Resistance Quantitative Trait Loci Research Articles

The RppC-AvrRppC NLR-effector interaction mediates the resistance to southern corn rust in maize

Southern corn rust (SCR), caused by the fungal pathogen Puccinia polysora, is a major threat to maize production worldwide. Efficient breeding and deployment of resistant hybrids are key to achieving durable control of SCR. Here, we report the molecular cloning and characterization of RppC, which encodes an NLR-type immune receptor and is responsible for a major SCR resistance quantitative trait locus. Furthermore, we identified the corresponding avirulence effector, AvrRppC, which is secreted by P. polysora and triggers RppC-mediated resistance. Allelic variation of AvrRppC directly determines the effectiveness of RppC-mediated resistance, indicating that monitoring of AvrRppC variants in the field can guide the rational deployment of RppC-containing hybrids in maize production. Currently, RppC is the most frequently deployed SCR resistance gene in China, and a better understanding of its mode of action is critical for extending its durability.

Mapping a stable adult-plant stripe rust resistance QTL on chromosome 6AL in Chinese wheat landrace Yibinzhuermai

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases threatening the yield and stability of wheat production in China and many other countries. Identification and utilization of new genes for durable stripe rust resistance are important for ongoing control of this disease. The objectives of this study were to identify quantitative trait loci (QTL) associated with adult-plant stripe rust resistance in the Chinese wheat landrace Yibinzhuermai (YBZR) and to provide wheat breeders with new sources of potentially durable resistance. A total of 117 recombinant inbred lines (RILs) (F5:8) derived from a cross between YBZR and highly susceptible cultivar Taichung 29 (TC29) were assessed for stripe rust severity in field experiments at Wenjiang in 2016 and 2017 and Chongzhou in 2016, 2017, 2018, and 2019 in Sichuan following inoculation with a mixture of current Pst races. The RILs were genotyped using the Wheat55K single nucleotide polymorphism (SNP) array. Three QTL were identified on chromosome arms 6AL, 5BL and 7DS. QYr.YBZR-6AL and QYr.YBZR-7DS conferred major effects in all field environments, explaining 10.6% to 14.7% and 11.5% to 21.2% of phenotypic variation, respectively. The QTL on 5BL and 7DS likely correspond to previously known QTL, whereas QYr.YBZR-6AL is probably novel. Haplotype analysis revealed that the resistance allele at QYr.YBZR-6AL was present in 2.8% of 324 Chinese wheat landraces. SNP markers closely linked with QYr.YBZR-6AL were converted to kompetitive allele-specific PCR markers and validated in the RIL population and a subset of 92 wheat cultivars. QYr.YBZR-6AL and its markers should be useful in breeding programs to improve the level and durability of stripe rust resistance.

Identification and Fine-Mapping of Clubroot (Plasmodiophora brassicae) Resistant QTL in Brassica rapa

European fodder turnips (Brassica rapa ssp. rapifera) were identified as sources of clubroot resistance (CR) and have been widely used in Brassica resistance breeding. An F2 population derived from a cross between a resistant turnip and a susceptible Chinese cabbage was used to determine the inheritance and locating the resistance Quantitative Trait Loci (QTLs). The parents showed to be very resistant/susceptible to the field isolates (pathotype 4) of clubroot from Henan in China. After inoculation, 27 very resistant or susceptible individuals were selected to construct bulks, respectively. Next-generation-sequencing-based Bulk Segregant Analysis Sequencing (BSA-Seq) was used and located resistance QTL on chromosome A03 (3.3–7.5 Mb) and A08 (0.01–6.5 Mb), named Bcr1 and Bcr2, respectively. Furthermore, an F3 population including 180 families derived from F2 individuals was phenotyped and used to verify and narrow candidate regions. Ten and seven Kompetitive Allele-Specific PCR (KASP) markers narrowed the target regions to 4.3–4.78 Mb (A03) and 0.02–0.79 Mb (A08), respectively. The phenotypic variation explained (PVE) of the two QTLs were 33.3% and 13.3% respectively. The two candidate regions contained 99 and 109 genes. In the A03 candidate region, there were three candidate R genes, namely Bra006630, Bra006631 and Bra006632. In the A08 candidate region, there were two candidate R genes, namely Bra030815 and Bra030846.

