Genotype imputation in winter wheat using first-generation haplotype map SNPs improves genome-wide association mapping and genomic prediction of traits

Genome-wide single nucleotide polymorphism (SNP) variation allows for the capture of haplotype structure in populations and prediction of unobserved genotypes based on inferred regions of identity-by-descent (IBD). Here we have used a first-generation wheat haplotype map created by targeted re-sequencing of low-copy genomic regions in the reference panel of 62 lines to impute marker genotypes in a diverse panel of winter wheat cultivars from the U.S. Great Plains. The IBD segments between the reference population and winter wheat cultivars were identified based on SNP genotyped using the 90K iSelect wheat array and genotyping by sequencing (GBS). A genome-wide association study and genomic prediction of resistance to stripe rust in winter wheat cultivars showed that an increase in marker density achieved by imputation improved both the power and precision of trait mapping and prediction. The majority of the most significant marker-trait associations belonged to imputed genotypes. With the vast amount of SNP variation data accumulated for wheat in recent years, the presented imputation framework will greatly improve prediction accuracy in breeding populations and increase resolution of trait mapping hence, facilitate cross-referencing of genotype datasets available across different wheat populations

Development of expressed sequence tags-simple sequence repeats (EST-SSRs) for Musa and their applicability in authentication of a Musa breeding population

Maintaining identity of clones is essential in breeding programs. New EST-SSR markers have been developed for banana and used to screen a diploid population for clonal identity. A total of 410 primer pairs were designed from an EST database, validated using polyacrylamide gel electrophoresis (PAGE) and a subset was optimized for accurate genotyping on a capillary genetic analyzer. Combining PAGE and capillary electrophoresis, about 44% of the designed primers were informative in the diploid population. The majority of markers produced two alleles as expected in a diploid population. However, some showed three to four alleles, possibly indicating closely-related members of gene families. Screening of field samples using SSR markers revealed genotype identity issues in the target population. The present study demonstrates the applicability of SSRs in the  establishment of parentage and relatedness between accessions. The newly-developed SSRs will be valuable tools in the understanding of Musa genetics, in marker-trait associations, thereby enhancing the effectiveness of breeding programs.Key words: EST, SSRs, markers, Musa, breeding

Genomic prediction in a multiploid crop: genotype by environment interaction and allele dosage effects on predictive ability in banana

Open Access Journal; Published online: 2 March 2018Improving the efficiency of selection in conventional crossbreeding is a major priority in banana (Musa spp.) breeding. Routine application of classical marker assisted selection (MAS) is lagging in banana due to limitations in MAS tools. Genomic selection (GS) based on genomic prediction models can address some limitations of classical MAS, but the use of GS in banana has not been reported to date. The aim of this study was to evaluate the predictive ability of six genomic prediction models for 15 traits in a multi-ploidy training population. The population consisted of 307 banana genotypes phenotyped under low and high input field management conditions for two crop cycles. The single nucleotide polymorphism (SNP) markers used to fit the models were obtained from genotyping by sequencing (GBS) data. Models that account for additive genetic effects provided better predictions with 12 out of 15 traits. The performance of BayesB model was superior to other models particularly on fruit filling and fruit bunch traits. Models that included averaged environment data were more robust in trait prediction even with a reduced number of markers. Accounting for allele dosage in SNP markers (AD-SNP) reduced predictive ability relative to traditional bi-allelic SNP (BA-SNP), but the prediction trend remained the same across traits. The high predictive values (0.47– 0.75) of fruit filling and fruit bunch traits show the potential of genomic prediction to increase selection efficiency in banana breeding

Supraconductivité du Silicium sur Isolant et MOSFET supraconducteur à base de siliciure pour les technologies quantiques

