水稻糯性相关基因的全基因组关联分析

利用1 090 071个SNP标记, 对419份广西地方稻种资源核心种质的糯性进行全基因组关联分析。结果表明, 运用混合线性模型, 在P<4.72×10^-8 (4.72E-8)水平下, 检测到45个与糯性显著关联的SNP位点, 均位于第6号染色体上。通过筛选显著关联位点上、下游各150 kb区域内的基因, 共找到305个候选基因, 其中包含2个与淀粉合成酶相关的Wx和SSIIa基因; 同时在第6号染色体5.69-5.89 Mb区域发现4个与糯性显著关联的SNP位点, 该区域可能是影响水稻(Oryza sativa)糯性的重要候选区域。     

普通菜豆抗菜豆象性状的全基因组关联分析

普通菜豆(Phaseolus vulgaris)具有丰富的营养价值, 菜豆象(Acanthoscelides obtectus)是危害菜豆的主要害虫, 利用抗虫种质资源防治菜豆象是最安全且经济有效的方法。该研究利用改良的室内人工接虫方法, 对625份普通菜豆种质资源进行2次菜豆象抗性重复鉴定, 筛选出2份抗性稳定且种子受害率均在10%以下的高抗种质。利用种子受害率和蛀孔总数的表型数据, 基于3 767 432个SNP标记进行全基因组关联分析, 鉴定出15个与种子受害率相关的显著关联遗传位点, 8个与蛀孔总数相关的显著关联位点, 解释了4.54%-5.56%的表型变异。在候选位点筛选出包括编码蛋白酶抑制剂、凝集素和过氧化物酶等在内的20个与抗虫防御相关的候选基因。     

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。采用混合线性模型(MLM)对700 000个单核苷酸多态性(SNP)基因型和苗期的稻瘟病表型数据进行GWAS研究,在水稻基因组中鉴定了24个抗性关联位点,除4号和7号染色体外,在其余10条染色体上均有分布。在这些关联位点中,5个位点包含已克隆或定位的6个稻瘟病基因,其余19个位点是新的抗性位点。此外,通过对水稻亚群抗性规律分析发现,热带粳稻亚群的平均抗性水平最高,温带粳稻亚群的平均抗性水平最低。这些研究结果为分子辅助抗稻瘟病育种提供了分子标记,也为后续抗稻瘟病基因的克隆提供了基因组定位信息。     

利用紧缩线性模型和贝叶斯模型对猪总产仔数和产活仔数性状的全基因组关联研究

全基因组关联分析策略已逐渐成为家畜重要经济性状研究的强有力工具。文章使用猪60K SNP芯片对一个具多胎繁殖性状记录的商业母猪群(n=820)进行分型检测,共计57 814个SNP通过设定质控标准。主成分分析显示群体内不存在显著的群体分层现象,而后分别运用两种统计模型Compressed Mixed Linear Model(GAPIT程序包)、Bayes CPi(GenSel软件)进行第1和第2胎次总产仔数和产活仔数性状的全基因组关联分析。从两种分析方法所得结果中各取最显著的50个SNP位点进行比较:对于第1胎次总产仔数,两种方法分析结果存在31个重合SNP位点,对于第1胎次产活仔数,有20个重合SNP位点;且两种统计分析结果中最显著的SNP位点都在另一方法中得到验证。与第1胎次总产仔数显著关联的SNP位于1、2、3、7、13、16和18号染色体,与第1胎次产活仔数显著关联的SNP位于1、3、4、13和16号染色体上的11个区域内。在1、3、13和16染色体上共有5个区域同时与这两个性状显著关联。与第2胎次总产仔数和产活仔数显著关联的区域主要位于7、10、12、13、14和16号染色体的6个重叠区域内。     

