QTL associated with heat susceptibility index in wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.) under short-term reproductive stage heat stress

Heat stress adversely affects wheat production in many regions of the world and is particularly detrimental during reproductive development and grain-filling. The objective of this study was to identify quantitative trait loci (QTL) associated with heat susceptibility index (HSI) of yield components in response to a short-term heat shock during early grain-filling in wheat. The HSI was used as an indicator of yield stability and a proxy for heat tolerance. A recombinant inbred line (RIL) population derived from the heat tolerant cultivar ‘Halberd’ and heat sensitive cultivar ‘Cutter’ was evaluated for heat tolerance over 2 years in a controlled environment. The RILs and parental lines were grown in the greenhouse and at 10 days after pollination (DAP) half the plants for each RIL received a three-day heat stress treatment at 38°C/18°C day/night, while half were kept at control conditions of 20°C/18°C day/night. At maturity, the main spike was harvested and used to determine yield components. A significant treatment effect was observed for most yield components and a HSI was calculated for individual components and used for QTL mapping. QTL analysis identified 15 and 12 QTL associated with HSI in 2005 and 2006, respectively. Five QTL regions were detected in both years, including QTL on chromosomes 1A, 2A, 2B, and 3B. These same regions were commonly associated with QTL for flag leaf length, width, and visual wax content, but not with days to flowering. Pleiotropic trade-offs between the maintenance of kernel number versus increasing single kernel weight under heat stress were present at some QTL regions. The results of this study validate the use of the main spike for detection of QTL for heat tolerance and identify genomic regions associated with improved heat tolerance that can be targeted for future studies.     

QTL for yield, yield components and canopy temperature depression in wheat under late sown field conditions

A wheat (Triticum aestivum L.) recombinant inbred line (RIL) population was used to identify quantitative trait loci (QTL) associated with yield, yield components, and canopy temperature depression (CTD) under field conditions. The RIL population, consisting of 118 lines derived from a cross between the stress tolerant cultivar ‘Halberd’ and heat stress sensitive cultivar ‘Karl92’, was grown under optimal and late sown conditions to impose heat stress. Yield and yield components including biomass, spikes m^?2, thousand kernel weight, kernel weight and kernel number per spike, as well as single kernel characteristics were determined. In addition, CTD was measured during both moderate (32–33 °C) and extreme heat stress (36–37 °C) during grain-filling. Yield traits showed moderate to high heritability across environments with a large percentage of the variance explained by genetic effects. Composite interval mapping detected 25 stable QTL for the 15 traits measured, with the amount of phenotypic variation explained by individual QTL ranging from 3.5 to 27.1 %. Two QTL for both yield and CTD were co-localized on chromosomes 3BL and 5DL and were independent of phenological QTL. At both loci, the allele from Halberd was associated with both higher yield and a cooler crop canopy. The QTL on 3BL was also pleiotropic for biomass, spikes m^?2, and heat susceptibility index. This region as well as other QTL identified in this study may serve as potential targets for fine mapping and marker assisted selection for improving yield potential and stress adaptation of 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.     

Mapping quantitative trait loci associated with grain filling duration and grain number under terminal heat stress in bread wheat (Triticum aestivum L.)

Terminal heat stress has the potential negative impact on wheat production across the world, especially in South Asia. Under the threat of terminal heat stress, wheat genotypes with stay green trait would suffer from high temperature stress during their long grain filling duration (GFD). The genotypes with short GFD would be advantageous. To identify quantitative trait loci (QTL) for heat tolerance, a RIL population of K 7903 (heat tolerant) and RAJ 4014 (heat sensitive) wheat genotypes was investigated under timely and late‐sown conditions. Heat susceptibility index of GFD, yield components and traits under late‐sown condition were used as phenotypic data for QTL identification. Stable QTLs associated with these traits were identified on chromosomes 1B, 2B, 3B, 5A and 6B. The LOD value ranged from 2.9 to 5.0 and the corresponding phenotyping variation explained ranged from 12.0–22%. QTL for heat susceptibility index for the grain filling duration were colocalized with QTL for productive tillers under late sown and GFD under late‐sown condition on chromosomes 1B and 5A, respectively. These genomic regions could be exploited for molecular wheat breeding programmes targeting heat tolerance.     

