Sat-BSA: an NGS-based method using local de novo assembly of long reads for rapid identification of genomic structural variations associated with agronomic traits

Advances in next generation sequencing (NGS)-based methodologies have accelerated the identifications of simple genetic variants such as point mutations and small insertions/deletions (InDels). Structural variants (SVs) including large InDels and rearrangements provide vital sources of genetic diversity for plant breeding. However, their analysis remains a challenge due to their complex nature. Consequently, novel NGS-based approaches are needed to rapidly and accurately identify SVs. Here, we present an NGS-based bulked-segregant analysis (BSA) technique called Sat-BSA (SVs associated with traits) for identifying SVs controlling traits of interest in crops. Sat-BSA targets allele frequencies at all SNP positions to first identify candidate genomic regions associated with a trait, which is then reconstructed by long reads-based local de novo assembly. Finally, the association between SVs, RNA-seq-based gene expression patterns and trait is evaluated for multiple cultivars to narrow down the candidate genes. We applied Sat-BSA to segregating F₂ progeny obtained from crosses between turnip cultivars with different tuber colors and successfully isolated two genes harboring SVs that are responsible for tuber phenotypes. The current study demonstrates the utility of Sat-BSA for the identification of SVs associated with traits of interest in species with large and heterozygous genomes.     

Conservation of a permanent hypersaline lake: management options evaluated from decadal variability of Coleofasciculus chthonoplastes microbial mats

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Genetic analysis of the population structure of the rice false smut fungus,Villosiclava virens,in China using microsatellite markers mined from a genome assembly

Studies on population genetics of Villosiclava virens are limited because of the lack of polymorphic markers. Based on a draft genome sequence of isolate HWD‐2 produced in this study, 20 of 403 potential simple sequence repeats (SSR) loci showed polymorphisms in preliminary screening using eight diverse V. virens isolates. Among polymorphic loci, most of them with tetra‐ to hexanucleotide unit motifs showed higher levels of polymorphism than loci with smaller motifs. After testing with 20 polymorphic SSR markers, the 87 isolates of V. virens from eight populations in China showed a high level of genetic diversity, with each as a unique haplotype. This differs from some previous findings showing little to no genetic variation based on random amplified polymorphic DNA and amplified fragment length polymorphism analyses. Among eight populations from major rice production areas of China, the population from Guangxi province in south China showed the highest levels of polymorphism, which led to the speculation that it might be closer to the centre of origin of this pathogen. The northern, central and eastern populations (Jilin, Liaoning, Hubei, Hunan, Jiangxi and Zhejiang), when considered together as a group, showed significant molecular variation compared to the southern populations (Fujian and Guangxi) (Φ_PT = 0·043, P = 0·037). A significant relationship (Mantel test, P = 0·027) but with low correlation (R² = 0·23) was also found between geographic distance and genetic distance. The 20 polymorphic SSR primer pairs designed in this study provide a tool for further research on the population diversity of this emerging fungal pathogen of rice.     

Molecular characterization of storage proteins for selected durum wheat varieties grown in different environments

The variations of the amounts of individual high molecular weight glutenin subunits (HMW-GS), of the ratios HMW-GSy to HMW-GSx and HMW-GS to low molecular weight glutenin subunits (LMW-GS) and of protein content were evaluated for eight durum wheat cultivars in two regions using four fertilizer combinations during two successive years. All measured parameters showed significant variation with genotypes (G), environments (E) and fertilizers (F). The interaction E × G × F was highly significant for glutenin amount variation. Amongst cultivars possessing HMW-GS 20, landraces seem to better value the N-fertilizer use for the accumulation of HMW-GSy than high yielding cultivars. Both HMW-GSy to HMW-GSx and HMW-GS to LMW-GS ratios were found to be positively correlated (p < 0.05) with total protein content.     

Acute-phase protein response in pigs experimentally infected with Haemophilus parasuis

The acute-phase protein (APP) response to an infection caused by Haemophilus parasuis, the etiological agent of Glässer's disease in pigs, was characterized measuring serum concentrations of pig major acute-phase protein (pig MAP), haptoglobin (HPT), C-reactive protein (CRP) and apolipoprotein A-I (ApoA-I) in colostrum-deprived pigs. They were divided into six experimental groups: non-immunized control group (I); immunized with a non-commercial bacterin (II); with an OMP-vaccine (III); with a sublethal dose (IV); and with two commercial bacterins (V and VI). All groups were challenged intratracheally with 5 × 10⁹ CFU of H. parasuis 37 days after immunisation. The highest levels of the positive APPs (pig MAP, HPT and CRP) and the lowest levels of the negative APPs (ApoA-I) were observed in the animals that died as a consequence of the infection, both those in the non-inmunized and in the immunized groups. However, the surviving animals (all of them in groups II, V and VI, two pigs in group III, and three in group IV) showed a minor variation in APP response, mainly on day 1 post-challenge (p.c.), and then tended to recover the initial values. APP response was still less pronounced in the groups of pigs previously immunized with bacterins. In conclusion, APP response can reflect Glässer-disease ongoing, showing a correlation between the severity and duration of the clinical signs and lesions and the magnitude of changes in the APP levels.     

