QTL mapping for six ear leaf architecture traits under water‐stressed and well‐watered conditions in maize (Zea mays L.)

Morphological traits for ear leaf are determinant traits influencing plant architecture and drought tolerance in maize. However, the genetic controls of ear leaf architecture traits remain poorly understood under drought stress. Here, we identified 100 quantitative trait loci (QTLs) for leaf angle, leaf orientation value, leaf length, leaf width, leaf size and leaf shape value of ear leaf across four populations under drought‐stressed and unstressed conditions, which explained 0.71%–20.62% of phenotypic variation in single watering condition. Forty‐five of the 100 QTLs were identified under water‐stressed conditions, and 29 stable QTLs (sQTLs) were identified under water‐stressed conditions, which could be useful for the genetic improvement of maize drought tolerance via QTL pyramiding. We further integrated 27 independent QTL studies in a meta‐analysis to identify 21 meta‐QTLs (mQTLs). Then, 24 candidate genes controlling leaf architecture traits coincided with 20 corresponding mQTLs. Thus, new/valuable information on quantitative traits has shed some light on the molecular mechanisms responsible for leaf architecture traits affected by watering conditions. Furthermore, alleles for leaf architecture traits provide useful targets for marker‐assisted selection to generate high‐yielding maize varieties.     

Identification of QTL for stalk sugar-related traits in a population of recombinant inbred lines of maize

Increasing sugar content in silage maize stalk improves its forage quality and palatability. The genetic mapping and characterization of quantitative trait loci (QTLs) is considered a valuable tool for trait enhancement, yet little information on QTL for stalk sugar content in maize has been reported. To this end, we investigated QTLs associated with stalk sugar traits including Brix, plant height (PHT), three ear leaves area (TELA), and days to silking (DTS) in two environments using a population of 202 recombinant inbred lines from a cross between YXD053, which has a high stalk sugar content, and Y6-1, which has a low stalk sugar content. A genetic map with 180 SSR and 10 AFLP markers was constructed, which spanned 1,648.6 cM of the maize genome with an average marker distance of 8.68 cM, and QTLs were detected using composite interval mapping. Seven QTLs controlling Brix were mapped on chromosomes 1, 2, 6 and 9 in the combined environments. These QTLs could explain 2.69–13.08 % of the phenotypic variance. One major QTL for Brix on chromosome 2 located between the markers bnlg1909 and umc1635 explained 13.08 % of the phenotypic variance. Y6-1 also contributed QTL allele for increased Brix on chromosome 6. One major QTLs controlling PHT on chromosome 1 and TELA on chromosome 4 were also identified and accounted for 13.68 and 12.49 % of the phenotypic variance, respectively. QTL alleles for increased DTS were located on chromosomes 1 and 5 of YXD053. Significant epistatic effects were identified in four traits, but no significant QTL × environment interactions were observed. The information presented here may be valuable for stalk sugar content improvement via marker-assisted selection in silage maize breeding programs.     

Identification of quantitative trait loci for leaf‐related traits in an IBM Syn10 DH maize population across three environments

Leaf‐related traits (leaf length, leaf width, leaf area and leaf angle) are very important for the yield of maize (Zea mays L) due to their influence on plant type. Therefore, it is necessary to identify quantitative trait loci (QTLs) for leaf‐related traits. In this report, 221 doubled haploid lines (DHLs) of an IBM Syn10 DH population were provided for QTL mapping. In total, 54 QTLs were detected for leaf‐related traits in single environments using a high‐density genetic linkage map. Among them, only eight common QTLs were identified across two or three environments, and the common QTLs for the four traits explained 4.38%–19.99% of the phenotypic variation. qLL‐2‐1 (bin 2.09), qLW‐2‐2 (bin 2.09), qLW‐6‐3 (bin 6.07) and qLA‐5‐2 (bin 2.09) were detected in previous studies, and qLL‐1‐1, qLAr‐1‐1, qLAr‐2‐1 and qLA‐7‐1 may be new QTLs. Notably, qLW‐6‐3 and qLA‐5‐2 were found to be major QTLs explaining 19.99% and 10.96% of the phenotypic variation, respectively. Interestingly, we found three pairs of QTLs (qLW‐2‐2 and qLAr‐2‐1, qLW‐8‐1 and qLL‐8‐2, qLL‐3‐3 and qLAr‐3‐3) that control different traits and that were located on the same chromosome or in a nearby location. Moreover, nine pairs of loci with epistatic effects were identified for the four traits. These results may provide the foundation for QTL fine mapping and for an understanding of the genetic basis of variation in leaf‐related traits.     

