Development of molecular markers for crown rot resistance in wheat: mapping of QTLs for seedling resistance in a '2-49' × 'Janz' population

Crown rot, caused by Fusarium pseudograminearum, is an important disease of wheat in Australia and elsewhere. In order to identify molecular markers associated with partial seedling resistance to this disease, bulked segregant analysis and quantitative trait loci (QTL) mapping approaches were undertaken using a population of 145 doubled haploid lines constructed from ‘2‐49’ (partially resistant) × ‘Janz’ (susceptible) parents. Phenotypic data indicated that the trait is quantitatively inherited. The largest QTLs were located on chromosomes 1D and 1A, and explained 21% and 9% of the phenotypic variance, respectively. Using the best markers associated with five QTLs identified by composite interval mapping, the combined effect of the QTLs explained 40.6% of the phenotypic variance. All resistance alleles were inherited from ‘2‐49’ with the exception of a QTL on 2B, which was inherited from ‘Janz’. A minor QTL on 4B was loosely linked (19.8 cM) to the Rht1 locus in repulsion. None of the QTLs identified in this study were located in the same region as resistance QTLs identified in other populations segregating for Fusarium head blight, caused by Fusarium graminearum.     

Identification of novel QTL for resistance to crown rot in the doubled haploid wheat population 'W21MMT70' × 'Mendos'

Crown rot (causal agent Fusarium pseudograminearum) is a fungal disease of major significance to wheat cultivation in Australia. A doubled haploid wheat population was produced from a cross between line ‘W21MMT70’, which displays partial seedling and adult plant (field) resistance to crown rot, and ‘Mendos’, which is moderately susceptible in seedling tests but partially resistant in field trials. Bulked segregant analysis (BSA) based on seedling trial data did not reveal markers for crown rot resistance. A framework map was produced consisting of 128 microsatellite markers, four phenotypic markers, and one sequence tagged site marker. To this map 331 previously screened AFLP markers were then added. Three quantitative trait loci (QTL) were identified with composite interval mapping across all of the three seedling trials conducted. These QTL are located on chromosomes 2B, 2D and 5D. The 2D and 5D QTL are inherited from the line ‘W21MMT70’, whereas the 2B QTL is inherited from ‘Mendos’. These loci are different from those associated with crown rot resistance in other wheat populations that have been examined, and may represent an opportunity for pyramiding QTL to provide more durable resistance to crown rot.     

Molecular mapping of soybean seed tocopherols in the cross ‘OAC Bayfield’ × ‘OAC Shire’

Soybean (Glycine max [L.] Merr.) is cultivated primarily for its protein and oil in the seed. In addition, soybean seeds contain nutraceutical compounds such as tocopherols (vitamin E), which are powerful antioxidants with health benefits. The objective of this study was to identify molecular markers linked to quantitative trait loci (QTL) that affect accumulation of soybean seed tocopherols. A recombinant inbred line (RIL) population derived from the cross ‘OAC Bayfield’ × ‘OAC Shire’ was grown in three locations over 2 years. A total of 151 SSR markers were polymorphic of which a one‐way analysis of variance identified 42 markers whereas composite interval mapping identified 26 markers linked to tocopherol QTL across 17 chromosomes. Individual QTL explained from 7% to 42% of the total phenotypic variation. Significant two‐locus epistatic interactions were identified for a total of 122 combinations in 2009 and 152 in 2010. The multiple‐locus models explained 18.4–72.2% of the total phenotypic variation. The reported QTL may be used in marker‐assisted selection (MAS) to develop high tocopherol soybean cultivars.     

