Genetic dissection of wheat panicle traits using linkage analysis and a genome-wide association study

Key message

Coincident regions on chromosome 4B for GW, on 5A for SD and TSS, and on 3A for SL and GNS were detected through an integration of a linkage analysis and a genome-wide association study (GWAS). In addition, six stable QTL clusters on chromosomes 2D, 3A, 4B, 5A and 6A were identified with high PVE% on a composite map.

Abstract

The panicle traits of wheat, such as grain number per spike and 1000-grain weight, are closely correlated with grain yield. Superior and effective alleles at loci related to panicles developments play a crucial role in the progress of molecular improvement in wheat yield breeding. Here, we revealed several notable allelic variations of seven panicle-related traits through an integration of genome-wide association mapping and a linkage analysis. The linkage analysis was performed using a recombinant inbred line (RIL) population (173 lines of F_8:9) with a high-density genetic map constructed with 90K SNP arrays, Diversity Arrays Technology (DArT) and simple sequence repeat (SSR) markers in five environments. Thirty-five additive quantitative trait loci (QTL) were discovered, including eleven stable QTLs on chromosomes 1A, 2D, 4B, 5B, 6B, and 6D. The marker interval between EX_C101685 and RAC875_C27536 on chromosome 4B exhibited pleiotropic effects for GW, SL, GNS, FSN, SSN, and TSS, with the phenotypic variation explained (PVE) ranging from 5.40 to 37.70%. In addition, an association analysis was conducted using a diverse panel of 205 elite wheat lines with a composite map (24,355 SNPs) based on the Illumina Infinium assay in four environments. A total of 73 significant marker-trait associations (MTAs) were detected for panicle traits, which were distributed across all wheat chromosomes except for 4D, 5D, and 6D. Consensus regions between RAC875_C27536_611 and Tdurum_contig4974_355 on chromosome 4B for GW in multiple environments, between QTSS5A.7-43 and BS00021805_51 on 5A for SD and TSS, and between QSD3A.2-164 and RAC875_c17479_359 on 3A for SL and GNS in multiple environments were detected through linkage analysis and a genome-wide association study (GWAS). In addition, six stable QTL clusters on chromosomes 2D, 3A, 4B, 5A, and 6A were identified with high PVE% on a composite map. This study provides potentially valuable information on the dissection of yield-component traits and valuable genetic alleles for molecular-design breeding or functional gene exploration.

     

Rhizosphere processes induce changes in dissimilatory iron reduction in a tidal marsh soil: a rhizobox study

Background and aims

Although the role of microbial iron respiration in tidal marshes has been recognized for decades, the effect of rhizosphere processes on dissimilatory ferric iron reduction (FeR) is poorly known. Herein, we examined the FeR surrounding the root zone of three tidal marsh plants.

Methods

Using in situ rhizoboxes, we accurately separated rhizobox soil as one rhizosphere zone, and three bulk soil zones. Dissimilatory and sulfidic-mediated FeR were quantified by accumulation of non-sulfidic Fe(II) and Fe sulfides over time, respectively.

Results

The rates of dissimilatory FeR attained 42.5 μmol Fe g^?1 d^?1 in the rhizosphere, and logarithmically declined by up to 19.1 μmol Fe g^?1 d^?1 in the outer bulk soil. The rates of sulfidic-mediated FeR were less than 2 μmol Fe g^?1 d^?1 among all zones. Poorly crystalline Fe(III), DOC and DON, porewater Fe²⁺, and SO₄^2? were all enriched in the rhizosphere, whereas non-sulfidic Fe(II) and Fe sulfides gradually accumulated away from the roots. Iron reducers (Geobacter, Bacillus, Shewanella, and Clostridium) had higher populations in the rhizosphere than in the bulk soil. Higher rates of dissimilatory FeR were observed in the Phragmites australis and Spartina alterniflora rhizoboxes than in the Cyperus malaccensis rhizoboxes.

Conclusions

The radial change pattern of dissimilatory FeR rates were determined by allocation of poorly crystalline Fe(III) and dissolved organic carbon. The interspecies difference of rhizosphere dissimilatory FeR was associated with the root porosity and aerenchyma of the tidal marsh plants.

