Characterization and precise mapping of a QTL increasing spike number with pleiotropic effects in wheat

Tiller number (TN) and spike number per plant (SN) are key components of grain yield and/or biomass in wheat. In this study, an introgression line 05210, developed by introgression of chromosomal segments from a synthetic exotic wheat Am3 into an elite cultivar Laizhou953, showed a significantly increased TN and SN, but shorter spike length (SL) and fewer grain number per spike (GNS) than Laizhou953. To investigate the quantitative trait locus (QTL) responsible for these variations, the introgressed segments in 05210 were screened by SSR markers and one follow-up segregation population was developed from the cross 05210/Laizhou953. The population showed 3:1 segregation ratios for SN, SL and GNS, indicating that QTLs for these traits have been dissected into single Mendelian factors. Bulked segregation analysis showed that the markers located on the 4B introgressed segment were polymorphic between the two bulks. Therefore, they were further analyzed in the F₂ population to construct a linkage map. Three new QTLs, QSn.sdau-4B, QSl.sdau-4B and QGns.sdau-4B, were detected for SN, SL and GNS, respectively, which explained a large portion of the phenotypic variation (30.1–67.6%) for these traits with overlapping peaks. Correlation analysis and multiple-trait, multiple-interval mapping (MMIM) suggested pleiotropic effects of the QTL on SN, SL and GNS. Therefore, the QTL was designated as QSn.sdau-4B. By a progeny test based on F₃ families using SN, the QTL was mapped as a Mendelian factor to the proximal region of 4BL. It is a key QTL responsible for variation in spike number and size, which had not been reported previously. Thus, it is an important QTL for wheat to achieve high and stable biomass and grain yield. Dissection and mapping of this QTL as a Mendelian factor laid a solid foundation for map-based cloning of grain yield-related QTLs in wheat.     

A new intervarietal linkage map and its application for quantitative trait locus analysis of "gigas" features in bread wheat.

A doubled-haploid (DH) population from an intervarietal cross between the Japanese cultivar 'Fukuho-komugi' and the Israeli wheat line 'Oligoculm' was produced by means of wheat x maize crosses. One hundred seven DH lines were genotyped to construct a simple sequence repeat (SSR) based linkage map with RFLP, RAPD, and inter-simple sequence repeat markers. Out of 570 loci genotyped, 330 were chosen based on their positions on the linkage map to create a "framework" map for quantitative trait locus (QTL) analysis. Among the 28 linkage groups identified, 25 were assigned to the 21 chromosomes of wheat. The total map length was 3948 cM, including the three unassigned linkage groups (88 cM), and the mean interval between loci was 12.0 cM. Loci with segregation distortion were clustered on chromosomes 1A, 4B, 4D, 5A, 6A, 6B, and 6D. After vernalization, the DH lines were evaluated for spike number per plant (SN) and spike length (SL) in a greenhouse under 24-h daylength to assess the "gigas" features (extremely large spikes and leaves) of 'Oligoculm'. The DH lines were also autumn-sown in the field in two seasons (1990-1991 and 1997-1998) for SN and SL evaluation. QTL analysis was performed by composite interval mapping (CIM) with the framework map to detect QTLs for SN and SL. A major QTL on 1AS, which was stable in both greenhouse and field conditions, was found to control SN. This QTL was close to the glume pubescence locus (Hg) and explained up to 62.9% of the total phenotypic variation. The 'Oligoculm' allele restricted spike number. The SSR locus Xpsp2999 was the closest locus to this QTL and is considered to be a possible marker for restricted tillering derived from 'Oligoculm'. Eight QTLs were detected for SL. The largest QTL detected on 2DS was common to the greenhouse and field environments. It explained up to 33.3% of the total phenotypic variation. The second largest QTL on 1AS was common to the greenhouse and the 1997-1998 season. The position of this QTL was close to that for the SN detected on 1AS. The association between SN and SL is discussed.     

