<Emphasis Type="Italic">FaRCg1</Emphasis>: a quantitative trait locus conferring resistance to Colletotrichum crown rot caused by <Emphasis Type="Italic">Colletotrichum gloeosporioides</Emphasis> in octoploid strawberry

Colletotrichum crown rot (CCR) is an important disease of strawberry (Fragaria?×ananassa) throughout the Southeastern US and in subtropical climates around the world, where hot and humid conditions facilitate rapid disease development. Yet no resistance loci have been described to date, as genetic studies have been historically difficult in allo-octoploid (2n?=?8x?=?56) strawberry. In the present study, we investigate the genetic architecture of resistance to CCR. Four population sets from the University of Florida were inoculated in four different seasons from 2013–2014 to 2016–2017. Two large, multiparental discovery population sets were used for QTL discovery, and two validation sets of cultivars and advanced selections representing the parent pool of the breeding program were also assessed. Subgenome-specific single-nucleotide polymorphism (SNP) markers were mapped, and FlexQTL? software was utilized to perform a Bayesian, pedigree-based QTL analysis. A quantitative trait locus on linkage group 6B, which we name FaRCg1, accounts for most of the genetic variation for resistance in the discovery sets (26.8–29.8% in 2013–2014 and 17% in 2015–2016). High-throughput marker assays were developed for the most significant SNPs which correlated with the mode of the QTL region. The discovery and characterization of the FaRCg1 locus and the molecular tools developed from it will be utilized to achieve increased genetic gains for resistance.     

A rapid and sensitive method for the detection of Xanthomonas fragariae, causal agent of angular leafspot disease in strawberry plants

Angular leaf spot is a bacterial disease caused by Xanthomonas fragariae. It has become a serious disease in the USA and Europe in recent years. Several detection procedures are described for this plant pathogen. However, they are either too time-consuming, too insensitive or impractical when handling a large number of samples routinely. Here we describe a modified protocol of the REDExtract-N-Amp Plant PCR-Kit for the detection of X. fragariae in planta and demonstrate that it provides greater sensitivity, speed and high throughput potential than methods previously described.     

Resistance to Phytophthora fragariae var. fragariae in strawberry: the Rpf2 gene

  Phytophthora fragariae var. fragariae is the causal agent of red stele (red core) root rot in strawberry (Fragaria spp.). The inheritance of resistance to one isolate of this fungus was studied in 12 segregating populations of F.×ananassa derived from crosses between four resistant cultivars (‘Climax’, ‘Redgauntlet’, ‘Siletz’, and ‘Sparkle’) and three susceptible cultivars (‘Blakemore’, ‘Glasa’, and ‘Senga’ Sengana’). The analysis clearly supports the hypothesis of a single segregating dominant resistance gene. It is proposed that this gene be designated Rpf2. Received 12 November 1996 / Accepted: 22 November 1996     

High-resolution mapping reveals linkage between genes in common bean cultivar Ouro Negro conferring resistance to the rust,anthracnose, and angular leaf spot diseases

Key message

Co-segregation analysis and high-throughput genotyping using SNP, SSR, and KASP markers demonstrated genetic linkage between Ur-14 and Co-3 ⁴ /Phg-3 loci conferring resistance to the rust, anthracnose and angular leaf spot diseases of common bean.

