Orientation of mouse H19 ICR affects imprinted H19 gene expression through promoter methylation-dependent and -independent mechanisms

The mouse Igf2/H19 locus is regulated by genomic imprinting, in which the paternally methylated H19 imprinting control region (ICR) plays a critical role in mono-allelic expression of the genes in the locus. Although the maternal allele-specific insulator activity of the H19 ICR in regulating imprinted Igf2 expression has been well established, the detailed mechanism by which the H19 ICR controls mono-allelic H19 gene expression has not been fully elucidated. In this study, we evaluated the effect of H19 ICR orientation on imprinting regulation in mutant mice in which the H19 ICR sequence was inverted at the endogenous locus. When the inverted-ICR allele was paternally inherited, the methylation level of the H19 promoter was decreased and the H19 gene was derepressed, suggesting that methylation of the H19 promoter is essential for complete repression of H19 gene expression. Unexpectedly, when the inverted allele was maternally inherited, the expression level of the H19 gene was lower than that of the WT allele, even though the H19 promoter remained fully hypomethylated. These observations suggested that the polarity of the H19 ICR is involved in controlling imprinted H19 gene expression on each parental allele, dependent or independent on DNA methylation of the H19 promoter.

Patterns of stability and change in the maize genome: a case study of small RNA transcriptomes in two recombinant inbred lines and their progenitors

Small RNAs (sRNAs) are epigenetic regulators of eukaryotic genes and transposable elements (TEs). Diverse sRNA expression patterns exist within a species, but how this diversity arises is not well understood. To provide a window into the dynamics of maize sRNA patterning, sRNA and mRNA transcriptomes were examined in two related Zea mays recombinant inbred lines (RILs) and their inbred parents. Analysis of these RILs revealed that most clusters of sRNA expression retain the parental sRNA expression level. However, expression states that differ from the parental allele were also observed, predominantly reflecting decreases in sRNA expression. When RIL sRNA expression differed from the parental allele, the new state was frequently similar between the two RILs, and similar to the expression state found at the allele in the other parent. Novel sRNA expression patterns, distinct from either parent, were rare. Additionally, examination of sRNA expression over TEs revealed one TE family, Gyma, that showed consistent enrichment for RIL sRNA expression differences compared to those found at parental alleles. These findings provide insights into how sRNA silencing might evolve over generations and suggest that further inquiry into the molecular nature of sRNA trans regulators is warranted.

PATRIOT: A Pipeline for Tracing Identity-by-Descent for Chromosome Segments to Improve Genomic Prediction in Self-Pollinating Crop Species

The lowering genotyping cost is ushering in a wider interest and adoption of genomic prediction and selection in plant breeding programs worldwide. However, improper conflation of historical and recent linkage disequilibrium between markers and genes restricts high accuracy of genomic prediction (GP). Multiple ancestors may share a common haplotype surrounding a gene, without sharing the same allele of that gene. This prevents parsing out genetic effects associated with the underlying allele of that gene among the set of ancestral haplotypes. We present “Parental Allele Tracing, Recombination Identification, and Optimal predicTion” (i.e., PATRIOT) approach that utilizes marker data to allow for a rapid identification of lines carrying specific alleles, increases the accuracy of genomic relatedness and diversity estimates, and improves genomic prediction. Leveraging identity-by-descent relationships, PATRIOT showed an improvement in GP accuracy by 16.6% relative to the traditional rrBLUP method. This approach will help to increase the rate of genetic gain and allow available information to be more effectively utilized within breeding programs.

APOK3, a pollen killer antidote in Arabidopsis thaliana

According to the principles of heredity, each parental allele of hybrids equally participates in the progeny. At some loci, however, it happens that one allele is favored to the expense of the other. Gamete killers are genetic systems where one allele (the killer) triggers the death of the gametes carrying the other (killed) allele. They have been found in many organisms, and are of major interest to understand mechanisms of evolution and speciation. Gamete killers are particularly prevalent in plants, where they can compromise crop breeding. Here, we deciphered a pollen killer in Arabidopsis thaliana by exploiting natural variation, de novo genomic sequencing and mutants, and analyzing segregations in crosses. We found that the killer allele carries an antidote gene flanked by two elements mandatory for the killing activity. We identified the gene encoding the antidote, a chimeric protein addressed to mitochondria. This gene appeared in the species by association of domains recruited from other genes, and it recently underwent duplications within a highly variable locus, particularly in the killer genotypes. Exploring the species diversity, we identified sequence polymorphisms correlated with the antidote activity.