Family-based QTL mapping of heat stress tolerance in primitive tetraploid wheat (Triticum turgidum L.)

Identification of quantitative trait loci (QTL) and markers associated with heat and drought tolerance is warranted for marker-assisted selection in wheat (Triticum aestivum L.) breeding programs in areas prone to these abiotic stresses. Our study used a family-based mapping approach in which 19 families consisting of 384 individuals were developed by three-way crosses involving the heat tolerant, tetraploid cultivated emmer (Triticum turgidum L. var dicoccum) genotype IG45069 and ten heat susceptible tetraploid genotypes, IG44999, IG44961, IG45413, IG83047, IG45441, IG127682, IG45448, IG110572, IG88723 and IG54073, in order to detect QTL and markers associated with heat tolerance. The 384 individuals were phenotyped for physiological traits associated with heat tolerance and genotyped by SSR markers. The QTL associated with heat stress tolerance, as measured by chlorophyll content, flag leaf temperature depression (FLTD) and individual kernel weight (IKW) were mapped on chromosomes 1B (QChlc.tamu-1B), 2B (QFlt.tamu-2B), and 5A (QIkw.tamu-5A), respectively, using linkage analysis. Alleles from IG45069 possessed the highest associations with the phenotypic data for the studied traits. This study demonstrates that a family-based mapping approach can be utilized in rapid detection of QTL associated with heat tolerance in wheat based on linkage and association analyses.     

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.     

Quantitative trait loci for resistance to Fusarium head blight in the Chinese wheat landrace Huangfangzhu

The Chinese wheat landrace Huangfangzhu (HFZ) has a high level of resistance to Fusarium head blight (FHB). To identify chromosomal regions that are responsible for FHB resistance in HFZ, F₈ recombinant inbred lines (RIL) were developed from a cross between HFZ and Wheaton, a U.S. hard spring wheat. FHB was evaluated by single floret inoculation in both greenhouse and field environments. Two quantitative trait loci (QTL) with major effects were identified. One QTL was located on the short arm of chromosome 3B, and explained 35.4% of the phenotypic variation; the other QTL was assigned to 7AL and explained 18.0% of the phenotypic variation for FHB response. In addition, three minor QTL were detected on chromosomes 1AS, 1B and 5AS by single marker regression. HFZ contributed all favorable alleles. The RIL with HFZ alleles at the QTL on 3BS and 7AL displayed significantly lower percentages of infected spikelets than RIL without these alleles in both greenhouse and field environments. HFZ combined several alleles from germplasm reported previously and is a promising alternative source for improving wheat FHB resistance.     

冬小麦品种生育后期的耐热性评价

冬小麦品种生育后期耐热性遗传差异的表现受环境影响较大。通过1997～2000年间在北京对群体气-冠温差、灌浆特性、热感指数等三种耐热性评价方法有效性的比较研究，认为热感指数反映品种对后期热胁迫的敏感程度，利用千粒重热感指数可鉴定出后期耐热性较好的基因型。气-冠温差法快速、简便、准确，但叶片持绿期长的品种气-冠温差一般较大，可结合对灌浆速率的评价来筛选生育期适中的耐热基因型。在3年的试验中，小麦品种鲁936098表现耐热性强，千粒重稳定。     

Identification of QTLs associated with heat tolerance at the heading and flowering stage in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