Mapping QTL for grain yield, yield components, and spike features in a doubled haploid population of bread wheat

A doubled haploid (DH) population derived from a cross between the Japanese cultivar 'Fukuho-kumogi' and the Israeli wheat line 'Oligoculm' was used to map genome regions involved in the expression of grain yield, yield components, and spike features in wheat (Triticum aestivum L). A total of 371 markers (RAPD, SSR, RFLP, AFLP, and two morphological traits) were used to construct the linkage map that covered 4190 cM of wheat genome including 28 linkage groups. The results of composite interval mapping for all studied traits showed that some of the quantitative trait loci (QTL) were stable over experiments conducted in 2004 and 2005. The major QTL located in the Hair-Xpsp2999 interval on chromosome 1A controlled the expression of grains/spike (R(2) = 12.9% in 2004 and 22.4% in 2005), grain weight/spike (R(2) = 21.4% in 2004 and 15.8% in 2005), and spike number (R(2) = 15.6% in 2004 and 5.4% in 2005). The QTL for grain yield located on chromosomes 6A, 6B, and 6D totally accounted for 27.2% and 31.7% of total variation in this trait in 2004 and 2005, respectively. Alleles inherited from 'Oligoculm' increased the length of spikes and had decreasing effects on spike number. According to the data obtained in 2005, locus Xgwm261 was associated with a highly significant spike length QTL (R(2) = 42.33%) and also the major QTL for spikelet compactness (R(2) = 26.1%).     

Kernel weight per spike: what contributes to it at the individual QTL level?

Spike length (SL), spikelet number (SPN) per spike, kernel number per spike (KNPS), and thousand-kernel weight (TKW) have strong genetic associations with kernel weight per spike (KWPS) in wheat. To investigate their genetic relationships at the individual quantitative trait locus (QTL) level, both unconditional and conditional QTL mapping for KWPS with respect to SL, SPN, KNPS, and TKW were conducted. Two related F_8:9 recombinant inbred line populations, comprising 485 and 229 lines, respectively, were used. The trait phenotypic performances of each population were evaluated in four different environments. Unconditional QTL mapping analysis identified 22 putative additive QTL for KWPS, five of which were stable QTL, and only QKwps-WJ-1B.2 showed significant additive-by-environment interaction effects. In comparison with unconditional QTL mapping analysis, conditional QTL mapping analysis indicated that, at the QTL level, KNPS and TKW contributed more to KWPS than did SL and SPN. Any unconditional QTL for KWPS detected in this study was associated with at least one of its four related traits. The present study will provide assistance in the understanding of the genetic relationships between KWPS and its related traits.     

Identification of QTL for flag leaf length in common wheat and their pleiotropic effects

Leaf size is an important factor contributing to the photosynthetic capability of wheat plants. It also significantly affects various agronomic traits. In particular, the flag leaves contribute significantly to grain yield in wheat. A recombinant inbred line (RIL) population developed between varieties with significant differences in flag leaf traits was used to map quantitative trait loci (QTL) of flag leaf length (FLL) and to evaluate its pleiotropic effects on five yield-related traits, including spike length (SL), spikelet number per spike (SPN), kernel number per spike (KN), kernel length (KL), and thousand-kernel weight (TKW). Two additional RIL populations were used to validate the detected QTL and reveal the relationships in different genetic backgrounds. Using the diversity arrays technology (DArT) genetic linkage map, three major QTL for FLL were detected, with single QTL in different environments explaining 8.6–23.3% of the phenotypic variation. All the QTL were detected in at least four environments, and validated in two related populations based on the designed primers. These QTL and the newly developed primers are expected to be valuable for fine mapping and marker-assisted selection in wheat breeding programs.     

Genetic insight into yield-associated traits of wheat grown in multiple rain-fed environments

Background

Grain yield is a key economic driver of successful wheat production. Due to its complex nature, little is known regarding its genetic control. The goal of this study was to identify important quantitative trait loci (QTL) directly and indirectly affecting grain yield using doubled haploid lines derived from a cross between Hanxuan 10 and Lumai 14.