Abstract

Rust, anthracnose, and angular leaf spot are major diseases of common bean in the Americas and Africa. The cultivar Ouro Negro has the Ur-14 gene that confers broad spectrum resistance to rust and the gene cluster Co-3 ⁴ /Phg-3 containing two tightly linked genes conferring resistance to anthracnose and angular leaf spot, respectively. We used co-segregation analysis and high-throughput genotyping of 179 F_2:3 families from the Rudá (susceptible) × Ouro Negro (resistant) cross-phenotyped separately with races of the rust and anthracnose pathogens. The results confirmed that Ur-14 and Co-3 ⁴ /Phg-3 cluster in Ouro Negro conferred resistance to rust and anthracnose, respectively, and that Ur-14 and the Co-3 ⁴ /Phg-3 cluster were closely linked. Genotyping the F_2:3 families, first with 5398 SNPs on the Illumina BeadChip BARCBEAN6K_3 and with 15 SSR, and eight KASP markers, specifically designed for the candidate region containing Ur-14 and Co-3 ⁴ /Phg-3, permitted the creation of a high-resolution genetic linkage map which revealed that Ur-14 was positioned at 2.2 cM from Co-3 ⁴ /Phg-3 on the short arm of chromosome Pv04 of the common bean genome. Five flanking SSR markers were tightly linked at 0.1 and 0.2 cM from Ur-14, and two flanking KASP markers were tightly linked at 0.1 and 0.3 cM from Co-3 ⁴ /Phg-3. Many other SSR, SNP, and KASP markers were also linked to these genes. These markers will be useful for the development of common bean cultivars combining the important Ur-14 and Co-3 ⁴ /Phg-3 genes conferring resistance to three of the most destructive diseases of common bean.

     

Identification of RAPD markers linked to a Phytophthora fragariae resistance gene (Rpf1) in the cultivated strawberry

 Bulked segregant analysis (BSA) was used to identify seven random amplified polymorphic DNA (RAPD) markers linked to the Rpf 1 gene. Rpf 1 confers resistance to Phytophthora fragariae var. fragariae, the causal agent of red stele root rot in Fragaria spp. The bulked DNAs represented subsets of a F₁ population obtained from the cross Md683×Senga Sengana which consisted of 60 plants and segregated in a 1:1 ratio for resistance or susceptibility to race 2.3.4 isolate NS2 of P.  fragariae. Seven markers were shown to be linked to Rpf 1 and were generated from four primers; five of these markers were in coupling phase and two in repulsion phase with respect to the gene. A linkage map of this resistance gene region was generated using JoinMap 2.0^TM. The manner in which Rpf 1 and the linked markers co-segregated indicated that they are inherited in a disomic fashion. These markers could enable gene pyramiding and marker-assisted selection of resistance genes in strawberry breeding programmes. Received: 26 August 1996 / Accepted: 20 December 1996     

Forecasting model of bacterial leaf spot disease of mulberry caused by Xanthomonas campestris pv. mori

In order to develop weather-based forecasting model of bacterial leaf spot (BLS) disease of mulberry caused by Xanthomonas campestris pv. mori, weekly disease severity data were recorded for three years on the ruling cultivar S-1. Daily meteorological data viz. maximum temperature, minimum temperature, maximum relative humidity, minimum relative humidity, rainfall and number of rainy days were also recorded. It was observed that BLS appeared in April/May and continued up to November with maximum severity in July. The correlation coefficient between disease severity and meteorological parameters revealed that the BLS disease severity has significant positive correlation with minimum temperatures, maximum and minimum relative humidity, rainfall and number of rainy days and negative correlation with maximum temperature. Multiple regressions analysis revealed that average of maximum temperature, minimum temperature and rainfall of preceding seven days and maximum relative humidity, minimum relative humidity of previous 9–15 days was found to maximally influence BLS disease severity. The contribution of the meteorological factors was found to be highest of minimum temperature (40.65%) followed by maximum temperature (24.20%), maximum relative humidity (16.41%), minimum relative humidity (8.07%), rainfall (5.29%) and number of rainy days (5.38%).     