Transcriptional network of the industrial hybrid Saccharomyces pastorianus reveals temperature-dependent allele expression bias and preferential orthologous protein assemblies

Saccharomyces pastorianus is an industrial natural yeast evolved from different hybridisation events between the mesophilic S. cerevisiae and the cold-tolerant S. eubayanus. This complex aneuploid hybrid carries multiple copies of the parental alleles alongside specific hybrid genes and encodes for multiple protein isoforms which impart novel phenotypes, such as the strong ability to ferment at low temperature. These characteristics lead to agonistic or antagonistic competition for substrates and a plethora of biochemical activities, resulting in a unique cellular metabolism. Here, we investigated the transcriptional signature of the different orthologous alleles in S. pastorianus during temperature shifts. We identified temperature-dependent media-independent genes and showed that 35% have their regulation dependent on extracellular leucine uptake, suggesting an interplay between leucine metabolism and temperature response. The analysis of the expression of ortholog parental alleles unveiled that the majority of the genes express preferentially one parental allele over the other, and that S. eubayanus-like alleles are significantly over-represented among the genes involved in cold acclimatisation. The presence of functionally redundant parental alleles may impact on the nature of protein complexes established in the hybrid, where both parental alleles are competing. Our expression data indicate that the majority of the protein complexes established in the hybrid are likely to be either exclusively chimeric or uni-specific, and that the redundancy is discouraged, a scenario which fits well with the stoichiometric balance-hypothesis. This study offers a first overview of the transcriptional pattern of S. pastorianus and provide a rationalisation for its unique industrial traits at expression level.

Identifying Wild Versus Cultivated Gene-Alleles Conferring Seed Coat Color and Days to Flowering in Soybean

Annual wild soybean (G. soja) is the ancestor of the cultivated soybean (G. max). To reveal the genetic changes from soja to max, an improved wild soybean chromosome segment substitution line (CSSL) population, SojaCSSLP5, composed of 177 CSSLs with 182 SSR markers (SSR-map), was developed based on SojaCSSLP1 generated from NN1138-2(max)×N24852(soja). The SojaCSSLP5 was genotyped further through whole-genome resequencing, resulting in a physical map with 1366 SNPLDBs (SNP linkage-disequilibrium blocks), which are composed of more markers/segments, shorter marker length and more recombination breakpoints than the SSR-map and caused 721 new wild substituted segments. Using the SNPLDB-map, two loci co-segregating with seed-coat color (SCC) and six loci for days to flowering (DTF) with 88.02% phenotypic contribution were identified. Integrated with parental RNA-seq and DNA-resequencing, two SCC and six DTF candidate genes, including three previously cloned (G, E2 and GmPRR3B) and five newly detected ones, were predicted and verified at nucleotide mutant level, and then demonstrated with the consistency between gene-alleles and their phenotypes in SojaCSSLP5. In total, six of the eight genes were identified with the parental allele-pairs coincided to those in 303 germplasm accessions, then were further demonstrated by the consistency between gene-alleles and germplasm phenotypes. Accordingly, the CSSL population integrated with parental DNA and RNA sequencing data was demonstrated to be an efficient platform in identifying candidate wild vs. cultivated gene-alleles.

Predicting the purebred-crossbred genetic correlation from the genetic variance components in the parental lines

Background The genetic correlation between purebred and crossbred performance ($${r}_{pc}$$ r pc ) is an important parameter in pig and poultry breeding, because response to selection in crossbred performance depends on the value of $${r}_{pc}$$ r pc when selection is based on purebred (PB) performance. The value of $${r}_{pc}$$ r pc can be substantially lower than 1, which is partly due to differences in allele frequencies between parental lines when non-additive genetic effects are present. This relationship between $${r}_{pc}$$ r pc and parental allele frequencies suggests that $${r}_{pc}$$ r pc can be expressed as a function of genetic parameters for the trait in the parental lines. In this study, we derived expressions for $${r}_{pc}$$ r pc based on genetic variances within, and the genetic covariance between parental lines. It is important to note that the variance components used in our expressions are not the components that are typically estimated in empirical data. The expressions were derived for a genetic model with additive and dominance effects (D), and additive and epistatic additive-by-additive effects (EAA). We validated our expressions using simulations of purebred parental lines and their crosses, where the parental lines were either selected or not. Finally, using these simulations, we investigated the value of $${r}_{pc}$$ r pc for genetic models with both dominance and epistasis or with other types of epistasis, for which expressions could not be derived. Results Our simulations show that when non-additive effects are present, $${r}_{pc}$$ r pc decreases with increasing differences in allele frequencies between the parental lines. Genetic models that involve dominance result in lower values of $${r}_{pc}$$ r pc than genetic models that involve epistasis only. Using information of parental lines only, our expressions provide exact estimates of $${r}_{pc}$$ r pc for models D and EAA, and accurate upper and lower bounds of $${r}_{pc}$$ r pc for two other genetic models. Conclusion This work lays the foundation to enable estimation of $${r}_{pc}$$ r pc from information collected in PB parental lines only.

