Genetic Basis Of Heterosis Research Articles

Synergy of gut microbiota and host genome in driving heterosis expression of chickens

Heterosis has been widely utilized in agricultural production. Despite over a century of extensive research, the underlying mechanisms of heterosis remain elusive. Most hypotheses and research have focused on the genetic basis of heterosis. However, the potential role of gut microbiota in heterosis has been largely ignored. Here, we carefully design a crossbreeding experiment with two distinct broiler breeds and conduct 16S rRNA amplicon and transcriptome sequencing to investigate the synergistic role of gut microbiota and host genes in driving heterosis. We find that the breast muscle weight of hybrids exhibits a high heterosis, 6.28% higher than the mid-parent value. A notable difference is observed in the composition and potential function of cecal microbiota between hybrids and their parents. Over 90% of differentially colonized microbiota and differentially expressed genes exhibit nonadditive patterns. Integrative analyses uncover associations between nonadditive genes and nonadditive microbiota, including a connection between the expression of cellular signaling pathways and metabolism-related genes and the abundance of Odoribacter, Oscillibacter, and Alistipes in hybrids. Moreover, higher abundances of these microbiota are related to better meat yield. In summary, these findings highlight the importance of gut microbiota in heterosis, serving as crucial factors that modulate heterosis expression in chickens.

Transcriptome profiling of two super hybrid rice provides insights into the genetic basis of heterosis

BackgroundHeterosis is a phenomenon that hybrids show superior performance over their parents. The successful utilization of heterosis has greatly improved rice productivity, but the molecular basis of heterosis remains largely unclear.ResultsHere, the transcriptomes of young panicles and leaves of the two widely grown two-line super hybrid rice varieties (Jing-Liang-You-Hua-Zhan (JLYHZ) and Long-Liang-You-Hua-Zhan (LLYHZ)) and their parents were analyzed by RNA-seq. Transcriptome profiling of the hybrids revealed 1,778 ~ 9,404 differentially expressed genes (DEGs) in two tissues, which were identified by comparing with their parents. GO, and KEGG enrichment analysis showed that the pathways significantly enriched in both tissues of two hybrids were all related to yield and resistance, like circadian rhythm (GO:0,007,623), response to water deprivation (GO:0,009,414), and photosynthetic genes (osa00196). Allele-specific expression genes (ASEGs) were also identified in hybrids. The ASEGs were most significantly enriched in ionotropic glutamate receptor signaling pathway, which was hypothesized to be potential amino acid sensors in plants. Moreover, the ASEGs were also differentially expressed between parents. The number of variations in ASEGs is higher than expected, especially for large effect variations. The DEGs and ASEGs are the potential reasons for the formation of heterosis in the two elite super hybrid rice.ConclusionsOur results provide a comprehensive understanding of the heterosis of two-line super hybrid rice and facilitate the exploitation of heterosis in hybrid rice breeding with high yield heterosis.

