger SG, Herrera-Foessel S, et al. (2009). Gene-specific markers for the wheat gene Lr34/Yr18/Pm38 which confers resistance to multiple fungal pathogens. Theoret Appl Genet, 119, 889–98
  • Lata C, Prasad M. (2013). Validation of an allele-specific marker associated with dehydration stress tolerance in a core set of foxtail millet accessions. Plant Breed, 132, 496–9
  • Liu Y, He Z, Appels R, Xia X. (2012). Functional markers in wheat: current status and future prospects. Theoret Appl Genet, 125, 1–10
  • Liu S, Chao S, Anderson JA. (2008). New DNA markers for high molecular weight glutenin subunits in wheat. Theoret Appl Genet, 118, 177–83
  • Liu Y, Nie Y-D, Han F-X, et al. (2014). Allelic variation of a soluble acid invertase gene (SAI-1) and development of a functional marker in sweet sorghum [Sorghum bicolor (L.) Moench]. Mol Breed, 33, 721–30
  • Lu Y, Zhao G, Li Y, et al. (2013). Identification of two novel waxy alleles and development of their molecular markers in sorghum. Genome, 56, 283–8
  • Lübberstedt T, Melchinger AE, Fähr S, et al. (1998). QTL mapping in testcrosses of flint lines of maize: III. Comparison across populations for forage traits. Crop Sci, 38, 1278–89
  • Lübberstedt T, Zein I, Andersen JR, et al. (2005). Development and application of functional markers in maize. Euphytica, 146, 101–8
  • Madsen L, Collins NC, Rakwalska M, et al. (2003). Barley disease resistance gene analogs of the NBS-LRR class: identification and mapping. Mol Genet Genomics, 269, 150–61
  • McCartney C, Somers D, Fedak G, et al. (2007). The evaluation of FHB resistance QTLs introgressed into elite Canadian spring wheat germplasm. Mol Breed, 20, 209–21
  • Miedaner T, Korzun V. (2012). Marker-assisted selection for disease resistance in wheat and barley breeding. Phytopathology, 102, 560–6
  • Mohamed A, Ali R, Elhassan O, et al. (2014). First products of DNA marker-assisted selection in sorghum released for cultivation by farmers in sub-saharan Africa. J Plant Sci Mol Breed, 3, 1–10
  • Mohler V, Bauer A, Bauer C, et al. (2011). Genetic analysis of powdery mildew resistance in German winter wheat cultivar Cortez. Plant Breed, 130, 35–40
  • Morgante M, Olivieri A. (1993). PCR-amplified microsatellites as markers in plant genetics. Plant J, 3, 175–82
  • Nasu S, Suzuki J, Ohta R, et al. (2009). Search for and analysis of single nucleotide polymorphisms (SNPs) in rice (Oryza sativa, Oryza rufipogon) and establishment of SNP markers. DNA Res, 9, 163–71
  • Neeraja C, Maghirang-Rodriguez R, Pamplona A, et al. (2007). A marker-assisted backcross approach for developing submergence-tolerant rice cultivars. Theoret Appl Genet, 115, 767–76
  • Palaisa KA, Morgante M, Williams M, Rafalski A. (2003). Contrasting effects of selection on sequence diversity and linkage disequilibrium at two phytoene synthase loci. Plant Cell Online, 15, 1795–806
  • Pandey B, Sharma P, Pandey D, et al. (2013). Identification of new aquaporin genes and single nucleotide polymorphism in bread wheat. Evol Bioinform Online, 9, 437–52
  • Panwar P, Jha A, Pandey PK, et al. (2011). Functional markers based molecular characterization and cloning of resistance gene analogs encoding NBS-LRR disease resistance proteins in finger millet (Eleusine coracana). Mol Biol Rep, 38, 3427–36
  • Percudani R. (2001). Restricted wobble rules for eukaryotic genomes. Trends Genet, 17, 133–5
