1前言
分子标记广泛应用于植物遗传育种研究，对基因或染色体片段的标记辅助选择有利于提高品种选育的效率(Francia et al., 2005)。根据质量性状基因在遗传图谱中的位置，利用分子标记能对其进行分离(Jander et al., 2002)，而对于受多因子控制的性状，通过分子标记可鉴定每个因子，包括遗传因子和环境因子(Cooper et al., 2009)。此外，在植物遗传研究中，分子标记也常用于分析群体结构、进化关系以及模式植物全基因组水平的个体遗传结构(Bomblies and Weigel, 2007)。

近年来，单核苷酸多态性(single nucleotide polymorphism, SNP)研究备受关注(Shi et al., 2009)。由于个体间核苷酸序列存在很大差异，SNP的数量几乎是无限的，且每个SNP可能是潜在的有用标记。SNP标记的潜力已在人类基因分型中得到很好的展示。随着科研经费的大量投入，目前已从人类基因组序列中开发出几百万个SNP标记(International HapMap Consortium et al., 2007)，并发展出能同时检测上百万个SNP位点的技术。这使得通过全基因组扫描分析特定性状与标记的关联性成为可能，也就是所谓的全基因组扫描(whole-genome scanning, WGS)、全基因组关联分析(genome-wide association studies, GWAS)、或关联遗传学(association genetics) (McCarthy et al., 2008)。 

SNP标记已广泛应用于人类和动物基因组分析，但在植物上仍处于起步阶段。植物关联分析要求同时检测上千个标记和成百上千个群体单株，除水稻、拟南芥和玉米外，其他植物尚没有在关联作图群体中大规模检测SNP报道(Huang et al., 2010; Li et al., 2010; Poland et al., 2011) 。

2SNP开发技术
当前已有几种技术用于大规模植物SNP的开发。下面章节将在总结相关SNP论文的基础上讨论这些技术在模式植物和模式作物中的应用性、需求性及极限性。

2.1基于EST序列数据开发SNP
随着测序效率的不断提高，现已在多个作物获得大量EST序列。当前NCBI EST数据库(URL:http://www.ncbi.nlm.nih.gov/dbEST)收录的作物EST序列少的不到10 000条，多则达上百万条。截止2011年7月15日，GenBank收录的模式植物拟南芥EST序列达到1 529 700条，模式作物水稻EST序列1 252 989条。EST序列主要通过国际合作产生，且其供体大多由少数几个品系组成，因此可直接用于SNP的开发。基因组纯合的自花授粉作物，如拟南芥(Schmid et al., 2003)、水稻等，可通过比较不同品系间EST序列鉴定SNP位点。而针对基因组高度杂合的异花授粉作物，利用生物信息学方法则可直接从单个品系的EST序列中开发SNP (Pavy et al., 2006)。尽管利用EST序列开发SNP优点大，但缺点却比优点多几倍。首先是EST序列质量不高(通常EST的Phred值≈20，意味着平均每100 bp序列产生1个碱基的错误)。为确保SNP的可靠性，用于SNP分析的EST簇至少包含几个EST序列。其次，除均一化文库外，由于基因表达水平不同，每个文库中可用于比对的EST序列数量有限。最后，如何区分直系同源序列(来自同一个基因)和旁系同源序列(来自相关基因或基因家族)是个棘手的问题。

由于上述缺点，通过EST序列开发的SNP数量少，且准确率不高(50%~85%)。利用EST序列开发SNP标记的植物包括拟南芥(Schmid et al., 2003)、玉米(Batley et al., 2003)、大麦(Kota et al., 2003)、番茄(Yamamoto et al., 2005)、豇豆(Muchero et al., 2009)、甜瓜(Deleu et al., 2009) 、鳗草(Ferber et al., 2008)、苹果(Chagné et al., 2008)和松树(Dantec et al., 2004)。

2.2利用微阵列芯片开发SNP
开发SNP的另一个策略是大量采用来自不同基因的EST序列设计寡核苷酸微阵列芯片。微阵列芯片不仅能检测个体基因表达水平，还能与不同个体的cDNA或DNA杂交，根据结果差异开发SNP，即所谓的SFPs (single feature polymorphisms)。短片段寡核苷酸微阵列芯片能灵敏检测到序列的变异，尤其是寡核苷酸探针中间位置所检测的序列。与利用EST序列开发SNP比较，微阵列芯片能够在表达水平上无偏差地分析大量基因(10 000~20 000)。利用微阵列芯片已在拟南芥(Borevitz et al., 2003; Borevitz et al., 2007; Singer et al., 2006)、水稻(Kumar et al., 2007)、小麦(Bernardo et al., 2009)、大麦(Cui et al., 2005; Rostoks et al., 2005)、桉树(Neves et al., 2011)、番茄(Sim et al., 2009)、大豆(O'Rourke et al., 2009)和玉米(Krist et al., 2006)上鉴定出大量SFPs。微阵列芯片除适用于提供核苷酸序列的物种，还可用于基因序列多态性低的近缘物种。现已利用大豆基因组微阵列芯片成功从豇豆中开发出SFPs (Das et al., 2008)。尽管微阵列芯片开发SNP存在诸多优点，但也存在高假阳性率(25%-50%)的缺点，这是由于芯片与大基因组物种核酸杂交容易出错造成。解决途径是采用一系列降低基因组复杂度的方法，如甲基化过滤法(methyl filtration)、c₀t-过滤法(c₀t-filtration)、源自mRNA的cRNA或AFLP法。但经过处理后SFPs假阳性率仍高达20%，只有部分高度可信(Gore et al., 2007)。

2.3扩增子重测序开发SNP
该方法主要用于人类单倍型遗传变异研究(URL: http://www.hapmap.org)。它包括设计引物(用于扩增基因、ESTs或其他单拷贝基因组序列片段)、全测序PCR产物(扩增一系列代表品系)、序列比对三个步骤。此法的优点是扩增子通过双向测序后，SNP假阳性率通常低于5%。其他优点还包括：当测序片段足够大时，除开发SNP外，还可鉴定单倍型；可准确区分来自直系同源序列和旁系同源序列的SNP；可估计种质资源中SNP位点的等位频率。此法的主要缺点是所分析基因数量多时工作量大，这是由于每个受检测基因均需设计一对特异引物，同时需要扩增和测序大量品系。扩增子重测序在玉米上应用最广，现已从玉米的一套品系中测序几千个基因(Wright et al., 2005; Yamasaki et al., 2005; Yan et al., 2009)，相关数据可从Panzea 数据库(URL: http://www.panzea.org)获得。国外种子公司已对超过10 000个基因和5 000个玉米品系进行扩增子重测序(Beló et al., 2008)。除玉米外，大豆中有关扩增子重测序的研究也较多，目前已从大豆中获得4240个扩增子(Choi et al., 2007)。其他采用扩增子重测序方法开发SNP且所检测基因数量达几百个的植物包括拟南芥(Nordborg et al., 2005; Schmid et al., 2005)、水稻(Nasu et al., 2002)、番茄(Van et al., 2007)、甜菜(Schneider et al., 2007)、大麦(Kota et al., 2008)、云杉(Pavy et al., 2008)和油菜(Westermeier et al., 2009; Durstewitz et al., 2010)。

