分子标记辅助渗入佳辐占基因组约800kb区间定向改良珍汕97B外观品质

稻米的外观品质性状主要包括粒长、粒宽、长宽比、垩白和透明度。外观性状是稻米商品品质的第一要素,直接影响稻米的商品价值。中国杂交稻以产量高著名,但常因品质欠佳,尤其是外观品质差而影响杂交稻的推广应用。杂交稻汕优63是中国最著名的杂交稻组合,也因品质欠佳而不能持续应用。本研究构建了三个遗传群体,对稻米外观性状进行了经典和分子遗传学研究,并试图利用分子标记辅助手段改良我国三系杂交稻著名保持系“珍汕97B”,以期提高杂交稻汕优63的品质并使之持续应用。主要的研究结果如下:通过整合已发表的分子遗传图谱和基因组数据库,选用45个与外观性状相关的分子标记,在珍佳群体和广佳群体中进行稻米外观性状分子连锁群重建,并用区间作图法对稻米外观性状进行OTL分析。研究表明:在珍佳群体中,检测到9个与稻米外观性状相关的OTL,其中5号染色体的RM169-RM516是粒宽、长宽比、垩白和腹白的共同座位,贡献率分别为10.9％、14.9％、12.0％和14.2％;7号染色体RM214、8号染色体RM339都是垩白和腹白的共同座位,贡献率分别为9.4％和10.0％、11.0％和12.1％;3号染色体上检测到1个长宽比基因座位RM347,贡献率为10.3％。在广佳群体中,检测到5个与稻米外观性状的OTL,其中5号染色体RM169-RM516是粒宽、垩白和腹白性     

不同环境基于高密度遗传图谱的稻米外观品质QTL定位

为解析稻米外观品质遗传基础, 挖掘稳定存在的控制稻米外观品质性状的QTL, 本研究以籼稻品种V20B和爪哇稻品种CPSLO17作为亲本, 构建包含150个重组自交家系(recombinantion inbred line, RIL)的RIL作图群体, 进行外观品质性状QTL定位分析。利用特定位点扩增长度测序(SLAF-seq)技术, 构建了一个由12个连锁群包含8602个标记, 平均间距为0.29 cM的高密度遗传图谱。采用IciMapping 4.0软件的ICIM-ADD方法在3种环境(贵阳、贵定、三亚)对4个外观品质性状(粒长、粒宽、垩白度和垩白粒率)进行QTL (quantitative trait locus)定位分析。结果表明: 3种环境共检测到9个粒长QTL、6个粒宽QTL、3个垩白度QTL和4个垩白粒率QTL; 有5个QTL在多个环境被重复检测到, 其中3种环境都定位到的粒宽QTL qGW5-1和垩白度QTL qCha5-1为同一定位区间(第5染色体的Marker1642127-Marker1514505); 此外, 垩白度QTL qCha5-2的定位区间(Marker1554573-Marker1554589)和垩白粒率QTL qCGP5-2也是一样的。序列比对发现QTL qCha5-1定位区间仅51.5 kb, 是新的垩白性状主效QTL。本研究结果不仅为挖掘新的外观品质性状基因奠定基础, 也有助于开发新的分子标记进行水稻外观品质性状遗传改良。     

水稻外观品质性状QTL分析

为发掘控制水稻外观品质相关性状的稳定QTL,利用籼稻品种‘贵9B’(Gui 9B)和粳稻品种‘热研2号’(Reyan No.2)为亲本,构建了包含100个家系的重组自交系群体为作图群体。分别于2014年12月和2015年5月将该群体种植于海南三亚和贵州贵阳2个不同生态环境,对稻米粒长和垩白粒率等外观品质性状进行了QTL分析。结合相应的分子连锁图谱及完备区间作图定位方法,对外观品质性状进行QTL定位分析。QTL检测结果表明:2个环境中共定位到16个外观品质QTL,分布在第1、第2、第3、第5、第9、第10和第11条染色体上,LOD值介于2.50~10.98之间,贡献率介于7.64%~19.89%之间。其中,有8个QTL为首次发现,有2个影响粒长的QTL在2个环境下均被检测到。本研究有利于推动水稻外观品质性状基因遗传研究和分子辅助育种。     