Methodology/Principal Findings

Ten yield-associated traits, including yield per plant (YP), number of spikes per plant (NSP), number of grains per spike (NGS), one-thousand grain weight (TGW), total number of spikelets per spike (TNSS), number of sterile spikelets per spike (NSSS), proportion of fertile spikelets per spike (PFSS), spike length (SL), density of spikelets per spike (DSS) and plant height (PH), were assessed across 14 (for YP) to 23 (for TGW) year × location × water regime environments in China. Then, the genetic effects were partitioned into additive main effects (a), epistatic main effects (aa) and their environment interaction effects (ae and aae) by using composite interval mapping in a mixed linear model.

Conclusions/Significance

Twelve (YP) to 33 (PH) QTLs were identified on all 21 chromosomes except 6D. QTLs were more frequently observed on chromosomes 1B, 2B, 2D, 5A and 6B, and were concentrated in a few regions on individual chromosomes, exemplified by three striking yield-related QTL clusters on chromosomes 2B, 1B and 4B that explained the correlations between YP and other traits. The additive main-effect QTLs contributed more phenotypic variation than the epistasis and environmental interaction. Consistent with agronomic analyses, a group of progeny derived by selecting TGW and NGS, with higher grain yield, had an increased frequency of QTL for high YP, NGS, TGW, TNSS, PFSS, SL, PH and fewer NSSS, when compared to low yielding progeny. This indicated that it is feasible by marker-assisted selection to facilitate wheat production.     

Saturation and mapping of a majorFusarium head blight resistance QTL on chromosome 3BS of Sumai 3 wheat

Fusarium head blight (FHB) is a destructive disease in wheat. The major quantitative trait locus (QTL) on 3BS from Sumai 3 and its derivatives has been used as a major source of the resistance to FHB worldwide, but the discrepancy in reported location of the major QTL could block its using in map based cloning and marker assisted selection. In this study, Chinese Spring-Sumai 3 chromosome 3B substitution line was used as resistant parent of the mapping population to reduce the confounded effect of genetic background in Sumai 3. The major QTL region was saturated with the Sequence Tagged Microsatellite (STM) and Sequence Tagged Site (STS) markers. A linkage map of chromosome 3B with 36 markers covering a genetic distance of 112.4 cM was constructed. Twelve new markers were inserted into the chromosome region where the major QTL was located. The average interval distance between markers was 1.5 cM. Multiple QTL Models (MQM) mapping indicated that the major QTL was located in the interval ofXgwm533 — Xsts9-1, and explained 45.6% of phenotypic variation of the resistance to FHB. The SSR (simple sequence repeat) markerXgwm533 and STM markerXstm748tcac are closely linked to the major QTL.     

Identification and mapping of genetic loci affecting the free-threshing habit and spike compactness in wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.)

Recombinant inbred lines of the International Triticeae Mapping Initiative (ITMI) mapping population were used to localize genetic loci that affect traits related to the free-threshing habit (percent threshability, glume tenacity, and spike fragility) and to spike morphology (spike length, spikelet number, and spike compactness) of wheat (Triticum aestivum L.). The ITMI population was planted in three environments during 1999 and 2000, and phenotypic and genotypic data were used for composite interval mapping. Two quantitative trait loci (QTL) that consistently affected threshability-associated traits were localized on chromosomes 2D and 5A. Coincident QTL on the short arm of 2D explained 44% of the variation in threshability, 17% of the variation in glume tenacity, and 42% of the variation in rachis fragility. QTL on chromosomes 2D probably represent the effect of Tg, a gene for tenacious glumes. Coincident QTL on the long arm of 5A explained 21% and 10% of the variation in glume tenacity and rachis fragility, respectively. QTL on 5A are believed to represent the effect of Q. Overall, free-threshing-related characteristics were predominantly affected by Tg and to a lesser extent by Q. Other QTL that were significantly associated with threshability-related traits in at least one environment were localized on chromosomes 2A, 2B, 6A, 6D, and 7B. Four QTL on chromosomes 1B, 4A, 6A, and 7A consistently affected spike characteristics. Coincident QTL on the short arm of chromosome 1B explained 18% and 7% of the variation in spike length and spike compactness, respectively. QTL on the long arm of 4A explained 11%, 14%, and 12% of the variation in spike length, spike compactness, and spikelet number, respectively. A QTL on the short arm of 6A explained 27% of the phenotypic variance for spike compactness, while a QTL on the long arm of 7A explained 18% of the variation in spikelet number. QTL on chromosomes 1B and 6A appear to affect spike dimensions by modulating rachis internode length, while QTL on chromosomes 4A and 7A do so by affecting the formation of spikelets. Other QTL that were significantly associated with spike morphology-related traits, in at least one environment, were localized on chromosomes 2B, 3A, 3D, 4D, and 5A.Communicated by J. Dvorak     