Increasing the density of markers around a major QTL controlling resistance to angular leaf spot in common bean

Angular leaf spot (ALS) causes major yield losses in the common bean (Phaseolus vulgaris L.), an important protein source in the human diet. This study describes the saturation around a major quantitative trait locus (QTL) region, ALS10.1, controlling resistance to ALS located on linkage group Pv10 and explores the genomic context of this region using available data from the P. vulgaris genome sequence. DArT-derived markers (STS-DArT) selected by bulk segregant analysis and SCAR and SSR markers were used to increase the resolution of the QTL, reducing the confidence interval of ALS10.1 from 13.4 to 3.0 cM. The position of the SSR ATA220 coincided with the maximum LOD score of the QTL. Moreover, a new QTL (ALS10.2^UC) was identified at the end of the same linkage group. Sequence analysis using the P. vulgaris genome located ten SSRs and seven STS-DArT on chromosome 10 (Pv10). Coincident linkage and genome positions of five markers enabled the definition of a core region for ALS10.1 spanning 5.3 Mb. These markers are linked to putative genes related to disease resistance such as glycosyl transferase, ankyrin repeat-containing, phospholipase, and squamosa-promoter binding protein. Synteny analysis between ALS10.1 markers and the genome of soybean suggested a dynamic evolution of this locus in the common bean. The present study resulted in the identification of new candidate genes and markers closely linked to a major ALS disease resistance QTL, which can be used in marker-assisted selection, fine mapping and positional QTL cloning.     

Rapid location of Glomerella leaf spot resistance gene locus in apple by whole genome re-sequencing

Glomerella leaf spot (GLS) is a new fungal disease of apple that damages apple leaves mainly during the summer in China. For efficient GLS-resistant apple breeding by marker-assisted selection (MAS) and a better understanding of the molecular mechanisms of the resistance, it is important to find molecular markers that are tightly linked to GLS resistance genes and construct fine mapping. However, the development and selection of DNA markers are time-consuming and labor-intensive processes. Next-generation sequencing technology provides a powerful tool to overcome this limitation and is faster and more efficient in establishing the association of GLS resistance with molecular markers or searching for candidate genes. In this study, we report a method for rapid location of a GLS resistance gene locus (R _gls ) in apple by whole genome re-sequencing technology coupled with bulked segregant analysis (BSA). A total of 3,399,950 single nucleotide polymorphisms (SNPs) were identified. Through the genome-wide comparison of SNP profiles between the resistant and the susceptible bulks constructed from F₁ individuals derived from a cross between “Golden Delicious” and “Fuji,” the R _gls locus was identified on apple chromosome 15 between 2 and 5 Mb. In this region, eight SNP markers were validated using high resolution melting (HRM), and the fine genetic mapping of the eight markers was constructed. The R _gls locus was sandwiched by two flanking markers SNP4208 and SNP4257, with the recombination frequency of 0.97% (2/207). The marker SNP4236 co-segregated with R _gls . The physical size of the R _gls locus was estimated to be 49 kb. In this genetic interval, nine genes were predicted. Our study provides an effective method for rapid identification of genomic regions and development of the diagnostic markers for MAS. This strategy is potentially useful for other agronomic traits or plant species.     

Mapping of the quantitative trait locus (QTL) conferring partial resistance to rice leaf blast disease

Malaysian rice, Pongsu Seribu 2, has wide-spectrum resistance against blast disease. Chromosomal locations conferring quantitative resistance were detected by linkage mapping with SSRs and quantitative trait locus (QTL) analysis. For the mapping population, 188 F₃ families were derived from a cross between the susceptible cultivar, Mahsuri, and a resistant variety, Pongsu Seribu 2. Partial resistance to leaf blast in the mapping population was assessed. A linkage map covering ten chromosomes and consisting of 63 SSR markers was constructed. 13 QTLs, including 6 putative and 7 putative QTLs, were detected on chromosomes 1, 2, 3, 5, 6, 10, 11 and 12. The resulting phenotypic variation due to a single QTL ranged from 2 to 13 %. These QTLs accounted for approx. 80 % of the total phenotypic variation within the F₃ population. Therefore, partial resistance to blast in Pongsu Seribu 2 is due to combined effects of multiple loci with major and minor effects.     

