小麦耐低磷相关性状的全基因组关联分析

通过对小麦耐低磷相关性状进行全基因组关联分析(GWAS,genome-wide association study),挖掘与小麦耐低磷性显著相关的单核苷酸多态性标记(SNP,single nucleotide polymorphism)位点及候选基因,为小麦耐低磷性状的遗传基础和分子机制研究提供理论参考。本试验以198份黄淮麦区小麦品种(系)为试验材料,设置低磷和正常磷营养液水培试验,利用小麦35K芯片对分布于小麦全基因组的11896个SNP,采用Q+K关联模型对小麦耐低磷性相关性状进行关联分析。结果表明,小麦耐低磷性状表现出广泛的表型变异,变异系数为15.65%~26.59%,多态性信息含量(PIC,polymorphic information content)为0.095~0.500。群体结构分析表明,试验所用自然群体可分为2个亚群,GWAS共检测到67个与小麦耐低磷相关性状显著关联的SNP位点(P≤0.001),这些位点分布在除3A、3B和3D以外的18条染色体上,单个SNP位点可解释5.826%~9.552%的表型变异。在这些显著位点中有4个SNP位点同时关联到了2个不同的耐低磷性状。对67个SNP位点进行发掘,筛选到7个可能与小麦耐低磷性有关的候选基因。TraesCS6A02G001000和TraesCS6A02G001100在锌指合成中有重要作用;TraesCS6A02G118100可能为低磷胁迫诱导基因;TraesCS5D02G536400、TraesCS1B02G154200和TraesCS5D02G536500与低磷胁迫相关酶类基因家族有关;TraesCS1D02G231200与植物DUF 538结构域蛋白有关,是植物胁迫相关调控蛋白候选基因。     

玉米开花期相关性状的QTL分析

利用玉米强优势组合(Mo17×黄早四)自交衍生的191个F_2单株构建了由SSR和AFLP标记组成的分子连锁图谱,用F2进一步自交产生的184个F_(2:3)家系调查散粉期、吐丝期和开花-吐丝间隔期(ASI)的表型值,采用基于混合线性模型的复合区间作图法和相应的作图软件QTLmapper/V2.0,在两个生长环境下定位了与散粉期、吐丝期和ASI相关的QTL数目分别为13、7和5个,检测到3对控制散粉期、17对控制吐丝期和5对控制ASI的上位性效应位点;同时发现了与环境存在显著互作的3个散粉期、3个吐丝期和2个ASI单位点标记区域以及1对散粉期、3对吐丝期和2对ASI上位性效应区域.对玉米散粉期、吐丝期和ASI遗传基础中遗传因素相对作用大小分析表明,加性效应、部分显性效应和上位性效应是玉米开花期相关性状的重要遗传基础.     

玉米dbf1基因与耐旱相关性状的关联分析

脱水响应元件结合因子(DBF1蛋白)是高等植物体内DRE/CRT顺式元件的结合因子,是水分胁迫信号传导的核心构件。本文以玉米自交系郑22为材料,采用PCR技术分离得到dbf1基因区域基因组DNA(gDNA)全长949 bp,起始密码子至终止密码子序列长654 bp。该基因由1个外显子组成,无内含子。dbf1基因在175份玉米自交系中共检测到9个SNP变异(平均每57.3 bp一个),没有检测到In/Del变异,在3个多态性位点间存在较高程度的连锁不平衡(r20.5)。在干旱胁迫下,dbf1基因中的多态性位点397与ASI和单穗粒重显著关联(P0.05),位点477与单穗粒重和结实株数百分率存在显著关联(P0.05)。位点397对ASI和单穗粒重的贡献率分别为6.94%和10.03%;位点477对单穗粒重和结实株数百分率的贡献率分别是1.01%和3.66%。根据2个位点将175份自交系分成4种单体型,其中单体型4含有能使ASI减小、结实株数百分率增加的等位基因位点,包含早49、丹598、丹黄02等耐旱和中度耐旱自交系,推测单体型4可能是dbf1基因的耐旱单体型。研究结果为基于dbf1因开发耐旱功能标记提供信息。     

