绵羊心脏脂肪酸结合蛋白基因单核苷酸多态性分析

试验旨在探讨心脏脂肪酸结合蛋白（heart fatty acid-binding protein，H-FABP）基因在绵羊中的遗传多态性，并寻找可用于辅助选择的分子标记。本研究以滩羊（250只）及滩羊×湖羊杂交F1代（174只）为试验动物，利用SNaPshot分型技术对H-FABP基因（GenBank登录号：AY157617）的多态位点进行单核苷酸多态性（SNP）分析，统计基因频率和基因型频率，进行Hardy-Weinberg平衡性检测，计算期望杂合度（He）、多态信息含量（PIC）和有效等位基因数（Ne）等遗传多态指标，分析候选基因不同基因型与体重、体长、体高、胸围、胸深、胸宽和管围等生长性状的关联性。结果显示：①检测到9个多态位点：939[A/G]、980[G/A]、1018[T/C]、2878[C/T]、2956[C/T]、3017[G/A]、3341[G/C]、3394[T/A]、1056[-/G]，其中有6处转换、2处颠换、1处单碱基插入。②939[A/G]、980[G/A]、2956[C/T]、3341[G/C]、3394[T/A]和1018[T/C]的He为0.3200~0.4666，PIC为0.2688~0.3577；2878[C/T]、3017[G/A]位点的He为0.0283~0.1272，PIC为0.0279~0.1191，为低度多态；1056[-/G]位点的He在滩羊、滩羊×湖羊杂交F1代群体中分别为0.0120和0，PIC在滩羊、滩羊×湖羊杂交F1代群体中分别为0.0119和0；9个多态位点在滩羊、滩羊×湖羊杂交F1代群体中均符合Hardy-Weinberg平衡定律。③5个多态位点：939[A/G]、980[G/A]、2956[C/T]、3341[G/C]、3394[T/A]处于紧密连锁（D'>0.99），将H-FABP基因分为3个单倍型：AA、AB和BB。④在41只滩羊×湖羊杂交F1代羊中，BB单倍型在各生产性状上具有最大值，但各单倍型间差异不显著（P>0.05）。结果表明，绵羊H-FABP基因具有丰富的遗传多态性，939[A/G]、980[G/A]、2956[C/T]、3341[G/C]、3394[T/A]5个位点紧密连锁，BB单倍型可能是与绵羊生产性状相关的优势单倍型。     

茶氨酸合成酶基因的SNP挖掘和遗传定位

茶氨酸合成酶(Theanine synthetase,TS)基因是茶树茶氨酸代谢过程中的关键酶基因。本研究以氨基酸含量差异明显的亲本及其杂交所得F_1子代为研究材料,克隆TS基因的c DNA序列,挖掘其SNPs位点,并成功将杂合SNP位点定位在遗传连锁群上。研究结果显示,通过序列比对在亲本间检测到3个SNPs,验证得到1个杂合的位点SNP735。将此位点成功转化为dCAPS标记,该标记在子代中的基因型分离比为1∶1,利用该群体已构建的茶树遗传图谱进行遗传定位,将dCAPS标记定位在连锁群LG03上,相邻标记为TM299和TM517。联合此标记及其相邻标记与游离氨基酸总含量和茶氨酸含量进行统计分析,表明具有显著的相关性。     

贝母属植物叶绿体基因组候选SNP位点应用分析

贝母属植物是中国中药材的宝库,由于形态上难以区分,在民间应用、临床应用和中药市场中还存在混淆应用、以次充好的现象,急需开发基于新型分子标记位点的精准检测方法。本研究应用多重序列比对、SNP筛选等生物信息学分析手段,对贝母属15种植物28条叶绿体基因组序列进行分析。结果发现,贝母属叶绿体基因组DNA同源性达97.22%,通过分析共发现SNP位点5879个,其中川贝母类鉴别候选位点71个,川贝母鉴别候选位点4个,瓦布贝母鉴别候选位点37个,太白贝母鉴别候选位点147个,浙贝母鉴别候选位点91个,湖北贝母鉴别候选位点271个,平贝母鉴别候选位点1393个,伊贝母鉴别候选位点89个。本研究还对SNP位点在精准鉴定、精确定量应用方面进行了讨论,可为川贝母中药资源鉴定提供技术支撑。     