2.4从基因组序列中开发SNP
目前已公布全基因组序列的植物仅有少数，拟南芥是第一个完成全基因组测序的植物(The Arabidopsis Genome Initiative, 2000)，而水稻则是首个公布全基因组序列的作物(International Rice Genome Sequencing Project, 2005)。毛果杨(Tuskan et al., 2006)、葡萄(Jaillon et al., 2007)、番木瓜(Ming et al., 2008)、玉米(Schnable et al., 2009)、大豆(Schmutz et al., 2010)、 高粱(Paterson et al., 2009)、蒺藜苜蓿(http://www.medicago.org/)的全基因组序列虽已公布，但组装尚不完整。其他全基因组测序即将完成的作物还包括短柄草、木薯、番茄、马铃薯和百脉根。利用已测序的基因组大规模开发SNP的方法有几种。对于杂合体如毛果杨，其测序数据包含两套基因组序列，可直接从单个品系的基因组序列中挖掘SNP。针对水稻(Yu et al., 2005)和葡萄(Velasco et al., 2007)等纯合体，则需要同时测序两个不同品系，根据两者基因组序列差异鉴定SNP (Shen et al., 2004; Feltus et al., 2004)。利用拟南芥Col-0基因组序列，Clark等开发出拟南芥基因组重测序芯片，并被成功用于拟南芥SNP标记开发(Clark et al., 2007; Zeller et al., 2008)，McNally等也成功利用水稻重测序芯片分析水稻地方种与栽培品种的SNP遗传变异(McNally et al., 2009)。

2.5利用第二代测序技术开发SNP
如何迅速挖掘大量SNP，人们对第二代高通量基因组测序技术(454、Solexa、SOLiD)寄予厚望。由于每个run能产生几亿到几十亿碱基序列数据，利用第二代测序技术能够以非常低廉的价格开发大量SNP (Mardis, 2008)。上述方法已应用于拟南芥(Ossowski et al., 2008)、水稻(Arai-Kichise et al., 2011)、大豆(Wu et al., 2011; Hyten et al., 2010)、高粱(Nelson et al., 2011)和毛果杨(Geraldes et al., 2011)等完全测序的物种。而对于其他未完成测序的物种，尽管已取得一些进展(Han et al., 2011; You et al., 2011)，但仍处于起步阶段。为了用足够的冗余序列开发可信SNP，通常要求在不影响测序通量的前提下，将供测DNA序列的复杂度降低到相当水平(占基因组的1/10至1/100)。此法已成功从玉米(Barbazuk et al., 2007)和桉树(Novaes et al., 2008)中开发出数量庞大的SNP，其假阳性率大概为20%。另一个减少序列复杂性的方法是利用AFLP技术从不同个体中选择特定的限制片段进行扩增(Van et al., 2007)，所得SNP假阳性率约25%。

2.6多倍体植物SNP的开发
遗传研究表明，许多植物并非只拥有单纯的二倍体遗传背景，多倍化现象普通存在，例如四倍体的棉花(Gossypium hirsutum)、油菜(Brassica napus)、花生(Arachis hypogea)和烟草(Nicotiana tabacum)，六倍体的小麦(Triticum aestivum)。其他植物如甘蔗和马铃薯则是高度杂合的同源多倍体，通常含有4个或更多个基因组拷贝。上述介绍用于鉴定二倍体植物SNP的方法部分已在多倍体植物中应用，特别是同源多倍体。由于直系同源序列间的差异足以作为真实的SNP，通过扫描大量同源多倍体ESTs序列可从中鉴定SNP (Cordeiro et al., 2006; Tang et al., 2006)。扩增子重测序方法在不同DNA剂量上检测SNP均足够灵敏，因此也可用于同源多倍体植物SNP的开发(Simko et al., 2006; Li et al., 2008)。微阵列芯片杂交则只能鉴定个体间完全不同的SNP(例如某一个体全套基因组上某一位点上的碱基序列均为A，而另一个体对应的位点为G)，而难于鉴定杂合性多倍体的SNP。与同源多倍体相比，异源多倍体SNP的开发则更加复杂，因为必须区分基因组之间(无用)和基因组之内的SNP。尽管在某些情况下有办法区分异源多倍体中不同基因组间的EST序列(Somers et al., 2003; Trick et al., 2009)，然而这是一个复杂的过程，需要熟练掌握生物信息学知识并分析不同个体间大量的EST序列。当前异源多倍体植物SNP开发方法主要采用扩增子测序。在异源四倍体植物如油菜(Brassica napus)中，由于两套基因组(A和C)序列差异小，其SNP的开发可效仿同源多倍体植物，同时扩增A和C基因组并直接测序PCR产物(Westermeier et al., 2009)。另一个鉴定油菜SNP的途径是利用二倍体祖先种(如Brassica rapa和Brassica oleracea) (Durstewitz et al., 2010)。然而，由于多倍化通常与遗传瓶颈关联，祖先二倍体基因组往往比四倍体含有更多的遗传变异，这无疑增加SNP开发的难度。而对于其他物种如六倍体小麦，直接对三套基因组的扩增子测序是不够的，因为基因组间存在的插入/缺失使测序结果分析困难，甚至无法分析。对此，变通的方法是采用基因组特异引物进行扩增子测序(增序列只来自其中的一套基因组) (Ganal et al., 2007)。此法已在几个小麦SNP鉴定的项目中实施，现已设计出几千对基因组特异性引物(URL: http://wheat.pw.usda.gov/SNP)用于扩增子测序和小麦品种间的SNP分析(Ravel et al., 2006; Chao et al., 2009)。

3问题与展望
在SNP开发过程中，为了避免由于资源库遗传背景狭窄所造成的测量偏倚，必须仔细挑选一套具有代表性的材料。只从少数几个感兴趣的品系或带有不同等位基因频率的材料中鉴定出的SNP可能在其他与之差异明显的资源中没有多态性或者用处不大。通过大量扩增子测序并结合品系混合基因池测序可在最大程度上避免测量偏倚，后者的目的在于估计等位基因频率。将来，利用第二代测序技术能够在一个特定的资源库中同时分析大量品系，届时等位基因频率能被可靠地估算。

目前，不管从整个基因组或者只针对基因的编码区进行大规模SNP开发仍面临很大挑战，因为完成主要作物的全基因组测序还需要一定时间。例如，虽然现在玉米基因组的序列草图已经可用(URL: http://www.maizesequence.org)，但为完成剩余序列的测序，至少仍需要1~2年甚至更长时间才能够得到高质量的玉米全基因组序列，而对于像大麦和小麦等基因组大于5 pg的作物，将需要花费更多时间。

由于全基因组测序只是大规模SNP鉴定的开始，在主要二倍体作物中通过测序几个个体去获得详细的SNP数据将需要更长时间。而对尚未完成全基因组测序的植物，大规模鉴定SNP的最可靠方法仍是扩增并测序尽可能多的基因。对于已获得完整全基因组序列的植物，利用第二代测序技术对全基因组进行重测序是大规模开发SNP并进行全基因组关联分析的不二选择。最近在拟南芥(Atwell et al., 2010)和水稻(Huang et al., 2010)上的两个研究成果已充分展示全基因组重测序结合第二代测序技术的强大能量。Huang等(2010)采用第二代测序技术Solexa对517个水稻地方品种进行全基因组重测序，从中鉴定出大约360万个SNP位点，构建了超高密度的水稻单倍型图谱，并在此基础上对14个农艺性状进行全基因组关联分析。该研究标示着水稻全基因组关联作图时代的到来。

除了前面提到的SNP开发方法之外，目前人们正对一种涉及序列捕获的SNP鉴定新方法颇感兴趣。这种方法已成功用于探测人类基因组外显子区域的SNP (Hodges et al., 2007)。其原理是利用基因序列(如外显子)合成芯片，并通过与基因组总DNA杂交富集目的DNA，接着用第二代测序技术测序。最后以芯片上的序列为参考序列，快速而有效地鉴定大量SNP。然而，此法迄今尚未在植物上应用。由于该法同样能捕获旁系同源序列，它在直系同源序列中鉴定SNP的成效如何尚不清楚，将其应用于异源多倍体或古多倍体(如玉米)则更具挑战性。