Genetic basis of heterosis in a common wheat cross withstrong-heterosis

<p indent="0mm">Heterosis refers to the phenomenon that a heterozygous hybrid exhibits superior performances over its parents, which has been suggested as a solution to overcome yield stagnation of wheat. However, the molecular basis of wheat heterosis is still poorly understood. We have previously found that a cross derived from the winter common wheat Nongda3338 (ND3338) and Jingdong 6 (JD6) showed strong mid-parent heteroses on plant height (PH) and thousand grain weight (TGW). In this study, we further aimed to investigate the genetic underpinnings of PH and TGW using an “immortalized F₂” (IF₂) derived from the ND3338/JD6 doubled haploid (DH) population. The PH and TGW of DH and IF₂ populations were evaluated across two different environments, and the mid-parent heterosis value (HV) was used to measure heterosis. The direction and magnitude of HV greatly varied between PH and TGW across the environments. A two-way analysis of variance (ANOVA) was performed for PH and TGW in the IF₂ population, revealing that genetic variation was the main source, despite the significant variations found from the environments and genotype by environment interaction. The broad sense heritability of PH and TGW in IF₂ population was 94.05% and 88.14%, respectively. Pearson’s correlation coefficients of PH, TGW, HV_PH and HV_TGW in the IF₂ population were estimated based on the best linear unbiased prediction (BLUP) values of two environments, showing that PH was significantly positively correlated with TGW and HV_TGW, TGW was significantly positively correlated with HV_TGW and negatively correlated with HV_PH, while HV_PH had a strong positive correlation with HV_TGW. The genotypes of the IF₂ population were deduced from corresponding DH parents. Based on the inclusive composite interval mapping method, quantitative trait locus (QTL) mapping was separately conducted with PH, TGW, HV_PH and HV_TGW using the QTL IciMapping software. We identified a total of 32 and 25 QTL that exhibited additive, dominant and overdominant pattern associated with PH and TGW, which accounted for 0.54%–36.05% and 0.87%–25.78% of the variance, respectively. Consistent with the results found in the ND3338/JD6 DH population, major and stable QTL on chromosomes 2D (<italic>QPh</italic>.<italic>2D</italic>.<italic>1</italic> and <italic>QTgw</italic>.<italic>2D</italic>), 4B (<italic>QPh</italic>.<italic>4B</italic>.<italic>1</italic> and <italic>QTgw</italic>.<italic>4B</italic>.<italic>1</italic>) and 4D (<italic>QPh</italic>.<italic>4D </italic>and <italic>QTgw</italic>.<italic>4D</italic>) that were coincident with the dwarfing genes <italic>Rht1</italic>, <italic>Rht2</italic> and <italic>Rht8</italic> were detected, suggesting that the IF₂ population design is feasible and reliable for identifying the genetic components of heterosis. Furthermore, 13 QTL for HV_PH and 15 QTL for HV_TGW were identified, of which most of these loci exhibited overdominant pattern. However, only few of the QTL controlling PH and TGW were overlapped with those controlling HV_PH and HV_TGW, suggesting potentially different genetic mechanisms between phenotypic traits and heterosis. In addition, epistasis analysis for PH and TGW revealed that four types of digenic interactions, including additive by additive (AA), additive by dominance (AD), dominance by additive (DA) and dominance by dominance (DD), were involved in the genetic basis of hybrid performance and heterosis in the IF₂ population. Notably, the DD-oriented QTL with the greatest interactive effects possessed the highest frequency. Overall, this study provides strong evidence for supporting the classical genetic hypotheses of heterosis (dominance, overdominance, and epistasis) with an IF₂ population, establishing the foundation to develop and select crosses with strong heterosis.

Screening of Grain Development Heterosis Candidate Genes by Integrating QTL Mapping and RNA-Seq in Super Hybrid Rice WFYT025

The application of heterosis during plant breeding increases rice grain yield. However, there have been limited studies on heterosis during rice grain development during the grain-filling stage; therefore, the genetic basis of heterosis for grain development during the grain-filling stage should be highly valued. In this study, a hybrid combination with the super hybrid rice WFYT025 was used to perform a transcriptomic dynamic analysis in grains at the beginning and middle grain-filling stages. A total of 1556 and 1507 transcripts that were differentially expressed between WFYT025 and its parents (DGHP) were identified at 1-day post-anthesis (DPA) and at 10 DPA, respectively. The analysis of the genetic effects of heterosis showed that the over-dominant effect (66.90% and 55.87%) was the main mode of action during grain development. The KEGG pathway and GO analysis of the DGHP indicated that the gibberellin biosynthetic, starch metabolic, and diterpenoid biosynthetic signaling pathways may be associated with heterosis during grain development. To further explore the candidate genes for grain development heterosis, a recombinant inbred line (RILs) population with a high-density genetic map of 2578 bin markers was constructed by crossing the parents of WFYT025, and nine stable QTLs for grain weight-related traits were identified. By comparing the DGHP with 20 QTLs, LOC_Os02g28820, LOC_Os02g32580, LOC_Os04g25440, and LOC_Os12g04980 were identified as grain development heterosis-related candidate genes. These findings provide resources for the study of heterosis during the grain development of super hybrid rice and provide valuable theoretical references for the cloning and functional analysis of heterosis-related genes.