基于SNP标记的爆裂玉米农家品种遗传多样性

为了评价广西爆裂玉米农家品种的遗传多样性,利用56K SNP芯片技术对中国广西45个爆裂玉米农家品种、中国2个爆裂玉米杂交种和6个南美爆裂玉米种质进行全基因组扫描,获得多态性标记14 338个,基因分型为6 种类型。其中A/G类型最多,为5 805个;A/T类型最少,为149个。1号染色体的多态性SNP位点最多,为2 302个;10号染色体最少,为848个。45个农家品种间平均遗传相似系数为0.62,变幅为0.41~0.99,总体遗传相似度高。聚类分析将参试品种划分为三大类群,相同来源的农家品种大多聚在一起;主成分分析显示大部分农家品种聚在一起,与杂交品种和南美品种之间没有交集,表明农家品种遗传相似性较高,与杂交品种和南美品种遗传差异较大。     

Genome wide association studies (GWAS) of element contents in grain with a special focus on zinc and iron in a world collection of barley (Hordeum vulgare L.)

Genome wide association studies (GWAS) were carried out to map Quantitative Trait Loci (QTL) associated with element contents in the grain using 336 spring barley. Of the elements analyzed, Fe content ranged from 21.9 to 91.0 mg kg⁻¹, Zn from 10.4 to 54.5 mg kg⁻¹, Ba from 0.2 to 8.9, Ca from 186.4 to 977.5, Cu from 1.5 to 9.8, K from 353.2 to 7721.5, Mg from 1049.8 to 2024.2, Mn from 8.1 to 22.9, Na from 55.9 to 627.9, P from 2272.9 to 5428.8, S from 880.7 to 1898.0, Si from 19.1 to 663.2, and Sr from 0.35 to 2.62 mg kg⁻¹. GWAS were carried out using 6519 SNP markers and multiple elements in MLM:PCA + K model in TASSEL software. Population analyses showed two sub-populations, primarily based on row types. GWAS for row types showed association with INTERMEDIUM-C, a modifier gene for lateral spikelet fertility in the 4H chromosome, validating current GWAS approach. GWAS also showed that 2 QTL for Ba, 2 for Ca, 4 for Cu, 11 for Fe, 2 for K, 3 for Mg, 6 for Mn, 4 for Na, 3 for S, 5 for Si, and 3 for Zn were mapped in barley chromosomes. The QTL identified in the current study are valuable for breeding nutrient dense barley cultivars in the future, especially Zn and Fe.     

Development of a core set of KASP markers for assaying genetic diversity in Brassica rapa subsp. chinensis Makino

Single‐nucleotide polymorphisms (SNPs) are rapid, economical and reliable genotyping tools. Non‐heading Chinese cabbage (Brassica rapa L. subsp. chinensis Makino) is now an economically important vegetable crop worldwide. In this study, 1,167 SNPs were evaluated for 7polymorphism among 70 representative non‐heading Chinese cabbage inbred lines using a Kompetitive Allele Specific PCR (KASP) genotyping assay. On the basis of identified polymorphisms and the results of a principal component analysis, we selected 50 core SNPs that were balanced sufficiently to provide adequate information for genetic identification. The core SNPs were used for construction of a neighbour‐joining dendrogram that separated the 70 inbred lines into four main groups and several subgroups corresponding to Caixin, Heiyebaicai, Huangxinwu, Naibaicai, Taitsai, Pak‐choi, and Wutatsai. This categorization was superior to that achieved using a dataset of 479 polymorphic SNPs. To confirm the utility of the core SNP markers in genetic identification, we tested their stability and resolution using 162 commercial hybrid cultivars. The SNPs, which represent a cost‐effective, accurate marker set for germplasm analysis and cultivar identification, are suitable for molecular marker‐assisted breeding in non‐heading Chinese cabbage.     