  • Periyannan S, Bansal U, Bariana H, et al. (2014). Identification of a robust molecular marker for the detection of the stem rust resistance gene Sr45 in common wheat. Theoret Appl Genet, 127, 947–55
  • Picoult-Newberg L, Ideker TE, Pohl MG, et al. (1999). Mining SNPs from EST databases. Genome Res, 9, 167–74
  • Prasanna B, Pixley K, Warburton ML, Xie C-X. (2010). Molecular marker-assisted breeding options for maize improvement in Asia. Mol Breed, 26, 339–56
  • Pushpa D, Yogendra KN, Gunnaiah R, et al. (2014). Identification of late blight resistance-related metabolites and genes in potato through nontargeted metabolomics. Plant Mol Biol Rep, 32, 584–95
  • Rafalski A. (2005). Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol, 5, 94–100
  • Rajaram S. (2005). Role of conventional plant breeding and biotechnology in future wheat production. Turk J Agric Forest, 29, 105–11
  • Ramkumar G, Sivaranjani A, Pandey MK, et al. (2010). Development of a PCR-based SNP marker system for effective selection of kernel length and kernel elongation in rice. Mol Breed, 26, 735–40
  • Reddy RN, Madhusudhana R, Mohan SM, et al. (2012). Characterization, development and mapping of unigene-derived microsatellite markers in sorghum [Sorghum bicolor (L.) Moench]. Mol Breed, 29, 543–64
  • Risch NJ. (2000). Searching for genetic determinants in the new millennium. Nature, 405, 847–56
  • Robertson D. (2004). VIGS vectors for gene silencing: many targets, many tools. Annu Rev Plant Biol, 55, 495–519
  • Roessner U, Luedemann A, Brust D, et al. (2001). Metabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems. Plant Cell Online, 13, 11–29
  • Rooney WL, Klein RR, (eds). (2000). Potential of marker-assisted selection for improving grain mold resistance in sorghum. Technical and institutional options for sorghum grain mold management: proceedings of an international consultation, ICRISAT, Patancheru, India
  • Sakthivel K, Rani NS, Pandey MK, et al. (2009). Development of a simple functional marker for fragrance in rice and its validation in Indian Basmati and non-Basmati fragrant rice varieties. Mol Breed, 24, 185–90
  • Salgotra RK, Gupta BB, Stewart Jr CN. (2014). From genomics to functional markers in the era of next-generation sequencing. Biotechnol Lett, 36, 417–26
  • Salvi S, Sponza G, Morgante M, et al. (2007). Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize. Proc Natl Acad Sci USA, 104, 11376–81
  • Samadder P, Sivamani E, Lu J, et al. (2008). Transcriptional and post-transcriptional enhancement of gene expression by the 5′ UTR intron of rice rubi3 gene in transgenic rice cells. Mol Geneti Genomics, 279, 429–39
  • Sauna ZE, Kimchi-Sarfaty C. (2011). Understanding the contribution of synonymous mutations to human disease. Nat Rev Genet, 12, 683–91
  • Savadi SB, Fakrudin B, Nadaf H, Gowda M. (2012). Transferability of sorghum genic microsatellite markers to peanut. Am J Plant Sci, 3, 1169–80
  • Scofield SR, Brandt AS. (2012). Virus-induced gene silencing in hexaploid wheat using barley stripe mosaic virus vectors. Methods Mol Biol (Clifton, NJ),894, 93–112
  • Senthil-Kumar M, Anand A, Uppalapati SR, Mysore KS. (2008). Virus-induced gene silencing and its applications. CAB Rev: Perspect Agric Vet Sci Nutr Nat Resources, 3, 1–18
  • Senthilvel S, Jayashree B, Mahalakshmi V, et al. (2008). Development and mapping of simple sequence repeat markers for pearl millet from data mining of expressed sequence tags. BMC Plant Biol, 8, 119
  • Septiningsih EM, Pamplona AM, Sanchez DL, et al. (2009). Development of submergence-tolerant rice cultivars: the Sub1 locus and beyond. Ann Bot, 103, 151–60
