QTL mapping for flour and noodle colour components and yellow pigment content in common wheat

Improvement of flour colour is an important breeding objective for various wheat-based end-products. The objectives of this study were to identify quantitative trait loci (QTL) for flour colour components and yellow pigment content (YPC), using 240 recombinant inbred lines (RILs) derived from a cross between the Chinese wheat cultivars PH82-2 and Neixiang 188. Field trials were performed in a Latinized α-lattice design in Anyang and Jiaozuo, Henan Province and Taian, Shandong, in the 2005–2006 and 2006–2007 cropping seasons providing data for six environments. One hundred and eighty-eight polymorphic SSR markers, rye secalin marker Sec1, STS markers YP7A for a phytoene synthase gene (Psy-A1), and four glutenin subunit markers, were used to genotype the population and construct the linkage map for subsequent QTL analysis. Two major QTL were detected for YPC, associated with 1RS (1B.1R translocation) and the Psy-A1 (7A) gene, explaining 31.9% and 33.9% of the phenotypic variances, respectively. 1RS also had large influences on Fa*, Fb*, KJ, NL*and Nb*, and Psy-A1 genes showed large effects on Fa*, Fb*, Kj, Fci, NL*, Na* and Nb*, explaining from 4.5 to 26.1% and 4.3 to 35.9% of the phenotypic variances, respectively. In addition, QTL for flour colour parameters and yellow pigment content were also detected on chromosomes 1A and 4A, accounting for 1.5–4.1% of the phenotypic variance. The genetic effect of the 1B.1R translocation on flour colour parameters was also discussed.     

Rapid genotyping with DNA micro-arrays for high-density linkage mapping and QTL mapping in common buckwheat (Fagopyrum esculentum Moench)

For genetic studies and genomics-assisted breeding, particularly of minor crops, a genotyping system that does not require a priori genomic information is preferable. Here, we demonstrated the potential of a novel array-based genotyping system for the rapid construction of high-density linkage map and quantitative trait loci (QTL) mapping. By using the system, we successfully constructed an accurate, high-density linkage map for common buckwheat (Fagopyrum esculentum Moench); the map was composed of 756 loci and included 8,884 markers. The number of linkage groups converged to eight, which is the basic number of chromosomes in common buckwheat. The sizes of the linkage groups of the P1 and P2 maps were 773.8 and 800.4 cM, respectively. The average interval between adjacent loci was 2.13 cM. The linkage map constructed here will be useful for the analysis of other common buckwheat populations. We also performed QTL mapping for main stem length and detected four QTL. It took 37 days to process 178 samples from DNA extraction to genotyping, indicating the system enables genotyping of genome-wide markers for a few hundred buckwheat plants before the plants mature. The novel system will be useful for genomics-assisted breeding in minor crops without a priori genomic information.     

QTL analysis for grain weight in common wheat

Quantitative trait loci (QTL) analysis for grain weight (GW = 1000 grain weight) in common wheat was conducted using a set of 100 recombinant inbred lines (RILs) derived from a cross ‘Rye Selection 111 (high GW) × Chinese Spring (low GW)’. The RILs and their two parental genotypes were evaluated for GW in six different environments (three locations × two years). Genotyping of RILs was carried out using 449 (30 SSRs, 299 AFLP and 120 SAMPL) polymorphic markers. Using the genotyping data of RILs, framework linkage maps were prepared for three chromosomes (1A, 2B, 7A), which were earlier identified by us to carry important/major genes for GW following monosomic analysis. QTL analysis for GW was conducted following genome-wide single marker regression analysis (SMA) and composite interval mapping (CIM) using molecular maps for the three chromosomes. Following SMA, 12 markers showed associations with GW, individual markers explaining 6.57% to 10.76% PV (phenotypic variation) for GW in individual environments. The high grain weight parent, Rye Selection111, which is an agronomically superior genotype, contributed favourable alleles for GW at six of the 12 marker loci identified through SMA. The CIM identified two stable and definitive QTLs, one each on chromosome arms 2BS and 7AS, which were also identified through SMA, and a third suggestive QTL on 1AS. These QTLs explained 9.06% to 19.85% PV for GW in different environments. The QTL for GW on 7AS is co-located with a QTL for heading date suggesting the occurrence of a QTL having a positive pleiotropic effect on the two traits. Some of the markers identified during the present study may prove useful for marker-assisted selection, while breeding for high GW in common wheat.     

