BackgroundSoybean (Glycine max [L.] Merr.) is one of the most important oil and protein crops. Ever-increasing soybean consumption necessitates the improvement of varieties for more efficient production. However, both correlations among different traits and genetic interactions among genes that affect a single trait pose a challenge to soybean breeding.ResultsTo understand the genetic networks underlying phenotypic correlations, we collected 809 soybean accessions worldwide and phenotyped them for two years at three locations for 84 agronomic traits. Genome-wide association studies identified 245 significant genetic loci, among which 95 genetically interacted with other loci. We determined that 14 oil synthesis-related genes are responsible for fatty acid accumulation in soybean and function in line with an additive model. Network analyses demonstrated that 51 traits could be linked through the linkage disequilibrium of 115 associated loci and these links reflect phenotypic correlations. We revealed that 23 loci, including the known Dt1, E2, E1, Ln, Dt2, Fan, and Fap loci, as well as 16 undefined associated loci, have pleiotropic effects on different traits.ConclusionsThis study provides insights into the genetic correlation among complex traits and will facilitate future soybean functional studies and breeding through molecular design.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-017-1289-9) contains supplementary material, which is available to authorized users.

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat. Here we report a 110-Mb draft sequence of Pst isolate CY32, obtained using a ‘fosmid-to-fosmid’ strategy, to better understand its race evolution and pathogenesis. The Pst genome is highly heterozygous and contains 25,288 protein-coding genes. Compared with non-obligate fungal pathogens, Pst has a more diverse gene composition and more genes encoding secreted proteins. Re-sequencing analysis indicates significant genetic variation among six isolates collected from different continents. Approximately 35% of SNPs are in the coding sequence regions, and half of them are non-synonymous. High genetic diversity in Pst suggests that sexual reproduction has an important role in the origin of different regional races. Our results show the effectiveness of the ‘fosmid-to-fosmid’ strategy for sequencing dikaryotic genomes and the feasibility of genome analysis to understand race evolution in Pst and other obligate pathogens.

Background Bread wheat is one of the most important and broadly studied crops. However, due to the complexity of its genome and incomplete genome collection of wild populations, the bread wheat genome landscape and domestication history remain elusive. Results By investigating the whole-genome resequencing data of 93 accessions from worldwide populations of bread wheat and its diploid and tetraploid progenitors, together with 90 published exome-capture data, we find that the B subgenome has more variations than A and D subgenomes, including SNPs and deletions. Population genetics analyses support a monophyletic origin of domesticated wheat from wild emmer in northern Levant, with substantial introgressed genomic fragments from southern Levant. Southern Levant contributes more than 676 Mb in AB subgenomes and enriched in the pericentromeric regions. The AB subgenome introgression happens at the early stage of wheat speciation and partially contributes to their greater genetic diversity. Furthermore, we detect massive alien introgressions that originated from distant species through natural and artificial hybridizations, resulting in the reintroduction of ~ 709 Mb and ~ 1577 Mb sequences into bread wheat landraces and varieties, respectively. A large fraction of these intra- and inter-introgression fragments are associated with quantitative trait loci of important traits, and selection events are also identified. Conclusion We reveal the significance of multiple introgressions from distant wild populations and alien species in shaping the genetic components of bread wheat, and provide important resources and new perspectives for future wheat breeding. Electronic supplementary material The online version of this article (10.1186/s13059-019-1744-x) contains supplementary material, which is available to authorized users.

Pathogenesis-related (PR) proteins, induced in plants in response to various biotic and abiotic stresses, have been assumed to play a role in plant defense system. Proteins of the PR5 family, also named thaumatin-like proteins (TLPs), have been detected in numerous plant species. In this research, a novel PR5 gene, designated as TaPR5, was isolated and characterized from wheat leaves (cv. Suwon 11) infected by the stripe rust pathotype CY23 (incompatible interaction) using the rapid amplification of cDNA ends (RACE). TaPR5 was predicted to encode a protein of 173 amino acids with an estimated molecular mass of 17.6 kDa and a theoretical pI of 4.64. The deduced amino acid sequence of TaPR5 showed a significant sequence similarity with PR5 and TLPs from barley and other plants and contained a putative signal peptide at the amino terminus. Southern blot analysis indicated that TaPR5 is coded by a single-copy gene. Quantitative real-time polymerase chain reaction (qRT-PCR) analyses revealed that TaPR5 transcript is significantly induced and upregulated in the incompatible interaction while in the compatible interaction a relative low level of the transcript was detected. TaPR5 was also induced by phytohormones (SA, JA and ABA) and stress stimuli (wounding, cold temperature and high salinity). Using an assay of onion epidermal cells indicated accumulation of TaPR5 protein in the apoplast. The immunocytochemical method showed that the TaPR5 protein was detected on cell walls of wheat leaves in the incompatible interaction at markedly higher labeling density compared with the compatible interaction.

Genomic selection is a promising molecular breeding strategy enhancing genetic gain per unit time. The objectives of our study were to (1) explore the prediction accuracy of genomic selection for plant height and yield per plant in soybean [Glycine max (L.) Merr.], (2) discuss the relationship between prediction accuracy and numbers of markers, and (3) evaluate the effect of marker preselection based on different methods on the prediction accuracy. Our study is based on a population of 235 soybean varieties which were evaluated for plant height and yield per plant at multiple locations and genotyped by 5361 single nucleotide polymorphism markers. We applied ridge regression best linear unbiased prediction coupled with fivefold cross-validations and evaluated three strategies of marker preselection. For plant height, marker density and marker preselection procedure impacted prediction accuracy only marginally. In contrast, for grain yield, prediction accuracy based on markers selected with a haplotype block analyses-based approach increased by approximately 4 % compared with random or equidistant marker sampling. Thus, applying marker preselection based on haplotype blocks is an interesting option for a cost-efficient implementation of genomic selection for grain yield in soybean breeding.Electronic supplementary materialThe online version of this article (doi:10.1007/s11032-016-0504-9) contains supplementary material, which is available to authorized users.