本研究比较H/L选育群体和非选育群体的基因组数据和沙门氏菌感染后的脾脏转录组数据，旨在鉴定H/L选育过程中参与脾脏抗菌能力的关键基因。在选择系第10代，从H/L选育系和对照系分别选取41只和31只个体采集外周血样本提取DNA，并基于55K SNP芯片进行基因分型进行选择信号分析；分别选取选育系和对照系群体于7日龄进行鼠伤寒沙门氏菌（ST）感染试验，感染后3d测定肝组织载菌量和血液溶菌酶含量，同时采集脾脏组织（N=9）进行转录组分析；结合选择信号和脾脏转录组结果共同鉴定脾脏中参与沙门氏菌抵抗的候选基因。结果表明，与对照系群体相比，H/L选育群体对鼠伤寒沙门氏菌的抗性更强（P<0.05）。在选育系和对照系之间，鉴定的分化基因主要参与TGF-β信号通路、FoxO信号通路和沙门氏菌感染通路。对所有鉴定得到的脾脏差异表达基因（DEGs）的分析结果表明，沙门氏菌感染途径涉及的G蛋白偶联受体（GPCR）和胰岛素样生长因子（IGF-I）信号通路被显著富集（p<0.01）。基于DEGs和Fst（Fixation index）的综合分析鉴定了参与沙门氏菌感染途径的候选基因，如GPR39、NTRK2和ANXA1。广泛的基因组变化显示了在鸡群中免疫反应的多基因遗传基础。许多与免疫防御功能相关的基因在H/L选育和对照系中差异表达，选育系群体对沙门氏菌表现出更强的抗性。该研究确定了在用ST攻击后易感鸡和抗性鸡中差异表达的基因和通路，以更好地了解宿主对ST感染的免疫抗性。本研究利用动物模型（H/L定向选育系和对照系）的基因组数据和脾脏转录组数据进行了系统性的研究，解析了H/L定向选育后脾脏影响沙门氏菌抗性的分子机制。

早在2011年，研究者已对其进行了全基因组测序，并发现此基因组中有超过30%的编码基因是假定基因。另外，水平基因转移(horizontal gene transfer，HGT)已被认为是细菌基因组创新和进化的驱动力之一。前人在Xoc应对氧化应激的分子机制研究中，鉴定到了一个参与BLS256响应氧化胁迫并对毒性有贡献的水平转移基因(xoc_2868)。然而，xoc_2868作为一个转录因子的未知编码基因，其调控机制尚未被揭示。本研究基于BLAST序列比对和系统发育分析，初步判断其下游基因(xoc_2866和xoc_2867)与xoc_2868一样，均可能是BLS256在长期进化过程中通过水平转移从伯克氏菌科(Burkholderiaceae)获得的。为探索xoc_2868在BLS256响应氧胁迫过程中的潜在作用，我们分别对野生型(BLS256)和突变株(Δxoc_2868)在氧胁迫处理后进行了转录组测序。RNA-seq数据分析表明，在氧胁迫条件下，突变株中几个参与胞外多糖(EPS)和黄原胶(xanthan)生物合成基因的表达相较野生型显著下调，但未检测到其下游基因(xoc_2866和xoc_2867)的表达。为进一步鉴定受XOC_2868直接调控的基因，我们在野生型xoc_2868 C端融合了His6标签，并对此重组菌株进行了染色质免疫共沉淀 (ChIP-seq)分析。结合转录组分析发现，XOC_2868直接调控一个编码细胞色素bd氧化酶的两个亚基并参与氧化还原平衡的操纵子(cydAB)。与野生型菌株相比，cydA和cydAB缺失突变菌株与Δxoc_2868菌株一致出现对外源H₂O₂敏感性增强和细菌毒力减弱的表型。综上所述，本研究探讨了一种HGT形成和选择驱动的调控回路进化的可能性，xoc_2868与其两个下游基因可能是作为一个基因簇转移的，但它们在BLS256中各自进化，并在外界选择压下得以保留，XOC_2868通过结合新的调控位点直接调控了细胞色素bd氧化酶表达的通路，通过清除H₂O₂和其他ROS保护细胞免受氧化应激。此外，对胞外多糖和黄原胶合成相关基因的间接激活，也促进了其在宿主体内的定植和传播，从而参与了BLS256的致病力。本研究结果强调了在BLS256进化过程中，HGT现象对其毒力和适应性影响的可能性。