Fine mapping of QPm.caas-3BS, a stable QTL for adult-plant resistance to powdery mildew in wheat (Triticum aestivum L.).

A stable QTL QPm.caas-3BS for adult-plant resistance to powdery mildew was mapped in an interval of 431kb, and candidate genes were predicted based on gene sequences and expression profiles. Powdery mildew is a devastating foliar disease occurring in most wheat-growing areas. Characterization and fine mapping of genes for powdery mildew resistance can benefit marker-assisted breeding. We previously identified a stable quantitative trait locus (QTL) QPm.caas-3BS for adult-plant resistance to powdery mildew in a recombinant inbred line population of Zhou8425B/Chinese Spring by phenotyping across four environments. Using 11 heterozygous recombinants and high-density molecular markers, QPm.caas-3BS was delimited in a physical interval of approximately 3.91Mb. Based on re-sequenced data and expression profiles, three genes TraesCS3B02G014800, TraesCS3B02G016800 and TraesCS3B02G019900 were associated with the powdery mildew resistance locus. Three gene-specific kompetitive allele-specific PCR (KASP) markers were developed from these genes and validated in the Zhou8425B derivatives and Zhou8425B/Chinese Spring population in which the resistance gene was mapped to a 0.3cM interval flanked by KASP14800 and snp_50465, corresponding to a 431kb region at the distal end of chromosome 3BS. Within the interval, TraesCS3B02G014800 was the most likely candidate gene for QPm.caas-3BS, but TraesCS3B02G016300 and TraesCS3B02G016400 were less likely candidates based on gene annotations and sequence variation between the parents. These results not only offer high-throughput KASP markers for improvement of powdery mildew resistance but also pave the way to map-based cloning of the resistance gene.

Characterization of non-specific lipid transfer protein (nsLtp) gene families in the Brassica napus pangenome reveals abundance variation

BackgroundBrassica napus is an important agricultural species, improving stress resistance was one of the main breeding goals at present. Non-specific lipid transfer proteins (nsLTPs) are small, basic proteins which are involved in some biotic or abiotic stress responses. B. napus is susceptible to a variety of fungal diseases, so identify the BnLTPs and their expression in disease responses is very important. The common reference genome of B. napus does not contain all B. napus genes because of gene presence/absence variations between individuals. Therefore, it was necessary to search for candidate BnLTP genes in the B. napus pangenome.ResultsIn the present study, the BnLTP genes were identified throughout the pangenome, and different BnLTP genes were presented among varieties. Totally, 246 BnLTP genes were identified and could be divided into five types (1, 2, C, D, and G). The classification, phylogenetic reconstruction, chromosome distribution, functional annotation, and gene expression were analyzed. We also identified potential cis-elements that respond to biotic and abiotic stresses in the 2 kb upstream regions of all BnLTP genes. RNA sequencing analysis showed that the BnLTP genes were involved in the response to Sclerotinia sclerotiorum infection. We identified 32 BnLTPs linked to blackleg resistance quantitative trait locus (QTL).ConclusionThe identification and analysis of LTP genes in the B. napus pangenome could help to elucidate the function of BnLTP family members and provide new information for future molecular breeding in B. napus.

Unravelling cucumber resistance to several viruses via genome-wide association studies highlighted resistance hotspots and new QTLs.

The mapping and introduction of sustainable resistance to viruses in crops is a major challenge in modern breeding, especially regarding vegetables. We hence assembled a panel of cucumber elite lines and landraces from different horticultural groups for testing with six virus species. We mapped 18 quantitative trait loci (QTL) with a multiloci genome wide association studies (GWAS), some of which have already been described in the literature. We detected two resistance hotspots, one on chromosome 5 for resistance to the cucumber mosaic virus (CMV), cucumber vein yellowing virus (CVYV), cucumber green mottle mosaic virus (CGMMV) and watermelon mosaic virus (WMV), colocalizing with the RDR1 gene, and another on chromosome 6 for resistance to the zucchini yellowing mosaic virus (ZYMV) and papaya ringspot virus (PRSV) close to the putative VPS4 gene location. We observed clear structuring of resistance among horticultural groups due to plant virus coevolution and modern breeding which have impacted linkage disequilibrium (LD) in resistance QTLs. The inclusion of genetic structure in GWAS models enhanced the GWAS accuracy in this study. The dissection of resistance hotspots by local LD and haplotype construction helped gain insight into the panel's resistance introduction history. ZYMV and CMV resistance were both introduced from different donors in the panel, resulting in multiple resistant haplotypes at same locus for ZYMV, and in multiple resistant QTLs for CMV.

