Transcriptome Analysis of Heterosis in Survival in the Hybrid Progenies of‘Haida No.1’and Orange-Shelled Lines of the Pacific Oyster Crassostrea gigas

Heterosis has been exploited to enhance the yield and adaptability in various shellfish species;however,the molecular basis of it remains unclear.The Pacific oyster Crassostrea gigas is one of the most economically important aquaculture species,and its productive traits can be improved by hybridization.Here,an intraspecific cross between orange shell(O,10th generation)and‘Haida No.1’(H,13th generation)of C.gigas was performed to assess the heterosis of survival trait.Survival rates of hybrid family(OH)and inbred families(HH and OO)were compared at larval stage,and eyed-pediveliger larvae of three families were subjected to transcriptome analysis.The analysis results of best-parent heterosis and mid-parent heterosis showed that the hybrid family exhi-bited a high heterosis in survival relative to the parental families.The OH-M(OH vs.OO)and OH-P(OH vs.HH)had 425 and 512 dif-ferentially expressed genes(DEGs),respectively.Functional enrichment analysis of these DEGs revealed that the significantly enrich-ed genes function in virion binding,C-type lectin receptor signaling pathway,cellular defense response and other immune-related pro-cesses,which involves perlucin-like protein,CD209 antigen-like protein,ZNFX1,caspase-3 and acan genes.These differentially ex-pressed genes in OH-M and OH-P,together with the immune-related processes mentioned above may play an important role in the larval survival of C.gigas.In addition,three genes(CYP450,fucolectin and perlucin-like)are associated with the orange shell and low survival of maternal oyster OO.These findings provide support for the application of hybrid with superior survival and will facilitate the understanding of heterosis formation in the Pacific oyster.

Dissection of two QTL clusters underlying yield-related heterosis in the cabbage founder parent 01–20

Cabbage has significant heterosis and most commercial cultivars are hybrids.To explore genetic basis of cabbage heterosis and promote cabbage heterosis utilization,we constructed two populations by crossing 100 DH lines derived from a cabbage hybrid 01–20×96–100 with two female parents.Hybrids exhibited different extents of heterosis,the mean value of economic yield was 2.6 times bigger than parents.We identified 66 and 73 QTLs associated with mid-parent heterosis and transgressive heterosis of twelve yield-related traits,respectively.Some QTLs could be detected under the two-year experiment existed in two populations with different testers,showing relatively high phenotypic contribution rate(15.8%–20.0%).Heterosis QTLs exhibited clustered distribution in several cabbage chromosome regions.Two dominant genetic regions,mk300–316 and mk258–268,originated from the elite parent 01–20,exhibited significant genetic effects for yield-related heterosis,which were first identified.Three elite DH lines(D22,D46,D83)harboring these two dominant regions were selected as having strong heterosis in cabbage production.Candidate gene analysis revealed that some genes participating in biosynthetic processes of carbohydrates and some responses to auxin might affect cabbage yield heterosis.QTL identification and genetic dissection of yield-related traits provide new insights into the genetic effects of cabbage heterosis.

Comparative DNA-methylome and transcriptome analysis reveals heterosis-and polyploidy-associated epigenetic changes in rice

Heterosis and polyploidy have an overwhelming influence on plant evolution.Recently,polyploid rice hybrids have been used to breed new rice varieties because they combine the advantages of both heterosis and polyploidy.In this study,we generated six rice lines:autotetraploid rice hybrids and their autotetraploid parents,diploid donors,and hybrids of the diploid donors.To investigate the molecular mechanism controlling the effects of both hybridization and polyploidization,we performed bisulfite and RNA sequencing on young panicles at the pollen meiosis stage to compare the DNA metabolomes and transcriptomes among the six rice lines.The hybrids lines were hypermethylated compared to their corresponding parents and the autotetraploid lines showed globally increased DNA methylation of their transposable elements compared to the diploid donors.The alteration in DNA methylation level corresponded to the differential gene expressions among the rice genotypes,suggesting that methylation changes induced by polyploidization and hybridization may affect gene expression.Groups of gene candidates were identified that may be associated with heterosis and polyploidy.Our results provide DNA information that can be used to investigate epigenetic modification during heterosis and polyploidy in rice.

