Genetic dissection and origin of pleiotropic loci underlying multilevel fiber quality traits in upland cotton(Gossypium hirsutum L.)

Cotton fiber quality is a persistent concern that determines planting benefits and the quality of finished textile products.However,the limitations of measurement instruments have hindered the accurate evaluation of some important fiber characteristics such as fiber maturity,fineness,and neps,which in turn has impeded the genetic improvement and industrial utilization of cotton fiber.Here,12 single fiber quality traits were measured using Advanced Fiber Information System(AFIS)equipment among 383 accessions of upland cotton(Gossypium hirsutum L.).In addition,eight conventional fiber quality traits were assessed by the High Volume Instrument(HVI)System.Genome-wide association study(GWAS),linkage disequilibrium(LD)block genotyping and functional identification were conducted sequentially to uncover the associated elite loci and candidate genes of fiber quality traits.As a result,the previously reported pleiotropic locus FL_D11 regulating fiber length-related traits was identified in this study.More importantly,three novel pleiotropic loci(FM_A03,FF_A05,and FN_A07)regulating fiber maturity,fineness and neps,respectively,were detected based on AFIS traits.Numerous highly promising candidate genes were screened out by integrating RNA-seq and qRT-PCR analyses,including the reported GhKRP6 for fiber length,the newly identified GhMAP8 for maturity and GhDFR for fineness.The origin and evolutionary analysis of pleiotropic loci indicated that the selection pressure on FL_D11,FM_A03 and FF_A05 increased as the breeding period approached the present and the origins of FM_A03 and FF_A05 were traced back to cotton landraces.These findings reveal the genetic basis underlying fiber quality and provide insight into the genetic improvement and textile utilization of fiber in G.hirsutum.

Surveying the genomic landscape of silage-quality traits in maize(Zea mays L.)

Despite the longstanding importance of silage as a critical feed source for ruminants,its quality improvement has been largely overlooked.Although numerous quantitative trait loci(QTL)and genes affecting silage quality in maize have been reported,only a few have been effectively incorporated into breeding programs.Addressing this gap,the present study undertook a comprehensive meta-QTL(MQTL)analysis involving 523 QTL associated with silage-quality traits collected from 14 published studies.Of the 523 QTL,405 were projected onto a consensus map comprising 62,424 genetic markers,resulting in the identification of 60 MQTL and eight singletons.The average confidence interval(CI)of the MQTL was 3.9-fold smaller than that of the source QTL.Nine of the 60 identified MQTL were classified as breeder’s MQTL owing to their small CIs,involvement of more QTL,and large contribution to phenotypic variation.One-third of the MQTL co-localized with DNA marker-trait associations identified in previous genomewide association mapping studies.A set of 78 high-confidence candidate genes influencing silage quality were identified in the MQTL regions.These genes and associated markers may advance marker-assisted breeding for maize silage quality.

Expression Profiling Identifies Candidate Genes for Fiber Yield and Quality

Gene expression profiling at early stages(0～2 DPA) of fiber development in Gossypium hirsutum identified a number of transcription factors which were down regulated in fiberless mutants relative to wild type controls and which could play a role in controlling early fiber development.Chief among these was GhMYB25,a Mixta-like MYB gene.Transgenic GhMYB25-silenced cotton

Identification of candidate genes controlling fiber quality traits in upland cotton through integration of meta-QTL,significant SNP and transcriptomic data

Background:Meta-analysis of quantitative trait locus(QTL)is a computational technique to identify consensus QTL and refine QTL positions on the consensus map from multiple mapping studies.The combination of meta-QTL intervals,significant SNPs and transcriptome analysis has been widely used to identify candidate genes in various plants.Results:In our study,884 QTLs associated with cotton fiber quality traits from 12 studies were used for meta-QTL analysis based on reference genome TM-1,as a result,74 meta-QTLs were identified,including 19 meta-QTLs for fiber length;18 meta-QTLs for fiber strength;11 meta-QTLs for fiber uniformity;11 meta-QTLs for fiber elongation;and 15 meta-QTLs for micronaire.Combined with 8589 significant single nucleotide polymorphisms associated with fiber quality traits collected from 15 studies,297 candidate genes were identified in the meta-QTL intervals,20 of which showed high expression levels specifically in the developing fibers.According to the function annotations,some of the 20 key candidate genes are associated with the fiber development.Conclusions:This study provides not only stable QTLs used for marker-assisted selection,but also candidate genes to uncover the molecular mechanisms for cotton fiber development.

