Lipoxygenase from the leaves of wheat grown under different water supply conditions

Lipoxygenase (LOG) in protein fractions isolated from the leaves of substituted wheat lines was investigated. Three molecular forms of the enzyme were detected. A water deficiency caused the induction of a membrane-bound form (mLOG) and resulted in a decrease in the activity of “soluble” enzymes (s1LOG) and (s2LOG) in most genotypes. A correlation analysis demonstrated the dependence between the level of enzymatic activity and indices of resistance to drought. A genetic control of the s1LOG and s2LOG activity at an optimal water supply level was associated with chromosomes 1A, 1D, 3A, 5A, 5B, and 5D, while under the conditions of the modeled soil drought, it was associated with chromosomes 1B and 1D.     

Leaf dehydroascorbate reductase and catalase activity is associated with soil drought tolerance in bread wheat

A number of morphological, physiological and phenological traits have been suggested as significant markers of adaptation to drought in bread wheat (Triticum aestivum L.). This study was aimed at the identification of a relationship between dehydroascorbate reductase (DHAR, EC 1.8.5.1) and catalase (CAT, EC 1.11.1.6) activities in leaves of wheat plants and stability of yield components under water deficit. The single chromosome substitution lines of cv. Chinese Spring carrying separate chromosomes from the donor Synthetic 6x, an artificial hexaploid combining the genomes of the two wild species, Triticum dicoccoides (AABB) and Aegilops tauschii (DD), were the objects of the investigations. The activities of the DHAR and CAT were correlated with flag leaf relative water content and two indexes of stability of grain yield components under drought across the set substitution lines. The lines carrying a synthetic hexaploid homologous pair of chromosomes 1B, 1D, 2D, 3D or 4D all expressed a low constitutive level of DHAR and the lines carrying chromosomes 3B, 1D, 2D and 3D a low constitutive level of CAT. All were able to increase this level (by fourfold for DHAR and by 1.5-fold for CAT) in response to stress caused by water deficit. When challenged by drought stress, these lines tended to be the most effective in retaining the water status of the leaves and preventing the grain yield components from being compromised. The discovered genetic variability for enzymes activity in leaves of wheat might be a useful selection criterion for drought tolerance.     

小麦叶片水分利用效率及相关生理性状基因的染色体定位

利用中国春-埃及红代换系对控制小麦水分利用效率、光合速率、蒸腾速率、POD活性以及SOD活性等的基因进行了染色体定位。结果表明,控制高水分利用效率的基因可能位于5A和5D染色体上;控制高光效的基因可能位于3A和3D染色体上;控制高蒸腾速率的基因可能位于7B染色体上;诱导POD和SOD活性增强的有利培因可能分别位于7D和6D、2B染色体上。这些研究结果可以为小麦机抗旱节水的遗传育种研究提供一定参号信息。     

Conditional and unconditional QTL mapping of drought-tolerance-related traits of wheat seedling using two related RIL populations

For discovering the quantitative trait loci (QTLs) contributing to early seedling growth and drought tolerance during germination, conditional and unconditional analyses of 12 traits of wheat seedlings: coleoptile length, seedling height, longest root length, root number, seedling fresh weight, stem and leaves fresh weight, root fresh weight, seedling dry weight, stem and leaves dry weight, root dry weight, root to shoot fresh weight ratio, root-to-shoot dry weight ratio, were conducted under two water conditions using two F_8:9 recombinant inbred line (RIL) populations. The results of unconditional analysis are as follows: 88 QTLs accounting for 3.33–77.01% of the phenotypic variations were detected on chromosomes 1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 4A, 4B, 4D, 5A, 5B, 5D, 6A, 6B, 6D, 7A, 7B and 7D. Among these QTLs, 19 were main-effect QTLs with a contribution rate greater than 10%. The results of the conditional QTL analysis of 12 traits under osmotic stress on normal water conditions were as follows: altogether 22 QTLs concerned with drought tolerance were detected on chromosomes 1B, 2A, 2B, 3B, 4A, 5D, 6A, 6D, 7B, and 7D. Of these QTLs, six were main-effect QTLs. These 22 QTLs were all special loci directly concerned with drought tolerance and most of them could not be detected by unconditional analysis. The finding of these QTLs has an important significance for fine-mapping technique, map-based cloning, and molecular marker-assisted selection of early seedling traits, such as growth and drought tolerance.     

