Co-occurrence of amyotrophic lateral sclerosis and Leber's hereditary optic neuropathy: is mitochondrial dysfunction a modifier?

N

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Introduction: Wheat (Triticum aestivum L.) is the most widely cultivated crop on Earth, contributing about a fifth of the total calories consumed by humans. Consequently, wheat yields and production affect the global economy, and failed harvests can lead to social unrest. Breeders continuously strive to develop improved varieties by fine-tuning genetically complex yield and end-use quality parameters while maintaining stable yields and adapting the crop to regionally specific biotic and abiotic stresses. Rationale: Breeding efforts are limited by insufficient knowledge and understanding of wheat biology and the molecular basis of central agronomic traits. To meet the demands of human population growth, there is an urgent need for wheat research and breeding to accelerate genetic gain as well as to increase and protect wheat yield and quality traits. In other plant and animal species, access to a fully annotated and ordered genome sequence, including regulatory sequences and genome-diversity information, has promoted the development of systematic and more time-efficient approaches for the selection and understanding of important traits. Wheat has lagged behind, primarily owing to the challenges of assembling a genome that is more than five times as large as the human genome, polyploid, and complex, containing more than 85% repetitive DNA. To provide a foundation for improvement through molecular breeding, in 2005, the International Wheat Genome Sequencing Consortium set out to deliver a high-quality annotated reference genome sequence of bread wheat. Results: An annotated reference sequence representing the hexaploid bread wheat genome in the form of 21 chromosome-like sequence assemblies has now been delivered, giving access to 107,891 high-confidence genes, including their genomic context of regulatory sequences. This assembly enabled the discovery of tissue- and developmental stage–related gene coexpression networks using a transcriptome atlas representing all stages of wheat development. The dynamics of change in complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. Aspects of the future value of the annotated assembly for molecular breeding and research were exemplarily illustrated by resolving the genetic basis of a quantitative trait locus conferring resistance to abiotic stress and insect damage as well as by serving as the basis for genome editing of the flowering-time trait. Conclusion: This annotated reference sequence of wheat is a resource that can now drive disruptive innovation in wheat improvement, as this community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding. Importantly, the bioinformatics capacity developed for model-organism genomes will facilitate a better understanding of the wheat genome as a result of the high-quality chromosome-based genome assembly. By necessity, breeders work with the genome at the whole chromosome level, as each new cross involves the modification of genome-wide gene networks that control the expression of complex traits such as yield. With the annotated and ordered reference genome sequence in place, researchers and breeders can now easily access sequence-level information to precisely define the necessary changes in the genomes for breeding programs. This will be realized through the implementation of new DNA marker platforms and targeted breeding technologies, including genome editing

Durum wheat genome highlights past domestication signatures and future improvement targets

PubMedID: 30962619The domestication of wild emmer wheat led to the selection of modern durum wheat, grown mainly for pasta production. We describe the 10.45 gigabase (Gb) assembly of the genome of durum wheat cultivar Svevo. The assembly enabled genome-wide genetic diversity analyses revealing the changes imposed by thousands of years of empirical selection and breeding. Regions exhibiting strong signatures of genetic divergence associated with domestication and breeding were widespread in the genome with several major diversity losses in the pericentromeric regions. A locus on chromosome 5B carries a gene encoding a metal transporter (TdHMA3-B1) with a non-functional variant causing high accumulation of cadmium in grain. The high-cadmium allele, widespread among durum cultivars but undetected in wild emmer accessions, increased in frequency from domesticated emmer to modern durum wheat. The rapid cloning of TdHMA3-B1 rescues a wild beneficial allele and demonstrates the practical use of the Svevo genome for wheat improvement. © 2019, The Author(s), under exclusive licence to Springer Nature America, Inc.Western Grains Research Foundation Ministry of Agriculture - Saskatchewan Israel Science Foundation: 1137/17 031A536 FP7 Food, Agriculture and Fisheries, Biotechnology: DROPS ID244347 Natural Sciences and Engineering Research Council of Canada InterOmics PB05 Genome Prairie United States-Israel Binational Science Foundation: 2015409 Genome Canada Saskatchewan Canola Development Commission 2819103915 PIR01_00017 3060-21000-038-00-DWe acknowledge the funding support of: the Italian Ministry of Education and Research with projects CNR Flagship InterOmics PB05 (L.M., A.C., G.S.), PON ELIXIR CNR-BiOmics PIR01_00017 (L.M., M.G., M.Mo.) and PON ISCOCEM (P.D.); CREA project Interomics (L.C.); Fondazione in rete per la ricerca agroalimentare AGER project From Seed to Pasta (R.T.); FP7-KBBE Project DROPS ID244347 (R.T.); Genome Canada (A.G.S., C.P.); the Western Grain Research Foundation (A.G.S., C.P.); the Manitoba Wheat and Barley Commission (A.G.S., C.P.); the Saskatchewan Wheat Development Commission (A.G.S., C.P.); the Alberta Wheat Development Commission (A.G.S., C.P.); the Saskatchewan Ministry of Agriculture (A.G.S., C.P.); the administrative support of Genome Prairie (A.G.S., C.P.); Canadian Triticum Applied Genomics -CTAG2-(A.G.S., C.P.); Binational Science Foundation grant no. 2015409 (I.H., A.D.); Israel Science Foundation grant no. 1137/17 (A.D.); USDA-Agricultural Research Service Current Research Information System project 3060-21000-038-00-D (J.D.F., S.S.X.); German Federal Ministry of Food and Agriculture grant no. 2819103915 (N.S., K.F.X.M.); German Ministry of Education and Research grant no. 031A536 (K.F.X.M.); and Natural Sciences and Engineering Council of Canada grant nos. SPG 336119-06 and RGPIN 92787 (G.J.T., C.P.). The authors are grateful to E. Elias (North Dakota State University) for providing nine DW cultivars, included in the Global Tetraploid Wheat Collection and E. Scarpella (University of Alberta, Edmonton, Canada) for assistance with confocal microscopy