Identification of Heterotic Loci with Desirable Allelic Interaction to Increase Yield in Rice

Heterosis denotes the superiority of a hybrid plant over its parents. The use of heterosis has contributed significantly to yield improvement in crops. However, the genetic and molecular bases on heterosis are not fully understood. A large number of heterotic loci were identified for 12 yield-related traits in one parental population of chromosome segment substitution lines (CSSLs) and two test populations, which were interconnected by CSSLs derived from two rice genome-sequenced cultivars, Nipponbare and Zhenshan 97. Seventy-five heterotic loci were identified in both homozygous background of Zhenshan 97 and heterogeneous background of an elite hybrid cultivar Shanyou 63. Among the detected loci, at least 11 were colocalized in the same regions encompassing previously reported heterosis-associated genes. Furthermore, a heterotic locus Ghd8NIP for yield advantage was verified using transgenic experiments. Various allelic interaction at Ghd8 exhibited different heterosis levels in hetero-allelic combinations of five near-isogenic lines that contain a particular allele. The significant overdominance effects from some hetero-allelic combinations were found to improve yield heterosis in hybrid cultivars. Our findings support the role of allelic interaction at heterotic loci in the improvement of yield potential, which will be helpful for dissecting the genetic basis of heterosis and provide an optional strategy for the allele replacement in molecular breeding programs in hybrid rice.

Genetic dissection of heterosis of indica\u2013japonica by introgression line, recombinant inbred line and their testcross populations

The successful implementation of heterosis in rice has significantly enhanced rice productivity, but the genetic basis of heterosis in rice remains unclear. To understand the genetic basis of heterosis in rice, main-effect and epistatic quantitative trait loci (QTLs) associated with heterosis for grain yield-related traits in the four related rice mapping populations derived from Xiushui09 (XS09) (japonica) and IR2061 (indica), were dissected using single nucleotide polymorphism bin maps and replicated phenotyping experiments under two locations. Most mid-parent heterosis of testcross F1s (TCF1s) of XS09 background introgression lines (XSILs) with Peiai64S were significantly higher than those of TCF1s of recombinant inbred lines (RILs) with PA64S at two locations, suggesting that the effects of heterosis was influenced by the proportion of introgression of IR2061’s genome into XS09 background. A total of 81 main-effect QTLs (M-QTLs) and 41 epistatic QTLs were identified for the phenotypic variations of four traits of RILs and XSILs, TCF1s and absolute mid-parent heterosis in two locations. Furthermore, overdominance and underdominance were detected to play predominant effects on most traits in this study, suggesting overdominance and underdominance as well as epistasis are the main genetic bases of heterosis in rice. Some M-QTLs exhibiting positive overdominance effects such as qPN1.2, qPN1.5 and qPN4.3 for increased panicle number per plant, qGYP9 and qGYP12.1 for increased grain yield per plant, and qTGW3.4 and qTGW8.2 for enhanced 1000-grain weight would be highly valuable for breeding to enhance grain yield of hybrid rice by marker-assisted selection.