QTL mapping for germination of seeds obtained from previous wheat generation under drought

The QTLs controlling germination and early seedling growth were mapped using seeds acquired from mapping population and parental lines of Chinese Spring and SQ1 grown under water-limited conditions, severe drought (SDr) and well-watered plants (C). Germination ability was determined by performing a standard germination test based on the quantification of the germination percentage (GP24) of seeds incubated for 24 h at 25°C in the dark. Early seedling growth was evaluated on the basis of the length of the root and leaf at the 6th day of the experiment. QTLs were identified by composite interval mapping method using Windows QTLCartographer 2.5 software. For the traits studied, a total of thirty eight additive QTLs were identified. Seventeen QTLs were mapped in C on chromosomes: 1A, 2A, 7A, 1B, 2B, 3B, 4B, 5B, 6B, 7B, 2D, 3D, 4D and 6D, while twenty one QTLs were identified in SDr on chromosomes: 1A, 2A, 5A, 2B, 3B, 4B, 5B, 6B, 7B, 3D, 5D and 6D. Most of the QTLs for GP and early leaf growth parameters were clustered on chromosome 4B (associated with the Rht-B1 marker) both in C and SDr plants. The results indicate the complex and polygenic nature of germination.     

12057单体系及其二体抗旱生理指标的比较

利用１２０５７单体及其二体连续两年进行抗旱生理招标的比较,结果表明：１２０５７单体系珉春二体在灌浆中期旗叶相对含水量、细胞膜稳定性、叶片渗透势以及渗透调节能力等均存在差异。其中２Ｂ、３Ｂ、６Ｂ单体相对含水量较高;５Ａ单体叶组织膜稳定性较高;４Ｂ、５Ｂ、４Ｄ、６Ｂ、３Ａ单体的渗透势较低;６Ｂ、４Ｂ、３Ｂ、４Ｄ、、Ｂ单体的渗透调节能力较高。此外看出部分同源染色体群对上述生理招标的反应具有相似性。     

普通小麦品种Hope细胞膜热稳定性基因的染色体定位

利用全部 21个“中国春”的“Hope”染色体代换系及其亲本品种“中国春” (受体)和“Hope”(供体)对六倍体普通小麦的细胞膜热稳定性基因进行了染色体定位研究。结果表明:普通小麦品种“Hope”的1A、2A、2B、 2D、3A、3B、3D、5D和6B等9条染色体上具有耐热性基因,而其余染色体与“Hope”的耐热性无关。 Abstract:All 21 substitutions of common wheat(T.aestivum L.)and their parental cultivars“Chinese Spring”(recipient)and “Hope”(donor)were evaluated for their relative heat tolerance as measured by membrane thermostability to determine the chromosomal locations of genes controlling this trait.Results indicate that chromosomes 1A,2A,2B,2D,3A,3B,3D,5D and 6B were associated with heat tolerance of cv.Hope,while the others were not related to heat tolerance.     

