Abstract
Heterosis is defined as the ability of hybrids to outperform their parents with respect to various characteristics and agronomical important traits (Shull 1948). Various plant traits and particularly pronounced yield display heterosis. Hybrid breeding is based upon the phenomenon and prediction of hybrid performance and heterosis are important applications to increase the efficiency of hybrid breeding programs. Traditional phenotypic evaluation is still the common methodology to estimate general combining abilities for the predictions of hybrid traits (Choudhary et al. 2008). Molecular markers like RFLPs (restriction fragment length polymorphism), RAPDs (randomly amplified polymorphic DNA) or AFLPs (amplified fragment length polymorphism) can be employed to improve the prediction of complex traits like yield. An example is the application of AFLP-Markers in a linear regression approach to predict hybrid performance and SCA in intergroup-crosses of maize (Vuylsteke et al. 2000). For a long time molecular marker-based genetic distances has not proven to be a reliable approach for the prediction of hybrid characteristics in crops (Melchinger 1999) and might have limitations for prediction, as e.g. in Arabidopsis the correlation between heterosis and genetic distance was not significant (Meyer et al. 2004; Stokes et al. 2007). However, the improvement of DNA marker based approaches and its application to factorial crosses in maize led to a prediction accuracy that is comparable to phenotype based estimates (Schrag et al. 2006, 2007). To further increase prediction abilities for hybrid breeding, various molecular compounds of the plant, like DNA methylation states, transcripts, proteins and metabolites, are currently considered and tested as new markers with diagnostic and predictive potential. Current results related to specific compounds are discussed in the various chapters of this section. Here we address the development and applicability of RNA expression data for the prediction of heterosis and hybrid performance.
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References
Auger DL, Gray AD, Ream TS, Kato A, Coe EH, Birchler JA (2005) Nonadditive gene expression in diploid and triploid hybrids of maize. Genetics 169:389–397
Birchler JA, Auger DL, Riddle NC (2003) In search of the molecular basis of heterosis. Plant Cell 15:2236–2239
Boppenmaier J, Melchinger AE, Seitz G, Geiger HH, Herrmann RG (1993) Genetic diversity for RFLPs in European maize inbreds.3. Performance of crosses within versus between heterotic groups for grain traits. Plant Breeding 111:217–226
Broadley MR, White PJ, Hammond JP, Graham NS, Bowen HC, Emmerson ZF, Fray RG, Iannetta PP, McNicol JW, May ST (2008) Evidence of neutral transcriptome evolution in plants. New Phytol 180(3):587–593
Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ, Browne C, Ersoz E, Flint-Garcia S, Garcia A, Glaubitz JC et al (2009) The genetic architecture of maize flowering time. Science 325:714–718
Charcosset A, Essioux L (1994) The effect of population-structure on the relationship between heterosis and heterozygosity at marker loci. Theor Appl Genet 89:336–343
Choudhary K, Choudhary OP, Shekhawat NS (2008) Marker assisted selection: a novel approach for crop improvement. American-Eurasian J Agron 1:26–30
Frisch M, Thiemann A, Fu JJ, Schrag TA, Scholten S, Melchinger AE (2010) Transcriptome-based distance measures for grouping of germplasm and prediction of hybrid performance in maize. Theor Appl Genet 120:441–450
Fu J, Thiemann A, Schrag TA, Melchinger AE, Scholten S, Frisch M (2010) Dissecting grain yield pathways and their interactions with grain dry matter content by a two-step correlation approach with maize seedling transcriptome. BMC Plant Biol 10:63
Gärtner T, Steinfath M, Andorf S, Lisec J, Meyer RC, Altmann T, Willmitzer L, Selbig J (2009) Improved heterosis prediction by combining information on DNA- and metabolic markers. PLoS One 4(4):e5220
Groszmann M, Greaves IK, Albert N, Fujimoto R, Helliwell CA, Dennis ES, Peacock WJ (2011a) Epigenetics in plants-vernalisation and hybrid vigour. Biochim Biophys Acta 1809(8):427–437
Groszmann M, Greaves IK, Albertyn ZI, Scofield GN, Peacock WJ, Dennis ES (2011b) Changes in 24-nt siRNA levels in Arabidopsis hybrids suggest an epigenetic contribution to hybrid vigor. Proc Natl Acad Sci USA 108:2617–2622