Breeding cherry tomato grown under open field conditions for simultaneous improvement in yield, nutritional quality, and leaf curl virus disease tolerance

ABSTRACTCherry tomato [Solanum lycopersicum var. cerasiforme (Dunnal) A. Gray] has the potential for improvement through heterosis breeding, which can be further utilized for the development of desirable recombinants. However, genetic control of yield, fruit quality, and disease severity traits are not well known. Six phenotypically diverse parents were crossed in half-diallel mating design to determine the extent of heterobeltiosis, mode of gene action, combining ability effects, and dominance effects for 18 quantitative traits to produce information that could lead to the development of improved genotypes. The predictability ratio indicated an overwhelming response of non-additive gene action in controlling the expression of most traits studied. Based on general combining ability effects, and average performance, genitors ‘16/TOCVAR-1ʹ and ‘16/TOCVAR-3ʹ could be potential donor parents in breeding. Based on average performance, heterosis manifested, and specific combining ability effects, crosses ‘16/TOCVAR-1 × 16/TOCVAR-3ʹ and ‘16/TOCVAR-1 × 16/TOCVAR-4ʹ were best in respect to yield, nutritional quality, and level of field tolerance against leaf curl virus disease under tropical and sub-tropical conditions. Partial- to over-dominance reactions for the inheritance of fruit yield, and other economically important traits, reflect the genetic basis of heterosis. Commercially exploitable cherry tomato hybrids with high antioxidant activity, tolerance to leaf curl virus disease, could be developed with the involvement of a single parent tolerant to this disease.

Genetic control of economic traits and evidence of economic heterosis in crosses involving monoecious cucumber genotypes

ABSTRACT A cucumber (Cucumis sativus L.) hybrid could be acceptable to growers of tropical and subtropical climates if it is a high yielder with good fruit quality, and has tolerance against downy mildew disease. Six phenotypically diverse parents were crossed in half-diallel mating design to determine the extent of heterobeltiosis and standard heterosis, mode of gene action, combining ability effects, and dominance effects for 15 quantitative characters to produce information that could lead to development of improved genotypes. The predictability ratio indicated response of non-additive gene action in controlling expression of most traits under study. Two genitors ‘Debstar’ and ‘Pusa Barkha’ could be potential donors in breeding. The crosses ‘Debstar × Pusa Barkha’ and ‘Pusa Barkha × Samrat 7 Star’ were identified as having promise based on average values, heterobeltiosis and standard heterosis manifested, and relevance of specific combining ability effects, for possible commercialization in cucumber growing zones of tropical and subtropical climates after critical testing. Isolation of pure lines from the segregating generation of heterotic F1s is an alternative approach to improve fruit yield, fruit quality, and downy mildew disease tolerance. Partial- to overdominance response in inheritance of most traits contributes to the genetic basis of heterosis. A commercially useful downy mildew tolerant hybrid with involvement of a single genotype tolerant to this disease might be able to be developed.

Overdominance is the major genetic basis of lint yield heterosis in interspecific hybrids between G. hirsutum and G. barbadense.

The genetic basis of heterosis has not been resolved for approximately a century, although the role of loci with overdominant (ODO) effects has continued to be discussed by biologists. In the present investigation, a proposed model was studied in Gossypium hirsutum L. introgression lines (ILs) harbouring a segment of G. barbadense. These introgressions were confirmed by a single marker of G. barbadense. These ILs contained 396 quantitative trait loci (QTLs) for 11 yield and non-yield traits that were recorded in the field on homozygous and heterozygous plants for 5 years. After comparing the different types of QTLs between the yield group and the non-yield group, it was found that the yield group had significantly higher ODO QTL ratios. Moreover, 16 ODO QTLs identified for 5 yield-related traits were consistently detected during 5 cotton growing seasons (2010-2011 and 2013-2015): 6 of 7 for boll weight, 3 of 11 for seed-cotton yield per plant, 4 of 17 for boll number, 2 of 13 for lint yield per plant and 1 of 11 for lint percentage. Therefore, we propose that overdominance is the major genetic basis of lint yield heterosis in interspecific hybrids between G. barbadense and G. hirsutum. These findings have important implications in cotton breeding in that the boll weight can be improved by utilizing ODO QTLs via heterosis; thus, the stagnant yield barrier can be smashed to achieve sustainable increases in cotton production. Additionally, this concept can be translated to other field crops for improving their yield potential.

