Widespread genetic incompatibility in C. elegans maintained by balancing selection

Natural selection is expected to eliminate genetic incompatibilities from interbreeding populations. We have discovered a globally distributed incompatibility in the primarily selfing species Caenorhabditis elegans that has been maintained despite its negative consequences for fitness. Embryos homozygous for a naturally occurring deletion of the zygotically acting gene zeel-1 arrest if their sperm parent carries an incompatible allele of a second, paternal-effect locus, peel-1. The two interacting loci are tightly linked, with incompatible alleles occurring in linkage disequilibrium in two common haplotypes. These haplotypes exhibit elevated sequence divergence, and population genetic analyses of this region indicate that natural selection is preserving both haplotypes in the population. Our data suggest that long-term maintenance of a balanced polymorphism has permitted the incompatibility to persist despite gene flow across the rest of the genome.     

The structure of haplotype blocks in the human genome

Haplotype-based methods offer a powerful approach to disease gene mapping, based on the association between causal mutations and the ancestral haplotypes on which they arose. As part of The SNP Consortium Allele Frequency Projects, we characterized haplotype patterns across 51 autosomal regions (spanning 13 megabases of the human genome) in samples from Africa, Europe, and Asia. We show that the human genome can be parsed objectively into haplotype blocks: sizable regions over which there is little evidence for historical recombination and within which only a few common haplotypes are observed. The boundaries of blocks and specific haplotypes they contain are highly correlated across populations. We demonstrate that such haplotype frameworks provide substantial statistical power in association studies of common genetic variation across each region. Our results provide a foundation for the construction of a haplotype map of the human genome, facilitating comprehensive genetic association studies of human disease.     

Molecular identification of a taste receptor gene for trehalose in Drosophila

The molecular nature of sweet taste receptors has not been fully explored. Employing a differential screening strategy, we identified a taste receptor gene, Tre1, that controls the taste sensitivity to trehalose in Drosophila melanogaster. The Tre1 gene encodes a novel protein with similarity to G protein-coupled seven-transmembrane receptors. Disruption of the Tre1 gene lowered the taste sensitivity to trehalose, whereas sensitivities to other sugars were unaltered. Overexpression of the Tre1 gene restored the taste sensitivity to trehalose in the Tre1 deletion mutant. The Tre1 gene is expressed in taste sensory cells. These results provide direct evidence that Tre1 encodes a putative taste receptor for trehalose in Drosophila.     

基于叶绿体DNA变异的山荆子种质遗传多样性和系统演化

【目的】山荆子是中国原产苹果属植物中分布最广泛的种,母系遗传的叶绿体基因组的非编码区适用于较低的分类阶元（如科、属）的系统研究。对野外考察新收集的山荆子种质的叶绿体DNA（cpDNA）非编码区进行测序,解析其序列遗传变异,从母系遗传基因的角度探究山荆子不同居群的遗传多样性和系统演化关系,为我国山荆子种质资源的起源演化以及收集和保护提供理论依据。【方法】利用4对叶绿体DNA引物扩增新收集的215份山荆子种质资源的4个非编码区trnH-psbA、trnS-trnG spacer+intron、trnT-5'trnL和5'trnL-trnF,对每个基因间区正反向测序获得的序列进行人工校对后,使用MEGA 7.0进行序列拼接和比对,并构建山荆子不同居群间基于遗传距离的Neighbour-Joining系统发育树;使用DnaSP ver5.10.01计算叶绿体DNA的遗传多样性参数,计算不同居群间的基因流和基因分化;利用Arlequin v3.5分析标准分子变异（AMOVA）;运用NetWork ver4.6.1.2构建种内居群间的叶绿体DNA单倍型邻接网络关联图。【结果】4个叶绿体DNA非编码区经测序、拼接、比对和合并之后的片段长度为3 777 bp,共有171个多态性变异位点,其中包含150个插入-缺失位点、20个简约信息位点和1个单一突变位点。在215份山荆子种质中,trnH-psbA、trnS-trnG spacer + intron、trnT-5'trnL和5'trnL-trnF区域的变异位点数量分别为26、32、103和10个,单倍型数量分别为8、8、6和4个,合并之后的叶绿体DNA片段的单倍型为24个。核苷酸多样性最高的区域为trnT-5'trnL（Pi=0.01174）,单倍型（基因）多样性最高的为trnS-trnG spacer+intron（Hd=0.599）,最低的为5'trnL-trnF（Hd=0.228）。215份山荆子种质叶绿体DNA多样性较高（Hd=0.727,Pi=0.00577）。Tajima’s D检验中,4个cpDNA区域在各检验水平上均不显著,检测的4个cpDNA区域在进化上遵循中性模型。AMOVA分析表明遗传变异主要存在于群体内部。【结论】供试4个叶绿体DNA非编码区适合苹果属山荆子种质遗传多样性和系统演化分析。在叶绿体DNA水平导致山荆子群体进化的原因不是自然选择,而是突变压力和遗传漂变。群体间遗传分化与其地理距离不完全相关。山荆子可能为多点起源,推测黑龙江和吉林,内蒙古,甘肃和山西为3个可能的起源地区。     