在中国南方稻作区，传统的早稻-晚稻双季稻模式（DR）种植面积迅速减少，同时，再生稻（RR）和稻虾（RC）作为两种新兴稻作模式正快速发展。本文采用能值分析法和生命周期评价法评估了稻作模式转变对水稻生产经营经济效益和生态可持续性的影响。经济效益分析结果表明：RC的生产产值和利润远大于RR和DR，RR和RC比DR的产投比分别提高了25.5和122.7%。与DR相比，由于较高的灌溉水、电力、幼虾苗和饲料等生产资料的投入，RC增加了能值投入，而RR则具有较低的总能值和不可再生能值投入，如灌溉水、电力、肥料和农药等。当稻作模式从DR转变为RR或者RC时，水稻生产的环境负载率分别减少了20.4和38.2%，而能值可持续性指标增加了34.8和65.2%。生命周期评价结果表明：RR和RC具有较低的潜在环境影响，它们的综合环境影响指数比DR分别低35.0和61.0%。与DR相比，RR的稻谷产量没有明显下降，但显著减少了经济成本和能值投入，而RC模式下稻谷产量下降严重（与RR相比减少了53.6%）。综上，再生稻模式是一种更有利于全面实现粮食安全、经济效益和生态可持续的种植模式。

水稻细菌性穗枯病又称水稻细菌性谷枯病，是一种由颖壳伯克氏菌 (Burkholderia glumae) 引起的严重的水稻种传病害，对全球水稻生产和食品安全造成了巨大威胁。由于缺乏对B. glumae在植物宿主中的适应性和发病机制的深入了解，迄今生产上还没有有效的防治措施。水平基因转移 (HGT) 已被证明是原核生物进化的主要驱动力。先前对60个Burkholderia全基因组的比较分析推断，大多数Burkholderia基因在其进化过程中至少经历过一次HGT，并在其菌株分化和致病性决定因素中起着重要作用。在本研究中，我们通过对LMG 2196菌株进行全基因组分析，鉴定到了42个潜在的水平转移基因。其中，一个注释为非核糖体肽合成酶(KS03_RS09665)的基因被确定为候选基因。进一步通过系统进化树的建立，发现该基因仅出现在与植物致病相关的Burkholderia菌属，并且在进化分枝上更接近于假单胞菌(Pseudomonas)中编码丁香肽合成酶(SypA)的sypA基因。为研究该基因在B. glumae致病性中的潜在作用，我们构建了syp基因缺失突变株。表型观察结果表明，sypA基因参与调控了该病菌的游动性、生物膜的形成、类似丁香肽代谢物的合成和致病性等重要生理表型。其中，与野生型菌株接种稻穗相比，sypA突变体接种稻穗后发病指数降低了20%。另外，与野生型菌株相比，sypA缺失突变菌株表现为游动能力显著下降、生物膜形成和类似丁香肽代谢物的合成受到抑制。综上所述，本研究探讨了水平转移基因sypA在颖壳伯克氏菌毒力中的作用。结果表明，sypA基因可能参与了颖壳伯克氏菌毒性物质丁香肽的合成，并且正向调控了其游动性和生物膜的形成，从而参与了颖壳伯克氏菌的致病力。本研究的结果强调了在颖壳伯克氏菌进化过程中，HGT现象对其毒力和适应性影响的可能性。