Patterns of genome-wide allele-specific expression in hybrid rice and the implications on the genetic basis of heterosis

Utilization of heterosis has greatly increased the productivity of many crops worldwide. Although tremendous progress has been made in characterizing the genetic basis of heterosis using genomic technologies, molecular mechanisms underlying the genetic components are much less understood. Allele-specific expression (ASE), or imbalance between the expression levels of two parental alleles in the hybrid, has been suggested as a mechanism of heterosis. Here, we performed a genome-wide analysis of ASE by comparing the read ratios of the parental alleles in RNA-sequencing data of an elite rice hybrid and its parents using three tissues from plants grown under four conditions. The analysis identified a total of 3,270 genes showing ASE (ASEGs) in various ways, which can be classified into two patterns: consistent ASEGs such that the ASE was biased toward one parental allele in all tissues/conditions, and inconsistent ASEGs such that ASE was found in some but not all tissues/conditions, including direction-shifting ASEGs in which the ASE was biased toward one parental allele in some tissues/conditions while toward the other parental allele in other tissues/conditions. The results suggested that these patterns may have distinct implications in the genetic basis of heterosis: The consistent ASEGs may cause partial to full dominance effects on the traits that they regulate, and direction-shifting ASEGs may cause overdominance. We also showed that ASEGs were significantly enriched in genomic regions that were differentially selected during rice breeding. These ASEGs provide an index of the genes for future pursuit of the genetic and molecular mechanism of heterosis.

Identification of heterotic loci associated with grain yield and its components using two CSSL test populations in maize.

Heterosis has widely been used to increase grain yield and quality. In this study, the genetic basis of heterosis on grain yield and its main components in maize were examined over 2 years in two locations in two test populations constructed from a set of 184 chromosome segment substitution lines (CSSLs) and two inbred lines (Zheng58 and Xun9058). Of the 169 heterotic loci (HL) associated with grain yield and its five components identified in CSSL × Zheng58 and CSSL × Xun9058 test populations, only 25 HL were detected in both populations. The comparison of quantitative trait loci (QTLs) detected in the CSSL population with HL detected in the two test populations revealed that only 15.46% and 17.35% of the HL in the given populations respectively, shared the same chromosomal regions as that of the corresponding QTLs and showed dominant effects as well as pleiotropism with additive and dominant effects. In addition, most of the HL (74.23% and 74.49%) had overdominant effects. These results suggest that overdominance is the main contributor to the effects of heterosis on grain yield and its components in maize, and different HL are associated with heterosis for different traits in different hybrids.

Genetic analysis of Upland cotton dynamic heterosis for boll number per plant at multiple developmental stages.

Yield is an important breeding target. As important yield components, boll number per plant (BNP) shows dynamic character and strong heterosis in Upland cotton. However, the genetic basis underlying the dynamic heterosis is poorly understood. In this study, we conducted dynamic quantitative trait loci (QTL) analysis for BNP and heterosis at multiple developmental stages and environments using two recombinant inbred lines (RILs) and two corresponding backcross populations. By the single-locus analysis, 23 QTLs were identified at final maturity, while 99 QTLs were identified across other three developmental stages. A total of 48 conditional QTLs for BNP were identified for the adjacent stages. QTLs detected at later stage mainly existed in the partial dominance to dominance range and QTLs identified at early stage mostly showed effects with the dominance to overdominance range during plant development. By two-locus analysis, we observe that epistasis played an important role not only in the variation of the performance of the RIL population but also in the expression of heterosis in backcross population. Taken together, the present study reveals that the genetic basis of heterosis is dynamic and complicated, and it is involved in dynamic dominance effect, epistasis and QTL by environmental interactions.

Formation of diploid and triploid hybrid groupers (hybridization of Epinephelus coioides ♀ × Epinephelus lanceolatus ♂) and their 5S gene analysis.