陕北地区秦川牛及其多个杂交后代群体的遗传多样性

为了解陕北地区黄牛的遗传多样性及遗传背景,采用直接测序技术对55头饲养在陕北榆林地区的秦川牛及其多个杂交后代群体的线粒体DNA D-loop区826bp序列进行测定。结果表明,榆林地区黄牛D-loop区序列A+T平均含量为61.5%,G+C含量38.5%;共检测到33种单倍型和84个变异位点,核苷酸多样度(π)为0.021 43,单倍型多样度(h)为0.970,表明陕北榆林地区的黄牛具有丰富的遗传多样性。NJ法聚类结果显示,该地区的黄牛品种或群体有2个母系起源。     

藏绵羊DQA1基因多态性分析

 【目的】研究藏绵羊DQA1基因多态性,确定其等位基因数、核苷酸多态位点、氨基酸多态位点及各等位基因间的遗传关系,同时分析其进化意义。【方法】采用PCR-SSCP方法检测了900只藏绵羊DQA1基因第2外显子多态性;克隆、测序群体内变异产生的各等位基因序列,并分析序列数据。【结果】发现了17个DQA1的等位基因,包括缺失的1种基因,其中5个为发现的新等位基因。16个单倍型序列中发现56个核苷酸多态位点,27个氨基酸多态位点。【结论】藏绵羊DQA1基因第2外显子具有丰富的多态性,群体中可能蕴藏着更多的遗传资源;藏绵羊DQA1基因最初可能是由2个等位基因突变分化成两大类等位基因的;藏绵羊DQA1基因第2外显子序列与牛的DQA1基因第2外显子序列具有较高的同源性,预示绵羊和牛的DQA1基因最早可能来源于它们分歧以前的共同祖先原始序列;DQA1基因在与其相关的特定抗原刺激下发生的免疫应答反应在绵羊和牛上具有相似性;新等位基因C的139位发现了1个新的核苷酸突变位点（A/G）,属同义突变;5个新发现的DQA1等位基因遗传关系较近,可能由同一等位基因突变产生。     

中华鲟野生群体及迁地群体的MHCⅠa基因遗传多样性变异研究

利用特异性引物MHCⅠf和MHCⅠr,分别从30尾野生中华鲟(Acipenser sinensis)、30尾中华鲟子一代和30尾中华鲟子二代的基因组DNA中扩增MHCⅠa基因的多肽结合位点(PBR)片段,扩增产物长度为127 bp。中华鲟野生群体30个样品265个有效克隆中共检测出50条特异序列(单倍型),中华鲟子一代群体30个样品的278个有效克隆中共检测出66条特异序列(单倍型),中华鲟子二代群体30个样品的257个克隆中检测出64条特异序列(单倍型)。单倍型Acsi-UAB*0101在3个群体中所占的百分比最高,分别为58.1%、38.8%和60.7%。单倍型分布及群体内遗传多样性参数分析表明,中华鲟子一代群体的MHC基因遗传多样性最丰富,野生中华鲟群体的MHCⅠa基因遗传多样性较低。中华鲟野生群体非同义替代与同义替代比率为1.33,分析表明正向选择可能是中华鲟MHCⅠa多态性的主要因素。该研究结果提供了中华鲟从野生群体到子二代群体MHCⅠa基因的部分遗传信息和遗传变异规律,为中华鲟全人工种群优化和繁殖管理提供理论依据。     