Mapping QTL involved in powdery mildew resistance of the apple clone U 211

Scab and powdery mildew, caused by Venturia inaequalis (Cke.) Wint. and Podosphaera leucotricha (Ellis et Ev.) Salm. are the most important apple diseases. The apple clone U 211 is resistant to scab and is also highly resistant to powdery mildew under field conditions. The interval mapping method was applied for the identification of genomic regions conferring U 211 resistance to powdery mildew. The genetic maps of the ‘Idared’ and U 211 genome sectors were constructed using amplified fragment lenght polymorphism and simple sequence repeat markers and 98 individuals from the progeny of the cross ‘Idared’× U 211. On the basis of the phenotypic and molecular marker data 10 powdery mildew resistance quantitative trait loci (QTL) were identified in U 211 and ‘Idared’. One of the QTL in the clone U 211 explained 48‐72% of the phenotypic variation and its effect was stable over years.     

Molecular mapping of quantitative trait loci for field resistance to Fusarium head blight in a European winter wheat population

Fusarium head blight (FHB), one of the most destructive diseases of wheat in many parts of the world, can reduce the grain quality due to mycotoxin contamination up to rejection for usage as food or feed. Objective of this study was to map quantitative trait loci (QTL) associated with FHB resistance in the winter wheat population ‘G16‐92’ (resistant)/‘Hussar’. In all, 136 recombinant inbred lines were evaluated in field trials in 2001 and 2002 after spray inoculation with a Fusarium culmorum suspension. The area under disease progress curve was calculated based on the visually scored FHB symptoms. For means across all environments two FHB resistance QTL located on chromosomes 1A, and 2BL were identified. The individual QTL explained 9.7% and 14.1% of the phenotypic variance and together 26.7% of the genetic variance. The resistance QTL on 1A coincided with a QTL for plant height in contrast to the resistance QTL on 2BL that appeared to be independently inherited from morphological characteristics like plant height and ear compactness. Therefore, especially the QTL on 2BL could be of great interest for breeding towards FHB resistance.     

Deployment of cold tolerance loci from Oryza sativa ssp. Japonica cv. ‘Nipponbare’ in a high‐yielding Indica rice cultivar ‘93‐11’

Cold tolerance is a complex trait, and QTL pyramiding is required for rice breeding. In this study, a total of seven QTLs for cold tolerance in the Japonica rice variety ‘Nipponbare’ were identified in an F_2:3 population. A stably inherited major QTL, called qCTS11, was detected in the region adjacent to the centromere of chromosome 11. In a near‐isogenic line population, the QTL was further dissected into two linked loci, qCTS11.1 and qCTS11.2. Both of the homozygous alleles of qCTS11.1 and qCTS11.2 from ‘Nipponbare’ showed major positive effects on cold tolerance. Through pyramiding the linked QTLs in the cold‐sensitive Indica rice cultivar ‘93‐11’, we have developed a new elite, high‐yielding Indica variety with cold tolerance.     

Validation of a major QTL for scab resistance with SSR markers and use of marker-assisted selection in wheat

The objectives of this study were to validate the major quantitative trait locus (QTL) for scab resistance on the short arm of chromosome 3B in bread wheat and to isolate near‐isogenic lines for this QTL using marker‐assisted selection (MAS). Two resistant by susceptible populations, both using ‘Ning7840’ as the source of resistance, were developed to examine the effect of the 3BS QTL in different genetic backgrounds. Data for scab resistance and simple sequence repeat (SSR) markers linked to the resistance QTL were analyzed in the F_2:3 lines of one population and in the F_3:4 lines of the other. Markers linked to the major QTL on chromosome 3BS in the original mapping population (‘Ning7840’/‘Clark’) were closely associated with scab resistance in both validation populations. Marker‐assisted selection for the QTL with the SSR markers combined with phenotypic selection was more effective than selection based solely on phenotypic evaluation in early generations. Marker‐assisted selection of the major QTL during the seedling stage plus phenotypic selection after flowering effectively identified scab resistant lines in this experiment. Near‐isogenic lines for this 3BS QTL were isolated from the F₆ generation of the cross ‘Ning7840’/‘IL89‐7978’ based on two flanking SSR markers, Xgwm389 and Xbarc147. Based on these results, MAS for the major scab resistance QTL can improve selection efficiency and may facilitate stacking of scab resistance genes from different sources.     