Lr68: a new gene conferring slow rusting resistance to leaf rust in wheat

The common wheat cultivar Parula possesses a high level of slow rusting, adult plant resistance (APR) to all three rust diseases of wheat. Previous mapping studies using an Avocet-YrA/Parula recombinant inbred line (RIL) population showed that APR to leaf rust (Puccinia triticina) in Parula is governed by at least three independent slow rusting resistance genes: Lr34 on 7DS, Lr46 on 1BL, and a previously unknown gene on 7BL. The use of field rust reaction and flanking markers identified two F₆ RILs, Arula1 and Arula2, from the above population that lacked Lr34 and Lr46 but carried the leaf rust resistance gene in 7BL, hereby designated Lr68. Arula1 and Arula2 were crossed with Apav, a highly susceptible line from the cross Avocet-YrA/Pavon 76, and 396 F₄-derived F₅ RILs were developed for mapping Lr68. The RILs were phenotyped for leaf rust resistance for over 2 years in Ciudad Obregon, Mexico, with a mixture of P. triticina races MBJ/SP and MCJ/SP. Close genetic linkages with several DNA markers on 7BL were established using 367 RILs; Psy1-1 and gwm146 flanked Lr68 and were estimated at 0.5 and 0.6 cM, respectively. The relationship between Lr68 and the race-specific seedling resistance gene Lr14b, located in the same region and present in Parula, Arula1 and Arula2, was investigated by evaluating the RILs with Lr14b-avirulent P. triticina race TCT/QB in the greenhouse. Although Lr14b and Lr68 homozygous recombinants in repulsion were not identified in RILs, γ-irradiation-induced deletion stocks that lacked Lr68 but possessed Lr14b showed that Lr68 and Lr14b are different loci. Flanking DNA markers that are tightly linked to Lr68 in a wide array of genotypes can be utilized for selection of APR to leaf rust.     

Narrowing down the single homoeologous FaPFRU locus controlling flowering in cultivated octoploid strawberry using a selective mapping strategy

Extending the period of fruit production is a way to substantially increase crop yield in many fruit or ornamental species. In the cultivated octoploid strawberry (Fragaria × ananassa), the most consumed small fruit worldwide, fruit production season can be extended by selecting the perpetual flowering (PF) cultivars. This trait is of considerable interest to growers and to the food industry. Four homoeologous loci controlling a single trait can be expected in such a complex octoploid species. However, we recently showed that the PF trait is under the control of the single dominant FaPFRU locus (J. Exp. Bot., 2013, 64 , 1837), making it potentially amenable to marker‐assisted selection (MAS). Here, we report the successful use of a strategy, based on a selective mapping using a reduced sample of individuals, to identify nine markers in close linkage to the FaPFRU allelic variant. Thus, this strategy can be used to fine map the target homoeologous loci in other complex polyploid crop species. Recombinant analysis further enabled us to reduce the locus to a region flanked by two markers, Bx083_206 and Bx215_131, corresponding to a 1.1 Mb region in the diploid F. vesca reference genome. This region comprises 234 genes, including 15 flowering associated genes. Among these, the FLOWERING LOCUS T (FT) is known to be a key activator of flowering. The close association between the PF trait and the FaPFRU flanking markers was validated using an additional segregating population and genetic resources. This study lays the foundation for effective and rapid breeding of PF strawberry cultivars by MAS.     

Mapping of QTLs conferring resistance to bacterial leaf streak in rice

A large F₂ and a RI population were separately derived from a cross between two indica rice varieties, one of which was highly resistant to bacterial leaf streak (BLS) and the other highly susceptible. Following artificial inoculation of the RI population and over 2 years of testing, 11 QTLs were mapped by composite interval mapping (CIM) on six chromosomes. Six of the QTLs were detected in both seasons. Eight of the QTLs were significant following stepwise regression analysis, and of these, 5 with the largest effects were significant in both seasons. The detected QTLs explained 84.6% of the genetic variation in 1997. Bulked segregant analysis (BSA) of the extremes of the F₂ population identified 3 QTLs of large effect. The 3 QTLs were dentical to 3 of the 5 largest QTLs detected by CIM. The independent detection of the same QTLs using two methods of analysis in separate mapping populations verifies the existence of the QTLs for BLS and provides markers to ease their introduction into elite varieties. Received: 13 October 1999 / Accepted: 29 October 1999     