Distribution, Etiology, Molecular Genetics and Management Perspectives of Northern Corn Leaf Blight of Maize (Zea mays L.)

Maize is cultivated extensively throughout the world and has the highest production among cereals. However, Northern corn leaf blight (NCLB) disease caused by <i>Exherohilum turcicum</i>, is the most devastating limiting factor of maize production. The disease causes immense losses to corn yield if it develops prior or during the tasseling and silking stages of crop development. It has a worldwide distribution and its development is favoured by cool to moderate temperatures with high relative humidity. The prevalence of the disease has increased in recent years and new races of the pathogen have been reported worldwide. The fungus <i>E. turcicum</i> is highly variable in nature. Though different management strategies have proved effective to reduce economic losses from NCLB, the development of varieties with resistance to <i>E. turcicum</i> is the most efficient and inexpensive way for disease management. Qualitative resistance for NCLB governed by Ht genes is a race-specific resistance which leads to a higher level of resistance. However, some Ht genes can easily become ineffective under the high pressure of virulent strains of the pathogen. Hence, it is imperative to understand and examine the consistency of the genomic locations of quantitative trait loci for resistance to NCLB in diverse maize populations. The breeding approaches for pyramiding resistant genes against <i>E. turcicum</i> in maize can impart NCLB resistance under high disease pressure environments. Furthermore, the genome editing approaches like CRISPR-cas9 and RNAi can also prove vital for developing NCLB resistant maize cultivars. As such this review delivers emphasis on the importance and current status of the disease, racial spectrum of the pathogen, genetic nature and breeding approaches for resistance and management strategies of the disease in a sustainable manner.

Mapping of partial resistance to Phytophthora sojae in soybean PIs using whole‐genome sequencing reveals a major QTL

In the last decade, more than 70 quantitative trait loci (QTL) related to soybean [Glycine max (L.) Merr.] partial resistance (PR) against Phytophthora sojae have been identified by genome-wide association studies (GWAS). However, most of them have either a minor effect on the resistance level or are specific to a single phenotypic variable or one isolate, thereby limiting their use in breeding programs. In this study, we have used an analytical approach combining (a) the phenotypic characterization of a diverse panel of 357 soybean accessions for resistance to P. sojae captured through a single variable, corrected dry weight; (b) a new hydroponic assay allowing the inoculation of a combination of P. sojae isolates covering the spectrum of commercially relevant Rps genes; and (c) exhaustive genotyping through whole-genome resequencing (WGS). This led to the identification of a novel P. sojae resistance QTL with a relatively major effect compared with the previously reported QTL. The QTL interval, spanning ∼500 kb on chromosome (Chr) 15, does not colocalize with previously reported QTL for P. sojae resistance. Plants carrying the favorable allele at this QTL were 60% more resistant. Eight genes were found to reside in the linkage disequilibrium (LD) block containing the peak single-nucleotide polymorphism (SNP) including Glyma.15G217100, which encodes a major latex protein (MLP)-like protein, with a functional annotation related to pathogen resistance. Expression analysis of Glyma.15G217100 indicated that it was nearly eight times more highly expressed in a group of plant introductions (PIs) carrying the resistant (R) allele compared with those carrying the susceptible (S) allele within a short period after inoculation. These results offer new and valuable options to develop improved soybean cultivars with broad resistance to P. sojae through marker-assisted selection.

Identification of Quantitative Trait Loci for Leaf Rust and Stem Rust Seedling Resistance in Bread Wheat Using a Genome-Wide Association Study.