The antioxidant enzymes activity in leaves of inter-varietal substitution lines of wheat (Triticum aestivum L.) with different tolerance to soil water deficit

Understanding of the genetic basis of physiological properties, which are most relevant to water-deficit tolerance would be helpful for genomic-assisted improvement of bread wheat. A set of bread wheat inter-varietal single chromosome substitution lines (ISCSLs) of variety ‘Janetzkis Probat’ (JP) in the genetic background of ‘Saratovskaya’ 29 (S29) were used to reveal the critical chromosomes in wheat genome controlling tolerance to water deficit. The same lines were involved in the identification of chromosomes associated with the activity of antioxidant enzymes that are closely related to the detoxification of H₂O₂ [catalase (CAT), ascorbate peroxidase, dehydroascorbate reductase and glutathione reductase (GR)]. The recipient cultivar S29 was highly drought tolerant while the donor JP was sensitive. Using non-metric multidimensional scaling of yield components and indices of drought tolerance/susceptibility chromosomes 2A and 4D, substitution in the genetic background of S29 was found to lead to a critical decrease of water-deficit tolerance. The drop of tolerance correlated with a sharp decline of cumulative activity of the catalase and the enzymes of ascorbate–glutathione cycle in wheat leaves. Clear evidence was obtained for the involvement of genes present on the homoeologous group 2 chromosomes in the control of GR and CAT activity. Substitution of the chromosome 4D had a significant reducing impact on the CAT activity level.     

小麦萌发期抗旱和耐盐性状的QTL分析

该研究以‘山农0431×鲁麦21’RIL群体及其父母本为材料,用20%PEG-6000溶液和100 mmol·L-1 NaCl溶液分别模拟干旱和盐环境,对12个小麦萌发期抗旱耐盐相关性状进行测定,结合已构建的分子标记遗传图谱对小麦萌发期抗旱、耐盐的相关性状进行QTL分析,为小麦抗旱、耐盐基因的克隆和分子标记辅助选择提供参考。结果表明:(1)正常、干旱和盐胁迫3种处理下共检测到143个QTL。检测到相对高频QTL(RHF-QTL)29个,平均贡献率范围为4.39%~13.28%,贡献率在10%以上的主效RHF-QTL有10个。(2)检测到胁迫下特异表达的RHF-QTL共17个,正常处理下特异表达的RHF-QTL为8个,稳定表达的RHF-QTL为4个。(3)QTL分析结果表明,7个RHF-QTL形成了3个QTL簇,且分布在2D、4D和5B等3条染色体上,其中:QC1位于2D染色体的wPt-6847~D-1172783区间,包括3个QTL(QRl-2D.2、QSdw-2D.3、QTdw-2D);QC2位于4D染色体短臂的D-2245724~D-1108531区间,包括2个QTL(QSl-4D、QShl-4D);QC3位于5B染色体的D-982263~S-1083095区间,包括2个QTL(QSl-5B.2、QTdw-5B.1)。     

小麦ARF基因家族生物信息学分析及在干旱胁迫下的表达特性研究

植物生长素响应因子ARF(auxin response factor)参与调节了植物的向性运动、顶端优势、微观的分化、侧根和茎的形态发生等众多生理反应,在植物生长发育的整个过程都起到重要调控作用。本研究通过对小麦最新基因组数据进行分析,获得了61个ARF家族基因,命名为TaARFs,根据染色体编号排列为TaARF1~TaARF61,对61个TaARFs基因进行系统生物信息学分析后发现ARF家族基因结构较为复杂,外显子数量从1个到15个变化不等,除了4号染色体和5A和5B染色体之外,其余的染色体均有ARF家族基因分布。ARF家族基因大多包含B3 DNA结构域、ARF结构域(Auxin-resp)和Aux/IAA结构域;同源进化分析表明,小麦ARF家族基因的旁系同源基因数量明显多于大麦和二穗短柄草。通过拟南芥数据库比对获得14个高同源的根系发育相关的小麦ARF家族基因,利用二系杂交小麦京麦6号及父母本根系为试材进行干旱胁迫处理及实时荧光定量PCR(qPCR)筛选。结果表明,7个小麦ARF基因不同程度受到干旱胁迫诱导,其在旱胁迫下的表达量显著高于正常条件下的表达量,可能参与干旱胁迫应答;此外本研究还发现,ARF基因在F1杂交种中表达量显著高于双亲,表现出超亲表达模式,可能参与了根系抗旱杂种优势基因表达调控网络。     