FINE-MAPPING OF QSBM.UBO-2BS=SBM2, A MAJOR QTL FOR RESISTANCE TO SOIL-BORNE CEREAL MOSAIC VIRUS (SBCMV)

QSbm.ubo - 2BS=Sbm2, a major QTL controlling the response to Soil - Borne Cereal Mosaic Virus (SB CMV) in durum wheat, was c haracterized in two recombinant inbred line populations, namely Meridiano (resistant, R) x Claudio (moderately susceptible, MS) and Simeto (susceptible, S) x Levante (R). B y means of meta - QTL analysis QSbm.ubo - 2BS was mapped as a unique QTL within a 2 cM - wide interval (LOD - 2) in the distal region of chromosome arm 2BS (Maccaferri et al., 2012) . The addition of the Illumina 90K SNPs array to the durum linkage maps allowed to identify 36 transcripts - associated SNPs tightly associated with the Mendelized QTL (Maccaferri et al., 2014) . Nine SNPs from the Illumina 90K wheat array were converted to KASP markers, which provided fluorescent high - throughput assays spanning the QTL region. Marker - assisted selection (MAS) was performed on 3c 2,000 RILs from the Svevo (R) x Ciccio (S) population (Gadaleta et al., 2009) with two KAS P markers flanking the QTL interval , KUBO 9 and KUBO 13. MAS identified 291 lines recombinant between the two markers. These lines were characterized for SBCMV response in the 2016 field nursery under severe and uniform SBCMV infection. The lines were scor ed for symptom severity (SS) on a 0 to 4 scale , where 0 = very res istant and 4 = very susceptible (Vallega and Rubies Autonell, 1985). They were also genotyped with seven KASP markers distributed along the QTL interval ( KUBO 1 , KUBO 3 , KUBO 27 , KUBO 29 , KU BO 38, KUBO 40 and KUBO 41 ) and with the DArT marker wPt - 2106 , the marker most associated with the phenotype in the Meridiano x Claudio RIL population (Maccaferri et al., 2012). The bimodal distribution of SS reflects the segregation of the resistance trai t in the QTL interval: frequency peaks were observed around values of 1.7 and 3.8. The fine - mapping allowed to narrow the most probable support interval to 0,2 cM between KUBO 27 and KUBO 1 based on the Svevo x Ciccio RILs population. Work is in progress to analyze other - 1,000 RILs of the same population in order to confirm the results obtained with the first part of the study and to improve the ongoing fine - mapping of the gene responsible for the resistance

TRANSCRIPTOME ANALYSIS OF 13 ELITE DURUM WHEAT VARIETIES SPANNING THE COMPLETE BREEDING ERA DECADES

Variation of gene content and gene expression in terms of relative quantitative expression and tissue/organ specificity is a substantial factor affecting phenotypic diversity. In crops, particularly in cereals, the pantran scriptome and pan - genome concepts raised soon after the reference genomes were made available. Characterizing the gene expression presence - absence variation (ePAV) of tetraploid durum wheat ( Triticum turgidum ssp. durum) enables to investigate the associat ion between the genotypic and phenotypic variation at an unprecedented level of precision. The current study presents the transcriptome analysis for 13 elite varieties from worldwide germplasm spanning from 1969 up to 2005. We aim to describe the gene expr ession variation in relation to a high - quality reference genome sequence assembly of durum wheat cv. Svevo (c/o International Durum Wheat Genome Sequencing Consortium). cDNA libraries for the 13 varieties were produced from roots and leaves at the seedling stage, and developing grains. In order to study the gene expression pattern, RNA - seq libraries of 13 varieties were aligned to the durum wheat genome using HISAT2. The transcript abundance was calculated using StringTie and Ballgown. Expression matrix was then normalized using R package DESeq2 for further clustering and variance analysis. The annotation of the Svevo assembled genome resulted in 66,559 high confidence gene models. Overall, 75.0% (48,007 genes), 70.5% (45,142) and 74.5% (47,702) of genes wer e expressed in grain, leaf and roots, respectively. Considering the cultivars and the tissue/organ libraries overall, the percentage of genes mapped to the Svevo genome reference varied from 48.0% (Altar84, Capeiti 8, Claudio, Saragolla leaves) to a maximu m of 61.0% (Meridiano, Strongfield roots and grains). Principal Component Analysis (PCA) analysis showed a clear gene expression clustering lead by organs (leaves, grains and roots accounting for 33.0 % variance). Hierarchical clustering based on the stron gest PC1 \u2013 PC2 scores clearly differentiated up - and down - regulated gene clusters based on tissues and varieties. Variance expression analysis projected on the Svevo assembly allowed us to identify the chromosome regions that drove the major expression varia tion patterns. Presence/absence of expression polymorphism could also be observed for several of the genes sorted by PCA. Interestingly, by clustering the gene expression profiles and the cultivar\u2019s expression profiles several gene expression patterns rela ted to the ancestry relationship among cultivars were evidenced, particularly for the grains. The functional annotation of these gene clusters is ongoing. Towards assembly of a pan - transcriptome in durum, the cultivar - specific reads that could not be mappe d on the Svevo genome (4 - 30% referred to the Svevo Illumina sequencing data) are being de novo assembled. This expression pattern database could also be useful to identify genes regulated by eQTLs and to elucidate the function of candidate gene

