A role for heritable transcriptomic variation in maize adaptation to temperate environments

Background: Transcription bridges genetic information and phenotypes. Here, we evaluated how changes in transcriptional regulation enable maize (Zea mays), a crop originally domesticated in the tropics, to adapt to temperate environments. Result: We generated 572 unique RNA-seq datasets from the roots of 340 maize genotypes. Genes involved in core processes such as cell division, chromosome organization and cytoskeleton organization showed lower heritability of gene expression, while genes involved in anti-oxidation activity exhibited higher expression heritability. An expression genome-wide association study (eGWAS) identified 19,602 expression quantitative trait loci (eQTLs) associated with the expression of 11,444 genes. A GWAS for alternative splicing identified 49,897 splicing QTLs (sQTLs) for 7614 genes. Genes harboring both cis-eQTLs and cis-sQTLs in linkage disequilibrium were disproportionately likely to encode transcription factors or were annotated as responding to one or more stresses. Independent component analysis of gene expression data identified loci regulating co-expression modules involved in oxidation reduction, response to water deprivation, plastid biogenesis, protein biogenesis, and plant-pathogen interaction. Several genes involved in cell proliferation, flower development, DNA replication, and gene silencing showed lower gene expression variation explained by genetic factors between temperate and tropical maize lines. A GWAS of 27 previously published phenotypes identified several candidate genes overlapping with genomic intervals showing signatures of selection during adaptation to temperate environments. Conclusion: Our results illustrate how maize transcriptional regulatory networks enable changes in transcriptional regulation to adapt to temperate regions

A role for heritable transcriptomic variation in maize adaptation to temperate environments

Background: Transcription bridges genetic information and phenotypes. Here, we evaluated how changes in transcriptional regulation enable maize (Zea mays), a crop originally domesticated in the tropics, to adapt to temperate environments. Result: We generated 572 unique RNA-seq datasets from the roots of 340 maize genotypes. Genes involved in core processes such as cell division, chromosome organization and cytoskeleton organization showed lower heritability of gene expression, while genes involved in anti-oxidation activity exhibited higher expression heritability. An expression genome-wide association study (eGWAS) identified 19,602 expression quantitative trait loci (eQTLs) associated with the expression of 11,444 genes. A GWAS for alternative splicing identified 49,897 splicing QTLs (sQTLs) for 7614 genes. Genes harboring both cis-eQTLs and cis-sQTLs in linkage disequilibrium were disproportionately likely to encode transcription factors or were annotated as responding to one or more stresses. Independent component analysis of gene expression data identified loci regulating co-expression modules involved in oxidation reduction, response to water deprivation, plastid biogenesis, protein biogenesis, and plant-pathogen interaction. Several genes involved in cell proliferation, flower development, DNA replication, and gene silencing showed lower gene expression variation explained by genetic factors between temperate and tropical maize lines. A GWAS of 27 previously published phenotypes identified several candidate genes overlapping with genomic intervals showing signatures of selection during adaptation to temperate environments. Conclusion: Our results illustrate how maize transcriptional regulatory networks enable changes in transcriptional regulation to adapt to temperate regions

Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish

White-blooded Antarctic icefishes, a family within the adaptive radiation of Antarctic notothenioid fishes, are an example of extreme biological specialization to both the chronic cold of the Southern Ocean and life without hemoglobin. As a result, icefishes display derived physiology that limits them to the cold and highly oxygenated Antarctic waters. Against these constraints, remarkably one species, the pike icefish Champsocephalus esox, successfully colonized temperate South American waters. To study the genetic mechanisms underlying secondarily temperate adaptation in icefishes, we generated chromosome-level genome assemblies of both C. esox and its Antarctic sister species, Champsocephalus gunnari. The C. esox genome is similar in structure and organization to that of its Antarctic congener; however, we observe evidence of chromosomal rearrangements coinciding with regions of elevated genetic divergence in pike icefish populations. We also find several key biological pathways under selection, including genes related to mitochondria and vision, highlighting candidates behind temperate adaptation in C. esox. Substantial antifreeze glycoprotein (AFGP) pseudogenization has occurred in the pike icefish, likely due to relaxed selection following ancestral escape from Antarctica. The canonical AFGP locus organization is conserved in C. esox and C. gunnari, but both show a translocation of two AFGP copies to a separate locus, previously unobserved in cryonotothenioids. Altogether, the study of this secondarily temperate species provides an insight into the mechanisms underlying adaptation to ecologically disparate environments in this otherwise highly specialized group

Exploring the Phenotypic Space and the Evolutionary History of a Natural Mutation in Drosophila melanogaster