Transcriptome and QTL analyses reveal candidate genes for fiber quality in Upland cotton

With increasing demand for high-quality cotton,it is desirable to identify genes involved in fiber development for molecular improvement of cotton.In this study,780 differentially expressed genes(DEGs)were identified in developing fibers at 10 days post-anthesis(DPA)in Gossypium hirsutum acc.DH962 and G.hirsutum cv.Jimian 5 using RNA-seq.Of 15 stable QTL for fiber quality identified in the same two parents in previous studies,4,3,6,1,and 1 QTL were associated with fiber length(FL),fiber strength(FS),micronaire(MIC),fiber elongation(FE)and fiber length uniformity ratio(FU),respectively.Integration of DEGs and QTL allowed the identification of 31 genes in 9 QTL regions,of which 25 were highly expressed in fibers based on the transcriptome datasets and 9 were preferentially expressed in different stages of fiber development.Gh_A01G0453(GhDTX19),Gh_D07G1581 and Gh_D04G0942 were expressed specifically in 5 and 10 DPA fibers,with Gh_D04G0942 showing low expression in other tissues except pistil.Gh_D07G1799(GhGAUT9),Gh_D11G0326(GhVPS29),Gh_D11G0333(GhTCP14),and Gh_D11G0334(GhNRP2)were preferentially expressed in 5 or 10 DPA fibers;Gh_A01G0397(GhABCG10)and Gh_D07G1744 were expressed specifically in 20 and 25 DPA fibers.These results suggest candidate genes for molecular improvement of cotton fiber quality.

Genetic dissection of rice appearance quality and cooked rice elongation by genome-wide association study

Appearance and cooked rice elongation are key quality traits of rice. Although some QTL for these traits have been identified, understanding of the genetic relationship between them remains limited. In the present study, large phenotypic variation was observed in 760 accessions from the 3 K Rice Genomes Project for both appearance quality and cooked rice elongation. Most component traits of appearance quality and cooked rice elongation showed significant pairwise correlations, but a low correlation was found between appearance quality and cooked rice elongation. A genome-wide association study identified 74 QTL distributed on all 12 chromosomes for grain length, grain width, length to width ratio, degree of endosperm with chalkiness, rice elongation difference, and elongation index. Thirteen regions containing QTL stably expressed in multiple environments and/or exerting pleiotropic effects on multiple traits were detected. By gene-based association analysis and haplotype analysis, 46 candidate genes, including five cloned genes, and 49 favorable alleles were identified for these 13 QTL. The effect of the candidate gene Wx on rice elongation difference was validated by a transgenic strategy. These results shed light on the genetic bases of appearance quality and cooked rice elongation and provide gene resources for improving rice quality by molecular breeding.

羊肉品质重要候选基因研究进展

羊肉凭借高蛋白、低胆固醇、低脂肪等特点受到消费者的喜爱。现阶段,育种学家们通过分子生物学的方式筛选与羊肉品质相关的候选基因,为肉羊品种改良等分子育种提供依据,以促进羊肉品质的提升。该文就与羊肉pH、肌内脂肪沉积以及脂肪酸分布等相关的候选基因进行综述,以期为后续羊的遗传改良、羊肉品质提高以及新育种技术的研发提供参考。

基于垂体全长转录组测序分析鸡睾丸性状相关基因

【背景】睾丸是雄性动物重要生殖器官,具有产生精子和分泌雄激素的功能,睾丸质量与繁殖性能有直接联系。睾丸性状受下丘脑-垂体-性腺轴多基因共同调控,其分子机理尚不清楚。宁都黄鸡睾丸性状变异系数大,繁殖性能一致性差。【目的】通过对不同睾丸性状个体垂体组织进行全长转录组测序,挖掘候选基因以及关键信号通路,探究影响睾丸性状的遗传基础,以期为发展地方鸡种睾丸性状的选种选育提供依据。【方法】以70只22周龄宁都黄公鸡为研究对象,分为大睾丸组和小睾丸组,从两组中分别选取3个个体,构建垂体组织的全长转录本表达谱,筛选高表达量及两组个体差异表达基因或转录本,对差异基因或转录本进行功能富集分析。随机选取6个基因,进行基因表达水平验证。参考已知垂体细胞的标记基因,筛选与8种细胞标记基因对应的差异表达基因或转录本,并分析这些差异基因或转录本以及高表达量基因或转录本与睾丸性状相关性。【结果】在6个宁都黄鸡垂体组织中,检测到21834个基因,29355个全长转录本。其中,332个基因及229个转录本在两组个体中差异表达。KEGG通路分析结果显示,这些差异基因或转录本主要富集于Apelin信号、甘油磷脂代谢等通路。一共发现5个促性腺细胞标记基因或其对应转录本与部分睾丸性状显著相关,包括NFASC(neurofascin)及其对应转录本XM_015298904.2、TESC(tescalcin)及其对应转录本XM_025155510.1、FSHB(folliclestimulatinghormonebeta)转录本ONT.20974.4、RLN3(relaxin 3)、NDUFB2(NADH:ubiquinone oxidoreductase subunit B2)转录本ONT.1176.4。1个催乳素细胞标记基因EGR1(early growth response 1),2个滤泡星状细胞标记基因TMSB4X(thymosin beta 4,X-linked)、C1H12ORF57(chromosome 1 open reading frame),1个促甲状腺细胞标记基因CHGB(chromogranin B)均与部分睾丸性状显著相关。2个高表达量基因TMSB4X、HSP90AA1(heat shock protein 90 alpha family class A member 1)与部分睾丸性状显著相关。FSHB、EGR1均为基因互作网络中节点基因。【结论】经初步功能分析,EGR1、TMSB4X、FSHB、RLN3为睾丸性状调控的关键基因。MAPK信号通路、神经活性配体-受体相互作用、GnRH信号通路为睾丸性状调控的关键基因通路。