In recent years, leaf rust (LR) and stem rust (SR) have become a serious threat to bread wheat production in Kazakhstan. Most local cultivars are susceptible to these rusts, which has affected their yield and quality. The development of new cultivars with high productivity and LR and SR disease resistance, including using marker-assisted selection, is becoming an important priority in local breeding projects. Therefore, the search for key genetic factors controlling resistance in all plant stages, including the seedling stage, is of great significance. In this work, we applied a genome-wide association study (GWAS) approach using 212 local bread wheat accessions that were phenotyped for resistance to specific races of Puccinia triticina Eriks. (Pt) and Puccinia graminis f. sp. tritici (Pgt) at the seedling stages. The collection was genotyped using a 20 K Illumina iSelect SNP assay, and 11,150 polymorphic SNP markers were selected for the association mapping. Using a mixed linear model, we identified 11 quantitative trait loci (QTLs) for five out of six specific races of Pt and Pgt. The comparison of the results from this GWAS with those from previously published work showed that nine out of eleven QTLs for LR and SR resistance had been previously reported in a GWAS study at the adult plant stages of wheat growth. Therefore, it was assumed that these nine common identified QTLs were effective for all-stage resistance to LR and SR, and the two other QTLs appear to be novel QTLs. In addition, five out of these nine QTLs that had been identified earlier were found to be associated with yield components, suggesting that they may directly influence the field performance of bread wheat. The identified QTLs, including novel QTLs found in this study, may play an essential role in the breeding process for improving wheat resistance to LR and SR.

Registration of the slow‐darkening pinto common bean cultivar ‘Wildcat’

AbstractSlow‐darkening pinto common bean (Phaseolus vulgaris L.) cultivar ‘Wildcat’ (Reg. no. CV‐345, PI 698190) was released by the University of Nebraska dry bean breeding program in 2018. It was bred for adaptation to western Nebraska growing conditions and enhanced resistance to bean rust, common bacterial blight (CBB), and Bean common mosaic virus (BCMV). The yield of Wildcat was comparable to conventional and slow‐darkening pinto bean cultivars grown in Nebraska from 2015 to 2020. During the 2017 Western Regional Bean Trial, 2017 Midwest Regional Performance Nursery, and 2018 Cooperative Dry Bean Nursery, Wildcat had a higher seed yield than ‘Twin Falls’, ‘Nez Perce’, ‘Black Foot’, ‘Montrose’, ‘Buster’, ‘ND‐Palomino’, and ‘La Paz’ at some locations. Wildcat has the Ur‐11 gene that confers resistance to all but one known bean rust race and carries the Indel NDSU_IND_11_48.459.896 marker tagging the Ur‐11 locus. Wildcat also has the SAP6 sequence characterized amplified region (SCAR) marker linked to a major CBB resistance quantitative trait locus, with an intermediate CBB rating (5.0) under field conditions at western Nebraska in 2020. Wildcat also carries the single dominant I gene that confers resistance to all non‐necrotic strains of BCMV and the SW13 SCAR marker linked to the I gene for resistance to BCMV. Wildcat has white flowers, blooms 46 d after planting, and is a full‐season bean, maturing 93 d after planting. The seed size of Wildcat, 43.3 g 100 seeds–1 on average, was significantly larger than current conventional and slow‐darkening pinto beans.

Quantitative Trait Loci Mapping of Adult Plant and Seedling Resistance to Stripe Rust (Puccinia striiformis Westend.) in a Multiparent Advanced Generation Intercross Wheat Population.

Stripe rust caused by the biotrophic fungus Puccinia striiformis Westend. is one of the most important diseases of wheat worldwide, causing high yield and quality losses. Growing resistant cultivars is the most efficient way to control stripe rust, both economically and ecologically. Known resistance genes are already present in numerous cultivars worldwide. However, their effectiveness is limited to certain races within a rust population and the emergence of stripe rust races being virulent against common resistance genes forces the demand for new sources of resistance. Multiparent advanced generation intercross (MAGIC) populations have proven to be a powerful tool to carry out genetic studies on economically important traits. In this study, interval mapping was performed to map quantitative trait loci (QTL) for stripe rust resistance in the Bavarian MAGIC wheat population, comprising 394 F6 : 8 recombinant inbred lines (RILs). Phenotypic evaluation of the RILs was carried out for adult plant resistance in field trials at three locations across three years and for seedling resistance in a growth chamber. In total, 21 QTL for stripe rust resistance corresponding to 13 distinct chromosomal regions were detected, of which two may represent putatively new QTL located on wheat chromosomes 3D and 7D.

Genome-Wide Association Analysis of Stable Stripe Rust Resistance Loci in a Chinese Wheat Landrace Panel Using the 660K SNP Array.