Association and Validation of Yield-Favored Alleles in Chinese Cultivars of Common Wheat (Triticumaestivum L.)

Common wheat is one of the most important crops in China, which is the largest producer in the world. A set of 230 cultivars was used to identify yield-related loci by association mapping. This set was tested for seven yield-related traits, viz. plant height (PH), spike length (SL), spikelet number per spike (SNPS), kernel number per spike (KNPS), thousand-kernel weight (TKW), kernel weight per spike (KWPS), and sterile spikelet number (SSN) per plant in four environments. A total of 106 simple sequence repeat (SSR) markers distributed on all 21 chromosomes were used to screen the set. Twenty-one and 19 of them were associated with KNPS and TKW, respectively. Association mapping detected 73 significant associations across 50 SSRs, and the phenotypic variation explained (R²) by the associations ranged from 1.54 to 23.93%. The associated loci were distributed on all chromosomes except 4A, 7A, and 7D. Significant and potentially new alleles were present on 8 chromosomes, namely1A, 1D, 2A, 2D, 3D, 4B, 5B, and 6B. Further analysis showed that genetic effects of associated loci were greatly influenced by association panels, and the R² of crucial loci were lower in modern cultivars than in the mini core collection, probably caused by strong selection in wheat breeding. In order to confirm the results of association analysis, yield-related favorable alleles Xgwm135-1A₁₃₈, Xgwm337-1D₁₈₆, Xgwm102-2D₁₄₄, and Xgwm132-6B₁₂₈ were evaluated in a double haploid (DH) population derived from Hanxuan10 xLumai14.These favorable alleles that were validated in various populations might be valuable in breeding for high-yield.     

小麦株高性状的QTL分析

自20世纪60年代农林10号矮秆基因被用于小麦育种以来,矮化育种成为世界范围内势不可挡的趋势,矮秆基因研究被越来越多的育种专家重视,先后鉴定出20余个矮秆基因,并应用其中6,7个基因,培育了大批丰产潜力大的半矮秆品种,应用矮秆冬小麦吕系DN3338（♀）和F390（♂）杂交得到的F2：3群体,研究小麦株高的遗传基础,以控制株高的数量性状基因座进行定位,利用240个F2：3家系,构建了含215个微卫星标记,覆盖3600cM,由21个连锁群组成的遗传 连锁图谱,并对该群体进行了4个环境（2年：2000年和2001年,2点：北京和石家庄）3重复的田间种植;采用区间作图法,对该群体的株高性状进行了QTL分析。结果表明：7个影响株高的QTL分别位于染色体1B,4B(2个）,6A（2个）,6D和7A上,每个QTL能解释5．2％－50．1％的表型变异,每个环境条件下检测出的所有QTL能解释64．8％－75％,的表型变异,除了7A上的QTL外,其他6个降低株高的QTL均来自ND3338,其效应介于0．94cm-9.33cm之间,且其中的4个在所有的环境下都能被检测出来,具有较高的稳定性,在4BS的Xgwm113标记附近有一主效QTL,其在不同的环境下能降低株高7．91cm-9.33cm,解释27．8％－36．2％,的表型变异,有着同农林10号中Rht-Blb相近的效应;同时在4BS上还发现一个和地点互作的QTL,该QTL在石家庄的两年试验中均被检测到,且有较大的效应值（80cm和7.6cm),因此,认为大部分的QTL能在所有的环境中检测到,这些QTO可以被用于品种改良和分子标记辅助选择育种。     

