Combining Single Nucleotide Polymorphism Genotyping Array with Bulked Segregant Analysis to Map a Gene Controlling Adult Plant Resistance to Stripe Rust in Wheat Line 03031-1-5 H62

KASP: a high-throughput genotyping system and its applications in major crop plants for biotic and abiotic stress tolerance

Advances in plant molecular breeding have resulted in the development of new varieties with superior traits, thus improving the crop germplasm. Breeders can screen a large number of accessions without rigorous and time-consuming phenotyping by marker-assisted selection (MAS). Molecular markers are one of the most imperative tools in plant breeding programmes for MAS to develop new cultivars possessing multiple superior traits. Single nucleotide polymorphisms (SNPs) are ideal for MAS due to their low cost, low genotyping error rates, and reproducibility. Kompetitive Allele Specific PCR (KASP) is a globally recognized technology for SNP genotyping. KASP is an allele-specific oligo extension-based PCR assay that uses fluorescence resonance energy transfer (FRET) to detect genetic variations such as SNPs and insertions/deletions (InDels) at a specific locus. Additionally, KASP allows greater flexibility in assay design, which leads to a higher success rate and the capability to genotype a large population. Its versatility and ease of use make it a valuable tool in various fields, including genetics, agriculture, and medical research. KASP has been extensively used in various plant-breeding applications, such as the identification of germplasm resources, quality control (QC) analysis, allele mining, linkage mapping, quantitative trait locus (QTL) mapping, genetic map construction, trait-specific marker development, and MAS. This review provides an overview of the KASP assay and emphasizes its validation in crop improvement related to various biotic and abiotic stress tolerance and quality traits.

Identification and validation of major-effect quantitative trait locus QMS-5B associated with male sterility in photo-thermo-sensitive genic male sterile wheat

KEY MESSAGE

QMS-5B, a major QTL for photo-thermo-sensitive genic male sterility in wheat, was fine mapped in a 2.15 Mb region harboring a serine/threonine protein kinase gene TraesCS5B03G0887500, which was the most likely candidate gene. Genic male sterility is an essential trait in the utilization of heterosis and hybrid seed production for wheat. Currently, genic male sterile genes have been reported in wheat mutants, but the sterile genes controlling photo-thermo-sensitive genic male sterility in wheat have not been studied systematically. Here, 235 doubled haploid lines derived from a cross between photo-thermo-sensitive genic male sterile line BS462 and its restorer line CP279 were used to map male sterile gene by GenoBaits® Wheat 100 K Panel, bulked segregant exome sequencing (BSE-Seq) and wheat 660 K array. As a result, the major stable QTL on chromosome 5B, QMS-5B, was identified in all four environments, accounting for 7.3-36.4% of the phenotypic variances. Ulteriorly, QMS-5B was delimited to an approximate 2.15 Mb physical interval between KASP-5B5 and KASP-5B6 using kompetitive allele-specific PCR (KASP) markers. Within the interval, twenty-nine high-confidence genes were predicted according to Chinese Spring RefSeq v2.1. TraesCS5B03G0887500, encoding a serine/threonine protein kinase, was identified as the most likely candidate gene for QMS-5B based on weighted gene co-expression network analysis. Expression analysis confirmed that TraesCS5B03G0887500 was significantly differentially expressed in anthers of BS462 and CP279 at different stages under fertile and sterile environments. In addition, flanking KASP marker KASP-5B6 can effectively genotype male sterile lines and restorer lines, and can be used for molecular marker-assisted selection. This study provides insights into for exploring the mechanism of photo-thermo-sensitive genic male sterility in wheat.

Identification and Molecular Mapping of the Gene YrFL in Wheat Cultivar Flanders with Durable Resistance to Stripe Rust

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most severe diseases of wheat (Triticum aestivum L.) worldwide. Identification and characterization of resistance genes is advantageous to cultivating wheat varieties with durable resistance, which is the most economic and effective strategy to control stripe rust. Flanders, a common wheat cultivar released in France in 1986, confers effective resistance to stripe rust both at the seedling and adult plant stages. To elucidate the genetic basis of resistance in Flanders, F1, F2, and F2:3 generations derived from the cross Mingxian169 × Flanders were evaluated with the most prevalent Chinese Pst race CYR33 at the seedling stage. Inheritance analysis showed that the stripe rust resistance of Flanders was controlled by a single dominant gene, temporarily designated as YrFL. Bulked segregant analysis (BSA) combined with a wheat 660K single-nucleotide polymorphism (SNP) array indicated that polymorphic SNP markers were mainly located in the 0 to 150 Mb on wheat chromosome 5A. One hundred and eleven kompetitive allele-specific PCR (KASP) and 39 simple sequence repeat (SSR) markers on chromosome 5A were used to locate the YrFL. Linkage analysis mapped YrFL with 19 KASP and three SSR markers on wheat chromosome 5AS, and the genetic distances of the closest flanking markers AX108925494 and Xbarc56 to YrFL were 0.6 and 2.0 cM, respectively. Chromosome location, resistance characterization, and molecular marker positions indicated that YrFL is likely a novel stripe rust resistance gene on wheat chromosome 5AS and could be pyramided with other resistance genes to improve resistance in wheat breeding programs.

