Quantitative Trait Loci Mapping Of Resistance Research Articles

Genome-Wide Association Study Reveals a QTL Region for Ashy Stem Blight Resistance in PRA154 Andean Common Bean.

Ashy stem blight (ASB) caused by Macrophomina phaseolina (Tassi) Goidanich affects the common bean (Phaseolus vulgaris L.) at all growing stages. Higher levels of resistance were observed in Andean common beans, but specific resistant quantitative trait loci (QTLs) conferring resistance to this pathogen have not been reported in this gene pool. The objectives of this research were to: (i) conduct a genome-wide association study (GWAS) and QTL mapping for resistance in the Andean breeding line PRA154; and (ii) identify single nucleotide polymorphism (SNP) markers and candidate genes for ASB resistance. Phenotyping was conducted under greenhouse conditions by inoculating the 107 F6:7 recombinant inbred lines (RILs) derived from the cross between the susceptible cultivar 'Verano' and the partial-resistant breeding line PRA154 twice with the M. phaseolina isolate PRI21. Genotyping was performed with 109,040 SNPs distributed across all 11 P. vulgaris chromosomes. A novel major QTL was located between 28,761,668 and 31,263,845 bp, extending 2.5 Mbp on chromosome Pv07, and the highest significant SNP markers were Chr07_28761668_A_G, Chr07_29131720_G_A, and Chr07_31263845_C_T with the highest LOD (more than 10 in most of the cases) and R-squared values, explaining 40% of the phenotypic variance of the PRI21 isolate. The gene Phvul.007G173900 (methylcrotonyl-CoA carboxylase alpha chain and mitochondrial 3-methylcrotonyl-CoA carboxylase 1 [MCCA]) with a size of 10,891 bp, located between 29,131,591 and 29,142,481 bp on Pv07, was identified as one candidate for ASB resistance in PRA154, and it contained Chr07_29131720_G_A. The QTL and genetic marker information could be used to assist common bean breeders to develop germplasm and cultivars with ASB resistance through molecular breeding.

Parametric mapping of QTL for resistance to European canker in apple in ‘Aroma’ × ‘Discovery’

Resistance to European canker (Neonectria ditissima) in apple is currently one of the most important breeding targets for commercial production in Sweden. Previous research has identified significant genetic variation in susceptibility to the disease, with the local Swedish cultivar ‘Aroma’ considered as one of the most resistant cultivars. Identification of genetic regions underlying the resistance of this cultivar would be a valuable tool for future breeding. Thus, we performed Bayesian quantitative trait loci (QTL) mapping for resistance to European canker in a full-sib family of ‘Aroma’ × ‘Discovery’. Mapping was performed with the area under the disease progression curves (AUDPCs) from all seven (AUDPC_All7) and the first four assessments (AUDPC_First4), and three parameters of a sigmoid growth model for lesion length. As a scale for the effect of the different parameters, historic phenotypic data from screenings of a genetically diverse germplasm was compiled and re-analyzed. The parametrization of the data on lesion growth increased the number of QTL that could be identified with high statistical power, and provided some insight into their roles during different stages of disease development in the current experimental setup. Five QTL regions with strong or decisive evidence were identified on linkage groups 1, 8, 15, and 16. The QTL regions could be assigned to either of the parameters lesion length at the first assessment (‘LL_A1’), the maximal lesion growth rate (lesion length doubling time, ‘t_gen’), and the lesion length at girdling (‘LL_G’). Three of these QTL were traced along the pedigrees of some known relatives of the FS family, and discussed in relation to future crosses for breeding and genetic research.

QTL Mapping of Resistance to Bacterial Wilt in Pepper Plants (Capsicum annuum) Using Genotyping-by-Sequencing (GBS)

