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Abstract Heterosis, recognized for improving crop performance, especially in the first filial (F1) generation, remains an area of significant study in the tobacco industry. The low utilization of leaf veins in tobacco contributes to economic inefficiency and resource waste. Despite the positive impacts of heterosis on crop genetics, investigations into leaf-vein ratio heterosis in tobacco have been lacking. Understanding the mechanisms underlying negative heterosis in leaf vein ratio at the molecular level is crucial for advancing low vein ratio leaf breeding research. This study involved 12 hybrid combinations and their parental lines to explore heterosis associated with leaf vein ratios. The hybrids displayed diverse patterns of positive or negative leaf vein ratio heterosis across different developmental stages. Notably, the F1 hybrid (G70 × Qinggeng) consistently exhibited substantial negative heterosis, reaching a maximum of -19.79% 80 days after transplanting. A comparative transcriptome analysis revealed that a significant proportion of differentially expressed genes (DEGs), approximately 39.04% and 23.73%, exhibited dominant and over-dominant expression patterns, respectively. These findings highlight the critical role of non-additive gene expression, particularly the dominance pattern, in governing leaf vein ratio heterosis. The non-additive genes, largely associated with various GO terms such as response to abiotic stimuli, galactose metabolic process, plant-type cell wall organization, auxin-activated signaling pathway, hydrolase activity, and UDP-glycosyltransferase activity, were identified. Furthermore, KEGG enrichment analysis unveiled their involvement in phenylpropanoid biosynthesis, galactose metabolism, plant hormone signal transduction, glutathione metabolism, MAPK signaling pathway, starch, and sucrose metabolism. Among the non-additive genes, we identified some genes related to leaf development, leaf size, leaf senescence, and cell wall extensibility that showed significantly lower expression in F1 than in its parents. These results indicate that the non-additive expression of genes plays a key role in the heterosis of the leaf vein ratio in tobacco. This study marks the first exploration into the molecular mechanisms governing leaf vein ratio heterosis at the transcriptome level. These findings significantly contribute to understanding leaf vein ratios in tobacco breeding strategies.

Heterosis, recognized for improving crop performance, especially in the first filial (F1) generation, remains an area of significant study in the tobacco industry. The low utilization of leaf veins in tobacco contributes to economic inefficiency and resource waste. Despite the positive impacts of heterosis on crop genetics, investigations into leaf-vein ratio heterosis in tobacco have been lacking. Understanding the mechanisms underlying negative heterosis in leaf vein ratio at the molecular level is crucial for advancing low vein ratio leaf breeding research. This study involved 12 hybrid combinations and their parental lines to explore heterosis associated with leaf vein ratios. The hybrids displayed diverse patterns of positive or negative leaf vein ratio heterosis across different developmental stages. Notably, the F1 hybrid (G70 × Qinggeng) consistently exhibited substantial negative heterosis, reaching a maximum of -19.79% 80 days after transplanting. A comparative transcriptome analysis revealed that a significant proportion of differentially expressed genes (DEGs), approximately 39.04% and 23.73%, exhibited dominant and over-dominant expression patterns, respectively. These findings highlight the critical role of non-additive gene expression, particularly the dominance pattern, in governing leaf vein ratio heterosis. The non-additive genes, largely associated with various GO terms such as response to abiotic stimuli, galactose metabolic process, plant-type cell wall organization, auxin-activated signaling pathway, hydrolase activity, and UDP-glycosyltransferase activity, were identified. Furthermore, KEGG enrichment analysis unveiled their involvement in phenylpropanoid biosynthesis, galactose metabolism, plant hormone signal transduction, glutathione metabolism, MAPK signaling pathway, starch, and sucrose metabolism. Among the non-additive genes, we identified some genes related to leaf development, leaf size, leaf senescence, and cell wall extensibility that showed significantly lower expression in F1 than in its parents. These results indicate that the non-additive expression of genes plays a key role in the heterosis of the leaf vein ratio in tobacco. This study marks the first exploration into the molecular mechanisms governing leaf vein ratio heterosis at the transcriptome level. These findings significantly contribute to understanding leaf vein ratios in tobacco breeding strategies. [ABSTRACT FROM AUTHOR]