Molecular and physical mapping of genes affecting awning in wheat

Quantitative trait loci (QTL) for three traits related to awning (awn length at the base, the middle and the top of the ear) in wheat were mapped in a doubled‐haploid line (DH) population derived from the cross between the cultivars ‘Courtot’ (awned) and ‘Chinese Spring’ (awnless) and grown in Clermont‐Ferrand, France, under natural field conditions. A molecular marker linkage map of this cross that was previously constructed based on 187 DH lines and 550 markers was used for the QTL mapping. The genome was well covered (more than 95%) and a set of anchor loci regularly spaced (one marker every 20.8 cM) was chosen for marker regression analysis. For each trait, only two consistent QTL were identified with individual effects ranging from 8.5 to 45.9% of the total phenotypic variation. These two QTL cosegregated with the genes Hd on chromosome 4A and B2 on chromosome 6B, which are known to inhibit awning. The results were confirmed using ‘Chinese Spring’ deletion lines of these two chromosomes, which have awned spikes, while ‘Chinese Spring’ is usually awnless. No quantitative trait locus was detected on chromosome 5A where the B1 awn‐inhibitor gene is located, suggesting that both ‘Courtot’ and ‘Chinese Spring’ have the same allelic constitution at this locus. The occurrence of awned speltoid spikes on the deletion lines of this chromosome suggests that ‘Chinese Spring’ and ‘Courtot’ have the dominant B1 allele, indicating that B1 alone has insufficient effect to induce complete awn inhibition.     

Identification of quantitative trait loci controlling soybean seed weight in recombinant inbred lines derived from PI 483463 (Glycine soja) × ‘Hutcheson’ (G. max)

The objective of this study was to identify quantitative trait loci (QTLs) controlling 100‐seed weight in soybean using 188 recombinant inbred lines (RIL) derived from a cross of PI 483463 and ‘Hutcheson’. The parents and RILs were grown for 4 years (2010–2013), and mature, dry seeds were used for 100‐seed weight measurement. The variance components of genotype (a), environment (e) and a × e interactions for seed weight were highly significant. The QTL analysis identified 14 QTLs explaining 3.83–12.23% of the total phenotypic variation. One of the QTLs, qSW17‐2, was found to be the stable QTL, being identified in all the environments with high phenotypic variation as compared to the other QTLs. Of the 14 QTLs, 10 QTLs showed colocalization with the seed weight QTLs identified in earlier reports, and four QTLs, qSW5‐1, qSW14‐1, qSW15‐1 and qSW15‐2, found to be the novel QTLs. A two‐dimensional genome scan revealed 11 pairs of epistatic QTLs across 11 chromosomes. The QTLs identified in this study may be useful in genetic improvement of soybean seed weight.     

Dissection of genetic architecture for oil content in soybean seed using two backcross populations

Soybean seed oil was valued in foods, animal feed and some industrial applications. Molecular marker‐assisted selection (MAS) for high‐oil‐content cultivars was an important method for soybean breeders. The objective of this study was to identify quantitative trait loci (QTL) and epistatic QTL underlying the seed oil content of soybeans across two backcross (BC) populations (with one common male parent ‘Dongnong47’) and two different environments. Two molecular genetic maps were constructed. They encompassed 1046.8 cM [with an average distance of 6.75 cM in the ‘Dongnong47’  ×  ‘Jiyu89’ (DJ) population] and 846.10 cM [with an average distance of 5.76 cM in the ‘Dongnong47’  ×  ‘Zaoshu18’ (DZ) population]. Nine and seven QTL were identified to be associated with oil content in the DJ and DZ populations, respectively. The phenotypic variation explained by most of the QTL was usually less than 10%. Among the identified QTL, those stable ones across multiple environments and populations often had stronger additive effects. In addition, three stable QTL in the DZ populations were identified in the similar genomic region of the three QTL in the DJ population [qDJE and qDZE‐1 were located near Satt151 of Chromosome 15 (Chr15), qDJA1 and qDZA1 were located near Satt200 of Chr15 (LG A1), and qDJD2‐1 and qDZD2‐1 were located near Sat365 of Chr17]. In conclusion, MAS will be able more effectively to combine beneficial alleles of the different donors to design new genotypes with higher soybean seed oil content using the BC populations.     