A major challenge of modern Biology is elucidating the functional consequences of natural mutations. Although we have a good understanding of the effects of laboratory-induced mutations on the molecular- and organismal-level phenotypes, the study of natural mutations has lagged behind. In this work, we explore the phenotypic space and the evolutionary history of a previously identified adaptive transposable element insertion. We first combined several tests that capture different signatures of selection to show that there is evidence of positive selection in the regions flanking FBti0019386 insertion. We then explored several phenotypes related to known phenotypic effects of nearby genes, and having plausible connections to fitness variation in nature. We found that flies with FBti0019386 insertion had a shorter developmental time and were more sensitive to stress, which are likely to be the adaptive effect and the cost of selection of this mutation, respectively. Interestingly, these phenotypic effects are not consistent with a role of FBti0019386 in temperate adaptation as has been previously suggested. Indeed, a global analysis of the population frequency of FBti0019386 showed that climatic variables explain well the FBti0019386 frequency patterns only in Australia. Finally, although FBti0019386 insertion could be inducing the formation of heterochromatin by recruiting HP1a (Heterochromatin Protein 1a) protein, the insertion is associated with upregulation of sra in adult females. Overall, our integrative approach allowed us to shed light on the evolutionary history, the relevant fitness effects, and the likely molecular mechanisms of an adaptive mutation and highlights the complexity of natural genetic variants.A.U. is an FPI fellow (BES-2012-052999) and J.G. is a Ramón y Cajal fellow (RYC-2010-07306). This work was supported by grants from the European Comission (Marie Curie CIG PCIG-2011-293860) and from the Spanish Government (Fundamental Research Projects Grant BFU-2011-24397) to J.G.Peer reviewe

The Complex Demographic History and Evolutionary Origin of the Western Honey Bee, Apis Mellifera.

The western honey bee, Apis mellifera, provides critical pollination services to agricultural crops worldwide. However, despite substantial interest and prior investigation, the early evolution and subsequent diversification of this important pollinator remain uncertain. The primary hypotheses place the origin of A. mellifera in either Asia or Africa, with subsequent radiations proceeding from one of these regions. Here, we use two publicly available whole-genome data sets plus newly sequenced genomes and apply multiple population genetic analysis methods to investigate the patterns of ancestry and admixture in native honey bee populations from Europe, Africa, and the Middle East. The combination of these data sets is critical to the analyses, as each contributes samples from geographic locations lacking in the other, thereby producing the most complete set of honey bee populations available to date. We find evidence supporting an origin of A. mellifera in the Middle East or North Eastern Africa, with the A and Y lineages representing the earliest branching lineages. This finding has similarities with multiple contradictory hypotheses and represents a disentangling of genetic relationships, geographic proximity, and secondary contact to produce a more accurate picture of the origins of A. mellifera. We also investigate how previous studies came to their various conclusions based on incomplete sampling of populations, and illustrate the importance of complete sampling in understanding evolutionary processes. These results provide fundamental knowledge about genetic diversity within Old World honey bee populations and offer insight into the complex history of an important pollinator

Quality Protein Maize Germplasm Characterized for Amino Acid Profiles and Endosperm Opacity

Quality protein maize (QPM) is improved over normal (non-QPM) maize in grain concentrations of the essential amino acids lysine and tryptophan. Quality protein maize has a long history as tropical adapted germplasm, but little effort has been made to incorporate temperate or sub-tropical germplasm for temperate adaptation and interactions between different modifier loci in these backgrounds are poorly understood. A design-II mating scheme including new temperate and subtropical lines produced 69 hybrids. Large hybrid genetic variation components resulted in substantial broad-sense heritability H2 estimates, specifically tryptophan (0.46) and endosperm opacity (0.82). A microbial assay for amino acid estimation proved robust across diverse environments with minimal genotype × environment (G×E) effects. Endosperm opacity had no G×E effects across both Texas and Iowa locations demonstrating stability for this trait. Endosperm opacity primarily followed an additive, midparent trend, with a few hybrids deviating from the trend (36%) suggesting a complex nature of multiple modifier loci across diverse germplasm. The top QPM hybrid outperformed the top commercial hybrid by 35 and 30% for lysine and tryptophan as a proportion of grain, respectively. QPM line Tx832 was a parent of top hybrids for lysine and tryptophan, and the highest noncommercial hybrids for methionine. Minimal correlations with yield and other traits suggest that future breeding should result in QPM hybrids with increasingly competitive yields

Seasonal changes in metabolic rates in muskoxen following twenty- four hours of starvation

Timing of seasonal trends in post-prandial energy expenditure (EE) was measured in muskoxen (2 males and 1 female) given a standardized meal followed by a 24-26 h starvation during 10 months over the course of a year. EE was significantly lower in winter than summer. CH4 production (EctM) was reversed with winter highs and summer lows. Ratio of ECH4:EE indicates a change in dietary efficiency but this difference was not associated with a seasonal shift in RQ which was constant. The main increase in EE from winter to summer occurred between April and May and the summer to winter decrease between August and Septembet