Heterosis of Vine Decline Disease Resistance Caused by the Fungus Monosporascus cannonballus in Melons (Cucumis melo L)

Vine decline disease (VDD) constitutes a menace to melons worldwide. Especially, the one caused by the fungus Monosporascus cannonballus. Thus, resistant plant material must be released to help growers. Hence, our goal was to develop resistant plant material to VDD. More than 600 melon accessions are expected to be tested for disease resistance in M. cannonballus infested soil in Weslaco, Texas, USA, to identify resistance to VDD, and other important traits. So far, at most 7 lines were found to be resistant to VDD and some of them were used to develop elite, muskmelon inbred lines by pedigree breeding following single or double backcrosses. These elite parents were crossed to each other to develop the hybrids M3 and M4. They were also tested in the same infested field in Weslaco. The hybrids were grown using standard commercial practices followed by growers and when their fruits were ready, their roots were sampled as well as scored for disease severity to estimate high and mid-parent heterosis Our results indicate the existence of heterosis regarding resistance to VDD. Thus, resistant plant material can be developed and selection for resistance can be accomplished.

The Relation between Genetic Difference for Parents of Hybrid Rice and Heterosis

Exploring the indica-japonica differentiation in parents of hybridization can provide theoretical bases for utilizing inter-subspecific heterosis. In this study, 5 sterile lines and 18 self-bred restorer lines were used as female parents and male parents respectively. Then 90 combinations were constructed by incomplete diallel cross followed by relationship analysis between parental Cheng’s index difference value and Euclidean distance and heterosis. The results showed a significant correlation between several phenotype values, super male parent heterosis and control heterosis and Euclidean distance or Cheng’s index difference value. However, it was no significant correlation for yield. Further analysis found a common interval, 3.41 - 3.46 for Euclidean distance and 3 - 4 for cheng’s index difference value of parents, which was significant or high significant positive correlated with phenotype value, super male parent and control heterosis of main yield traits. This illustrates that the larger the genetic difference of parents was, the stronger the heterosis combinations were, when the genetic differences of parents were in an appropriate range.

Determination of Heterotic Groups and Heterosis Analysis of Yield Performance in indica Rice

To compare the heterosis levels among various groups of parental lines used extensively in China, identify foundational heterotic groups in parental pools and understand the relationship between genetic distance and heterosis performance, 16 parental lines with extensive genetic variation were selected from various sub-groups, and 39 hybrid combinations were generated and evaluated in Fujian and Hainan Provinces of China. The main results were as follows： （1） The 16 parental lines can be grouped into 7 sub-groups consisting of 1 maintainer sub-group and 6 restorer sub-groups; （2） Mean grain yield of the restorer lines was higher than that of the maintainer lines, and mean yield of parental lines was higher than that of the hybrid combinations; （3） The two best heterotic patterns were II-32A × G5 and II-32A × G6, moreover, the order of restorer sub-groups according to grain yield, from the highest to lowest, was G7, G6, G5, G4, G3 and G2; High specific combining ability values were observed for combinations of II-32A × G5, II-32A × G6 and Tianfeng A × G7; （4） Hybrid combinations derived from II-32A crossed with 13 restorer lines had higher yield trait values （mid-parent heterosis, better-parent heterosis, standard heterosis over check and specific combining ability） than any other combinations; （5） Genetic distance was positively correlated with panicle number, grain length and length-to-width ratio （P 〈 0.05） and negatively correlated with grain width, grain yield, seed-setting rate, as well as mid-parent heterosis, standard heterosis over check, and specific combining ability for grain yield （P 〈 0.01）. These heterotic groups and patterns and their argonomic traits will provide useful information for future hybrid rice breeding programs.

Analysis of Genetic Effects for Heterosis of Erucic Acid and Glucosinolate Contents in Rapeseed (Brassica napus L.)

The embryo, cytoplasmic, and maternal heterosis for erucic acid content （EAC） and glucosinolate content （GLS） of rapeseed （Brassica napus L.） were studied by using the genetic models for quantitative traits of seeds in diploid crops. Eight parents were included in a diallel mating design in two years. It was found that the heterosis of EAC and GLS was simultaneously controlled by genetic main effects and genotype×environment （GE） interaction effects. The general heterosis of most crosses for EAC was significantly positive, while it was not for GLS. The general heterosis was more important for two quality traits of rapeseed because of the low GE interaction heterosis in both years, especially for GLS. Among different genetic systems, significant positive embryo general heterosis and the negative maternal general heterosis were found for EAC and GLS in most hybrid crosses. Some hybrids with significant negative interaction heterosis were detected for either of EAC or GLS. In general, maternal general and interaction heterosis was more important for reducing EAC and GLS of rapeseed.