Analysis of quantitative trait loci associated with leaflet types in two recombinant inbred lines of soybean

Leaf area, length and width affect the photosynthetic capability of a plant and so increasing the photosynthetic rate per unit leaf area may improve seed yield in soybean. In this study, simple sequence repeat (SSR) markers were used to identify the genomic regions significantly associated with the quantitative trait locus (QTL) that controls length, width and the length/width ratio of the terminal and lateral leaflet in two segregating F_2:10 recombinant inbred line (RIL) populations, ‘Keounolkong’ × ‘Shinpaldalkong’ (K/S) and ‘Keounolkong’ × ‘Iksan10’ (K/I). In the K/S population, one QTL was identified for terminal leaflet length (TLL), two for lateral leaflet length (LLL), four for terminal leaflet width (TLW), four for lateral leaflet width (LLW), two for terminal leaflet length/width ratio (TLR) and four for lateral leaflet length/width ratio (LLR), with total phenotypic variations of 7.43, 10.9, 26.57, 23.46, 20.25 and 23.31%, respectively. In the K/I population, two QTLs were identified for TLL, two for LLL, three for TLW, and two for LLW, four for TLR and two for LLR with total phenotypic variations of 29.89, 22.77, 18.5, 12.15, 22.96 and 17.85%, respectively. Only a few QTLs coincided among the leaflet traits and no relationships were observed between the two populations. Many QTLs were associated with leaflet traits but each single QTL made only a minimal contribution. Thus, pyramiding the favourable alleles for leaflet traits in soybean breeding programmes may accelerate vegetative growth and perhaps lead to higher yields by maximizing total photosynthetic performance.     

QTL analysis of resistance to Fusarium head blight in wheat using a 'Wangshuibai'-derived population

Fusarium head blight (FHB) is a devastating disease that reduces the yield, quality and economic value of wheat. For quantitative trait loci (QTL) analysis of resistance to FHB, F₃ plants and F_3:5 lines, derived from a ‘Wangshuibai’ (resistant)/‘Seri82’(susceptible) cross, were spray inoculated during 2001 and 2002, respectively. Artificial inoculation was carried out under field conditions. Of 420 markers, 258 amplified fragment length polymorphism and 39 simple sequence repeat (SSR) markers were mapped and yielded 44 linkage groups covering a total genetic distance of 2554 cM. QTL analysis was based on the constructed linkage map and area under the disease progress curve. The analyses revealed a QTL in the map interval Xgwm533‐Xs18/m12 on chromosome 3BS accounting for up to 17% of the phenotypic variation. In addition, a QTL was detected in the map interval Xgwm539‐Xs15/m24 on chromosome 2DL explaining up to 11% of the phenotypic variation. The QTL alleles originated from ‘Wangshuibai’ and were tagged with SSR markers. Using these SSR markers would facilitate marker‐assisted selection to improve FHB resistance in wheat.     