Traditionally, Chinese indigenous cattle is geographically widespread.  The present study analyzed based on genome-wide variants to evaluate the genetic background among 157 individuals from four representative indigenous cattle breeds of Hubei Province of China: Yiling yellow cattle (YL), Bashan cattle (BS), Wuling cattle (WL), Zaobei cattle (ZB), and 21 individuals of Qinchuan cattle (QC) from the nearby Shanxi Province of China.  Linkage disequilibrium (LD) analysis showed the LD of YL was the lowest (r2=0.32) when the distance between markers was approximately 2 kb.  Principle component analysis (PCA), and neighbor-joining (NJ)-tree revealed a separation of Yiling yellow cattle from other geographic nearby local cattle breeds.  In PCA plot, the YL and QC groups were segregated as expected; moreover, YL individuals clustered  together more obviously.  In the NJ-tree, the YL group formed an independent branch and BS, WL, ZB groups were mixed.  We then used the FST statistic approach to reveal long-term selection sweep of YL and other 4 cattle breeds.  According to the selective sweep, we identified the unique pathways of YL, associated with production traits.  Based on the results, it can be proposed that YL has its unique genetic characteristics of excellence resource, and it is an indispensable cattle breed in China.   

Genomic selection has been demonstrated as a powerful technology to revolutionize animal breeding.  However, marker density and minor allele frequency can affect the predictive ability of genomic estimated breeding values (GEBVs).  To investigate the impact of marker density and minor allele frequency on predictive ability, we estimated GEBVs by constructing the different subsets of single nucleotide polymorphisms (SNPs) based on varying markers densities and minor allele frequency (MAF) for average daily gain (ADG), live weight (LW) and carcass weight (CW) in 1 059 Chinese Simmental beef cattle.  Two strategies were proposed for SNP selection to construct different marker densities: 1) select evenly-spaced SNPs (Strategy 1), and 2) select SNPs with large effects estimated from BayesB (Strategy 2).  Furthermore, predictive ability was assessed in terms of the correlation between predicted genomic values and corrected phenotypes from 10-fold cross-validation.  Predictive ability for ADG, LW and CW using autosomal SNPs were 0.13±0.002, 0.21±0.003 and 0.25±0.003, respectively.  In our study, the predictive ability increased dramatically as more SNPs were included in analysis until 200K for Strategy 1.  Under Strategy 2, we found the predictive ability slightly increased when marker densities increased from 5K to 20K, which indicated the predictive ability of 20K (3% of 770K) SNPs with large effects was equal to the predictive ability of using all SNPs.  For different MAF bins, we obtained the highest predictive ability for three traits with MAF bin 0.01–0.1.  Our result suggested that designing a low-density chip by selecting low frequency markers with large SNP effects sizes should be helpful for commercial application in Chinese Simmental cattle.

Methanotrophs play a vital role in the mitigation of methane emission from soils. However, the influences of cover crops incorporation on paddy soil methanotrophic community structure have not been fully understood. In this study, the impacts of two winter cover crops (Chinese milk vetch (Astragalus sinicus L.) and ryegrass (Lolium multiflorum Lam.), representing leguminous and non-leguminous cover crops, respectively) on community structure and abundance of methanotrophs were evaluated by using PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) and real-time PCR technology in a double-rice cropping system from South China. Four treatments were established in a completely randomized block design: 1) double-rice cropping without nitrogen fertilizer application, CK; 2) double-rice cropping with chemical nitrogen fertilizer application (200 kg ha–1 urea for entire double-rice season), CF; 3) Chinese milk vetch cropping followed by double-rice cultivation with Chinese milk vetch incorporation, MV; 4) ryegrass cropping followed by double-rice cultivation with ryegrass incorporation, RG. Results showed that cultivating Chinese milk vetch and ryegrass in fallow season decreased soil bulk density and increased rice yield in different extents by comparison with CK. Additionally, methanotrophic bacterial abundance and community structure changed significantly with rice growth. Methanotrophic bacterial pmoA gene copies in four treatments were higher during late-rice season (3.18×107 to 10.28×107 copies g–1 dry soil) by comparison with early-rice season (2.1×107 to 9.62×107 copies g–1 dry soil). Type I methanotrophs absolutely predominated during early-rice season. However, the advantage of type I methanotrophs kept narrowing during entire double-rice season and both types I and II methanotrophs dominated at later stage of late-rice.