基于简化基因组测序的大黄鱼耐高温性状全基因组关联分析

利用Illumina HiSeqTM 2500测序平台, 对通过高温胁迫实验筛选得到的20尾耐高温和20尾不耐高温的大黄鱼(Larimichthys crocea)进行了简化基因组测序(SLAF-seq), 每个样本的平均测序深度达到10.26×, 共获得419211个高质量的群体单核苷酸多态性(SNP)位点 。利用TASSEL软件的混合线性模型(MLM)进行全基因组关联分析(GWAS), 共筛选到38个与大黄鱼耐高温性状显著相关的SNP位点(P<2.39E–08)。利用BLAST程序定位每个SNP位点在大黄鱼基因组中的位置, 并分析其周围的功能基因。结果在38个SNPs附近共找到26个已知的功能基因, 这些基因主要与细胞转录、代谢、免疫等功能相关。研究结果可为下一步大黄鱼耐高温分子机制解析及耐高温品种的选育提供参考。     

玉米叶片叶绿素含量的全基因组关联性分析

植物叶片的叶绿素含量与叶片的光合作用效率和产量潜力紧密相关,因此是作物的一个重要生理指标。但是,目前已克隆的控制叶绿素含量的基因大多来自拟南芥和水稻,尚不清楚玉米自然群体中哪些基因控制叶片叶绿素含量的变异。本研究发现玉米苗期第一片叶片的叶绿素含量和吐丝期穗位叶的叶绿素含量高度相关,且与后者相比具有更高的遗传力。进一步分析了287份玉米自交系的第一片叶的叶绿素含量,利用558 269个单核苷酸多态性分子标记进行全基因组关联性分析,获得9个显著关联SNP位点和16个候选基因。通过候选基因的序列分析和功能预测,发现两个可能和叶绿素含量相关的基因,包括拟南芥Tic22基因的同源基因和水稻衰老相关基因SAG12的同源基因。     

ORMDL3基因多态性与哮喘的相关性

哮喘是一种非常复杂的表型异质性疾病,是受遗传和环境因素双重影响的多基因遗传病,通过全基因组关联研究显示,1 7号染色体ORMDL3基因是迄今为止发现的与哮喘关联最有充分证据的基因,而SNP(rs7216389)是哮喘最显著的相关标记。本综述将概述ORMDL3基因、ORMDL3基因产物功能、ORMDL3基因多态性与哮喘的相关性,及哮喘主要相关位点SNP(rs7216389)和SNP(rs1051740)等方面的研究成果。     

中国汉族高原肺水肿易感基因的全基因组关联研究

高原肺水肿(High-altitude pulmonary edema, HAPE)是一种特发于高原低氧环境的肺水肿, 是遗传和环境因素共同作用的结果。为了寻找与中国汉族高原肺水肿相关的单核苷酸多态性(Single nucleotide polymorphism, SNP)位点及易感基因, 文章利用Affymetrix SNP Array 6.0芯片, 对2010年5月至2012年7月在青海省玉树地区执行援建任务时来自平原地区的40例HAPE患者和33例健康对照进行全基因组SNP分型, 通过PLINK软件对芯片结果进行全基因组关联分析(Genome-wide association study, GWAS), 筛选出在病例组和对照组中间有显著差异(P < 10E-7)的SNP位点57个, 通过对57个SNP位点附近74个基因进行GO与Pathway富集分析, 发现这些基因与“前列腺素代谢”、“四烯酸代谢”、“氮代谢”显著相关(adjust P < 0.05), 以上代谢过程与HAPE病理生理机制相关。结果表明, 高原肺水肿受遗传多态性影响, 与多个基因以及位点相关。     

显性E1基因背景下大豆开花和成熟期的全基因组关联分析

【目的】深入解析大豆开花期和成熟期的遗传基础,发掘控制性状的重要基因组区间,为分子标记辅助选择育种和新基因克隆提供依据。【方法】以224份携带显性E1基因的大豆种质为试验材料,在4个种植环境下调查表型数据,采用R-mrMLM软件包中的6种多位点关联分析模型对大豆开花和成熟期进行全基因组关联分析。【结果】共检测到91个开花期和83个成熟期QTNs（quantitative trait nucleotides）,其中6个开花期和10个成熟期QTNs能在多环境中检测到。这些环境稳定QTNs分布于15个区间大小在90~490 Kb的单倍型（基因组）内,并有6个基因组区间为本研究新检测到。【结论】研究表明显性E1基因背景下大豆开花和成熟期的QTN构成复杂,位于5号染色体39.52~40.01Mb等15个基因组区间是该群体中控制大豆开花期或成熟期的重要位点。     

