Traits to Differentiate Lineages and Subspecies of Aegilops tauschii, the D Genome Progenitor Species of Bread Wheat

Aegilops tauschii Coss., the D genome donor of hexaploid wheat (Triticum aestivum L.), is the most promising resource used to broaden the genetic diversity of wheat. Taxonomical studies have classified Ae. tauschii into two subspecies, ssp. tauschii and ssp. strangulata. However, molecular analysis revealed three distantly related lineages, TauL1, TauL2 and TauL3. TauL1 and TauL3 includes the only ssp. tauschii, whereas TauL2 includes both subspecies. This study aimed to clarify the phylogeny of Ae. tauschii and to find the traits that can differentiate between TauL1, TauL2 and TauL3, or between ssp. tauschii and ssp. strangulata. We studied the genetic and morpho-physiological diversity in 293 accessions of Ae. tauschii, covering the entire range of the species. A total of 5880 high-quality SNPs derived from DArTseq were used for phylogenetic cluster analyses. As a result, we observed wide morpho-physiological variation in each lineage and subspecies. Despite this variation, no key traits can discriminate lineages or subspecies though some traits were significantly different. Of 124 accessions previously lacking the passport data, 66 were allocated to TauL1, 57 to TauL2, and one to TauL3.

Privacy-Utility Equilibrium Protocol for Federated Aggregating Multiparty Genome Data

Cloud server aggregates a large amount of genome data from multi genome donors to facilitate scientific research. However, the untrusted cloud server is prone to violate privacy of aggregating genome data. Thus, each genome donor can randomly perturb her genome data using differential privacy mechanism before aggregating. But this is easy to lead to utility disaster of aggregating genome data due to the different privacy preferences of each genome donor, and privacy leakage of aggregating genome data because of the kinship between genome donors. The key challenge here is to achieve an equilibrium between privacy preserving and data utility of aggregating multiparty genome data. To this end, we proposed federated aggregation protocol of multiparty genome data (MGD-FAP) with privacy-utility equilibrium for guaranteeing desired privacy protection and desired data utility. First, we regarded the privacy budget and the accuracy as the desired privacy-utility metrics of genome data respectively. Second, we constructed the federated aggregation model of multiparty genome data by combining random perturbation method of genome data guaranteeing desired data utility with federated comparing update method of local privacy budget achieving desired privacy preserving. Third, we presented the MGD-FAP maintaining privacy-utility equilibrium under the federated aggregation model of multiparty genome data. Finally, our theoretical and experimental analysis showed that MGD-FAP can maintain privacy-utility equilibrium. The MGD-FAP is practical and feasible to ensure the privacy-utility equilibrium of cloud server aggregating multiparty genome data.

Ancestry of the two subgenomes of maize

Maize (Zea mays ssp. mays) is not only one of the world’s most important crops, but it also is a powerful tool for studies of genetics, genomics, and cytology. The genome of maize shows the unmistakable signature of an ancient hybridization event followed by whole genome duplication (allopolyploidy), but the parents of this event have been a mystery for over a century, since studies of maize cytogenetics began. Here we show that the whole genome duplication event preceded the divergence of the entire genus Zea and its sister genus Tripsacum. One genome was donated, in whole or in part, by a plant related to the modern African genera Urelytrum and Vossia, although genomic rearrangement has been extensive. The other genome donor is less well-supported, but may have been related to the modern Rottboellia-Hemarthria clade, which is also African. Thus Zea and Tripsacum together represent a New World radiation derived from African ancestors.

Structure and expression analysis of genes encoding ADP-glucose pyrophosphorylase large subunit in wheat and its relatives

ADP-glucose pyrophosphorylase (AGP), which consists of two large subunits (AGP-L) and two small subunits (AGP-S), controls the rate-limiting step in the starch biosynthetic pathway. In this study, a full-length open reading frame (ORF) of AGP-L gene (named as Agp2) in wheat and a series of Agp2 gene sequences in wheat relatives were isolated. The coding region of Agp2 contained 15 exons and 14 introns including a full-length ORF of 1566 nucleotides, and the deduced protein contained 522 amino acids (57.8 kDa). Generally, the phylogenetic tree of Agp2 indicated that sequences from A- and D-genome donor species were most similar to each other and sequences from B-genome donor species contained more variation. Starch accumulation and Agp2 expression in wheat grains reached their peak at 21 and 15 days post anthesis (DPA), respectively.

Phylogenetic analysis of Leymus (Poaceae: Triticeae) based on random amplified polymorphic DNA

To investigate the Ns genome donor of

Systematic Comparisons of Orthologous Selenocysteine Methyltransferase and Homocysteine Methyltransferase Genes from Seven Monocots Species

Identifying and manipulating genes underlying selenium metabolism could be helpful for increasing selenium content in crop grain, which is an important way to overcome diseases resulted from selenium deficiency. A reciprocal smallest distance algorithm (RSD) approach was applied using two experimentally confirmed Homocysteine S-Methyltransferases genes (HMT1 and HMT2) and a putative Selenocysteine Methyltransferase (SMT) from dicots plant Arabidopsis thaliana, to explore their orthologs in seven sequenced diploid monocot species: Oryza sativa, Zea mays, Sorghum bicolor, Brachypodium distachyon, Hordeum vulgare, Aegilops tauschii (the D-genome donor of common wheat) and Triticum urartu (the A-genome donor of common wheat). HMT1 was apparently diverged from HMT2 and most of SMT orthologs were the same with that of HMT2 in this study, leading to the hypothesis that SMT and HMT originate from one common ancestor gene. Identifying orthologs provide candidates for further experimental confirmation; also it could be helpful in designing primers to clone SMT or HMT orthologs in other crops.

Phylogenetic relationships among Elymus and related diploid genera (Triticeae: Poaceae) based on nuclear rDNA ITS sequences

To investigate the phylogenetic relationships among Elymus and related diploid genera, the genome donor of Elymus, and the evolutionary history of polyploid Elymus species, nuclear ribosomal internal transcribed spacer (ITS) sequences were analyzed for 10 Elymus species, together with 17 diploid taxa from 5 monogenomic genera. The phylogenetic analyses (Neighbor-Joining) supported two major clades (St and H). Sequence diversity and genealogical analysis suggested that (1) Elymus species were unambiguously closely related to Pseudoroegeria; (2) Pse. stipifolia might be serve as the St genome donor of polyploid Elymus species; (3) the Y genome might be originated from ancestral lineage of Pseudoroegneria (St); (4) the ITS sequences of Elymus were evolutionarily distinct and may clarify parental lineages and phylogenetic relationships in Elymus.