Production of wheat-rye substitution lines and identification of chromosome composition of karyotypes using C-banding, GISH, and SSR markers

Based on the cross (Triticum aestivum L. x Secale cereale L.) x T. aestivum L., wheat-rye substitution lines (2n = 42) were produced with karyotypes containing, instead of a pair of homologous wheat chromosomes, a homeologous pair of rye chromosomes. The chromosome composition of these lines was described by GISH and C-banding methods, and SSR analysis. The results of genomic in situ hybridization demonstrated that karyotype of these lines included one pair of rye chromosomes each and lacked wheat--rye translocations. C-banding and SSR markers were used to identify rye chromosomes and determine the wheat chromosomes at which the substitution occurred. The lines were designated 1R(1D), 2R(2D)2, 2R(2D)3, 3R(3B), 6R(6A)2. The chromosome composition of lines IR(1A), 2R(W)1, 5R(W), 5R(5A), and 6R(W)1, which were earlier obtained according to the same scheme for crossing, was characterized using methods of telocentric analysis, GISH, C-banding, and SSR analysis. These lines were identified as 1R(1A), 2R(2D)1, 5R(5D), 5R(5A), and 6R(6A)1, C-banding of chromosomes belonging to line 1R(1A) revealed the presence of two translocated chromosomes (3DS.3DL-del. and 4AL.W) during simultaneous amplification of SSR markers located on 3DL and 4AS arms. The "combined" long arm of the newly derived chromosome 4A is assumed to be formed from the long arm of chromosome 4AS itself and a deleted segment 3DL. All examined lines are cytologically stable, except for 3R(3B), which does not affect the stability of rye 3R chromosome transfer. Chromosome identification and classification of the lines will permit them to be models for genetic studies that can be used thereafter as promising "secondary gene pools" for the purpose of plant breeding.     

Identification of Loci Associated with Drought Resistance Traits in Heterozygous Autotetraploid Alfalfa (Medicago sativa L.) Using Genome-Wide Association Studies with Genotyping by Sequencing

Drought resistance is an important breeding target for enhancing alfalfa productivity in arid and semi-arid regions. Identification of genes involved in drought tolerance will facilitate breeding for improving drought resistance and water use efficiency in alfalfa. Our objective was to use a diversity panel of alfalfa accessions comprised of 198 cultivars and landraces to identify genes involved in drought tolerance. The panel was selected from the USDA-ARS National Plant Germplasm System alfalfa collection and genotyped using genotyping by sequencing. A greenhouse procedure was used for phenotyping two important traits associated with drought tolerance: drought resistance index (DRI) and relative leaf water content (RWC). Marker-trait association identified nineteen and fifteen loci associated with DRI and RWC, respectively. Alignments of target sequences flanking to the resistance loci against the reference genome of M. truncatula revealed multiple chromosomal locations. Markers associated with DRI are located on all chromosomes while markers associated with RWC are located on chromosomes 1, 2, 3, 4, 5, 6 and 7. Co-localizations of significant markers between DRI and RWC were found on chromosomes 3, 5 and 7. Most loci associated with DRI in this work overlap with the reported QTLs associated with biomass under drought in alfalfa. Additional significant markers were targeted to several contigs with unknown chromosomal locations. BLAST search using their flanking sequences revealed homology to several annotated genes with functions in stress tolerance. With further validation, these markers may be used for marker-assisted breeding new alfalfa varieties with drought resistance and enhanced water use efficiency.     