Marker-assisted selection of common beans for resistance to common bacterial blight: efficacy and economics

The possibility of using random amplified polymorphic DNA (RAPD) markers previously mapped in the common bean PC50/XANI59 population to select for resistance to common bacterial blight (CBB) in different populations was examined. Two out of 02 selected RAPD markers were polymorphic in HR56 and W0633d, the parental lines used in this experiment. Cosegregation analysis of the two polymorphic markers and disease reaction in a recombinant inbred (RI) population derived from HR67/W1744d confirmed that one of the two RAPD markers, BC420₉₀₀, was significantly associated with a major quantitative trait locus‐conditioning resistance to CBB in HR67. This locus accounted for approximately 51) of the phenotypic variation. The RAPD marker was transformed into a sequence characterized amplified region (SCAR) marker and used for selection in a different population derived from ‘Envoy’/HR67. Prediction for resistance to CBB with the BC420_.990 SCAR marker was 94.2% accurate in this population. A comparison between marker‐assisted selection (MAS) and conventional greenhouse screening showed that the cost of MAS is about one‐third less than that of the greenhouse test.     

QTL mapping for anthocyanin and proanthocyanidin content in red rice

Anthocyanins and proanthocyanidins are the primary pigments of red rice and are also important functional nutrients for human health. To identify novel quantitative trait loci (QTLs) underlying anthocyanins and proanthocyanidins (ANC and PAC) in rice, a recombinant inbred line (RIL) derived from a cross of red rice ‘Hong Xiang 1’ (‘HX1’) and white rice ‘Song 98-131’ (‘S98-131’) was cultivated in six environments. A genetic map containing 126 markers covering 1833.4 cM with an average of 14.55 cM between markers was constructed. A total of 21 additive QTLs (A-QTLs) for ANC and PAC were identified from six environments using the IciMapping v3.3 software. Two new QTLs, qANC3 and qPAC12-4, were detected in several environments, and explained significant phenotypic variance. Nine QTLs of ANC and PAC were detected with additive × environmental interaction effects (AE effects) by QTLNetwork 2.1 software, but no epistatic and epistatic × environmental interaction effects (AA and AAE effects) were detected. The information obtained in this study could be useful for fine mapping and molecular marker-assisted selection of ANC and PAC in rice.     

花生种子大小相关性状QTL定位研究进展

花生是我国重要的油料作物和经济作物,目前国内花生的产量远远不能满足消费者的所需,进一步提高花生单产是解决花生生产供不应求的重要途径。花生种子大小相关性状是花生的重要农艺性状,对提高花生单产至关重要。本文综述了植物种子大小的调控途径以及近年来花生分子标记、遗传图谱构建、种子大小相关性状QTL定位研究中取得的进展,探讨了目前花生种子大小相关性状研究中面临的挑战和机遇,对花生产量遗传改良进行了展望。     

QTL mapping of yield-related traits in the wheat germplasm 3228

The new wheat germplasm 3228, a putative derivative of tetraploid Agropyron cristatum Z559 and the common wheat Fukuhokomugi, has superior features in yield-related traits, particularly in spike morphological traits, such as large spike and superior grain number. To identify favorable alleles of these traits in 3228, 237 F_2:3 families were developed from the cross 3228/Jing 4839. A genetic map was constructed using 179 polymorphic SSR and EST-SSR markers. A total of 76 QTL controlling spike number per plant (SNP), spike length (SL), spikelet number per spike (SNS), floret number per spikelet (FNS), grain number per spike (GNS) and thousand-grain weight (TGW) were detected on 16 chromosomes. Each QTL explained 1.24–27.01% of the phenotypic variation, and 9 QTL (28.95%) were detected in two or all environments. Additive effects of 45 QTL were positive with 3228 alleles increasing the QTL effects, 31 QTL had negative effects indicating positive contributions from Jing 4839. Three important clusters involving all traits were located on chromosomes 5A, 6A and 4B, and several co-located QTL were also found. Most of the QTL detected on the three chromosome regions could contribute to the use of 3228 in breeding for grain yield improvement.     