Prospects of utilization of inter-subspecific heterosis between indica and japonica rice

The Asian cultivated rice(Oryza sativa L.) grown worldwide is divided into two subspecies, indica and japonica. It is well known that the heterosis of inter-subspecies is usually stronger than that of intra-subspecies. Since the 1970 s, indica hybrid rice, an intra-subspecific hybrid rice, has being widely used in China and even in the world. However, the inter-subspecific hybrid rice between indica and japonica is still unavailable. The major obstacle is the hybrid sterility of the inter-subspecies. In recent decades, the genetic and molecular basis of indica-japonica hybrid sterility was understood more and more clearly. Some breeding approaches for overcoming inter-subspecific hybrid sterility were proposed and used to develop the indicajaponica hybrid rice. The updated understanding will offer new approaches for development of breeding lines for overcoming indica-japonica hybrid sterility, which facilitates developing of inter-subspecific hybrid rice.

Heterosis and Combining Ability for Major Yield Traits of a New Wheat Germplasm Shannong 0095 Derived from Thinopyrum intermedium

The wheatgrass, Thinopyrum intermedium （Host） Barkworth ＆ DR Dewey, shows many beneficial characteristics, such as big spikes and high resistance to many diseases. To transfer the beneficial genes of this species, many wheat- Thinopyrum intermedium alien chromosome lines were developed. Of them, Shannong 0095 （SN0095）, a disomic substitution, has long spikes and flag-leaves, and thus may be an important genetic resource for wheat yield improvement. In order to realize its heterosis and combining ability on major yield traits, a 7 ×7 complete diallel design was made according to Griffing＇s Method-1. The results showed that heterosis for spike length （SPL）, flag-leaf area （FLA）, number of spikes per plant （NSP）, number of spikelets per spike （NSL）, kernels per spike （KPS）, 1 000-kernel weight （TKW） and grain yield per plant （GYP） existed in all the crosses by SN0095, but heterobeltiosis occurred only for KPS, TKW, and GYP. The relative mid-parent heterosis （RMH） and relative high-parent heterosis （RHH） for GYP, which valued as high as 35.32 and 29.92% respectively, were the highest among all the traits mearsured. Though additive and non-additive gene effects and cytoplasmic effects （or cytoplasmic-nuclear interaction effects） were found in governing all the traits measured above, additive gene action played a predominant role. The results also showed that SN0095 was the best-general combiner for SPL and FLA, and high-general combiner for NSP amongst all the parents. Estimates of specific combining ability （SCA） showed that SN0095 could also make high-SCA combinations for GYP, such as SN0095 × Jimai 19 （JMI9）. SN0095 could be a unique and important parent in hybrid wheat breeding programs.

Relationship Between Heterosis and Parental Genetic Distance Based on Molecular Markers for Functional Genes Related to Yield Traits in Rice

The genetic distances among 18 cytoplasmic male sterile lines and 11 restorer lines were analyzed with molecular markers derived from yield-related functional genes. The correlation between parental genetic distance and heterosis was investigated by analyzing the performance of 47 combinations. The results showed that the genetic distance was significantly correlated with yield heterosis （r=0.29^＊）, but not significantly correlated with heterosis for other traits, such as number of effective panicles per plant, seed setting rate, 1000-grain weight, number of grains per panicle and theoretical yield. However, the correlation coefficient was so small that the parental genetic distance could not to be used to predict heterosis.

Genome-Wide Transcriptional Analysis of Yield and Heterosis-Associated Genes in Maize (Zea mays L.)