Simple Summary: Mitogen-activated protein kinases (MAPKs) are serine/threonine kinases that play a crucial role in regulating multiple processes, including protein degradation and localization, mRNA stability, endocytosis, apoptosis, cytoskeleton dynamics, and cell migration. To investigate the regulation of MAPKs' gene expression variation in hybrid tilapia (Oreochromis niloticus ♀ × O. aureus ♂), we focused on p38 mapk. Our study uncovered a compensatory interaction between cis- and trans-acting elements of the Nile tilapia and blue tilapia sub-genomes, resulting in a nonadditive expression pattern of p38 in hybrid tilapia. In addition, we identified eight specific single-nucleotide polymorphisms (SNPs) in transcription factor binding sites between Nile tilapia and blue tilapia and demonstrated that it is promoter differences that differentiate parental gene expression using a dual-luciferase reporting system. Overall, this study reveals the non-additive expression patterns of functionally important genes in hybrid fish, particularly in growth and immune responses. Hybridization is a widely used breeding technique in fish species that enhances desirable traits in cultured species through heterosis. However, the mechanism by which hybrids alter gene expression to form heterosis remains unclear. In this study, a group of hybrid tilapia was used to elucidate heterosis through interspecies crossing. Specifically, p38 was analyzed to describe the regulation of gene expression variation in hybrid tilapia. Transcripts from the Nile tilapia allele were found to be significantly higher than those from the blue tilapia allele in hybrid individuals, indicating that the expression of p38 was dominated by Nile tilapia sub-genomic alleles. The study also found a compensatory interaction of cis- and trans-acting elements of the Nile tilapia and blue tilapia sub-genomes, inducing a non-additive expression of p38 in hybrids. Eight specific SNPs were identified in the p38 promoter regions of Nile tilapia and blue tilapia, and were found to be promoter differences leading to differences in gene expression efficiencies between parental alleles using a dual-luciferase reporter system. This study provides insights into the non-additive expression patterns of key functional genes in fish hybrids related to growth and immunity response. [ABSTRACT FROM AUTHOR]

Heterosis is a complex biological phenomenon regulated by genetic variations and epigenetic changes. However, the roles of small RNAs (sRNAs), an important epigenetic regulatory element, on plant heterosis are still poorly understood. Here, an integrative analysis was performed with sequencing data from multi-omics layers of maize hybrids and their two homologous parental lines to explore the potential underlying mechanisms of sRNAs in plant height (PH) heterosis. sRNAome analysis revealed that 59 (18.61%) microRNAs (miRNAs) and 64,534 (54.00%) 24-nt small interfering RNAs (siRNAs) clusters were non-additively expressed in hybrids. Transcriptome profiles showed that these non-additively expressed miRNAs regulated PH heterosis through activating genes involved in vegetative growth-related pathways while suppressing those related to reproductive and stress response pathways. DNA methylome profiles showed that non-additive methylation events were more likely to be induced by non-additively expressed siRNA clusters. Genes associated with low-parental expression (LPE) siRNAs and trans-chromosomal demethylation (TCdM) events were enriched in developmental processes as well as nutrients and energy metabolism, whereas genes associated with high-parental expression (HPE) siRNAs and trans-chromosomal methylation (TCM) events were gathered in stress response and organelle organization pathways. Our results provide insights into the expression and regulation patterns of sRNAs in hybrids and help to elucidate their potential targeting pathways contributing to PH heterosis. [ABSTRACT FROM AUTHOR]