A intervarietal genetic map and QTL analysis for yield traits in wheat

A new genetic linkage map was constructed based on recombinant inbred lines (RILs) derived from the cross between the Chinese winter wheat (Triticum aestivum L.) varieties, Chuang 35050 and Shannong 483 (ChSh). The map included 381 loci on all the wheat chromosomes, which were composed of 167 SSR, 94 EST-SSR, 76 ISSR, 26 SRAP, 15 TRAP, and 3 Glu loci. This map covered 3636.7 cM with 1327.7 cM (36.5%), 1485.5 cM (40.9%), and 823.5 cM (22.6%) for A, B, and D genome, respectively, and contained 13 linkage gaps. Using the RILs and the map, we detected 46 putative QTLs on 12 chromosomes for grain yield (GY) per m², thousand-kernel weight (TKW), spike number (SN) per m², kernel number per spike (KNS), sterile spikelet number per spike (SSS), fertile spikelet number per spike (FSS), and total spikelet number per spike (TSS) in four environments. Each QTL explained 4.42–70.25% phenotypic variation. Four QTL cluster regions were detected on chromosomes 1D, 2A, 6B, and 7D. The most important QTL cluster was located on chromosome 7D near the markers of Xwmc31, Xgdm67, and Xgwm428, in which 8 QTLs for TKW, SN, SSS and FSS were observed with very high contributions (27.53–67.63%).     

Quantitative trait loci responsible for Fusarium head blight resistance in Chinese landrace Baishanyuehuang

Fusarium head blight (FHB), mainly caused by Fusarium graminearum, is a destructive disease that can significantly reduce grain yield and quality. Deployment of quantitative trait loci (QTLs) for FHB resistance in commercial cultivars has been the most effective approach for minimizing the disease losses. 'Baishanyuehuang' is a highly FHB-resistant landrace from China. Recombinant inbred lines (RILs) developed from a cross of 'Baishanyuehuang' and 'Jagger' were evaluated for FHB resistance in three greenhouse experiments in 2010 and 2011 by single-floret inoculation. Percentage of symptomatic spikelets in an inoculated spike was recorded 18 days post-inoculation. The RIL population was screened with 251 polymorphic simple sequence repeats. Four QTLs were associated with FHB resistance and mapped on three chromosomes. Two QTLs were located on the short arm of chromosome 3B (3BS) with one in distal of 3BS and another near centromere (3BSc), designated as Qfhb.hwwg-3BSc. The QTL in the distal of 3BS is flanked by Xgwm533 and Xgwm493, thus corresponds to Fhb1. This QTL explained up to 15.7 % of phenotypic variation. Qfhb.hwwg-3BSc flanked by Xwmc307 and Xgwwm566 showed a smaller effect than Fhb1 and explained up to 8.5 % of phenotypic variation. The other two QTLs were located on 3A, designated as Qfhb.hwwg-3A, and 5A, designated as Qfhb.hwwg-5A. Qfhb.hwwg-3A was flanked by Xwmc651 and Xbarc356 and explained 4.8-7.5 % phenotypic variation, and Qfhb.hwwg-5A was flanked by markers Xgwm186 and Xbarc141, detected in only one experiment, and explained 4.5 % phenotypic variation for FHB resistance. 'Baishanyuehuang' carried all resistance alleles of the four QTL. Qfhb.hwwg-3BSc and Qfhb.hwwg-3A were new QTLs in 'Baishanyuehuang'. 'Baishanyuehuang' carries a combination of QTLs from different sources and can be a new source of parent to pyramid FHB-resistant QTLs for improving FHB resistance in wheat.     

QTL analysis of falling number and seed longevity in wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.)