A Locus Controlling Leaf Rolling Degree in Wheat under Drought Stress Identified by Bulked Segregant Analysis

Drought stress frequently occurs, which seriously restricts the production of wheat (Triticum aestivum L.). Leaf rolling is a typical physiological phenomenon of plants during drought stress. To understand the genetic mechanism of wheat leaf rolling, we constructed an F₂ segregating population by crossing the slight-rolling wheat cultivar “Aikang 58” (AK58) with the serious-rolling wheat cultivar ″Zhongmai 36″ (ZM36). A combination of bulked segregant analysis (BSA) with Wheat 660K SNP Array was used to identify molecular markers linked to leaf rolling degree. A major locus for leaf rolling degree under drought stress was detected on chromosome 7A. We named this locus LEAF ROLLING DEGREE 1 (LERD1), which was ultimately mapped to a region between 717.82 and 720.18 Mb. Twenty-one genes were predicted in this region, among which the basic helix-loop-helix (bHLH) transcription factor TraesCS7A01G543300 was considered to be the most likely candidate gene for LERD1. The TraesCS7A01G543300 is highly homologous to the Arabidopsis ICE1 family proteins ICE/SCREAM, SCREAM2 and bHLH093, which control stomatal initiation and development. Two nucleotide variation sites were detected in the promoter region of TraesCS7A01G543300 between the two wheat cultivars. Gene expression assays indicated that TraesCS7A01G543300 was higher expressed in AK58 seedlings than that of ZM36. This research discovered a candidate gene related to wheat leaf rolling under drought stress, which may be helpful for understanding the leaf rolling mechanism and molecular breeding in wheat.

Quick mapping and characterization of a co-located kernel length and thousand-kernel weight-related QTL in wheat

A co-located KL and TKW-related QTL with no negative effect on PH and AD was rapidly identified using BSA and wheat 660 K SNP array. Its effect was validated in a panel of 218 wheat accessions. Kernel length (KL) and thousand-kernel weight (TKW) of wheat (Triticum aestivum L.) contribute significantly to kernel yield. In the present study, a recombinant inbred line (RIL) population derived from the cross between the wheat line S849-8 with larger kernels and more spikelets per spike and the line SY95-71 was developed. Further, of both the bulked segregant analysis (BSA) and the wheat 660 K single nucleotide polymorphism (SNP) array were used to rapidly identify genomic regions for kernel-related traits from this RIL population. Kompetitive Allele Specific PCR markers were further developed in the SNP-enriched region on the 2D chromosome to construct a genetic map. Both QKL.sicau-SSY-2D for KL and QTKW.sicau-SSY-2D for TKW were identified at multiple environments on chromosome arm 2DL. These two QTLs explained 9.68-23.02% and 6.73-18.32% of the phenotypic variation, respectively. The effects of this co-located QTL were successfully verified in a natural population consisting of 218 Sichuan wheat accessions. Interestingly, the major QTL was significantly and positively correlated with spike length, but did not negatively affect spikelet number per spike (SNS), plant height, or anthesis date. These results indicated that it is possible to synchronously improve kernel weight and SNS by using this QTL. Additionally, several genes associated with kernel development and filling rate were predicted and sequenced in the QTL-containing physical intervals of reference genomes of 'Chinese spring' and Aegilops tauschii. Collectively, these results provide a QTL with great breeding potential and its linked markers which should be helpful for fine mapping and molecular breeding.

Identification of Genomic Regions Associated with Vine Growth and Plant Height of Soybean

Vining growth (VG) and high plant height (PH) are the physiological traits of wild soybean that preclude their utilization for domesticated soybean breeding and improvement. To identify VG- and PH-related quantitative trait loci (QTLs) in different genetic resources, two populations of recombinant inbred lines (RILs) were developed by crossing a cultivated soybean, Zhonghuang39 (ZH39), with two wild soybean accessions, NY27-38 and NY36-87. Each line from the two crosses was evaluated for VG and PH. Three QTLs for VG and three for PH, detected in the ZH39 × NY27-38 population of the RILs, co-located on chromosomes 2, 17 and 19. The VG- and PH-related QTL in the ZH39 × NY36-87 population co-located on chromosome 19. A common QTL shared by the two populations was located on chromosome 19, suggesting that this major QTL was consistently selected for in different genetic backgrounds. The results suggest that different loci are involved in the domestication or adaptations of soybean of various genetic backgrounds. The molecular markers presented here would benefit the fine mapping and cloning of candidate genes underlying the VG and PH co-localized regions and thus facilitate the utilization of wild resources in breeding by avoiding undesirable traits.