Genetic analysis of tolerance to photo-oxidative stress induced by high light in winter wheat （Triticum aestivum L.）

High light induced photooxidation (HLIP) usually leads to leaf premature senescence and causes great yield loss in winter wheat. In order to explore the genetic control of wheat tolerance to HLIP stress, a quantitative trait loci (QTL) analysis was conducted on a set of doubled haploid population, derived from two winter wheat cultivars. Actual values of chlorophyll content (Chl), minimum fluorescence level (Fo), maximum fluorescence level (Fm), and the maximum quantum efficiency of photosystem Ⅱ (Fv/Fm) under both HLIP and non-stress conditions as well as the ratios of HLIP to non-stress were evaluated. HLIP considerably reduced Chl, Fm, and Fv/Fm, but increased Fo, compared with that under non-stress condition. A total of 27, 16, and 28 QTLs were associated with the investigated traits under HLIP and non-stress and the ratios of HLIP to non-stress, respectively. Most of the QTLs for the ratios of HLIP to non-stress collocated or nearly linked with those detected under HLIP condition. HLIP-induced QTLs were mapped on 15 chromosomes, involving in 1A, 1B, 1D,2A, 2B, 2D, 3A, 3B, 4A, 4D, 5B, 6A, 6B, 7A, and 7D while those expressed under non-stress condition involved in nine chromosomes, including 1B, 1D, 2A, 2B, 3B, 4A, 5A, 5B, and 7A. The expression patterns of QTLs under HLIP condition were different from that under non-stress condition except for six loci on five chromosomes. The phenotypic variance explained by individual QTL ranged from 5.0% to 19.7% under HLIP, 8.3% to 20.8% under non-stress, and 4.9% to 20.2% for the ratios of HLIP to non-stress, respectively. Some markers, for example,Xgwm192 and WMC331 on 4D regulating Chl, Fo, Fm, and Fv/Fm under HLIP condition, might be used in marker assistant selection.     

Somatic karyotype,heterochromatin distribution,and nature of chromosome differentiation in common wheat,Triticum aestivum L. em Thell

Heterochromatin distribution and structural differentiation of somatic chromosomes of five common wheat cultivars — Chinese Spring, Wichita, Cheyenne, Timstein, and Hope — were studied by an acetocarmine/N-banding technique. Detailed morphological observations on acetocarmine stained somatic chromosomes of Chinese Spring were made on all A genome chromosomes (except 1A), all B genome chromosomes, and chromosomes 1D, 2D, and 7D. N-banding patterns of chromosomes 2A, 3A, 5A, 6A, 1D, 2D, and 7D were described for the first time. Substitution lines of 21 individual chromosomes each of Cheyenne, Timstein, and Hope in Chinese Spring were analyzed by N-banding. A high frequency of N-band polymorphism was observed, especially for most of the B genome chromosomes. Chromosomes 3A, 5A, 2D, and 7D showed a constant banding pattern. Three cases of doubtful substitutions, Hope 2A, 2B, and Timstein 7A, and several cases of incomplete and chromosomally modified substitutions were observed. The reduced level of chromosome pairing that is often observed in intercultivar hybrids of wheat may be due to heterochromatic differentiation, genic and structural heterozygosity, or hybrid dysgenesis.     

Mapping of the quantitative trait loci (QTL) associated with grain quality characteristics of the common wheat grown under different environmental conditions

The quantitative trait loci (QTL) associated with individual characteristics of grain and flour quality in wheat lines grown under contrasting environmental conditions were mapped. Overall, 22 QTL that manifested under contrasting environmental conditions with various significances were detected on 10 chromosomes. Grain hardness and vitreousness were associated with three loci on chromosomes 5D, 6A, and 3A, while the gluten content, with two loci on chromosomes 5B and 7A. Dough extensibility was associated with only one QTL localized in the region of Glu-A1 locus. One of the loci determining flour and dough strengths is located in the region of Gli-B1 and Glu-B3 loci and the rest, in various regions of chromosomes 1B, 5D, and 4B, where no particular genes associated with grain quality have been yet found. The detected QTL can be used in further experiments on genetic control of gluten formation and quality in wheat.     