BackgroundInterspecies hybridization is widely used to achieve heterosis or hybrid vigor, which has been observed and harnessed by breeders for centuries. Natural allopolyploid hybrids generally exhibit more superior heterosis than both the diploid progenies and their parental species. However, polyploid formation processes have been long ignored, the genetic basis of heterosis in polyploids remains elusive.ResultsIn the present study, triploid hybrids had been demonstrated to contain two sets of chromosomes from mother species and one set from father species. Cellular polyploidization process in the embryos had been traced. The triploid hybrids might be formed by failure formation of the second polarized genome during the second meiosis stage. Four spindle centers were observed in anaphase stage of the first cell division. Three spindle centers were observed in side of cell plate after the first cell division.The 5S rDNA genes of four types of groupers were cloned and analyzed. The diploid and triploid hybrids had been proved to contain the tandem chimera structures which were recombined by maternal and paternal monomer units. The results indicated that genome re-fusion had occurred in the hybrid progenies.To further elucidate the genetic patterns of diploid and triploid hybrids, fluorescence chromosome location had been carried out, maternal 5S gene (M-386) were used as the probe. The triploid hybrids contained fewer fluorescence loci numbers than the maternal species. The results indicated that participation of paternal 5S gene in the triploid hybrid genome had degraded the match rates of M-386 probe.ConclusionsOur study is the first to investigate the cellular formation processes of natural allopolyploids in hybrid fish, the cellular polyploidization process may be caused by failure formation of the second polarized genome during the meiosis, and our results will provide the molecular basis of hybrid vigor in interspecies hybridization.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0443-9) contains supplementary material, which is available to authorized users.

Genomic prediction of crossbred performance based on purebred Landrace and Yorkshire data using a dominance model.

BackgroundIn pig breeding, selection is usually carried out in purebred populations, although the final goal is to improve crossbred performance. Genomic selection can be used to select purebred parental lines for crossbred performance. Dominance is the likely genetic basis of heterosis and explicitly including dominance in the genomic selection model may be an advantage when selecting purebreds for crossbred performance. Our objectives were two-fold: (1) to compare the predictive ability of genomic prediction models with additive or additive plus dominance effects, when the validation criterion is crossbred performance; and (2) to compare the use of two pure line reference populations to a single combined reference population.MethodsWe used data on litter size in the first parity from two pure pig lines (Landrace and Yorkshire) and their reciprocal crosses. Training was performed (1) separately on pure Landrace (2085) and Yorkshire (2145) sows and (2) the two combined pure lines (4230), which were genotyped for 38 k single nucleotide polymorphisms (SNPs). Prediction accuracy was measured as the correlation between genomic estimated breeding values (GEBV) of pure line boars and mean corrected crossbred-progeny performance, divided by the average accuracy of mean-progeny performance. We evaluated a model with additive effects only (MA) and a model with both additive and dominance effects (MAD). Two types of GEBV were computed: GEBV for purebred performance (GEBV) based on either the MA or MAD models, and GEBV for crossbred performance (GEBV-C) based on the MAD. GEBV-C were calculated based on SNP allele frequencies of genotyped animals in the opposite line.ResultsCompared to MA, MAD improved prediction accuracy for both lines. For MAD, GEBV-C improved prediction accuracy compared to GEBV. For Landrace (Yorkshire) boars, prediction accuracies were equal to 0.11 (0.32) for GEBV based on MA, and 0.13 (0.34) and 0.14 (0.36) for GEBV and GEBV-C based on MAD, respectively. Combining animals from both lines into a single reference population yielded higher accuracies than training on each pure line separately. In conclusion, the use of a dominance model increased the accuracy of genomic predictions of crossbred performance based on purebred data.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-016-0220-2) contains supplementary material, which is available to authorized users.