     

Detection of Insertions/Deletions Within <Emphasis Type="Italic">SIRT1</Emphasis>, <Emphasis Type="Italic">SIRT2</Emphasis> and <Emphasis Type="Italic">SIRT3</Emphasis> Genes and Their Associations with Body Measurement Traits in Cattle

Growth traits are complex quantitative traits controlled by numerous candidate genes, and they can be well-evaluated using body measurement traits. As the members of the nicotinamide adenine dinucleotide-dependent family of histone deacetylases, class I sirtuin genes (including SIRT1, SIRT2 and SIRT3) play crucial roles in regulating lipid metabolism, cellular growth and metabolism, suggesting that they are potential candidate genes affecting body measurement traits in animals. Hence, the objective of this work aimed to detect novel insertions/deletions (indels) of SIRT1, SIRT2 and SIRT3 genes in 955 cattle belonging to five breeds, as well as to evaluate their effects on body measurement traits. Herein, the novel 12-bp indel of SIRT1 gene, the 7-bp indel of SIRT2 gene and the 26-bp indel of SIRT3 gene were firstly reported, respectively. The association analysis indicated that the indels within SIRT1 and SIRT2 genes were significantly associated with body measurement traits such as body weight, chest circumference, height at hip cross, hip width, body height, etc. (P?<?0.05 or P?<?0.01). Therefore, based on these findings, the two novel indel variants within bovine SIRT1 and SIRT2 genes could be considered as potential molecular markers for growth traits in cattle selection practices and breeding.     

Gene expression profile of Ralstonia Solanacearum for the rhizosphere ecological niche of Solanum tuberosum

Plant root secretion can be regarded as signal molecules, which exerts impact on microorganisms in the rhizosphere ecological niche. We obtained gene expression profile of Ralstonia solanacearumPO41 under the root secretions environment of Solanum tuberosum at the time points of 8 hrs, 16 hrs and 24 hrs, respectively, after infection with RNA microarray technology. Bioinformatics tools of differential genes expression analysis, GO functional analysis, cluster analysis and pathway analysis were conducted to find out the pathogenic genes and other related genes. We found that the virulence factors of R. solanacearum mainly focused on the output pathways of toxic protein (Sec pathway, Tat pathway and type III secretion system (T3SS)), the aggregation and transfer of exopolysaccharides and the chemotactic movement and adhesion of flagellum in the potato root secretion ecological niche, while the virulence factors in the atypical output pathway mainly distributed in Sec (secB, secDF, yidc) and Tat (tatA, tatC) pathways to promote the output of folded and unfolded toxic proteins. The fliIATPase was obviously upregulated 8 hrs postinoculation, suggesting that type III secretion system was only active at the early stage of PO41 infection. The upregulated expression of phosphoglucomutase and epimerase showed that the virulence factor of exopolysaccharides (EPS) was synthesized at the early stage of R. solanacearum infection. Chemotactic receptor and motor protein were obviously upregulated within 24 hrs postinoculation. Our study revealed that R. solanacearumPO41 had already colonized to the roots within 24 hrs with the stimulating of root secretion. Some pathogenic genes were upregulated during this period.     

Effects of NMDAR Antagonist on the Regulation of P-MARCKS Protein to Aβ<Subscript>1−42</Subscript> Oligomers Induced Neurotoxicity

Alzheimer’s disease (AD) is a well-known neurodegenerative disease. Deposition of β-amyloid protein (Aβ) oligomers plays a crucial role in the disease progression. Previous studies showed that toxicity induced by Aβ oligomers in cultured neurons and adult rat brain was partially mediated by activation of glutamatergic N-methyl-d-aspartate receptors (NMDAR). Additionally, memantine, a noncompetitive NMDAR antagonist, can significantly improve cognitive functions in some AD patients. However, little is currently known about the potential role of NMDAR antagonist on the regulation of P-MARCKS protein to Aβ_1?42 oligomers induced neurotoxicity. The protective effect and mechanism of NMDAR antagonist on primary neurons exposed to Aβ_1?42 oligomers were investigated in the study. We have defined that the Aβ_1?42 treatment decreased cell viability and increased apoptosis. Moreover, Aβ_1?42 oligomers exposure increased P-MARCKS and PIP2 expressions, while decreased SYP expression. However, NMDAR antagonist pretreatment ameliorates Aβ_1?42 oligomers induced neuronal apoptosis and partially reverses the expression of P-MARCKS, PIP2 and SYP. In conclusion, NMDAR antagonist may ameliorate neurotoxicity induced by Aβ_1?42 oligomers through reducing neuronal apoptosis and protecting synaptic plasticity in rat primary neurons. The mechanism involved may be mediated by the variation of protein P-MARCKS.     