Bacterial wilt (BW) disease, which is caused by Ralstonia solanacearum, is one globally prevalent plant disease leading to significant losses of crop production and yield with the involvement of a diverse variety of monocot and dicot host plants. In particular, the BW of the soil-borne disease seriously influences solanaceous crops, including peppers (sweet and chili peppers), paprika, tomatoes, potatoes, and eggplants. Recent studies have explored genetic regions that are associated with BW resistance for pepper crops. However, owing to the complexity of BW resistance, the identification of the genomic regions controlling BW resistance is poorly understood and still remains to be unraveled in the pepper cultivars. In this study, we performed the quantitative trait loci (QTL) analysis to identify genomic loci and alleles, which play a critical role in the resistance to BW in pepper plants. The disease symptoms and resistance levels for BW were assessed by inoculation with R. solanacearum. Genotyping-by-sequencing (GBS) was utilized in 94 F2 segregating populations originated from a cross between a resistant line, KC352, and a susceptible line, 14F6002-14. A total of 628,437 single-nucleotide polymorphism (SNP) was obtained, and a pepper genetic linkage map was constructed with putative 1550 SNP markers via the filtering criteria. The linkage map exhibited 16 linkage groups (LG) with a total linkage distance of 828.449 cM. Notably, QTL analysis with CIM (composite interval mapping) method uncovered pBWR-1 QTL underlying on chromosome 01 and explained 20.13 to 25.16% by R2 (proportion of explained phenotyphic variance by the QTL) values. These results will be valuable for developing SNP markers associated with BW-resistant QTLs as well as for developing elite BW-resistant cultivars in pepper breeding programs.

Fine mapping of QTLs for resistance to Phytophthora nicotianae in flue-cured tobacco using a high-density genetic map

Tobacco (Nicotiana tabacum L.) is an important agronomic crop and model system for studies of plant-pathogen interactions. Black shank, caused by Phytophthora nicotianae, is an important disease affecting tobacco production worldwide. In this study, a mapping population of 177 F7:8-9 recombinant inbred lines was generated from a cross between the highly resistant cultivar ‘Yunyan 85’ and a susceptible line ‘Dabaijin 599’. A high-density genetic linkage map containing 7734 single-nucleotide polymorphic markers based on restriction site-associated DNA tag sequencing technology was used to finely map quantitative trait loci (QTL) for resistance to P. nicotianae. A total of 10 QTLs were detected as being associated with resistance to P. nicotianae across multiple environments, and two major QTL qBS7 and qBS14 were repeatedly identified under all five environments. They explained 16.48-62.20% and 3.94-11.29% of the phenotypic variance with high LOD score, respectively. One hundred thirty-eight candidate genes were identified for two major QTLs qBS7 and qBS14, and annotation analysis showing that several predicted genes encoded proteins associated with plant defense response to pathogens. This high-density single-nucleotide polymorphic genetic linkage map of flue-cured tobacco based on restriction site-associated DNA sequencing was useful in the QTL finely mapping of resistance to P. nicotianae. This study increases our understanding of the genetics of resistance to P. nicotianae and aids in marker-assisted selection.

QTL mapping for resistance to and tolerance for the rice root-knot nematode, Meloidogyne graminicola

BackgroundThe root-knot nematode Meloidogyne graminicola is an obligate biotrophic pathogen considered to be the most damaging nematode species that causes significant yield losses to upland and rainfed lowland rice production in South and Southeast Asia. Mapping and identification of quantitative trait loci (QTL) for resistance to and tolerance for M. graminicola may offer a safe and economic management option to farmers. In this study, resistance to and tolerance for M. graminicola in Asian rice (Oryza sativa L.) were studied in a mapping population consisting of 300 recombinant inbred lines (RILs) derived from IR78877–208-B-1-2, an aerobic rice genotype with improved resistance to and tolerance for M. graminicola, and IR64, a popular, high-yielding rice mega-variety susceptible to M. graminicola. RILs were phenotyped for resistance and tolerance in the dry seasons of 2012 and 2013. QTL analysis was performed using 131 single nucleotide polymorphism (SNP) and 33 simple sequence repeat (SSR) markers.ResultsThree QTLs with main effects on chromosomes 4 (qMGR4.1), 7 (qMGR7.1) and 9 (qMGR9.1) and two epistatic interactions (qMGR3.1/ qMGR11.1 and qMGR4.2/ qMGR8.1) associated with nematode reproduction that were consistent in the two seasons were detected. A QTL affecting root galling was found on chromosomes 4 (qGR4.1) and 8 (qGR8.1), and QTLs for nematode tolerance were found on chromosomes 5 (qYR5.1) and 11 (qYR11.1). These QTLs were consistent in both seasons. A QTL for grain yield was found on chromosome 10 (qGYLD10.1), a QTL affecting filled grains per panicle was detected on chromosome 11 (qFG11.1) and a QTL for fresh root weight was found on chromosomes 2 (qFRWt2.1), 8 (qFRWt8.1) and 12 (qFRWt12.1) in both seasons. The donor of the alleles for qMGR4.1, qMGR7.1, qMGR9.1, qGR4.1, qGR8.1, qYR5.1 and qFRWt2.1 was IR78877–208-B-1-2, whereas for qYR11.1, qGYLD10.1 and qFG11.1, qFRWt8.1 and qFRWt12.1 was IR64. Lines having favorable alleles for resistance, tolerance and yield provided better yield under nematode-infested conditions and could be a starting point of marker-assisted breeding (MAB) for the improvement of M. graminicola resistance and tolerance in Asian rice.ConclusionThis study identified a total of 12 QTLs with main effects and two epistatic interactions in the 1st season and 2nd season related to M. graminicola resistance and tolerance, and other agronomic traits such as plant yield, percentage of filled grains, and fresh and dry root weight. Rice genotypes that have the favorable alleles for resistance (qMGR4.1, qMGR7.1, qMGR9.1, qGR4.1, qGR8.1) and tolerance (qYR5.1, and qYR11.1,) QTLs, and which are either resistant or partially resistant and tolerant, were also selected. These selected genotypes and the identified QTLs are vital information in designing MAB for the improvement of high-yielding rice genotypes but are susceptible to M. graminicola infection.