The ongoing rise in temperatures caused by global climate change is a critical climatic risk factor for rice production, and enhancing rice heat tolerance is an area of particular research interest. A recombinant inbred line (RIL) mapping population was developed from heat sensitive, rice cultivar IAPAR-9 crossed with heat tolerant, Liaoyan241. RIL and parental lines were exposed to high temperature at the heating and flowering stage in experiments in 2014 and 2015. As indicators of heat tolerance, the seed setting rate under natural (NS) and heat stress (HTS) conditions were measured, and the reduction rate of seed set (RRS) was calculated. Quantitative trait loci (QTL) analysis revealed eleven heat tolerance QTLs located on chromosomes 1, 3, 4, 5, and 6. Single QTL contribution rates were 4.75–13.81% and effect values were ? 5.98 to 5.00. Four major QTLs (qNS1, qNS4, qNS6, and qRRS1) were stable detected in different environments in both years. Thirteen QTLs with epistatic interactions and nine QTLs with environmental interactions were also detected. Major QTLs were all involved in epistatic and environmental interactions. Three QTLs from the SSR marker interval RM471 to RM177 region of chromosome 4 (qNS4, qHTS4, and qRRS4) were all involved in epistatic and environmental interactions and contributed to phenotypic variation, indicating that this region constituted a major QTL hotspot. The major QTL for heat tolerance identified in this study will aid in breeding tolerant cultivars and facilitating investigation of the molecular underpinnings of heat tolerance in rice.     

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。     

Several stably expressed QTL for spike density of common wheat (Triticum aestivum) in multiple environments

Spike density (SD), an important spike morphological trait associated with wheat yield, is the spikelet number per spike (SNS) divided by spike length (SL). In this study, phenotypic data from eight environments were collected and a recombinant inbred line population (RIL) constructed by the wheat line 20828 and the cultivar 'Chuannong16' and a Wheat55K SNP array-based constructed genetic linkage map were used to identify SD quantitative trait locus (QTL). Correlation between SD and other agronomic traits was calculated. Genes associated with plant growth and development for major loci were predicted. The results showed that 24 QTLs associated with SD were detected in eight environments. Among them, three major QTL, namely QSd.sicau-5B.2, QSd.sicau-2D.3 and QSd.sicau-4B.1, explained up to 35.62%, 14.21% and 11.23% of phenotypic variation, respectively. The positive alleles of them were all derived from 'Chuannong16'. The significant relationships between SD and other agronomic traits were detected and discussed. Taken together, the stably expressed SD QTL under different environments identified in this study provided theoretical guidance for further fine mapping and germplasm improvement.     

Flag Leaf Variation and the Analysis of Diversity in Durum Wheat

Flag leaf in wheat (Triticum spp.) is a major source of photosynthate for the developing grain and its size contributes to interplant competition. Flag leaf length, width, and area in a sample of 778 entries of durum wheat (T. turgidum L. durum group) germplasm obtained from the U.S. National Small Grains Collection showed considerable phenotypic variation. Correlations between flag leaf and eight spike quantitative characters showed significant values greater than 0.30 for kernel weight per spike with all three flag leaf measurements and for awn length with flag leaf length and area. Larger flag leaf area appeared to be associated with accessions having a history of some deliberate plant breeding for high grain yield. A multivariate approach was used to assess how discrimination among 26 countries of origin obtained with spike characters in a previous study was affected by reducing the sample size from about 3,000 to 735 and by the addition of flag leaf measurements to the analysis. The reduced sample size had little impact on the results of the previous analysis on the whole collection of about 3,000 entries. The addition of flag leaf characters to the analysis caused a rearrangement in the clusters of countries, mostly from Asia, where less germplasm modified by plant breeding was included in the collection. Five clusters were identified: (1) 11 Mediterranean basin countries, (2) USA, UdSSR, and Yugoslavia, (3) four Near East Countries and Bulgaria, (4) three Middle East countries and Greece, India and Ethiopia, and (5) Afghanistan. Phenotypic differentiation of durum wheat, and probably many other crops, on a geographic basis is more pronounced in areas where plant breeding has had little impact.     

水稻孕穗期耐热性QTLs分析

水稻籼粳亚种间杂种优势利用是提高水稻产量的重要途径。然而，异常高温或低温导致籼粳亚种间杂种育性下降是影响其优势利用的主要因素之一。本研究以USSR5（粳稻）/广解9号（籼稻）//USSR5回交群体为供试材料，构建了相应的分子连锁图谱，分别以高温处理下直接小穗育性及小穗育性热敏感指数为指标，对水稻孕穗期高温耐热性及其相对耐热性进行数量性状位点（QTLs）分析。结果表明，在第2、4和5染色体上检测到孕穗期耐热性相关的QTL各一个，对表型变异的解释率为6.4%~15.8%；在第4、8染色体上分别检测到与孕穗期相对耐热性相关的QTL，qhts-4和qhts-8，LOD值分别为3.81和2.86，对表型变异的解释率分别为16.8%和9.9%。对其进一步的上位性分析表明，有8条染色体的4对位点存在基因间互作，小穗育性耐热性除受主效QTL控制外，还受基因间互作及修饰基因的影响。     