随着基因分型芯片平行分析SNP的数量(10 000~60 000)不断增加，精确测序显得格外重要。为开发成千上万个伴随着25%~50%误差率或者没有单倍型信息的SNP而设计芯片是不明智的，因为用于鉴定假阳性SNP或者来自同一单倍型的几个SNP的费用比利用可靠但不高效的SNP鉴定方法多花的费用还高。就此而言，先进的生物信息学算法和高精度测序将和第二代测序技术一样变得非常重要。

4结语
尽管当前几种大规模SNP开发方法被证明行之有效，在第二代测序技术的推动下，多数植物的SNP开发速度也将加快，但在SNP大规模用于关联分析和育种研究之前，仍存在许多需要解决的难题。由于短期内无法获得主要农作物的完整全基因组序列，SNP开发应主要通过分析尽可能多的品系和基因。即使缺乏全基因组序列，利用扩增子重测序或者序列捕获技术并结合第二代测序技术，我们仍将能够在几年时间内从一种作物30 000~60 000个基因中鉴定出SNP或单倍型。此外，我们的重点应该放在能反映育种材料真正遗传变异的SNP开发上，经过验证的SNP可通过作图群体进行精确定位。

目前，许多作物上大范围的SNP分析仍基于个体型SNP。将来，为了像分析人类基因组一样更有效地进行关联分析，需要转向单倍型特异性SNP的开发。一旦作物单倍型特异SNP鉴定出来，将能在全基因组水平上详细分析种质资源，高效地进行SNP标记与植物性状的关联分析，并最终在育种上有效地利用植物的遗传多样性。

作者贡献
洪彦彬参与题目选定、初稿撰写与修改润色；李杏瑜参与资料的收集及稿件格式的修改；梁炫强参与总体思路和文章结构的确立、文章结构修改、文字润色。全体作者都阅读并同意最终的文本。

致谢
本研究由国家自然科学基金项目(30900907、30971819)、广东省自然科学基金项目(9151007010000001)和粤港关键领域重点突破项目(2008A024200009)资助。

参考文献
Arai-Kichise Y., Shiwa Y., Nagasaki H., Ebana K., Yoshikawa H., Yano M., and Wakasa K., 2011, Discovery of genome-wide DNA polymorphisms in a landrace cultivar of Japonica rice by whole-genome sequencing, Plant Cell Physiol., 52(2): 274-282
http://dx.doi.org/10.1093/pcp/pcr003
PMid:21258067 PMCid:3037082

Atwell S., Huang Y.S., Vilhjálmsson B.J., Willems G., Horton M., Li Y., Meng D., Platt A., Tarone A.M., Hu T.T., Jiang R., Muliyati N.W., Zhang X., Amer M.A., Baxter I., Brachi B., Chory J., Dean C., Debieu M., de Meaux J., Ecker J.R., Faure N., Kniskern J.M., Jones J.D., Michael T., Nemri A., Roux F., Salt D.E., Tang C., Todesco M., Traw M.B., Weigel D., Marjoram P., Borevitz J.O., Bergelson J., and Nordborg M., 2010, Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines, Nature, 465(7298): 627-631
http://dx.doi.org/10.1038/nature08800
PMid:20336072 PMCid:3023908

Barbazuk W.B., Emrich S.J., Chen H.D., and Schnable P.S., 2007, SNP discovery via 454 transcriptome sequencing, Plant J., 51(5): 910-918
http://dx.doi.org/10.1111/j.1365-313X.2007.03193.x
PMid:17662031 PMCid:2169515

Batley J., Barker G., O’Sullivan H., Edwards K.J., and Edwards D., 2003, Mining for single nucleotide polymorphisms in insertions/deletions in maize expressed sequence tag data, Plant Physiol., 132(1): 84-91
http://dx.doi.org/10.1104/pp.102.019422
PMid:12746514 PMCid:166954

Beló A., Zheng P., Luck S., Shen B., Meyer D.J., Li B., Tingey S., and Rafalski A., 2008, Whole genome scan detects an allelic variant of fad2 associated with increased oleic acid levels in maize, Mol. Genet. Genomics, 279(1): 1-10
http://dx.doi.org/10.1007/s00438-007-0289-y
PMid:17934760

Bernardo A.N., Bradbury P.J., Ma H., Hu S., Bowden R.L., Buckler E.S., and Bai G., 2009, Discovery and mapping of single feature polymorphisms in wheat using Affymetrix arrays, BMC Genomics, 10: 251
http://dx.doi.org/10.1186/1471-2164-10-251
PMid:19480702 PMCid:2698007

Bomblies K., and Weigel D., 2007, Arabidopsis: a model genus for speciation, Curr. Opin. Genet. Dev., 17(6): 500-504
http://dx.doi.org/10.1016/j.gde.2007.09.006

Borevitz J.O., Hazen S.P., Michael T.P., Morris G.P., Baxter I.R., Hu T.T., Chen H., Werner J.D., Nordborg M., Salt D.E., Kay S.A., Chory J., Weigel D., Jones J.D., and Ecker J.R., 2007, Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana, Proc. Natl. Acad. Sci. USA., 104(29): 12057-12062
http://dx.doi.org/10.1073/pnas.0705323104
PMid:17626786 PMCid:1914337

Borevitz J.O., Liang D., Plouffe D., Chang H.S., Zhu T., Weigel D., Berry C.C., Winzeler E., and Chory J., 2003, Large-scale identification of single-feature polymorphisms in complex genomes., Genome Res., 13: 513-523
http://dx.doi.org/10.1101/gr.541303
PMid:12618383 PMCid:430246

Chagné D., Gasic K., Crowhurst R.N., Han Y., Bassett H.C., Bowatte D.R., Lawrence T.J., Rikkerink E.H., Gardiner S.E., and Korban S.S., 2008, Development of a set of SNP markers present in expressed genes of the apple, Genomics, 92(5): 353-358
http://dx.doi.org/10.1016/j.ygeno.2008.07.008
PMid:18721872

Chao S.M., Zhang W.J., Akhunov E., Sherman J., Ma Y.Q., Luo M.C., and Dubcovsky J., 2009, Analysis of gene-derived SNP marker polymorphism in US wheat (Triticum aestivum L.) cultivars, Mol. Breed., 23: 23-33
http://dx.doi.org/10.1007/s11032-008-9210-6

Choi I.Y., Hyten D.L., Matukumalli L.K., Song Q., Chaky J.M., Quigley C.V., Chase K., Lark K.G., Reiter R.S., Yoon M.S., Hwang E.Y., Yi S.I., Young N.D., Shoemaker R.C., van Tassell C.P., Specht J.E., and Cregan P.B., 2007, A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysis, Genetics, 176(1): 686-696
http://dx.doi.org/10.1534/genetics.107.070821
PMid:17339218 PMCid:1893076

Clark C., Schweikert G., Toomajian C., Ossowsksi S., Zeller G., Shinn P., Warthmann N., Hu T., Fu G., Hinds G., Chen H., Frazer K.A., Huson D.H., Schölkopf B., Nordborg M., Rätsch G., Ecker J.R., and Weigel D., 2007, Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana, Science, 317(5836): 338-342
http://dx.doi.org/10.1126/science.1138632
PMid:17641193

Cooper M., van Eeuwijk F.A., Hammer G.L., Podlich D.W., and Messina C., 2009, Modeling QTL for complex traits: detection and context for plant breeding, Curr. Opin. Plant Biol., 12(2): 231-240
http://dx.doi.org/10.1016/j.pbi.2009.01.006
PMid:19282235