镉（Cd）胁迫下蓖麻蛋白质组学筛查及RcBSK7抗性功能研究

为揭示蓖麻（Ricinus communis）植株响应重金属镉（Cd）胁迫相关机制,筛选出蓖麻中参与Cd胁迫的抗性基因。本研究通过观察种子发芽及植株生长状态,最终确定以水处理的蓖麻植株为对照,研究其在3种剂量（300、700、1 000 mg·L^-1）Cd胁迫处理下的反应机制,以期为揭示蓖麻响应Cd胁迫的防御和解毒机制提供新思路。利用差异蛋白质组学分析蓖麻在Cd胁迫下的网络调控机制,即随着Cd胁迫浓度的增加,蓖麻植株分别通过阻隔根系对重金属Cd的吸收、提高自身抗氧化能力、抑制Cd²⁺运转以及诱导细胞程序性死亡等防御解毒过程以抵抗Cd胁迫损伤。根据组学分析结果筛选出差异显著基因RcBSK7,通过在拟南芥（Arabidopsis thaliana）中进行功能验证可知,该基因对提高蓖麻对Cd耐受性具有重要的作用。本研究增强了对蓖麻植株在3种Cd胁迫下多样性和复杂性的认识,为耐Cd基因鉴定和土壤中重金属污染修复提供了有价值的理论依据。     

高原肺水肿易感基因多态性的全基因组关联分析

目的：高原肺水肿严重影响高原人群的健康。筛选高原肺水肿易感基因以用于高原肺水肿易感者的评估及防护。方法：利用Affymetrix SNP Array6．0芯片对23例高原肺水肿患者和17个健康对照进行全基因组SNP分型,利用PLINK软件进行了全基因组关联分析,利用Go和Pathway软件进行分析及作图。结果：全基因组关联分析获得39个相对显著的SNPs位点（P〈10^-4）。通过对这些SNP位点附近27个基因的c0和Pathway富集分析,发现这些基因主要参与细胞增殖调控过程、氮代谢过程和G蛋白耦联受体蛋白信号转导通路等。结论：本文发现的多态性位点及相关基因可能与高原肺水肿易感性相关。     

Meta-Analysis of Flowering-Related Traits and Mining of Candidate Genes in Maize

Maize flowering is an important agronomic character, which is controlled by quantitative trait loci (QTL). Over the years, a large number of flowering-related QTL have been found in maize and exist in public databases. However, combining these data, re-analyzing and mining candidate loci and fine mapping of flowering-related traits to reduce confidence intervals has become a hot issue in maize. In this study, the QTL of 6 important agronomic traits of maize flowering were collected from 15 published articles, including flowering period (DA), Days to tasseling (DTT), Days to silking (DS), Days to pollen shedding (DTP), anthesis-silking interval (ASI) and the photosensitive (PS). Through meta-analysis, 622 QTL were integrated into 26 meta-QTLs (MQTL). Finally, the candidate genes related to maize flowering (Gene IDs: ZM00001D005791, ZM00001D019045, ZM00001D050697, ZM00001D011139) were identified by Gene Ontology (GO) enrichment and hierarchical cluster analysis of expression profile. Based on the results of this study, the genetic characteristics of maize flowering traits will be further analyzed, which is of great significance to guide the improvement of important agronomic characters and improve the efficiency of breeding.     

Identification of genetic variants associated with maize flowering time using an extremely large multi‐genetic background population

Flowering time is one of the major adaptive traits in domestication of maize and an important selection criterion in breeding. To detect more maize flowering time variants we evaluated flowering time traits using an extremely large multi‐ genetic background population that contained more than 8000 lines under multiple Sino‐United States environments. The population included two nested association mapping (NAM) panels and a natural association panel. Nearly 1 million single‐nucleotide polymorphisms (SNPs) were used in the analyses. Through the parallel linkage analysis of the two NAM panels, both common and unique flowering time regions were detected. Genome wide, a total of 90 flowering time regions were identified. One‐third of these regions were connected to traits associated with the environmental sensitivity of maize flowering time. The genome‐wide association study of the three panels identified nearly 1000 flowering time‐associated SNPs, mainly distributed around 220 candidate genes (within a distance of 1 Mb). Interestingly, two types of regions were significantly enriched for these associated SNPs – one was the candidate gene regions and the other was the approximately 5 kb regions away from the candidate genes. Moreover, the associated SNPs exhibited high accuracy for predicting flowering time.     