Superconducting transport through a silicon MOSFET can open up many new possibilities ranging from fundamental research to industrial applications. In this thesis, we investigate the electric transport properties of a MOSFET built with superconducting source and drain contacts. Due to their advantages in terms of scalability and reproducibility, we want to integrate superconducting materials compatible with CMOS technology, thus exploiting the reliable and mature silicon technology. The idea is to realize a new type of superconducting circuits in a transistor geometry in which a non-dissipative supercurrent owing through the device from source to drain will be modulated by a gate: a JOFET (Josephson Field Effect Transistor). One important outcome is the realization of superconducting qubits in a perfectly reproducible and mature technology. However, at low temperature and with the reduction of the size of the devices, two antagonistic phenomena appear. The dissipation-free transport of Cooper pairs competes with lossy single-particle processes due to Coulomb interactions. The goal is to understand how these two conflicting properties manifest in such hybrid devices. In this thesis, I studied two different ways of introducing superconductivity in the devices. We deployed a high boron doping and a laser annealing provided by well-controlled out-of-equilibrium doping techniques to make the silicon superconducting. Although highly boron-doped silicon has been known to be superconducting since 2006, superconductivity of SOI, the basic brick of some transistors, was never tested before. We aim at adapting those doping techniques on SOI in order to make it superconducting and to integrate it in transistor-like devices. In a second project, we study source and drain contacts fabricated with superconducting silicides such as PtSi. Such Schottky barrier MOSFETs with superconducting PtSi contacts are elaborated at the CEA/LETI. Measurements at very low temperature revealed the competition between superconductivity and Coulomb interactions and moreover, have brought evidence of superconductivity in PtSi based silicon Schottky barrier MOSFET.L'introduction de la supraconductivité dans des structures de type MOSFET en silicium ouvre de nouvelles perspectives dans la recherche en nanophysique. Dans cette thèse, on s'intéresse aux propriétés de transport électronique au sein d'un MOSFET fabriqué avec des sources et drains supraconducteurs. Afin de garantir la reproductibilité de ces dispositifs, il est important d'intégrer des matériaux supraconducteurs compatibles avec la technologie CMOS exploitant la technologie silicium qui a pour énorme avantage d'être véritablement fiable et mature. L'idée fondamentale est de réaliser un nouveau type de circuit supraconducteur avec une géométrie de type transistor dans lequel un supercourant non dissipatif circulant au sein du dispositif, de la source vers le drain, serait modulé par une tension de grille : un JOFET (Josephson Field Effect Transistor). Une perspective importante est la réalisation d'un qubit supraconducteur grâce à une technologie parfaitement reproductible et mature. Cependant, à très basse température et avec la diminution de la taille des dispositifs, deux phénomènes a priori antagonistes entrent en compétition, à savoir la supraconductivité qui implique un grand nombre d'électrons condensés dans le même état quantique macroscopique et l'interaction Coulombienne qui décrit des processus de transport à une particule. L'intérêt de l'étude est donc de réaliser de tels transistors afin de mieux comprendre comment ce genre de dispositif hybride peut s'adapter à des propriétés opposées. Dans cette thèse, j'ai étudié deux façons d'introduire la supraconductivité dans nos dispositifs. La première option est de réaliser des sources et drains en silicium rendus supraconducteurs par dopage en bore et recuit laser effectué grâce à des techniques de dopage hors-équilibre robustes et bien maîtrisées. Même si la supraconductivité du silicium très fortement dopé en bore est connue depuis 2006 et son état supraconducteur a été très bien caractérisée sur des couches bidimensionnelles, la supraconductivité du SOI, qui est le substrat initial à la base de certains transistors, n'a jamais encore été testée et étudiée. L'objectif est de pouvoir adapter ces techniques de dopage au SOI afin de le rendre supraconducteur et de pouvoir l'intégrer par la suite dans des dispositifs de type MOSFET. La seconde option considérée est la réalisation de source et drain à base de siliciures supraconducteurs tel que le PtSi. Ce siliciure est intéressant du point de vue de sa température critique relativement haute de 1K. D'un point de vue technologique, les MOSFETs à barrière Schottky présentant des contacts en PtSi supraconducteur ont été élaborés au CEA/LETI. Les mesures à très basse température au sein d'un cryostat à dilution ont mis en évidence cette compétition entre la supraconductivité et les effets d'interaction Coulombienne et ont également révélé la supraconductivité dans le MOSFET comportant des contacts en PtSi grâce notamment à l'observation du gap induit dans le dispositif