  • Setter TL, Yan J, Warburton M, et al. (2010). Genetic association mapping identifies single nucleotide polymorphisms in genes that affect abscisic acid levels in maize floral tissues during drought. J Exp Bot, 62, 701–16
  • Shao G, Tang A, Tang S, et al. (2011). A new deletion mutation of fragrant gene and the development of three molecular markers for fragrance in rice. Plant Breed, 130, 172–6
  • Shattuck-Eidens DM, Bell RN, Neuhausen SL, Helentjaris T. (1990). DNA sequence variation within maize and melon: observations from polymerase chain reaction amplification and direct sequencing. Genetics, 126, 207–17
  • Shi W, Yang Y, Chen S, Xu M. (2008). Discovery of a new fragrance allele and the development of functional markers for the breeding of fragrant rice varieties. Mol Breed, 22, 185–92
  • Sorensen MA, Kurland C, Pedersen S. (1989). Codon usage determines translation rate in Escherichia coli. J Mol Biol, 207, 365–77
  • Spielmeyer W, Ellis M, Robertson M, et al. (2004). Isolation of gibberellin metabolic pathway genes from barley and comparative mapping in barley, wheat and rice. Theoret Appl Genet, 109, 847–55
  • Su Z, Hao C, Wang L, et al. (2011). Identification and development of a functional marker of TaGW2 associated with grain weight in bread wheat (Triticum aestivum L.). Theoret Appl Genet, 122, 211–23
  • Tadege M, Ratet P, Mysore KS. (2005). Insertional mutagenesis: a swiss army knife for functional genomics of Medicago truncatula. Trends Plant Sci, 10, 229–35
  • Tao Y, Jiang L, Liu Q, et al. (2013). Combined linkage and association mapping reveals candidates for Scmv1, a major locus involved in resistance to sugarcane mosaic virus (SCMV) in maize. BMC Plant Biol, 13, 162
  • Thornsberry JM, Goodman MM, Doebley J, et al. (2001). Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet, 28, 286–9
  • Tohge T, Fernie AR. (2010). Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function. Nat Protoc, 5, 1210–27
  • Tommasini L, Yahiaoui N, Srichumpa P, Keller B. (2006). Development of functional markers specific for seven Pm3 resistance alleles and their validation in the bread wheat gene pool. Theoret Appl Genet, 114, 165–75
  • Toojinda T, Baird E, Booth A, et al. (1998). Introgression of quantitative trait loci (QTLs) determining stripe rust resistance in barley: an example of marker-assisted line development. Theoret Appl Genet, 96, 123–31
  • Tucker EJ, Huynh BL. (2014). Genotyping by high-eesolution melting analysis. Methods Mol Biol, 1145, 59–66
  • Varshney RK, Graner A, Sorrells ME. (2005a). Genomics-assisted breeding for crop improvement. Trends Plant Sci, 10, 621–30
  • Varshney RK, Thiel T, Stein N, et al. (2002). In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cell Mol Biol Lett, 7, 537–46
  • Varshney RK, Graner A, Sorrells ME. (2005b). Genic microsatellite markers in plants: features and applications. Trends Biotechnol, 23, 48–55
  • Varshney RK, Sigmund R, Börner A, et al. (2005c). Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice. Plant Sci, 168, 195–202
  • Varshney RK, Marcel TC, Ramsay L, et al. (2007). A high density barley microsatellite consensus map with 775 SSR loci. Theoret Appl Genet, 114, 1091–103
  • Venuprasad R, Bool M, Quiatchon L, et al. (2012). A large-effect QTL for rice grain yield under upland drought stress on chromosome 1. Mol Breed, 30, 535–47
