作物学报 | 综述: 花生种子大小相关性状QTL定位研究进展
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黄 莉* 陈玉宁 罗怀勇 周小静 刘念
陈伟刚 雷永 廖伯寿 姜慧芳
中国农业科学院油料作物研究所 / 农业农村部油料作物生物学与遗传育种重点实验室，湖北武汉 430062
摘要 Abstract
花生是我国重要的油料作物和经济作物，目前国内花生的产量远远不能满足消费者的所需，进一步提高花生单产是解决花生生产供不应求的重要途径。花生种子大小相关性状是花生的重要农艺性状，对提高花生单产至关重要。本文综述了植物种子大小的调控途径以及近年来花生分子标记、遗传图谱构建、种子大小相关性状QTL定位研究中取得的进展，探讨了目前花生种子大小相关性状研究中面临的挑战和机遇，对花生产量遗传改良进行了展望。
花生(Arachis hypogaea L.)是我国重要的油料作物和经济作物，是食用植物油和蛋白质的重要来源。花生及其制品以其优良的风味、品质及保健功能，深得消费者喜爱，在国民经济和社会发展占有重要地位。我国是世界上最大的花生生产国，年产量在1700万吨以上，种植面积在国际上仅次于印度居全球第2位，占全球花生面积约17%[1]。近几年来我国花生总产约52%用于榨油，是花生最大的利用途径。随着人民生活水平的不断改善，国内花生油的市场需求量持续上升，国内花生产量远远不能满足持续增长的消费需求。目前，我国人均耕地资源短缺，我国花生种植面积难以大幅增加，花生生产供不应求的矛盾只能依靠提高花生单产来解决，因此，进一步提高花生单产是满足我国植物油日益增长需求的重要途径。
花生种子大小是衡量花生单产的重要指标，花生的种子长、种子宽和籽仁重直接显著地影响花生产量。花生优良品种的选育以及新品种的推广应用极大地提高了花生的单产水平。自20世纪50年代以来，花生品种实现了5次更新，每次品种更新均显著提高了花生的单产[2]。研究花生种子大小的遗传基础，能为花生优良亲本组合的选配、优良高产种质的创制以及高产分子育种提供坚实的理论基础，有助于加快花生高产育种进程。本文主要总结了植物种子大小的调控途径以及近年来花生在分子标记、遗传图谱构建、种子大小相关性状QTL定位研究中取得的进展。探讨了目前花生种子大小相关性状研究中面临的挑战和机遇，对花生产量遗传改良进行了展望，以期为相关研究提供参考。
01
植物种子大小的调控途径研究进展
种子大小是影响产量的一个重要因素，同时，也是作物驯化过程中的一个主要农艺性状。种子的大小由植物自身的遗传机制决定[3]。单子叶和双子叶植物的种子均从双受精开始发育，受精后，胚珠发育成种子，珠被发育成种皮。双子叶植物种子的发育过程主要包括胚乳的增殖和胚的生长，胚乳由于快速增殖，形成多核体，使种腔变大，之后胚乳细胞化形成多个单细胞。当胚乳细胞化完成时，即确定了该种子的大小[4]。而单子叶植物的胚乳并未消失，成为种子的重要组成部分。此外，不论是双子叶植物还是单子叶植物，其珠被经过细胞化以及色素和淀粉粒的积累，形成了种皮。种皮的存在会限制种子的最终大小[5]。因此，胚、胚乳以及珠被共同调控种子的大小[6]。种子生长发育的过程，从细胞学水平看，是由细胞增殖和细胞膨大相互协调控制，它们分别控制着细胞的数目和大小[7]。细胞增殖或细胞膨大均会导致种子的大小发生改变，其中细胞增殖，即改变细胞数目对种子大小的影响更大[8]。
近年来，在植物中已经图位克隆了一批控制种子大小的基因或者调控因子，比如水稻中的GS3[9]、GW2[10]、GW5[11]、GS5[12]、GLW7[13]。这些基因或者调控因子通过植物激素途径、IKU途径、泛素-蛋白酶体途径等调控细胞增殖和细胞数目，从而影响胚、胚乳和珠被的发育，进而影响种子的大小(图1)。
图1 植物种子大小的主要调控途径及关键基因
植物激素途径是种子大小调控网络中一个重要的途径，其涉及到的激素包括生长素(Auxin, IAA)、油菜素内酯(Brassinolide, BR)、细胞分裂素(Cytokinin, CTK)以及赤霉素(Gibberellin, GA)等，这些激素在种子生长发育过程中具有重要的作用[14]。生长素主要是通过auxin response factors(ARFs)调控生长素介导的基因来调控种子的大小。拟南芥中已经鉴定到ARF2基因通过限制珠被内的细胞增殖来控制种子的大小[15]，并且该基因在调控种子大小性状上具有母体效应[16]。此外，油菜中也已经图位克隆到基因ARF18，该基因同时调控油菜的千粒重以及角果长，并且该基因也具有母体效应[17]。BR是一种类固醇激素，研究表明，BR通过改变胚和胚乳从而调控种子的大小，也可以通过调控其他种子大小相关基因的表达从而调控种子大小[18]。在细胞分裂素缺失突变体中，细胞数目增多，胚细胞增大，种子变大，表明CTK通过调控细胞增殖来调控种子的大小[19]。GA通过抑制DELLA蛋白的活性而促进种子的发育[20]，GA信号途径中的部分基因调控了细胞的膨大[21]。