Stripe rust (caused by Puccinia striiformis f. sp. tritici) is one of the most severe diseases affecting wheat production. The disease is best controlled by developing and growing resistant cultivars. Chinese wheat (Triticum aestivum) landraces have excellent resistance to stripe rust. The objectives of this study were to identify wheat landraces with stable resistance and map quantitative trait loci (QTL) for resistance to stripe rust from 271 Chinese wheat landraces using a genome-wide association study (GWAS) approach. The landraces were phenotyped for stripe rust responses at the seedling stage with two predominant Chinese races of P. striiformis f. sp. tritici in a greenhouse and the adult-plant stage in four field environments and genotyped using the 660K wheat single-nucleotide polymorphism (SNP) array. Thirteen landraces with stable resistance were identified, and 17 QTL, including eight associated to all-stage resistance and nine to adult-plant resistance, were mapped on chromosomes 1A, 1B, 2A, 2D, 3A, 3B, 5A, 5B, 6D, and 7A. These QTL explained 6.06–16.46% of the phenotypic variation. Five of the QTL, QYrCL.sicau-3AL, QYrCL.sicau-3B.4, QYrCL.sicau-3B.5, QYrCL.sicau-5AL.1 and QYrCL.sicau-7AL, were likely new. Five Kompetitive allele specific PCR (KASP) markers for four of the QTL were converted from the significant SNP markers. The identified wheat landraces with stable resistance to stripe rust, significant QTL, and KASP markers should be useful for breeding wheat cultivars with durable resistance to stripe rust.

Unravelling consensus genomic regions conferring leaf rust resistance in wheat via meta‐QTL analysis

Leaf rust, caused by the fungus Puccinia triticina Erikss (Pt), is a destructive disease affecting wheat (Triticum aestivum L.) and a threat to food security. Developing resistant cultivars represents a useful method of disease control, and thus, understanding the genetic basis for leaf rust resistance is required. To this end, a comprehensive bibliographic search for leaf rust resistance quantitative trait loci (QTL) was performed, and 393 QTL were collected from 50 QTL mapping studies. Afterward, a consensus map with a total length of 4,567 cM consisting of different types of markers (simple sequence repeat [SSR], diversity arrays technology [DArT], chip-based single-nucleotide polymorphism [SNP] markers, and SNP markers from genotyping-by-sequencing) was used for QTL projection, and meta-QTL (MQTL) analysis was performed on 320 QTL. A total of 75 MQTL were discovered and refined to 15 high-confidence MQTL (hcmQTL). The candidate genes discovered within the hcmQTL interval were then checked for differential expression using data from three transcriptome studies, resulting in 92 differentially expressed genes (DEGs). The expression of these genes in various leaf tissues during wheat development was explored. This study provides insight into leaf rust resistance in wheat and thereby provides an avenue for developing resistant cultivars by incorporating the most important hcmQTL.

A high-density linkage map of finger millet provides QTL for blast resistance and other agronomic traits.

Finger millet [Eleusine coracana (L.) Gaertn.] is a critical subsistence crop in eastern Africa and southern Asia but has few genomic resources and modern breeding programs. To aid in the understanding of finger millet genomic organization and genes underlying disease resistance and agronomically important traits, we generated a F2:3 population from a cross between E. coracana (L.) Gaertn. subsp. coracana accession ACC 100007 and E. coracana (L.) Gaertn. subsp. africana , accession GBK 030647. Phenotypic data on morphology, yield, and blast (Magnaporthe oryzae) resistance traits were taken on a subset of the F2:3 population in a Kenyan field trial. The F2:3 population was genotyped via genotyping-by-sequencing (GBS) and the UGbS-Flex pipeline was used for sequence alignment, nucleotide polymorphism calling, and genetic map construction. An 18-linkage-group genetic map consisting of 5,422 markers was generated that enabled comparative genomic analyses with rice (Oryza sativa L.), foxtail millet [Setaria italica (L.) P. Beauv.], and sorghum [Sorghum bicolor (L.) Moench]. Notably, we identified conserved acrocentric homoeologous chromosomes (4A and 4B in finger millet) across all species. Significant quantitative trait loci (QTL) were discovered for flowering date, plant height, panicle number, and blast incidence and severity. Sixteen putative candidate genes that may underlie trait variation were identified. Seven LEUCINE-RICH REPEAT-CONTAINING PROTEIN genes, with homology to nucleotide-binding site leucine-rich repeat (NBS-LRR) disease resistance proteins, were found on three chromosomes under blast resistance QTL. This high-marker-density genetic map provides an important tool for plant breeding programs and identifies genomic regions and genes of critical interest for agronomic traits and blast resistance.