Guo M, Rupe MA, Zinselmeier C, Habben J, Bowen BA, Smith OS (2004) Allelic variation of gene expression in maize hybrids. Plant Cell 16:1707–1716
Guo M, Rupe MA, Yang XF, Crasta O, Zinselmeier C, Smith OS, Bowen B (2006) Genome-wide transcript analysis of maize hybrids: allelic additive gene expression and yield heterosis. Theor Appl Genet 113:831–845
Hamblin MT, Warburton ML, Buckler ES (2007) Empirical comparison of simple sequence repeats and single nucleotide polymorphisms in assessment of maize diversity and relatedness. PLoS One 2:e1367
He G, Zhu X, Elling AA, Chen L, Wang X, Guo L, Liang M, He H, Zhang H, Chen F, Qi Y, Chen R, Deng XW (2010) Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell 22:17–33
Hochholdinger F, Hoecker N (2007) Towards the molecular basis of heterosis. Trends Plant Sci 12:427–432
Hoecker N, Keller B, Muthreich N, Chollet D, Descombes P, Piepho HP, Hochholdinger F (2008) Comparison of maize (Zea mays L.) F1-hybrid and parental inbred line primary root transcriptomes suggests organ-specific patterns of nonadditive gene expression and conserved expression trends. Genetics 179:1275–1283
Huang Y, Zhang L, Zhang J, Yuan D, Xu C, Li X, Zhou D, Wang S, Zhang Q (2006) Heterosis and polymorphisms of gene expression in an elite rice hybrid as revealed by a microarray analysis of 9198 unique ESTs. Plant Mol Biol 62:579–591
Jahnke S, Sarholz B, Thiemann A, Kühr V, Gutiérrez-Marcos JF, Geiger HH, Piepho HP, Scholten S (2010) Heterosis in early seed development: a comparative study of F1 embryo and endosperm tissues 6 days after fertilization. Theor Appl Genet 120:389–400
Maenhout S, De Baets G, Haesaert G, Bockstaele EV (2007) Support vector machine regression for the prediction of maize hybrid performance. Theor Appl Genet 115:1003–1013
Mallory AC, Vaucheret H (2006) Functions of microRNAs and related small RNAs in plants. Nat Genet 38:S31–S36
McMullen MD, Kresovich S, Villeda HS, Bradbury P, Li HH, Sun Q et al (2009) Genetic properties of the maize nested association mapping population. Science 325:737–740
Melchinger AE (1999) Genetic diversity and heterosis. In: Coors JG, Pandey S (eds) The genetics and exploitation of heterosis in crops. ASA-CSSA, Madison, pp 99–118
Meyer RC, Torjek O, Becher M, Altmann T (2004) Heterosis of biomass production in Arabidopsis. Establishment during early development. Plant Physiol 134:1813–1823
Meyer S, Pospisil H, Scholten S (2007) Heterosis associated gene expression in maize embryos 6 days after fertilization exhibits additive, dominant and overdominant pattern. Plant Mol Biol 63:381–391
Moghaddam AM, Fuchs J, Czauderna T, Houben A, Mette MF (2010) Intraspecific hybrids of Arabidopsis thaliana revealed no gross alterations in endopolyploidy, DNA methylation, histone modifications and transcript levels. Theor Appl Genet 120:215–226
Moghaddam AM, Roudier F, Seifert M, Bérard C, Magniette ML, Ashtiyani RK, Houben A, Colot V, Mette MF (2011) Additive inheritance of histone modifications in Arabidopsis thaliana intra-specific hybrids. Plant J. doi:10.1111/j.1365-313X.2011.04628.x
Mosher RA, Melnyk CW, Kelly KA, Dunn RM, Studholme DJ, Baulcombe DC (2009) Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature 460:283–286
Ni Z, Sun Q, Liu Z, Wu L, Wang X (2000) Identification of a hybrid-specific expressed gene encoding novel RNA-binding protein in wheat seedling leaves using differential display of mRNA. Mol Gen Genet 263:934–938
Nobuta K, Lu C, Shrivastava R, Pillay M, De Paoli E, Accerbi M, Arteaga-Vazquez M, Sidorenko L, Jeong DH, Yen Y, Green PJ, Chandler VL, Meyers BC (2008) Distinct size distribution of endogenous siRNAs in maize: evidence from deep sequencing in the mop1-1 mutant. Proc Natl Acad Sci USA 105:14958–14963
Omholt SW, Plahte E, Øyehaug L, Xiang K (2000) Gene regulatory networks generating the phenomena of additivity, dominance and epistasis. Genetics 155:969–981
Schön C, Dhillon B, Utz H, Melchinger A (2010) High congruency of QTL positions for heterosis of grain yield in three crosses of maize. Theor Appl Genet 120:321–332
Schrag TA, Melchinger AE, Sorensen AP, Frisch M (2006) Prediction of single-cross hybrid performance for grain yield and grain dry matter content in maize using AFLP markers associated with QTL. Theor Appl Genet 113:1037–1047
Schrag TA, Maurer HP, Melchinger AE, Piepho HP, Peleman J, Frisch M (2007) Prediction of single-cross hybrid performance in maize using haplotype blocks associated with QTL for grain yield. Theor Appl Genet 114:1345–1355