      Annual ryegrass (Lolium multiflorum Lam.), a non-leguminous winter cover crop, has been adopted to absorb soil native N to minimize N loss from an intensive double rice cropping system in southern China, but a little is known about its effects on rice grain yield and rice N use efficiency. In this study, effects of ryegrass on double rice yield, N uptake and use efficiency were measured under different fertilizer N rates. A 3-year (2009–2011) field experiment arranged in a split-plot design was undertaken. Main plots were ryegrass (RG) as a winter cover crop and winter fallow (WF) without weed. Subplots were three N treatments for each rice season: 0 (N₀), 100 (N₁₀₀) and 200 kg N ha^–1 (N₂₀₀). In the 3-year experiment, RG reduced grain yield and plant N uptake for early rice (0.4–1.7 t ha^–1 for grain yield and 4.6–20.3 kg ha^–1 for N uptake) and double rice (0.6–2.0 t ha^–1 for grain yield and 6.3–27.0 kg ha^–1 for N uptake) when compared with WF among different N rates. Yield and N uptake decrease due to RG was smaller in N₁₀₀ and N₂₀₀ plots than in N₀ plots. The reduction in early rice grain yield in RG plots was associated with decrease number of panicles. Agronomic N use efficiency and fertilizer N recovery efficiency were higher in RG plots than winter fallow for early rice and double rice among different N rates and experimental years. RG tended to have little effect on grain yield, N uptake, agronomic N use efficiency, and fertilizer N recovery efficiency in the late rice season. These results suggest that ryegrass may reduce grain yield while it improves rice N use efficiency in a double rice cropping system.

Methane (CH4) and nitrous oxide (N2O) emissions from paddy soils have seldom been estimated when leguminous green manure is applied as a nitrogen source. In this paper, gas fluxes were measured by using a pot sampling device combined with a static chamber method to estimate the effects of Chinese milk vetch (Astragalus sinicus L., CMV) on CH4 and N2O emissions and their integrated global warming potentials (GWP) in a double-rice cropping system. Four treatments (no nitrogen fertilizer, NF; urea as chemical fertilizer, CF; CMV incorporation, MV; 50% CMV incorporation and 50% urea, MVCF) were established. CH4 flux peaked on the 15th d after treatment application. Total season CH4 emission was increased by MV and MVCF by 370 and 209%, 152 and 66%, when compared with NF and CF, respectively. Most of the increased CH4 was emitted in the first two months after incorporation of CMV. N2O emission from CF was 17- and 5.6-fold higher than that from MV and MVCF, respectively. Application of CMV restricted N2O emission caused by the application of urea. Improved CMV residue management was needed to minify CH4 emission induced by the input of organic material. Despite the highest GWP being found in MV, we recommend CMV, when applied as an N source in paddy fields, as a potential mitigation tool for greenhouse gas emissions.

Horizontal gene transfer (HGT) plays key roles in the evolution of pathogenetic bacteria, especially in pathogenetic associated genes. In this study, the evolutionary dynamics of Xanthomonas at species level were determined by the comparative analysis of the complete genomes of 15 Xanthomonas strains. A concatenated multiprotein phyletic pattern and a dataset with Xanthomonas clusters of orthologous genes were constructed. Mathematical extrapolation estimates that the core genome will reach a minimum of about 1 547 genes while the pan-genome will increase up to 22 624 genes when sequencing 1 000 genomes. The HGT extent in this genus was assessed by using a Markov-based probabilistic method. The reconstructed gene gain/loss history, which contained several features consistent with biological observations, showed that nearly 60% of the Xanthomonas genes were acquired by HGT. A large fraction of variability was in the clade ancestor nodes and “leaves of the tree”. Coexpression analysis suggested that the pathogenic and metabolic variation between Xanthomonas oryzae pv. oryzicola and Xanthomonas oryzae pv. oryzae might due to recently-transferred genes. Our results strongly supported that the gene gain/loss may play an important role in divergence and pathogenicity variation of Xanthomonas species.