玉米主要株型性状与产量的全基因组关联分析

为了深入剖析玉米的株型性状和产量性状的遗传基础及其相关关系,本研究以204份玉米自交系作为关联群体,利用分布于玉米全基因组上的558 529个单核苷酸多态性标记(SNPs)对5个相关性状进行全基因组关联分析。结果表明,供试自交系各性状基本呈正态分布,且各性状间存在丰富的变异,变异系数在9.00%~50.00%之间;通过相关性分析和热图层次聚类分析株型和产量相关性状间彼此紧密关联;且由主成分分析筛选出总体方差累计贡献率达到71.667%的主成分2个;以P≤1×10^-5为显著阙值,利用Q+K模型对供试材料的5个相关性状进行全基因组关联分析,在株高、穗位高和单穗重间共检测到13个显著的SNP位点,分别分布于玉米的第3、第5、第6、第7号染色体上,而在总叶片数和穗上叶数间未检测到显著的SNP位点;在显著SNP上下游各50 kb范围共搜索到39个相关候选基因,其中有注释的基因12个,并对株高与穗位高最佳候选基因进行了预测。本研究通过对玉米株型及产量相关性状进行全基因组关联分析,为后期基因功能的验证与新功能的开发奠定了良好的基础。     

中国农耕区土壤有机质含量及其与酸碱度和容重关系

对我国农耕区土壤有机质区域变化及其与酸碱度和容重关系进行系统分析，为耕地地力提升和改善土壤结构提供支撑。基于国家级耕地长期定位监测点913个，统计分析全国及7大区域（东北NE、华北NC、西北NW、长江中游MYR、长三角YRD、华南SC、西南SW）耕层土壤有机质含量、酸碱度及容重变化特征。结果表明，全国农耕区耕层土壤有机质含量平均值为22.4~24.8 g/kg。其中有机质含量中等偏低的监测点位占比达72.5%。不同区域耕层土壤有机质含量差异显著（p<0.05），MYR耕层土壤有机质含量显著高于其他6个区域。全国农耕区耕层土壤pH和容重平均分别为（6.90±1.20），（1.30±0.15） g/cm³。不同土壤利用方式对土壤有机质、酸碱度及容重产生影响。水田耕层土壤有机质含量显著高于旱地，旱地耕层土壤pH和容重则显著高于水田。亚当斯方程和指数函数分别推荐拟合土壤容重对有机质含量响应关系（R²=0.09，RMSE=0.17，n=759），以及土壤pH对土壤有机质含量响应（R²=0.16，RMSE=1.24，n=886）。全国农耕区耕层土壤有机质含量总体中等偏低，呈现出东南向西北依次降低趋势。土壤pH及容重与土壤有机质呈现显著的负相关关系。亚当斯模型及指数方程能较好地拟合土壤容重及pH对有机质的响应关系，可用于非线性插值法补充土壤容重及pH缺失值。     

Identification of potential genomic regions for egg weight by a haplotype-based genome-wide association study using Bayesian methods

ABSTRACT

1. Theoretically, haplotype blocks might be a more suitable alternative to SNP genotypes as they are usually better at capturing multi-allelic QTL effects, compared to individual SNP genotypes in genome-wide association studies. The objectives of this study were to identify genomic regions related to egg weight traits by Bayesian methods (BayesA, BayesB, and BayesN) that fit fixed-length haplotypes using GenSel software.

2. Genotypes at 294,705 SNPs, that were common on a 600K Affymetrix chip, were phased for an egg-laying hen population of 1,063 birds. Recorded traits included first egg weight (FEW) and average egg weight at 28, 36, 56, 66, 72 and 80 weeks of age.

2. Fitting 1Mb haplotypes from BayesB resulted in the highest proportion of genetic variance explained for the egg weight traits. Based on the trait, the genetic variance explained by each marker ranged from 27% to 76%.

3. Different haplotype windows associated with egg weight traits only explained a small percentage of the genetic variance.

4. The top one 1-Mb window on GGA1 explained approximately 4.05% of total genetic variance for the FEW. Candidate genes, including PRKAR2B, HMGA2, LEMD3, GRIP1, EHBP1, MAP3K7, and MYH were identified for egg weight traits.

5. Several genomic regions, potentially associated with egg weight traits, were identified, some of which overlapped with known genes and previously reported QTL regions for egg production traits.