Cordeiro G.M., Eliott F., McIntyre C.L., Casu R.E., and Henry R.J., 2006, Characterization of single nucleotide polymorphisms in sugarcane ESTs, Theor. Appl. Genet., 113(2): 331-343
http://dx.doi.org/10.1007/s00122-006-0300-8
PMid:16791699

Cui X., Xu J., Asghar R., Condamine P., Svensson J.T., Wanamaker S., Stein N., Roose M., and Close T.J., 2005, Detecting single feature polymorphisms using oligonucleotide arrays and robustified projection pursuit, Bioinfomatics, 21(20): 3852-3858
http://dx.doi.org/10.1093/bioinformatics/bti640
PMid:16118260

Dantec L.L., Chagne´ D., Pot D., Cantin O., Garnier-Géré P., Bedon F., Frigerio J.M., Chaumell P., Leéger P., Garcia V., Laigret F., De Daruvar A., and Plomion C., 2004, Automated SNP detection in expressed sequence tags: statistical considerations and applications to maritime pine sequences, Plant Mol. Biol., 54(3): 461-470
http://dx.doi.org/10.1023/B:PLAN.0000036376.11710.6f
PMid:15284499

Das S., Bhat P.R., Sudhakar C., Ehlers J.D., Wanamaker S., Roberts P.A., Cui X., and Close T.J., 2008, Detection and validation of single feature polymorphisms in cowpea (Vigna unguiculata L. Walp) using a soybean genome array., BMC Genomics., 9: 107
http://dx.doi.org/10.1186/1471-2164-9-107
PMid:18307807 PMCid:2270837

Deleu W., Esteras C., Roig C., González-To M., Fernández-Silva I., Gonzalez-Ibeas D., Blanca J., Aranda M.A., Arús P., Nuez F., Monforte A.J., Picó M.B., and Garcia-Mas J., 2009, A set of EST-SNPs for map saturation and cultivar identification in melon, BMC Plant Biol., 9: 90
http://dx.doi.org/10.1186/1471-2229-9-90
PMid:19604363 PMCid:2722630

Durstewitz G., Polley A., Plieske J., Luerssen H., Graner E.M., Wieseke R., and Ganal M.W., 2010, SNP discovery by amplicon sequencing and multiplex SNP genotyping in the allopolyploid species Brassica napus, Genome, 53(11): 948-956
PMid:21076510

Feltus F.A., Wan J., Schulze S.R., Estill J.C., Jiang N., and Paterson A.H., 2004, An SNP resource for rice genetics and breeding based on subspecies indica and japonica alignments, Genome Res., 14(9): 1812-1819
http://dx.doi.org/10.1101/gr.2479404
PMid:15342564 PMCid:515328

Ferber S., Reusch T.B., Stam W.T., and Olsen J.L., 2008, Characterization of single nucleotide polymorphism markers for eelgrass (Zostera marina), Mol. Ecol. Resour., 8(6): 1429-1435
http://dx.doi.org/10.1111/j.1755-0998.2008.02251.x
PMid:21586067

Francia E., Tacconi G., Crosatti C., Barabaschi D., Bulgarelli D., Dall’Aglio E., and Valè G., 2005, Marker assisted selection in crop plants, Plant Cell, 82(3): 317-342

Ganal M.W., and Röder M.S., 2007, Microsatellite and SNP markers in wheat breeding, In: Varshney R.K., Tuberosa R.(eds.), Genomic assisted crop improvement: genomics applications in crops, Springer, The Netherlands, pp.1-24.
http://dx.doi.org/10.1007/978-1-4020-6297-1_1

Geraldes A., Pang J., Thiessen N., Cezard T., Moore R., Zhao Y., Tam A., Wang S., Friedmann M., Birol I., Jones S.J., Cronk Q.C., and Douglas C.J., 2011, SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing, Mol. Ecol. Resour., 11(Suppl 1): 81-92
http://dx.doi.org/10.1111/j.1755-0998.2010.02960.x
PMid:21429165

Gore M., Bradbury P., Hogers R., Kirst M., Verstege E., van Oeveren J., Peleman J., Buckler Iv E.S., and van Eijk M., 2007, Evaluation of target preparation methods for single-feature polymorphism detection in large complex plant genomes, Crop Sci., 47: S135-S148
http://dx.doi.org/10.2135/cropsci2007.02.0085tpg

Han Y., Kang Y., Torres-Jerez I., Cheung F., Town C.D., Zhao P.X., Udvardi M.K., and Monteros M.J., 2011, Genome-wide SNP Discovery in Tetraploid Alfalfa Using 454 Sequencing and High Resolution Melting Analysis, BMC Genomics, 12: 1-11
http://dx.doi.org/10.1186/1471-2164-12-350
PMid:21733171 PMCid:3154875

Hodges E., Xuan Z., Balija V., Kramer M., Molla M.N., Smith S.W., Middle C.M., Rodesch M.J., Albert T.J., Hannon G.J., and McCombie W.R., 2007, Genome-wide in situ exon capture for selective resequencing, Nat. Genet., 39(12): 1522-1527
http://dx.doi.org/10.1038/ng.2007.42
PMid:17982454

Huang X.H., Wei X.H., Sang T., Zhao Q., Feng Q., Zhao Y., Li C.Y., Zhu C.R., Lu T.T., Zhang Z.W., Li M., Fan D.L., Guo Y.L., Wang A.H., Wang L., Deng L.W., Li W.J., Lu Y.Q., Weng Q.J., Liu K.Y., Huang T., Zhou T.Y., Jing Y.F., Li W., Lin Z., Buckler E.S., Qian Q., Zhang Q.F., Li J.Y., and Han B., 2010, Genome-wide association studies of 14 agronomic traits in rice landraces, Nat. Genet., 42(11): 961-967
http://dx.doi.org/10.1038/ng.695
PMid:20972439

Hyten D.L., Cannon S.B., Song Q., Weeks N., Fickus E.W., Shoemaker R.C., Specht J.E., Farmer A.D., May G.D., and Cregan P.B., 2010, High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence, BMC Genomics, 11: 38
http://dx.doi.org/10.1186/1471-2164-11-38
PMid:20078886 PMCid:2817691

