Broadening the avenue of intersubgenomic heterosis in oilseed Brassica

Accumulated evidence has shown that each of the three basic Brassica genomes (A, B and C) has undergone profound changes in different species, and has led to the concept of the “subgenome”. Significant intersubgenomic heterosis was observed in hybrids between traditional Brassica napus and first generation lines of new type B. napus. The latter were produced by the partial introgression of subgenomic components from different species into B. napus. To increase the proportion of exotic subgenomic components and thus achieve stronger heterosis, lines of first generation new type B. napus were intercrossed with each other, and subjected to intensive marker-assisted selection to develop the second generation of new type B. napus. The second generation showed better agronomic traits and a higher proportion of introgression of subgenomic components than did the first generation. Compared with the commercial hybrid and the hybrids produced with the first generation new type B. napus, the novel hybrids showed stronger heterosis for seed yield during the 2 years of field trials. The extent of heterosis showed a significant positive correlation with the introgressed subgenomic components in the parental new type B. napus. To increase the content of the exotic subgenomic components further and to allow sustainable breeding of novel lines of new type B. napus, we initiated the development of a gene pool for new type B. napus that contained a substantial amount of genetic variation in the A^r and C^c genome. We discuss new approaches to broaden the avenue of intersubgenomic heterosis in oilseed Brassica.     

Relationship between genetic distance and heterosis for yield and morphological traits in winter canola (Brassica napus L.)

Genetic distance among canola cultivars was estimated through multivariate analysis. Thirty cultivars from various sources were analyzed and clustered based upon five morphological characteristics and yield components-crown diameter, number of branches plant^-1, number of pods plant^-1, number of seeds pod^-1 and yield plant^-1 -and placed in three distinct clusters. Two cultivars from each cluster were selected as parents and 15 partial-diallel inter- and intra-cluster crosses were made between the six selected parents and evaluated at two locations in Michigan in 1990/1991. The association between genetic distance and mid-parent heterosis was investigated. The correlation between genetic distance and heterosis was positive and highly significant for seed yield, number of pods plant^-1, and number of seeds pod^-1. Clustering, based on yield and yield-component traits, demonstrated that inter-cluster heterosis was greater than intra-cluster heterosis in the majority of cases.     

Comparison of phenotypic and molecular distances to predict heterosis and F1 performance in Ethiopian mustard (Brassica carinata A. Braun)

Predicting heterosis and F₁ performance from the parental generation could largely enhance the efficiency of breeding hybrid or synthetic cultivars. This study was undertaken to determine the relationship between parental distances estimated from phenotypic traits or molecular markers with heterosis, F₁ performance and general combining ability (GCA) in Ethiopian mustard (Brassica carinata). Nine inbred lines representing seven different geographic regions of Ethiopia were crossed in half-diallel. The nine parents along with their 36 F₁s were evaluated in a replicated field trail at three locations in Ethiopia. Distances among the parents were calculated from 14 phenotypic traits (Euclidean distance, ED) and 182 random amplified polymorphic DNA (RAPD) markers (Jaccard’s distances, JD), and correlated with heterosis, F₁ performance and GCA sum of parents (GCA_sum). The correlation between phenotypic and molecular distances was low (r=0.34, P≤0.05). Parents with low molecular distance also had low phenotypic distance, but parents with high molecular distance had either high, intermediate or low phenotypic distance. Phenotypic distance was highly significantly correlated with mid-parent heterosis (r=0.53), F₁ performance (r=0.61) and GCA (r=0.79) for seed yield. Phenotypic distance was also positively correlated with (1) heterosis, F₁ performance and GCA for plant height and seeds plant⁻¹, (2) heterosis for number of pods plant⁻¹, and (3) F₁ performance for 1,000 seed weight. Molecular distance was correlated with GCA_sum (r=0.36, P≤0.05) but not significantly with heterosis and F₁ performance for seed yield. For each parent a mean distance was calculated by averaging the distances to the eight other parents. Likewise, mean heterosis was estimated by averaging the heterosis obtained when each parent is crossed with the other eight. For seed yield, both mean ED and JD were significantly correlated with GCA (r=0.90, P≤0.01 for ED and r=0.68, P≤0.05 for JD) and mean heterosis (r=0.79, P≤0.05 for ED and r=0.77, P≤0.05 for JD). In conclusion, parental distances estimated from phenotypic traits better predicted heterosis, F₁ performance and GCA than distances estimated from RAPD markers. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Gene expression analyses in maize inbreds and hybrids with varying levels of heterosis

Background  

Heterosis is the superior performance of F₁ hybrid progeny relative to the parental phenotypes. Maize exhibits heterosis for a wide range of traits, however the magnitude of heterosis is highly variable depending on the choice of parents and the trait(s) measured. We have used expression profiling to determine whether the level, or types, of non-additive gene expression vary in maize hybrids with different levels of genetic diversity or heterosis.     