Genetic diversity of maize kernel starch-synthesis genes with SNAPs.

Measuring genetic diversity in populations of a crop species is very important for understanding the genetic structure of and subsequently improving the crop species by genetic manipulation. Single-nucleotide amplified polymorphisms (SNAPs) among and within maize populations of waxy, dent, and sweet corns at 25 single-nucleotide polymorphism (SNP) sites in 6 kernel starch-synthesis genes (sh2, bt2, su1, ae1, wx1, and sh1) were determined. Because of the intensive selection of some favorable alleles in starch-synthesis genes during the breeding process, and the resultant strong linkage disequilibrium (LD), the number of haplotypes in each population was far less than expected. Subsequent phenetic clustering analysis with the SNAPs indicated that the dent, waxy, and sweet corns formed distinct subclusters, except in a few incidences. LD was surveyed among SNAPs of intragenic, intergenic, and intrachromosomal SNPs in whole and subpopulations, which revealed that some SNAPs showed high LD with many other SNAPs, but some SNAPs showed low or no significant LD with others, depending on the subpopulation, indicating that these starch genes have undergone different selection in each subpopulation during the breeding process. Because the starch synthesis genes used in this study are important in maize breeding, the genetic diversity, LD, and accessions having rare SNAP alleles might be valuable in maize improvement programs.     

Genetic analysis of the related traits of flowering and silk for hybrid seed production in maize

In the field, asynchrony of flowering and silk for male and female plants always occurs under different abiotic stresses, and reduces yield in the seed industry. Under stress conditions, a female parent with a short duration of silk emergence and a long time of silk receptivity can decrease the risk of the asynchrony for flowering and silking in the process of hybrid seed production. For dissecting the genetic basis of the related traits of flowering and silk in maize, a set of recombinant inbred lines (RIL) was evaluated at three different environments. Correlation analysis showed that anthesis silk interval (ASI) had a significant positive relationship with day to silk (DTS) and duration of silk emergence (DSE). Silk receptivity (SR) had a significant negative correlation to DTS, DSE, and ASI. This implied that the female parent with a long DTS, DSE, and ASI could easy lose its SR, and required synchrony of pollen shedding for the male parent in the field. A total of sixteen different QTLs were identified for the seven traits of flowering and silking traits, including three QTLs for day to tassel (DTT), two for day to pollen (DTP), two for duration of pollen shedding (DPS), three for SR, two for DTS, two for DSE, and two for ASI. The QTLs detected for the related traits of flowering and silk could select ideal traits for male and female parents to raise the yield in the seed industry under certain stress conditions.     

Identification of quantitative trait loci under drought conditions in tropical maize. 1. Flowering parameters and the anthesis-silking interval

Drought is an important climatic phenomenon which, after soil infertility, ranks as the second most severe limitation to maize production in developing countries. When drought stress occurs just before or during the flowering period, a delay in silking is observed, resulting in an increase in the length of the anthesis-silking interval (ASI) and in a decrease in grain yield. Selection for reduced ASI in tropical open-pollinated varieties has been shown to be correlated with improved yields under drought stress. Since efficient selection for drought tolerance requires carefully managed experimental conditions, molecular markers were used to identify the genomic segments responsible for the expression of ASI, with the final aim of developing marker-assisted selection (MAS) strategies. An F₂population of 234 individuals was genotyped at 142 loci and F₃ families were evaluated in the field under several water regimes for male flowering (MFLW), male sterility (STER), female flowering (FFLW) and ASI. The genetic variance of ASI increased as a function of the stress intensity, and the broad-sense heritabilites of MFLW, FFLW and ASI were high under stress conditions, being 86%, 82% and 78%, respectively. Putative quantitative trait loci (QTLs) involved in the expression of MFLW and/or FFLW under drought were detected on chromosomes 1, 2, 4, 5, 8, 9 and 10, accounting for around 48% of the phenotypic variance for both traits. For ASI, six putative QTLs were identified under drought on chromosomes 1, 2, 5, 6, 8 and 10, and together accounted for approximately 47% of the phenotypic variance. Under water stress conditions, four QTLs were common for the expression of MFLW and FFLW, one for the expression of ASI and MFLW, and four for the expression of ASI and FFLW. The number of common QTLs for two traits was related to the level of linear correlation between these two traits. Segregation for ASI was found to be transgressive with the drought-susceptible parent contributing alleles for reduced ASI (4 days) at two QTL positions. Alleles contributed by the resistant line at the other four QTLs were responsible for a 7-day reduction of ASI. These four QTLs represented around 9% of the linkage map, and were stable over years and stress levels. It is argued that MAS based on ASI QTLs should be a powerful tool for improving drought tolerance of tropical maize inbred lines.     

