水稻苗期抗稻瘟病基因全基因组关联分析

含抗性基因的水稻品种易被病原菌克服,因此为进一步发掘新的稻瘟病抗性基因,利用水稻多样性群体II(RDP-II)中的470份种质资源,在湖南省桃江县稻瘟病高发区的自然病圃中进行水稻苗期的抗病性鉴定,并通过全基因组关联分析(GWAS)鉴定稻瘟病的抗性相关位点,最终鉴定出25份苗期抗性较好的品种,可作为抗性育种材料.采用混合...     

水稻资源开花期耐热性的全基因组关联分析

水稻在开花期对高温非常敏感,挖掘耐热种质并解析耐热性的遗传机制,有助于水稻的耐热性遗传改良.本研究选取205份国内外种质资源,在抽穗开花期对遇高温的稻穗进行标记,以高温下标记穗的结实率作为耐热指标,结合高密度SNP标记进行全基因组关联分析并初步预测候选基因.结果 表明:不同水稻种质的耐热性差异明显,高温下的结实率最低为...     

羊重要性状全基因组关联分析研究进展

全基因组关联分析(genome-wide association study, GWAS)是一种复杂性状功能基因鉴定的分析策略,已成为挖掘畜禽重要经济性状候选基因的重要手段。随着绵羊和山羊基因组完成和公布,以及不同密度的SNP (single nucleotide polymorphism)芯片的推出并进行商业化推广,不仅大大丰富了羊标记辅助选择可利用的分子标记,而且还为开展重要性状的分子机理的探索提供了重要技术支撑。本文主要针对羊角、羊毛、羊奶、生长发育、肉质、繁殖和疾病等重要性状的GWAS研究所用的群体、主要研究方法和研究结果进行了综述,并对GWAS方法研究现状进行了归纳,以期为进一步利用GWAS进行羊的各种性状的遗传基础研究提供参考。     

京海黄鸡体重性状全基因组关联分析

体重性状是肉鸡重要的经济性状。为了寻找可用于京海黄鸡体重性状遗传改良的分子标记及候选基因,本文以400只京海黄鸡核心群母鸡为基础,测定了0~14周龄体重,利用简化基因组测序技术(Specific-locus amplified fragment sequencing, SLAF-seq)对京海黄鸡体重性状进行全基因组关联研究(Genome-wide association stndy, GWAS),筛选与京海黄鸡体重性状相关的SNPs位点。结果共检测到100个与京海黄鸡体重相关的SNPs位点,其中15个位点效应达到全基因组显著水平(P<1.87E-06),85个位点效应达到全基因组潜在显著水平(P<3.73E-05)。通过筛选每个显著SNP周围1 Mb区域内的基因,共找到9个可能的候选基因,其中FAM124A(Family with sequence similarity 124A)、QDPR(Quinoid dihydropteridine reductase)、WDR1(WD repeat domain 1)和SLC2A9(Solute carrier family 2 (facilitated glucose transporter), member 9) 4个基因可能是影响体重性状的重要候选基因。同时还发现,4号染色体75.6~80.7 Mb区域集中了大部分与京海黄鸡中后期体重性状显著相关的SNPs位点,该区域可能是影响京海黄鸡中后期生长体重的重要候选区域。     

中国精神分裂症的全基因组关联分析及其转化医学进展

我国在精神分裂症的遗传学和生命组学研究方面取得了很大进展,如在全基因组关联分析(genome-wide association study,GWAS)方面工作获得了一系列成果.随着我国对重大疾病转化医学的逐步关注和重视,利用在精神分裂症上已经获得的广泛和深入的研究结果,寻找精神分裂症各种临床应用的生物标记物研究,系统性地建立适合于类似精神分裂症这类复杂疾病的早期诊断、干预和预防的临床咨询和应用体系等将是该疾病转化医学方面可实施的方法和案例.精神分裂症的转化医学方面还涉及精神分裂症患者的个体化用药方案建立.药物疗效和药物不良反应的个体差异具有较复杂的环境和遗传背景,结合精神分裂症的遗传学病因和药物作用的遗传学差异,将有效发挥治疗药物的功效,并降低重大不良反应在敏感个体上的发生.对精神分裂症这类给国家和社会带来极其重大负担的重大疾病,积极推动我国在此类疾病上的基础研究成果转化和转化医学的实施具有重要的社会效应和积极的带动作用.     