  • Viard F, Franck P, Dubois M-P, et al. (1998). Variation of microsatellite size homoplasy across electromorphs, loci, and populations in three invertebrate species. J Mol Evol, 47, 42–51
  • Wang J, Nakazaki T, Chen S, et al. (2009a). Identification and characterization of the erect-pose panicle gene EP conferring high grain yield in rice (Oryza sativa L.). Theoret Appl Genet, 119, 85–91
  • Wang L, Zhao X, He Z, et al. (2009b). Characterization of low-molecular-weight glutenin subunit Glu-B3 genes and development of STS markers in common wheat (Triticum aestivum L.). Theoret Appl Genet, 118, 525–39
  • Wei B, Jing R, Wang C, et al. (2009). Dreb1 genes in wheat (Triticum aestivum L.): development of functional markers and gene mapping based on SNPs. Mol Breed, 23, 13–22
  • Wen W, Li D, Li X, et al. (2014). Metabolome-based genome-wide association study of maize kernel leads to novel biochemical insights. Nat Commun, 5, 3438
  • Woodward J. (2014). Bi-allelic SNP genotyping using the TaqMan® assay. Methods Mol Biol, 1145, 67–74
  • Yamanaka S, Nakamura I, Watanabe KN, Sato Y-I. (2004). Identification of SNPs in the waxy gene among glutinous rice cultivars and their evolutionary significance during the domestication process of rice. Theoret Appl Genet, 108, 1200–4
  • Yang Z, Bai Z, Li X, et al. (2012). SNP identification and allelic-specific PCR markers development for TaGW2, a gene linked to wheat kernel weight. Theoret Appl Genet, 125, 1057–68
  • Yogendra KN, Pushpa D, Mosa KA, et al. (2014). Quantitative resistance in potato leaves to late blight associated with induced hydroxycinnamic acid amides. Funct Integr Genomics, 14, 285–98
  • Yu J, Buckler ES. (2006). Genetic association mapping and genome organization of maize. Curr Opin Biotechnol, 17, 155–60
  • Yu J-K, La Rota M, Kantety R, Sorrells M. (2004). EST derived SSR markers for comparative mapping in wheat and rice. Mol Genet Genomics, 271, 742–51
  • Yundaeng C, Somta P, Tangphatsornruang S, et al. (2013). Gene discovery and functional marker development for fragrance in sorghum (Sorghum bicolor (L.) Moench). Theoret Appl Genet, 126, 2897–906
  • Zhang Z, Gerstein M. (2003). Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. Nucl Acids Res, 31, 5338–48
  • Zhang C, Dong C, He X, et al. (2011). Allelic variants at the locus on wheat chromosome 2DL and their association with yellow pigment content. Crop Sci, 51, 1580–90
  • Zhang L, Zhao YL, Gao LF, et al. (2012). TaCKX6-D1, the ortholog of rice OsCKX2, is associated with grain weight in hexaploid wheat. New Phytol, 195, 574–84
  • Zhang Y, Miao X, Xia X, He Z. (2014). Cloning of seed dormancy genes (TaSdr) associated with tolerance to pre-harvest sprouting in common wheat and development of a functional marker. Theoret Appl Genet, 127, 855–66
  • Zhang X, Yang S, Zhou Y, et al. (2006). Distribution of the Rht-B1b, Rht-D1b and Rht8 reduced height genes in autumn-sown Chinese wheats detected by molecular markers. Euphytica, 152, 109–16
  • Zhou Y, Han Y, Li Z, et al. (2012). ZmcrtRB3 encodes a carotenoid hydroxylase that affects the accumulation of α-carotene in maize kernel. J Integr Plant Biol, 54, 260–9
  • Zhou L, Chen Z, Lang X, et al. (2013). Development and validation of a PCR-based functional marker system for the brown planthopper resistance gene Bph14 in rice. Breed Sci, 63, 347--52
  • Zhu Y, Song Q, Hyten D, et al. (2003). Single-nucleotide polymorphisms in soybean. Genetics, 163, 1123–34–352

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.