Mapping QTLs for chlorophyll content and chlorophyll fluorescence in wheat under heat stress

Heat stress, one of the major abiotic stresses in wheat, affects chlorophyll fluorescence and chlorophyll content and thereby photosynthesis. To identify quantitative trait loci (QTLs) associated with these traits under terminal heat stress, 251 recombinant inbred lines (RILs) derived from a cross HD 2808/HUW510 were phenotyped. Using composite interval mapping, 40 QTLs were identified; 17 were related to conditions after timely sowing and 23 to heat stress after late sowing. The various parameters of chlorophyll fluorescence were associated with 23 QTLs, which were located on chromosomes 1A, 2A, 3A, and 2D and explained 3.67 to 18.04 % of phenotypic variation, whereas chlorophyll content was associated with 17 QTLs on chromosomes 2A, 2B, 2D, 5B, and 7A explaining 3.49 to 31.36 % of phenotypic variation. Most of the identified QTLs were clustered on chromosome 2D followed by 2A and 1A. The QTL Qchc.iiwbr-2A for chlorophyll content linked with marker gwm372 was stable over conditions and explained 3.81 to 18.05 % of phenotypic variation. In addition, 7 epistatic QTL pairs were also detected which explained 1.67 to 11.0 % of phenotypic variance. These identified genomic regions can be used in marker assisted breeding after validation for heat tolerance in wheat.     

Wheat chromosome instability in the selfed progeny of the double monosomics 1Rv-1A

Structural alterations of chromosomes are often found in wheat-rye hybrids. In the majority of cases modifications are observed for rye chromosomes, yet chromosome aberration cases are described for wheat, including the progeny of Triticum aestivum disomic and monosomic addition lines. Since wheat-rye substitution and translocation lines are the source of rye chromatin in wheat breeding programs, the information on possible chromosome changes in the genomes of introgressive forms is important. Chromosome behavior in F₁ meiosis and chromosomal composition of F₂ karyotypes for double monosomics 1Rv-1A were studied by applying C-banding, genomic in situ hybridisation (GISH) using rye genomic DNA, and sequential in situ hybridization using repetitive sequences pAs1, pSc119.2 and centromere specific pAet-06 as probes. The double monosomics 1Rv-1A were obtained by crossing of disomic substitution line with chromosome 1A replaced by Secale cereale 1Rv in the bread wheat Saratovskaya 29 (S29) background with S29. The results indicated a high frequency of bipolar chromosome 1Rv orientation, as compared to 1A, at metaphase I (MI) (58.6 and 34.7 % of meiocytes, respectively), and, at anaphase I (AI), chromatid segregation of 1Rv compared to 1A (70.53 and 32.14 % of meiocytes, respectively). In few cases desynapsis of wheat homologues was observed, at AI, the chromosomes randomly distributed between the poles or underwent chromatid segregation. At AI, the two wheat homologues separated onto sister chromatids in 10.89 % of cells.The plants F2 karyotypes were marked with aneuploidy not only of chromosomes 1A and 1Rv, but also of 1D, 2D, 3D, 3B, 3A, 4A, 6D, 6B, 6A, and 7D. Structural changes were observed for the chromosomes of the first homoeologous group (1Rv, 1A, 1D, 1B), as well as for 2B, 5D, 6B, and 7B. The chromosomes 1Rv and 6B often demonstrated aberrations. The types of aberrations were centromeric break, deletions of various sizes, and a changed repeat pSc119.2 localization pattern.     

Introduction of d-genome chromosomes from Aegilops squarrosa L. into tetraploid triticale (AB)(AB)RR (2n=28)