QTL Mapping and Candidate Gene Identification of Swollen Root Formation in Turnip

The swollen root is an important agronomic trait and is a determinant of yield for turnips, which are cultivated as both vegetables and fodder. However, the genetic mechanism of swollen root formation is poorly understood. In this study, we analyzed the F2 and BC1P2 populations derived from a cross between “10601” (European turnip with swollen root, Brassica rapa ssp. rapifera, AA, 2n = 2× = 20) and “10603” (Chinese cabbage with normal root, Brassica rapa ssp. pekinensis, AA, 2n = 2× = 20), and suggested that the swollen root is a quantitative trait. Two major quantitative trait loci (QTLs), FR1.1 (Fleshy root 1.1) and FR7.1 (Fleshy root 7.1), were identified by QTL-seq analysis and further confirmed by QTL mapping in F2 and BC1P2 populations. The QTL FR1.1 with a likelihood of odd (LOD) of 7.01 explained 17.2% of the total phenotypic variations for root diameter and the QTL FR7.1 explained 23.0% (LOD = 9.38) and 31.0% (LOD = 13.27) of the total phenotypic variations in root diameter and root weight, respectively. After a recombinant screening, the major QTL FR7.1 was further narrowed down to a 220 kb region containing 47 putative genes. A candidate gene, Bra003652, which is a homolog of AT1G78240 that plays an essential role in cell adhesion and disorganized tumor-like formation in Arabidopsis thaliana, was identified in this region. In addition, expression and parental allele analysis supported that Bra003652 was a possible candidate gene of QTL FR7.1 for swollen root formation in turnip. Our research may provide new insight into the molecular mechanism of swollen root formation in root crops.

Recovery from hybrid breakdown reveals a complex genetic architecture of mitonuclear incompatibilities

Reproductive isolation is often achieved when genes that are neutral or beneficial in their genomic background become functionally incompatible in a foreign genome, causing inviability, sterility or low fitness in hybrids. Recent studies suggest that mitonuclear interactions are among the initial incompatibilities to evolve at early stages of population divergence across taxa. Yet, it is unclear whether mitonuclear incompatibilities involve few or many regions in the nuclear genome. We employ an experimental evolution approach starting with unfit F2 interpopulation hybrids of the copepod Tigriopus californicus, in which compatible and incompatible nuclear alleles compete in a fixed mitochondrial background. After about nine generations, we observe a generalized increase in population size and in survivorship, suggesting efficiency of selection against maladaptive phenotypes. Whole genome sequencing of evolved populations showed some consistent allele frequency changes across the three replicates of each reciprocal cross, but markedly different patterns between mitochondrial background. In only a few regions (~6.5% of the genome), the same parental allele was overrepresented irrespective of the mitochondrial background. About 33% of the genome shows allele frequency changes consistent with divergent selection, with the location of these genomic regions strongly differing between mitochondrial backgrounds. The dominant allele matches the mitochondrial background in 87 and 89% of these genomic regions, consistent with mitonuclear coadaptation. These results suggest that mitonuclear incompatibilities have a complex polygenic architecture that differs between populations, potentially generating genome wide barriers to gene flow between closely related taxa.

Maternal DOT1L is dispensable for mouse development

A battery of chromatin modifying enzymes play essential roles in remodeling the epigenome in the zygote and cleavage stage embryos, when the maternal genome is the sole contributor. Here we identify an exemption. DOT1L methylates lysine 79 in the globular domain of histone H3 (H3K79). Dot1l is an essential gene, as homozygous null mutant mouse embryos exhibit multiple developmental abnormalities and die before 11.5 days of gestation. To test if maternally deposited DOT1L is required for embryo development, we carried out a conditional Dot1l knockout in growing oocytes using the Zona pellucida 3-Cre (Zp3-Cre) transgenic mice. We found that the resulting maternal mutant Dot1lmat−/+ offspring displayed normal development and fertility, suggesting that the expression of the paternally inherited copy of Dot1l in the embryo is sufficient to support development. In addition, Dot1l maternal deletion did not affect the parental allele-specific expression of imprinted genes, indicating that DOT1L is not needed for imprint establishment in the oocyte or imprint protection in the zygote. In summary, uniquely and as opposed to other histone methyltransferases and histone marks, maternal DOT1L deposition and H3K79 methylation in the zygote and in the preimplantation stage embryo is dispensable for mouse development.