Detection of quantitative trait locus for leaffolder (Cnaphalocrocis medinalis (Guenée)) resistance in rice on linkage group 1 based on damage score and flag leaf width

Rice leaffolder (RLF) (Cnaphalocrocis medinalis (Guenée) is a destructive and widespread insect pest throughout the rice growing regions in Asia. The genetics of resistance to RLF in rice is very complex and not thoroughly explored. The present study was conducted to detect the quantitative trait loci (QTL) associated with RLF resistance involving 176 recombinant inbred lines (RILs) of F₈ generation derived from a cross between IR36, a leaffolder susceptible variety and TNAULFR831311, a moderately resistant indica rice culture. Simple sequence repeat (SSR) markers were used to construct specific linkage groups of rice. All the RILs were screened to assess their level of resistance to RLF by measuring the leaf area damaged. Besides this, the length and width of the flag leaf of each RIL were measured since these two parameters were considered as correlated traits to the RLF resistance in rice. All the above parameters observed across the RILs showed quantitative variation. Correlation analysis revealed that damage score based on greenhouse screening was positively correlated with length and width of the flag leaf. Out of 364 SSR markers analysed, 90 were polymorphic between the parents. Multi-point analysis carried out on segregating 69 SSR marker loci linkage group wise resulted in construction of linkage map with eleven groups of 42 SSR markers. Through single marker analysis, 19 SSR markers were found to have putative association with the three phenotypic traits studied. Of these markers, RM472 was identified as a locus having major effect on RLF resistance trait based on length of the flag leaf. Interval mapping detected two QTLs on linkage group 1. Among these QTLs, the QTL flanked by RM576–RM3412 were found to be associated with width of the flag leaf and RLF resistance. The putative SSR markers associated with leaffolder resistance identified in the present study may be one of the loci contributing resistance to RLF in rice.     

燕大1817/北农6号重组自交系群体穗部性状的QTL定位

小麦穗部性状与单株产量密切相关。本研究以小麦骨干亲本燕大1817与优良品系北农6号衍生的269个重组自交系为材料,通过在北京和河北石家庄的2年田间试验数据,利用本实验室已构建的高密度SNP和SSR遗传连锁图谱进行穗长、穗粒数和穗粒重QTL定位。采用完备复合区间作图法共检测到29个穗部性状加性效应QTL,其中10个穗长QTL分布于1B、2D、3A、3B、4A、5A、5B、6A和7D染色体上,解释的表型变异率为2.96%~9.63%,QSl.cau-4A.2在所有5个环境中均能被检测到,解释的表型变异为5.89%~9.62%,另有7个QTL能在2个或2个以上环境中被检测到;8个穗粒数相关QTL分布于1A、3A、3D、4A和5B染色体上,解释的表型变异为4.06%~11.17%,为单个环境QTL。11个与穗粒重相关QTL分布于1A、1B、2A、2D、3A、4D、5A、5B和6B染色体上,解释的表型变异为2.79%~16.12%,其中QGws.cau-1B、QGws.cau-3A和QGws.cau-6B.2在2个或者2个以上环境中能被检测到。另外,鉴定出6个分布于1A、2D、3A、4A和5B染色体上的QTL富集区段。     

Dissection of the genetic architecture for grain quality‐related traits in three RIL populations of maize (Zea mays L.)