Summary Tetraploid triticale with the genome constitution (ABD) (ABD)RR (2n=4x=28) selected from the progenies of DDRR x (AB)(AB)RR hybrids (D(AB)RR) were karyotyped using C-banding. The aneuploidy frequency was 10.7% with 4.4% hypoploids and 6.3% hyperploids in the F₅. Among 67 plants having 28 chromosomes, 41.8% had a stabilized karyotype, while 58.2% were unstabilized with at least one homoeologous group segregating for A-, B- or D-genome chromosomes. The stabilized plants represented ten different karyotypes that contained one to five disome substitutions of D-genome chromosomes for A- or B-genome chromosomes. Two (BD) (BD)RR tetraploids had no A-genome chromosomes. The average number of D substitutions was 3.0 per line. Of the seven substitutions possible only one, 4D(4B), was not present. In the progeny of plants selected for fertility a selection pressure acted against wheat chromosomes 1B, 3B, 4D and 7D. The most favoured chromosome constitution of the (ABD) mixed genome was 1D, 2A, 3D, 4B, 5B, 6A and 7B. Plants of that karyotype but with a heterologous pair of chromosomes 5B and 5D had the best seed set. Evolutionary and breeding aspects of tetraploid triticale are discussed.     

Chromosomal location of powdery mildew resistance genes and cytogenetic analysis of meiosis in common wheat cultivar Meri

Common wheat cv. Meri was crossed to a set of 21 Chinese Spring monosomic lines to characterize resistance to powdery mildew and to determine the chromosomal location of the gene(s). Monosomic F1 plants were allowed to self-pollinate and to produce F2 seeds. Seedlings of F2 and F3 plants and their parents were inoculated with isolates Ns 2 and 9 of Erysiphe graminis f. sp. tritici. Analysis of obtained data revealed that one major dominant gene conferring resistance is located on chromosome 1B of cv. Meri. The new gene is designated by symbol Pm28. On the basis of the trivalent configuration frequency (without univalent) at the 1st metaphase of meiosis it was found that two reciprocal translocations involving chromosomes 2A/5A and 5B/5D differentiate cv. Meri from cv. Chinese Spring. In the F1 monosomic hybrids, genes causing a decrease in pairing are found on chromosomes 4D and 6D, and genes enhancing pairing--on chromosomes 3A and 7B.     

Genetic dissection of interactions between wheat flour starch and its components in two populations using two QTL mapping methods

Starch content and its components are important for determining wheat end-use quality and yield. However, little information is available about their interactions at the QTL/gene level in more than one population using different QTL mapping methods. Therefore, to dissect these interactions, two mapping populations from two locations over 2 years were used. The QTLs for the populations were analyzed by unconditional and conditional QTL mapping by two different analysis methods. In the two populations, there were a total of 24 unconditional additive QTLs detected for flour amylose (FAMS), flour amylopectin (FAMP), flour total starch (FTSC), and the ratio of FAMS to FAMP using ICIMapping4.1 methods, but 26 unconditional QTLs were found using QTLNetwork2.0 methods. Of these QTLs, 10 stable major additive QTLs were identified in more than one environment, mainly distributed on chromosomes 3B, 4A, 5A, and 7D. The maximum percentage of phenotypic variance explained (PVE) reached 54.31%. Two new unconditional major additive QTLs on chromosome 3B (Qftsc3B and Qfamp3B) were found. A total of 23 and 19 conditional additive QTLs were identified in the two populations using two different methods, respectively. Of which, eight and six stable major conditional QTLs were detected on chromosomes 3B, 4A, and 7D, respectively. New repressed QTLs were identified, such as Qftsc/fams5B-1 and Qftsc/fams5B-2. There were 20 epistatic unconditional and 15 conditional QTLs detected. In all, important QTLs on chromosomes 3B, 4A, and 7A were found in both populations. However, the number of important QTLs in the special recombinant inbred line (RIL) population was higher than that in the double haploid (DH) population, especially on chromosomes 7D and 5B. Moreover, the QTLs on chromosomes 4A, 7A, and 7D were close to the Wx-1 loci in the RIL population. These indicated better results can be obtained by a special population to target traits than by a common population. The important QTLs on key chromosomes can always be detected no matter what kinds of populations are used, such as the QTLs on chromosome 4A. In addition, QTL clusters were found on chromosomes 4A, 3B, 7A, 7D, and 5A in the two populations, indicating these chromosome regions were very important for starch biosynthesis.