Rice diversity panel provides accurate genomic predictions for complex traits in the progenies of biparental crosses involving members of the panel

KEY MESSAGE

Rice breeding programs based on pedigree schemes can use a genomic model trained with data from their working collection to predict performances of progenies produced through rapid generation advancement. So far, most potential applications of genomic prediction in plant improvement have been explored using cross validation approaches. This is the first empirical study to evaluate the accuracy of genomic prediction of the performances of progenies in a typical rice breeding program. Using a cross validation approach, we first analyzed the effects of marker selection and statistical methods on the accuracy of prediction of three different heritability traits in a reference population (RP) of 284 inbred accessions. Next, we investigated the size and the degree of relatedness with the progeny population (PP) of sub-sets of the RP that maximize the accuracy of prediction of phenotype across generations, i.e., for 97 F5-F7 lines derived from biparental crosses between 31 accessions of the RP. The extent of linkage disequilibrium was high (r 2 = 0.2 at 0.80 Mb in RP and at 1.1 Mb in PP). Consequently, average marker density above one per 22 kb did not improve the accuracy of predictions in the RP. The accuracy of progeny prediction varied greatly depending on the composition of the training set, the trait, LD and minor allele frequency. The highest accuracy achieved for each trait exceeded 0.50 and was only slightly below the accuracy achieved by cross validation in the RP. Our results thus show that relatively high accuracy (0.41-0.54) can be achieved using only a rather small share of the RP, most related to the PP, as the training set. The practical implications of these results for rice breeding programs are discussed.

High-density SNP assay development for genetic analysis in maritime pine (Pinus pinaster)

Maritime pine provides essential ecosystem services in the south-western Mediterranean basin, where it covers around 4 million ha. Its scattered distribution over a range of environmental conditions makes it an ideal forest tree species for studies of local adaptation and evolutionary responses to climatic change. Highly multiplexed single nucleotide polymorphism (SNP) genotyping arrays are increasingly used to study genetic variation in living organisms and for practical applications in plant and animal breeding and genetic resource conservation. We developed a 9k Illumina Infinium SNP array and genotyped maritime pine trees from (i) a three-generation inbred (F2) pedigree, (ii) the French breeding population and (iii) natural populations from Portugal and the French Atlantic coast. A large proportion of the exploitable SNPs (2052/8410, i.e. 24.4%) segregated in the mapping population and could be mapped, providing the densest ever gene-based linkage map for this species. Based on 5016 SNPs, natural and breeding populations from the French gene pool exhibited similar level of genetic diversity. Population genetics and structure analyses based on 3981 SNP markers common to the Portuguese and French gene pools revealed high levels of differentiation, leading to the identification of a set of highly differentiated SNPs that could be used for seed provenance certification. Finally, we discuss how the validated SNPs could facilitate the identification of ecologically and economically relevant genes in this species, improving our understanding of the demography and selective forces shaping its natural genetic diversity, and providing support for new breeding strategies.

The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release

BACKGROUND

Many northern-hemisphere forests are dominated by oaks. These species extend over diverse environmental conditions and are thus interesting models for studies of plant adaptation and speciation. The genomic toolbox is an important asset for exploring the functional variation associated with natural selection.

RESULTS

The assembly of previously available and newly developed long and short sequence reads for two sympatric oak species, Quercus robur and Quercus petraea, generated a comprehensive catalog of transcripts for oak. The functional annotation of 91 k contigs demonstrated the presence of a large proportion of plant genes in this unigene set. Comparisons with SwissProt accessions and five plant gene models revealed orthologous relationships, making it possible to decipher the evolution of the oak genome. In particular, it was possible to align 9.5 thousand oak coding sequences with the equivalent sequences on peach chromosomes. Finally, RNA-seq data shed new light on the gene networks underlying vegetative bud dormancy release, a key stage in development allowing plants to adapt their phenology to the environment.

CONCLUSION

In addition to providing a vast array of expressed genes, this study generated essential information about oak genome evolution and the regulation of genes associated with vegetative bud phenology, an important adaptive traits in trees. This resource contributes to the annotation of the oak genome sequence and will provide support for forward genetics approaches aiming to link genotypes with adaptive phenotypes.

[Detection of anti-DNA antibodies for the diagnosis of disseminated lupus erythematosus. Comparative study of immunoenzyme methods and a Farr test]

Among the biological assays used for the diagnosis of systemic lupus erythematosus, the detection of anti-double strand DNA (dsDNA) antibodies is highly specific, especially at a high level. Different methods are using for the detection of this specificity, particularly enzyme-based immunoassay (EIA) kits that become widespread in autoimmunity because of several advantages like standardization, simple use and automation. We selected 80 sera in order to evaluate six commercial anti-dsDNA EIA kits and a Farr assay. The results were compared with clinical data, to appreciate both the sensitivity and the specificity of each method. EIA assays are highly sensitive, but are less specific than the Farr assay. These EIA methods should remain organized in an integrative biological step, following an evocative clinical examination. Moreover, the EIA results require confirmations with a more specific assay.

Mortality in 504 infants weighing less than 1501 g at birth and treated in four neonatal intensive care units of south-Belgium between 1976 and 1980

Mortality was studied in 504 infants weighing less than 1501 g at birth and treated in four neonatal intensive care units of South-Belgium between 1976 and 1980. Two hundred and twenty-one babies died during their stay at the hospital, a mortality rate of 438 per 1000 live births. The neonatal mortality rate (mortality during the first 28 days of life) was 373 per 1000 live-births. Thirty-three infants died after the neonatal period, which is 15% of the total number of deaths. Two-thirds of these post-neonatal deaths were related to complications of diseases associated with pre-term delivery. Mortality rates were higher in infants of less than 1001 g than in those of 1001-1250 g or 1251-1500 birth weight. In each birth weight category, patients born in their own obstetrical departments and referred infants has similar mortality rates. Longitudinal analysis showed improving mortality rates between 1976 and 1977 in the total population of VLBW infants, between 1977 and 1978 in infants of less than 1001 g and in 1980 compared to 1976 in the 1251-1500 g group. There were higher incidences of need for ventilatory assistance, patent ductus arteriosus, necrotising enterocolitis and septicaemia in referred patients of less than 1001 g than in patients born in their own obstetrical departments with comparable birth weight. Artificial ventilation was more often required in referred infants of 1251-1500 g. This study confirms the importance of considering at least the complete hospital stay when analysing mortality in VLBW infants. Infants of less than 1001 g had high mortality, particularly after the neonatal period.(ABSTRACT TRUNCATED AT 250 WORDS)