Afatinib Decreases P‐Glycoprotein Expression to Promote Adriamycin Toxicity of A549T Cells

We investigated the reversal effect of afatinib (AFT) on activity of adriamycin (ADR) in A549T cells and clarified the related molecular mechanisms. A549T cells overexpressing P‐glycoprotein (P‐gp) were resistant to anticancer drug ADR. AFT significantly increased the antitumor activity of ADR in A549T cells. AFT increased the intracellular concentration of ADR by inhibiting the function and expression of P‐gp at mRNA and protein levels in A549T cells. Additionally, the reversal effect of AFT on P‐gp mediated multidrug resistance (MDR) might be related to the inhibition of PI3K/Akt pathway. Cotreatment with AFT and ADR could enhance ADR‐induced apoptosis and autophagy in A549T cells. Meanwhile, the co‐treatment significantly induced cell apoptosis and autophagy accompanied by increased expression of cleaved caspase‐3, PARP, LC3B‐II, and beclin 1. Apoptosis inhibitors had no significant effect on cell activity, while autophagy inhibitors decreased cell viability, suggesting that autophagy may be a self protective mechanism of cell survival in the absence of chemotherapy drugs. Interestingly, when combined with AFT and ADR, inhibition of apoptosis and/or autophagy could enhance cell viability. These results indicated that in addition to inhibit P‐gp, ADR‐induced apoptosis, and autophagy promoted by AFT contributed to the antiproliferation effect of combined AFT and ADR on A549T cells. These findings provide evidence that AFT combined ADR may achieve a better therapeutic effect to lung cancer in clinic. J. Cell. Biochem. 119: 414–423, 2018. © 2017 Wiley Periodicals, Inc.     

Genetic Dissection of Wheat Kernel Hardness Using Conditional QTL Mapping of Kernel Size and Protein-Related Traits

Kernel hardness (KH) is one of the primary quality parameters for common wheat (Triticum aestivum L.) and has a major impact on milling, flour quality, and end-product properties. In addition to Puroindoline (Pin) mutations and differences in Pin expression, other factors, such as kernel size and protein-related traits, play noticeable roles in determining hardness, but at the quantitative trait locus (QTL) level, the influence of these factors remains unclear. In this study, genetic relationships between KH and kernel size traits and between KH and protein-related traits were demonstrated by unconditional and conditional mapping using a wheat 90K genotyping assay with a segregating population of 173 recombinant inbred lines in four environments. Eight additive QTL for KH were detected using unconditional QTL mapping analysis; these QTL were primarily distributed on chromosomes 4B, 5A, 5B, and 6D, with phenotypic variation that ranged from 0.2 to 17.7%. In addition, one pair of epistatic QTL (QKH3B.4-65/QKH4B.6-2) was identified by unconditional mapping, and this pair accounted for 1.6% of the phenotypic variation. Through conditional mapping, after excluding the influences of kernel size and protein-related traits, 14 QTL were discovered and accounted for 0.6–18.5% of the phenotypic variation. Of them, the stable QTL QKH4B.4-17 made the largest contribution, which was partially contributed by the kernel length (KL), kernel thickness (KT), and dry gluten content (DGC). Furthermore, QKH4B.4-17 was crucially contributed by the kernel width (KW), kernel diameter (KD), kernel protein content (KPC), and wet gluten content (WGC) and was independent of the sedimentation volume (SV) and gluten index (GI). Another major QTL, QKH5B.10-63, was independent of the KW and KT; partly due to the variations in KL, KD, DGC, and WGC; and conclusively contributed by the KPC, SV, and GI. Seven additional QTL were only detected in the conditional analysis and were crucially contributed by kernel size or protein-related traits. These results demonstrated that kernel size and protein-related traits play significant roles in determining KH. The present study increases the understanding of the relationships between KH and kernel size and between KH and protein-related traits at the QTL level.     

Sinopestalotiollides A–D,cytotoxic diphenyl ether derivatives from plant endophytic fungus Pestalotiopsis palmarum

Four new diphenyl ether derivatives, sinopestalotiollides A–D (1–4), one new natural α-pyrone product (11), as well as twelve known compounds (5–1?7), were obtained from the ethyl acetate extract of the endophytic fungus Pestalotiopsis palmarum isolated from the leaves of medicinal plant Sinomenium acutum (Thunb.) Rehd et Wils. The structures were elucidated by HR-ESI-MS and NMR spectrometry data. Bioassay experiments revealed that compounds 1–4 and 11 exhibited strong to weak cytotoxicities against three human tumor cell lines Hela, HCT116 and A549.