Detection of QTLs for bread‐making quality in wheat using a recombinant inbred line population

Whereas gluten fraction accounts for 30–60% of the variation in wheat bread‐making quality, there remains substantial variation determined by non‐gluten factors. The objective of this study was to detect new loci for wheat quality. The genetics of sodium dodecyl sulphate‐sedimentation volume (Ssd), grain hardness (GH), grain protein content, wet gluten content (WGC) and water absorption (Abs) in a set of 198 recombinant inbred lines derived from two commercial varieties was studied by quantitative trait loci (QTL) analysis. A genetic map based on 255 marker loci, consisting of 250 simple sequence repeat markers and five glutenin loci, Glu‐A1, Glu‐B1, Glu‐D1, Glu‐B3 and Glu‐D3, was constructed. A total of 73 QTLs were detected for all traits. A major QTL for GH was detected on chromosome 1B and its relative contribution to phenotypic variation was 27.7%. A major QTL for Abs on chromosome 5D explained more than 30% of the phenotypic variation. Variations in Ssd were explained by four kinds of genes. Some QTLs for correlated traits mapped to the same regions forming QTL clusters or indicated pleiotropic effects.     

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。     

Mapping QTLs for potassium-deficiency tolerance at the seedling stage in wheat (Triticum aestivum L.)

Potassium (K) deficiency is a major factor limiting crop development and yield. In this study, 20 traits were investigated at the seedling stage using a doubled-haploid population subjected to normal K and K deprivation treatments. Evaluation of phenotypes expressed under the two K supply conditions revealed that K deprivation was able to decrease values of ten measured traits, whereas values of the other ten traits increased. A total of 65 QTLs were detected across all 21 chromosomes, except for chromosomes 2B, 5A, and 7B. Individual QTLs in the two K supply treatments explained between 5.35 and 39.64 % of the phenotypic variation. Nine QTL clusters (C1–C9) involving 34 QTLs under the different K supply treatments were mapped to chromosomes 1A, 1B, 1D, 3B, 4A, 5B, 6A, and 7B. Our results are helpful for understanding the genetic basis of K deficiency in wheat, and provide useful information for genetic improvement of K deficiency in wheat by marker-assisted selection.     

Identification and characterization of quantitative trait loci related to lodging resistance and associated traits in bread wheat

Lodging is a major constraint to increasing yield in many crops, but is of particular importance in the small‐grained cereals. This study investigated the genetic control of lodging and component traits in wheat through the detection of underlying quantitative trait loci (QTL), The analysis was based on the identification of genomic regions which affect various traits related to lodging resistance in a population of 96‐doubled haploid lines of the cross ‘Milan’בCatbird’, mapped using 126‐microsatellite markers. Although major genes related to plant height (Rht genes) were responsible for increasing lodging resistance in this cross, several other traits independent of plant height were shown to be important such as fool and shoot traits, and various components of plant yield. Yield components such as grain number and weight were shown to be an indicator of plant susceptibility to lodging. QTL for lodging and associated traits were found on chromosomes IB, ID. 2B. 2D. 4B, 4D. 6D and 7D. QTL for yield and associated traits were identified on chromosomes IB, ID. 2A. 2B. 2D. 4D and 6A,     

Mapping quantitative trait loci controlling pre-harvest sprouting resistance in a red × white seeded spring wheat cross

Hard white wheat (Triticum aestivum L.) is a value-added product because of its processing advantages over red wheat; however, white wheat tends to be more susceptible to pre-harvest sprouting (PHS). To identify quantitative trait loci (QTLs) associated with PHS tolerance, we developed a doubled haploid (DH) mapping population from the cross AC Domain (red seeded) × White-RL4137 (white seeded). A genetic map was constructed using microsatellite markers located on chromosome groups 3, 4, 5 and 6. A population of 174 DH lines was characterized for important aspects of PHS including sprouting index, germination index, Hagberg falling number and seed coat colour. A total of 11 QTLs were identified on group 3 chromosomes and on chromosome 5D. Seven QTLs associated with the PHS traits were found to be co-incident with seed coat colour on chromosomes 3A, 3B and 3D. The 5D PHS QTL was notable because it is independent of seed coat colour.     