两个人工选择奥利亚罗非鱼群体系统发育 及其遗传多样性分析

[目的]了解人工选择偏好对奥利亚罗非鱼遗传多样性的影响,为今后人工选育及生产提供参考依据.[方法]对两个奥利亚罗非鱼群体(那马群体和武鸣群体)各70尾个体的线粒体DNA的D-loop区序列、CoI基因和Cytb基因进行测序及系统进化研究,并选用20对微卫星标记对其遗传多样性进行分析.[结果]基于D-loop区序列两个群体共检测出32个单倍型,其中共享单倍型6个;基于CoI基因共检测出23个单倍型,其中共享单倍型16个;基于Cytb基因共检测出14个单倍型,其中共享单倍型10个.基于D-loop区序列、CoI基因和Cytb基因单倍型分别构建的系统发育进化树显示,武鸣群体和那马群体的个体交错在一起,地理差异不明显,且采用NJ法和ME法构建系统发育进化树的进化拓扑结构基本相似.20对微卫星引物均能在奥利亚罗非鱼中获得稳定有效的扩增条带,其中有18个微卫星位点呈多态性;那马、武鸣群体的平均等位基因数(Na)分别为6.5000和7.9444,平均有效等位基因数(Ne)分别是3.9857和4.7268,平均观测杂合度(Ho)分别为0.7123和0.7752,平均期望杂合度(He)分别为0.9614和0.9711、平均Nei期望杂合度分别为0.7017和0.7636,均表现为武鸣群体略高于那马群体.两个群体的遗传分化系数(Fst)在不同微卫星位点间差异明显,其变化范围为0.0173(GM241)~0.2318(UNH868),平均0.0997;从单群体近交系数(Fis)和总群体近交系数(Fit)来看,所有微卫星位点的数值均为负值.[结论]经短期人工选择的武鸣群体奥利亚罗非鱼遗传多样性较被长期人工选择的那马群体遗传多样性丰富,即短期内的不同人工选择偏好对线粒体DNA的遗传影响较小.     

Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure

Catechol-O-methyltransferase (COMT) is a key regulator of pain perception, cognitive function, and affective mood. Three common haplotypes of the human COMT gene, divergent in two synonymous and one nonsynonymous position, code for differences in COMT enzymatic activity and are associated with pain sensitivity. Haplotypes divergent in synonymous changes exhibited the largest difference in COMT enzymatic activity, due to a reduced amount of translated protein. The major COMT haplotypes varied with respect to messenger RNA local stem-loop structures, such that the most stable structure was associated with the lowest protein levels and enzymatic activity. Site-directed mutagenesis that eliminated the stable structure restored the amount of translated protein. These data highlight the functional significance of synonymous variations and suggest the importance of haplotypes over single-nucleotide polymorphisms for analysis of genetic variations.     

基于CO Ⅰ和Cytb基因的浙江不同抗性水平二化螟种群的遗传结构分析

本研究利用线粒体细胞色素氧化酶亚基Ⅰ(COⅠ)和细胞色素b(Cytb)基因的遗传学方法分析了浙江省8个不同抗性水平二化螟地理种群的遗传多样性及种群遗传结构。种群遗传多样性分析表明：PCR扩增测序分别获得长度为627 bp的COⅠ基因片段和长度为455 bp的Cytb基因片段。355条同源COⅠ序列监测出了68个多态性位点,其中单突变位点22个,简约突变位点46个,共定义了85个单倍型,每个群体的平均单倍型为18.25个,其中瑞安(RA)种群中单倍型最多,为27个单倍型。326条Cytb同源序列监测出了45个多态性位点,其中单突变位点19个,简约突变位点26个,共定义了64个单倍型,每个群体的平均单倍型为14.375个,其中乐清(YQ)种群中单倍型最多,为25个单倍型。此外,各群体中最高的单倍型多样度h分别为0.896 3和0.934 4,反映出二化螟群体较低的遗传多样性水平。种群遗传结构分析表明：二化螟不同地理种群间遗传变异大多数来自于群体内个体间,占80.30%(COⅠ基因)和78.16%(Cytb基因)。较少部分的遗传差异来自于组间,仅占19.43%(COⅠ基因)和21.22%(C...     