IKU途径是植物种子早期发育阶段的一个重要调控机制，涉及HAIKU1 (IKU1)、HAIKU2 (IKU2)、MINISEED3 (MINI3)和SHORT HYPOCOTYL UNDER BIUE1 (SHB1)。其中IKU1和IKU2分别编码一个含有VQ结构域的蛋白和亮氨酸受体激酶，它们使胚乳细胞化提前，抑制胚细胞增殖和珠被细胞的伸长，从而导致种子变小[4]。MINI3编码WRKY10转录因子，可以与IKU1和IKU2相互作用[22]。SHB1正调控细胞的大小和数目，在种子发育过程中，可以结合IKU2和MINI3的启动子区域，促进IKU2和MINI3的表达，使胚乳生长加快，提高胚细胞增殖和扩展的速度[23]。
泛素-蛋白酶体途径是泛素首先被泛素活化酶E1、泛素结合酶E2和泛素连接酶E3依次催化，形成泛素化的蛋白质，然后被分解为短肽或氨基酸，该途径也参与调控种子大小，例如基因DA1、SOD2、SOD7等。拟南芥的DA1基因为种子大小的抑制子，通过限制细胞增殖时间而调控种子大小；SOD7基因通过抑制珠被和细胞增殖来调控种子大小[24-25]。研究发现，过量表达SOD7基因，会使转基因植株的种子显著变小，而敲除SOD7基因，会使转基因植株的种子显著变大[26]。DA1基因和SOD7基因对种子大小性状的调控均具有母体效应[24]。此外，SOD2基因编码泛素特异的蛋白酶UBIQUITIN-SPECIFIC PROTEASE15 (UBP15)，负调控拟南芥种子的种子大小，并且同样具有母体效应[27]。
除以上3种途径，种子大小还受其他因子的调控，比如转录因子(AP2类、MADS-box类、bHLH类)、G-蛋白、激酶、microRNA等[28]。这些调控因子相互影响、相互制约，构成了一个复杂的调控网络，从而对种子的胚、胚乳和珠被进行调控，进而调控种子大小。
02
花生种子大小相关性状QTL定位研究进展
2.1 花生分子标记
早在20世纪90年代，限制性片段长度多态性(restriction fragment length polymorphism，RFLP)、随机扩增DNA多态性(random amplified polymorphic DNA，RAPD)和扩增片段长度多态性(amplified fragments length polymorphism，AFLP)就开始应用于花生遗传多样性分析和遗传图谱构建。Kochert等[29]利用RFLP标记对8份美国花生品种和14份野生花生资源进行了遗传多样性分析。后来，Hopkins等[30]发现栽培种花生中存在大量CT和GT重复序列，认为花生与其他作物一样，基因组中也存在简单重复序列(simple sequence repeats，SSR)，能够开发大量的SSR标记进行遗传分析与研究。随后，研究发现SSR标记在花生栽培种资源中存在较高的遗传多态性，可以进行群体遗传学分析[31]。目前，国内外研究者通过SSR富集文库[32]、BAC末端序列[33]、cDNA文库[34-35]、转录组序列[36]、公共数据库[37]、二倍体野生花生基因组[38]和栽培种花生基因组[39]已开发了上万个花生SSR标记，这些SSR标记已广泛应用于花生资源遗传多样性、遗传图谱构建及QTL定位研究中。
随着高通量测序技术的发展，单核苷酸多态性(SNP)标记由于具有基因组分布广、数量大、可实现高通量检测的优点，被认为是最具有利用潜力的分子标记。目前，芯片杂交技术和新一代测序技术是常用的SNP高通量检测手段。Pandey等[40]利用30份花生栽培种材料和来源于6个不同二倍体野生种的11份野生花生材料，构建了花生的第一张SNP芯片“Axiom_Arachis”芯片，该芯片包含58,000个SNP位点，目前已成功应用于分析花生资源遗传多样性[40]、重要性状QTL定位[41]等研究中。随着测序技术的飞速发展，二倍体野生种Arachis duranensis [42-43]和A. ipaensis[42,44]、四倍体野生种A. monticola[45]和四倍体栽培种Tifrunner[46]、狮头企[47]、伏花生[48]基因组陆续发表，使得利用全基因组重测序技术从基因组中检测SNP分子标记这种快捷有效的技术手段在花生研究中成为可能。但是，由于花生栽培种基因组较大(约2.7 G)，群体重测序花费较高，限制了其被大规模应用。于是，以RAD-seq (restriction-site-associated DNA sequencing)技术和SLAF-seq (specific-locus amplified fragment sequencing)技术为代表的“简化基因组测序(reduced-representation sequencing)”便应运而生。它利用限制性核酸内切酶将基因组DNA进行酶切，并制备一批DNA片段文库，这些DNA片段文库可以作为全基因的简化代表，从而降低了测序的费用。简化基因组测序技术的发展促进了SNP标记在花生遗传多样性分析[49]、高密度遗传图谱构建[50-56]及数量性状位点[51-57]研究中的应用。