Alleles on the two dwarfing loci on 4B and 4D are main drivers of FHB‐related traits in the Canadian winter wheat population “Vienna” × “25R47”

Fusarium head blight (FHB), leaf rust and stem rust are among the most destructive wheat diseases. High‐yielding, native disease resistance sources are available in North America. The objective of this study was to map loci associated with FHB traits, leaf rust, stem rust and plant height in a “Vienna”/”25R47” population. DArT markers were used to generate a genetic map, and quantitative trait loci (QTL) analysis was performed by evaluating 113 doubled haploid lines across three environments in Ontario, Canada. FHB resistance QTL were identified on chromosomes 4D, 4B, 2D and 7A, while a QTL for leaf and stem rust resistance was identified on chromosome 1B. The dwarfing alleles of both Rht‐B1 and Rht‐D1 were associated with increased FHB index and DON content.     

Identification of QTLs for rice grain size and shape of Iranian cultivars using SSR markers

Grain size is a main component of rice appearance quality. In this study, we performed the SSR mapping of quantitative trait loci (QTLs) controlling grain size (grain length and breadth) and shape (length/breadth ratio) using an F₂ population of a cross between two Iranian cultivars, Domsephid and Gerdeh, comprising of 192 individuals. A linkage map with 88 markers was constructed, which covered 1367.9 cM of the rice genome with an average distance of 18 cM between markers. Interval mapping procedure was used to identify the QTLs controlling three grain traits, and QTLs detected were further confirmed using composite interval mapping. A total of 11 intervals carrying 18 QTLs for three traits were identifed, that included five QTLs for grain length, seven QTLs for grain breadth, and six QTLs for grain shape. A major QTL for grain length was detected on chromosome 3, that explained 19.3% of the phenotypic variation. Two major QTLs for grain breadth were mapped on chromosomes 3 and 8, which explained 34.1% and 20% of the phenotypic variation, respectively. Another two major QTLs were identified for grain shape on chromosomes 3 and 8, which accounted for 27.1% and 20.5% of the phenotypic variance, respectively. The two QTLs that were mapped for grain shape coincided with the major QTLs detected for grain length and grain breadth. Intrestingly, gs2 QTL specific to grain shape was detected on chromosome 2 that explained 15% of the phenotypic variation.     

普通小麦籽粒黄色素含量的QTL分析

小麦面粉黄色度b*值是反映面粉颜色的重要指标，主要与籽粒黄色素含量有关。利用122对SSR引物、4对贮藏蛋白STS引物和10对AFLP引物组合，分析了中优9507´CA9632的71个DH系，构建了由173个位点组成的遗传连锁图，在小麦21个连锁群上覆盖2 881 cM。将该群体种植2年共计5个地点，测定籽粒黄色素和面粉黄色度b*值含量。采用复合区间作图法（CIM）进行了籽粒黄色素含量和面粉黄色度QTL分析。结果表明，面粉黄色度b*值的QTL位于染色体1DS、2DL、3A、4D、5D、6AL、6D和7AL上，其中7AL的QTL效应最大，贡献率为12.9%~37.6%；籽粒黄色素含量的QTL位于染色体2DL、3DL、4A、5A和7AL，其中7AL的QTL效应最大，贡献率为12.1%~33.9%。面粉黄色度b*值与籽粒黄色素含量共同的QTL位于7AL，与Xgwm264b紧密连锁，遗传距离分别为0~3.9 cM和0~0.9 cM。     

QTL analysis for cooking traits of super rice with a high‐density SNP genetic map and fine mapping of a novel boiled grain length locus