Mapping of Candidate Genes Involved in Bud Dormancy and Flowering Time in Sweet Cherry (Prunus avium)

The timing of flowering in perennial plants is crucial for their survival in temperate climates and is regulated by the duration of bud dormancy. Bud dormancy release and bud break depend on the perception of cumulative chilling during endodormancy and heat during the bud development. The objectives of this work were to identify candidate genes involved in dormancy and flowering processes in sweet cherry, their mapping in two mapping progenies ‘Regina’ × ‘Garnet’ and ‘Regina’ × ‘Lapins’, and to select those candidate genes which co-localized with quantitative trait loci (QTLs) associated with temperature requirements for bud dormancy release and flowering. Based on available data on flowering processes in various species, a list of 79 candidate genes was established. The peach and sweet cherry orthologs were identified and primers were designed to amplify sweet cherry candidate gene fragments. Based on the amplified sequences of the three parents of the mapping progenies, SNPs segregations in the progenies were identified. Thirty five candidate genes were genetically mapped in at least one of the two progenies and all were in silico mapped. Co-localization between candidate genes and QTLs associated with temperature requirements and flowering date were identified for the first time in sweet cherry. The allelic composition of the candidate genes located in the major QTL for heat requirements and flowering date located on linkage group 4 have a significant effect on these two traits indicating their potential use for breeding programs in sweet cherry to select new varieties adapted to putative future climatic conditions.     

Identification of Genetic Differentiation between Waxy and Common Maize by SNP Genotyping

Waxy maize (Zea mays L. var. ceratina) is an important vegetable and economic crop that is thought to have originated from cultivated flint maize and most recently underwent divergence from common maize. In this study, a total of 110 waxy and 110 common maize inbred lines were genotyped with 3072 SNPs to evaluate the genetic diversity, population structure, and linkage disequilibrium decay as well as identify putative loci that are under positive selection. The results revealed abundant genetic diversity in the studied panel and that genetic diversity was much higher in common than in waxy maize germplasms. Principal coordinate analysis and neighbor-joining cluster analysis consistently classified the 220 accessions into two major groups and a mixed group with mixed ancestry. Subpopulation structure in both waxy and common maize sets were associated with the germplasm origin and corresponding heterotic groups. The LD decay distance (1500–2000 kb) in waxy maize was lower than that in common maize. Fourteen candidate loci were identified as under positive selection between waxy and common maize at the 99% confidence level. The information from this study can assist waxy maize breeders by enhancing parental line selection and breeding program design.     

Mapping quantitative trait loci associated with southern leaf blight resistance in maize (Zea mays L.)

Southern leaf blight (SLB) caused by the fungus Cochliobolus heterostrophus (Drechs.) Drechs. is a major foliar disease of maize worldwide. Our objectives were to identify quantitative trait loci (QTL) for resistance to SLB and flowering traits in recombinant inbred line (RIL) population derived from the cross of inbred lines LM5 (resistant) and CM140 (susceptible). A set of 207 RILs were phenotyped for resistance to SLB at three time intervals for two consecutive years. Four putative QTL for SLB resistance were detected on chromosomes 3, 8 and 9 that accounted for 54% of the total phenotypic variation. Days to silking and anthesis–silking interval (ASI) QTL were located on chromosomes 6, 7 and 9. A comparison of the obtained results with the published SLB resistance QTL studies suggested that the detected bins 9.03/02 and 8.03/8.02 are the hot spots for SLB resistance whereas novel QTL were identified in bins 3.08 and 8.01/8.04. The linked markers are being utilized for marker‐assisted mobilization of QTL conferring resistance to SLB in elite maize backgrounds. Fine mapping of identified QTL will facilitate identification of candidate genes underlying SLB resistance.