马铃薯晚疫病菌交配型研究概述

晚疫病是严重危害全球马铃薯生产、且具有毁灭性的一种卵菌病害。该文在简要介绍马铃薯晚疫病菌起源、分类地位和生活史的基础上,着重概述了晚疫病菌卵孢子形成的可能机制、交配型遗传规律及检测方法的主要进展。     

Biogenic calcium phosphate transformation in soils over millennial time scales

Background, aim, and scope  Changes in bioavailability of phosphorus (P) during pedogenesis and ecosystem development have been shown for geogenic calcium phosphate (Ca-P). However, very little is known about long-term changes of biogenic Ca-P in soil. Materials and methods  Long-term transformation characteristics of biogenic Ca-P were examined using anthropogenic soils along a chronosequence from centennial to millennial time scales. Results and discussion  Phosphorus fractionation of Anthrosols resulted in overall consistency with the Walker and Syers model of geogenic Ca-P transformation during pedogenesis. The biogenic Ca-P (e.g., animal and fish bones) disappeared to 3% of total P within the first ca. 2,000 years of soil development. This change concurred with increases in P adsorbed on metal-oxides surfaces, organic P, and occluded P at different pedogenic time. Phosphorus K-edge X-ray absorption near-edge structure (XANES) spectroscopy revealed that the crystalline and therefore thermodynamically most stable biogenic Ca-P was transformed into more soluble forms of Ca-P over time. While crystalline hydroxyapatite (34% of total P) dominated Ca-P species after about 600–1,000 years, β-tricalcium phosphate increased to 16% of total P after 900–1,100 years, after which both Ca-P species disappeared. Iron-associated P was observable concurrently with Ca-P disappearance. Soluble P and organic P determined by XANES maintained relatively constant (58–65%) across the time scale studied. Conclusions  Disappearance of crystalline biogenic Ca-P on a time scale of a few thousand years appears to be ten times faster than that of geogenic Ca-P.     

菊花黄化突变体初步研究

以菊花‘霞光飞跃’叶色突变体和正常植株为试验材料,对其叶绿素含量进行测定,并进行无参转录组测序分析。结果表明：突变体与正常植株相比,叶绿素含量有较大幅度的下降,仅为正常植株的18%左右,叶绿素a/b比值(Chl a/b)显著升高。利用转录组测序技术分别从突变体与正常植株叶片中获得4.75 Gb和4.96 Gb有效数据(Clean Data),de novo组装后得到105 456条通用基因(Unigenes),其中长度大于1 kb的有15 493条,N50为1 556 bp。对Unigenes表达分析,共获得3 762条差异表达基因(DEGs)。对得到的DEGs进行生物学功能性注释,获得总注释信息为2 741。通过对注释信息进行GO和KEGG富集分析,结合定量PCR验证表明,菊花‘霞光飞跃’叶色突变体形成的原因可能是 dmGLK2低水平表达和dmGLK1 不表达导致叶绿体合成和分裂受阻,叶片细胞内叶绿体数量大大降低,进而叶绿素含量下降。     

3种自根无性系砧木对接穗PR107产量的影响初报

比较了3种由巴西橡胶树花药离体组织培养的无性系组成的嫁接组合材料(热研8813、海垦2和大丰99为砧木,PR107为接穗)接穗胶乳在不同季节的干含(DRC)和干胶产量,分析不同砧木对它们的影响。结果表明:①砧木对接穗产量有显著影响,优良的可大幅提高橡胶产量,对接穗干含影响显著。砧木对接穗干含和干胶产量的影响因砧木材料不同而有较大变化。比较3种芽接树年平均产量,PR107/大丰99比PR107/热研88-13高6.22%、比PR107/海垦2高31.83%,PR107/热研88-13比PR107/海垦2高24.15%。②同一芽接树接穗胶乳干含和干胶产量随季节发生波动,在不同季节胶乳干含和干胶产量存在显著差异,表明它们受季节影响明显。不同的芽接树接穗胶乳干含和产量受季节的影响程度有较大差异,这种差异来源于砧木对接穗的影响。