International HapMap Consortium, Frazer K.A., Ballinger D.G., Cox D.R., Hinds D.A., Stuve L.L., Gibbs R.A., Belmont J.W., Boudreau A., Hardenbolo P., Leal S.M., Pasternak S., Wheeler D.A., Willis T.D., Yu F., Yang H., Zeng C., Gao Y., Hu H., Hu W., Li C., Lin W., Liu S., Pan H., Tang X., Wang J., Wang W., Yu J., Zhang B., Zhang Q., Zhao H., Zhao H., Zhou J., Gabriel S.B., Barry R., Blumenstiel B., Camargo A., Defelice M., Faggart M., Goyette M., Gupta S., Moore J., Nguyen H., Onofrio R.C., Parkin M., Roy J., Stahl E., Winchester E., Ziaugra L., Altshuler D., Shen Y., Yao Z., Huang W., Chu X., He Y., Jin L., Liu Y., Shen Y., Sun W., Wang H., Wang Y., Wang Y., Xiong X., Xu L., Waye M.M., Tsui S.K., Xue H., Wong J.T., Galver L.M., Fan J.B., Gunderson K., Murray S.S., Oliphant A.R., Chee M.S., Montpetit A., Chagnon F., Ferretti V., Leboeuf M., Olivier J.F., Phillips M.S., Roumy S., Sallée C., Verner A., Hudson T.J., Kwok P.Y., Cai D., Koboldt D.C., Miller R.D., Pawlikowska L., Taillon-Miller P., Xiao M., Tsui L.C., Mak W., Song Y.Q., Tam P.K., Nakamura Y., Kawaguchi T., Kitamoto T., Morizono T., Nagashima A., Ohnishi Y., Sekine A., Tanaka T., Tsunoda T., Deloukas P., Bird C.P., Delgado M., Dermitzakis E.T., Gwilliam R., Hunt S., Morrison J., Powell D., Stranger B.E., Whittaker P., Bentley D.R., Daly M.J., de Bakker P.I., Barrett J., Chretien Y.R., Maller J., McCarroll S., Patterson N., Pe'er I., Price A., Purcell S., Richter D.J., Sabeti P., Saxena R., Schaffner S.F., Sham P.C., Varilly P., Altshuler D., Stein L.D., Krishnan L., Smith A.V., Tello-Ruiz M.K., Thorisson G.A., Chakravarti A., Chen P.E., Cutler D.J., Kashuk C.S., Lin S., Abecasis G.R., Guan W., Li Y., Munro H.M., Qin Z.S., Thomas D.J., McVean G., Auton A., Bottolo L., Cardin N., Eyheramendy S., Freeman C., Marchini J., Myers S., Spencer C., Stephens M., Donnelly P., Cardon L.R., Clarke G., Evans D.M., Morris A.P., Weir B.S., Tsunoda T., Mullikin J.C., Sherry S.T., Feolo M., Skol A., Zhang H., Zeng C., Zhao H., Matsuda I., Fukushima Y., Macer D.R., Suda E., Rotimi C.N., Adebamowo C.A., Ajayi I., Aniagwu T., Marshall P.A., Nkwodimmah C., Royal C.D., Leppert M.F., Dixon M., Peiffer A., Qiu R., Kent A., Kato K., Niikawa N., Adewole I.F., Knoppers B.M., Foster M.W., Clayton E.W., Watkin J., Gibbs R.A., Belmont J.W., Muzny D., Nazareth L., Sodergren E., Weinstock G.M., Wheeler D.A., Yakub I., Gabriel S.B., Onofrio R.C., Richter D.J., Ziaugra L., Birren B.W., Daly M.J., Altshuler D., Wilson R.K., Fulton L.L., Rogers J., Burton J., Carter N.P., Clee C.M., Griffiths M., Jones M.C., McLay K., Plumb R.W., Ross M.T., Sims S.K., Willey D.L., Chen Z., Han H., Kang L., Godbout M., Wallenburg J.C., L'Archevêque P., Bellemare G., Saeki K., Wang H., An D., Fu H., Li Q., Wang Z., Wang R., Holden A.L., Brooks L.D., McEwen J.E., Guyer M.S., Wang V.O., Peterson J.L., Shi M., Spiegel J., Sung L.M., Zacharia L.F., Collins F.S., Kennedy K., Jamieson R., and Stewart J., 2007, A second generation human haplotype map of over 3.1 million SNPs, Nature, 449: 851-861

International Rice Genome Sequencing Project, 2005, The map-based sequence of the rice genome, Nature, 436(7052): 793-800
http://dx.doi.org/10.1038/nature03895
PMid:16100779

Jaillon O., Aury J.M., Noel B., Policriti A., Clepet C., Casagrande A., Choisne N., Aubourg S., Vitulo N., Jubin C., Vezzi A., Legeai F., Hugueney P., Dasilva C., Horner D., Mica E., Jublot D., Poulain J., Bruyère C., Billault A., Segurens B., Gouyvenoux M., Ugarte E., Cattonaro F., Anthouard V., Vico V., Del Fabbro C., Alaux M., Di Gaspero G., Dumas V., Felice N., Paillard S., Juman I., Moroldo M., Scalabrin S., Canaguier A., Le Clainche I., Malacrida G., Durand E., Pesole G., Laucou V., Chatelet P., Merdinoglu D., Delledonne M., Pezzotti M., Lecharny A., Scarpelli C., Artiguenave F., Pè M.E., Valle G., Morgante M., Caboche M., Adam-Blondon A.F., Weissenbach J., Quétier F., Wincker P., and French-Italian Public Consortium for Grapevine Genome Characterization., 2007, The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla, Nature, 449(7161): 463-467
http://dx.doi.org/10.1038/nature06148
PMid:17721507

Jander G., Norris S.R., Rounsley S.D., Bush D.F., Levin I.M., and Last R.L., 2002, Arabidopsis map-based cloning in the post-genome era, Plant Physiol., 129(2): 440-450
http://dx.doi.org/10.1104/pp.003533
PMid:12068090 PMCid:1540230

Kota R., Rudd S., Facius A., Kolesov G., Thiel T., Zhang H., Stein N., Mayer K., and Graner A., 2003, Snipping polymorphisms from large EST collections in barley (Hordeum vulgare L.), Mol. Genet. Genomics, 270(1): 24-33
http://dx.doi.org/10.1007/s00438-003-0891-6
PMid:12938038

Kota R., Varshney R.K., Prasad M., Zhang H., Stein N., and Graner A., 2008, EST derived single nucleotide polymorphism markers for assembling genetic and physical maps of the barley genome, Funct. Integr. Genomics, 8(3): 223-233
http://dx.doi.org/10.1007/s10142-007-0060-9

Krist M., Caldo R., Casati P., Tanimoto G., Walbot V., Wise R.P., and Buckler E.S., 2006, Genetic diversity contribution to errors in short oligonucleotide microarray analysis, Plant Biotechnol. J., 4(5): 489-498
PMid:17309725

Kumar R., Qiu J., Joshi T., Valliyodan B., Xu D., and Nguyen H.T., 2007, Single feature polymorphism discovery in rice, PLoS One, 2(3): e284
http://dx.doi.org/10.1371/journal.pone.0000284
PMid:17372626 PMCid:1808426

Li L., Paulo M.J., Strahwald J., Lübeck J., Hofferbert H.R., Tacke E., Junghans H., Wunder J., Draffehn A., van Eeuwijk F., and Gebhardt C., 2008, Natural DNA variation at candidate loci is associated with potato chip color, tuber starch content, yield and starch yield, Theor. Appl. Genet., 116(8): 1167-1181
http://dx.doi.org/10.1007/s00122-008-0746-y
PMid:18379755 PMCid:2358939

Li Y., Huang Y., Bergelson J., Nordborg M., and Borevitz J.O., 2010, Association mapping of local climate-sensitive quantitative trait loci in Arabidopsis thaliana, Proc. Natl. Acad. Sci. USA., 107(49): 21199-21204
http://dx.doi.org/10.1073/pnas.1007431107
PMid:21078970 PMCid:3000268

Mardis E.R., 2008, The impact of next-generation sequencing technology on genetics, Trends Genet., 24(3): 133-141
http://dx.doi.org/10.1016/j.tig.2007.12.007
PMid:18262675 PMCid:2680276

McCarthy M.I., Abecasis G.R., Cardon L.R., Goldstein D.B., Little J., Ioannidis J.P.A., and Hirschhorn J.N., 2008, Genome-wide association studies for complex traits: consensus, uncertainty and challenges, Nat. Rev. Genet., 9: 356-369
http://dx.doi.org/10.1038/nrg2344
PMid:18398418