稻米外观品质的研究进展与分子改良策略

本文综述了稻米外观品质(长、宽、长宽比和垩白)的经典遗传及分子遗传研究状况，归纳列举了已定位的外观品质性状的QTLs，提出了稻米外观品质改良的分子策略。     

利用DH群体定位水稻谷粒外观性状的QTL

采用混合线性模型的复合区间作图方法，对水稻“圭630”和“02428”组合的DH群体的谷粒外观性状——粒长、粒宽和粒形进行了数量性状基因定位，同时对定位的主效应和上位性进行了环境效应分析。2002年对粒长、粒宽和粒形分别检测到5、4和2个QTLs；2003年对以上3个性状分别检测到3、4和4个QTLs。其中4个QTLs在2年均检测到，且其贡献率较大。位于第4染色体C22．RG449d区间的QTL效应大，同时影响粒长和粒宽，2年内均被检测到。联合2年数据分析分别检测到6个粒长QTLs、6个粒宽QTLs和3个粒形QTLs，共解释各自性状变异的67．7l％、50．08％和29．17％，且影响粒形的3个QTLs同时影响粒长或粒宽。对粒形和粒宽分别检测到4个QTLs与环境之间存在显著互作。本实验中检测到主效应和上位性对谷粒外观性状均具有重要作用，但上位性贡献率相对主效应较小，环境互作效应更小。     

利用BIL和CSSL群体鉴定外观品质主效QTL

为进一步探究稻米外观品质分子调控机制,挖掘新的环境钝感型主效QTL,本研究以‘屉锦’和‘北陆129’杂交衍生的回交重组自交系(BIL)和染色体片段代换系(CSSL)群体为试验材料,对稻米外观品质进行QTL鉴定。结果显示,双亲外观品质存在明显差异,‘屉锦’整精米率较高、垩白少和粒型短圆,外观品质性状间存在明显的相关性。BIL群体检测到32个调控外观品质的QTL,15个QTL稳定表达;CSSL群体鉴定了16个相关QTL,主效QTL在不同群体中共性表达;QTL成簇分布于第1、2、3、8、9和11染色体上,6个区段包含30个位点,占QTL总数的62.50%,其中主效QTL簇qAQ1、qAQ8和qAQ9在不同群体与环境下效应明显、重演性较好,是进一步深入研究的"热点"区域。这将进一步丰富外观品质性状的分子调控机理,也为主效QTL簇的精细鉴定提供坚实基础。     

用全基因组关联分析解析籼稻垩白的遗传基础

利用272份全球籼稻微核心种质的重测序SNP基因型,对海南三亚、广东深圳、浙江杭州和湖北荆州4个地点收集到的垩白粒率和垩白度性状采用TASSEL软件进行全基因组关联分析,解析籼稻垩白的遗传基础和挖掘影响垩白粒率和垩白度的优异等位基因。结果表明,依据SNP数据,可将籼稻微核心种质分成3个亚群。4个地点分别检测到42个和44个与垩白粒率和垩白度显著关联的位点,位于全部12条染色体上。2个性状分别有21个和19个位点在2个以上环境下同时被检测到,这些位点中有12个位点同时影响垩白粒率和垩白度,11个位点附近都有已克隆的水稻品质相关基因。其中,第5染色体3.3~5.3 Mb区间在4个地点都被检测到与垩白粒率显著关联,以杭州点对垩白粒率的贡献最大,优异等位基因载体品种为IRGC121689;第12染色体的17.5~18.0 Mb区间在三亚和杭州都被检测到与垩白度显著关联,以三亚点的垩白度贡献最大,优异等位基因载体品种为IRGC122285。这些位点和品种资源可作水稻外观品质分子改良的重要基因和品种资源。     

旱稻导入系碾磨品质和垩白粒率的QTL定位及其与土壤水分的互作分析

以优质水稻品种越富为遗传背景,具有旱稻品种IRAT109导入片段的271份导入系为材料,在水、旱田2个土壤水分环境下调查糙米率、精米率、整精米率和垩白粒率4个品质性状,研究旱田栽培对稻米品质性状的影响,进行QTL定位及基因型与环境的互作分析。结果表明,整精米率和垩白粒率易受土壤水分环境的影响,糙米率和精米率相对稳定。适当水分胁迫能提高稻米的整精米率,减少垩白粒率。利用混合线性模型,水、旱田条件下共检测到4个品质性状的10个加性QTL和2对上位性互作QTL,分别位于第3、4、7、8和9染色体。3个加性QTL (qMR9、qHMR7和qHMR9)和一对上位性互作QTL (qHMR3~qHMR9)的贡献率大于10%。7个QTL与前人研究结果相一致。第4染色体RM1112~RM1272和第9染色体RM1189~RM410是QTL集中分布的区域。根据不同性状对干旱胁迫的反应特点,分别选择水、旱田条件下贡献率大、稳定的QTL或者具有旱田特异性的QTL,进行标记辅助聚合育种是培育抗旱、优质稻的一个有效途径。     