Genetic mapping of quantitative trait locus for the leaf morphological traits in a recombinant inbred line population by ultra-high–density maps across multi-environments of maize (Zea mays)

Leaf is the main organ of photosynthetic reaction of plants. Studying the genetic mechanism that affects the leaf shape is very important for the improvement of maize production. In this study, a RIL population, derived from a cross between Ye478 and Qi319, was planted in four different environments, and six leaf morphological traits were measured, including the leaf angle of first leaf above ear, the leaf angle of first leaf below ear, leaf orientation value, leaf area of first leaf above ear, leaf area of ear and leaf area of first leaf below ear. By combining with a genetic map containing 4,602 bin markers, 39 QTLs associated with leaf morphological traits were identified. Among them, four QTLs explained more than 10% of the phenotypic variance, and the QTL qLOV8-2 which controlled LOV not only had a phenotypic contribution rate of 13.86% but also was detected in four environments, which could be considered as a stable major QTL. These results provide useful information for understanding the molecular mechanisms controlling maize leaf morphological traits.     

利用BC2F2高代回交群体定位水稻籽粒大小和形状QTL

以我国优良籼稻恢复系蜀恢527为轮回亲本, 以来自菲律宾的Milagrosa为供体亲本, 培育了样本容量为199株的BC₂F₂高代回交群体。选取85个均匀分布在12条染色体上的多态性SSR标记进行基因型分析, 同时对粒长、粒宽、长宽比和千粒重4种性状进行了表型鉴定。采用性状－标记间的单向和双向方差分析对上述性状进行了QTL定位。单向方差分析(P<0.01)共检测到了10个控制粒长、粒宽、长宽比和千粒重的QTL, 其中有3个具有多效性。由于粒长和长宽比的高度相关性, 控制长宽比的2个QTL均能在粒长QTL中检测到。位于第3染色体着丝粒区域的qgl3b是一个控制粒长、长宽比和千粒重的主效QTL, 它可以分别解释粒长、长宽比和千粒重表型变异的29.37%、26.15%和17.15%。该QTL对于粒长、长宽比和千粒重均表现较大的加性效应(来自蜀恢527的等位基因为增效)和负向超显性。位于第8染色体的qgw8位点是一个控制粒宽的主效QTL, 同时也是控制千粒重的微效QTL, 能解释粒宽表型变异的21.47%和千粒重表型变异的5.16%。该QTL对粒宽和千粒重均具有较大的加性效应(来自蜀恢527的等位基因为增效)和正向部分显性。双向方差分析(P<0.005)共检测到61对显著的上位性互作, 涉及54个QTL, 其中23个是能同时影响2~4个性状的多效位点, 且有8个位点与单向方差分析检测到的相同。控制长宽比的13对上位性互作位点中, 与控制粒长的上位性互作位点完全相同的有8对。以上结果为进一步开展水稻籽粒大小和形状有利基因的精细定位、克隆和分子设计育种奠定了基础。     

利用BC2F2高代回交群体定位水稻籽粒大小和形状QTL

以我国优良籼稻恢复系蜀恢527为轮回亲本, 以来自菲律宾的Milagrosa为供体亲本, 培育了样本容量为199株的BC₂F₂高代回交群体。选取85个均匀分布在12条染色体上的多态性SSR标记进行基因型分析, 同时对粒长、粒宽、长宽比和千粒重4种性状进行了表型鉴定。采用性状－标记间的单向和双向方差分析对上述性状进行了QTL定位。单向方差分析(P<0.01)共检测到了10个控制粒长、粒宽、长宽比和千粒重的QTL, 其中有3个具有多效性。由于粒长和长宽比的高度相关性, 控制长宽比的2个QTL均能在粒长QTL中检测到。位于第3染色体着丝粒区域的qgl3b是一个控制粒长、长宽比和千粒重的主效QTL, 它可以分别解释粒长、长宽比和千粒重表型变异的29.37%、26.15%和17.15%。该QTL对于粒长、长宽比和千粒重均表现较大的加性效应(来自蜀恢527的等位基因为增效)和负向超显性。位于第8染色体的qgw8位点是一个控制粒宽的主效QTL, 同时也是控制千粒重的微效QTL, 能解释粒宽表型变异的21.47%和千粒重表型变异的5.16%。该QTL对粒宽和千粒重均具有较大的加性效应(来自蜀恢527的等位基因为增效)和正向部分显性。双向方差分析(P<0.005)共检测到61对显著的上位性互作, 涉及54个QTL, 其中23个是能同时影响2~4个性状的多效位点, 且有8个位点与单向方差分析检测到的相同。控制长宽比的13对上位性互作位点中, 与控制粒长的上位性互作位点完全相同的有8对。以上结果为进一步开展水稻籽粒大小和形状有利基因的精细定位、克隆和分子设计育种奠定了基础。     

