Yaxi Liu

Effects of Dietary Copper on Growth, Digestive, and Brush Border Enzyme Activities and Antioxidant Defense of Hepatopancreas and Intestine for Young Grass Carp ( Ctenopharyngodon idella )

To investigate the effects of dietary copper (Cu) on fish growth, digestive and absorptive enzyme activities, and antioxidant status in the hepatopancreas and intestine, young grass carp (Ctenopharyngodon idella) (282±2.8 g) were fed six diets containing 0.74 (basal diet), 2.26, 3.75, 5.25, 6.70, and 8.33 mg Cu /kg diet for 8 weeks. Results showed that percentage weight gain (PWG) and feed intake were increased with dietary Cu levels up to 3.75 mg/kg diet. In addition, the positive effects of dietary Cu at a level 3.75 or 5.25 mg/kg diet on trypsin, chymotrypsin, and lipase activities in the hepatopancreas and of Na+, K+-ATPase, alkaline phosphatase, creatine kinase, and γ-glutamyl transpeptidase activities in three intestine segments produced significantly (P<0.05) better feed efficiency (FE). However, amylase activity in the hepatopancreas was decreased by dietary Cu levels up to 3.75 mg/kg diet (P<0.05). In addition, dietary Cu at 3.75 or 5.25 mg/kg diet decreased malondialdehyde and protein carbonyl content partly by significantly (P<0.05) increasing the activities of superoxide dismutase, catalase, glutathione peroxidase, glutathione reductase, glutathione-S-transferase, and glutathione content in the hepatopancreas and intestine. Collectively, dietary Cu improved growth and digestive and absorptive capacity and decreased lipid peroxidation and protein oxidation partly by enhancing antioxidant defense in the hepatopancreas and intestine. The dietary Cu requirement for PWG, plasma ceruloplasmin activity, and FE of young grass carp (282–688 g) were 4.78, 4.95, and 4.70 mg/kg diet, respectively.

Identification and validation of a major QTL conferring crown rot resistance in hexaploid wheat

Crown rot (CR), caused by various Fusarium species, is a chronic wheat disease in Australia. As part of our objective of improving the efficiency of breeding CR resistant wheat varieties, we have been searching for novel sources of resistance. This paper reports on the genetic control of one of these newly identified resistant genotypes, ‘CSCR6’. A population derived from a cross between CSCR6 and an Australian variety ‘Lang’ was analyzed using two Fusarium isolates belonging to two different species, one Fusarium pseudograminearum and the other Fusarium graminearum. The two isolates detected QTL with the same chromosomal locations and comparable magnitudes, indicating that CR resistance is not species-specific. The resistant allele of one of the QTL was derived from ‘CSCR6’. This QTL, designated as Qcrs.cpi-3B, was located on the long arm of chromosome 3B and explains up to 48.8% of the phenotypic variance based on interval mapping analysis. Another QTL, with resistant allele from the variety ‘Lang’, was located on chromosome 4B. This QTL explained up to 22.8% of the phenotypic variance. A strong interaction between Qcsr.cpi-3B and Qcsr.cpi-4B was detected, reducing the maximum effect of Qcrs.cpi-3B to 43.1%. The effects of Qcrs.cpi-3B were further validated in four additional populations and the presence of this single QTL reduced CR severity by up to 42.1%. The fact that significant effects of Qcrs.cpi-3B were detected across all trials with different genetic backgrounds and with the use of isolates belonging to two different Fusarium species make it an ideal target for breeding programs as well as for further characterization of the gene(s) involved in its resistance.

Identification of candidate genes for drought tolerance by whole-genome resequencing in maize

BackgroundDrought stress is one of the major limiting factors for maize production. With the availability of maize B73 reference genome and whole-genome resequencing of 15 maize inbreds, common variants (CV) and clustering analyses were applied to identify non-synonymous SNPs (nsSNPs) and corresponding candidate genes for drought tolerance.ResultsA total of 524 nsSNPs that were associated with 271 candidate genes involved in plant hormone regulation, carbohydrate and sugar metabolism, signaling molecules regulation, redox reaction and acclimation of photosynthesis to environment were detected by CV and cluster analyses. Most of the nsSNPs identified were clustered in bin 1.07 region that harbored six previously reported QTL with relatively high phenotypic variation explained for drought tolerance. Genes Ontology (GO) analysis of candidate genes revealed that there were 35 GO terms related to biotic stimulus and membrane-bounded organelle, showing significant differences between the candidate genes and the reference B73 background. Changes of expression level in these candidate genes for drought tolerance were detected using RNA sequencing for fertilized ovary, basal leaf meristem tissue and roots collected under drought stressed and well-watered conditions. The results indicated that 70% of candidate genes showed significantly expression changes under two water treatments and our strategies for mining candidate genes are feasible and relatively efficient.ConclusionsOur results successfully revealed candidate nsSNPs and associated genes for drought tolerance by comparative sequence analysis of 16 maize inbred lines. Both methods we applied were proved to be efficient for identifying candidate genes for complex traits through the next-generation sequencing technologies (NGS). These selected genes will not only facilitate understanding of genetic basis of drought stress response, but also accelerate genetic improvement through marker-assisted selection in maize.