水稻粒形和垩白的QTL分析

水稻的产量和品质性状一直都是水稻育种长期关注的两个重要方面。本研究利用两个在粒形和垩白上有显著差异的籼稻品种R287和中早35为亲本,构建了一个含有192个单株的F2群体及衍生的F2:3群体,对其粒长、粒宽、长宽比、千粒重和腹白等性状进行了表型鉴定,并结合分子标记遗传连锁图谱进行了QTL(Quantitative trait locus)分析,结果表明:共检测到29个QTL,其中与粒重相关的QTL有6个,与粒形性状相关的QTL有12个,与垩白性状相关的QTL有11个。它们分布在第1号、第2号、第3号、第4号、第5号、第6号、第7号和第11号染色体上,表型变异贡献率介于0.10%~36.84%之间。     

水稻抽穗期数量性状基因的定位及遗传效应分析

本研究利用特早抽穗粳稻品种石狩白毛和籼稻品种明恢63杂交的F2分离群体共116株,构建了含88个共显性分子标记的连锁图谱,对水稻(Oryza sativA L．)抽穗期进行基因定位。利用2种分析软件MAPMAKER／QTL和QTLMapper进行分析,共检测到3个抽穗期的数量性状基因座(QTLs)。2个软件共同发现第7染色体上RM214与A5106标记区间内存在1个主效QTL Hd7a（Hd7c),来自明恢63的这个位点的等位基因可使抽穗期延迟。其余2个QTLs分别位于第7、9染色体上。同时检测到有5对位点间存在上位性作用,但相对贡献率较小,表明上位性效应也是影响抽穗期的遗传基础。     

Quantitative trait loci for grain-quality traits across a rice F2 population and backcross inbred lines

Improving grain-quality is an important goal in rice breeding programs. One vital step is to find major quantitative trait loci (QTLs) for quality related traits and then investigate the relationships among them. We crossed ‘N22’, an indica variety with good appearance but low grain weight, to a japonica variety, ‘Nanjing35’, with superior grain yield but poor appearance. This enabled us to construct an F₂ population and a set of backcross inbred lines (BILs) for QTL-mapping for the traits related grain appearance. In all, 37 QTLs were identified for grain length (GL), grain width (GW), grain thickness (GT), thousand-grain weight (TGW), and the percentage of grains with chalkiness (PGWC). Of these, 17 QTLs detected from 184 plants in the F₂ population explained 4.97–27.26 % of the phenotypic variance, another 20 QTLs were identified using BILs from 2009 to 2010. Quantitative trait loci for major effects were detected in different populations and across years. A new QTL hot spot (marker interval RM504–RM520) was found on Chromosome 3, which harbored QTLs for GL, GW, GT, and TGW. Among our five examined traits, grain shape was significantly correlated with TGW and PGWC. The PGWC values of two heavier grains BILs, L93, and L145 are much lower than Nanjiing35, the analysis of genotype showed that this greater weight may due to the locus for GL occurring within RM504–RM520 on Chromosome 3. Therefore, those two lines will allow us to develop a long-grain high-yield rice variety with less chalkiness.     

Improvement of Appearance Traits of elite Rice Zhenshan 97B by Molecular Introgression of Targeted about 800 kb Interval from Indica Rice Jiafuzhan Genome