水稻地方品种Pi-ta的3'-UTR遗传多态分析

【目的】分析Pi-ta的3'-UTR区遗传变异与该基因抗性功能之间的关系,了解Pi-ta的抗性决定机制,为培养更持久的抗性品种提供依据。【方法】以遗传多样性极高的云南水稻地方品种为研究对象,收集了137个云南地方水稻品种。育苗后提取三叶一心期的水稻幼苗总DNA,设计引物扩增了Pi-ta的3'-UTR区的DNA序列,并扩增了关键功能位点6 640到终止密码子第6 675处这一段的DNA序列。通过双向序列测定获得了137条3'-UTR区的DNA序列并提交至Gen Bank,通过变异位点检测分析云南水稻地方品种Pi-ta的3'-UTR区的遗传多样性程度,并基于最大简约法构建单倍型网络图,分析不同单倍型之间的谱系关系。同时,联合编码区关键抗病位点6 640的碱基状态对3'-UTR单倍型的分布进行分析,讨论3'-UTR区与Pi-ta抗性功能之间的关系。【结果】云南水稻地方品种Pi-ta的3'-UTR区呈现出高度的遗传多样性,长度为1.1 kb的3'-UTR区共有12个SNP位点,由这些SNP可将137个品种划分成7个单倍型。不同单倍型之间没有重组的信号。Pi-ta的3'-UTR对应的DNA编码区长为1 120bp,是植物基因3'-UTR平均长度(200 bp)的5倍多,G+C含量相对较低,为40.43%,不存在插入或缺失导致的长度多态性。Pi-ta的3'-UTR序列中存在多个非保守的潜在poly A位点,此外,Pi-ta的3'-UTR区还存在非常高频率的TTTT序列,提示Pi-ta在转录终止时可能具有复杂的调控机制;而对Pi-ta的不同转录本的分析也表明3'-UTR对应于DNA编码区序列时呈现复杂多变的剪切方式,3'-UTR这种选择性拼接可能与抗性决定作用有关。对遗传多态的进一步分析表明,3'-UTR的SNP高度多态性都出现在感病品种中,所有抗性品种只共享一种单倍型。有趣的是,唯一的3'-UTR抗性单倍型与Pi-ta编码区唯一的抗性单倍型相对应,也即是6 640G所在单倍型也是3'-UTR唯一抗性单倍型。这表明3'-UTR与其编码区是紧密关联的,在功能上和所受到的选择压力方面是连续和一致的。Pi-ta的抗性单倍型区域已从编码区扩展到了3'-UTR区,在研制广谱抗性品种引入Pi-ta时需要同时保证其3'-UTR区不能有额外的SNP,必须是抗性单倍型特有的SNPs。【结论】Pi-ta的3'-UTR与其编码区紧密连锁,抗性品种的3'-UTR受到纯净化选择,维持单一单倍型,3'-UTR对于Pi-ta的抗性功能具有不可或缺的作用。     

我国不同品种黑羽鸡MC1R基因多态性研究

为了研究我国地方黑羽鸡品种MC1R基因的多态性,采用PCR的方法扩增了我国7个黑羽鸡品种(狼山鸡、寿光鸡、东乡绿壳蛋鸡、盐津乌骨鸡、余干乌骨鸡、鸿光黑鸡和新杨黑鸡)的MC1R基因,并对不同品种鸡MC1R基因序列的多态性进行生物信息学分析。结果显示：7个品种MC1R基因编码区全长均为945 bp,共编码315个氨基酸。7个品种210条序列,总计发现10个多态位点,位于编码区的有9个,其中有7个导致编码氨基酸发生变化,共界定了14种单倍型,定义为Hap1—Hap14,其中东乡绿蛋鸡和寿光鸡有2种单倍型,其他品种单倍型数都在2个以上。系统发育树分化为两个分支,分支I仅包含新杨黑鸡,分支II包含其他6个黑羽鸡品种。我国黑羽鸡MC1R基因表现出丰富的多态性,中国本土黑羽鸡品种和国外血缘黑羽品种存在MC1R基因多态位点上存在差别。该研究结果为我国黑羽地方鸡遗传资源的种质保护、品种选育和鉴定工作提供了参考。     

利用线粒体序列分析野生唇(鱼骨)群体的遗传结构

运用PCR直接测序法,对8个野生唇(鱼骨)群体线粒体ATP6和ND4基因部分序列进行测定,共获得1 629bp序列,序列变异率为4.97％,核酸多样性为0.007 5,表明野生唇(鱼骨)群体保持了较好的遗传多样性;在8个野生唇(鱼骨)群体中共检测出21个单倍型,其中HQ1和HT2单倍型共包含了45.24％的个体,且单倍...     