Fine mapping of a major flowering time QTL on soybean chromosome 6 combining linkage and association analysis

Flowering time is a key trait in the plant life cycle and an important selection criterion for soybean. Here, we combine the advantages of genome-wide association and linkage mapping to identify and fine map quantitative trait loci (QTLs) associated with flowering time. Linkage mapping was performed using 152 recombinant inbred lines and a major QTL, qFT6, affecting flowering time was found on chromosome 6. To refine the qFT6, the 192 natural accessions were genotyped using eight new simple sequence repeats and 10 single nucleotide polymorphisms markers covering the qFT6 region Haplotype analysis showed that the haplotype between markers BARC-014947-01929 and Satt365 could explain more phenotypic variation (26.5 %) than any other combination of markers. These results suggested that the target flowering time gene was located in ~300 kb between BARC-014947-01929 and Satt365, including three predicted genes. High-resolution map in qFT6 region will be useful not only for marker-assisted selection of flowering time but also for further positional cloning of the target gene. These results indicate that combining association and linkage mapping provides an efficient approach for fine mapping of soybean genes.     

Development of STS markers and QTL validation for common bacterial blight resistance in common bean

Common bacterial blight (CBB) of common bean ( Phaseolus vulgaris L.), is one of the major diseases that decrease yield and quality. A major quantitative trait locus (QTL) for CBB resistance from line XAN 159 was transferred into two bean lines, HR45 and HR67. Previous studies identified that two markers are linked to this QTL but the chromosome location was not consistent. To identify more tightly linked markers and to verify the chromosome location, 65 additional markers were mapped using 81 recombinant inbred lines (RILs) derived from a cross HR67 × OAC95-4. The QTL was mapped to a 13 cM region on chromosome 1 and defined by eight molecular markers that explained 25–52% of the phenotypic variation. Six tightly linked amplified fragment length polymorphism markers (0.6–9.7 cM from the QTL peak) were converted into seven sequence tagged site markers, three of which were mapped to this QTL. Five tightly linked markers were used to screen 907 F₂ plants derived from a cross HR45 × 'OAC Rex' and four of them were linked to each other within 4.2 cM. These markers may be useful in marker-assisted selection and map-based cloning of this major QTL.     

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.     

Genetic mapping and QTL analysis for sugar yield-related traits in sugarcane

Genetic improvement of sugar content in sugarcane would benefit from the availability of sufficient DNA markers and a genetic map. Genetic linkage maps were constructed to identify quantitative trait loci (QTLs) for seedling brix (SB), brix (B), sucrose percent in juice (SUC), stalk number (SN), stalk length (SL), stalk diameter (SD), internodes (INT), number of green leaves (NGL), at three crop cycles across seven environments in a segregating population with 207 individuals derived from a bi-parental cross of sugarcane elite cultivars. Linkage analysis led to the construction of eight linkage groups (LGs) for Co86011 and sixteen LGs for CoH70. The combined length of the two linkage maps was 2606.77 cM distributed over 24 LGs. 31 QTLs were identified: 2 for SB, 7 for B, 6 for SUC, 4 for SN, 1 for SL, 3 for SD, 6 for INT and 2 for NGL at LOD scores ranging from 2.69 to 4.75. 7 QTLs (22 %) had stable effect across crop year and locations. Markers from parents were found to be associated with both positive and negative effect on all of the traits analyzed. The most important QTLs intervals identified in this study using single-dose marker, were qB2, qSUC2, qINT2 and qB2, qSUC2, qSL2, qINT2 located between SSR markers UGSM31₅₄₈ and UGSM31₆₄₉. These QTLs could be put into use in marker assisted breeding.     