Hybrid rice has contributed substantially to the improvement of grain production worldwide, yet its poor cooking and tasting characteristics have long been recognized. In this study, 132 recombinant inbred lines derived from LYPJ were used to identify quantitative trait loci (QTLs) for 12 cooking traits with the high‐density SNP linkage map recently developed by our team. We identified 17 QTLs on chromosomes 1, 2, 4, 5, 6, 7, 8, 9 and 11, which accounted for 7.50% to 23.50% of the phenotypic variations. A novel major QTL qBGL7 for boiled grain length was further fine‐mapped to an interval of 440 Kb between the two markers RM21906 and gl3 using a BC₃F₂ population. Two near‐isogenic lines with extreme boiled grain length, GX5‐176 and GX5‐101, could be directly used in improving cooking quality. We also identified a QTL for soaked grain width expansion rate, qSGWE6, in the Wx gene region on chromosome 6. The Wx differential regulation coincided with sequential variation between the two parents. Our work offered a theoretical basis for molecular breeding of high‐quality hybrid rice.     

Variation in quality traits in common wheat as related to Chinese fresh white noodle quality

The variation in grain compositional traits related to Chinese fresh white noodle (CFWN) quality was examined in 25 leading Chinese common wheat cultivars and advanced lines. Large variations were observed in flour yield, flour particle size, protein and ash contents, farinograph and rapid visco-analyzer (RVA) parameters, flour colour components, and polyphenol oxydase (PPO) activity. An improved sensory method was proposed for adequately evaluating CFWN quality of common wheat flour based on methodology used in the Japanese quality scoring system for white salted noodles, but with major modifications in the score weight given to each noodle quality parameter. Large differences in CFWN quality were observed among Chinese wheat cultivars. The correlation coefficients (r) between starch paste breakdown (RVA) and noodle viscoelasticity and smoothness were 0.63 and 0.59, respectively, suggesting that in breeding wheat for high CFWN quality, the starch pasting properties are of major importance. Low ash content was significantly correlated (r = – 0.66) with bright white noodle colour.     

Detection of quantitative trait loci (QTLs) for seedling traits and drought tolerance in wheat using three related recombinant inbred line (RIL) populations

In order to detect quantitative trait loci (QTLs) for drought tolerance in wheat during seed germination conditional and unconditional QTL analyses of eight seedling traits were conducted under two water regimes using three related F₉ recombinant inbred line populations with a common female parent. A total of 87 QTLs for the eight seedlings traits and 34 specific QTLs related to drought tolerance were detected. Seventy-one of these QTLs were major QTLs with contributions to phenotypic variance of >10 %. Of the 34 QTLs related to drought tolerance only eight were also detected by unconditional analysis of seedling traits under osmotic stress conditions indicating that most of the QTLs related to drought tolerance could not be detected by unconditional QTL analysis. Therefore, conditional QTL analysis of stress-tolerance traits such as drought tolerance was feasible and effective. Of 11 important QTL clusters located on chromosomes 1BL, 1D, 2A, 2B, 2D, 4A, 6B, and 7B, nine were detected in multiple populations and eight were detected by both unconditional and conditional analyses.     

Mapping QTLs for pre-harvest sprouting traits in the spring wheat cross ‘RL4452/AC Domain’

Pre-harvest sprouting (PHS) in spring wheat (Triticum aestivum L.) is a major downgrading factors for grain producers and can significantly reduce end-use quality. PHS resistance is a complex trait influenced by genotype, environment and plant morphological factors. A population of 185 doubled haploid (DH) lines from the spring wheat cross ‘RL4452/AC Domain’ were used as the mapping population to detect quantitative trait loci (QTLs) associated with three PHS traits, germination index (GI), sprouting index (SI) and falling number (FN). Six major QTLs linked with PHS traits were mapped on bread wheat chromosomes 3A, 3D, 4A (2 loci), 4B and 7D. ‘AC Domain’ alleles contributed to PHS resistance on 3A, 4A (locus-2) and 4B, and ‘RL4452’ alleles contributed resistance on 3D, 4A (locus-1) and 7D. QTLs detected on chromosome 4B controlling FN (QFN.crc-4B), GI (QGI.crc-4B) and SI (QSI.crc-4B) were coincident, and explained the largest amount of phenotypic variation in FN (22%), GI (67%) and SI (26%), respectively.     

