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Regulation of microRNAs (miRNAs) on various biological processes has been a surprising and exciting field. Identification of miRNAs is the first step to comprehensively understand their functions. However, attempts on global identification and functional verification of miRNAs are very limited in penaeid shrimp Marsupenaeus japonicus, an economically important aquatic species. By performing an integrated analysis of transcriptomic profile from gastrula embryos of M. japonicus, 21 conserved miRNAs in M. japonicas (mja-miRNAs), belonging to 19 miRNA families, were identified and characterized. Of the 21 mja-miRNAs, 15 miRNAs were successfully verified to be predominantly expressed in gastrula stage, where they displayed dynamic expression patterns compared with those in naupliuin stage. Based on perfect or near-perfect match to target region, 120 target genes were predicted at transcriptome-wide level. Noteworthy, gene ontology (GO) classification and metabolic pathway annotation revealed eight targets that were actively involved in developmental processes. Of the predicted miRNA-mRNA pairs, six targets were then randomly selected and experimentally validated by dual luciferase reporter assay, where three pairs were proved with potential targeting activity. Overall, to search for conserved miRNAs potentially involved in early development of M. japonicus, we combined in silico and experimental methods, which can be applied in other organisms as well. Our data implied important roles of miRNAs in the early embryonic development and also suggested the presence of complex miRNA-mRNA functional networks in M. japonicus. [ABSTRACT FROM AUTHOR]

Rice bean (Vigna umbellata) is an underexploited domesticated legume crop consumed for dietary protein in Asia, yet little is known about the genetic diversity of this species. Here, we present a high-quality reference genome for a rice bean landrace (FF25) built using PacBio long-read data and a Hi-C chromatin interaction map, and assess the phylogenetic position and speciation time of rice bean within the Vigna genus. We sequence 440 landraces (two core collections), and GWAS based on data for growth sites at three widely divergent latitudes reveal loci associated with flowering and yield. Loci harboring orthologs of FUL (FRUITFULL), FT (FLOWERING LOCUS T), and PRR3 (PSEUDO-RESPONSE REGULATOR 3) contribute to the adaptation of rice bean from its low latitude center of origin towards higher latitudes, and the landraces which pyramid early-flowering alleles for these loci display maximally short flowering times. We also demonstrate that copy-number-variation for VumCYP78A6 can regulate seed-yield traits. Intriguingly, 32 landraces collected from a mountainous region in South-Central China harbor a recently acquired InDel in TFL1 (TERMINAL FLOWER1) affecting stem determinacy; these materials also have exceptionally high values for multiple human-desired traits and could therefore substantially advance breeding efforts to improve rice bean. Rice bean is an underexploited legume crop that has many desirable properties against bio and abiotic stresses. Here, the authors report the genome assembly of this species, conduct population genetics studies and reveal the genetic variations associated with adaptation and yield traits. [ABSTRACT FROM AUTHOR]

A narrow genetic basis in modern cultivars and strong linkage disequilibrium in peach (Prunus persica) has restricted resolution power for association studies in this model fruit species, thereby limiting our understanding of economically important quality traits including fruit flavor. Here, we present a high-quality genome assembly for a Chinese landrace, Longhua Shui Mi (LHSM), a representative of the Chinese Cling peaches that have been central in global peach genetic improvement. We also map the resequencing data for 564 peach accessions to this LHSM assembly at an average depth of 26.34× per accession. Population genomic analyses reveal a fascinating history of convergent selection for sweetness yet divergent selection for acidity in eastern vs. western modern cultivars. Molecular-genetics and biochemical analyses establish that PpALMT1 (aluminum-activated malate transporter 1) contributes to their difference of malate content and that increases fructose content accounts for the increased sweetness of modern peach fruits, as regulated by PpERDL16 (early response to dehydration 6-like 16). Our study illustrates the strong utility of the genomics resources for both basic and applied efforts to understand and exploit the genetic basis of fruit quality in peach. Longhua Shui Mi (LHSM) is a representative of the Chinese Cling peaches that have been central in global peach genetic improvement. Here, the authors assemble the genome of LHSM and show convergent selection for sweetness yet divergent selection for acidity in eastern vs. western cultivars through population genomics analyses. [ABSTRACT FROM AUTHOR]

Genetic parameters and response to selection were estimated for harvest body weight in turbot. The data consisted of 10 952 individuals of 508 full-sib families from three generations (G0, G1, and G2). The heritability estimates for G0, G1, and G2 were 0.11±0.08, 0.18±0.09, and 0.17±0.07, respectively. Over three generations, the heritability estimate was 0.19±0.04. Maternal and common environmental effects were 0.10±0.04, 0.14±0.04, and 0.13±0.03 within each generation and 0.12±0.01 across generations. The selection differential in growth was 18.24 g in G0 and 21.19 g in G1 corresponding to an average of 19.72 g per generation. The genetic gains were also calculated, they were 22.06 g in G1 and 11.93 g in G2, corresponding to 6.36% and 3.52% body weight. The total genetic gain after two generations was 10.10% body weight, which indicated that the selective breeding program for the body weight trait in turbot was successful. [ABSTRACT FROM AUTHOR]

Bayesian and restricted maximum likelihood (REML) approaches were used to estimate the genetic parameters in a cultured turbot Scophthalmus maximus stock. The data set consisted of harvest body weight from 2 462 progenies (17 months old) from 28 families that were produced through artificial insemination using 39 parent fish. An animal model was applied to partition each weight value into a fixed effect, an additive genetic effect, and a residual effect. The average body weight of each family, which was measured at 110 days post-hatching, was considered as a covariate. For Bayesian analysis, heritability and breeding values were estimated using both the posterior mean and mode from the joint posterior conditional distribution. The results revealed that for additive genetic variance, the posterior mean estimate (σ=9 320) was highest but with the smallest residual variance, REML estimates (σ=8 088) came second and the posterior mode estimate (σ=7 849) was lowest. The corresponding three heritability estimates followed the same trend as additive genetic variance and they were all high. The Pearson correlations between each pair of the three estimates of breeding values were all high, particularly that between the posterior mean and REML estimates (0.996 9). These results reveal that the differences between Bayesian and REML methods in terms of estimation of heritability and breeding values were small. This study provides another feasible method of genetic parameter estimation in selective breeding programs of turbot. [ABSTRACT FROM AUTHOR]

The estimation of genetic parameters has played an important role in animal selective breeding for growth traits. Recently studies show that molecular markers can be incorporated into genetic evaluations. In order to improve the performance of an incomplete pedigree (i.e, only parents are known) in the genetic evaluations, 12 microsatellite markers have been applied in the estimation of the genetic parameters for body weight in a farmed population ( n=1 890) of juvenile turbot ( Scophthalmus maximus L.). A new relatedness called parental molecular relatedness (PMR) is estimated based on results of genotyping of 48 parents (31 males, 17 females) with microsatellites markers. The feasibility of PMR in estimation of genetic parameters is verified by comparison with pedigree related (PR) which is obtained from a complete pedigree. The results demonstrate that a high correlation (0.872) between them is found. Heritabilities are estimated using the PMR (0.52±0.13) and PR (0.55±0.22) with the same animal model. A cross-validation shows that the predictive abilities of models using the PMR and the PR are identical (0.81). From that, a conclusion can be made that PMR and PR predicted genetic values equally well in a population of juvenile turbot. Therefore PMR can be applied as an alternative of the PR when only parents are known. However, for a better performance, more markers and more families should be included in a further study. [ABSTRACT FROM AUTHOR]