基于线粒体DNA控制区的斑翅草螽不同地理种群遗传分化研究

采用PCR扩增结合DNA克隆测序技术,分析了斑翅草螽Conocephalus maculates 9个地理种群mtDNA控制区序列的变异及遗传多样性.切除侧翼RNA基因序列后,最终获得的斑翅草螽mtDNA控制区比对后全长为676 bp,平均碱基组成T(37.8％),C(11.7％),A(41.3％)和G(9.1％).共检测到98个可变位点,占总位点数的14.5％,其中,9处碱基插入/缺失,74处转换(40个T/C,34个A/G),50处颠换(18个A/T,11个T/G,15个A/C,6个C/G).共定义46个单倍型,其中,4个为种群间共享单倍型(H02、H05、H08和H10),其余42个为各种群独有单倍型,包括6个种群内共享单倍型(H09、H11、H15、H18、H26和H38).单倍型总数占实验个体总数的69.7％,除四川峨眉山外,其余种群单倍型百分比均＞50％.通过两两地理种群间的FST值差异显著性检验,将这些群体分为4组,分别为SC+CQ,GX+FLB+HN+YN,XZ和HB.以长瓣草螽C.gladiatus、峨眉草螽C.emeiensis、悦鸣草螽C.melaenus、竹草螽C.bambusanus为外群,构建的斑翅草螽mtDNA控制区单倍型NJ法系统树形成3个自举支持度较高的分支,其中,分支A由28种单倍体组成,包括本研究中除四川峨眉山(SC)和重庆万州(CQ)以外的7个种群;分支B由12种单倍体组成,包含除菲律宾拉乌尼翁(FLB)和江西南昌(JX)以外的7个种群;分支C由6种单倍型组成,全部来自西藏林芝(XZ)的单倍型.聚类结果表明,斑翅草螽不同地理种群间的遗传分化并不明显,即使是两两群体间FST值差异显著的群体,也未能形成完全独立的分支.     

烟草Ti245抗烟草花叶病毒的遗传分析及抗性基因定位

以含抗烟草花叶病毒(TMV)基因的烟草Ti245为抗病亲本,以K326为感病亲本,经杂交得到F1,F1自交得到F2群体,分析了Ti245抗TMV的遗传规律,并对抗性基因进行SSR标记定位.结果表明:Ti245对TMV的抗性由1对隐性基因控制;基因定位发现,Ti245抗TMV的位点位于LG9连锁群,标记*Tp217200...     

The Mining of Citrus EST-SNP and Its Application in Cultivar Discrimination

Single nucleotide polymorphisms （SNPs） are the most abundant sequence variations found in plant genomes and are widely used as molecular genetic markers in cultivar identification and genetic diversity studies. The objective of this study was to identify SNP markers useful for discrimination of citrus cultivars, since large numbers of expressed sequence tags （ESTs） of sweet orange are available from the National Center for Biotechnology Information （NCBI）. We now have the opportunity to discover SNP markers suitable for determining the haplotypes with which to distinguish very closely related cultivars and to assess genetic diversity within or between related species of citrus. SNPs and small insertions/deletions （Indels） from ESTs of sweet orange and satsuma were identified by the in silico SNP discovery strategy. 55 296 EST sequences of sweet orange and 2 575 of satsuma retrieved from the NCBI repository were mined for potential SNPs. Cleaved amplified polymorphic sequences （CAPS） and sequencing approaches were used to validate putative SNPs in a sample of 30 citrus accessions. A total of 3 348 putative SNPs were identified based on the abundance of sequences and haplotype cosegregation. Of these 3 348 SNPs, the transitions, transversions and Indels ratios were 47.9, 36.1 and 16.0%, respectively. The SNPs occurred on average at a frequency of 1 per 164 bp in the coding region of citrus. 14 SNPs were randomly selected and genotyped according to 30 citrus accessions including 23 accessions of sweet orange; 11 SNPs displayed polymorphism with an average polymorphism information content （PIC） of 0.20 among 30 citrus accessions. The genetic diversity present in sweet orange was low, so the 14 SNP markers failed to discriminate different cultivars of sweet orange, but they did succeed in distinguishing accessions of inter-species of citrus. In this study, SNPs were mined from EST sequences of sweet orange and satsuma, which displayed potential capability as molecular markers to discriminate inter-species accessions of citrus. It is anticipated that these putative SNPs could be applied in citrus genetics research and breeding.     