A limited set of starch related genes explain several interrelated traits in potato

To understand the molecular basis of potato starch related traits and the underlying starch biosynthesis and degradation, a Quantitative Trait Locus (QTL) analysis in combination with a candidate gene approach was performed. The diploid mapping population C × E, consisting of 249 individuals, was assayed over two consecutive years, for chipping colour, cold induced sweetening, starch content, starch granule size, starch gelling temperature, starch enthalpy, amylose content and degree of starch phosphorylation. QTLs were observed for all traits, except enthalpy on eight out of the twelve potato chromosomes. Several QTLs were found to be consistent over 2 years. Clustering of co-localizing QTLs was observed on some chromosomes, indicating common genetic factors for the different traits. On chromosome 2, Soluble Starch Synthase 2 mapped on the same position as QTLs for starch phosphorylation, starch gelling temperature and amylose content. α-glucan, water dikinase co-localizes on chromosome 5 together with QTLs for starch phosphorylation and cold induced sweetening. Furthermore, the genes coding for two phosphorylases (StPho1a and StPho2) coincide with QTLs for starch gelling temperature, chipping colour and starch granule size on chromosome 2 and a QTL for starch phosphorylation on chromosome 9, respectively. The results suggest allelic variation acting on the genetics of the different traits.     

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.     

小麦GMP含量发育动态的QTL定位

利用小麦京771和Pm97034杂交后代重组自交系（RIL）群体,对小麦谷蛋白大聚合体（GMP）含量发育动态进行了QTL定位研究。结果表明,在籽粒灌浆的5个不同时期,共检测到8个条件QTL和10个非条件QTL,但没有一个QTL能在测定的5个时期都有效应。花后12 d,控制GMP形成的基因就已经有了一定的表达量,条件QTL能解释6.21%的表型变异,该基因位于1A染色体上。花后17 d,在1D染色体上测到了1个新表达的条件QTL位点,单独能解释14.14%的表型变异。花后22 d,控制GMP形成的基因的表达比较活跃,非条件分析检测到3个QTL位点,条件分析检测到2个QTL位点,这5个QTL位点分别位于1B、5B、6B和7B染色体上,其效应值都比较低,2个条件QTL共同能解释12.67%的净表型变异。花后27 d,在2D和3B染色体上各检测到2个条件和非条件QTL位点,加性效应值比较大。条件QTL能解释16.37%的表型变异,非条件QTL能解释23.94%的变异。花后32 d,仍有2个新的基因位点在表达,但此时QTL的净表达量已经开始下降,条件QTL仅能解释11.43%的表型变异。     

利用“永久F2”群体进行小麦幼苗根系性状QTL分析

为了研究小麦苗期根系性状的遗传,以小麦品种花培3号和豫麦57的杂交DH群体组配了一套含168个杂交组合的“永久F₂”群体。利用WinRHIZO根系分析系统测定四叶一心期小麦水培幼苗根系总长度、直径、表面积、体积、根尖数、最大根长、茎叶干重、根干重及根茎干重比9个性状。采用复合区间作图法分析幼苗根系8个性状的QTL,定位了7个加性效应QTL和12对上位性互作QTL,包括加性效应、显性效应,加加互作、加显互作和显显互作,分布在1A、1D、2A、2B、2D、3A、3B、5D、6D和7D染色体上,单个QTL可解释0.01%~11.91%的遗传变异。在染色体2D上XWMC41至XBARC349.2区间检测到同时控制总根长和根干重的一个QTL。上位性对苗期根系生长发育有重要作用。试验结果表明,苗期根系性状的遗传机制较复杂, 因此在育种中要综合考虑根系各性状之间的关系,保证根系协调统一、发达健壮。     