Quantitative Trait Locus Mapping of Resistance to Turnip Yellows Virus in Brassica rapa and Brassica oleracea and Introgression of These Resistances by Resynthesis Into Allotetraploid Plants for Deployment in Brassica napus.

Turnip yellows virus (TuYV) is aphid-transmitted and causes considerable yield losses in oilseed rape (OSR, Brassica napus, genome: AACC) and vegetable brassicas. Insecticide control of the aphid vector is limited due to insecticide resistance and the banning of the most effective active ingredients in the EU. There is only one source of TuYV resistance in current commercial OSR varieties, which has been mapped to a single dominant quantitative trait locus (QTL) on chromosome A04. We report the identification, characterisation, and mapping of TuYV resistance in the diploid progenitor species of OSR, Brassica rapa (genome: AA), and Brassica oleracea (genome: CC). Phenotyping of F1 populations, produced from within-species crosses between resistant and susceptible individuals, revealed the resistances were quantitative and partially dominant. QTL mapping of segregating backcross populations showed that the B. rapa resistance was controlled by at least two additive QTLs, one on chromosome A02 and the other on chromosome A06. Together, they explained 40.3% of the phenotypic variation. In B. oleracea, a single QTL on chromosome C05 explained 22.1% of the phenotypic variation. The TuYV resistance QTLs detected in this study are different from those in the extant commercial resistant varieties. To exploit these resistances, an allotetraploid (genome: AACC) plant line was resynthesised from the interspecific cross between the TuYV-resistant B. rapa and B. oleracea lines. Flow cytometry confirmed that plantlets regenerated from the interspecific cross had both A and C genomes and were mixoploid. To stabilise ploidy, a fertile plantlet was self-pollinated to produce seed that had the desired resynthesised, allotetraploid genome AACC. Phenotyping of the resynthesised plants confirmed their resistance to TuYV. Genotyping with resistance-linked markers identified during the mapping in the progenitors confirmed the presence of all TuYV resistance QTLs from B. rapa and B. oleracea. This is the first report of TuYV resistance mapped in the Brassica C genome and of an allotetraploid AACC line possessing dual resistance to TuYV originating from both of its progenitors. The introgression into OSR can now be accelerated, utilising marker-assisted selection, and this may reduce selection pressure for TuYV isolates that are able to overcome existing sources of resistance to TuYV.

Mapping pre-harvest sprouting resistance loci in AAC Innova \xd7 AAC Tenacious spring wheat population

BackgroundPre-harvest sprouting (PHS) is a major problem for wheat production due to its direct detrimental effects on wheat yield, end-use quality and seed viability. Annually, PHS is estimated to cause > 1.0 billion USD in losses worldwide. Therefore, identifying PHS resistance quantitative trait loci (QTLs) is crucial to aid molecular breeding efforts to minimize losses. Thus, a doubled haploid mapping population derived from a cross between white-grained PHS susceptible cv AAC Innova and red-grained resistant cv AAC Tenacious was screened for PHS resistance in four environments and utilized for QTL mapping.ResultsTwenty-one PHS resistance QTLs, including seven major loci (on chromosomes 1A, 2B, 3A, 3B, 3D, and 7D), each explaining ≥10% phenotypic variation for PHS resistance, were identified. In every environment, at least one major QTL was identified. PHS resistance at most of these loci was contributed by AAC Tenacious except at two loci on chromosomes 3D and 7D where it was contributed by AAC Innova. Thirteen of the total twenty-one identified loci were located to chromosome positions where at least one QTL have been previously identified in other wheat genotype(s). The remaining eight QTLs are new which have been identified for the first time in this study. Pedigree analysis traced several known donors of PHS resistance in AAC Tenacious genealogy. Comparative analyses of the genetic intervals of identified QTLs with that of already identified and cloned PHS resistance gene intervals using IWGSC RefSeq v2.0 identified MFT-A1b (in QTL interval QPhs.lrdc-3A.1) and AGO802A (in QTL interval QPhs.lrdc-3A.2) on chromosome 3A, MFT-3B-1 (in QTL interval QPhs.lrdc-3B.1) on chromosome 3B, and AGO802D, HUB1, TaVp1-D1 (in QTL interval QPhs.lrdc-3D.1) and TaMyb10-D1 (in QTL interval QPhs.lrdc-3D.2) on chromosome 3D. These candidate genes are involved in embryo- and seed coat-imposed dormancy as well as in epigenetic control of dormancy.ConclusionsOur results revealed the complex PHS resistance genetics of AAC Tenacious and AAC Innova. AAC Tenacious possesses a great reservoir of important PHS resistance QTLs/genes supposed to be derived from different resources. The tracing of pedigrees of AAC Tenacious and other sources complements the validation of QTL analysis results. Finally, comparing our results with previous PHS studies in wheat, we have confirmed the position of several major PHS resistance QTLs and candidate genes.