鱼和熊掌的选择: 反向重复序列变异介导的玉米环境适应与产量平衡

作物育种的目标是找到产量和抗性的最佳平衡点, 其中涉及“鱼和熊掌”二者兼得的选择策略。哪些逆境负调控位点影响产量性状, 以及如何调控等是突破育种瓶颈的重要科学问题。近百年来, 高产玉米(Zea mays)育种使玉米单产不断提高, 同时现代玉米品种对干旱的敏感性也呈现出增强趋势, 故而存在高产稳产的潜在风险。可对于这一现象背后确切的遗传机制却知之甚少, 从而限制了既高产又高抗玉米新品种的培育。玉米的非生物胁迫抗性与产量性状均为多基因控制的复杂数量性状, 涉及全基因组范围内大量基因的表达与调控。玉米基因组内存在大量的小RNA (sRNA), 其对基因表达起精细调控作用, 但人们对sRNA调控作物环境胁迫应答与产量性状机制的理解仍然有限。近日, 华中农业大学代明球课题组与李林和李峰两个课题组合作, 基于对338份玉米关联群体在不同环境下的sRNA表达组分析, 鉴定到大量干旱应答的sRNA, 以及调控这些sRNA表达的遗传位点(eQTL); 并克隆了8号染色体上1个干旱特异性eQTL热点DRESH8。生物信息学分析显示, DRESH8是1个由转座子组成的长度约为21.4 kb的反向重复序列(TE-IR)。DRESH8通过产生小干扰RNA (siRNA)介导抗旱基因的转录后沉默, 并间接抑制产量负调控因子的表达, 在负调控干旱应答的同时正调控产量性状。进一步研究发现, DRESH8在玉米驯化和改良过程中受到了人工选择。据此, 他们认为DRESH8可能是玉米平衡抗旱性和产量的关键遗传位点。该研究在全基因组水平上揭示了作物调控产量和环境胁迫抗性平衡的关键遗传机制, 同时也鉴定到大量IR位点, 为未来“高抗、高产”玉米设计育种提供了有价值的操控靶点。     

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19.0%,平均值为64.0%,中位值为65.9%,最高值为86.6%,其中06-32、剪刀齐、娄早籼5号等17份种质的耐热性较强;全基因组关联分析共筛选到130个与耐热性显著关联的SNP标记,并鉴定到18个耐热QTL,其中6个QTL与已报道的耐热相关QTL共定位;qHT4-6与耐热性的关联度最高,根据该区间lead SNP的单倍型分类,G单倍型材料的开花期耐热性显著强于A单倍型材料,该区间附近有7个基因可能受高温调控。     

小麦根部耐盐性状全基因组关联分析

为了解小麦耐盐相关性状的遗传机理,挖掘与小麦耐盐性显著相关的SNP位点及候选基因,本研究利用浓度200 mmol/L的NaCl溶液和正常营养液对全国300份小麦品种(系)进行耐盐性试验,并利用小麦90 K芯片对分布于小麦全基因组的16650个SNP,采用Q+K关联混合模型对小麦最长根长、根干重、根鲜重、根平均直径、根尖数、根表面积、根体积和总根长等8个根部耐盐性相关性状进行全基因组关联分析(GWAS,genome-wide association study)。研究结果表明,小麦根部性状表现出广泛的表型变异,变异系数为24.3%~50.0%,多态性信息含量(PIC,polymorphic information content)为0.170~0.562,全基因组LD衰减距离为6 Mb;群体结构分析表明,试验所用300份小麦品种(系)可分为3个亚群,亚群1包含143个(47.67%)试验材料,主要来自河南、陕西和四川;亚群2包含74个(24.67%)试验材料,主要来自北京;亚群3包含83个(27.67%)试验材料,主要来自河南。GWAS共检测到77个与小麦耐盐相关性状显著关联的SNP位点(P≤0.001),这些位点分布在小麦除6D外的20条染色体上,单个SNP位点可解释3.70%~19.45%的表型变异,其中位于1A、3A、4A、7A、3D和5D染色体上的RAC875_c13169_459等6个位点同时关联到2个或2个以上性状,贡献率为3.78%~19.45%;对77个SNP位点进行发掘,筛选到17个可能与小麦耐盐性有关的候选基因。TraesCS5B01G031800(阳离子反转运蛋白)在Na+等阳离子转运中起重要作用,TraesCS5A01G329000(防御素)可以在阻断Na+等阳离子进入过程中起作用,TraesCS2A01G079000(重复富脯氨酸细胞壁蛋白)在细胞壁的形成中起重要作用,这些候选基因可作为耐盐性重要基因。     

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。     

基于简化基因组的花生InDel标记开发和功能解析

InDel在基因组中的分布密度仅次于SNP,可作为动植物群体遗传分析、分子辅助育种等研究领域的有效分子标记。花生是世界范围内重要的油料作物之一。目前,花生栽培种全基因组已经公布,为准确挖掘花生基因组信息提供了重要参考。本研究通过169份花生核心种质的GBS(Genotyping-by-sequencing)测序和比对,共获得大小分布在1～14 bp范围内的10401个InDels。染色体Arahy.16上分布的InDels最多,达741个;而在染色体Arahy.08上分布的最少,有263个。参考基因组注释信息,仅有1167个InDels分布在功能基因相关区域。经GO注释,InDel分子功能主要包括催化活性(catalytic activity)和结合(binding);生物过程主要涉及代谢过程(metabolic process)、单组织过程(single-organism process)和细胞过程(cellular process)。经KEGG通路分析发现,InDels所在的基因区域的功能主要与代谢相关。本研究开发出全基因组水平的InDel标记,并做了相应功能分类和注释,为进一步分子验证和利用提供丰富的基因资源。     