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。     

桃基因组及全基因组关/联分析研究进展

桃(Prunus persica [L.] Batsch)是蔷薇科重要的核果类果树, 适应性强, 栽培范围广, 果实口感好, 深受消费者喜欢。提高桃果实品质及增加抗病、抗虫性一直是桃遗传育种者关注的焦点。文章对近年来桃遗传分子标记连锁图谱和物理图谱构建、分子标记开发应用、全基因组和转录组测序工作中所取得的最新成果进行综述, 同时阐述了高密度SNP芯片标记技术在桃以及其它作物上所开展的全基因组关联分析应用实例, 为桃进一步开展全基因组关联分析, 挖掘目标性状QTLs以及高效育种选择标记提供理论基础     

全基因组关联分析的进展与反思

全基因组关联分析(genomewide association study,GWAS)是应用人类基因组中数以百万计的单核苷酸多态性(single nucleotide polymorphism,SNP)为标记进行病例-对照关联分析,以期发现影响复杂性疾病发生的遗传特征的一种新策略。近年来,随着人类基因组计划和基因组单倍体图谱计划的实施,人们已通过GWAS方法发现并鉴定了大量与人类性状或复杂性疾病关联的遗传变异,为进一步了解控制人类复杂性疾病发生的遗传特征提供了重要的线索。然而,由于造成复杂性疾病/性状的因素较多,而且GWAS研究系统较为复杂,因此目前GWAS本身亦存在诸多的问题。本文将从研究方式、研究对象、遗传标记,以及统计分析等方面,探讨GWAS的研究现状以及存在的潜在问题,并展望GWAS今后的发展方向。     

拷贝数变异的全基因组关联分析

基因组拷贝数变异(copy number variations,CNVs)是指与基因组参考序列相比,基因组中≥1 kb的DNA片段插入、缺失和/或扩增,及其互相组合衍生出的复杂变异．由于其具有分布范围广、可遗传、相对稳定和高度异质性等特点,目前认为,CNVs是一种新的可以作为疾病易感标志的基因组DNA多态性,其变异引起的基因剂量改变可以导致表型改变．最近,一种基于CNVs的新的疾病易感基因鉴定策略——CNV全基因组关联分析开始出现,这一策略和传统的基于单核苷酸多态性的关联分析具有互补性,通过认识基因组结构变异可以认识复杂疾病的分子机制和遗传基础．     

利用全基因组重测序分析鹿茸重量相关基因

茸角是鹿科动物特有的器官,具有重要的生物学意义。鹿茸生长是一个复杂的生物代谢过程,其重量与遗传因素有一定关联。本研究对饲养条件基本一致的5个梅花鹿(Cervus nippon)群体进行调查,获得高产和低产梅花鹿个体共100只,利用全基因组重测序分析这些个体与鹿茸重量相关的遗传变异。结果表明,共得到94个与鹿茸重量可能相关的遗传变异,其中有2个变异位点分别定位于OAS2和ALYREF/THOC4基因的外显子区,且ALYREF/THOC4基因在鹿茸中表达量很高。功能富集分析发现,这些遗传变异与鹿茸生长发育密切相关,可作为潜在的鹿茸重量相关遗传变异。本研究首次通过全基因组重测序直接筛选与鹿茸重量相关的遗传变异,并分析关联基因的生物学功能,对揭示鹿茸生长发育和鹿茸重量差异形成的遗传机制具有重要意义。     

Genome-wide association study for flowering time,maturity dates and plant height in early maturing soybean (Glycine max) germplasm

Background

Soybean (Glycine max) is a photoperiod-sensitive and self-pollinated species. Days to flowering (DTF) and maturity (DTM), duration of flowering-to-maturity (DFTM) and plant height (PH) are crucial for soybean adaptability and yield. To dissect the genetic architecture of these agronomically important traits, a population consisting of 309 early maturity soybean germplasm accessions was genotyped with the Illumina Infinium SoySNP50K BeadChip and phenotyped in multiple environments. A genome-wide association study (GWAS) was conducted using a mixed linear model that involves both relative kinship and population structure.

Results

The linkage disequilibrium (LD) decayed slowly in soybean, and a substantial difference in LD pattern was observed between euchromatic and heterochromatic regions. A total of 27, 6, 18 and 27 loci for DTF, DTM, DFTM and PH were detected via GWAS, respectively. The Dt1 gene was identified in the locus strongly associated with both DTM and PH. Ten candidate genes homologous to Arabidopsis flowering genes were identified near the peak single nucleotide polymorphisms (SNPs) associated with DTF. Four of them encode MADS-domain containing proteins. Additionally, a pectin lyase-like gene was also identified in a major-effect locus for PH where LD decayed rapidly.