Heterosis has contributed greatly to yield in maize, but the nature of its contribution is not completely clear. In this study, two strategies using whole-genome oligonucleotide microarrays were employed to identify differentially expressed genes （DEGs） associated with heterosis and yield. The analysis revealed 1 838 heterosis-associated genes （HAGs）, 265 yield- associated genes （YAGs）, and 85 yield heterosis-associated genes （YHAGs）. 37.1% of HAGs and 22.4% of YHAGs expressed additively. The remaining genes expressed non-additively, including those with high/low-parent dominance and over/under dominance, which were prevalent in this research. Pathway enrichment analysis and quantitative trait locus （QTL） co-mapping demonstrated that the metabolic pathways for energy and carbohydrates were the two main enriched pathways influencing heterosis and yield. Therefore, the DEGs participating in energy and carbohydrate metabolism were considered to contribute to heterosis and yield significantly. The investigation of potential groups of HAGs, YAGs, and YHAGs might provide valuable information for exploiting heterosis to improve yield in maize breeding. In addition, our results support the view that heterosis is contributed by multiple, complex molecular mechanisms.

Analysis on Dynamic Heterosis for Allelopathy in Rice Under Different Environment Conditions

In this study, 5 parental rice varieties with different allelopathic potentials were employed in diallel cross [P(P+1)/2] to get a set of genetic materials including parental lines and two generations of F1s. The dynamic heterosis for allelopathy in rice under different environmental conditions, was analyzed by using additive-dominant developmental genetic model. The results indicated that heterosis in both F1 and F2 showed inhibitory effects on shoot and root length of receiver plant(Lactuca sativa L.). Heterosis over mid-parent based on population mean(HMP)in F2 was lower than that in differental environmental conditions, showing 1/2 HMP in F1 The heterosis in rice allelopathy was much higher under the field environmental conditions with lower temperature and weaker sunlight than that under favorable environment, implying that the allel-opthic potential could be increased by stress environment. This finding interpreted the genetic reason that plant could produce more allelochemicals under unfavorable environment.

Understanding the genetic basis of rice heterosis: Advances and prospects

Heterosis,which describes the superior vigor and yield of F_1 hybrids with respect to their parents,is observed in many rice hybrid crosses.The exploitation of heterosis is a great leap in the history of rice breeding.With advances in genomics and genetics,high-resolution mapping and functional identification of heterosis-associated loci have been performed in rice.Here we summarize advances in understanding the genetic basis of grain yield heterosis in hybrid rice and provide a vision for the genetic study and breeding application of rice heterosis in the future.

Combining ability and heterosis analysis over two environments in a diallel cross of three families of the clam Meretrix meretrix

A 3×3 complete diallel cross comprising three families of the clam Meretrix meretrix（P1, P2 and P3） was used to determine the combining ability of parental families and heterosis of F1 under indoor and openair environments for growth traits. Analysis of variance for shell length and whole body weight indicated highly significant cross effects, environment effects and the interaction of cross by environment. General combining ability（GCA） and specific combing ability exhibited great variation among crosses and between two environments. Pooled over environments, P2 was the top combiner among the three parental families for both traits studied. The cross of P1 and P3 had the highest SCA. Additionally, significant reciprocal effects were observed. For individual environment, about half of the crossbred combinations showed favorable Mid-parent heterosis（MPH）（〉1%） for the shell length and whole body weight. Our data has shown that non-additive genetic and reciprocal effects constituted the major sources of genetic variation for both shell length and whole body weight, which indicates that crossbreeding among selective families could further explore the heterotic effects.

Experimental evaluation of heterobeltiosis and heterosis between two populations of Pacific abalone Haliotis discus hannai Ino

A2 × 2 factorial cross between two populations of Pacific abalone Haliotis discus hannai Ino, collected separately from Dalian （D） in China and Miyagi （M） in Japan, was conducted to compare performances in fertilization rate, hatching rate, metamorphosis rate and growth at days 20, 43, 160 and 330 between purebreds （DD and MM） and crossbreds （DM and MD） and investigate the magnitude of heterobeltiosis （better parent） and heterosis （mid-parent）. Heterobeltiosis and heterosis for all the traits analyzed were evidently different between crossbreds DM and MD. Heterobeltiosis in the crossbred DM varied among traits, with values of 2.5% for the fertilization rate, 2.2% for the hatching rate, - 1.9% for the metamorphosis rate and 7.4% for the growth at the day 330. The crossbred DM displayed positive heterotic values for fertilization rate （5.4%）, hatching rate （7.4%）, metamorphosis rate （7.6%） and growth （ 12.0% ） at the day 330. However, both heterobeltiosis and heterosis for all the traits in the crossbred MD were negative except those for the growth at days 20 and 43. The results indicate the importance of selecting superior hybrid varieties if the exploitation of hybrid vigor is considered in the Pacific abalone breeding program.