梯棱羊肚菌全基因组SNP/Indel分析及基于Indel标记的遗传连锁图谱构建

基于梯棱羊肚菌Morchella importuna两个子囊孢子培养物的全基因组测序数据,对全基因组范围内的变异位点进行分析。共鉴定到18 438个变异位点,平均每Mbp的变异位点数量为361个;变异位点以单核苷酸多态性SNP为主,共计17 104个,基因组中SNP的频率为335SNPs/Mbp;Indel多态性位点1 334个,以2-10bp的插入缺失为主;73.4% SNP/Indel位于基因间隔区域,外显子区域共检测到3 042个变异位点,占总数的16.50%;对基因功能产生确定影响的移码突变有1 088个,占5.90%,错义突变916个,占比4.97%;不同Scaffold上的SNP/Indel出现频率不同,SNP频率最大的为Scaffold80,平均每Mbp包含2 856个SNP,频率最低为Scaffold60和Scaffold75,分别为16SNPs/Mbp和30SNPs/Mbp;对≥11bp的Indel变异位点进行标记开发和多态性群体分析,成功开发出75对Indel标记。采用原生质体单细胞分离技术,获得了梯棱羊肚菌M04的两个可亲和的同核体菌株M04P01和M04P40,同时采用来自M04子囊果的58个单孢菌株作为作图群体,初步构建了包含75个Indel标记和1个交配型基因的梯棱羊肚菌遗传连锁图谱,共获得12个连锁群,连锁群总长度273.7cM。     

Genome-wide association studies of Ca and Mn in the seeds of the common bean (Phaseolus vulgaris L.)

SNP markers linked to genes controlling Ca and Mn uptake were identified in the common bean seeds using DArT-based association mapping (AM). The Ca concentration in the seeds varied between 475 and 3,100 mg kg⁻¹ with an average of 1,280.9 mg kg⁻¹ and the Mn concentration ranged from 4.87 to 27.54 mg kg⁻¹ with a mean of 11.76 mg kg⁻¹. A total of 19,204 SNP markers were distributed across 11 chromosomes that correspond to the haploid genome number of the common bean. The highest value of ΔK was determined as K = 2, and 173 common bean genotypes were split into two main subclusters as POP1 (Mesoamerican) and POP2 (Andean). The results of the UPGMA dendrogram and PCA confirmed those of STRUCTURE analysis. MLM based on the Q + K model identified a large number of markers-trait associations. Of the 19,204 SNPs, five (on Pv2, 3, 8, 10 and 11) and four (on Pv2, 3, 8 and 11) SNPs were detected to be significantly related to the Ca content of the beans grown in Bornova and Menemen, respectively in 2015. In 2016, six SNPs (on Pv1–4, 8 and 10) were identified to be significantly associated with the Ca content of the seeds obtained from Bornova and six SNPs (on Pv1–4, 8 and 10) from Menemen. Eight (on Pv3, 5 and 11) and four (on Pv2, 5 and 11) SNPs had a significant association with Mn content in Bornova in 2015 and 2016, respectively. In Menemen, eight (on Pv3, 5, 8 and 11) and 11 (on Pv1, 2, 5, 10 and 11) SNPs had a significant correlation with Mn content in 2015 and 2016, respectively.     

Association mapping of days to flowering in common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.) revealed by DArT markers

In the current study, 173 common bean genotypes from several geographic regions were studied. Days to flowering (DF) was evaluated in two experimental locations in Izmir, Turkey (Bornova and Menemen) in 2 years (2015 and 2016) and was found to range from 30 to 62.7 days with a mean value of 41.5 days. A total of 22,848 SNPs based on diversity array technology were developed, and after filtering, the remaining 20,766 SNP markers were used for calculating linkage disequilibrium. Chromosomes 1–11 contained 1846, 2342, 2184, 1153, 1351, 1520, 1953, 2080, 2065, 1199, and 1511 SNPs, respectively. A total of 1562 SNPs were identified as scaffold markers. The PIC value was 0.25, ranging from 0.005 to 0.500. Common bean accessions were divided into two main subpopulations, namely POP1 (Mesoamerican) and POP2 (Andean). Mixed linear model using the Q + K model showed that three SNPs had a significant association (p?<?0.01) in Bornova in 2015 and seven SNPs had a significant association (p?<?0.01) in the same location in 2016. Five significant associations (p?<?0.01) were identified in 2015 while six (p?<?0.01) were identified in Menemen in 2016. When the data from both locations and both years was combined, six SNPs were significant (p?<?0.01). For DF, 11 putative candidate genes were predicted from the sequences representing homology to linked SNPs. We conclude that the markers, which were significantly associated with the DF of the common bean genotypes in the current study, can be used for marker-assisted selection in plant breeding program of common bean.     