Conclusions

This study identified multiple new loci and refined chromosomal regions of known loci associated with DTF, DTM, DFTM and/or PH in soybean. It demonstrates that GWAS is powerful in dissecting complex traits and identifying candidate genes although LD decayed slowly in soybean. The loci and trait-associated SNPs identified in this study can be used for soybean genetic improvement, especially the major-effect loci associated with PH could be used to improve soybean yield potential. The candidate genes may serve as promising targets for studies of molecular mechanisms underlying the related traits in soybean.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1441-4) contains supplementary material, which is available to authorized users.     

Natural variation in GmGBP1 promoter affects photoperiod control of flowering time and maturity in soybean

The present study screened for polymorphisms in coding and non‐coding regions of the GmGBP1 gene in 278 soybean accessions with variable maturity and growth habit characteristics under natural field conditions in three different latitudes in China. The results showed that the promoter region was highly diversified compared with the coding sequence of GmGBP1. Five polymorphisms and four haplotypes were closely related to soybean flowering time and maturity through association and linkage disequilibrium analyses. Varieties with the polymorphisms SNP_‐796G, SNP_‐770G, SNP_‐307T, InDel_‐242normal, SNP_353A, or haplotypes Hap‐3 and Hap‐4 showed earlier flowering time and maturity in different environments. The shorter growth period might be largely due to higher GmGBP1 expression levels in soybean that were caused by the TCT‐motif with SNP_‐796G in the promoter. In contrast, the lower expression level of GmGBP1 in soybean caused by RNAi interference of GmGBP1 resulted in a longer growth period under different day lengths. Furthermore, the gene interference of GmGBP1 also caused a reduction in photoperiod response sensitivity (PRS) before flowering in soybean. RNA‐seq analysis on GmGBP1 underexpression in soybean showed that 94 and 30 predicted genes were significantly upregulated and downregulated, respectively. Of these, the diurnal photoperiod‐specific expression pattern of three significant flowering time genes GmFT2a, GmFT5a, and GmFULc also showed constantly lower mRNA levels in GmGBP1‐i soybean than in wild type, especially under short day conditions. Together, the results showed that GmGBP1 functioned as a positive regulator upstream of GmFT2a and GmFT5a to activate the expression of GmFULc to promote flowering on short days.     

Genome-wide association study reveals the genetic architecture of flowering time in rapeseed (Brassica napus L.)

Flowering time adaptation is a major breeding goal in the allopolyploid species Brassica napus. To investigate the genetic architecture of flowering time, a genome-wide association study (GWAS) of flowering time was conducted with a diversity panel comprising 523 B. napus cultivars and inbred lines grown in eight different environments. Genotyping was performed with a Brassica 60K Illumina Infinium SNP array. A total of 41 single-nucleotide polymorphisms (SNPs) distributed on 14 chromosomes were found to be associated with flowering time, and 12 SNPs located in the confidence intervals of quantitative trait loci (QTL) identified in previous researches based on linkage analyses. Twenty-five candidate genes were orthologous to Arabidopsis thaliana flowering genes. To further our understanding of the genetic factors influencing flowering time in different environments, GWAS was performed on two derived traits, environment sensitivity and temperature sensitivity. The most significant SNPs were found near Bn-scaff_16362_1-p380982, just 13 kb away from BnaC09g41990D, which is orthologous to A. thaliana CONSTANS (CO), an important gene in the photoperiod flowering pathway. These results provide new insights into the genetic control of flowering time in B. napus and indicate that GWAS is an effective method by which to reveal natural variations of complex traits in B. napus.     

Diverse flowering responses subjecting to ambient high temperature in soybean under short-day conditions

Flowering time is one of important agronomic traits determining the crop yield and affected by high temperature. When facing high ambient temperature, plants often initiate early flowering as an adaptive strategy to escape the stress and ensure successful reproduction. However, here we find opposing ways in the short-day crop soybean to respond to different levels of high temperatures, in which flowering accelerates when temperature changes from 25 to 30 °C, but delays when temperature reaches 35 °C under short day. phyA-E1, possibly photoperiodic pathway, is crucial for 35 °C-mediated late flowering, however, does not contribute to promoting flowering at 30 °C. 30 °C-induced up-regulation of FT2a and FT5a leads to early flowering, independent of E1. Therefore, distinct responsive mechanisms are adopted by soybean when facing different levels of high temperatures for successful flowering and reproduction.     

Natural variation in the genes responsible for maturity loci E1, E2, E3 and E4 in soybean

Background and Aims

The timing of flowering has a direct impact on successful seed production in plants. Flowering of soybean (Glycine max) is controlled by several E loci, and previous studies identified the genes responsible for the flowering loci E1, E2, E3 and E4. However, natural variation in these genes has not been fully elucidated. The aims of this study were the identification of new alleles, establishment of allele diagnoses, examination of allelic combinations for adaptability, and analysis of the integrated effect of these loci on flowering.