Mapping QTL for stay-green and agronomic traits in wheat under diverse water regimes

Wheat (Triticum aestivum L.) yield is directly proportional to physio-morphological traits. A high-density genetic map consisting of 2575 markers was used for mapping QTL controlling stay-green and agronomic traits in wheat grown under four diverse water regimes. A total of 108 additive QTL were identified in target traits. Among them, 28 QTL for chlorophyll content (CC) were detected on 11 chromosomes, 43 for normalized difference vegetation index (NDVI) on all chromosomes except 5B, 5D, and 7D, five for spikes per plant (NSP) on different chromosomes, nine for plant height (PH) on four chromosomes, and 23 for thousand-kernel weight (TKW) on 11 chromosomes. Considering all traits, the phenotypic variation explained (PVE) ranged from 3.61 to 41.62%. A major QTL, QNDVI.cgb-5A.7, for NDVI with a maximum PVE of 20.21%, was located on chromosome 5A. A stable and major PH QTL was observed on chromosome 4D with a PVE close to 40%. Most distances between QTL and corresponding flanking markers were less than 1 cM, and approximately one-third of the QTL coincided with markers. Each of 16 QTL clusters on 10 chromosomes controlled more than one trait and therefore could be regarded as pleiotropic regions in response to different water regimes. Forty-one epistatic QTL were identified for all traits having PVE of 6.00 to 25.07%. Validated QTL closely linked to flanking markers will be beneficial for marker-assisted selection in improving drought-tolerance in wheat.     

QTL for flag leaf size and their influence on yield-related traits in wheat

Flag leaf-related traits (FLRTs) are determinant traits affecting plant architecture and yield potential in wheat (Triticum aestivum L.). In this study, three related recombinant inbred line (RIL) populations with a common female parent were developed to identify quantitative trait loci (QTL) for flag leaf width (FLW), length (FLL), and area (FLA) in four environments. A total of 31 QTL were detected in four environments. Two QTL for FLL on chromosomes 3B and 4A (QFll-3B and QFll-4A) and one for FLW on chromosome 2A (QFlw-2A) were major stable QTL. Ten QTL clusters (C1–C10) simultaneously controlling FLRTs and yield-related traits (YRTs) were identified. To investigate the genetic relationship between FLRTs and YRTs, correlation analysis was conducted. FLRTs were found to be positively correlated with YRTs especially with kernel weight per spike and kernel number per spike in all the three RIL populations and negatively correlated with spike number per plant. Appropriate flag leaf size could benefit the formation of high yield potential. This study laid a genetic foundation for improving yield potential in wheat molecular breeding programs.     

Quantitative trait loci mapping and epistatic analysis for grain yield and yield components using molecular markers with an elite maize hybrid

