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。     

Genetics and mapping of quantitative traits for nodule number, weight, and size in soybean (Glycine max L.[Merr.])

Soybean research has found that nodule traits, especially nodule biomass, are associated with N₂ fixation ability. Two genotypes, differing in nodule number per plant and individual nodule weight, KS4895 and Jackson, were mated to create 17 F₃- and 80 F₅-derived RILs. The population was mapped with 664 informative markers with an average distance of less than 20 cM between adjacent markers. Nodule traits were evaluated in 3-year field trials. Broad-sense heritability for nodule number (no. plant^?1), individual nodule dry weight (mg nodule^?1), individual nodule size (mm nodule^?1), and total nodule dry weight (g plant^?1) was 0.41, 0.42, 0.45, and 0.27, respectively. Nodule number was negatively correlated with individual nodule weight and size. Nodule number, individual nodule weight, and size are major components which likely contributed to increased total nodule weight per plant. Composite interval mapping (CIM) identified eight QTLs for nodule number with R² values ranging from 0.14 to 0.20. Multiple interval mapping (MIM) identified two QTLs for nodule number, one of which was located close to the QTL identified with CIM. Six QTLs for individual nodule weight were detected with CIM, and one QTL was identified with MIM. For nodule size, CIM identified seven QTLs with R² values ranging from 0.14 to 0.27. Five QTLs for total nodule weight were detected with CIM, one of which was located close to a QTL identified with MIM. These results document the first QTL information on nodule traits in soybean from field experiments utilizing a dense, complete linkage map.     

不同生态环境条件下小麦籽粒灌浆速率及千粒重QTL分析

以142个和尚麦/豫8679的F7:8重组自交系及其亲本为试验材料, 分析了籽粒平均灌浆速率、最高灌浆速率及千粒重在北京(2006, 2007)、安徽合肥(2007)和四川成都(2007)4个生态环境下的性状表现, 并利用已构建的含有170个SSR标记和2个EST标记的遗传图谱, 对这3个性状进行了QTL定位分析。共检测到54个QTLs, 涉及小麦1A、1B、2A、2D、3A、3B、3D、4A、4D、5A、5B、6D 和7D染色体。其中, 17个与平均灌浆速率相关, 可解释表型变异的7.17%~20.83%; 16个与最高灌浆速率相关, 可解释表型变异的6.31%~15.95%; 21个与千粒重相关, 可解释表型变异的4.36%~16.80%。另外, 在1A、1B、2A、3B、4D、6D和7D染色体上发现10个涉及“一因多效”或紧密连锁位点的基因组区段, 有助于了解籽粒灌浆和籽粒产量相关性状的遗传基础。     

Comparison and analysis of main effects,epistatic effects,and QTL × environment interactions of QTLs for agronomic traits using DH and RILs populations in rice

Two genetic linkage maps based on doubled haploid (DH) and recombinant inbred lines (RILs) populations, derived from the same indica-japonica cross ‘Samgang × Nagdong’, were constructed to analyze the quantitative trait loci (QTLs) affecting agronomic traits in rice. The segregations of agronomic traits in RILs population showed larger variations than those in DH population. A total of 10 and 12 QTLs were identified on six chromosomes using DH population and seven chromosomes using RILs population, respectively. Three stable QTLs including pl9.1, ph1.1, and gwp11.1 were detected through different years. The percentages of phenotypic variation explained by individual QTLs ranged from 8 to 18% in the DH population and 9 to 33% in the RILs population. Twenty-three epistatic QTLs were identified in the DH population, while 21 epistatic QTLs were detected in the RILs population. Epistatic interactions played an important role in controlling the agronomic traits genetically. Four significant main-effect QTLs were involved in the digenic interactions. Significant interactions between QTLs and environments (QE) were identified in two populations. The QTLs affecting grain weight per panicle (GWP) were more sensitive to the environmental changes. The comparison and QTLs analysis between two populations across different years should help rice breeders to comprehend the genetic mechanisms of quantitative traits and improve breeding programs in marker-assisted selection (MAS).     