Analysis of combining ability for stem-related traits and its correlations with lodging resistance heterosis in hybrid wheat

With the application of hybrid wheat, lodging is becoming one of the major factors limiting high yield in its production. However,few studies have focused on combining ability and heterosis analysis of stem-related traits. In this study, 24 crosses were made according to NCII genetic design, using the three(photo-sensitive male sterile lines)×eight(restorer lines) incomplete diallel crosses. The length of basal second internode(LBSI) and breaking strength of basal second internode(BSBSI)as well as other stem-related traits were used to perform the principal component analysis(PCA), combining ability and heterosis analysis. The PCA results showed that the variables could be classified into two main factors, which were named as the positive factor(factor 1) and the negative factor(factor 2), and accounted for 52.3 and 33.2%, respectively, of the total variance in different variables, combined with the analysis for index weight indicated that the factor 1-related traits play positive roles in lodging resistance formation of hybrids. Combining ability variance analysis indicated that its genetic performance was mainly dominated by additive gene effects, and the hybrid combinations with higher lodging resistance can be selected by using of 14 GF6085(R1), 14 GF6343-2(R4), 14 GF6937(R6), 14 GF7433-1(R7), and BS1086(M3),which are with the features with lower general combining ability(GCA) effects of factor 2-related traits whereas higher GCA effects of factor 1-related traits. The heterosis analysis showed that the wide range of heterosis varied with the traits and combinations, and GCA or specific combining ability(SCA) effects of factor 1-related traits except wall thickness of basal second internode(WTBSI) were positively and closely related to the heterosis of lodging resistance. Generally, the correlation coefficients of heterosis to GCA effects of sterile lines(GCAm) of factor 1-related traits are significantly higher than that to GCA of restorer lines(GCAr) and SCA, combined with the higher GCAm variance values of factor 1-related traits compared to GCAr, the GCAm of factor 1-related traits should be particularly considered when breeding hybrid combinations.The heritability analysis showed that the narrow-sense heritability of the diameter of basal second internode(DBSI) and the center of gravity height(TCGH) were obviously lower(<60%) than other traits, suggesting that these two traits were suitable for selection in higher generation for parental breeding. These could provide a theoretical basis for parental breeding and heterosis utilization of lodging resistance.

Dissection of heterosis for yield and related traits using populations derived from introgression lines in rice

Despite the great success achieved by the exploitation of heterosis in rice,the genetic basis of heterosis is still not well understood.We adopted an advanced-backcross breeding strategy to dissect the genetic basis of heterosis for yield and eight related traits.Four testcross(TC) populations with 228 testcross F1 combinations were developed by crossing57 introgression lines with four types of widely used male sterile lines using a North Carolina II mating design.Analysis of variance indicated that the effects of testcross F1 combinations and their parents were significant or highly significant for most of the traits in both years,and all interaction effects with year were significant for most of the traits.Positive midparent heterosis(HMP) was observed for most traits in the four TC populations in the two years.The relative HMPlevels for most traits varied from highly negative to highly positive.Sixty-two dominant-effect QTL were identified for HMPof the nine traits in the four TC populations in the two years.Of these,22 QTL were also identified for the performance of testcross F1.Most dominant-effect QTL could individually explain more than 10% of the phenotypic variation.Four QTL clusters were observed including the region surrounding the RM9–RM297 region on chromosome 1,the RM110–RM279–RM8–RM5699–RM452 region on chromosome 2,the RM5463 locus on chromosome 6 and the RM1146–RM147 region on chromosome 10.The identified QTL for heterosis provide valuable information for dissecting the genetic basis of heterosis.