Genomic regions and candidate genes linked with Phytophthora capsici root rot resistance in chile pepper (Capsicum annuum L.)

BackgroundPhytophthora root rot, caused by Phytophthora capsici, is a major disease affecting Capsicum production worldwide. A recombinant inbred line (RIL) population derived from the hybridization between ‘Criollo de Morellos-334’ (CM-334), a resistant landrace from Mexico, and ‘Early Jalapeno’, a susceptible cultivar was genotyped using genotyping-by-sequencing (GBS)-derived single nucleotide polymorphism (SNP) markers. A GBS-SNP based genetic linkage map for the RIL population was constructed. Quantitative trait loci (QTL) mapping dissected the genetic architecture of P. capsici resistance and candidate genes linked to resistance for this important disease were identified.ResultsDevelopment of a genetic linkage map using 1,973 GBS-derived polymorphic SNP markers identified 12 linkage groups corresponding to the 12 chromosomes of chile pepper, with a total length of 1,277.7 cM and a marker density of 1.5 SNP/cM. The maximum gaps between consecutive SNP markers ranged between 1.9 (LG7) and 13.5 cM (LG5). Collinearity between genetic and physical positions of markers reached a maximum of 0.92 for LG8. QTL mapping identified genomic regions associated with P. capsici resistance in chromosomes P5, P8, and P9 that explained between 19.7 and 30.4% of phenotypic variation for resistance. Additive interactions between QTL in chromosomes P5 and P8 were observed. The role of chromosome P5 as major genomic region containing P. capsici resistance QTL was established. Through candidate gene analysis, biological functions associated with response to pathogen infections, regulation of cyclin-dependent protein serine/threonine kinase activity, and epigenetic mechanisms such as DNA methylation were identified.ConclusionsResults support the genetic complexity of the P. capsici–Capsicum pathosystem and the possible role of epigenetics in conferring resistance to Phytophthora root rot. Significant genomic regions and candidate genes associated with disease response and gene regulatory activity were identified which allows for a deeper understanding of the genomic landscape of Phytophthora root rot resistance in chile pepper.

Soybean Cyst Nematode Resistance Quantitative Trait Locus cqSCN-006 Alters the Expression of a γ-SNAP Protein.

Soybean cyst nematode (SCN) is the most economically damaging pathogen of soybean and host resistance is a core management strategy. The SCN resistance quantitative trait locus cqSCN-006, introgressed from the wild relative Glycine soja, provides intermediate resistance against nematode populations, including those with increased virulence on the heavily used rhg1-b resistance locus. cqSCN-006 was previously fine-mapped to a genome interval on chromosome 15. The present study determined that Glyma.15G191200 at cqSCN-006, encoding a γ-SNAP, contributes to SCN resistance. CRISPR/Cas9-mediated disruption of the cqSCN-006 allele reduced SCN resistance in transgenic roots. There are no encoded amino acid polymorphisms between resistant and susceptible alleles. However, other cqSCN-006-specific DNA polymorphisms in the Glyma.15G191200 promoter and gene body were identified, and we observed differing induction of γ-SNAP protein abundance at SCN infection sites between resistant and susceptible roots. We identified alternative RNA splice forms transcribed from the Glyma.15G191200 γ-SNAP gene and observed differential expression of the splice forms 2 days after SCN infection. Heterologous overexpression of γ-SNAPs in plant leaves caused moderate necrosis, suggesting that careful regulation of this protein is required for cellular homeostasis. Apparently, certain G. soja evolved quantitative SCN resistance through altered regulation of γ-SNAP. Previous work has demonstrated SCN resistance impacts of the soybean α-SNAP proteins encoded by Glyma.18G022500 (Rhg1) and Glyma.11G234500. The present study shows that a different type of SNAP protein can also impact SCN resistance. Little is known about γ-SNAPs in any system, but the present work suggests a role for γ-SNAPs during susceptible responses to cyst nematodes.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