Genome-wide association study of 29 morphological traits in Aegilops tauschii.

Aegilops tauschii is the D-genome progenitor of hexaploid wheat (Triticum aestivum). It is considered to be an important source of genetic variation for wheat breeding, and its genome is an invaluable reference for wheat genomics. We conducted a genome-wide association study using 7,185 single nucleotide polymorphism (SNP) markers across 322 diverse accessions of Ae. tauschii that were systematically phenotyped for 29 morphological traits in order to identify marker-trait associations and candidate genes, assess genetic diversity, and classify the accessions based on phenotypic data and genotypic comparison. Using the general linear model and mixed linear model, we identified a total of 18 SNPs significantly associated with 10 morphological traits. Systematic search of the flanking sequences of trait-associated SNPs in public databases identified several genes that may be linked to variations in phenotypes. Cluster analysis using phenotypic data grouped accessions into four clusters, while accessions in the same cluster were not from the same Ae. tauschii subspecies or from the same area of origin. This work establishes a fundamental research platform for association studies in Ae. tauschii and also provides useful information for understanding the genetic mechanism of agronomic traits in wheat.

Quantitative Trait Loci Associated with Micronutrient Concentrations in Two Recombinant Inbred Wheat Lines

Micronutrient malnutrition affects over three billion people worldwide, especially women and children in developing countries. Increasing the bioavailable concentrations of essential elements in the edible portions of crops is an effective resolution to address this issue. To determine the genetic factors controlling micronutrient concentration in wheat, the quantitative trait locus (QTL) analysis for iron, zinc, copper, manganese, and selenium concentrations in two recombinant inbred line populations was performed. In all, 39 QTLs for five micronutrient concentrations were identified in this study. Of these, 22 alleles from synthetic wheat SHW-L1 and seven alleles from the progeny line of the synthetic wheat Chuanmai 42 showed an increase in micronutrient concentrations. Five QTLs on chromosomes 2A, 3D, 4D, and 5B found in both the populations showed significant phenotypic variation for 2–3 micronutrient concentrations. Our results might help understand the genetic control of micronutrient concentration and allow the utilization of genetic resources of synthetic hexaploid wheat for improving micronutrient efficiency of cultivated wheat by using molecular marker-assisted selection.

The non-gibberellic acid-responsive semi-dwarfing gene uzu affects Fusarium crown rot resistance in barley

BackgroundStudies in Arabidopsis show that DELLA genes may differentially affect responses to biotrophic and necrophic pathogens. A recent report based on the study of DELLA-producing reduced height (Rht) genes in wheat and barley also hypothesized that DELLA genes likely increased susceptibility to necrotrophs but increased resistance to biotrophs.ResultsEffects of uzu, a non-GA (gibberellic acid)-responsive semi-dwarfing gene, on Fusarium crown rot (FCR) resistance in barley were investigated. Fifteen pairs of near isogenic lines for this gene were generated and assessed under two different temperature regimes. Similar to its impacts on plant height, the semi-dwarfing gene uzu also showed larger effects on FCR severity in the high temperature regime when compared with that in the low temperature regime.ConclusionsResults from this study add to the growing evidence showing that the effects of plant height on Fusarium resistances are unlikely related to DELLA genes but due to direct or indirect effects of height difference per se. The interaction between these two characteristics highlights the importance of understanding relationships between resistance and other traits of agronomic importance as the value of a resistance gene could be compromised if it dramatically affects plant development and morphology.

Regulation, evolution, and functionality of flavonoids in cereal crops

Flavonoids are plant secondary metabolites that contribute to the adaptation of plants to environmental stresses, including resistance to abiotic and biotic stress. Flavonoids are also beneficial for human health and depress the progression of some chronic diseases. The biosynthesis of flavonoids, which belong to a large family of phenolic compounds, is a complex metabolic process with many pathways that produce different metabolites, controlled by key enzymes. There is limited knowledge about the composition, biosynthesis and regulation of flavonoids in cereals. Improved understanding of the accumulation of flavonoids in cereal grains would help to improve human nutrition through these staple foods. The biosynthesis of flavonoids, scope for altering the flavonoid composition in cereal crops and benefits for human nutrition are reviewed here.