Enriched partial correlations in genome-wide gene expression profiles of hybrids (A. thaliana): a systems biological approach towards the molecular basis of heterosis

Heterosis is a well-known phenomenon but the underlying molecular mechanisms are not yet established. To contribute to the understanding of heterosis at the molecular level, we analyzed genome-wide gene expression profile data of Arabidopsis thaliana in a systems biological approach. We used partial correlations to estimate the global interaction structure of regulatory networks. Our hypothesis states that heterosis comes with an increased number of partial correlations which we interpret as increased numbers of regulatory interactions leading to enlarged adaptability of the hybrids. This hypothesis is true for mid-parent heterosis for our dataset of gene expression in two homozygous parental lines and their reciprocal crosses. For the case of best-parent heterosis just one hybrid is significant regarding our hypothesis based on a resampling analysis. Summarizing, both metabolome and gene expression level of our illustrative dataset support our proposal of a systems biological approach towards a molecular basis of heterosis.     

Negative Complementation at the Notch Locus of DROSOPHILA MELANOGASTER

Four Abruptex alleles (Ax^E1, Ax^E₂, Ax^₉B₂, and Ax¹⁶¹⁷²) have been mapped within the Notch locus. Based on their visible phenotypes and their interactions with one another and with N mutations, the Ax alleles can be divided into two groups. Heterozygous combinations of members of the same group are intermediate in phenotype compared to the respective homozygotes, whereas heterozygotes of Ax alleles from different groups exhibit negative heterosis, being much less viable and more extremely mutant than either homozygote. It is suggested that the Notch locus is a multi-functional regulator ("integrator") gene, whose product possesses both "repressor" and "activator" functions for the processes it regulates.     

Relationships of differential gene expression in leaves with heterosis and heterozygosity in a rice diallel cross

Using differential display analysis, we assessed the patterns of differential gene expression in hybrids relative to their parents in a diallel cross involving 8 elite rice lines. The analysis revealed several patterns of differential expression including: (1) bands present in one parent and F₁ but absent in the other parent, (2) bands observed in both parents but not in the F₁, (3) bands occurring in only one parent but not in the F₁ or the other parent, and, (4) bands detected only in the F₁ but in neither of the parents. Relationships between differential gene expression and heterosis and marker heterozygosity were evaluated using data for RFLPs, SSRs and a number of agronomic characters. The analysis showed that there was very little correlation between patterns of differential expression and the F₁ means for all six agronomic traits. Differentially expressed fragments that occurred only in one parent but not in the other parent or in F₁ in each of the respective crosses were positively correlated with heterosis and heterozygosity. And conversely, fragments that were detected in F₁s but in neither of the respective parents were negatively correlated with heterosis and heterozygosity. The remaining patterns of differential expression were not correlated with heterosis or heterozygosity. The relationships between the patterns of differential expression and heterosis observed in this study were not consistent with expectations based on dominance or overdominance hypotheses.     

Cell number counts - The fw2.2 and CNR genes and implications for controlling plant fruit and organ size

Two key determinants of plant and organ size are cell number and cell size, and altering either one may affect the plant organ size, but cell number control often plays a predominant role in natural populations. Domesticated crops usually have larger fruit and harvested organ sizes than wild progenitors. Crop yields have increased significantly by breeding, often via heterosis, which is associated with increased plant and organ size primarily achieved by cell number increases. A small class of genes is now known that control plant and organ sizes though cell number or cell size. The fw2.2 gene was found to control a major QTL for tomato fruit size by negatively affecting cell numbers. Orthologs to these fw2.2 genes underlie QTLs for fruit sizes in other species, and their expression can be negatively correlated with increased cell number. In maize decreased or increased expression of the fw2.2 ortholog ZmCNR1, increases or decreases cell number, respectively, thereby affecting maize organ size throughout the plant and thus also whole plant size. Therefore, these genes should now be considered as more general regulators of plant cell number and organ size. The exact molecular function of these transmembrane domain proteins remains unknown, as does any clear relationship to the cell cycle. Because these genes control organ sizes in diverse plants and important crop species, and because they can affect whole plant size, interest arose into how effects of such genes could parallel agronomic crop improvements, in particular that by heterosis, as it also affects cell number. In joining these subjects here in discussion we speculate on how single gene cell number regulation and heterosis may cooperate in crop improvement.     