8种水旱环境下2个玉米群体穗部性状QTL间的上位性及环境互作效应分析

深入剖析干旱胁迫条件下玉米穗部性状的遗传机制可为玉米抗旱高产分子育种提供参考依据。以大穗型旱敏感自交系TS141为共同亲本,分别与小穗型强抗旱自交系廊黄和昌7-2杂交,构建了含有202个(LTPOP)和218个(CTPOP)家系的F2:3群体,在8种水旱环境下进行单穗重、穗轴重、穗粒重、百粒重、出籽率及穗长等6个穗部性状的表型鉴定,并采用复合区间作图法(CIM)和基于混合线性模型的复合区间作图法(MCIM)对其进行单环境和多环境联合数量性状位点(QTL)分析。结果表明,采用CIM法,单环境下在2套F2:3群体间检测到62个穗部性状QTL,其中干旱胁迫环境下检测到38个QTL,进一步在2套F2:3群体多个干旱胁迫环境下检测到10个稳定表达的QTL (sQTL),分别位于Bin 1.01–1.03、Bin 1.03–1.04、Bin 1.05、Bin 1.07、Bin 1.07–1.08、Bin 2.04、Bin 4.08、Bin 5.06–5.07、Bin6.05和Bin 9.04–9.06。采用MCIM法,联合分析定位到54个穗部性状联合QTL,其中24个表现显著的QTL与环境互作(QTL×E), 17对参与了显著的加性与加性/显性(AA/AD)上位性互作,其表型贡献率较低。这些研究结果可为系统地剖析玉米穗部性状的分子遗传机制提供理论依据;且这2套F2:3群体多个环境下检测到的sQTL可作为穗部性状改良的重要候选染色体区段,用于图位克隆或抗旱高产分子育种,但要注重环境及上位性互作效应的影响。     

水、旱栽培条件下稻谷粒型和粒重的相关分析及其QTL定位

为了解水、旱栽培条件下水稻粒形和粒重的表型及QTL变化,以陆稻品种IRAT109和水稻品种越富构建的双单倍体群体为材料,系统分析了稻谷粒长、粒宽、粒重及长宽比在水、旱栽培条件下的相关性,并进行了数量性状基因位点的比较定位。结果表明,水、旱条件下,粒长与长宽比和粒重均呈极显著正相关;粒宽与长宽比呈极显著负相关,与粒重极显著正相关,4个性状在水、旱条件间相关性都达极显著正相关。其中粒长的相关系数最高,达0.817,粒宽的相关系数最低,为0.457。表明粒长受水分影响最小而粒宽受水分影响较大。粒重、长宽比介于二者之间。两种条件下共检测到14个QTLs,分布于水稻1、5、6、7、10和12染色体上,其中控制粒长的5个,LOD值为1.93~5.11,贡献率为5.97%~28.85%;控制粒宽的1个,LOD值为2.39,贡献率为12.76%;控制长宽比的3个,LOD值为2.08~4.6,贡献率为7.78%~21.89%;控制粒重的5个,LOD值为2.68~9.45,贡献率为4.1%~14.8%。其中控制粒长的qGL-5及控制粒重的qGWt-1a和qGWt-1b在水、旱条件下均能检测到,在抗旱育种中可用于分子标记辅助选择籽粒性状。QTL分析的结果进一步验证了表型分析结果,粒宽相对易受土壤水分影响,粒长、粒重和长宽比,受水分胁迫影响较小,遗传比较稳定。     

