Multi-Trait Genomic Prediction Models Enhance the Predictive Ability of Grain Trace Elements in Rice.

Multi-trait (MT) genomic prediction models enable breeders to save phenotyping resources and increase the prediction accuracy of unobserved target traits by exploiting available information from non-target or auxiliary traits. Our study evaluated different MT models using 250 rice accessions from Asian countries genotyped and phenotyped for grain content of zinc (Zn), iron (Fe), copper (Cu), manganese (Mn), and cadmium (Cd). The predictive performance of MT models compared to a traditional single trait (ST) model was assessed by 1) applying different cross-validation strategies (CV1, CV2, and CV3) inferring varied phenotyping patterns and budgets; 2) accounting for local epistatic effects along with the main additive effect in MT models; and 3) using a selective marker panel composed of trait-associated SNPs in MT models. MT models were not statistically significantly (p < 0.05) superior to ST model under CV1, where no phenotypic information was available for the accessions in the test set. After including phenotypes from auxiliary traits in both training and test sets (MT-CV2) or simply in the test set (MT-CV3), MT models significantly (p < 0.05) outperformed ST model for all the traits. The highest increases in the predictive ability of MT models relative to ST models were 11.1% (Mn), 11.5 (Cd), 33.3% (Fe), 95.2% (Cu) and 126% (Zn). Accounting for the local epistatic effects using a haplotype-based model further improved the predictive ability of MT models by 4.6% (Cu), 3.8% (Zn), and 3.5% (Cd) relative to MT models with only additive effects. The predictive ability of the haplotype-based model was not improved after optimizing the marker panel by only considering the markers associated with the traits. This study first assessed the local epistatic effects and marker optimization strategies in the MT genomic prediction framework and then illustrated the power of the MT model in predicting trace element traits in rice for the effective use of genetic resources to improve the nutritional quality of rice grain.

Genome-wide development of miRNA-based SSR markers in Cleistogenes songorica and analysis of their transferability to Gramineae/non-Gramineae species.

Simple sequence repeat (SSR) markers are commonly used for many genetic applications, such as map construction, fingerprinting, and genetic diversity analyses, due to their high reproducibility, polymorphism, and abundance. Endogenous miRNAs play essential roles in plant development and gene expression under diverse biotic and abiotic stress conditions. In the present study, we predicted 110 miRNA-SSR primer pairs from 287 precursor miRNAs. Among 110 primer pairs, 85 were successfully amplified and examined for transferability to other Gramineae and non-Gramineae species. The results showed that all 82 primer pairs yielded unambiguous and strong amplification, and across the 23 studied Cleistogenes accessions, a total of 385 alleles were polymorphic. The number of alleles produced per primer varied from 3 to 11, with an average of 4.69 per locus. The expected heterozygosity (He) ranged from 0.44 to 0.88, with an average of 0.74 per locus, and the PIC (Polymorphism Information Content) values ranged from 0.34 to 0.87, with an average of 0.69 per locus. Furthermore, 1422 miRNA target genes were predicted and analyzed using the GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases. In conclusion, the results showed that an miRNA-based microsatellite marker system can be applicable for genetic diversity and marker-assisted breeding studies.

Mining Late Embryogenesis Abundant (LEA) Family Genes in Cleistogenes songorica, a Xerophyte Perennial Desert Plant.

Plant growth and development depends on its ability to maintain optimal cellular homeostasis during abiotic and biotic stresses. Cleistogenes songorica, a xerophyte desert plant, is known to have novel drought stress adaptation strategies and contains rich pools of stress tolerance genes. Proteins encoded by Late Embryogenesis Abundant (LEA) family genes promote cellular activities by functioning as disordered molecules, or by limiting collisions between enzymes during stresses. To date, functions of the LEA family genes have been heavily investigated in many plant species except perennial monocotyledonous species. In this study, 44 putative LEA genes were identified in the C. songorica genome and were grouped into eight subfamilies, based on their conserved protein domains and domain organizations. Phylogenetic analyses indicated that C. songorica Dehydrin and LEA_2 subfamily proteins shared high sequence homology with stress responsive Dehydrin proteins from Arabidopsis. Additionally, promoter regions of CsLEA_2 or CsDehydrin subfamily genes were rich in G-box, drought responsive (MBS), and/or Abscisic acid responsive (ABRE) cis-regulatory elements. In addition, gene expression analyses indicated that genes from these two subfamilies were highly responsive to heat stress and ABA treatment, in both leaves and roots. In summary, the results from this study provided a comprehensive view of C. songorica LEA genes and the potential applications of these genes for the improvement of crop tolerance to abiotic stresses.

Analysis of microRNA reveals cleistogamous and chasmogamous floret divergence in dimorphic plant.

Cleistogenes songorica, a grass species that exhibits two spatially different type of inflorescence, chastogamy (CH), flowers localized at the top, and cleistogamy (CL) flowers embedded in leaf sheath. This study aimed at dissecting reasons underlying these distinct floral development patterns at morphological and microRNA level. Phenotyping for CH and CL was conducted and four small RNA libraries were constructed from the CH and CL flowers for high-throughput sequencing to identify the differentiated miRNAs. As results, spikelet, stigma, anther, lemma and lodicule length of CH flowers were found larger than that of CL, and so was seed setting. Also, 17 flower-related differential expression miRNAs were identified which were associated with floral organ development and morphogenesis, and the flower development. Further results showed that miR159a.1-CL3996.Contig2 pair was related to anther development, miR156a-5p-CL1954.Contig2 was linked to response to high light intensity, miR408-3p/miR408d-Unigene429 was related to pollination and Unigene429 positively regulated flower development. To our knowledge, this is the first study on differential miRNA accumulation between CH and CL flowers and our study serves as a foundation to the future elucidation of regulatory mechanisms of miRNAs in the divergent development of CL and CH flowers in a single plant.

Genetic variation and diversity in 199 Melilotus accessions based on a combination of 5 DNA sequences.

Melilotus is an important genus of legume plants and an herbage with excellent nitrogen fixation; it can tolerate extreme environmental conditions and possesses important medicinal value. However, there is limited genetic information about the genus; thus, we analysed four chloroplast loci (rbcL, matK, psbA-trnH and trnL-F) and one nuclear region (ITS) to determine the genetic diversity of 199 accessions from 18 Melilotus species. The rbcL and matK sequences were highly conserved, whereas the trnL-F and ITS sequences contained variable and parsimony-informative sites. In our analyses of the single and combined regions, we calculated the pairwise distance, haplotype and nucleotide diversity and gaps and then constructed phylogenetic trees to assess the genetic diversity, and our results revealed significant variations among the different accessions. The genetic distance values were between zero and nine, and based on the combined regions, the highest frequency value was approximately four. Melilotus showed high haplotype and nucleotide diversity, particularly in the ITS sequences, with values of 0.86 and 0.0087, respectively. The single ITS sequence, psbA-trnH, and the combined matK+rbcL+trnL-F (MRT) and matK+rbcL+psbA-trnH+trnL-F+ITS (MRPTI) regions showed interspecific variation in the gap analysis. Phylogenetic trees calculated using ITS, psbA-trnH and MRPTI sequences indicated distinct genetic relationship in 18 species, and these species could be divided into two groups. By determining the genetic diversity of plants, we can evaluate the genetic relationships among species and accessions, providing a basis for preserving and utilizing the genetic resources of Melilotus.