Molecular loci associated with seed isoflavone content may underlie resistance to soybean pod borer (Leguminivora glycinivorella)

Soybean pod borer (SPB) (Leguminivora glycinivorella (Mats.) Obraztsov) causes severe loss of soybean (Glycine max L. Merr.) seed yield and quality in some regions of the world, especially in north‐eastern China, Japan and Russia. Isoflavones in soybean seed play a crucial role in plant resistance to diseases and pests. The aim of this study was to find whether SPB resistance QTL are associated with soybean seed isoflavone content. A cross was made between ‘Zhongdou 27’ (higher isoflavone content) and ‘Jiunong 20’ (lower isoflavone content). One hundred and twelve F_5:10 recombinant inbred lines were derived through single‐seed descent. A plastic‐net cabinet was used to cover the plants in early August, and thirty SPB moths per square metre were put in to infest the soybean green pods. The results indicated that the percentage of seeds damaged by SPB was positively correlated with glycitein content (GC), whereas it was negatively correlated with genistein (GT), daidzein (DZ) and total isoflavone content (TI). Four QTL underlying SPB damage to seeds were identified and the phenotypic variation for SPB resistance explained by the four QTL ranged from 2% to 14% on chromosomes Gm7, 10, 13 and 17. Moreover, eleven QTL underlying isoflavone content were identified, and ten of them were encompassed within the same four marker intervals as the SPB QTL (BARC‐Satt208‐Sat292, Satt144‐Sat074, Satt540‐Sat244 and Satt345‐Satt592). These QTL could be useful in marker‐assisted selection for breeding soybean cultivars with both SPB resistance and high seed isoflavone content.     

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

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

Mapping of quantitative trait loci conferring resistance to bacterial wilt in tobacco (Nicotiana tabacum L.)

Tobacco bacterial wilt (TBW) is one of the most serious tobacco diseases in the world. Studies have shown that tobacco resistance to TBW is quantitatively inherited. This study aimed to map quantitative trait loci (QTL) conferring TBW resistance. An F_2 : 3 population containing 237 lines was developed from a cross between two flue‐cured tobacco cultivars, ‘Yanyan 97’ (YY97; moderately resistant to TBW) and ‘Honghua Dajinyuan’ (HD; highly susceptible to TBW), and a linkage map consisting of 201 simple sequence repeats (SSR) markers and spanning a total length of 2326.7 cM was constructed based on the population. Field experiments were conducted 2011 and 2012, and disease symptoms were investigated three times in each year. The phenotypic data were analysed either separately or jointly for QTL mapping using the software QTLNetwork 2.1. Eight QTL with significant main effects were mapped on chromosomes 2, 6, 12, 17 and 24. A major QTL (qBWR17a) was detected on chromosome 17, which explained up to 30% of the phenotypic variation. The results can facilitate marker‐assisted selection (MAS) in TBW resistance breeding programme.     

黄瓜(Cucumis sativus L.)种子含油量性状的QTL定位与分析

应用SRAP和SSR技术,对黄瓜种子高含油量品系Ma7与低含油量品系M6杂交组合的F2群体进行检测,获得102个分子标记,构建了7个连锁群组成的分子标记遗传图谱;图谱总长764 cM,标记间平均长度7.49 cM.应用Windows QTL Cartographer 2.5对种子含油量性状进行QTL扫描,在2009年秋...     

Mapping quantitative trait loci for yield-related traits in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

Chinese cabbage (Brassica rapa L. ssp. pekinensis) is one of the most important vegetables in China. However, the inheritance of yield-related traits in Chinese cabbage is poorly understood to date. To map quantitative trait loci (QTL) for yield-related traits in Chinese cabbage, a genetic linkage map was constructed with 192 doubled haploid (DH) lines. The genetic map was constructed based on 190 sequence-related amplified polymorphisms and 43 simple sequence repeats. QTL mapping was conducted for 11 yield-related traits in 170 DH lines derived from a cross between two diverse Chinese cabbage lines, ‘WZ’ and ‘FT’, under different environmental conditions. A total of 46 main QTL (M-QTL) and 7 epistatic QTL (E-QTL) were identified. The phenotypic variation explained by each M-QTL and E-QTL ranged from 4.85 to 25.06 % and 1.85 to 13.29 %, respectively. The QTL-by-environment interactions were detected using the QTLNetwork 2.0 program in joint analyses of multi-environment phenotypic values. The phenotypic variation explained by each QTL and by QTL × environment interaction was 1.14–4.24 % and 0.00–1.26 %, respectively. Our results provide a better understanding of the genetic factors controlling leaf and head-related traits in Chinese cabbage.     