Partitioning of genetic effects on lifetime performance of mice

Summary A total of 2,457 lifetime performance records of 29 genetic groups of mice was analyzed using multiple regression of records on the proportion of gene contribution from 6 lines (designated as Lines M_P, m_Q, W_P, w_Q, C_P and c_Q). Genetic effects were partitioned into line additive, line maternal, direct heterosis, maternal heterosis and paternal heterosis effects. The line additive and line maternal effects were expressed as deviations from Line c_Q. Seventeen of 25 line additive effects differed significantly (P<0.05) from Line c_Q whereas only 4 of 25 line maternal effects deviated significantly from Line c_Q. Deviations in line additive effects from c_Q were negative in all lines examined whereas deviations in line maternal effects from c_Q were all positive, indicating a negative relationship between line additive and line maternal effects. Direct heterosis effects were all positive and significant (P < 0.01) except in the M_PxW_P cross which was produced by mating Lines M_P and W_P of the same base population (P). Maternal heterosis effects were significant in 10 of 20 cases whereas paternal heterosis effects were significant in 13 of 20 cases. Although direct heterosis is a major component of total heterosis effects (sum of direct, maternal and paternal heterosis), the results suggest that parental heterosis may need to be considered in producing multiple way crosses. The fitting of line additive, line maternal, direct heterosis, maternal heterosis and paternal heterosis effects in the multiple regression model effectively accounted for all genetic effects in lifetime performance.Animal Research Centre Contribution No. 1326     

QTL analysis of early stage heterosis for biomass in Arabidopsis

The main objective of this study was to identify genomic regions involved in biomass heterosis using QTL, generation means, and mode-of-inheritance classification analyses. In a modified North Carolina Design III we backcrossed 429 recombinant inbred line and 140 introgression line populations to the two parental accessions, C24 and Col-0, whose F ₁ hybrid exhibited 44% heterosis for biomass. Mid-parent heterosis in the RILs ranged from ?31 to 99% for dry weight and from ?58 to 143% for leaf area. We detected ten genomic positions involved in biomass heterosis at an early developmental stage, individually explaining between 2.4 and 15.7% of the phenotypic variation. While overdominant gene action was prevalent in heterotic QTL, our results suggest that a combination of dominance, overdominance and epistasis is involved in biomass heterosis in this Arabidopsis cross.     

Heterosis as investigated in terms of polyploidy and genetic diversity using designed Brassica juncea amphiploid and its progenitor diploid species

Fixed heterosis resulting from favorable interactions between the genes on their homoeologous genomes in an allopolyploid is considered analogous to classical heterosis accruing from interactions between homologous chromosomes in heterozygous plants of a diploid species. It has been hypothesized that fixed heterosis may be one of the causes of low classical heterosis in allopolyploids. We used Indian mustard (Brassica juncea, 2n = 36; AABB) as a model system to analyze this hypothesis due to ease of its resynthesis from its diploid progenitors, B. rapa (2n = 20; AA) and B. nigra (2n = 16; BB). Both forms of heterosis were investigated in terms of ploidy level, gene action and genetic diversity. To facilitate this, eleven B. juncea genotypes were resynthesized by hybridizing ten near inbred lines of B. rapa and nine of B. nigra. Three half diallel combinations involving resynthesized B. juncea (11×11) and the corresponding progenitor genotypes of B. rapa (10×10) and B. nigra (9×9) were evaluated. Genetic diversity was estimated based on DNA polymorphism generated by SSR primers. Heterosis and genetic diversity in parental diploid species appeared not to predict heterosis and genetic diversity at alloploid level. There was also no association between combining ability, genetic diversity and heterosis across ploidy. Though a large proportion (0.47) of combinations showed positive values, the average fixed heterosis was low for seed yield but high for biomass yield. The genetic diversity was a significant contributor to fixed heterosis for biomass yield, due possibly to adaptive advantage it may confer on de novo alloploids during evolution. Good general/specific combiners at diploid level did not necessarily produce good general/specific combiners at amphiploid level. It was also concluded that polyploidy impacts classical heterosis indirectly due to the negative association between fixed heterosis and classical heterosis.     

<Emphasis Type="Italic">Macrocystis</Emphasis> mariculture in Chile: growth performance of heterosis genotype constructs under field conditions

Recent progress in Macrocystis mariculture is based on clonal stock cultures of gametophyte parents. Batches of up to 10⁵ genetically identical sporophyte seedlings can be produced at any time in the laboratory and explanted in the field for production of biomass. Sexual crosses of selected Macrocystis pyrifera gametophyte parents of different geographic origin along the coast of Chile showed heterosis and produced sporophyte batches with superior growth performance. Starting from zygotes, after 10 weeks in the laboratory and 5 months in the sea, our best hybrid genotypes grew up to 11 kg fresh weight per frond, which corresponds to 66 kg m⁻¹ of line in a commercial mariculture installation. In contrast, average yields of 14.4 and 22 kg m⁻¹ are reported in the literature for traditional methods. Additional experiments, including inter-specific crosses M. pyrifera × M. integrifolia and their performance in different climate zones of Chile, confirm that heterosis is a powerful tool for crop improvement in Macrocystis. It opens the possibility to construct tailor-made heterosis genotypes with maximum productivity and/or other desired properties for any given locality.     