2.2 连锁分析
2.2.1 遗传连锁图谱的构建
综上，目前通过连锁分析获得的稳定的种子长主效QTL主要位于染色体A2[54]、A5[80]、B6[51,80]、B7[51]上，种子宽主效QTL位于染色体B6[80]和B7[51]上，种子长宽比主效QTL位于染色体A2[54]和A5[80]上，百仁重主效QTL位于染色体B6[80]和B7[51,81]上。这些主效QTL不仅调控种子大小相关性状，还调控着荚果长、荚果宽、百果重等性状[51,80]，这表明荚果和种子性状具有协同调控关系。虽然目前已报道的研究借助四倍体花生基因组信息已获得了种子大小性状QTL的物理位置，但是有的QTL物理区间仍然较大，所以目前研究结果仍然只是QTL初定位，后续还需要通过构建次级分离群体来进一步精细定位，从而将目标QTL缩小至某几个候选基因。
2.3 关联分析
2.3.1 关联分析群体
基于种质资源自然群体的关联分析是数量性状QTL定位的另一种重要有效分析方法。遗传多样性丰富的核心种质资源群体是花生数量性状关联分析的首选群体。美国农业部、印度国际半干旱地区热带作物研究所、以及中国农业科学院油料作物研究所分别构建了包含831份[82]、1704份[83]和576份[84]资源的美国、印度和中国花生核心种质群体。由于构建的核心种质群体包含的资源份数较多，不便于做大规模田间试验，于是又相继分别构建了包含112份[85]、184份[86]和298份[87]资源的微核心种质群体。此外，中国农业科学院油料作物研究所在此基础上，构建了一套包含99份资源的微微核心种质群体[88]，而印度国际半干旱地区热带作物研究所构建了一套来自48个国家的300份资源的“参考集” (reference set)[89]。此外，山东省农业科学院花生研究所[90]、山东农业大学[91]和河南省农业科学院[49]利用收集到的花生资源材料，分别构建了包含195份、268份和320份资源材料的关联分析群体，其中河南省农业科学院构建的群体包含了100份农家种、133份育种材料和87份美国微核心种质资源。由于自然群体的群体结构会对关联分析结果产生假阳性，为打破性状与群体结构的相关性，研究者通过交配设计构建了巢式关联作图(nested association mapping，NAM)群体[92]和多亲本高世代杂交(multiple parent advanced generation intercross, MAGIC)群体[93]进行全基因组关联分析。花生中，美国研究者首次利用2个常用的匍匐型花生品种Tifrunner和Florida-07，分别与8个不同的花生材料进行杂交，获得了16个RIL群体，构建了2个花生NAM群体[94]，通过表型调查发现，这些家系的产量性状、成熟期、耐盐性、晚斑病抗性等性状表型变异丰富[95]。这些遗传多样性丰富的资源材料群体都是花生全基因组关联分析的适宜群体。
2.3.2 花生种子大小关联分析QTL定位
与连锁分析相比，花生关联分析研究起步较晚，因此，目前通过关联分析鉴定到的花生大小QTL较少。Pandey等[89]利用154个SSR位点和4597个DArT位点对300份花生资源进行关联分析，鉴定到17个位点与种子大小显著关联，表型变异解释率为11.81%~30.09%。Zhao等[96]利用554个单位点SSR标记和104份花生资源，通过关联分析检测到30个SSR标记与种子大小显著关联，表型变异解释率为11.22%~32.30%，其中标记AHGA44686能够在多环境下重复检测到，且共定位到与种子长和百仁重显著关联。由于早期研究缺少基因组信息，Pandey等[89]和Zhao等[96]只能鉴定到显著关联的标记位点，无法进一步获得QTL区间以及候选基因。Wang等[90]对195份花生资源材料进行了GBS测序，获得了13,435个SNP，通过关联分析，鉴定到38个SNP与籽仁重显著关联，这些SNP主要位于染色体B6和B9上，将SNP位点与已报道的连锁分析结果进行比较发现，染色体A5上54.2~82.2 Mb之间存在4个共定位区域。Gangurde等[41]利用58K SNP芯片“Axiom_Arachis”对2个NAM群体NAM_Tifrunner (581个家系)和NAM_Florida-07 (496个家系)进行全基因关联分析，分别鉴定到28个和17个SNP位点与花生籽仁重显著关联，这些SNP位点主要集中位于染色体A5、A6、B5和B6上，依据这些SNP位点信息和基因组序列，分别鉴定到23个和14个基因可能与花生籽仁重相关。目前花生种子大小相关性状关联分析主要定位于染色体A5、A6、B5、B6和B9上，定位结果还仅仅局限于显著关联位点的获得，如何快速、准确地获得候选基因成为花生关联分析后续研究的重中之重。
03
问题与展望
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