Rice appearance trait is mainly mean grain length (GL), grain width (GW), ratio of length and width (L/W), chalkiness (CH) and transparence (TR). Appearance is the first impression, and rice appearance traits effect significantly the value of commodity. Hybrid rice is relatively low quality, especially on rice appearance quality,which restricts partially its extend and badly export of hybrid seed and rice in China.Shanyou 63, the most famous hybrid rice combination of China, could not be also sustainable application because of its poor qualities. In this studies, We attempt to improve appearance quality of the elite rice maintainer of Zhenshan 97B by using molecular approach of genomic interval targeted introgression. Three F2 populations were constructed to study the classical and molecular genetic of rice appearance traits, at the same time, molecular marker-asisted toimprove the main maintainer line, Zhenshan 97B were performed. There some following results:Three F2 populations were constructed based on crosses of Guangluai 4×Jiafuzhan (GJ popu.), Minghui 86×Jiafuzhan (MJ popu.) and Zhenshan 97B×Jiafuzhan (ZJ popu.). ZJ popu and GJ popu were produced to reconstruct the linkage maps related with rice appearance traits based on BSA, and detect QTL of target traits based on IM.In ZJ popu, 9 QTLs of target traits were detected. The interval, RM169～RM516 on Chromosome 5, was genetic locus of GW, L/W, CH and BW, and the explained variances were 10.9%, 14.9%, 12.0% and 14.2%, respectively.RM214 on chromosome 7, RM339 on chromosome 8 were genetic loci if CH and BW, and the explained variances were 9.4%, 10.0%, 11.0% and 12.1%. besides there is a genetic locus, RM347, of G/W on chromosome 3, and the explained varance was 10.3%. In GJ popu, 5 QTLs of rice appearance traits were detected. The interval, RM169-RM516 on Chromosome 5, were also the genetic loci of GW, CH and BW, and the explained variances were 9.0%, 12.5%, and 13.6%, respectively. RM264～RM80 on chromosome 8 was the genetic loci of GW amd L/W,and the explained variances were 14.7% and 13.4%. The genotypes of all QTLs, except RM214, from Jiafuzhan contributed to improving riee appearance traits.The research was to improve the rice appearance quality of Zhenshan 97B by introgressing QTLs of rice appearance traits from Jiafuzhan, a donor parent, by means of MAS in the process of recurrent backcrossing, 4 SSR markers were used to detect the target genotypes from donor parent, and 70 SSR primers to identify the genetic background of recurrent parent. Consequently, there were 19 target individuals in BC3, in which the mean value of GL, GW, L/W, CH and BW were 6.06±0.04mm, 2.50±0.02mm, 2.43±0.02, 29.5±2.7 and 29.4±2.7%, respectively,and the mean homologous degree (HD) to recurrent parent is up to 98.22%. Compared to Zhenshan 97B, GL, CH and BW decreased 0.17 mm, 34.9% and 34.5% respectively and however L/W increased 0.19. which accounted separately for 25.37%, 54.79%, 54.57% and 10.50% of thedifference of every trait between two parents. It is very luckly to find a individual, 13BC2-3BC3 line, whose GL, GW, G/W, CH and BW were 6.04 mm, 2.43 mm, 2.49,2.5% and 2.5% separately, There is very important signification for it to be used in hybrid rice breeding improving appearance traits. In the research, MAS efficiency of 3 loci (with 4 markers ) was 5.68% and coincident degree was 73.08%.     

杂交粳稻亲本米质性状优异配合力的标记基因型鉴定

杂交粳稻米质整体水平不如常规粳稻也是限制杂交粳稻广泛种植的原因之一。本研究选用115个SSR引物扩增6个粳稻BT型不育系和12个恢复系的标记基因型,并分析72个F₁组合谷粒长、谷粒宽、糙米率、精米率、整精米率、垩白米率、垩白度、糊化温度、胶稠度和直链淀粉含量10个米质性状的配合力,结合亲本SSR分子标记数据和性状配合力数据筛选了10个米质性状优异配合力的标记基因型。结果共鉴定出30个SSR标记基因型与亲本10个米质性状配合力显著相关,其中25个与亲本米质性状不良配合力相关,5个与优异配合力相关。标记基因型RM263-175/180和RM444-230/240可以使F₁整精米率分别提高3.2%和2.5%。RM3-120/150可以使F₁谷粒长缩短2.4%,RM444-180/240可以使F₁谷粒宽增加2.1%。RM428-273/294可以使F₁植株上的杂交稻米直链淀粉含量减少7.0%。有8个标记基因型同时也影响产量性状配合力。RM3-120/150同时可以使F₁的每穗总粒数和每穗实粒数分别增加15.9%和10.9%。RM1211-150/160可使F₁的糙米率和精米率分别减少0.9%和1.1%,同时使F₁的每穗总粒数和每穗实粒数分别增加21.8.%和20.4%。RM23-150/160可使F₁的垩白米粒率和垩白度分别增加44.1%和45.7%,同时使F₁的单株日产量和每穗总粒数分别增加11.2%和11.6%。这些结果可用于指导亲本米质性状和产量性状配合力的分子标记辅助改良以及未来杂交粳稻组合配置中的亲本选配。     

Identification and analysis of QTLs for grain quality traits in rice using an introgression lines population