Genetic divergence and hybrid performance in mung bean

Summary Genetic divergence in 35 populations (10 parents and 25 F₁'s) of mung bean was studied by D² and canonical analyses. The ten parents formed as many as eight separate clusters, suggesting that the genetic divergence between them was quite substantial. The parent BR-2 was highly divergent from all the other entries. It was found that flowering time, maturity, seed density and seed size (100-seed weight) contributed substantially to the divergence. Canonical analysis supported the divergence pattern obtained by D² analysis and the contribution of different characters to genetic divergence. The relationship between genetic divergence (D²) and heterosis was evaluated. In general, there was fair agreement between the extent of heterosis and the genetic divergence between the parents.     

Predicting heterosis for egg production traits in crossbred offspring of individual White Leghorn sires using genome-wide SNP data

Background

The development of a reliable method to predict heterosis would greatly improve the efficiency of commercial crossbreeding schemes. Extending heterosis prediction from the line level to the individual sire level would take advantage of variation between sires from the same pure line, and further increase the use of heterosis in crossbreeding schemes. We aimed at deriving the theoretical expectation for heterosis due to dominance in the crossbred offspring of individual sires, and investigating how much extra variance in heterosis can be explained by predicting heterosis at the individual sire level rather than at the line level. We used 53 421 SNP (single nucleotide polymorphism) genotypes of 3427 White Leghorn sires, allele frequencies of six White Leghorn dam-lines and cage-based records on egg number and egg weight of ~210 000 crossbred hens.

Results

We derived the expected heterosis for the offspring of individual sires as the between- and within-line genome-wide heterozygosity excess in the offspring of a sire relative to the mean heterozygosity of the pure lines. Next, we predicted heterosis by regressing offspring performance on the heterozygosity excess. Predicted heterosis ranged from 7.6 to 16.7 for egg number, and from 1.1 to 2.3 grams for egg weight. Between-line differences accounted for 99.0% of the total variance in predicted heterosis, while within-line differences among sires accounted for 0.7%.

Conclusions

We show that it is possible to predict heterosis at the sire level, thus to distinguish between sires within the same pure line with offspring that show different levels of heterosis. However, based on our data, variation in genome-wide predicted heterosis between sires from the same pure line was small; most differences were observed between lines. We hypothesise that this method may work better if predictions are based on SNPs with identified dominance effects.     

Comparative gene expression profiles between heterotic and non-heterotic hybrids of tetraploid Medicago sativa

Background  

Heterosis, the superior performance of hybrids relative to parents, has clear agricultural value, but its genetic control is unknown. Our objective was to test the hypotheses that hybrids expressing heterosis for biomass yield would show more gene expression levels that were different from midparental values and outside the range of parental values than hybrids that do not exhibit heterosis.     

Genetic control of the opaque-2 gene and background polygenes over some kernel traits in maize (Zea mays L.)

Some kernel traits of agronomical importance in maize are affected by the opaque-2 (o2) gene and background polygenes, which express in different genetic systems such as embryo, endosperm, cytoplasm and maternal plant. A genetic model for seed quantitative traits with the o2 gene effects and polygenic effects as well as their GE interactions was used for protein content, lysine content, oil content and kernel density in maize. The results suggested that the o2 gene was involved in the traits investigated but the effects of the o2 gene were distinctive on various traits. The effects of the o2 gene were large on lysine content and protein content while minor on oil content. There was a substantially wide quantitative variation from polygenes expressing in different genetic systems for the traits evaluated. Significant GE interactions of the o2 gene and background polygenes declared that not only the main effects but also specific expressions depending on environments were responsible for variation of the traits studied. There seemed to have strong maternal heterosis and slight embryo heterosis for kernel density.     

Fitness of Karyotypes in DROSOPHILA PSEUDOOBSCURA

In the dynamics of the survival of chromosomal polymorphism selection may be operating at the genic level, at the chromosomal level or at the supergene level. Tests designed to distinguish between these levels were run on Drosophila pseudoobscura. There was no evidence for heterosis, a necessary requirement for gene-determined chromosomal polymorphism. A strong chromosmal selection was observed. No evidence was found for the presence within one locality of more than a single superallele for each supergene (= gene order). These results are compared to those found by others.