Identification of Heterotic Loci for Yield and Ear Traits Using CSSL Test Population in Maize

Heterosis plays an important role in enhancing crop yield and quality. Dissecting the genetic basis of heterosis can promote hybrid maize selection, however it is unclear up to now. In this study, a set of chromosome segment substitution lines (CSSLs) population, which was constructed using the inbred line lx9801 as the receptor parent and the inbred line Chang 7-2 as the donor parent, was crossed with the inbred line T7296 to construct the corresponding test population. The test population was used to identify the heterotic loci (HL) for grain yield and ear traits in maize, which showed significant difference in heterosis between the corresponding chromosomal region of the inbred line Chang 7-2 and lx9801 as well as the test inbred line T7296. A total of 64 HL were identified for gain yield and ear traits, and among them 23 HL were identified at the two environments simul- taneously, including 4 HL for ear length, 4 HL for ear width, 4 HL for row number, 7 HL for kernels per row, and 4 HL for grain yield. Additionally, the HL for both grain yield and its components simultaneously were found on many chromosomal regions. This study could offer a basic material for thoroughly dissecting the genetic basis of heterosis for grain yield and its components in maize.

Maximizing crossbred performance through purebred genomic selection.

BackgroundIn livestock production, many animals are crossbred, with two distinct advantages: heterosis and breed complementarity. Genomic selection (GS) can be used to select purebred parental lines for crossbred performance (CP). Dominance being the likely genetic basis of heterosis, explicitly including dominance in the GS model may be an advantage to select purebreds for CP. Estimated breeding values for CP can be calculated from additive and dominance effects of alleles that are estimated using pure line data. The objective of this simulation study was to investigate the benefits of applying GS to select purebred animals for CP, based on purebred phenotypic and genotypic information. A second objective was to compare the use of two separate pure line reference populations to that of a single reference population that combines both pure lines. These objectives were investigated under two conditions, i.e. either a low or a high correlation of linkage disequilibrium (LD) phase between the pure lines.ResultsThe results demonstrate that the gain in CP was higher when parental lines were selected for CP, rather than purebred performance, both with a low and a high correlation of LD phase. For a low correlation of LD phase between the pure lines, the use of two separate reference populations yielded a higher gain in CP than use of a single reference population that combines both pure lines. However, for a high correlation of LD phase, marker effects that were estimated using a single combined reference population increased the gain in CP.ConclusionsUnder the hypothesis that performance of crossbred animals differs from that of purebred animals due to dominance, a dominance model can be used for GS of purebred individuals for CP, without using crossbred data. Furthermore, if the correlation of LD phase between pure lines is high, accuracy of selection can be increased by combining the two pure lines into a single reference population to estimate marker effects.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-015-0099-3) contains supplementary material, which is available to authorized users.

Genomic selection of purebred animals for crossbred performance in the presence of dominant gene action

BackgroundGenomic selection is an appealing method to select purebreds for crossbred performance. In the case of crossbred records, single nucleotide polymorphism (SNP) effects can be estimated using an additive model or a breed-specific allele model. In most studies, additive gene action is assumed. However, dominance is the likely genetic basis of heterosis. Advantages of incorporating dominance in genomic selection were investigated in a two-way crossbreeding program for a trait with different magnitudes of dominance. Training was carried out only once in the simulation.ResultsWhen the dominance variance and heterosis were large and overdominance was present, a dominance model including both additive and dominance SNP effects gave substantially greater cumulative response to selection than the additive model. Extra response was the result of an increase in heterosis but at a cost of reduced purebred performance. When the dominance variance and heterosis were realistic but with overdominance, the advantage of the dominance model decreased but was still significant. When overdominance was absent, the dominance model was slightly favored over the additive model, but the difference in response between the models increased as the number of quantitative trait loci increased. This reveals the importance of exploiting dominance even in the absence of overdominance. When there was no dominance, response to selection for the dominance model was as high as for the additive model, indicating robustness of the dominance model. The breed-specific allele model was inferior to the dominance model in all cases and to the additive model except when the dominance variance and heterosis were large and with overdominance. However, the advantage of the dominance model over the breed-specific allele model may decrease as differences in linkage disequilibrium between the breeds increase. Retraining is expected to reduce the advantage of the dominance model over the alternatives, because in general, the advantage becomes important only after five or six generations post-training.ConclusionUnder dominance and without retraining, genomic selection based on the dominance model is superior to the additive model and the breed-specific allele model to maximize crossbred performance through purebred selection.