Arbuscular mycorrhizal fungal-induced alteration to root architecture in strawberry and induced resistance to the root pathogenPhytophthora fragariae

Three strawberry cultivars Elsanta, Cambridge Favourite and Rhapsody were inoculated with eitherGlomus fasciculatum orGlomus etunicatum and their growth compared with non-inoculated plants. The roots of all inoculated plants were 55 to 70% colonised after 98 days. Increases in both root and shoot dry weights were measured. Root architecture was also determined and increases in branching were evident in AMF colonised root systems. The remaining plants were then inoculated with the root pathogenPhytophthora fragariae and allowed to grow for a further 58 days before harvest. In two of the cultivars, Cambridge Favourite and Elsanta, AMF reduced root necrosis by approximately 60 and 30% respectively. Only in the least susceptible cultivar, Rhapsody, was no reduction measured in AMF colonised plants. There were differences in the control conferred by the two arbuscular mycorrhizal fungi and this suggests there may be practical benefits of inoculation. Relationships between the presence of roots of different orders, on inoculation with the pathogen, and subsequent necrosis provided a mechanism for identifying root-architecture driven alteration to susceptibility. Root system necrosis was positively correlated with the proportion of the root system made up of higher order roots (3° to 4°) in non-colonised plants and negatively correlated in AMF colonised plants. These data suggest that root-architecture changes are not important per se but factors expressed concurrently may be.     

Genetic mapping of a major gene in triticale conferring resistance to bacterial leaf streak

Key message

A major gene conferring resistance to bacterial leaf streak was mapped to chromosome 5R in triticale.

Abstract

Bacterial leaf streak (BLS), caused by Xanthomonas translucens pv. undulosa (Xtu), is an important disease of wheat and triticale around the world. Although resistance to BLS is limited in wheat, several triticale accessions have high levels of resistance. To characterize the genetic basis of this resistance, we developed triticale mapping populations using a resistant accession (Siskiyou) and two susceptible accessions (UC38 and Villax St. Jose). Bulked segregant analysis in an F₂ population derived from the cross of Siskiyou × UC38 led to the identification of a simple sequence repeat (SSR) marker (XSCM138) on chromosome 5R that co-segregated with the resistance gene. The cross of Siskiyou × Villax St. Jose was advanced into an F_2:5 recombinant inbred line population and evaluated for BLS reaction. Genetic linkage maps on this population were assembled with markers generated using genotyping-by-sequencing as well as several SSR markers previously identified on 5R. Quantitative trait locus (QTL) mapping revealed a single major QTL on chromosome 5R, underlined by the same SSR marker as in the Siskiyou × UC38 population. The F₁ hybrids of the two crosses were highly resistant to BLS, indicating that resistance is largely dominant. This work will facilitate introgression of this rye-derived BLS resistance gene into the wheat genome by molecular marker-mediated chromosome engineering.

     

Mapping of the QTL (quantitative trait locus) conferring partial resistance to leaf blast in rice cultivar Chubu 32

The rice cultivar Chubu 32 possesses a high level of partial resistance to leaf blast. The number and chromosomal location of genes conferring this resistance were detected by restriction fragment length polymorphism (RFLP) linkage mapping and quantitative trait locus (QTL) analysis. For the mapping, 149 F₃ lines derived from the cross between rice cultivar Norin 29, with a low level of partial resistance, and Chubu 32 were used, and their partial resistance to leaf blast was assessed in upland nurseries. A linkage map covering six chromosomes and consisting of 36 RFLP markers was constructed. In the map, only one significant QTL (LOD>2.0) for partial resistance was detected on chromosome 11. This QTL explained 45.6% of the phenotypic variation. The segregation ratio of the F3 lines was 3:1 for partial resistance to susceptibility. These results suggest that the partial resistance in Chubu 32 is controlled by a major gene. Received: 15 March 2001 / Accepted: 13 August 2001     