Summary The aim of this investigation was to map quantitative trait loci (QTL) associated with grain yield and yield components in maize and to analyze the role of epistasis in controlling these traits. An F_2:3 population from an elite hybrid (Zong3 × 87-1) was used to evaluate grain yield and yield components in two locations (Wuhan and Xiangfan, China) using a randomized complete-block design. The mapping population included 266 F_2:3 family lines. A genetic linkage map containing 150 simple sequence repeats and 24 restriction fragment length polymorphism markers was constructed, spanning a total of 2531.6 cM with an average interval of 14.5 cM. A logarithm-of-odds threshold of 2.8 was used as the criterion to confirm the presence of one QTL after 1000 permutations. Twenty-nine QTL were detected for four yield traits, with 11 of them detected simultaneously in both locations. Single QTL contribution to phenotypic variations ranged from 3.7% to 16.8%. Additive, partial dominance, dominance, and overdominance effects were all identified for investigated traits. A greater proportion of overdominance effects was always observed for traits that exhibited higher levels of heterosis. At the P ≤ 0.005 level with 1000 random permutations, 175 and 315 significant digenic interactions were detected in two locations for four yield traits using all possible locus pairs of molecular markers. Twenty-four significant digenic interactions were simultaneously detected for four yield traits at both locations. All three possible digenic interaction types were observed for investigated traits. Each of the interactions accounted for only a small proportion of the phenotypic variation, with an average of 4.0% for single interaction. Most interactions (74.9%) occurred among marker loci, in which significant effects were not detected by single-locus analysis. Some QTL (52.2%) detected by single-locus analysis were involved in epistatic interactions. These results demonstrate that digenic interactions at the two-locus level might play an important role in the genetic basis of maize heterosis.     

水稻品种魔王谷粒形、剑叶性状和株高QTL定位

以粳稻魔王谷和籼稻CO39配组衍生的280个重组自交系为材料, 2015年和2016年对其粒形、剑叶形态、株高性状进行了相关性分析和QTL检测。剑叶长分别与粒厚和株高存在极显著负相关和正相关, 剑叶宽与粒宽存在极显著正相关。检测到17个粒形QTL, 分布于第1、第2、第3、第4、第5、第6、第7、第9和第10染色体上, 贡献率为3.51%~48.65%; 其中, 第3染色体RM6080-RM6283区间对粒长和千粒重兼具显著作用, 第5染色体RM8211-RM3381区间同时影响粒宽和粒厚。检测到12个控制剑叶形态性状的QTL, 分布于第1、第3、第4、第6、第7和第9染色体上, 贡献率为4.26%~38.40%; 有5个多效QTL区间, 其中, 第4染色体RM252-SFP4_6区间同时控制剑叶长、剑叶宽、剑叶面积和粒长, 第9染色体RM257-RM3909区间同时影响剑叶面积和粒长。只检测到一个控制株高的QTL, 位于第1染色体的RM6333-RM5536区间, 是一个主效QTL, 贡献率为28.76%。这些结果为进一步开展粒形、剑叶形态、株高基因的精细定位、克隆和分子辅助育种奠定了基础。     

Mapping and validation of the quantitative trait loci for leaf stay‐green‐associated parameters in maize

Functional stay‐green is generally regarded as a desirable trait of varieties in major crops including maize. In this study, we used an F_3:4 recombinant inbred line population with 165 lines from a cross between a stay‐green inbred line (Zheng58) and a model inbred line (B73) using 211 polymorphic simple sequence repeat markers to map quantitative trait loci for three stay‐green‐associated parameters, chlorophyll content, photosystem II photochemical efficiency and stay‐green area, at maturity stage, detected a total of 23 quantitative trait loci (QTL) on nine chromosomes. Single QTL explained 3.7–13.5% of the phenotypic variance. Additionally, we validated some important stay‐green QTL using a heterogeneous inbred family approach and found that the stay‐green‐associated parameters were significantly correlated with the plant yield. This study may contribute to a better insight into the regulatory mechanism behind leaf stay‐green in maize and a novel development of elite maize varieties with delayed leaf senescence through molecular marker‐assisted selection.     

小麦DH群体穗下节间直径、茎壁厚及茎壁面积的QTL定位

由小麦品种花培3号和豫麦57杂交获得168个DH株系,连续两年在山东泰安种植,利用324个SSR标记构建遗传连锁图谱,并基于混合线性模型对控制穗下节间直径、茎壁厚及茎壁面积的QTL遗传效应和环境互作效应进行分析。共检测到10个加性效应位点和6对上位效应位点,其中3个加性位点参与环境互作效应。检测到位于染色体2D、3D和5D(2个)控制穗下节间直径的4个加性QTLs,与控制茎壁厚的3个加性位点相同或相邻,表现出一因多效或紧密连锁效应。两个位于染色体2D和5D控制茎壁厚和茎壁面积QTL有较大遗传贡献率,分别为11.37%和10.98%,适用于分子标记辅助育种和聚合育种。6对上位性效应遗传贡献率较小、无环境互作效应。     