桑叶发酵菌株的生物学特性及发酵桑叶品质分析

本研究旨在分析桑叶发酵菌株的生物学特性和发酵桑叶品质,以得到优良发酵菌株,推动发酵桑叶在畜禽生产中替代豆粕等蛋白质饲料的广泛应用。本研究在对候选菌株的生物学特性分析的基础上,筛选优良菌株进行桑叶发酵,并对发酵桑叶的营养特性进行了分析。结果表明:候选菌株中乳酸片球菌(PA)、戊糖片球菌(PP)和敏捷乳杆菌(LA)对大肠杆菌等病原菌有广谱抑菌效果,4株芽孢杆菌有较强产纤维素酶和蛋白酶能力,11株菌对酸、温度、胆盐和人工胃肠液均具有耐受能力。经PA、PP、唾液乳杆菌(LS)、加氏乳杆菌(LG)和枯草芽孢杆菌1(BS1)发酵后桑叶的粗蛋白质含量显著高于未发酵桑叶(P<0.05);经凝结芽孢杆菌(BC)和枯草芽孢杆菌2(BS2)发酵后桑叶的粗纤维含量显著低于未发酵桑叶以及PP和LS发酵组(P<0.05);经PA和PP发酵后桑叶的pH显著低于其他组(P<0.05),其乳酸含量则显著高于其他组(P<0.05);7株乳酸菌发酵组乳酸菌数量显著高于其他组(P<0.05)。综合分析菌株生物学特性和发酵桑叶品质,选取的优良菌株为PA、PP、LS、LA、LR9、BS1和BL作为桑叶发酵菌株。

青贮玉米品质相关性状的全基因组关联分析

为了初步揭示玉米粗蛋白含量、淀粉含量、中性洗涤纤维(neutral detergent fiber,NDF)含量、酸性洗涤纤维(acid detergent fiber,ADF)含量、可溶性糖含量和体外干物质消化率等性状的遗传规律,按照随机区组设计将183份自交系为材料种植于贵阳,测定玉米粗蛋白含量、淀粉含量、NDF含量、ADF含量、可溶性糖含量和体外干物质消化率,利用Maize SNP 50芯片对供试材料进行基因分型,采用混合线性模型进行全基因组关联分析,结果显示,分别鉴定出31、61、11、36、20和42个与粗蛋白、淀粉、NDF、ADF、可溶性糖及体外干物质消化率显著相关的单核苷酸多态性位点(SNP)(P<0.001),对表型变异的解释率分别为5.80%~11.40%、5.78%~11.38%、5.78%~7.85%、5.81%~10.37%、5.78%~7.35%和5.79%~11.33%。同时,发现SYN6712、PHM1190.3、SYN7541和PZE-104072386属于一因多效位点;其中,6号染色体上的SYN6712、PHM1190.3和SYN7541同时与淀粉、体外干物质消化率显著关联,4号染色体上的PZE-104072386同时与ADF、可溶性糖显著关联,经过等位变异鉴定发现T/T基因型是SYN6712和PHM1190.3的优异等位变异,并挖掘到了Zm00001d037272、Zm00001d037386、Zm00001d037532和Zm00001d051166等候选基因。