The demand for superior grain quality represents a major issue in rice (Oryza sativa L.) breeding. To study the genetic basis of rice grain quality, including traits specifying grain dimension and percentage of grains with chalkiness, quantitative genetic analysis was conducted in a population of 37 introgression lines (ILs) of indica elite variety Habataki in the background of japonica cultivar Sasanishiki across two different environments. The ILs showed transgressive segregation for all of the investigated traits, including percentage of grains with chalkiness, brown grain length, width, thickness, length/width ratio, length/thickness ratio, volume and 1,000-brown grain weight, the result indicated that these rice grain quality traits were polygenic phenomenon. Fifty-four QTLs were identified on eleven chromosomes, and 44 QTLs were associated with more than one trait, as a cause of the observed phenotypic correlations between different traits. Five stable QTLs, namely QPGWC.NH-1.1, QPGWC.NH-1.2, QGW.NH-3.1, QLW.NH-7.1 and QGV.NH-8.2, were identified in this study. This study provides useful information for marker-aided improvement of grain quality (grain dimension and percentage of grains with chalkiness) in rice; moreover, ILs carrying these QTLs constitute good candidates for future fine mapping and positional cloning projects.     

影响水稻穗部性状及籽粒碾磨品质的QTL及其环境互作分析

利用优质恢复系测258为轮回亲本与粳型糯稻新品系IR75862杂交创制的BC₁F₇回交导入系群体,在广西南宁和海南三亚定位了产量相关性状(二次枝梗数、穗总粒数、穗实粒数、粒重和穗重)、粒型(粒长、宽、厚)和碾磨品质(糙米率、精米率和整精米率)的主效QTL并剖析其环境互作效应。双亲在穗实粒数、千粒重、粒长和粒宽及整精米率等性状上存在显著差异。各产量相关性状间呈极显著正相关,而与千粒重和粒长呈极显著负相关。多数产量及粒型相关性状与3种碾磨品质相关不显著。在南宁和三亚环境下检测到影响产量相关性状、粒型及碾磨品质的主效QTL共计57个,包括二次枝梗数的6个,穗实粒数4个,穗总粒数、粒重和穗重各5个,粒长9个,粒宽7个,粒厚1个,糙米率4个,精米率5个和整精米率6个,分布在除第11染色体外的所有染色体上。多数影响枝梗数、穗粒数和粒重的QTL成簇分布,而且与影响BR、MR和HR的QTL分布在不同染色体区域。在第2、第3、第4、第5和第6染色体上鉴定出影响穗粒数、粒重、粒型及碾磨品质的重要QTL,这些QTL在以往不同遗传背景和环境下被多次检测到。在第8染色体RM152~RM310区间鉴定到1个影响粒长和粒宽的新的QTL,能同步增加粒宽和粒长。鉴定出的这些稳定表达的QTL具有标记辅助选择育种的应用价值。整精米率是受环境影响最大的性状,其QTL的环境互作效应明显。对QTL的环境互作效应特点及其在品种标记辅助改良中的作用进行了深入探讨。     

水稻品种外观品质性状稳定性分析

基于AMMI模型,研究了18个水稻品种外观品质性状与环境的交互作用,并对参试品种的品质性状稳定性进行了分析。以6个外观品质性状表型值及相应的品种稳定性参数为指标,进行系统聚类分析,据此对供试品种外观品质性状进行了评价。结果表明,品种与环境互作效应在1%水平显著,外观品质性状的稳定性随品种而变化较大;随水稻品     

多环境下稻米粒重的QTL定位

以粳稻Asominori为遗传背景的染色体片段置换系（CSSLs）群体为材料,利用基于性状-标记多元回归分析方法对稻谷粒重和精米粒重进行多环境的QTL定位。结果在5个环境共检测到6个粒重相关QTL,分布于第1、6、7和8染色体上,对表型变异的贡献率介于13%~35%;其中控制精米粒重的qMRW-1a和稻谷粒重的qPRW-1在不同环境中均能稳定表达,且均位于第1染色体RFLP标记XNpb113附近,该基因座还同时控制着粒宽。qMRW-1a和qPRW-1共同对应的置换系AIS8和AIS11与Asominori 的粒重差异在不同环境中均显著(P < 0.05),表明该QTL的等位基因在不同环境中效应显著。比较发现该QTL在不同遗传群体中均能被重复检测到,且与蔗糖磷酸合酶基因（SPS）位置一致,推测该QTL与淀粉合成代谢有关。qMRW-1a 和qPRW-1在不同环境条件和遗传背景中表达,因此可用于进一步的精细定位研究。