Pre-harvest sprouting (PHS) and seed longevity (SL) are complex biological processes of major importance for agricultural production. In the present study, a recombinant inbred line (RIL) population derived from a cross between the German winter wheat (Triticum aestivum L.) cultivars History and Rubens was used to identify genetic factors controlling these two physiological seed traits. A falling number (FN) test was employed to evaluate PHS, while SL was measured using a germination test (and the speed of germination) after controlled deterioration. FN of the population was assessed in four environments; SL traits were measured in one environment. Four major quantitative trait loci (QTL) for FN were detected on chromosomes 4D, 5A, 5D, and 7B, whereas for SL traits, a major QTL was found on chromosome 1A. The FN QTL on chromosome 4D that coincided with the position of the dwarfing gene Rht-D1b only had effects in environments that were free of PHS. The remaining three QTL for FN were mostly pronounced under conditions conducive to PHS. The QTL on the long arm of chromosome 7B corresponded to the major gene locus controlling late maturity α-amylase (LMA) in wheat. The severity of the LMA phenotype became truly apparent under sprouting conditions. The position on the long arm of chromosome 1A of the QTL for SL points to a new QTL for this important regenerative seed trait.     

不同发育时期小麦粒重性状QTL的动态分析

利用6044×01-35构建的重组自交系(RIL)群体为试验材料,对小麦粒重性状进行发育动态QTL分析。结果表明,在小麦花后子粒灌浆的7个不同时期,两个试验点共检测到16个与粒重性状相关的QTL。其中开花后20d检测到的单穗粒重QTL位于2A染色体上,解释率达12%,遗传效应超过10;两环境下控制千粒重QTL在7个时期均被检测到。花后的各个时期均能在Xgwm448-Xgpw7399标记区间定位到千粒重QTL。其中花后10d检测到1个千粒重QTL,位于2A染色体的Xgwm448-Xgpw7399标记区间,解释较大的表型变异,达到18%。Qtl8、Qtl13和Qtl14均定位在Xgwm448-Xgpw7399标记区间的同一位置,共同解释11%的表型变异。花后20d和花后25d均检测到1个QTL,位于2A染色体的Xgwm372-Xgwm95标记区间的不同位点,均能解释4%的表型变异。花后40d检测到1个QTL,位于1D染色体的Xwmc93-Xgpw2224标记区间,解释1%的表型变异。从连锁群的位置上看,控制千粒重的QTL主要集中在2A染色体的Xgwm448-Xgpw7399标记区间,这是一个控制千粒重QTL的富集区域,以期进行精细定位和图位克隆。     

Analysis of agronomic and domestication traits in a durum × cultivated emmer wheat population using a high-density single nucleotide polymorphism-based linkage map

Key message

Development of a high-density SNP map and evaluation of QTL shed light on domestication events in tetraploid wheat and the potential utility of cultivated emmer wheat for durum wheat improvement.

Abstract

Cultivated emmer wheat (Triticum turgidum ssp. dicoccum) is tetraploid and considered as one of the eight founder crops that spawned the Agricultural Revolution about 10,000 years ago. Cultivated emmer has non-free-threshing seed and a somewhat fragile rachis, but mutations in genes governing these and other agronomic traits occurred that led to the formation of today’s fully domesticated durum wheat (T. turgidum ssp. durum). Here, we evaluated a population of recombinant inbred lines (RILs) derived from a cross between a cultivated emmer accession and a durum wheat variety. A high-density single nucleotide polymorphism (SNP)-based genetic linkage map consisting of 2,593 markers was developed for the identification of quantitative trait loci. The major domestication gene Q had profound effects on spike length and compactness, rachis fragility, and threshability as expected. The cultivated emmer parent contributed increased spikelets per spike, and the durum parent contributed higher kernel weight, which led to the identification of some RILs that had significantly higher grain weight per spike than either parent. Threshability was governed not only by the Q locus, but other loci as well including Tg-B1 on chromosome 2B and a putative Tg-A1 locus on chromosome 2A indicating that mutations in the Tg loci occurred during the transition of cultivated emmer to the fully domesticated tetraploid. These results not only shed light on the events that shaped wheat domestication, but also demonstrate that cultivated emmer is a useful source of genetic variation for the enhancement of durum varieties.     