Genomic Patterns of Introgression in Interspecific Populations Created by Crossing Wheat with Its Wild Relative

Introgression from wild relatives is a valuable source of novel allelic diversity for breeding. We investigated the genomic patterns of introgression from Aegilops tauschii, the diploid ancestor of the wheat D genome, into winter wheat (Triticum aestivum) cultivars. The population of 351 BC1F3:5 lines was selected based on phenology from crosses between six hexaploid wheat lines and 21 wheat-Ae. tauschii octoploids. SNP markers developed for this population and a diverse panel of 116 Ae. tauschii accessions by complexity-reduced genome sequencing were used to detect introgression based on the identity-by-descent analysis. Overall, introgression frequency positively correlated with recombination rate, with a high incidence of introgression at the ends of chromosomes and low in the pericentromeric regions, and was negatively related to sequence divergence between the parental genomes. Reduced introgression in the pericentromeric low-recombining regions spans nearly 2/3 of each chromosome arm, suggestive of the polygenic nature of introgression barriers that could be associated with multilocus negative epistasis between the alleles of wild and cultivated wheat. On the contrary, negative selection against the wild allele of Tg, controlling free-threshing trait and located in the high-recombining chromosomal region, led to reduced introgression only within ∼10 Mbp region around Tg. These results are consistent with the effect of selection on linked variation described by the Hill-Robertson effect, and offer insights into the introgression population development for crop improvement to maximize retention of introgressed diversity across entire genome

Genotype imputation in winter wheat using first-generation haplotype map SNPs improves genome-wide association mapping and genomic prediction of traits

Genome-wide single nucleotide polymorphism (SNP) variation allows for the capture of haplotype structure in populations and prediction of unobserved genotypes based on inferred regions of identity-by-descent (IBD). Here we have used a first-generation wheat haplotype map created by targeted re-sequencing of low-copy genomic regions in the reference panel of 62 lines to impute marker genotypes in a diverse panel of winter wheat cultivars from the U.S. Great Plains. The IBD segments between the reference population and winter wheat cultivars were identified based on SNP genotyped using the 90K iSelect wheat array and genotyping by sequencing (GBS). A genome-wide association study and genomic prediction of resistance to stripe rust in winter wheat cultivars showed that an increase in marker density achieved by imputation improved both the power and precision of trait mapping and prediction. The majority of the most significant marker-trait associations belonged to imputed genotypes. With the vast amount of SNP variation data accumulated for wheat in recent years, the presented imputation framework will greatly improve prediction accuracy in breeding populations and increase resolution of trait mapping hence, facilitate cross-referencing of genotype datasets available across different wheat populations

Association genetics of bunch weight and its component traits in East African highland banana (Musa spp. AAA group)

KEY MESSAGE: The major quantitative trait loci associated with bunch weight and its component traits in the East African highland banana-breeding population are located on chromosome 3. Bunch weight increase is one of the major objectives of banana improvement programs, but little is known about the loci controlling bunch weight and its component traits. Here we report for the first time some genomic loci associated with bunch weight and its component traits in banana as revealed through a genome-wide association study. A banana-breeding population of 307 genotypes varying in ploidy was phenotyped in three locations under different environmental conditions, and data were collected on bunch weight, number of hands and fruits; fruit length and circumference; and diameter of both fruit and pulp for three crop cycles. The population was genotyped with genotyping by sequencing and 27,178 single nucleotide polymorphisms (SNPs) were generated. The association between SNPs and the best linear unbiased predictors of traits was performed with TASSEL v5 using a mixed linear model accounting for population structure and kinship. Using Bonferroni correction, false discovery rate, and long-range linkage disequilibrium (LD), 25 genomic loci were identified with significant SNPs and most were localized on chromosome 3. Most SNPs were located in genes encoding uncharacterized and hypothetical proteins, but some mapped to transcription factors and genes involved in cell cycle regulation. Inter-chromosomal LD of SNPs was present in the population, but none of the SNPs were significantly associated with the traits. The clustering of significant SNPs on chromosome 3 supported our hypothesis that fruit filling in this population was under control of a few quantitative trait loci with major effects.status: publishe