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.

Heterosis Analysis in Endogenous Substances in Root Bleeding Sap of Sorghum

Despite hybrid dominance contributing to the genetic improvement of crops,little is known about heterosis and inheritance patterns of endogenous substances in sorghum(Sorghum bicolor(L.)Moench)root bleeding sap.In this study,six sterile and six restorer lines of sorghum and 36 hybrid sorghum combinations formulated as incomplete double-row crosses were selected as test materials,and heterosis,combining ability,heritability,and their interrelationships of root bleeding sap endogenous substances in different hybrid sorghum combinations and their parents were investigated.The results showed that the root bleeding sap of the F1 generation of hybrid sorghum had a high heterosis in both soluble sugar content and amino acid content at the flowering stage,and the average high-parent heterosis was 129.34%and 74.57%,respectively.Indole-3-acetic acid(IAA),cytokinins(CTK),gibberellic acid(GA_(3)),abscisic acid(ABA),soluble sugar,amino acid,and root bleeding intensity were mainly affected by non-additive genetic effects of the genes.Soluble protein was affected by additive genetic effects of the genes and had a high narrow heritability(75.50%),which could be selected at low generations in breeding.The combining ability analyses showed that the sterile lines 521A and 170A,and the restorer lines Ji318R and 0–30 were promising parents with high general combining ability.Correlation analysis showed that all endogenous substances of root bleeding sap were positively correlated with the sum of parental general combining ability(GCA)at highly significant levels,and IAA,CTK,GA_(3),ABA,soluble sugar,amino acid,and root bleeding intensity were positively correlated with male GCA at significant or highly significant levels.Therefore,the GCA of the restorer lines root bleeding sap endogenous material or the sum of both parents’GCA can be used to predict the performance of wounding endogenous material in the F1 generation of hybrid sorghum.Overall,this study results can help elucidate heterosis mechanisms of root bleeding sap endogenous material and improve sorghum quality.

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.

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.

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 Analysis of Nitrogen Use Efficiency for Grain Production of Brassica napus L.

[Objective]The aim was to study heterosis of N use efficiency for grain production （NUEg） of Brassica napus L. and provide theoretical basis for breeding N-efficient cultivars. [Method]Dry matter production and N content of six B.napus parents （Zheshuang 3,Yangyou 7,ZJ1,Shilijia,Ningyou 14 and Huyou 16） and their F1 combinations from 6 × 6 complete diallel cross in maturity stage under two N levels were measured; heterosis of NUEg,combining ability and heritability size were analyzed and calculated. [Result]The results showed that NUEg has obvious heterosis; combining ability variance analysis indicated that NUEg was mainly controlled by additive,dominant and cytoplasmic effects; genetic variance analysis showed that additive effects and dominance effects were all significant in low nitrogen fertilizer and dominance effects were significant in high nitrogen fertilizer. [Conclusion]NUEg of B.napus has obvious heterosis.

Genetic Effects and Heterosis in Plant Height and Internode Traits of Japonica-Indica Hybrid Rice

[Objective] This study aimed to investigate the genetic effects and heterosis of plant height and internode traits of japonica-indica hybrid rice. [Methed] Incomplete diallel crosses were made between six japonica CMS lines and nine indica widecompatibility restorer lines; the genetic effects of plant height and internode traits of japonica-indica hybrid rice were analyzed using the additive-dominance genetic model. [Result] The ple, nt height, panicle length and the length of internode 1 of japonica-in- dica hybrid rice were mainly controlled by the additive effects; but the length of in- ternode 3, internode 4 and internode 5 were mainly controlled by dominance effects. Both the narrow sense heritability and broad sense heritability of plant height, panicle length, number of elongated internodes and length of most internodes reached signifi- cance level. The positive phenotypic correlation, genetic correlation, additive correla- tion and dominance correlation between plant height and panicle length, number of e- longated internodes and internode length were significant; and most of the other paired traits were significantly positively correlated. Heterosis analysis showed that the positive heterosis value over mid-parent and positive heterosis value over better- parent of the length of internode 3, internode 4, internode 5 and internode 6 reached significant level, and the heterosis value over mid-parent of plant height reached extreme significance level. [Conclusion] This study will provide reliable theoretical basis for the genetic improvement and heterosis utilization of plant height and internode traits in japonica-indica hybrid rice.