Tolerancia del arroz a la temperatura baja

Tolerance of rice to low temperatures The damages caused to rice crops by low temperatures and cold are reviewed, and crop symptoms are indicated. The results of genetic improvement efforts regarding cold tolerance in rice are also discussed. Low temperatures limit rice production in the tropical and subtropical upland areas of temperate zones. The effects of cold temperatures during different stages of plant development include reduced yields, extended vegetative cycle, and deteriorated grain quality. The nature and extent of the damages caused to the crop will depend, among other factors, on the duration and intensity of the cold spell as well as on the stage of the crop when low temperatures occur. One way to deal with adverse climatic conditions is by using varieties tolerant to this type of stress. Rice improvement programs in the southernmost part of Latin America are selecting germplasm for tolerance to cold conditions at different phenological stages. This is usually done by exposing the germplasm to natural conditions—a methodology that works but is both expensive and time-consuming. The Latin American Fund for Irrigated Rice (FLAR) has recently developed several procedures under controlled conditions to accelerate germplasm selection. This strategy combines the cold tolerance of japonica rice with the yield potential and grain quality of indica rice. This objective has been persistently pursued by different agricultural research organizations in the affected areas. As a result, since 2001 one of FLAR’s programs has focused on combining high yields with cold tolerance to offer useful rice germplasm to its partners in temperate areas of South America, where the cold climate represents an ongoing threat to this crop.Se revisan los daños causados por las temperaturas bajas y el frío al cultivo del arroz, la sintomatología del daño y las investigaciones en mejoramiento genético con respecto a la tolerancia del frío. Las temperaturas bajas limitan la producción de arroz en las tierras altas de los trópicos y en las franjas subtropicales de las zonas templadas. Por los daños que causa el frío en varias etapas del desarrollo de las plantas, reducen el rendimiento del cultivo, alargan su ciclo vegetativo y deterioran la calidad del grano. La naturaleza de estos daños y su alcance en el tiempo dependen, entre otros factores, de la duración del período frío, de la intensidad del frío y de la etapa en que se halla el cultivo. Una forma de manejar esta adversidad climática es la tolerancia varietal de este tipo de estrés. Los programas de mejoramiento en el Cono Sur de América Latina hacen selección por tolerancia del frío en diferentes estados fenológicos. Generalmente, lo hacen por exposición del germoplasma a condiciones naturales, una metodología que funciona pero es costosa y lenta. Recientemente, el FLAR (Fondo Latinoamericano para Arroz de Riego) desarrolló algunos procedimientos en condiciones controladas para acelerar la selección de germoplasma, en los que combinó la tolerancia del frío del arroz tipo Japónica con el potencial de rendimiento y la calidad del arroz tipo Índica. Este objetivo ha sido perseguido constantemente por diversas organizaciones de investigación agrícola en las áreas afectadas. Por eso, el FLAR, desde el 2001, trabaja en un programa cuyo objetivo principal es combinar el alto rendimiento con la tolerancia del frío para ofrecer germoplasma útil a los socios ubicados en la zona templada de América del Sur donde el frío es una permanente amenaza del cultivo de arroz

Recent emergence of the wheat Lr34 multi-pathogen resistance: insights from haplotype analysis in wheat, rice, sorghum and Aegilops tauschii

Spontaneous sequence changes and the selection of beneficial mutations are driving forces of gene diversification and key factors of evolution. In highly dynamic co-evolutionary processes such as plant-pathogen interactions, the plant's ability to rapidly adapt to newly emerging pathogens is paramount. The hexaploid wheat gene Lr34, which encodes an ATP-binding cassette (ABC) transporter, confers durable field resistance against four fungal diseases. Despite its extensive use in breeding and agriculture, no increase in virulence towards Lr34 has been described over the last century. The wheat genepool contains two predominant Lr34 alleles of which only one confers disease resistance. The two alleles, located on chromosome 7DS, differ by only two exon-polymorphisms. Putatively functional homoeologs and orthologs of Lr34 are found on the B-genome of wheat and in rice and sorghum, but not in maize, barley and Brachypodium. In this study we present a detailed haplotype analysis of homoeologous and orthologous Lr34 genes in genetically and geographically diverse selections of wheat, rice and sorghum accessions. We found that the resistant Lr34 haplotype is unique to the wheat D-genome and is not found in the B-genome of wheat or in rice and sorghum. Furthermore, we only found the susceptible Lr34 allele in a set of 252 Ae. tauschii genotypes, the progenitor of the wheat D-genome. These data provide compelling evidence that the Lr34 multi-pathogen resistance is the result of recent gene diversification occurring after the formation of hexaploid wheat about 8,000years ag