Genetic analysis and molecular mapping of QTLs for resistance to rice black-streaked dwarf disease in rice.

Rice black-streaked dwarf disease, caused by rice black-streaked dwarf virus (RBSDV), is transmitted by small brown planthoppers (Laodelphax striatellus Fallén, SBPH) and causes severe yield loss in epidemic years in China and other East Asian countries. Breeding for resistance to RBSDV is a promising strategy to control the disease. We identified Tetep that showed resistance to RBSDV using a field test and artificial inoculation test. An evaluation of the resistance mechanism revealed that Tetep was resistant to RBSDV but not to SBPH. Genetic analysis showed that the resistance of Tetep to RBSDV was controlled by quantitative trait loci (QTLs). Three new QTLs for RBSDV resistance were identified in this study, i.e., qRBSDV-3, qRBSDV-10 and qRBSDV-11. The LOD scores of qRBSDV-3, qRBSDV-10 and qRBSDV-11 were 4.07, 2.24 and 2.21, accounting for 17.5%, 0.3% and 12.4% of the total phenotypic variation, respectively. All the resistance loci identified in this study were associated with virus resistance genes. The alleles for enhancing resistance on chromosomes 3 and 11 originated from Tetep, whereas the other allele on chromosome 10 originated from a susceptible parent. The identified new resistance QTLs in this study are useful resources for efficiently breeding resistant rice cultivars to RBSDV.

Molecular mapping of QTLs for resistance to Fusarium wilt (race 1) and Ascochyta blight in chickpea (Cicer arietinum L.)

AbstractFusarium wilt (FW) and Ascochyta blight (AB) are two important diseases of chickpea which cause 100 % yield losses under favorable conditions. With an objective to validate and/or to identify novel quantitative trait loci (QTLs) for resistance to race 1 of FW caused by Fusarium oxysporum f. sp. ciceris and AB caused by Ascochyta rabiei in chickpea, two new mapping populations (F2:3) namely ‘C 214’ (FW susceptible) × ‘WR 315’ (FW resistant) and ‘C 214’ (AB susceptible) × ‘ILC 3279’ (AB resistant) were developed. After screening 371 SSR markers on parental lines and genotyping the mapping populations with polymorphic markers, two new genetic maps comprising 57 (C 214 × WR 315) and 58 (C 214 × ILC 3279) loci were developed. Analysis of genotyping data together with phenotyping data collected on mapping population for resistance to FW in field conditions identified two novel QTLs which explained 10.4–18.8 % of phenotypic variation. Similarly, analysis of phenotyping data for resistance to seedling resistance and adult plant resistance for AB under controlled and field conditions together with genotyping data identified a total of 6 QTLs explaining up to 31.9 % of phenotypic variation. One major QTL, explaining 31.9 % phenotypic variation for AB resistance was identified in both field and controlled conditions and was also reported from different resistant lines in many earlier studies. This major QTL for AB resistance and two novel QTLs identified for FW resistance are the most promising QTLs for molecular breeding separately or pyramiding for resistance to FW and AB for chickpea improvement.