Identification of novel QTL for leaf traits in soybean

Several leaf traits of soybean (Glycine max L. Merr.), including leaf area (LA), leaf shape (LS) and specific leaf weight (SLW) may be related to soybean yield. The objective of this study was to identify novel quantitative trait loci (QTL) for LA, LS and SLW in a recombinant inbred line (RIL) population. The phenotype data were collected in 2011 and 2012 for 93 F_7:10 RILs using a randomized complete block design with 2 replicates each year. Five hundred and sixteen single‐nucleotide polymorphism (SNP) markers and the phenotype data were used to detect QTL using single marker analysis (SMA) and composite interval mapping (CIM). Single markers analysis identified 26 QTL for the three traits, of which 17 were novel and the rests were previously reported QTL. Most of these QTL were also identified by CIM. Most QTL reported in this study were in close proximity (<1 cM) of one or more SNP markers. These publicly available SNP markers with close linkage to LA, LS and SLW should be useful for marker‐assisted breeding for these traits.     

QTL mapping of resistance in lentil (Lens culinaris ssp. culinaris) to ascochyta blight (Ascochyta lentis)

Quantitative trait locus (QTL) analysis of ascochyta blight resistance in lentil was conducted using genomic maps developed from two F₂ populations, viz. ILL5588/ILL7537 and ILL7537/ILL6002. Five QTLs for ascochyta blight resistance were identified by composite interval mapping (CIM) across four linkage groups (LG) in population ILL5588/ILL7537. Three QTLs were identified by CIM in population ILL7537/ILL6002 (two in close proximity on LGI and one on LGII). Two of these coincided with regions identified using multiple interval mapping (MIM) and were shown to be conditioned by dominant and partial dominant gene action. Together, they accounted for approximately 50% of the phenotypic variance of disease severity. Comparison between the two populations revealed a potentially common QTL and several common regions that contained markers significantly associated with resistance. This study demonstrated the transferability of QTLs among populations and identified markers closely linked to the major QTL that may be useful for future marker‐assisted selection for disease resistance.     

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。     

低磷胁迫下水稻产量性状变化及其QTL定位

为研究低磷胁迫对水稻产量及其构成因素QTL表达的影响, 以耐低磷旱稻IRAT109和磷敏感水稻越富杂交的116个株系的DH群体为材料, 在低磷和正常栽培条件下, 调查了千粒重、结实率、有效穗数、穗粒数及单株产量等性状。结果表明, 结实率、有效穗数和单株产量对低磷胁迫的敏感性较大, 而千粒重、穗粒数对低磷胁迫的敏感性较小。利用水稻分子连锁图中94个RFLP标记和71个SSR标记, 依据以上5性状低磷胁迫下与对照的差值进行QTL定位。共检测出17个QTL, 其中12个对表型变异的贡献率大于10%。3、6和7号染色体上3个标记区域存在QTL成簇分布, 这些高贡献率QTL及成簇分布QTL可作为水稻耐低磷产量性状分子育种的重要候选区域。     

水稻粒长主效QTL的分子遗传效应分析

为了探索水稻粒长遗传机制,利用小穗小粒型水稻Milyang 46和大穗大粒型FJCD构建的含130个家系的重组自交群体及其包含119个分子标记的连锁图谱,分别在福建武夷山和莆田对水稻粒长进行数量性状基因位点(Quantitative trait loci,QTL)定位及其环境互作分析。结果共检测到16个控制粒长的加性QTL,包括在武夷山被检测到的7个QTL和在莆田检测到的9个QTL。它们分布在第1、2、4、5、6、7、10、11、12号染色体上,其中有2个QTL在2个环境下被重复检出。qGL-4-6在武夷山和莆田的表型变异贡献率分别为5.69%、3.58%,qGL-10-1在武夷山和莆田的表型变异贡献率分别为15.82%、8.06%。16个加性QTL中,qGL-5-3、qGL-10-1与环境存在显著互作,而互作效应对表型变异的贡献率为0。     