Field pea (Pisum sativum L.) is a highly nutritious winter-season pulse crop. It is used as food, feed, and fodder and offers nutritional security to low-income people in developing countries. Different graphical approaches like Principal Component Analysis (PCA) and Genotype + Genotype × Environment (GGE) biplots were used along with the conventional line × tester to identify efficient parents, combining ability effects and distinct heterotic groups in field pea (Pisum sativum L.). The study used a line tester design (9 × 3) for seed yield and its associated traits. In the conventional analysis, lines Aman and HFP 715 and the tester GP02/1108, as well as crosses HFP 715 × GP02/1108, Aman × GP02/1108, and Pant P-243 × HFP 1426 showed the best GCA (General Combining Ability) and SCA (Specific Combining Ability) effects, respectively, for seed yield and its attributes. The σ2SCA > σ2GCA, and σ2D > σ2A in almost all the traits indicated control of non-additive gene effects. High manifestations of heterobeltiosis for seed yield were evidenced by the superiority of 24 out of 27 crosses over the better parent. The highest significant heterobeltiosis was observed in the cross HFP 715 × GP02/1108, followed by IPF 14-16 × GP02/1108, IPF 14-16 × HFP 1426, DDR-23 × HFP 1426, DDR-23 × GP02/1108, and Aman × GP02/1108 for yield and its attributes. The biplot techniques were used to analyze data and compare their results with conventional line × tester analysis. Overall, graphical analysis results were very similar to those of traditional analysis. Consequently, it can surely be assumed that these methods could be helpful in presenting data from field pea breeding experiments carried out with line × tester design. [ABSTRACT FROM AUTHOR]

The objective of the present study was to quantify the association between both pedigree and genome-based measures of global heterozygosity and carcass traits, and to identify single nucleotide polymorphisms (SNPs) exhibiting non-additive associations with these traits. The carcass traits of interest were carcass weight (CW), carcass conformation (CC) and carcass fat (CF). To define the genome-based measures of heterozygosity, and to quantify the non-additive associations between SNPs and the carcass traits, imputed, high-density genotype data, comprising of 619,158 SNPs, from 27,213 cattle were used. The correlations between the pedigree-based heterosis coefficient and the three defined genomic measures of heterozygosity ranged from 0.18 to 0.76. The associations between the different measures of heterozygosity and the carcass traits were biologically small, with positive associations for CW and CC, and negative associations for CF. Furthermore, even after accounting for the pedigree-based heterosis coefficient of an animal, part of the remaining variability in some of the carcass traits could be captured by a genomic heterozygosity measure. This signifies that the inclusion of both a heterosis coefficient based on pedigree information and a genome-based measure of heterozygosity could be beneficial to limiting bias in predicting additive genetic merit. Finally, one SNP located on Bos taurus (BTA) chromosome number 5 demonstrated a non-additive association with CW. Furthermore, 182 SNPs (180 SNPs on BTA 2 and two SNPs on BTA 21) demonstrated a non-additive association with CC, while 231 SNPs located on BTA 2, 5, 11, 13, 14, 18, 19 and 21 demonstrated a non-additive association with CF. Results demonstrate that heterozygosity both at a global level and at the level of individual loci contribute little to the variability in carcass merit. [ABSTRACT FROM AUTHOR]

The objective of the present study was to quantify the association between both pedigree and genome-based measures of global heterozygosity and carcass traits, and to identify single nucleotide polymorphisms (SNPs) exhibiting non-additive associations with these traits. The carcass traits of interest were carcass weight (CW), carcass conformation (CC) and carcass fat (CF). To define the genome-based measures of heterozygosity, and to quantify the non-additive associations between SNPs and the carcass traits, imputed, high-density genotype data, comprising of 619,158 SNPs, from 27,213 cattle were used. The correlations between the pedigree-based heterosis coefficient and the three defined genomic measures of heterozygosity ranged from 0.18 to 0.76. The associations between the different measures of heterozygosity and the carcass traits were biologically small, with positive associations for CW and CC, and negative associations for CF. Furthermore, even after accounting for the pedigree-based heterosis coefficient of an animal, part of the remaining variability in some of the carcass traits could be captured by a genomic heterozygosity measure. This signifies that the inclusion of both a heterosis coefficient based on pedigree information and a genome-based measure of heterozygosity could be beneficial to limiting bias in predicting additive genetic merit. Finally, one SNP located on Bos taurus (BTA) chromosome number 5 demonstrated a non-additive association with CW. Furthermore, 182 SNPs (180 SNPs on BTA 2 and two SNPs on BTA 21) demonstrated a non-additive association with CC, while 231 SNPs located on BTA 2, 5, 11, 13, 14, 18, 19 and 21 demonstrated a non-additive association with CF. Results demonstrate that heterozygosity both at a global level and at the level of individual loci contribute little to the variability in carcass merit.