Single-strand conformational polymorphism markers associated with a major QTL for fusarium head blight resistance in wheat

A major quantitative trait locus (QTL) associated with resistance to Fusarium head blight (FHB) was identified on chromosome 3BS between simple sequence repeat (SSR) markers Xgwm389 and Xgwm493 in wheat 'Ning 7840', a derivative from 'Sumai 3'. However, the marker density of SSR in the QTL region was much lower than that required for marker-assisted selection (MAS) and map-based cloning. The objective of this study was to exploit new markers to increase marker density in this QTL region by using single-strand conformational polymorphism (SSCP) markers developed from wheat expressed sequence tags (ESTs) on 3BS bin 8-0.78-1.0. Sixty-nine out of 85 SSCP primer pairs amplified PCR (polymerase chain reaction) products from the genomic DNA of 'Chinese Spring'. Thirty-four primer pairs amplified PCR products that could form clear ssDNA (single strand DNA) bands through denaturation treatment. Ten SSCP markers had polymorphisms between 'Ning 7840' and 'Clark'. Five of the ten polymorphic SSCP markers were located on chromosome 3B by nulli-tetrasomic analysis. Three SSCP markers (Xsscp6, Xsscp20, and Xsscp21) were mapped into the region between Xgwm493 and Xgwm533, and possessed higher coefficient of determination (R2) than Xgwm493 and Xgwm533. The SSCP markers, Xsscp6, Xsscp20, and Xsscp21, can be used for map-based cloning of the QTL and for marker-assisted selection in FHB resistance breeding.     

Genetic dissection of wheat panicle traits using linkage analysis and a genome-wide association study

Key message

Coincident regions on chromosome 4B for GW, on 5A for SD and TSS, and on 3A for SL and GNS were detected through an integration of a linkage analysis and a genome-wide association study (GWAS). In addition, six stable QTL clusters on chromosomes 2D, 3A, 4B, 5A and 6A were identified with high PVE% on a composite map.

Abstract

The panicle traits of wheat, such as grain number per spike and 1000-grain weight, are closely correlated with grain yield. Superior and effective alleles at loci related to panicles developments play a crucial role in the progress of molecular improvement in wheat yield breeding. Here, we revealed several notable allelic variations of seven panicle-related traits through an integration of genome-wide association mapping and a linkage analysis. The linkage analysis was performed using a recombinant inbred line (RIL) population (173 lines of F_8:9) with a high-density genetic map constructed with 90K SNP arrays, Diversity Arrays Technology (DArT) and simple sequence repeat (SSR) markers in five environments. Thirty-five additive quantitative trait loci (QTL) were discovered, including eleven stable QTLs on chromosomes 1A, 2D, 4B, 5B, 6B, and 6D. The marker interval between EX_C101685 and RAC875_C27536 on chromosome 4B exhibited pleiotropic effects for GW, SL, GNS, FSN, SSN, and TSS, with the phenotypic variation explained (PVE) ranging from 5.40 to 37.70%. In addition, an association analysis was conducted using a diverse panel of 205 elite wheat lines with a composite map (24,355 SNPs) based on the Illumina Infinium assay in four environments. A total of 73 significant marker-trait associations (MTAs) were detected for panicle traits, which were distributed across all wheat chromosomes except for 4D, 5D, and 6D. Consensus regions between RAC875_C27536_611 and Tdurum_contig4974_355 on chromosome 4B for GW in multiple environments, between QTSS5A.7-43 and BS00021805_51 on 5A for SD and TSS, and between QSD3A.2-164 and RAC875_c17479_359 on 3A for SL and GNS in multiple environments were detected through linkage analysis and a genome-wide association study (GWAS). In addition, six stable QTL clusters on chromosomes 2D, 3A, 4B, 5A, and 6A were identified with high PVE% on a composite map. This study provides potentially valuable information on the dissection of yield-component traits and valuable genetic alleles for molecular-design breeding or functional gene exploration.