基于统计特征的Quality Phrase挖掘方法

Quality Phrase挖掘是从文本语料库中提取有意义短语的过程,是文档摘要、信息检索等任务的基础。然而现有的无监督短语挖掘方法存在候选短语质量不高、Quality Phrase的特征权重平均分配的问题。本文提出基于统计特征的Quality Phrase挖掘方法,将频繁N-Gram挖掘、多词短语组合性约束及单词短语拼写检查相结合,保证了候选短语的质量;引入公共知识库对候选短语添加类别标签,实现了Quality Phrase特征权重的分配,并考虑特征之间相互影响设置惩罚因子调整权重比例;按照候选短语的特征加权函数得分排序,提取Quality Phrase。实验结果表明,基于统计特征的Quality Phrase挖掘方法明显提高了短语挖掘的精度,与最优的无监督短语挖掘方法相比,精确率、召回率及F1-Score分别提升了5.97%,1.77%和4.02%。

数字化背景下高职院校专业设置与产业发展的适应性研究——基于2021年浙江省39所高职计算机类专业招生投档情况的分析

通过对浙江省39所高职院校计算机类专业的招生投档数据分析,发现专业设置与产业发展存在专业同质化严重、办学质量与特色不明显、与地方产业匹配度不高、与产业的融合度不深、师资力量不强等问题。高职院校应坚持质量立校、特色强校的办学理念,在对接地方区域核心产业、与企业共建产业学院及加强师资队伍建设等方面加大力度,增强专业与产业协同发展的适应性。

冬小麦籽粒主要品质性状的全基因组关联分析

【目的】小麦籽粒品质是影响小麦加工品质和营养价值的重要因素。挖掘与小麦籽粒品质性状显著关联的位点及候选基因,为拓宽对小麦品质性状遗传机理的理解和分子标记辅助优质小麦育种提供依据。【方法】通过对来自国内外259份冬小麦品种(系)的蛋白质含量、湿面筋含量、淀粉含量、沉降值和籽粒硬度等5个品质性状进行测定,并结合90K SNP芯片进行全基因组关联分析,将定位到的显著性关联位点进行单倍型分析。【结果】5个性状均符合正态分布且在不同环境间均表现出丰富的变异,沉降值的变异系数最大(20.11%—24.42%)。各性状在基因型、环境、基因型×环境间均呈现出极显著差异(P<0.001),广义遗传力为0.77—0.84。通过全基因组关联分析,共检测到44个与5个性状显著关联(P<0.001)的位点,分布在除1D和3D染色体外的其他19个连锁群。在2个及以上的环境中均稳定存在的位点18个,涉及蛋白质含量(12个)、湿面筋含量(9个)、淀粉含量(11个)、沉降值(12个)和籽粒硬度(7个)等5个性状,能解释遗传变异的4.27%—10.98%。其中13个为多效应位点,与蛋白质含量、湿面筋含量、沉降值和淀粉含量等性状相关联的多效应位点最多(7个)。位于2B、2D和3A染色体的GENE-0762_631、IAAV7742和RAC875_c66845_466位点同时在2个环境和BLUP值下被检测到,表型贡献率的范围为4.32%—7.07%。通过对多环境下存在且表型贡献率高的多效应位点进行单倍型分析,在5D染色体的D_GDS7LZN02F4FP5_176位点发掘到与蛋白质含量、沉降值和淀粉含量等性状显著相关的Hap1、Hap2、Hap3和Hap4等4个不同单倍型,其中,Hap1是高淀粉含量单倍型(P<0.001),而Hap2和Hap3均为高蛋白质含量和沉降值的单倍型(P<0.05),4个单倍型分别占74.22%、16.21%、6.92%和2.65%。对不同来源冬小麦的单倍型分布频率进行分析,其中,高蛋白质含量和沉降值单倍型Hap2的分布频率由高到低为黄淮冬麦区>北部冬麦区>国外品种>长江中下游冬麦区>西南冬麦区。对稳定遗传的位点进行候选基因的挖掘,筛选到10个可能与小麦籽粒品质相关的候选基因。【结论】检测到18个与籽粒品质性状显著关联的稳定位点,鉴定到4个不同单倍型,筛选出10个与籽粒品质相关的候选基因。

Genome-wide Scan for Seed Composition Provides Insights into Soybean Quality Improvement and the Impacts of Domestication and Breeding