Six parental genotypes and their fifteen F1 hybrids in a diallel cross system, without reciprocals, were used in the present study to estimate heterosis percentage relative to both mid and better parents, potence ratios and combining ability (general and specific) for some characters in pepper (Capsicum annum, L.). The experiment was conducted at the Experimental Station Farm of Fac. Agric. Minufiya Univ., Shebin El Kom, Egypt, during two successive summer seasons of 2012 and 2013. The obtained results reflected generally that the mean squares for general (GCA) and specific (SCA) combining abilities were highly significant for all the studied traits, suggesting the presence of both additive and non-additive gene effects in the inheritance of the various studied characters. However, the high ratio of GCA: SCA mean squares showed that GCA effect was more important than SCA effect. The preponderance of GCA effects implied that these characters would respond favorably to direct selection. Estimates of GCA effects showed that the best combiner parents werer found to be those of P3 and P1 for early fruits number, P6 and P1 for early fruits weight, P3 and P2 for total yield as fruits number and weight, P1 for fruit diameter, P4 and P6 for fruit length, P6 and P1 for average fruit weight. For pericarp thickness and vitamin C content, the parental genotype P1 was the best combiner, while P2 for TSS content. Estimates of SCA effects showed that the F1 cross 1×6 reflected the highest value in all the studied traits. For heterotic effect, hybrid vigour was detected in many characters; i.e., early fruits yield, total yield, fruit length, vitamin C and total soluble solids contents. These results suggested that hybrid vigour is available for commercial production of sweet pepper hybrid, and that isolation of pure lines from the progenies of heterotic F1's is a possible way to enhance the fruits yield and fruit quality. [ABSTRACT FROM AUTHOR]

• An improve heterosis prediction system including dominance and SCA models have been developed and applied to the prediction of heterosis in cucumber. • Genetic distance (GD) is not suitable for the prediction of heterosis in cucumber. • Compared with the GD model, the predictive abilities of the dominance model and the SCA model were improved by 0.15∼0.74 and 0.15∼0.59, respectively. The heterosis prediction has an essential role in hybrid breeding. The prediction of heterosis is highly dependable upon the selection of an efficient method, however, fewer methods have been used till date which lack or unable to explain several important aspects in heterosis prediction. Thus, in our experiment, we tried to explore a new heterosis prediction system based on genomic prediction, in cucumber breeding. Two models, SNP-BLUP and GBLUP were used for genomic prediction model training. The additive, and dominance components were estimated by SNP-BLUP; General combining ability (GCA), and special combining ability (SCA) components were estimated by GBLUP. We explored the correlation of these four model components, the genetics distances with heterosis. The our results show that both the dominance and SCA have stronger correlations with heterosis (r = 0.36∼0.73). While genetic distance, additive model component, and GCA have relatively weak or no significant correlations with heterosis, which may not be suitable for the prediction of heterosis. Therefore, the GD model, Dominance model, and SCA model based on genetic distance, dominance, and SCA predictors were established, respectively. Compared with the GD model, the predictive abilities of the Dominance model and the SCA model were improved by 0.15∼0.74 and 0.15∼0.59, respectively. In conclusion, we have developed an improved heterosis prediction system, which might offer valuable information for cucumber breeding and also provide a reference for the prediction of heterosis in other horticulture crops. [ABSTRACT FROM AUTHOR]