玉米抗穗粒腐病QTL定位

用已构建的包括88个AFLP标记和151个SSR标记的遗传图谱和230个F₂植株用于抗病QTL定位研究,在四川雅安、绵阳对F2株系进行抗病性鉴定,采用复合区间定位法进行抗病QTL检测。在雅安检测到位于第2、3、4、6和9染色体上的抗病QTL 6个,解释表型变异的8.3%~25.7%;在绵阳检测到位于第1、6、7和9染色体上的抗病QTL 4个,解释表型变异的11.3%~26.4%。在10个抗病QTL中,位于第6和第9染色体上的2个同时在两点被检测到,贡献率均超过15%,表明玉米穗粒腐病确实存在遗传抗病性。利用2个环境抗病指数的平均值进行抗性QTL检测,共检测到位于第1、6和7连锁群上的3个抗性QTL,单个QTL的贡献率在8.9%~17.2%之间。结果有助于了解玉米穗粒腐病的抗性机制,并为分子标记辅助选择提供理论支撑。     

Mapping quantitative trait loci for yield-related traits in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

Chinese cabbage (Brassica rapa L. ssp. pekinensis) is one of the most important vegetables in China. However, the inheritance of yield-related traits in Chinese cabbage is poorly understood to date. To map quantitative trait loci (QTL) for yield-related traits in Chinese cabbage, a genetic linkage map was constructed with 192 doubled haploid (DH) lines. The genetic map was constructed based on 190 sequence-related amplified polymorphisms and 43 simple sequence repeats. QTL mapping was conducted for 11 yield-related traits in 170 DH lines derived from a cross between two diverse Chinese cabbage lines, ‘WZ’ and ‘FT’, under different environmental conditions. A total of 46 main QTL (M-QTL) and 7 epistatic QTL (E-QTL) were identified. The phenotypic variation explained by each M-QTL and E-QTL ranged from 4.85 to 25.06 % and 1.85 to 13.29 %, respectively. The QTL-by-environment interactions were detected using the QTLNetwork 2.0 program in joint analyses of multi-environment phenotypic values. The phenotypic variation explained by each QTL and by QTL × environment interaction was 1.14–4.24 % and 0.00–1.26 %, respectively. Our results provide a better understanding of the genetic factors controlling leaf and head-related traits in Chinese cabbage.     

Genetic dissection of plant height by molecular markers using a population of recombinant inbred lines in maize

Plant height is an important trait for maize breeding because it is related to planting density and lodging resistance. It is influenced by many qualitative genes and quantitative trait loci (QTL). In this study, the genetic basis of plant height and its related traits were dissected, using simple sequence repeat (SSR) markers with a maize population of 294 recombinant inbred lines (RIL). Correlation results showed that plant height had a significant positive correlation with leaf number, average internode length and internode number. Increased plant height was affected most by average internode length. Six QTL for plant height were detected, which were consistent with those reported in previous studies. Moreover, eight QTL for leaf number, seven for internode number and six for average internode length were identified. Four of six QTL detected for average internode length were located on the same chromosomal region as the QTL affecting plant height and shared common molecular markers. This latter result strongly suggests that average internode length was the main contributor to plant height in maize.     

Quantitative trait loci mapping of maize (Zea mays) ear traits under low-phosphorus stress

We constructed an F_2:3 population of 180 individuals from a cross between the maize genotypes 082 (high phosphorus use efficiency) and Ye107 (low phosphorus use efficiency). We used the population to perform quantitative trait loci (QTL) mapping for eight ear traits (ear diameter [ED], ear length [EL], ear weight [EW], ear kernel weight [EKW], row number per ear [ERN], bald tip length [BTL], kernel number per row [RKN] and number of seeds per plant [NSP]) in three low-phosphorus environments. A total of 36 QTL for ear traits were detected in at least one of three single environments and were located on all maize chromosomes except for chromosome 10; the explained phenotypic variation ranged from 5.91% to 12.80%. The QTL JAqEKW5-1, JAqEL3-1, JAqEW1-1, JAqBTL1-1 and JAqNSP5-2 were identified and stably expressed in single-environment and joint-environment analyses. Some novel QTL that have not been reported previously were also detected. Most of the identified QTL had stable effects in all low-phosphorus environments, suggesting that they may be useful for molecular breeding to develop low-phosphorus tolerant maize varieties.     