Characterization of Lr46, a gene conferring partial resistance to wheat leaf rust

Components of resistance conferred by the Lr46 gene, reported as causing "slow rusting" resistance to leaf rust in wheat, were studied and compared with the effects of Lr34 and genes for quantitative resistance in cv. Akabozu. Lr34 is a gene that confers non-hypersensitive type of resistance. The effect of Lr46 resembles that of Lr34 and other wheats reported with partial resistance. At macroscopic level, Lr46 produced a longer latency period than observed on the susceptible recurrent parent Lalbahadur, and a reduction of the infection frequency not associated with hypersensitivity. Microscopically, Lr46 increased the percentage of early aborted infection units not associated with host cell necrosis and decreased the colony size. The effect of Lr46 is comparable to that of Lr34 in adult plant stage, but in seedling stage its effect is weaker than that of Lr34.     

QTL mapping of resistance to gray leaf spot in ryegrass

Gray leaf spot (GLS) is a serious fungal disease caused by Magnaporthe grisea, recently reported on perennial ryegrass (Lolium perenne L.), an important turfgrass and forage species. This fungus also causes rice blast and many other grass diseases. Rice blast is usually controlled by host resistance, but durability of resistance is a problem. Little GLS resistance has been reported in perennial ryegrass. However, greenhouse inoculations in our lab using one ryegrass isolate and one rice-infecting lab strain suggest presence of partial resistance. A high density linkage map of a three generation Italian × perennial ryegrass mapping population was used to identify quantitative trait loci (QTL) for GLS resistance. Potential QTL of varying effect were detected on four linkage groups, and resistance to the ryegrass isolate and the lab strain appeared to be controlled by different QTL. Of three potential QTL detected using the ryegrass isolate, the one with strongest effect for resistance was located on linkage group 3 of the MFB parent, explaining between 20% and 37% of the phenotypic variance depending on experiment. Another QTL was detected on linkage group 6 of the MFA parent, explaining between 5% and 10% of the phenotypic variance. The two QTL with strongest effect for resistance to the lab strain were located on linkage groups MFA 2 and MFB 4, each explaining about 10% of the phenotypic variance. Further, the QTL on linkage groups 3 and 4 appear syntenic to blast resistance loci in rice. This work will likely benefit users and growers of perennial ryegrass, by setting the stage for improvement of GLS resistance in perennial ryegrass through marker-assisted selection.     

Inheritance and development of molecular markers linked to angular leaf spot resistance genes in the common bean accession G10909

Angular leaf spot (ALS) is one of the major diseases of the common bean (Phaseolus vulgaris L.). Different sources of resistance have been identified but few have been characterized. Studies were conducted to elucidate the inheritance of ALS resistance in the bean accession G10909 and to identify molecular markers linked to these genes. Evaluation of parental genotypes, F₁, F₂ and backcross to susceptible parent (Sprite) populations revealed that two dominant and complementary genes conditioned ALS resistance. Allelism tests showed that the ALS resistance genes in G10909 were different from those in the Mesoamerican cultivars Mexico 54, MAR 2, G10474 and Cornell 49-242. Three sequence-characterized amplified region (SCAR) markers, PF13₃₁₀, PF9₂₆₀ and OPE04₇₀₉, and a microsatellite, Pv-gaat001, segregated in coupling with the resistance genes in G10909. Pairwise segregation analysis revealed that markers PF13₃₁₀, PF9₂₆₀ and OPE04₇₀₉ were linked, while Pv-gaat001 segregated in a 9:3:3:1 ratio from all markers. Markers PF13₃₁₀, PF9₂₆₀ and OPE04₇₀₉ were mapped to linkage group B08, and segregated with resistance gene Phg _G10909B at 4.9, 7.4 and 9.9 cM, respectively. Pv-gaat001, previously mapped to linkage group B04, segregated with resistance gene Phg _G10909A at 13 cM. The potential utility of these markers to aid breeding for ALS resistance is discussed.