Heterosis in locally adapted sorghum genotypes and potential of hybrids for increased productivity in contrasting environments in Ethiopia

Increased productivity in sorghum has been achieved in the developed world using hybrids.Despite their yield advantage,introduced hybrids have not been adopted in Ethiopia due to the lack of adaptive traits,their short plant stature and small grain size.This study was conducted to investigate hybrid performance and the magnitude of heterosis of locally adapted genotypes in addition to introduced hybrids in three contrasting environments in Ethiopia.In total,139 hybrids,derived from introduced seed parents crossed with locally adapted genotypes and introduced R lines,were evaluated.Overall,the hybrids matured earlier than the adapted parents,but had higher grain yield,plant height,grain number and grain weight in all environments.The lowland adapted hybrids displayed a mean better parent heterosis(BPH) of19%,equating to 1160 kg ha-1and a 29% mean increase in grain yield,in addition to increased plant height and grain weight,in comparison to the hybrids derived from the introduced R lines.The mean BPH for grain yield for the highland adapted hybrids was 16% in the highland and 52%in the intermediate environment equating to 698 kg ha-1and 2031 kg ha-1,respectively,in addition to increased grain weight.The magnitude of heterosis observed for each hybrid group was related to the genetic distance between the parental lines.The majority of hybrids also showed superiority over the standard check varieties.In general,hybrids from locally adapted genotypes were superior in grain yield,plant height and grain weight compared to the high parents and introduced hybrids indicating the potential for hybrids to increase productivity while addressing farmers' required traits.

Heterosis for water uptake by maize (Zea mays L.) roots under water deficit: responses at cellular, single-root and whole-root system levels

To examine the potential heterosis for water uptake by maize roots, the hydraulic properties of roots in the F1 hybrid （Hudan 4） were compared with those of its inbred parents （ 478 and Tian 4） at cellular, single-root and whole-root system levels under well-watered and water-deficit conditions. The cell hydraulic conductivity （Lpc） decreased under water deficit, but the Lpc of the F1 was higher than that of its inbred parents with or without stress from water deficit. Marked reductions in Lpc were observed following Hg2＋ treatment. The hydrostatic hydraulic conductivity of single roots （hydrostatic Lpsr） varied among genotypes under the two water treatments, with the highest in the F1 and the lowest in 478. Radial hydraulic conductivity （radial Lpsr） and axial hydraulic conductance （Lax） of the three genotypes varied similarly as Lpsr. The variations in hydraulic parameters were related to root anatomy. Radial Lpsr was negatively correlated with the ratio of cortex width to root diameter （R2=-0.77, P〈0.01）, whereas Lax was positively correlated with the diameter of the central xylem vessel （R2=0.75, P〈0.01） and the cross-sectional area of xylem vessels （R2=0.93, P〈0.01 ）. Hydraulic conductivity （Lpwr） and conductance （Lwr） of the whole-root system followed the same trend under the two water treatments, with the highest values in the F1. The results demonstrated that heterosis for water uptake by roots of the F1 occurred at cellular, single-root and whole-root system levels under well-watered and water-deficit conditions.

Combining Ability and Heterosis Between High Strength Lines and Transgenic Bt (Bacillus thuringiensis) Bollworm-Resistant Lines in Upland Cotton (Gossypium hirsutum L.)

To analyse the combining ability and heterosis between high-strength lines and transgenic Bt bollworm-resistant lines in upland cotton, 5 high-strength lines were crossed as female lines with 12 transgenic Bt bollworm-resistant lines according to NCII design. It was demonstrated that the compositions of variance in various traits were quite different. For seed cotton yield, lint yield, boll numbers per plant and boll weight, the dominant (special combining ability) effects were the major effects, accounting for 87.38, 84. 40, 80. 04 and 64. 46% of the total phenotypic variances, respectively, while for fibre strength and micronaire value, the additive (general combining ability) effects had the major effects, with a ratio of additive variance to phenotypic variance of 78.85 and 43.80%. As for lint percent and 2.5% span length, the dominant and additive variances had similar effects, in phenotypic variances (54.94 and 40.11% for lint percent, 45.76 and 42.49% for 2. 5% span length, respectively). The mid-parent heterosis (Hpm), surpassing parent heterosis (Hpb) and competitive heterosis (Hck) for seed cotton yield and lint yield were both extremely significant. For fibre properties, the Hck and Hpm of 2.5 % fibre span length were extremely significant, the Hck of fibre strength was significant, and the favorable negative Hck of micronaire was also extremely significant. The increments of hybrid over common variety were 17% for lint yield and fibre strength, 7% for fibre span length, and 4 % for fineness.