Cloning of Vgt3, a major QTL for flowering time in maize

Flowering time is a complex trait important for crop adaptation to local environments and an essential breeding target to face the challenge of global climate change. A major quantitative trait locus (QTL) for flowering time and number of nodes (ND), qVgt3.05 (Vgt3), was previously identified on chromosome 3, bin 3.05, in a maize introgression library (IL) derived from the cross B73 x Gasp\ue9 Flint (recipient and donor genotypes, respectively. Salvi et al. 2011). In order to clone Vgt3, B73 was crossed with its early isogenic line 39-1-2-33 which carries a 17-cM Gasp\ue9 Flint introgression on bin 3.05. Using this cross, Vgt3 showed an addictive effect of 1.4 nodes, explained 56.6% of the phenotypic variance and was mapped within 0.3 cM. For positional cloning, a total of 7,500 F2 plants were phenotyped and genotyped with SNPs and SSR markers flanking the QTL interval. One-hundred recombinants lines were derived and the QTL was further narrowed the target genomic region to a 380-kb interval. A MADS-box gene with no coding sequence variation between the two alleles was found in the physical interval. However, the MADS-box gene RNA expression profile and transgenics testing confirmed its effect on flowering time. We are currently searching for the Vgt3 causative regulatory region by studying chromosome structural variation between the B73 and Gasp\ue9 Flint alleles

The Italian reappraisal of the most frequent genetic defects in hereditary optic neuropathies and the global top 10

We read with great interest the recent publication by Rocatcher and colleagues1 entitled ‘The top 10 most frequently involved genes in hereditary optic neuropathies in 2186 probands’, reporting on the experience of a national diagnostic centre for hereditary optic neuropathies (HON) in France. Similarly, our scientific institute is a national referral and diagnostic centre for HON in Italy, and in this correspondence, we present our neurogenetic assessments of 1097 HON patients. We offer a comparison between the two studies and comment on the global results obtained by merging the data, thus commenting on the largest cohort of HON cases presented to date

Durum wheat genome highlights past domestication signatures and future improvement targets

The domestication of wild emmer wheat led to the selection of modern durum wheat, grown mainly for pasta production. We describe the 10.45 gigabase (Gb) assembly of the genome of durum wheat cultivar Svevo. The assembly enabled genome-wide genetic diversity analyses revealing the changes imposed by thousands of years of empirical selection and breeding. Regions exhibiting strong signatures of genetic divergence associated with domestication and breeding were widespread in the genome with several major diversity losses in the pericentromeric regions. A locus on chromosome 5B carries a gene encoding a metal transporter (TdHMA3-B1) with a non-functional variant causing high accumulation of cadmium in grain. The high-cadmium allele, widespread among durum cultivars but undetected in wild emmer accessions, increased in frequency from domesticated emmer to modern durum wheat. The rapid cloning of TdHMA3-B1 rescues a wild beneficial allele and demonstrates the practical use of the Svevo genome for wheat improvement

Data from: Genetic architecture of adaptation to novel environmental conditions in a predominantly selfing allopolyploid plant

Genetic architecture of adaptation is traditionally studied in the context of local adaptation, viz. spatially varying conditions experienced by the species. However, human made changes in the natural environment pose a new context to this issue, i.e. adaptation to an environment that is new for the species. In this study, we used crossbreeding to analyze genetic architecture of adaptation to conditions not currently experienced by the species but with high probability of encounter in the near future due to the global climate change. We performed targeted inter-population crossing using genotypes from two core and two peripheral Triticum dicoccoides populations and grew up the parents and three generations of hybrids in a greenhouse under simulated desert conditions to analyze the genetic architecture of adaptation to these conditions and an effect of gene flow from plants having different origin. The observed in allopolyploid T. dicoccoides low importance of epistatic gene interactions and low probability of hybrid breakdown appear to be the result of permanent fixation of heterozygosity and lack of inter-genomic recombination in this species. At the same time, predominant but not complete selfing combined with an advantage of bivalent pairing of homologous chromosomes appear to maintain high genetic variability in T. dicoccoides, greatly enhancing its adaptive ability