利用重组自交系定位棉花第22染色体短臂的纤维品质性状的QTL

 以TM-1的染色体片段代换系CSB22sh和TM-1杂交,构建了包含104个家系的重组自交系（RILs）群体。利用74对具有多态性位点的引物进行检测,构建了包含61个多态性位点,长度为76.93 cM的遗传图谱,平均标记间距离1.26 cM。利用此遗传图谱结合重组自交系群体4个环境下的5个纤维品质性状进行QTL定位,共定位出12个QTLs,解释性状表型变异的2.45%～21.11%;在1,2,3,4个环境中同时检测到的QTLs分别有9,1,1,1个。而利用4个环境平均值进行联合分析定位出个4个QTLs,纤维长度和纤维整齐度的QTLs均为2个,解释性状表型变异的14.37%～19.97%,并且纤维长度和整齐度的QTL在相同的位置。多环境下检测到的QTL可能对标记辅助选择有实际应用价值。     

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。     

QTL Mapping of Boll Weight Trait Based on Recombinant Inbred Lines in Gossypium hirsutum L.

[Objective] The aim of this study was to explore the quantitative trait locus (QTL) related to the boll weight. [Method] A single seed descended population of 137 recombinant inbred lines (RILs) was developed from the cross of upland cotton (Gossypium hirsutum L.) CCRI 36 and G2005, an introgression inbred line introgressed from G. barbadense. Using restriction-site associated DNA sequencing (RAD-seq), a genetic linkage map composed of 6 434 makers, including 6 295 single nucleotide polymorphisms (SNP) and 139 simple sequence repeat (SSR) markers, was developed from the RILs population. [Result] This map spanned 4 071.98 cM with an average distance of 0.63 cM between adjacent markers. QTL mapping was performed by using boll weight data of five environments through WinQTLCart 2.5 software. Thirty-two QTL, with 4.46%-15.84% explained phenotypic variation related boll weight, were detected and found distributing on 15 chromosomes. qBW-A4-1, qBW-A4-2, qBW-A5-2, qBW-D9-1, and qBW-D9-2 were detected in two environments, which explained 5.07%-15.84% of the phenotypic variation. [Conclusion] Major QTLs detected in this study will provide an important reference for analysis of the genetic mechanism of boll weight.     

Molecular mapping of quantitative trait loci for domestication traits and β-glucan content in a wheat recombinant inbred line population

Genetic maps are useful for analysis of quantitative trait loci (QTLs) and for marker-assisted selection (MAS) in breeding. A simple sequence repeat (SSR) marker linkage map of common wheat was constructed based on recombination inbred lines (RILs) derived from a cross between Chinese Spring and spelt wheat. The map included 264 loci on all wheat chromosomes covering 2,345.2 cM with 962, 794.6, and 588.6 cM for the A, B, and D genomes, respectively. Using the RILs and the map, we detected 42 putative QTLs on 15 chromosomes for ear length, spikelet number, spike compactness, kernel length, kernel width, kernel height and β-glucan content. Each QTL explained 4–45% of the phenotypic variation. Five QTL cluster regions were detected on chromosomes 1A, 5AL, 2B, 2D, and 4D. The first QTLs for β-glucan content in wheat were identified on chromosomes 3A, 1B, 5B, and 6D.     

基于单片段代换系的玉米百粒重QTL分析

籽粒大小是影响玉米产量的关键因素。本研究基于59份玉米染色体单片段代换系(SSSL)纯合体,对玉米百粒重性状进行2年6个试验环境的表型鉴定,利用t测验和重叠群作图的方法对SSSL内代换片段上的百粒重效应进行了QTL分析。共检测出20个百粒重QTL,分布在玉米的8条染色体上,其中14个(70.0%)在2个以上试验环境中被重复检出,4个(20.0%)在4个以上试验环境中被重复检出,在全部6个试验环境中重复检出且基因加性效应值较大的玉米百粒重QTL是位于玉米第5染色体Bin5.05区SSR分子标记bnlg278和umc1680附近的q100kw-5-3。研究结果为玉米籽粒大小性状相关基因的进一步精细定位和克隆奠定了基础。     