McNally K.L., Childs K.L., Bohnert R., Davidson R.M., Zhao K., Ulat V.J., Zeller G., Clark R.M., Hoen D.R., Bureau T.E., Stokowski R., Ballinger D.G., Frazer K.A., Cox D.R., Padhukasahasram B., Bustamante C.D., Weigel D., Mackill D.J., Bruskiewich R.M., Rätsch G., Buell C.R., Leung H., and Leach J.E., 2009, Genomewide SNP variation reveals relationships among landraces and modern varieties of rice, Proc. Natl. Acad. Sci. USA., 106(30): 12273-12278
http://dx.doi.org/10.1073/pnas.0900992106
PMid:19597147 PMCid:2718348

Ming R., Hou S., Feng Y., Yu Q., Dionne-Laporte A., Saw J.H., Senin P., Wang W., Ly B.V., Lewis K.L. Salzberg S.L., Feng L., Jones M.R., Skelton R.L., Murray J.E., Chen C., Qian W., Shen J., Du P., Eustice M., Tong E., Tang H., Lyons E., Paull R.E., Michael T.P., Wall K., Rice D.W., Albert H., Wang M.L., Zhu Y.J., Schatz M., Nagarajan N., Acob R.A., Guan P., Blas A., Wai C.M., Ackerman C.M., Ren Y., Liu C., Wang J., Wang J., Na J.K., Shakirov E.V., Haas B., Thimmapuram J., Nelson D., Wang X., Bowers J.E., Gschwend A.R., Delcher A.L., Singh R., Suzuki J.Y., Tripathi S., Neupane K., Wei H., Irikura B., Paidi M., Jiang N., Zhang W., Presting G., Windsor A., Navajas-Pérez R., Torres M.J., Feltus F.A., Porter B., Li Y., Burroughs A.M., Luo M.C., Liu L., Christopher D.A., Mount S.M., Moore P.H., Sugimura T., Jiang J., Schuler M.A., Friedman V., Mitchell-Olds T., Shippen D.E., dePamphilis C.W., Palmer J.D., Freeling M., Paterson A.H., Gonsalves D., Wang L., and Alam M., 2008, The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus), Nature, 452(7190): 991-996
http://dx.doi.org/10.1038/nature06856
PMid:18432245 PMCid:2836516

Muchero W., Diop N.N., Bhat P.R., Fenton R.D., Wanamaker S., Pottorff M., Hearne S., Cisse N., Fatokun C., Ehlers J.D., Roberts P.A., and Close T.J., 2009, A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs, Proc. Natl. Acad. Sci. USA., 106(43): 18159-18164
http://dx.doi.org/10.1073/pnas.0905886106
PMid:19826088 PMCid:2761239

Nasu S., Suzuki J., Ohta R., Hasegawa K., Yui R., Kitazawa N., Monna L., and Minobe Y., 2002, Search for and analysis of single nucleotide polymorphisms (SNPs) in rice (Oryza sativa, Oryza rufipogon) and establishment of SNP markers, DNA Res., 9(5): 163-171
http://dx.doi.org/10.1093/dnares/9.5.163
PMid:12465716

Nelson J.C., Wang S., Wu Y., Li X., Antony G., White F.F., and Yu J., 2011, Single-nucleotide polymorphism discovery by high-throughput sequencing in sorghum, BMC Genomics, 12: 352
http://dx.doi.org/10.1186/1471-2164-12-352
PMid:21736744 PMCid:3146956

Neves L.G., Mc Mamani E., Alfenas A.C., Kirst M., and Grattapaglia D., 2011, A high-density transcript linkage map with 1 845 expressed genes positioned by microarray-based Single Feature Polymorphisms (SFP) in Eucalyptus, BMC Genomics, 12: 189
http://dx.doi.org/10.1186/1471-2164-12-189
PMid:21492453 PMCid:3090358

Nordborg M., Hu T.T., Ishino Y., Jhaveri J., Toomajian C., Zheng H., Bakker E., Calabrese P., Gladstone J., Goyal R., Jakobsson M., Kim S., Morozov Y., Padhukasahasram B., Plagnol V., Rosenberg N.A., Shah C., Wall J.D., Wang J., Zhao K., Kalbfleisch T., Schulz V., Kreitman M., and Bergelson J., 2005, The pattern of polymorphism in Arabidopsis thaliana., PLoS Biol., 3(7): e196
http://dx.doi.org/10.1371/journal.pbio.0030196
PMid:15907155 PMCid:1135296

Novaes E., Drost D.R., Farmerie W.G., Pappas G.J. Jr, Grattapaglia D., Sederoff R.R., and Kirst M., 2008, High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome, BMC Genomics, 9: 312
http://dx.doi.org/10.1186/1471-2164-9-312
PMid:18590545 PMCid:2483731

O'Rourke J.A., Nelson R.T., Grant D., Schmutz J., Grimwood J., Cannon S., Vance C.P., Graham M.A., snd Shoemaker R.C., 2009, Integrating microarray analysis and the soybean genome to understand the soybeans iron deficiency response, BMC Genomics., 10: 376
http://dx.doi.org/10.1186/1471-2164-10-376
PMid:19678937 PMCid:2907705

Ossowski S., Schneeberger K., Clark R.M., Lanz C., Warthmann N., and Weigel D., 2008, Sequencing of natural strains of Arabidopsis thaliana with short reads, Genome Res., 18(12): 2024-2033
http://dx.doi.org/10.1101/gr.080200.108
PMid:18818371 PMCid:2593571

Paterson A.H., Bowers J.E., Bruggmann R., Dubchak I., Grimwood J., Gundlach H., Haberer G., Hellsten U., Mitros T., Poliakov A., Schmutz J., Spannagl M., Tang H., Wang X., Wicker T., Bharti A.K., Chapman J., Feltus F.A., Gowik U., Grigoriev I.V., Lyons E., Maher C.A., Martis M., Narechania A., Otillar R.P., Penning B.W., Salamov A.A., Wang Y., Zhang L., Carpita N.C., Freeling M., Gingle A.R., Hash C.T., Keller B., Klein P., Kresovich S., McCann M.C., Ming R., Peterson D.G., Mehboob-ur-Rahman, Ware D., Westhoff P., Mayer K.F., Messing J., and Rokhsar D.S., 2009, The Sorghum bicolor genome and the diversification of grasses, Nature, 457(7229): 551-556
http://dx.doi.org/10.1038/nature07723
PMid:19189423

Pavy N., Parsons L.S., Paule C., MacKay J., and Bousquet J., 2006, Automated SNP detection from a large collection of white spruce expressed sequences: contributing factors and approaches for the categorization of SNPs, BMC Genomics, 7: 174
http://dx.doi.org/10.1186/1471-2164-7-174
PMid:16824208 PMCid:1557672

Pavy N., Pelgas B., Beauseigle S., Blais S., Gagnon F., Gosselin I., Lamothe M., Isabel N., and Bousquet J., 2008, Enhancing genetic mapping of complex genomes through the design of highly-multiplexed SNP arrays: application to the large and unsequenced genomes of white and black spruce, BMC Genomics, 9: 21
http://dx.doi.org/10.1186/1471-2164-9-21
PMid:18205909 PMCid:2246113

Poland J.A., Bradbury P.J., Buckler E.S., and Nelson R.J., 2011, Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize, Proc. Natl. Acad. Sci. USA., 108(17): 6893-6898
http://dx.doi.org/10.1073/pnas.1010894108
PMid:21482771

Ravel C., Praud S., Murigneux A., Canaguier A., Sapet F., Samson D., Balfourier F., Dufour P., Chalhoub B., Brunel D., Beckert M., and Charmet G., 2006, Single nucleotide polymorphism frequency in a set of selected lines of bread wheat (Triticum aestivum L.), Genome, 49(9): 1131-1139
http://dx.doi.org/10.1139/g06-067
PMid:17110993

