title: Dissimilar Manifestation of Heterosis in Superhybrid Rice at Early-Tillering Stage under Nutrient-Deficient and Nutrient-Sufficient Condition.
abstract: Heterosis has long been exploited for crop breeding; however, the genetic mechanisms, particularly the initial establishment of heterosis during the early vegetative growth phase, remain elusive. The biggest challenge for that is to exclude noise genes from the identified heterosis-related candidates. Herein, we use nutrient-deficient hybrid with no measurable growth heterosis as control. After filtering these irrelevant genes, only 336 differentially expressed genes (DEGs), which is significantly lower than in previous reports, were identified as heterosis-related genes in a superhybrid rice of Liang-You-Pei-Jiu (LYP9) at early-tillering stage. Among the DEGs that could be mapped to quantitative trait loci (QTL), approximately 72.8% could be covered by yield or growth vigor-related QTL, thereby suggesting that our DEGs were reliable and may have potential value to rice breeding. Among the 336 DEGs identified, a majority showed intermediate expression relative to that of its parental lines (i.e. additive effects), particularly, expression was frequently more similar to the paternal line rather than the maternal line (44.1% versus 32.7%); the remaining 27.1% were exclusively up- or down-regulated between the hybrid and either parent. Interestingly, up-regulated genes encoded various enzymes, whereas down-regulated genes were enriched in responses to stress, indicating that hybrids may benefit from both activating metabolism-related pathways and alleviating fitness cost through allelic interactions. Furthermore, a significantly larger proportion of divergent genes and higher nonsynonymous substitutions rates were detected in these DEGs, suggesting a potential contribution to the establishment of heterosis in superhybrid rice LYP9.
authors.affiliation: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China (L.G., M.J., X.Z., D.T., S.Y.); Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850 (Y.W.); and National Engineering Laboratory of Crop Stress Resistance breeding, Anhui Agricultural University, Hefei 230036, China (L.G., W.S.).
authors.forename: Longjiang
authors.initials: L
authors.lastname: Gu
authors.affiliation: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China (L.G., M.J., X.Z., D.T., S.Y.); Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850 (Y.W.); and National Engineering Laboratory of Crop Stress Resistance breeding, Anhui Agricultural University, Hefei 230036, China (L.G., W.S.).
authors.forename: Ying
authors.initials: Y
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China (L.G., M.J., X.Z., D.T., S.Y.); Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850 (Y.W.); and National Engineering Laboratory of Crop Stress Resistance breeding, Anhui Agricultural University, Hefei 230036, China (L.G., W.S.).
authors.forename: Mengmeng
authors.initials: M
authors.lastname: Jiang
authors.affiliation: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China (L.G., M.J., X.Z., D.T., S.Y.); Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850 (Y.W.); and National Engineering Laboratory of Crop Stress Resistance breeding, Anhui Agricultural University, Hefei 230036, China (L.G., W.S.).
authors.forename: Weina
authors.initials: W
authors.lastname: Si
authors.affiliation: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China (L.G., M.J., X.Z., D.T., S.Y.); Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850 (Y.W.); and National Engineering Laboratory of Crop Stress Resistance breeding, Anhui Agricultural University, Hefei 230036, China (L.G., W.S.).
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China (L.G., M.J., X.Z., D.T., S.Y.); Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850 (Y.W.); and National Engineering Laboratory of Crop Stress Resistance breeding, Anhui Agricultural University, Hefei 230036, China (L.G., W.S.) dtian@nju.edu.cn sihaiyang@nju.edu.cn.
authors.forename: Dacheng
authors.identifier: 0000-0002-2327-0578
authors.initials: D
authors.lastname: Tian
authors.affiliation: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China (L.G., M.J., X.Z., D.T., S.Y.); Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850 (Y.W.); and National Engineering Laboratory of Crop Stress Resistance breeding, Anhui Agricultural University, Hefei 230036, China (L.G., W.S.) dtian@nju.edu.cn sihaiyang@nju.edu.cn.
authors.forename: Sihai
authors.identifier: 0000-0002-7862-6412
authors.initials: S
authors.lastname: Yang
mesh_terms: D000538:Aluminum Silicates / Q000737:chemistry; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D005308:Fertilizers; D020869:Gene Expression Profiling / Q000379:methods / Q000706:statistics & numerical data; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics; D006823:Hybrid Vigor / Q000235:genetics*; D006824:Hybridization, Genetic; D012275:Oryza / Q000235:genetics* / Q000254:growth & development; D018547:Plant Stems / Q000235:genetics / Q000254:growth & development; D040641:Quantitative Trait Loci / Q000235:genetics; D036226:Seedlings / Q000235:genetics / Q000254:growth & development; D012987:Soil / Q000737:chemistry; D013997:Time Factors
chemical_list: D000538:Aluminum Silicates; D005308:Fertilizers; D012987:Soil; C003760:vermiculite