发掘人工合成小麦中千粒重QTL的有利等位基因

以人工合成小麦Am3为供体亲本,普通小麦莱州953为轮回亲本,经5次回交然后自交,培育出含85个株系的F_2:3群体。以该群体为材料,用348对多态性SSR标记,进行全基因组扫描,发掘人工合成小麦中千粒重QTL的有利等位基因。利用复合区间作图法检测到3个千粒重QTL,其对表型变异的贡献率为10.9%~33.79%。其中,Am3的等位基因能够增加千粒重2.3~4.8 g。相关分析表明,该导入系群体的千粒重与穗粒数、穗数和株高无显著相关性。千粒重QTL与穗粒数、穗数性状的QTL不在同一位置,这有利于高千粒重基因与其他产量性状基因的聚合。采用混合线性模型作图法检测到1个千粒重QTL(QGw.caas-3D),该QTL与环境互作效应小,而且与复合区间作图法在3个环境中都检测到的QTL相同,表明QGw.caas-3D是一个稳定的主效QTL。     

Identification of quantitative trait loci controlling soybean seed weight in recombinant inbred lines derived from PI 483463 (Glycine soja) × ‘Hutcheson’ (G. max)

The objective of this study was to identify quantitative trait loci (QTLs) controlling 100‐seed weight in soybean using 188 recombinant inbred lines (RIL) derived from a cross of PI 483463 and ‘Hutcheson’. The parents and RILs were grown for 4 years (2010–2013), and mature, dry seeds were used for 100‐seed weight measurement. The variance components of genotype (a), environment (e) and a × e interactions for seed weight were highly significant. The QTL analysis identified 14 QTLs explaining 3.83–12.23% of the total phenotypic variation. One of the QTLs, qSW17‐2, was found to be the stable QTL, being identified in all the environments with high phenotypic variation as compared to the other QTLs. Of the 14 QTLs, 10 QTLs showed colocalization with the seed weight QTLs identified in earlier reports, and four QTLs, qSW5‐1, qSW14‐1, qSW15‐1 and qSW15‐2, found to be the novel QTLs. A two‐dimensional genome scan revealed 11 pairs of epistatic QTLs across 11 chromosomes. The QTLs identified in this study may be useful in genetic improvement of soybean seed weight.     

大豆百粒重QTL定位

大豆百粒重是产量构成的重要因素之一,与产量呈正相关。本研究以溧水中子黄豆和南农493-1的504个F2正反交单株及其亲本间具有多态性的150个SSR标记信息构建连锁图谱,2008年分别在江苏南京和山东临沂两地种植其衍生的正反交F2:4家系,鉴定其百粒重,应用Win QTL CartographerV2.5复合区间作图法和两地正反交联合分析进行QTL定位。结果表明,复合区间作图法检测到16个主效QTL,联合分析检测到24个主效QTL、环境效应与细胞质效应、1个环境×QTL互作和12个细胞质×QTL互作。其中,两方法共同检测到10个主效QTL,正反交群体在两地中共同检测到3个主效QTL;Meta分析发现与其他研究一致的4个QTL。这些结果为大豆产量遗传与标记辅助育种实践提供理论基础。     

基于SNP标记的玉米株高及穗位高QTL定位

为进一步弄清玉米株高和穗位高的遗传机理,为育种生产提供服务,本研究以K22×CI7、K22×Dan3402个F₂群体为作图群体,利用覆盖玉米10条染色体的SNP标记构建了2个连锁图谱。并将这2个F₂群体衍生的分别含237和218个家系的F_2:3群体用于田间性状的鉴定。用复合区间作图模型对2个群体的株高、穗位高表型进行QTL定位分析,结果显示,在武汉和南宁两种环境条件下共定位到21个株高QTL和27个穗位高QTL;单个QTL表型变异贡献率的变幅为4.9%~17.9%;株高和穗位高QTL的作用方式以加性和部分显性为主;第7染色体上可能存在控制株高和穗位高的主效QTL。