Next‐generation sequencing for identification of candidate genes for Fusarium wilt and sterility mosaic disease in pigeonpea (Cajanus cajan)

To map resistance genes for Fusarium wilt (FW) and sterility mosaic disease (SMD) in pigeonpea, sequencing‐based bulked segregant analysis (Seq‐BSA) was used. Resistant (R) and susceptible (S) bulks from the extreme recombinant inbred lines of ICPL 20096 × ICPL 332 were sequenced. Subsequently, SNP index was calculated between R‐ and S‐bulks with the help of draft genome sequence and reference‐guided assembly of ICPL 20096 (resistant parent). Seq‐BSA has provided seven candidate SNPs for FW and SMD resistance in pigeonpea. In parallel, four additional genotypes were re‐sequenced and their combined analysis with R‐ and S‐bulks has provided a total of 8362 nonsynonymous (ns) SNPs. Of 8362 nsSNPs, 60 were found within the 2‐Mb flanking regions of seven candidate SNPs identified through Seq‐BSA. Haplotype analysis narrowed down to eight nsSNPs in seven genes. These eight nsSNPs were further validated by re‐sequencing 11 genotypes that are resistant and susceptible to FW and SMD. This analysis revealed association of four candidate nsSNPs in four genes with FW resistance and four candidate nsSNPs in three genes with SMD resistance. Further, In silico protein analysis and expression profiling identified two most promising candidate genes namely C.cajan_01839 for SMD resistance and C.cajan_03203 for FW resistance. Identified candidate genomic regions/SNPs will be useful for genomics‐assisted breeding in pigeonpea.     

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.     

Genome-Wide Association Studies of Anthracnose and Angular Leaf Spot Resistance in Common Bean (Phaseolus vulgaris L.)

The common bean (Phaseolus vulgaris L.) is the world’s most important legume for human consumption. Anthracnose (ANT; Colletotrichum lindemuthianum) and angular leaf spot (ALS; Pseudocercospora griseola) are complex diseases that cause major yield losses in common bean. Depending on the cultivar and environmental conditions, anthracnose and angular leaf spot infections can reduce crop yield drastically. This study aimed to estimate linkage disequilibrium levels and identify quantitative resistance loci (QRL) controlling resistance to both ANT and ALS diseases of 180 accessions of common bean using genome-wide association analysis. A randomized complete block design with four replicates was performed for the ANT and ALS experiments, with four plants per genotype in each replicate. Association mapping analyses were performed for ANT and ALS using a mixed linear model approach implemented in TASSEL. A total of 17 and 11 significant statistically associations involving SSRs were detected for ANT and ALS resistance loci, respectively. Using SNPs, 21 and 17 significant statistically associations were obtained for ANT and angular ALS, respectively, providing more associations with this marker. The SSR-IAC167 and PvM95 markers, both located on chromosome Pv03, and the SNP scaffold00021_89379, were associated with both diseases. The other markers were distributed across the entire common bean genome, with chromosomes Pv03 and Pv08 showing the greatest number of loci associated with ANT resistance. The chromosome Pv04 was the most saturated one, with six markers associated with ALS resistance. The telomeric region of this chromosome showed four markers located between approximately 2.5 Mb and 4.4 Mb. Our results demonstrate the great potential of genome-wide association studies to identify QRLs related to ANT and ALS in common bean. The results indicate a quantitative and complex inheritance pattern for both diseases in common bean. Our findings will contribute to more effective screening of elite germplasm to find resistance alleles for marker-assisted selection in breeding programs.     