The complex genetic architecture of quality traits has hindered efforts to modify seed nutrients in soybean. Genome-wide association studies were conducted for seed composition, including protein, oil, fatty acids, and amino acids, using 313 diverse soybean germplasm accessions genotyped with a high-density SNP array. A total of 87 chromosomal regions were identified to be associated with seed composition, explain- ing 8%-89% of genetic variances. The candidate genes GmSAT1, AK-HSDH, SACPD-C, and FAD3A of known function, and putative MtN21 nodulin, FATB, and steroid-5-^-reductase involved in N2 fixation, amino acid biosynthesis, and fatty acid metabolism were found at the major-effect loci. Further analysis of additional germplasm accessions indicated that these major-effect loci had been subjected to domes- tication or modern breeding selection, and the allelic variants and distributions were relevant to geographic regions. We also revealed that amino acid concentrations related to seed weight and to total protein had a different genetic basis. This helps uncover the in-depth genetic mechanism of the intricate relationships among the seed compounds. Thus, our study not only provides valuable genes and markers for soybean nutrient improvement, both quantitatively and qualitatively, but also offers insights into the alteration of soybean quality during domestication and breeding.

畜禽肉质性状相关候选基因的研究进展

随着市场对优质畜禽肉的需求量逐年提升,畜禽肉质性状已成为食品科学和动物育种领域的研究热点。肉质性状受多种信号通路和转录因子的影响,深入了解影响肉质性状的候选基因对改善畜禽肉质和培育优良畜禽品种具有指导意义。对与肌内脂肪(intramuscular fat,IMF)含量、肌苷酸(inosinic acid,IMP)含量、嫩度、pH值、肉色等肉质性状密切相关的候选基因研究进展进行综述,以期为畜禽选育改良和分子标记辅助育种等研究提供理论参考。

影响动物肉质性状主要候选基因的研究进展

随着分子生物学在动物遗传育种中的应用,对数量性状主效基因的研究成为必然。本文对影响肉质的脂肪酸结合蛋白基因、肥胖基因、leptin基因、黑素皮质受体基因、脂蛋白脂酶基因、激素敏感脂酶基因的国内外研究状况加以综述。

优质细毛羊羊毛细度的候选基因分析

采用PCR-SSCP的分子标记技术,选择编码羊毛纤维组成蛋白基因中的KAP1.1、KAP1.3的部分序列、KAP6.1的外显子区作为候选基因,通过对其多态性的研究,探索将该基因作为候选基因来间接选择羊毛细度性状的可行性。得出其中在角蛋白辅助蛋白的多基因家族中的高硫蛋白辅助蛋白基因(KAP1.1、KAP1.3)中,位点W08667与羊毛细度有显著的相关性(P<0.05)。在甘氨酸酪氨酸角蛋白辅助蛋白中,外显子位点W06933的AA基因型和BB基因型与羊毛细度之间有显著的相关性(P<0.05)。

畜禽肉质特性研究进展

畜禽的肉质特性已经成为动物生产的一个重要研究方向。对影响肉质特性的蛋白质和脂肪构成,蛋白质组学和基因表达谱等高通量研究方法在肉质研究上的最新成果,以及通过研究影响肌肉生长发育和脂肪沉积的结构基因和microRNA以阐明肉质特性的分子机理进行了综述,并对生物信息学将在肉质形成机理研究中发挥的重要作用进行了展望。

猪钙蛋白酶抑制蛋白基因PCR-RFLP多态性与肉质性状及背膘厚间的关系分析

钙蛋白酶抑制蛋白(CAST)是钙蛋白酶系统的内源性抑制剂,并且已经被确定能影响宰后肉的嫩度。本研究采用PCR-RFLP技术,分析了CAST基因在125头PIC杂交猪中的多态性分布及其与肉质性状和背膘厚间的相关。结果发现,CAST基因在本研究所检测的位点均具有多态性。进一步分析表明,CASTA2A2基因型个体与其相应的另外两个基因型个体相比肌内脂肪含量有显著差异,CASTB1B2基因型个体对于肌内脂肪含量的影响也有相同的趋势;CASTB1B2基因型个体与其相应的另外两个基因型个体相比背膘厚有显著差异,CASTC1C2基因型个体和CASTD1D2基因型个体对于背膘厚的影响也有相同的趋势。因此可以把CAST基因作为影响猪肉质性状和屠体性状的候选基因。

硕士研究生教育质量调查分析——对全国69所高校硕士生导师调查

通过对全国69所高校500余名硕士生导师就研究生招生、培养及质量的调查发现,近年来研究生生源质量下降,学制过短,学生未能系统掌握本专业理论和知识,科研方法训练不足,科研能力不强,研究生教育质量下降。为此,应适度控制研究生招生规模,实行差异化的学制和个性化的培养方案,改善研究生教学科研条件及生活条件,确保研究生参与课题研究的数量和质量,扩大国内外学术交流,切实提高研究生综合素质和科研能力,以提高硕士研究生教育质量。