QTL and epistatic analyses of heterosis for seed yield and three yield component traits using molecular markers in rapeseed (Brassica napus L.)

Aiming to explore the basis of heterosis in rapeseed, QTLs for yield and three yield component traits were mapped and the digenic interactions were detected in an F2 population derived from a cross between two elite rapeseed lines, SI-1300 and Eagle, in this study. Twenty-eight QTLs were detected for the four yield traits, with only two of them detected simultaneously in the Wuhan and Jingmen environments. Additive, partial dominance, dominance, and overdominance effects were all identified for the investigated traits. Dominance (including partial dominance) was shown by 55% of the QTLs, which suggests that dominance is a major genetic basis ofheterosis in rapeseed. At the P < or = 0.01 level with 1000 random permutations, 108 and 104 significant digenic interactions were detected in Wuhan and Jingmen, respectively, for the four yield-related traits using all possible locus pairs of molecular markers. Digenic interactions, including additive by additive, additive by dominance, and dominance by dominance, were frequent and widespread in this population. In most cases (78.3%), the interactions occurred among marker loci for which significant effects were not detected by single-locus analysis. Some QTLs (57.1%) detected by single-locus analysis were involved in epistatic interactions. It was concluded that epistasis, along with dominance (including partial dominance), is responsible for the expression of heterosis in rapeseed.

Intra-specific hybridization: Generator of genetic diversification and heterosis in Andrographis paniculata Nees. A bridge from extinction to survival

Andrographis paniculata (AP) has been stated as a low-diverse, endangered and red-listed plant species. Self-pollinated mating system, being an introduced species and experiencing a bottleneck as well as over exploitation cause such a consequence. Inter and intra-specific hybridizations have been suggested as essential techniques for generating genetic diversity. To test the effect of intra-specific hybridization on diversification and heterosis of AP, seven accessions were outcrossed manually in all 21 possible combinations. Three types of markers including morphological, phytochemical and RAPD markers were employed to evaluate the mentioned hypothesis. The results revealed that hybridization acted as a powerful engine for diversification of AP as it caused heterotic expression of the studied traits, simultaneously. Initially, it seems that additive and non-additive gene effects both can be considered as the genetic basis of heterosis in AP for the investigated traits. Agronomic and morphological traits were differentiated from each other, while positive heterosis was recorded mainly for agronomic traits but not for the morphological traits. Intra-specific hybridization increased the genetic diversity in AP population. Nevertheless, a part of this variation could also be attributed to the negative heterosis. The current exploration demonstrated the first ever conducted manual intra-specific hybridization among AP accessions in a mass scale. However, the 17 RAPD primers produced a monomorph pattern, but perhaps increasing the number of markers can feature a new genetic profile in this plant.

Expression analysis of abiotic stress‐responsive genes in two rice heterotic crosses under cold, heat and drought stresses

With 6 figures and 4 tablesAbstractHeterosis refers to the phenomenon in which the hybrid progeny of two inbred varieties exhibits enhanced growth or agronomic performance. Although a century‐long history of research has generated several hypotheses regarding the genetic basis of heterosis, the molecular mechanisms underlying heterosis and heterotic gene activity remain elusive. In this study, two rice heterotic crosses PA64S×93‐11 and Y58S×93‐11 were used as plant materials to analyse the activities of 10 abiotic stress‐responsive genes under cold, heat and drought stresses by quantitative real‐time PCR. The obtained result demonstrated that the expression levels of genes analysed in hybrids is unexpectedly higher, compared to those of both parental lines. More than 50% of the cases displayed over‐parent expression levels. The combined allelic expression pattern was found in hybrid, and under different stress conditions, different alleles were differentially expressed in hybrid.