Rostoks N., Borevitz J.O., Hedley P.E., Russell J., Mudies S., Morris J., Cardie L., Marshall D.F., and Waugh R., 2005, Single-feature polymorphism discovery in the barley transcriptome, Genome Biol., 6(6): R54
http://dx.doi.org/10.1186/gb-2005-6-6-r54
PMid:15960806 PMCid:1175974

Schmid K.J., Ramos-Onsins S., Ringys-Beckstein H., Weisshaar B., and Mitchell-Olds T., 2005, A multilocus sequence survey in Arabidopsis thaliana reveals a genome-wide departure from a neutral model of DNA sequence polymorphism, Genetics, 169(3): 1601-1615.
http://dx.doi.org/10.1534/genetics.104.033795
PMid:15654111 PMCid:1449538

Schmid K.J., Sorensen T.R., Stracke R., Torjek O., Altmann T., Mitchell-Olds T., and Weisshaar B., 2003, Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana, Genome Res., 13: 1250-1257.
http://dx.doi.org/10.1101/gr.728603
PMid:12799357 PMCid:403656

Schmutz J., Cannon S.B., Schlueter J., Ma J., Mitros T., Nelson W., Hyten D.L., Song Q., Thelen J.J., Cheng J., Xu D., Hellsten U., May G.D., Yu Y., Sakurai T., Umezawa T., Bhattacharyya M.K., Sandhu D., Valliyodan B., Lindquist E., Peto M., Grant D., Shu S., Goodstein D., Barry K., Futrell-Griggs M., Abernathy B., Du J., Tian Z., Zhu L., Gill N., Joshi T., Libault M., Sethuraman A., Zhang X.C., Shinozaki K., Nguyen H.T., Wing R.A., Cregan P., Specht J., Grimwood J., Rokhsar D., Stacey G., Shoemaker R.C., and Jackson S.A., 2010, Genome sequence of the palaeopolyploid soybean, Nature, 463(7278): 178-183
http://dx.doi.org/10.1038/nature08670
PMid:20075913

Schnable P.S., Ware D., Fulton R.S., Stein J.C., Wei F., Pasternak S., Liang C., Zhang J., Fulton L., Graves T.A., Minx P., Reily A.D., Courtney L., Kruchowski S.S., Tomlinson C., Strong C., Delehaunty K., Fronick C. Courtney B., Rock S.M., Belter E., Du F., Kim K., Abbott R.M., Cotton M., Levy A., Marchetto P., Ochoa K., Jackson S.M., Gillam B., Chen W., Yan L., Higginbotham J., Cardenas M., Waligorski J., Applebaum E., Phelps L., Falcone J., Kanchi K., Thane T., Scimone A., Thane N., Henke J., Wang T., Ruppert J., Shah N., Rotter K., Hodges J., Ingenthron E., Cordes M., Kohlberg S., Sgro J., Delgado B., Mead K., Chinwalla A., Leonard S., Crouse K., Collura K., Kudrna D., Currie J., He R., Angelova A., Rajasekar S., Mueller T., Lomeli R., Scara G., Ko A., Delaney K., Wissotski M., Lopez G., Campos D., Braidotti M., Ashley E., Golser W., Kim H., Lee S., Lin J., Dujmic Z., Kim W., Talag J., Zuccolo A., Fan C., Sebastian A., Kramer M., Spiegel L., Nascimento L., Zutavern T., Miller B., Ambroise C., Muller S., Spooner W., Narechania A., Ren L., Wei S., Kumari S., Faga B., Levy M.J., McMahan L., Van Buren P., Vaughn M.W., Ying K., Yeh C.T., Emrich S.J., Jia Y., Kalyanaraman A., Hsia A.P., Barbazuk W.B., Baucom R.S., Brutnell T.P., Carpita N.C., Chaparro C., Chia J.M., Deragon J.M., Estill J.C., Fu Y., Jeddeloh J.A., Han Y., Lee H., Li P., Lisch D.R., Liu S., Liu Z., Nagel D.H., McCann M.C., SanMiguel P., Myers A.M., Nettleton D., Nguyen J., Penning B.W., Ponnala L., Schneider K.L., Schwartz D.C., Sharma A., Soderlund C., Springer N.M., Sun Q., Wang H., Waterman M., Westerman R., Wolfgruber T.K., Yang L., Yu Y., Zhang L., Zhou S., Zhu Q., Bennetzen J.L., Dawe R.K., Jiang J., Jiang N., Presting G.G., Wessler S.R., Aluru S., Martienssen R.A., Clifton S.W., McCombie W.R., Wing R.A., and Wilson R.K., 2009, The B73 maize genome: complexity, diversity, and dynamics, Science, 326(5956): 1112-1115
http://dx.doi.org/10.1126/science.1178534
PMid:19965430

Schneider K., Kulosa D., Soerensen T.R., Möhring S., Heine M., Durstewitz G., Polley A., Weber E., Jamsari, Lein J., Hohmann U., Tahiro E., Weisshaar B., Schulz B., Koch G., Jung C., and Ganal M., 2007, Analysis of DNA polymorphisms in sugar beet (Beta vulgaris L.) and development of an SNP-based map of expressed genes, Theor. Appl. Genet., 115(5): 601-615
http://dx.doi.org/10.1007/s00122-007-0591-4
PMid:17622508

Shen Y.J., Jiang H., Jin J.P., Zhang Z.B., Xi B., He Y.Y., Wang G., Wang C., Qian L., Li X., Yu Q.B., Liu H.J., Chen D.H., Gao J.H., Huang H., Shi T.L., and Yang Z.N., 2004, Development of genome-wide DNA polymorphism database for map-based cloning of rice genes, Plant Physiol., 135(3): 1198-1205
http://dx.doi.org/10.1104/pp.103.038463
PMid:15266053 PMCid:519040

Shi J., Wang Y., and Huang W., 2009, Development and application of genotyping technologies, Science in China Series C: Life Sciences, 52(1): 17-23
http://dx.doi.org/10.1007/s11427-009-0011-x
PMid:19152080

Sim S.C., Robbins M.D., Chilcott C., Zhu T., and Francis D.M., 2009, Oligonucleotide array discovery of polymorphisms in cultivated tomato (Solanum lycopersicum L.) reveals patterns of SNP variation associated with breeding, BMC Genomics., 10: 466
http://dx.doi.org/10.1186/1471-2164-10-466
PMid:19818135 PMCid:2763011

Simko I., Haynes K.G., and Jones R.W., 2006, Assessment of linkage disequilibrium in potato genome with single nucleotide polymorphism markers, Genetics, 173(4): 2237-2245
http://dx.doi.org/10.1534/genetics.106.060905
PMid:16783002 PMCid:1569688

Singer T., Fan Y., Chang H.S., Zhu T., Hazen S.P., and Briggs S.P., 2006, A high resolution map of Arabidopsis recombinant inbred lines by whole-genome exon array hybridization, PLoS Genet., 2(9): e144
http://dx.doi.org/10.1371/journal.pgen.0020144
PMid:17044735 PMCid:1564425

Somers D.J., Kirkpatrick R., Moniwa M., and Walsh A., 2003, Mining singlenucleotide polymorphisms from hexaploid wheat ESTs, Genome, 46(3): 431-437
http://dx.doi.org/10.1139/g03-027
PMid:12834059

Tang J., Vosman B., Voorrips R.E., van der Linden C.G., and Leunissen J.A., 2006, QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species, BMC Bioinformatics., 7: 438
http://dx.doi.org/10.1186/1471-2105-7-95
PMid:16504159 PMCid:1409801

http://dx.doi.org/10.1186/1471-2105-7-438
PMid:17029635 PMCid:1618865

The Arabidopsis Genome Initiative, 2000, Analysis of the genome sequence of the flowering plant Arabidopsis thaliana, Nature, 408(6814): 796-815
http://dx.doi.org/10.1038/35048692
PMid:11130711