Relationships between water-use traits and photosynthesis in Brassica oleracea resolved by quantitative genetic analysis

The genetic control of water‐use and photosynthetic traits in Brassica oleracea is resolved by genetic analysis of quantitative trait loci (QTL). Variations in leaf conductance, photosynthetic assimilation rate, leaf thickness and leaf nitrogen content were assessed in a segregating population of F₁‐derived doubled haploid (DH) B. oleracea lines. In addition, stable carbon isotope ratios in leaf organic material were used as a surrogate measure of plant water‐use efficiency. Analysis of an existing linkage map for the population revealed significant QTL on seven linkage groups. Single significant QTL explained between 3.4% and 36.6% of the phenotypic variance in each of the traits measured. The locations of QTL for several traits were found to coincide in a physiologically meaningful way; stable carbon isotope discrimination had QTL co‐locating with leaf level water‐use efficiency, photosynthetic capacity with leaf thickness and nitrogen content and stomatal density with leaf thickness. Taken together, these results suggest that single genes or clusters of genes at these loci may have an influence on the expression of physiologically related traits controlling water‐use and photosynthesis.     

利用永久F2群体定位小麦株高的QTL

为研究小麦株高的遗传机制,利用DH群体构建了一套包含168个杂交组合的小麦永久F₂群体, 并于2007年种植于山东泰安和山东聊城。构建了一套覆盖小麦21条染色体的遗传连锁图谱并利用该图谱的324个SSR标记对小麦株高进行QTL定位研究,使用基于混合线性模型的QTLNetwork 2.0软件进行QTL分析。在永久F₂群体中定位了7个株高QTL,包括4个加性QTL,一个显性QTL,一对上位性QTL,共解释株高变异的20%,其中位于4D染色体的qPh4D,具有最大的遗传效应,贡献率为7.5%;位于2D 染色体显性效应位点qPh2D,可解释1.6%的表型变异;位于5B~6D染色体上位效应位点,可解释1.7%的表型变异。还发现加性效应、显性效应和上位效应对小麦株高的遗传起重要作用,并且基因与环境具有互作效应,结果表明利用永久F₂群体进行QTL定位研究的方法有助于分子标记辅助育种。     

Multiple‐line cross QTL mapping for grain yield and thousand kernel weight in triticale

Grain yield and its component trait thousand kernel weight are important traits in triticale breeding programmes. Here, we used a large mapping population of 647 doubled haploid lines derived from four families to dissect the genetic architecture underlying grain yield and thousand kernel weight by multiple‐line cross QTL mapping. We identified 3 QTL for grain yield and 13 for thousand kernel weight which cross‐validated explained 5.2% and 48.2% of the genotypic variance, respectively. Both traits showed a positive phenotypic correlation, and we found two QTL overlapping between them. Full two‐dimensional epistasis scans revealed epistatic QTL for both traits, suggesting that epistatic interactions contribute to their genetic architecture. Based on QTL identified in our results, we conclude that the potential for marker‐assisted selection is limited for grain yield but more promising for thousand kernel weight.     

利用单片段代换系研究水稻产量相关性状QTL加性及上位性效应

产量及其相关性状如单株有效穗数、千粒重、穗实粒数、穗总粒数和结实率等是水稻重要的农艺性状,了解产量及其相关性状QTL的加性及上位性效应对以分子标记聚合育种改良水稻产量具有重要意义。本文以16个单片段代换系及15个双片段代换系分析了水稻产量相关性状QTL的加性及上位性效应。共检出影响产量及其相关性状的13个QTL,包括产量性状1个、单株有效穗数1个、千粒重4个、穗实粒数4个、穗总粒数2个和结实率1个,分布于第2、第3、第4、第7和第10染色体上。此外,检出12对双基因互作。结果显示,2个正向(或负向)产量性状QTL聚合,往往会产生负向(或正向)的上位性效应,能否产生更大(或更小)的目标性状,取决于双片段遗传效应(加性效应与上位效应代数和)绝对值与单片段最大加性效应绝对值的差。本研究结果对实施高产分子标记聚合育种方法有重要参考价值。