基于线粒体Cytb基因和D-loop区的野生与养殖小黄鱼群体遗传多样性

为研究野生与养殖小黄鱼群体的遗传多样性,基于mtDNA Cytb基因和D-loop控制区对舟山嵊泗海域(SS)和象山三门口海域(SMK)2个小黄鱼野生群体和1个养殖群体(YZ)的遗传结构与遗传分化等进行比较分析。序列分析结果显示,Cytb基因序列为841 bp,其A+T含量(50.2%)与C+G含量(49.8%)相似;D-loop区序列为629～635 bp, A+T含量(58.9%)远高于C+G含量(41.1%)。SS、SMK和YZ群体Cytb基因的单倍型数分别为26、27和12,SS和SMK群体共享2个单倍型(Hap1和Hap13),SMK和YZ群体共享1个单倍型(Hap41);SS、SMK和YZ群体D-loop区的单倍型数分别为27、30和10,SS和SMK群体共享1个单倍型(Hap4)。多样性分析结果显示,3个群体均属于高单倍型多样性(H_d>0.5),其中,SS和SMK群体单倍型多样性和核苷酸多样性高于YZ群体,表明野生群体多样性略高于养殖群体。遗传分化指数显示,2个小黄鱼野生群体间的分化程度极小,而养殖群体与野生群体间存在中度分化。遗传分化指数和A...     

基于线粒体标记的淮南麻黄鸡遗传结构及其遗传多样性分析

通过探究淮南麻黄鸡的遗传多样性和遗传结构,为淮南麻黄鸡的种质资源保护和开发利用提供遗传背景资料。对淮南麻黄鸡线粒体基因组(mitochondrial genome,mt DNA)控制区全序列进行测序,并结合红色原鸡的序列进行生物信息学分析。淮南麻黄鸡mt DNA控制区全长1 231~1 232 bp,共发现26处单核苷酸变异位点,核苷酸多样性(Pi)为0.006 6,单倍型多样性(Hd)为0.917,平均核苷酸差异(K)为7.573。群体共包含14种单倍型,可以分为A、B、C和E 4个分支分别包括3、3、7和1种单倍型。淮南麻黄鸡在线粒体水平上有较高的多态性,并且来自多个不同的母系,有很好的开发潜力。     

黄瓜白粉病抗性基因定位及候选基因分析

【目的】通过对黄瓜白粉病抗性基因的精细定位,明确抗性基因的候选区段,为进一步克隆基因及解析基因功能奠定基础。【方法】本研究选用高抗白粉病资源(自交系‘74’)和感白粉病资源(自交系‘80’)配制杂交组合,构建F_1、F_2群体,利用单囊壳白粉菌鉴定亲本及群体白粉病抗性并进行遗传分析;采用BSA-seq的方法对黄瓜白粉病抗性基因进行初步定位,在此基础上在候选区段开发分子标记,进一步精细定位白粉病抗性基因。【结果】分离群体单株表型鉴定结果表明,自交系74的抗性是由不完全隐性基因控制的。BSA-seq技术初步将抗性基因定位于5号染色体15—25 Mb位置,命名为PM 74。最终,利用分子标记将抗性基因定位于SSR15321和SSR07531之间,遗传距离为3.06 c M,物理距离为238 444 bp,可解释41.95%的表型变异。生物信息学分析表明在候选区段内包含有17个候选基因,其中Cucsa.275630为TIR-NBS-LRR类基因。【结论】本研究将黄瓜白粉病抗性基因精细定位到约238 kb的候选区段内,区段内包含有一个TIR-NBS-LRR基因,该基因将是今后研究的重点候选基因。     

Genomics-assisted breeding——A revolutionary strategy for crop improvement

Food shortages arise more frequently owing to unpredictable crop yield losses caused by biotic and abiotic stresses. With advances in molecular biology and marker technology, a new era of molecular breeding has emerged that has greatly accelerated the pace of plant breeding. High-throughput genotyping technology and phenotyping platforms have enabled large-scale marker-trait association analysis, such as genome-wide association studies, to precisely dissect the genetic architecture of plant traits. Large-scale mapping of agronomically important quantitative trait loci, gene cloning and characterization, mining of elite alleles/haplotypes, exploitation of natural variations, and genomic selection have paved the way towards genomics-assisted breeding(GAB). With the availability of more and more informative genomic datasets, GAB would become a promising technique to expedite the breeding cycle for crop improvement.