Trick M., Long Y., Meng J., and Bancroft I., 2009, Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing, Plant Biotechnol. J., 7(4): 334-346
http://dx.doi.org/10.1111/j.1467-7652.2008.00396.x
PMid:19207216

Tuskan G.A., Difazio S., Jansson S., Bohlmann J., Grigoriev I., Hellsten U., Putnam N., Ralph S., Rombauts S., Salamov A., Schein J., Sterck L., Aerts A., Bhalerao R.R., Bhalerao R.P., Blaudez D., Boerjan W., Brun A., Brunner A., Busov V., Campbell M., Carlson J., Chalot M., Chapman J., Chen G.L., Cooper D., Coutinho P.M., Couturier J., Covert S., Cronk Q., Cunningham R., Davis J., Degroeve S., Déjardin A., Depamphilis C., Detter J., Dirks B., Dubchak I., Duplessis S., Ehlting J., Ellis B., Gendler K., Goodstein D., Gribskov M., Grimwood J., Groover A., Gunter L., Hamberger B., Heinze B., Helariutta Y., Henrissat B., Holligan D., Holt R., Huang W., Islam-Faridi N., Jones S., Jones-Rhoades M., Jorgensen R., Joshi C., Kangasjärvi J., Karlsson J., Kelleher C., Kirkpatrick R., Kirst M., Kohler A., Kalluri U., Larimer F., Leebens-Mack J., Leplé J.C., Locascio P., Lou Y., Lucas S., Martin F., Montanini B., Napoli C., Nelson D.R., Nelson C., Nieminen K., Nilsson O., Pereda V., Peter G., Philippe R., Pilate G., Poliakov A., Razumovskaya J., Richardson P., Rinaldi C., Ritland K., Rouzé P., Ryaboy D., Schmutz J., Schrader J., Segerman B., Shin H., Siddiqui A., Sterky F., Terry A., Tsai C.J., Uberbacher E., Unneberg P., Vahala J., Wall K., Wessler S., Yang G., Yin T., Douglas C., Marra M., Sandberg G., Van de Peer Y., and Rokhsar D., 2006, The genome of black cottonwood, Populus trichocarpa (Torr. & Gray), Science, 313: 1596-1604
http://dx.doi.org/10.1126/science.1128691
PMid:16973872

Van Deynze A., Stoffel K., Buell C.R., Kozik A., Liu J., van der Knaap E., and Francis D., 2007, Diversity in conserved genes in tomato, BMC Genomics, 8: 465
http://dx.doi.org/10.1186/1471-2164-8-465
PMid:18088428 PMCid:2249608

van Orsouw N.J., Hogers R.C., Janssen A., Yalcin F., Snoeijers S., Verstege E., Schneiders H., van der Poel H., van Oeveren J., Verstegen H., and van Eijk M.J., 2007, Complexity reduction of polymorphic sequences (CRoPS): a novel approach for large-scale polymorphism discovery in complex genomes, PLoS One, 2(11): e1172
http://dx.doi.org/10.1371/journal.pone.0001172
PMid:18000544 PMCid:2048665

Velasco R., Zharkikh A., Troggio M., Cartwright D.A., Cestaro A. Pruss D., Pindo M., Fitzgerald L.M., Vezzulli S., Reid J., Malacarne G., Iliev D., Coppola G., Wardell B., Micheletti D., Macalma T., Facci M., Mitchell J.T., Perazzolli M., Eldredge G., Gatto P., Oyzerski R., Moretto M., Gutin N., Stefanini M., Chen Y., Segala C., Davenport C., Demattè L., Mraz A., Battilana J., Stormo K., Costa F., Tao Q., Si-Ammour A., Harkins T., Lackey A., Perbost C., Taillon B., Stella A., Solovyev V., Fawcett J.A., Sterck L., Vandepoele K., Grando S.M., Toppo S., Moser C., Lanchbury J., Bogden R., Skolnick M., Sgaramella V., Bhatnagar S.K., Fontana P., Gutin A., Van de Peer Y., Salamini F., and Viola R., 2007, A high quality draft consensus sequence of the genome of a heterozygous grapevine variety, PLoS One, 2(12): e1326
http://dx.doi.org/10.1371/journal.pone.0001326
PMid:18094749 PMCid:2147077

Westermeier P., Wenzel G., and Mohler V., 2009, Development and evaluation of single-nucleotide polymorphism markers in allotetraploid rapeseed (Brassica napus L.)., Theor. Appl. Genet., 119(7): 1301-1311
http://dx.doi.org/10.1007/s00122-009-1135-x
PMid:19756476

Wright S.I., Bi I.V., Schroeder S.G., Yamasaki M., Doebley J.F., McMullen M.D., and Gaut B.S., 2005, The effects of artificial selection on the maize genome, Science, 308(5726): 1310-1314
http://dx.doi.org/10.1126/science.1107891
PMid:15919994

Wu X., Ren C., Joshi T., Vuong T., Xu D., and Nguyen H.T., 2010, SNP discovery by high-throughput sequencing in soybean, BMC Genomics, 11: 469
http://dx.doi.org/10.1186/1471-2164-11-469
PMid:20701770 PMCid:3091665

Yamamoto N., Tsugane T., Watanabe M., Yano K., Maeda F., Kuwata C., Torki M., Ban Y., Nishimura S., and Shibata D., 2005, Expressed sequence tags from the laboratory-grown miniature tomato (Lycopersicon esculentum) cultivar Micro-Tom and mining for single nucleotide polymorphisms and insertions/deletions in tomato cultivars, Gene., 356: 127-134
http://dx.doi.org/10.1016/j.gene.2005.04.026
PMid:15975739

Yamasaki M., Tenaillon M.I., Bi I.V., Schroeder S.G., Sanchez-Villeda H., Doebley J.F., Gaut B.S., and McMullen M.D., 2005, A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement, Plant Cell, 17(11): 2859-2872
http://dx.doi.org/10.1105/tpc.105.037242
PMid:16227451 PMCid:1276015

Yan J., Shah T., Warburton M.L., Buckler E.S., McMullen M.D., and Crouch J., 2009, Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers, PLoS One, 4(12): e8451
http://dx.doi.org/10.1371/journal.pone.0008451
PMid:20041112 PMCid:2795174

You F.M., Huo N., Deal K.R., Gu Y.Q., Luo M.C., McGuire P.E., Dvorak J., and Anderson O.D., 2011, Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence, BMC Genomics, 12: 59
http://dx.doi.org/10.1186/1471-2164-12-59
PMid:21266061 PMCid:3041743

Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S., Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L., Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J., Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X., Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y., Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L., Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H., Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z., Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L., Fang L., Lei T., Chen C., Chen H., Xu Z., Li H., Huang H., Zhang F., Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q., Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J., Gao L., Zheng W., Hao B., Liu S., Wang W., Yuan L., Cao M., McDermott J., Samudrala R., Wang J., Wong G.K., and Yang H., 2005, The genome of Oryza sativa: a history of duplications, PLoS Biol., 3(2): e38
http://dx.doi.org/10.1371/journal.pbio.0030038
PMid:15685292 PMCid:546038

Zeller G., Clark R.M., Schneeberger K., Bohlen A., Weigel D., and Rätsch G. 2008, Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays, Genome Res., 18(6): 918-929
http://dx.doi.org/10.1101/gr.070169.107
PMid:18323538 PMCid:2413159