Analysis of the Evolutionary Significance of Heterosis——taking the contribution of fitness to the genetic diversity in random mating population as an example

Upon the analogy of definition of heterosis and inbreeding depresstion in terms of population genetics, the heterosis is thought to be evaluated overall with fitness. By establishing a mathematical model, the equilibrium status of three genotypes of random mating population （i. e. RR, Rr and rr） under different fitness, which exposes that heterosis is the precondition for multiallele to exist in the population. The heterosis protects the genetic diversity and makes the population owning a stronger self-control and evolution potential by improving the hetemzygote＇s fithess so as not to wash out different types of genes. It deepens Darwin＇s thoughts of individual section by making the individual fitness consonant with population fitness.

Relationship Between Heterosis and Endogenous Plant Hormones in Liriodendron

To investigate the possible involvement of endogenous plant hormones in heterosis of Liriodendron interspecific hybrid, growth traits and contents of endogenous GA 1/3 (gibberellin A 1, A 3), IAA (indole_3_acetic acid) and iPA (isopentenyl adenine) of tulip tree ( L. chinense (Hemsl.) Sarg.), yellow poplar ( L. tulipifera L.) and their interspecific hybrid ( L. chinense × L. tulipifera ) were examined. Results showed that: (1) the heterosis in height growth trait of the interspecific hybrid was mainly caused by the reletively greater elongation of internodes. Although the uppermost three internodes had the potential of elongation, the first one, which had the greatest elongation amount, contributed to the heterosis of the height growth trait; (2) the contents of endogenous GA 1/3 , IAA and iPA were greatly different among tulip tree, yellow poplar and their interspecific hybrid. All of the three interspecific hybrid families studied significantly contained higher amount of endogenous GA 1/3 and iPA in the uppermost first internode than their parental species. And thus, a correlation between the contents of endogenous GA 1/3 and iPA, and hybrid vigor for height growth trait in Liriodendron was observed; (3) the rankings of endogenous GA 1/3 and iPA contents in the uppermost first internode of three hybrid families studied were not similar to the ranking for height of 3_year_old trees. Therefore, the contents of endogenous GA 1/3 and iPA in the uppermost first internode could not be used in predicting hybrid vigor among hybrid families.

Relationship between SSR Genetic Distance and Heterosis in Hot Pepper

[Objective] This study aimed to predict the heterosis of hot pepper using SSR genetice distance. [Method] Twenty-five hybridized combinations between 10pepper parents were obtained through NCⅡ incomplete diallel cross to analyze the relationship between SSR genetic distance and heterosis. [Result] The genetic distance of the parents varied in a range from 0.13 to 0.33, and the average genetic distance was 0.25, indicating that the genetic difference was not obvious among the parents, namely, they shared a close genetic relationship. In addition, the SSR genetic distance was closely related to yield per plant and fruits per plant, but showed no obvious correlation with other traits. [Conclusion] This study proved that in a certain range the combinations between the parents with a distant genetic distance possessed stronger heterosis and a larger possibility to produce a high yield and vice versa.

Genetic Polymorphism of Ten Microsatellites in Two Goat Breeds and Its Relationship with Heterosis

[Objective] This study aimed to investigate the genetic diversity of Macheng black goat and its correlation with heterosis.[Method] Ten microsatellite markers were selected for polymorphism investigation and statistical analysis of Boer goat and Macheng black goat populations.[Result] The results showed that totally 175 alleles were found in 10 microsatellite loci; to be specific,the maximum number of detected alleles was 23,and the minimum number was 10; the effective number of alleles （Ne） was 6.4-18.1,with absolute difference value of 1.6-8.1 from the observed number of alleles.The highest gene frequency was 0.239 1 and the lowest was 0.002 7.The polymorphic information contents of all the ten microsatellite markers were above 0.95.The observed heterozygosity （Ho） ranged from 0.616 7 to 0.984 4 and the expected heterozygosity （He） ranged from 0.844 1 to 0.944 6.The average expected heterozygosity of Boer goat and Macheng black goat was respectively 0.894 0 and 0.906 7.Various body weight and body size indices of Boer goatxMacheng black goat hybrids were improved in varying degrees compared with Macheng black goat （with an increase range of 0.32％-30.06％）.The average heterosis rates of body height and chest girth were relatively high,while average heterosis rate of body weight was relatively low.[Conclusion] The genetic distance between Boer goat and Macheng black goat was 0.379 5,which is consistent with the geographical distribution of Boer goat and Macheng black goat populations and is fully relevant to the heterosis of Boer goat × Macheng black goat hybrids,indicating that investigating polymorphism via microsatellite loci is one of the feasible means to predict and analyze heterosis between varieties.