Shimkets RA, Lowe DG, Tai JT-N, Sehl P, Jin H, Yang R, Predki PF, Rothberg BEG, Murtha MT, Roth ME, Shenoy SG, Windemuth A, Simpson JW, Simons JF, Daley MP, Gold SA, McKenna MP, Hillan K, Went GT, Rothberg JM (1999) Gene expression analysis by transcript profiling coupled to a gene database query. Nat Biotechnol 17:798–803
Shull GH (1948) What is ‘Heterosis’? Genetics 33:439–446
Song RT, Messing J (2003) Gene expression of a gene family in maize based on noncollinear haplotypes. Proc Natl Acad Sci USA 100:9055–9060
Steinfath M, Gärtner T, Lisec J, Meyer RC, Altmann T, Willmitzer L, Selbig J (2010) Prediction of hybrid biomass in Arabidopsis thaliana by selected parental SNP and metabolic markers. Theor Appl Genet 120:239–247
Stokes D, Morgan C, O’Neill C, Bancroft I (2007) Evaluating the utility of Arabidopsis thaliana as a model for understanding heterosis in hybrid crops. Euphytica 156:157–171
Stokes D, Fraser F, Morgan C, O’Neill CM, Dreos R, Magusin A et al (2010) An association transcriptomics approach to the prediction of hybrid performance. Mol Breed 26:91–106
Stupar RM, Springer NM (2006) Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression patterns in the F-1 hybrid. Genetics 173:2199–2210
Stupar RM, Gardiner JM, Oldre AG, Haun WJ, Chandler VL, Springer NM (2008) Gene expression analyses in maize inbreds and hybrids with varying levels of heterosis. BMC Plant Biol 8:33
Sun QX, Ni ZF, Liu ZY (1999) Differential gene expression between wheat hybrids and their parental inbreds in seedling leaves. Euphytica 106:117–123
Swanson-Wagner RA, Jia Y, DeCook R, Borsuk LA, Nettleton D, Schnable PS (2006) All possible modes of gene action are observed in a global comparison of gene expression in a maize F-1 hybrid and its inbred parents. Proc Natl Acad Sci USA 103:6805–6810
Thiemann A, Fu J, Schrag TA, Melchinger AE, Frisch M, Scholten S (2010) Correlation between parental transcriptome and field data for the characterization of heterosis in Zea mays L. Theor Appl Genet 120:401–413
Uzarowska A, Keller B, Piepho HP, Schwarz G, Ingvardsen C, Wenzel G, Lübberstedt T (2007) Comparative expression profiling in meristems of inbred-hybrid triplets of maize based on morphological investigations of heterosis for plant height. Plant Mol Biol 63:21–34
Vuylsteke M, Kuiper M, Stam P (2000) Chromosomal regions involved in hybrid performance and heterosis: their AFLP-based identification and practical use in prediction models. Heredity 85:208–218
Vuylsteke M, van Eeuwijk F, Van Hummelen P, Kuiper M, Zabeau M (2005) Genetic analysis of variation in gene expression in Arabidopsis thaliana. Genetics 171:1267–1275
Wang X, Elling AA, Li X, Li N, Peng Z, He G, Sun H, Qi Y, Liu XS, Deng XW (2009) Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell 21:1053–1069
Wei G, Tao Y, Liu G, Chen C, Luo R, Xia H, Gan Q, Zeng H, Lu Z, Han Y, Li X, Song G, Zhai H, Peng Y, Li D, Xu H, Wei X, Cao M, Deng H, Xin Y, Fu X, Yuan L, Yu J, Zhu Z, Zhu L (2009) A transcriptomic analysis of superhybrid rice LYP9 and its parents. Proc Natl Acad Sci USA 106:7695–7701
Weil C, Martienssen R (2008) Epigenetic interactions between transposons and genes: lessons from plants. Curr Opin Genet Dev 18:188–192
Wittkopp PJ, Haerum BK, Clark AG (2004) Evolutionary changes in cis and trans gene regulation. Nature 430:85–88
Wu LM, Ni ZF, Meng FR, Lin Z, Sun QX (2003) Cloning and characterization of leaf cDNAs that are differentially expressed between wheat hybrids and their parents. Mol Genet Genomics 270:281–286
Xiong LZ, Yang GP, Xu CG, Zhang QF, Maroof MAS (1998) Relationships of differential gene expression in leaves with heterosis and heterozygosity in a rice diallel cross. Mol Breed 4:129–136
Zhang H, He H, Chen L, Li L, Liang M, Wang X, Liu X, He G, Chen R, Ma L, Deng XW (2008) A genome-wide transcription analysis reveals a close correlation of promoter INDEL polymorphism and heterotic gene expression in rice hybrids. Mol Plant 1:720–731
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Scholten, S., Thiemann, A. (2013). Transcriptome-Based Prediction of Heterosis and Hybrid Performance. In: Lübberstedt, T., Varshney, R. (eds) Diagnostics in Plant Breeding. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-5687-8_13
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DOI: https://doi.org/10.1007/978-94-007-5687-8_13
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