To manipulate the composition of the maize kernel to meet future needs, an understanding of the molecular regulation of kernel quality‐related traits is required. In this study, the quantitative trait loci (QTL) for the concentrations of grain protein, starch and oil were identified using three sets of RIL populations in three environments. The genetic maps and the initial QTL were integrated using meta‐analyses. A total of 38 QTL were identified, including 15 in population 1, 12 in population 2 and 11 in population 3. The individual effects ranged from 2.87% to 13.11% of the phenotypic variation, with seven QTL each contributing over 10%. One common QTL was found for the concentrations of grain protein and starch in bin 3.09 in the three environments and the three RIL populations. Of the 38 initial QTL, 22 were integrated into eight mQTL by meta‐analysis. mQTL3 and mQTL8 of the key mQTL in which the initial QTL displayed R² > 10% included six and three initial QTL for grain protein and starch concentrations from two or three populations, respectively. These results will provide useful information for marker‐assisted selection to improve the quality of the maize kernel.     

Genome-wide association study of differences in 14 agronomic traits under low- and high-density planting models based on the 660k SNP array for common wheat

One hundred and ninety-seven wheat accessions from Yellow and Huai Winter Wheat Region (YHW) were evaluated for differences of 14 agronomic traits under low- and high-density plantings. Compared with the high-density plantings, plant height, neck length, uppermost internode length, flag leaf angle and number of sterile spikelets under the low-density plantings reduced, while heading date, flowering date, flag leaf length and width, spike length, number of fertile spikelets, grain number per spike, thousand-kernel weight and grain weight per spike increased. A total of 1,118 markers were detected based on GWAS, and seven QTLs were confirmed. One QTL on chromosomes 5BL and two other QTLs on 5Dl were all tightly associated with flowering date difference. Bioinformatics analysis revealed that two haploblocks in 5Dl were involved, and the Vrn-D1 locus was located in this interval. A region on chromosome 5B at around 531.5 Mb was significantly associated with plant height difference. Two QTLs including AX-94840438 (7BL) and AX-94563647 (7DS) were responsible for neck length or uppermost internode length difference.     

水稻剑叶角度与主穗产量的遗传剖析

理想水稻株型的选育与高产育种密切相关,而剑叶角度则是构成水稻理想株型的重要指标之一,同时也是影响水稻产量的重要因素。合理开发利用水稻中控制剑叶角度及产量相关的数量性状基因座位（QTL）,并结合分子育种技术,可更好地为高产制繁种目标服务。通过应用由244个株系组成的珍汕97B/密阳46重组自交系（RIL）群体,构建含256个分子标记的连锁图谱,采用QTL区间作图法对剑叶角度及主穗产量等5个性状进行定位分析,共检测到17个QTL,分布于染色体1、2、3、5、6、9、10、11。这些QTL对相应性状的贡献率介于3.46%~25.64%之间。在第1染色体上检测到控制5个性状的QTL,其中控制剑叶角度的两个QTL;在第2、3、9、10、11染色体上分别检测到各一个QTL;第5染色体上检测到控制剑叶、每穗总粒数和每穗实粒数的3个QTL;1个每穗实粒数和2个每穗实粒重的QTL分布于第6染色体上。多个区间表现出对两个性状的显著作用,其中第1染色体2个,第6染色体1个。相关性分析表明,较小的剑叶角度可通过提高结实率进而显著增加产量。     

QTL analysis of kernel shape and weight using recombinant inbred lines in wheat

Quantitative trait locus (QTL) analysis of kernel shape and weight in common wheat was conducted using a set of 131 recombinant inbred lines (RIL) derived from ‘Chuan 35050’ × ‘Shannong 483’. The RIL and their two parental genotypes were evaluated for kernel length (KL), kernel width (KW), thousand-kernel weight (TKW), and test weight (TW) in four different environments. Twenty QTL were located on 12 chromosomes, 1A, 1B, 1D, 2A, 2B, 3B, 4A, 4B, 5D, 6A, 6B, and 7B, with single QTL in different environments explaining 5.9–26.4% of the phenotypic variation. Six, three, four, and seven QTL were detected for KL, KW, TKW, and TW, respectively. The additive effects for 17 QTL were positive with Chuan 35050 increasing the QTL effects, whereas the remaining three QTL were negative with Shannong 483 increasing the effects. Eight QTL (40%) were detected in two or more environments. Two QTL clusters relating to KW, TKW, and TW were located on chromosomes 2A and 5D, and the co-located QTL on chromosome 6A involved a QTL for KW found in two environments and a QTL for TKW detected in four environments.