QTL mapping for seedling traits under different nitrogen forms in wheat

The uptake and utilization of nitrogen (N) by plants are affected by the different forms of N in the soil. In this study, eight morphological traits at the seedling stage were investigated using a set of recombinant inbred lines (RILs). Three hydroponic culture experiments were conducted using three different NO₃ ^?/NH₄ ⁺ ratios (T1 at 50/50 %, T2 at 100/0 % and T3 at 0/100 %). The investigated traits in T2 and T1 were significantly higher than T3 in all three experiments, indicating that NO₃ ^? promoted or NH₄ ⁺ suppressed the production of biomass. Comparing T1 with T2, NO₃ ^? significantly increased the values of root fresh weight (RFW), total fresh weight (TFW) and root dry weight (RDW) and significantly decreased shoot dry weight (SDW). A total of 147 quantitative trait loci (QTLs) for the eight traits were detected on 18 chromosomes (except 2A, 3D and 4D). Among them, 16 QTLs (QRfw-1A, QRfw-1D, QSfw-1D, QSfw-2B.1, QTfw-1A, QTfw-1D, QRsfw-2B, QRsfw-3B.1, QRdw-1A.1, QRdw-1A.2, QSdw-6B.1, QSdw-7A.1, QTdw-1A.1, QRsdw-1A.1, QRsdw-5A.1 and QRsdw-7A.1) were detected in more than three of the nine treatment–experiments, and most of the 16 QTLs made large contributions of approximately 15 %. Surprisingly, QRsfw-4A.1 and QRsfw-4A.2 explained as much as 47.9 and 55.5 % of the phenotypic variation, respectively. Thirteen important QTL clusters (C1-C13) with more than four QTLs and involving 66 QTLs (44.9 %) were mapped on chromosomes 1A, 1D, 2B, 2D, 4A, 4B, 5B, 5D, 6B, 7A and 7B.     

QTL mapping for the tocopherols at milk stage of kernel development in sweet corn

Tocopherols have several beneficial effects in plants, and are indispensable micronutrients for humans. Sweet corn is a major source of tocopherols in high concentrations. In this investigation, tocopherol compounds in sweet corn were analyzed by high performance liquid chromatography. To detect quantitative trait loci (QTL) controlling accumulation of tocopherols at the milk stage in sweet corn, a F₂ population consisting of 229 F_2:3 lines was created from the cross between a high-total tocopherols line (A6) and a low-total tocopherols line (A57). A genetic map was constructed using 136 polymorphic molecular markers including one gene-targeted marker based on the tocopherol biosynthesis pathway (HPPD). Eleven putative QTLs for tocopherol content and composition were detected by composite interval mapping and located on Chr. 1, Chr. 2, Chr. 5, Chr. 6 and Chr. 10. Phenotypic variance explained by each QTL ranged from 4.74 to 41.16 %. Eight mapped QTLs were co-localized, suggesting that the same QTL affected the amounts of more than one tocopherol compound. One candidate gene-targeted marker (HPPD) showed co-localization with the major QTL for γ-tocopherol and total tocopherols. Only one interval (umc1177–bnlg1429) on chromosome one exhibited a QTL for α, δ, γ, and total tocopherols with high LOD and R² values. The primary conclusion of this work is that two major QTLs located on Chr. 1 and Chr. 5 can be used for improvement of sweet corn nutrition quality by marker-assisted selection.     

Dynamic QTL mapping for plant height in the hybrid population of Agropyron Gaertn.

Plant height (PH) plays a very important role for plant breeding and also serves as a model trait to dynamic development study. The dynamic quantitative trait locus (QTL) analysis for PH of Agropyron Gaertn. was carried out in a cross-pollination (CP) hybrid population of A. Gaertn. based on the phenotypic data of PH at different developmental stages in four year-sites and the constructed single-nucleotide polymorphism (SNP) genetic map. The results showed that 69 QTL and nine major QTL were detected by unconditional QTL mapping. A total of 107 QTL and 13 major QTL were found using conditional QTL mapping. Forty-seven QTL were detected by two methods. Two unconditional QTL, Qph2-5 and Qph3-4, were expressed as major and stable QTL for PH. Four major stable conditional QTL for PH, cQph4-1, cQph4-8, cQph6-2 and cQph6-7, were detected. Two conditional PH QTL, cQph3-5 and cQPh3-7, were identified in four environments over multiple stages. The gene/QTL controlling PH was expressed in a certain spatiotemporal manner. These results could also provide a reference for genetic and breeding research of related plant.