QTL mapping for resistance to southern leaf blight in sweet corn

To identify quantitative trait loci (QTL) associated with southern leaf blight (SLB) in sweet corn, a population consisting of 330 F2:3 families was developed from a T14 (resistant) × T4 (susceptible) cross. The genetic linkage map was constructed based on the F2 population, with 192 SSR markers covering a total map distance of 1260 cm, and an average interval length of 6.56 cm. These 330 F2:3 families were evaluated in 2009 and 2010 for SLB resistance following inoculation at the seedling stage and milk stage. Using composite interval mapping (CIM) in QTL Cartographer v.2.5, 7 QTL out of 18 total QTL were identified at the seedling stage on chromosomes 3, 4, 6 and 9, and the phenotypic variance explained by each QTL ranged from 4.02 to 35.4%. The 11 other QTL were identified at the milk stage on chromosomes 3, 4, 6, 8, 9 and 10 and accounted for 3.50 to 13.65% of the phenotypic variance. Two QTL were detected in both years; these were located on chromosome 3 and 4 in the marker intervals umc2275 to umc2008 and umc2287 to bnlg2162, respectively. One QTL, located on chromosome 3 between umc2275 and umc2008, was detected at both developmental stages. The findings in this study may provide useful information for marker-assisted selection (MAS) and with further genetic and breeding studies for maize SLB. Key words: Sweet corn, southern leaf blight (SLB), composite interval mapping (CIM), quantitative trait loci(QTL).

QTL mapping for resistance to strip virus disease in rice

With 2 figures and 5 tables Abstract To discover new resistance genes to rice stripe virus disease (RSVD), quantitative trait loci (QTL) analysis was conducted by using 162 recombinant inbred lines, derived from a cross between ‘Guichao 2’ and ‘Koshihikari’, RSVD resistances were evaluated using both artificial inoculation and natural infection methods by scoring the ratio of the disease rating index. Three QTL-controlling RSVD resistance were detected by the above two methods, which located on chromosomes 4(qStv4), 9(qStv9) and 12(qStv12), respectively. The qStv9 and qStv12 was repeatedly detected in artificial inoculation test in 2006 and 2008. In natural inoculation test, the qStv4 and qStv9 was detected in 2006, and the qStv12 was detected in 2008. As qStv9 and qStv12 explained 11.3–32.1% of the resistance effect from ‘Guichao 2’ across two environments, they should be a useful genetic resource in rice MAS breeding programme against RSVD. Further analysis revealed that the lines harbouring the alleles of qStv9 and qStv12 exhibited significantly increased resistance to RSVD, implying the possibility of breeding new resistant varieties by pyramiding resistant QTL through marker-assisted selection.

Mapping of QTL for resistance against Fusarium head blight in the winter wheat population Pelikan//Bussard/Ning8026

AbstractWe report on the identification of FHB (Fusarium head blight) resistance quantitative trait loci (QTL) of the donor ‘G93010’ (Bussard/Ning8026) in the background of elite breeding material adapted to the central European climate. With a multiple interval mapping method, two major resistance QTL were identified. Qfhs.lfl‐7BS/5BL and Qfhs.lfl‐6BS reduced FHB severity individually by 30% and 24%. The combination of both QTL decreased disease severity most effectively by about one half. Qfhs.lfl‐6BS is most likely identical to Fhb2, thus, the effectiveness of Fhb2 in central European breeding material has been validated. Qfhs.lfl‐7BS/5BL overlapped with QTL for plant height and heading date. Nevertheless, the selection of lines combining a good FHB resistance level with an acceptable plant height was possible. As the donors of the QTL have probably not yet been utilized in European breeding material, we identified well‐adapted lines of the mapping population as valuable donors for marker‐assisted breeding programmes.