Single nucleotide polymorphism discovery in common bean

Single nucleotide polymorphisms (SNPs) were discovered in common bean (Phaseolus vulgaris L.) via resequencing of sequence-tagged sites (STSs) developed by PCR primers previously designed to soybean shotgun and bacterial artificial chromosome (BAC) end sequences, and by primers designed to common bean genes and microsatellite flanking regions. DNA fragments harboring SNPs were identified in single amplicons from six contrasting P. vulgaris genotypes of the Andean (Jalo EEP 558, G 19833, and AND 277) and Mesoamerican (BAT 93, DOR 364, and Rudá) gene pools. These genotypes are the parents of three common bean recombinant inbred line mapping populations. From an initial set of 1,880 PCR primer pairs tested, 265 robust STSs were obtained, which could be sequenced in each one of the six common bean genotypes. In the resulting 131,120?bp of aligned sequence, a total of 677 SNPs were identified, including 555 single-base changes (295 transitions and 260 transversions) and 122 small nucleotide insertions/deletions (indels). The frequency of SNPs was 5.16 SNPs/kb and the mean nucleotide diversity, expressed as Halushka??s theta, was 0.00226. This work represents one of the first efforts aimed at detecting SNPs in P. vulgaris. The SNPs identified should be an important resource for common bean geneticists and breeders for quantitative trait locus discovery, marker-assisted selection, and map-based cloning. These SNPS will be also useful for diversity analysis and microsynteny studies among legume species.     

Polymorphisms of mitochondrial ATPase 8/6 genes and association with milk production traits in holstein cows

The maternal effect has been widely proposed to affect the production traits in domestic animals. However, the sequence polymorphisms of mitochondrial DNA (mtDNA) and association with milk production traits in Holstein cows have remained unclear. In this study, we investigated the single nucleotide polymorphisms (SNPs) of mtDNA ATPase 8/6 genes and association with four milk production traits of interest in 303 Holstein cows. A total of 18 SNPs were detected among the 842?bp fragment of ATPase 8/6 genes, which determined six haplotypes of B. taurus (H1-H4) and B. indicus (H5-H6). The mixed model analysis revealed that there was significant association between haplotype and 305-day milk yield (MY). The highest MY was observed in haplotype H4. However, we did not detect statistically significant differences among haplotypes for the traits of milk fat (MF), milk protein (MP), and somatic cell count (SC). The overall haplotype diversity and nucleotide diversity of ATPase 8/6 genes were 0.563?±?0.030 and 0.00609?±?0.00043, respectively. The results suggested that mitochondrial ATPase 8/6 genes could be potentially used as molecular marker to genetically improve milk production in Holstein cows.     

Detection of copy number variants in the horse genome and examination of their association with recurrent laryngeal neuropathy

We used the data from a recently performed genome‐wide association study using the Illumina Equine SNP50 beadchip for the detection of copy number variants (CNVs) and examined their association with recurrent laryngeal neuropathy (RLN), an important equine upper airway disease compromising performance. A total of 2797 CNVs were detected for 477 horses, covering 229 kb and seven SNPs on average. Overlapping CNVs were merged to define 478 CNV regions (CNVRs). CNVRs, particularly deletions, were shown to be significantly depleted in genes. Fifty‐two of the 67 common CNVRs (frequency ≥ 1%) were validated by association mapping, Mendelian inheritance, and/or Mendelian inconsistencies. None of the 67 common CNVRs were significantly associated with RLN when accounting for multiple testing. However, a duplication on chromosome 10 was detected in 10 cases (representing three breeds) and two unphenotyped parents but in none of the controls. The duplication was embedded in an 8‐Mb haplotype shared across breeds.     

Analyses of reaction norms reveal new chromosome regions associated with tick resistance in cattle

Despite single nucleotide polymorphism (SNP) availability and frequent cost reduction has allowed genome-wide association studies even in complex traits as tick resistance, the use of this information source in SNP by environment interaction context is unknown for many economically important traits in cattle. We aimed at identifying putative genomic regions explaining differences in tick resistance in Hereford and Braford cattle under SNP by environment point of view as well as to identify candidate genes derived from outliers/significant markers. The environment was defined as contemporary group means of tick counts, since they seemed to be the most appropriate entities to describe the environmental gradient in beef cattle. A total of 4363 animals having tick counts (n=10 673) originated from 197 sires and 3966 dams were used. Genotypes were acquired on 3591 of these cattle. From top 1% SNPs (410) having the greatest effects in each environment, 75 were consistently relevant in all environments, which indicated SNP by environment interaction. The outliers/significant SNPs were mapped on chromosomes 1, 2, 5, 6, 7, 9, 11, 13, 14, 15, 16, 18, 21, 23, 24, 26 and 28, and potential candidate genes were detected across environments. The presence of SNP by environment interaction for tick resistance indicates that genetic expression of resistance depends upon tick burden. Markers with major portion of genetic variance explained across environments appeared to be close to genes with different direct or indirect functions related to immune system, inflammatory process and mechanisms of tissue destruction/repair, such as energy metabolism and cell differentiation.