SNP-based identification of QTL for resistance to black point caused by Bipolaris sorokiniana in bread wheat

Black point disease caused by Bipolaris sorokiniana is a problem in wheat production worldwide. We aimed to identify major quantitative trait loci (QTL) for resistance to black point and develop molecular markers for marker-assisted selection (MAS). A recombinant inbred line (RIL) population derived from a cross between Wanyuanbai 1 (susceptible) and SN4143 (resistant) was evaluated for black point response at three locations during two years under artificial inoculation with B. sorokiniana, providing data for six environments. Thirty resistant and 30 susceptible RILs were selected to form resistant and susceptible bulks, respectively, that were genotyped by the wheat 660K SNP array; 685 single-nucleotide polymorphisms (SNPs) were identified, among which 385 (56.2%) and 115 (16.8%) were located on chromosomes 4A and 2B, respectively. Bulked segregant RNA-Seq analysis identified candidate regions on chromosomes 4A (4.60–40.28 Mb) and 5A (1.22–48.47 Mb). Genetic linkage maps were constructed for chromosomes 2B, 4A, and 5A using 59 polymorphic dCAPS and SSR markers. Finally, two QTL, designated QBB.hau-4A and QBB.hau-5A, were detected on chromosomes 4A and 5A, respectively. The resistance allele of QBB.hau-4A was derived from SN4143, and that of QBB.hau-5A came from Wanyuanbai 1. QBB.hau-4A with a large and consistent effect (15.1%) is likely to be a new locus for black point resistance. The markers linked to QBB.hau-4A and QBB.hau-5A have potential application in MAS-based breeding.

Wheat genetic loci conferring resistance to stripe rust in the face of genetically diverse races of the fungus Puccinia striiformis f. sp. tritici

Key messageAnalysis of a wheat multi-founder population identified 14 yellow rust resistance QTL. For three of the four most significant QTL, haplotype analysis indicated resistance alleles were rare in European wheat.Stripe rust, or yellow rust (YR), is a major fungal disease of wheat (Triticum aestivum) caused by Puccinia striiformis Westend f. sp. tritici (Pst). Since 2011, the historically clonal European Pst races have been superseded by the rapid incursion of genetically diverse lineages, reducing the resistance of varieties previously showing durable resistance. Identification of sources of genetic resistance to such races is a high priority for wheat breeding. Here we use a wheat eight-founder multi-parent population genotyped with a 90,000 feature single nucleotide polymorphism array to genetically map YR resistance to such new Pst races. Genetic analysis of five field trials at three UK sites identified 14 quantitative trait loci (QTL) conferring resistance. Of these, four highly significant loci were consistently identified across all test environments, located on chromosomes 1A (QYr.niab-1A.1), 2A (QYr.niab-2A.1), 2B (QYr.niab-2B.1) and 2D (QYr.niab-2D.1), together explaining ~ 50% of the phenotypic variation. Analysis of these four QTL in two-way and three-way combinations showed combinations conferred greater resistance than single QTL, and genetic markers were developed that distinguished resistant and susceptible alleles. Haplotype analysis in a collection of wheat varieties found that the haplotypes associated with YR resistance at three of these four major loci were rare (≤ 7%) in European wheat, highlighting their potential utility for future targeted improvement of disease resistance. Notably, the physical interval for QTL QYr.niab-2B.1 contained five nucleotide-binding leucine-rich repeat candidate genes with integrated BED domains, of which two corresponded to the cloned resistance genes Yr7 and Yr5/YrSp.Graphical abstract