Methods

The sequences of these genes and their flanking regions were determined for 39 accessions by primer walking. Systematic discrimination among alleles was performed using DNA markers. Genotypes at the E1–E4 loci were determined for 63 accessions covering several ecological types using DNA markers and sequencing, and flowering times of these accessions at three sowing times were recorded.

Key Results

A new allele with an insertion of a long interspersed nuclear element (LINE) at the promoter of the E1 locus (e1-re) was identified. Insertion and deletion of 36 bases in the eighth intron (E2-in and E2-dl) were observed at the E2 locus. Systematic discrimination among the alleles at the E1–E3 loci was achieved using PCR-based markers. Allelic combinations at the E1–E4 loci were found to be associated with ecological types, and about 62–66 % of variation of flowering time could be attributed to these loci.

Conclusions

The study advances understanding of the combined roles of the E1–E4 loci in flowering and geographic adaptation, and suggests the existence of unidentified genes for flowering in soybean,     

Mapping genetic loci for flowering time,maturity, and photoperiod insensitivity in soybean

Time of flowering and maturity in soybean (Glycine max (L.) Merr) are important reproductive characters of agronomic interest. These traits are useful for developing soybean cultivars with a wider geographical adaptation. The objective of this research was to use molecular markers to identify chromosomal regions that control traits for flowering time, maturity and photoperiod insensitivity in soybean. Two single-cross populations, IX132 (PI 317.336 × `Corsoy') consisting of 101 progeny, and IX136 (PI 317.334B × `Corsoy') consisting of 100 progeny, were used. Days to R1 (the day when 50% of the plants in a plot have an open flower at one of the top nodes with a fully expanded leaf) was observed among F_6:7 RI lines in the field during 1991 and 1992 and in the growth chamber at 12 h and 20 h photoperiods using fluorescent and incandescent lamps. Days to R3 (the number of days after emergence when 50% of the plants in a plot had presented the first 5 mm pod at one of the top four nodes with a fully expanded leaf was observed in the field during 1991 and in the growth chamber with 12 h photoperiod. Days to R7 (the number of days after emergence when 50% of pods in a plot had mature pod color) was observed in the field in 1991. A total of 139 markers (88 RFLPs and 51 SSRs) in the IX132 population and 125 markers (73 RFLPs and 52 SSRs) in the IX136 population were used to map quantitative trait loci (QTL) affecting these traits. Results show that a large-effect QTL for days to R1, R3, and R7, and photoperiod insensitivity was found at the same location on linkage group (LG) C2 in both populations. This result suggests that photoperiod insensitivity, flowering time, and maturity may be controlled by the same gene(s) or by tightly clustered genes in the same chromosomal region. In addition to the large effect QTL, minor QTL were also detected controlling the four traits in both populations. Minor QTL account for as much as 17.8% and 12.1% of phenotypic variance in populations IX132 and IX136, respectively. Thus, time of flowering, maturity, and photoperiod insensitivity in these soybean populations are proposed to be controlled by a major QTL with a large effect and modified by several minor QTL.     

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.     

植物开花时间的遗传调控通路研究进展

开花时间对植物的繁殖成功至关重要。广泛分布的物种经常发生开花时间的分化, 从而能够更好地适应不同的环境条件。为了探索植物开花行为发生适应性分化的分子机制, 首先要明确调控开花行为的遗传通路。本文梳理了植物各类群调控开花时间的遗传通路, 以期为开花时间适应性分化的分子机制研究提供依据。 植物从营养生长向繁殖转变时, 其开花行为主要受到光照、温度、水分等外界环境因子和赤霉素等内在因素的影响。通过对模式植物拟南芥(Arabidopsis thaliana)和其他类群的研究, 总结出了调控植物开花时间的6条通路, 包括日照长度和光质影响开花的光依赖通路, 长时间冷暴露后促进植物开花的春化通路, 高温或低温环境影响开花的温度通路, 以及赤霉素通路、年龄通路和自主通路3条内部调节过程。植物开花时间调控的6条上游通路信号传递到下游的开花整合基因FT(FLOWERING LOCUS T)和SOC1(SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1), 整合基因将这些复杂的调节因子整合后进一步传递到下游花分生组织, 从而启动开花。此外, 非编码RNA、转座子对开花时间的调控也具有重要作用。部分遗传通路被证实在植物适应环境的过程中起到了重要作用。目前对植物开花调控的研究已经有一百多年历史, 理论相对成熟。然而, 仍然存在许多具有争议和未解决的问题, 如开花基因的表达方式、开花行为的特殊调控机制、开花时间变异的适应性意义等等, 需要更进一步的研究。