Analysis of F_1 Heterosis of Potassium Content on Self-bred High-potassium New Strains of Flue-cured Tobacco

F1 potassium heterosis of 8 flue-cured tobacco varieties and 6 self-bred high-potassium new strains were studied. The results showed that the F1 mean het- erosis of potassium content had differences between different parts of plants, showing B2F （8.45%）〉X2F （7.59%）〉C3F （5.64%）; the F1 over-parent heterosis of potassium content of various parts was not obvious, showing X2F （0.05%）〉C3F （-0.43%） 〉B2F （-0.48%）; the F, control heterosis of potassium content of different parts showed B2F （17.81%）〉X2F （4.06%）〉C3F （1.12%）. The variance of GCA of potassium content in various parts of the 6 self-bred high-potassium new strains was significant or extremely significant, and all leaves of GK2 had greater GCA effect on potassium content; C3F and X2F of GK7 had good GCA effect on potassium con- tent, but GCA effect was bad in B2F; GK9 preformed well in B2F but badly in C3F. The variance of SCA in all combinations was extremely significant, and the good combinations included Duoye 87xGK7 （17.19%） in B2F, Duoye 87xGK2 （25.63%）, ChangbohuangxGK5 （19.43%）, Yunyan 87xGK7 （22.78%）, and Yunyan 87xGK9 （24.38%） in C3F, Coker176xGK7 （19.87%）, 101xGK9 （15.89%）, Yunyan 85xGK9 （19.15%）, and Yunyan 87xGK9 （20.74%） in X2F.

Analysis of Heterosis, Combining Ability and Heritability of Cadmium Content in Brown Rice of Three-line Indica Hybrid Rice

Five cytoplasmic male sterile （CMS） lines were used as parents in an incomplete diallet cross and six restorer lines of rice design （Nc II design）. Thirty hybrid combinations with the same growth period were selected as experimental ma- terials to investigate the heterosis, combined ability and heredity of Cd content in brown rice of indica hybrid rice. According to the results, Cd content in brown rice showed a significantly negative heterosis; the general combining ability and specific combination ability of Cd content in CMS and restorer lines both reached extremely significant level （P〈0.01）, indicating that both genetic improvement of parents and e- valuation of combinations are important to the breeding of hybrid combinations with low accumulation of Cd; the broad-sense heritabitity and narrow-sense heritability of Cd content were both relatively high with slight differences, which respectively reached 97.73% and 80.10%, indicating that Cd content in brown rice mainly de- pends on the additive action of genes; in addition, parent improvement showed bet- ter effect on the selection of early generation.

Relationship Between Differential Gene Expression and Heterosis During Ear Development in Maize (Zea mays L.)

Maize （Zea raays L.） is one of the most important crops because of the remarkable properties of its hybrid, which is responsible for the high commercial value of hybrid maize. The genetic basis of heterosis （hybrid vigor） is not well understood. A differential display technique was performed to identify genes with differential expression across twelve maize inbred lines and thirty-three hybrids during ear development. An incomplete diallel design was used to investigate the relationship between the global framework of differential gene expression and heterosis. It was found that the genes belonging to MONO pattern （i.e., genes expressed in both parental lines and in hybrid） was the highest in percentage among the total five patterns and illustrated that the properties of differentially expressed genes are not entirely responsible for heterosis. Furthermore,a larger number of differentially expressed genes in hybrid, which serves as a major reservoir for generating novel phenotypes that exhibit heterosis of certain agronomic traits during early development and differentiation of maize ear. Moreover, there were some silent genesin hybrids that are responsible for the arrest or abortion of spikelets and for the increase in kernels weight.

Correlation Analysis of Genetic Distance and Heterosis of the Major Brassica napus L. Cultivars in Yunnan Province

[Objective] The correlation between genetic distance and heterosis of the major Brassica napus L. cultivars in Yunnan Province was analyzed. [Method] The genetic distances among the 8 major Brassica napus L. cultivars in Yunnan Province were investigated with the SSR molecular marker technique. Moreover, the correlation between genetic distance and field appearance of heterosis was ana-lyzed. [Result] There was a certain correlation between the genetic distance and heterosis of crossing parents （P〉0.05）. [Conclusion] It is difficult to predict the het-erosis of Brassica napus L. cultivars and to screen parents by using the SSR molecular marker technique.

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.

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.

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.