A Novel and Major Quantitative Trait Locus for Fusarium Crown Rot Resistance in a Genotype of Wild Barley (Hordeum spontaneum L.)

Fusarium crown rot (FCR), caused by various Fusarium species, is a destructive disease of cereal crops in semiarid regions worldwide. As part of our contribution to the development of Fusarium resistant cultivars, we identified several novel sources of resistance by systematically assessing barley genotypes representing different geographical origins and plant types. One of these sources of resistance was investigated in this study by generating and analysing two populations of recombinant inbred lines. A major locus conferring FCR resistance, designated as Qcrs.cpi-4H, was detected in one of the populations (mapping population) and the effects of the QTL was confirmed in the other population. The QTL was mapped to the distal end of chromosome arm 4HL and it is effective against both of the Fusarium isolates tested, one F. pseudograminearum and the other F. graminearum. The QTL explains up to 45.3% of the phenotypic variance. As distinct from an earlier report which demonstrated co-locations of loci conferring FCR resistance and plant height in barley, a correlation between these two traits was not detected in the mapping population. However, as observed in a screen of random genotypes, an association between FCR resistance and plant growth rate was detected and a QTL controlling the latter was detected near the Qcrs.cpi-4H locus in the mapping population. Existing data indicate that, although growth rate may affect FCR resistance, different genes at this locus are likely involved in controlling these two traits.

Genetic map of Triticum turgidum based on a hexaploid wheat population without genetic recombination for D genome

BackgroundA synthetic doubled-haploid hexaploid wheat population, SynDH1, derived from the spontaneous chromosome doubling of triploid F1 hybrid plants obtained from the cross of hybrids Triticum turgidum ssp. durum line Langdon (LDN) and ssp. turgidum line AS313, with Aegilops tauschii ssp. tauschii accession AS60, was previously constructed. SynDH1 is a tetraploidization-hexaploid doubled haploid (DH) population because it contains recombinant A and B chromosomes from two different T. turgidum genotypes, while all the D chromosomes from Ae. tauschii are homogenous across the whole population. This paper reports the construction of a genetic map using this population.ResultsOf the 606 markers used to assemble the genetic map, 588 (97%) were assigned to linkage groups. These included 513 Diversity Arrays Technology (DArT) markers, 72 simple sequence repeat (SSR), one insertion site-based polymorphism (ISBP), and two high-molecular-weight glutenin subunit (HMW-GS) markers. These markers were assigned to the 14 chromosomes, covering 2048.79 cM, with a mean distance of 3.48 cM between adjacent markers. This map showed good coverage of the A and B genome chromosomes, apart from 3A, 5A, 6A, and 4B. Compared with previously reported maps, most shared markers showed highly consistent orders. This map was successfully used to identify five quantitative trait loci (QTL), including two for spikelet number on chromosomes 7A and 5B, two for spike length on 7A and 3B, and one for 1000-grain weight on 4B. However, differences in crossability QTL between the two T. turgidum parents may explain the segregation distortion regions on chromosomes 1A, 3B, and 6B.ConclusionsA genetic map of T. turgidum including 588 markers was constructed using a synthetic doubled haploid (SynDH) hexaploid wheat population. Five QTLs for three agronomic traits were identified from this population. However, more markers are needed to increase the density and resolution of this map in the future study.

QTL Mapping for Important Agronomic Traits in Synthetic Hexaploid Wheat Derived from Aegiliops tauschii ssp. tauschii

Aegiliops tauschii is classified into two subspecies: Ae. tauschii ssp. tauschii and Ae. tauschii ssp. strangulata. Novel genetic variations exist in Ae. tauschii ssp. tauschii that can be utilized in wheat improvement. We synthesized a hexaploid wheat genotype (SHW-L1) by crossing an Ae. tauschii ssp. tauschii accession (AS60) with a tetraploid wheat genotype (AS2255). A population consisting of 171 F8 recombinant inbred lines was developed from SHW-L1 and Chuanmai 32 to identify QTLs associated with agronomic traits. A new genetic map with high density was constructed and used to detect the QTLs for heading date, kernel width, spike length, spikelet number, and thousand kernel weight. A total of 30 putative QTLs were identified for five investigated traits. Thirteen QTLs were located on D genomes of SHW-L1, six of them showed positive effect on agronomic traits. Chromosome region flanked by wPt-6133–wPt-8134 on 2D carried five environment-independent QTLs. Each QTL accounted for more than 10% phenotypic variance. These QTLs were highly consistent across environments and should be used in wheat breeding.