Mapping QTLs for salt tolerance with additive,epistatic and QTL × treatment interaction effects at seedling stage in wheat

Quantitative trait loci (QTLs) for salt tolerance with additive, epistatic and QTL × treatment interaction effects at seedling stage in wheat were identified. A set of 131 recombinant inbred lines derived from cross Chuan 35050 × Shannong 483 were evaluated under salt stress and normal conditions. Wide variation was found for all studied traits. A total of 18 additive and 16 epistatic QTLs were detected, among which five and 11 were with significant QTL × treatment effects. Ten QTL clusters were identified, and each may represent a single gene or closely linked genes. The locus controlling shoot K⁺/Na⁺ concentration ratio and shoot Na⁺ concentration on chromosome 5A may be identical to Nax2. The interval Xgwm6‐Xgwm538 on chromosome 4B for total dry weight was also identified in a previous study, both near the marker Xgwm6. The marker Xgwm6 may be useful for marker‐assisted selection. Six pairs of homoeologous QTLs were detected, showing synteny among the A, B and D genomes. These results facilitate understanding the mechanisms and the genetic basis of salt tolerance in wheat.     

Identification of quantitative trait loci (QTLs) associated with maintenance of wheat (Triticum aestivum Desf.) quality characteristics under heat stress conditions

The goal of this study was to identify quantitative trait loci (QTLs) associated with the maintenance of wheat grain quality following post-anthesis heat stress in a recombinant inbred line (RIL) population. The response to heat stress was measured using the sodium dodecyl sulfate sedimentation test (SDSS), a significant predictor of bread baking quality. SDSS scores were used to identify QTLs associated with grain quality and QTLs associated with quality stability were identified based on percent change in SDSS score between the heat stress and control treatments. Four QTLs were identified, located one each on linkage groups 1B, 1D, 4A, and 7A. The 1B, 1D, and 4A QTLs were associated with grain quality; the QTL on linkage group 7A was associated with quality stability. To confirm the detected QTLs, eighty advanced lines grown at three Texas nurseries were tested for relationships between allelic polymorphism at QTL linked markers and quality traits. Quality trait stability in the advanced lines was estimated using the coefficient of variability (CV%) of quality traits between nurseries. The analysis supported the relationship of the predicted QTLs on linkage groups 1B, 1D, and 4A with quality traits. The confirmed QTLs may be used in marker assisted selection (MAS) to develop wheat lines possessing superior quality traits. In addition, identification of genetic regions associated with this trait will aid the identification of the underlying genes.     

利用90k芯片技术进行小麦穗部性状QTL定位

小麦穗部性状与产量密切相关,挖掘穗部性状基因及其关联分子标记具有重要意义。本研究以周8425B?小偃81衍生的RIL群体(F8)为材料,利用90k芯片标记构建的高密度遗传图谱对3个环境下的穗长、小穗数、不育小穗数、穗粒数、千粒重进行QTL定位。共检测到19条染色体上的71个QTL,变异解释率(PVE)范围为2.10%~45.25%,其中37个位点为主效QTL(PVE10%)。QSl.nafu-6A.2(穗长)、QSl.nafu-7A(穗长)、QSsn.nafu-2A.1(不育小穗数)、QSsn.nafu-2D(不育小穗数)和QGns.nafu-2B(穗粒数)在多个环境中被检测到,且LOD10,PVE20%。位于同一个基因簇中的QSl.nafu-6A.2(穗长)、QGns.nafu-6A(穗粒数)和QTgw.nafu-6A(千粒重)在多个环境中被检测到,且与已报道的相关位点位置相同或相近,在分子标记辅助育种中具有较大参考价值。     

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.