     

Fine mapping of the region on wheat chromosome 7D controlling grain weight

We report the fine mapping of the previously described quantitative trait loci (QTL) for grain weight QTgw.ipk-7D associated with microsatellite marker Xgwm1002-7D by using introgression lines (ILs) carrying introgressions of the synthetic wheat W-7984 in the genetic background of the German winter wheat variety ‘Prinz’. The BC₄F₃ ILs had a 10% increased thousand grain weight compared to the control group and the recurrent parent ‘Prinz’, and 84.7% of the phenotypic variance could be explained by the segregation of marker Xgwm1002-7D, suggesting the presence of a gene modulating grain weight, which was preliminarily designated gw1. It was possible to delimit the QTL QTgw.ipk-7D to the interval Xgwm295–Xgwm1002, which is located in the most telomeric bin 7DS4-0.61-1.00 in the physical map of wheat chromosome arm 7DS. Furthermore, our data suggest the presence of a novel plant height-reducing locus Rht on chromosome arm 7DS of ‘Prinz’. Larger grain and increased plant height may reflect the pleiotropic action of one gene or may be caused by two linked genes. In general, our data support the concept of using nearly isogenic ILs for validating and dissecting QTLs into single Mendelian genes and open the gateway for map-based cloning of a grain-weight QTL in wheat.     

Location of genes involved in ear compactness in wheat (Triticum aestivum) by means of molecular markers

Quantitative trait loci (QTLs) for three traits related to ear morphology (spike length, number of spikelets, and compactness as the ratio between number of spikelets and spike length) in wheat (Triticum aestivum L.) were mapped in a doubled-haploid (DH) population derived from the cross between the cultivars Courtot and Chinese Spring. A molecular marker linkage map of this cross that had previously been constructed based on 187 DH lines and 380 markers was used for QTL mapping. The genome was well covered (85%) except chromosomes 1D and 4D and a set of anchor loci regularly spaced (one marker each 15.5 cM) were chosen for marker regression analysis. The presence of a QTL was declared at a significance threshold = 0.001. The population was grown in one location under field conditions during three years (1994, 1995 and 1998). For each trait, 4 to 6 QTLs were identified with individual effects ranging between 6.9% and 21.8% of total phenotypic variation. Several QTLs were detected that affected more than one trait. Of the QTLs 50% were detected in more than one year and two of them (number of spikelets on chromosome 2B, and compactness on chromosome 2D) emerged from the data from the three years. Only one QTL co-segregated with the gene Q known to be involved in ear morphology, namely the speltoid phenotype. However, this chromosome region explained only a minor part of the variation (7.5–11%). Other regions had a stronger effect, especially two previously unidentified regions located on chromosomes 1A and 2B. The region on the long arm of chromosome 1A was close to the locus XksuG34-1A and explained 12% of variation in spike length and 10% for compactness. On chromosome 2B, the QTL was detected for the three traits near the locus Xfbb121-2B. This QTL explained 9% to 22% of variation for the traits and was located in the same region as the gene involved in photoperiod response (Ppd2). Other regions were located at homoeologous positions on chromosomes 2A and 2D.     

Characterization of a QTL affecting spike morphology on the long arm of chromosome 3H in barley (Hordeum vulgare L.) based on near isogenic lines and a NIL-derived population

Traits related to spike morphology (SM), including grain density (GD), spike length (SL) and awn length (AL), are of central importance in cereal improvement. A recent study based on a two-row landrace of barley, TX9425, detected QTL controlling all of the three traits in a similar region on the long arm of chromosome 3H. To further characterize this chromosomal region, 12 pairs of near isogenic lines (NILs) for GD were generated from two populations between TX9425 and two different commercial cultivars. A population consisting of 1,028 lines segregating primarily for the target region was also developed using materials generated during the production of these NILs. Results from the analysis of the NILs and the NIL-derived population showed that these three traits were likely controlled by a single-locus which was mapped to a 2.84?cM interval between two SSR markers, GBM1495 and HVM33. Across the 12 pairs of NILs, the presence of the 3HL locus increased GD by 53.4?%, reduced SL and AL by 38.8?% and 62.7?%, respectively. In the NIL-derived population, the presence of the 3HL locus increased GD by 64.6?%, reduced SL and AL by 33.7?% and 62.6?%, respectively. An interesting question arising from this research is why some loci such as the one reported here affect several SM-related traits while others appear to affect one of these traits only. The NILs and the NIL-derived population generated in this study will help answer such questions by providing the germplasm to enable cloning and comparative analysis of the genes responsible for these SM-related traits.