Mapping of QTL for resistance to powdery mildew and resistance gene analogues in perennial ryegrass

AbstractThe objective of this study was to map resistance gene analogues (RGA) and quantitative trait loci (QTL) for powdery mildew resistance in perennial ryegrass (Lolium perenne L.). The mapping population consisted of 184 F2 genotypes produced from a cross between one genotype of a synthetic perennial ryegrass variety Veyo and one genotype from the perennial ryegrass ecotype Falster. The greenhouse infection was measured as number of sporulating colonies on a 10‐cm leaf area with the maximum possible number of colonies to be counted set to 50. The range of infection scores in the population was 0–50 and the heritability was 71.7%. In total, two QTL for powdery mildew resistance were identified, and mapped to linkage groups (LG) LG3 and LG7. Individually, these QTL explained between 7.5% and 22.1% of the total phenotypic variation. Six RGA and three laccases were mapped to LG2, LG3, LG4, LG5 and LG7, however, no close linkage between RGA and QTL was observed.

Mapping of QTL for Resistance to White Mold Disease in Common Bean

White mold (WM), incited by Sclerotinia sclerotiorum (Lib.) de Bary, is a serious disease of common bean (Phaseolus vulgaris L.). However, plant breeders have had very limited success in developing resistant (R) cultivars. Molecular markers linked to genes for R to WM may improve selection for R. The objective was to identify random amplified polymorphic DNA (RAPD) markers linked to quantitative trait loci (QTL) for partial physiological resistance (PPR), partial field resistance (PFR), porosity over the furrow (POF), and plant height (PH) in a linkage map by means of recombinant inbred lines (RILs) from the cross ‘PC‐50’ (R) × XAN‐159 (susceptible). The parents and RILs were inoculated in two separate greenhouse experiments for each isolate and were also infected naturally in the field. Significant correlations (0.39, 0.47) were found for the WM reactions in the greenhouse and field. Nine candidate QTL were found affecting PPR isolate 152 (comparison‐wise P < 0.05) with strong evidence (genome‐wise P < 0.01) for three QTL on linkage groups (LGs) 4, 7, and 8, based on composite interval mapping analysis. Candidate QTL affecting PPR to isolate 279 were found on LGs 2, 3, 4, 7, and 8 with very strong evidence (genome‐wise P < 0.001) for a QTL linked to the C locus for seedcoat pattern. Seven candidate QTL for PFR were observed on LGs 4, 7, 8, and 11. Six of the seven candidate QTL for PFR were found in the same locations as QTL for PPR. However, two of the seven genomic regions were associated with PFR and POF that may contribute to disease avoidance.

QTL mapping for resistance against the European corn borer (Ostrinia nubilalis H.) in early maturing European dent germplasm

The European corn borer (ECB, Ostrinia nubilalis Hubner) is a major pest of maize in Central Europe. We mapped and characterized quantitative trait loci (QTLs) involved in resistance of maize against ECB damage, compared them with QTLs for agronomic traits, and evaluated the usefulness of marker-assisted selection (MAS) for improving ECB resistance in early maturing European maize germplasm. A total 226 F3 families from the cross D06 (resistant) × D408 (susceptible), together with 93 RFLP and two SSR markers were used for the QTL analyses. For each F3 family we measured the length of tunnels produced by larval stalk mining (TL), stalk damage ratings (SDR), and relative grain yield (RGY) in field experiments, with two replications in two environments in 1 year. The agronomic traits comprised grain yield under insecticide protection (GYP) and manual ECB larval infestation (GYI), the date of anthesis (ANT), and the in vitro digestibility of organic matter (IVDOM) of stover. Estimates of genotypic variance (σ2 g) were highly significant for all traits. Six QTLs for TL and five QTLs for SDR were detected, explaining about 50.0% of σ2 g. Most QTLs showed additive gene action for TL and dominance for SDR. No QTL was found for RGY. The number of QTLs detected for the agronomic traits ranged from two for GYI to 12 for ANT, explaining 12.5 to 57.3% of σ2 g, respectively. Only a single QTL was in common between the two resistance traits, as expected from the moderate trait correlation and the moderate proportions of σ2 g explained. Based on these results, MAS for improving ECB resistance can be competitive when cost-effective PCR-based marker systems are applied. However, it remains to be established whether the putative QTL regions for ECB resistance detected in the population D06 × D408 are consistent across other early maturing European maize germplasms.