Mapping quantitative trait loci controlling soybean seed starch content in an interspecific cross of ‘Williams 82’ (Glycine max) and ‘PI 366121’ (Glycine soja)

Seed starch content (SSC) greatly affects the taste, flavour and processing properties of soy foods. The objective in this study was to identify quantitative trait loci (QTL) for SSC in soybean. A total in 169 recombinant inbred lines (RILs) derived from a cross in ‘Williams 82’ and ‘PI 366121’ were grown for three consecutive years. The SSC of the RILs displayed continuous variation with transgressive segregation and hence amenable for QTL mapping. Nine significant QTL exhibiting 5.6–11.3% of the total phenotypic variation (PVE) were identified. The QTL qSTR06_2 showed highest PVE (9.1–11.3%) at LOD values of 4.25–5.39. No stable QTL over 3 years were identified, indicating strong environmental influence on SSC. The QTL qSTR11_1 and qSTR20_1 were found to colocalize with some of the previously reported QTL for sucrose content in soybean, implying the interrelationship between starch and sucrose biosynthesis. As the carbohydrate components may affect key constituents such as oil and protein in soybean seed, findings of the study may be useful in breeding soybeans with improved seed composition.     

Detection of downy and powdery mildew resistance QTL in a ‘Regent’ × ‘RedGlobe’ population

One hundred and eighty six F₁ plants from a ‘Regent’ × ‘RedGlobe’ cross were used to generate a partial linkage map with 139 microsatellite markers spanning all 19 chromosomes. Phenotypic scores for downy mildew, taken over two years, confirmed a major resistance QTL (Rpv3) against downy mildew in the interval VVIN16-cjvh to UDV108 on chromosome 18 of ‘Regent’. This locus explained up to 62 % of the phenotypic variance observed. Additionally a putative minor downy mildew resistance locus was observed on chromosome 1 in one season. A major resistance locus against powdery mildew (Ren3) was also identified on chromosome 15 of ‘Regent’ in the interval UDV116 to VChr15CenGen06. This study established the efficacy of and validated the ‘Regent’-derived downy and powdery mildew major resistance genes/QTL under South African conditions. Closely linked SSR markers for marker-assisted selection and gene pyramiding strategies were identified.     

Genome-wide detection of genetic loci associated with soybean aphid resistance in soybean germplasm PI 603712

Soybean aphid (Aphis glycines Matsumura) has become one of the major pests of soybean [Glycine max (L.) Merr.] in North America since 2000. At least four biotypes of soybean aphid have been confirmed in the United States. Genetic characterization of new sources of soybean aphid resistance will facilitate the expansion of soybean gene pool for soybean aphid resistance and thus will help to develop soybean aphid resistant cultivars. To characterize the genetic basis of soybean aphid resistance in PI 603712, a newly identified resistant germplasm line, 142 F₂ plants derived from the cross ‘Roberts’ × PI 603712 and their parents were evaluated for soybean aphid resistance in the greenhouse, and were genotyped with BARCSoySNP6K Illumina Infinium II BeadChip. A genome-wide molecular linkage map was constructed with 1495 polymorphic SNP markers. QTL analysis revealed that PI 603712 possessed two major loci associated with soybean aphid resistance, located on chromosome 7 and 16, respectively. The locus on chromosome 7 was dominantly expressed and positioned about one Mega-base-pair distant from the previously identified resistance locus Rag1. The locus on chromosome 16 was positioned near the previously identified resistance locus Rag3 and expressed partially dominance or additive effect. Interestingly, two minor loci were also detected on chromosomes 13 and 17 but the alleles from PI 603712 decreased the resistance. In developing soybean aphid resistant cultivars through marker-assisted selection, an appropriate combination of resistance loci should be selected when PI 603712 is used as a donor parent of resistance.