QTL mapping for adult plant resistance to wheat stripe rust in M96-5 × Guixie 3 wheat population

Development of cultivars with multiple resistances has proven to be an effective way to prevent diseases in wheat breeding. The Guixie 3 variety (GX3) has shown excellent performance in resistance to stripe rust in field for many years. The purpose of this study was to detect quantitative trait loci (QTL) associated with resistance to stripe rust in the adult plant stage and determine closely linked molecular markers. A population of recombinant inbred lines (n = 228) was derived from a cross between the susceptible landrace Mian 96-5 (M96-5) and GX3 variety and evaluated in multiple field studies, and QTL analysis enabled to elucidate genetic architecture of wheat resistance to stripe rust. A total of 19 QTL for stripe rust resistance were mapped on 12 chromosomes using phenotypic data from multiple field tests over the course of 6 years. These chromosomes included 1B (2), 1D (2), 2A (2), 2B (2), 2D (1), 4B (2), 4D (1), 5A (3), 5B (1), 6A (1), 6B (1), and 7B (1). Two stable QTL on chromosomes 2AS (Qyr.gaas.2A) and 6AL (Qyr.gaas.6A) were detected in six and five different environments, respectively; in both QTL, positive allele was contributed by GX3 variety. Qyr.gaas.2A was found to be crucial for increasing adult plant resistance, which may explain the large phenotypic variation of 45.52%. Our results provide theoretical and molecular insight for wheat breeding and suggest the cloning of genes associated with the GX3 variety may be beneficial in future studies.

Phenotyping and validation of molecular markers associated with rust resistance genes in wheat cultivars in Egypt

BACKGROUND

Thirteen Egyptian wheat cultivars were evaluated and characterized for adult plant resistance to yellow, leaf, and stem rusts. SSR markers linked to yellow, leaf and stem rust resistance genes were validated and subsequently used to identify wheat cultivars containing more than one rust resistance gene.

RESULTS

Results of the molecular marker detection indicated that several genes, either alone or in different combinations, were present among the wheat cultivars, including Yr, Yr78 (stripe rust), Lr, Lr70 (leaf rust), Sr. Sr33, SrTA10187, Sr13, and Sr35 (stem rust), and Lr34/Yr18 and Lr49/Yr29 (leaf/stripe rust). The cultivar Sakha-95 was resistant to leaf and stem rusts, and partially resistant to stripe rust; however, this cultivar contained additional rust resistance genes (Lr, Sr and Lr/Yr). The area under the disease progress curve (AUDPC) type for the various wheat cultivars differed depending on the type of rust infection (yellow, leaf, or stem rust, indicated by Yr, Lr, and Sr). The cultivars Gem-12, Sids-14, Giza-171, and Giza-168 had AUDPC types of partial resistance and resistance. All six cultivars, however, contained additional rust resistance genes.

CONCLUSIONS

Marker-assisted selection can be applied to improve wheat cultivars with efficient gene combinations that would directly support the development of durable resistance in Egypt. Once the expression of the resistance genes targeted in this study have been confirmed by phenotypic screening, the preferable cultivars can be used as donors by Egyptian wheat breeders. The results of this study will help breeders determine the extent of resistance under field conditions when breeding for rust resistance in bread wheat.

Application of Genomics Tools in Wheat Breeding to Attain Durable Rust Resistance

Wheat is an important source of dietary protein and calories for the majority of the world's population. It is one of the largest grown cereal in the world occupying over 215 M ha. Wheat production globally is challenged by biotic stresses such as pests and diseases. Of the 50 diseases of wheat that are of economic importance, the three rust diseases are the most ubiquitous causing significant yield losses in the majority of wheat production environments. Under severe epidemics they can lead to food insecurity threats amid the continuous evolution of new races of the pathogens, shifts in population dynamics and their virulence patterns, thereby rendering several effective resistance genes deployed in wheat breeding programs vulnerable. This emphasizes the need to identify, characterize, and deploy effective rust-resistant genes from diverse sources into pre-breeding lines and future wheat varieties. The use of genetic resistance has been marked as eco-friendly and to curb the further evolution of rust pathogens. Deployment of multiple rust resistance genes including major and minor genes in wheat lines could enhance the durability of resistance thereby reducing pathogen evolution. Advances in next-generation sequencing (NGS) platforms and associated bioinformatics tools have revolutionized wheat genomics. The sequence alignment of the wheat genome is the most important landmark which will enable genomics to identify marker-trait associations, candidate genes and enhanced breeding values in genomic selection (GS) studies. High throughput genotyping platforms have demonstrated their role in the estimation of genetic diversity, construction of the high-density genetic maps, dissecting polygenic traits, and better understanding their interactions through GWAS (genome-wide association studies) and QTL mapping, and isolation of R genes. Application of breeder's friendly KASP assays in the wheat breeding program has expedited the identification and pyramiding of rust resistance alleles/genes in elite lines. The present review covers the evolutionary trends of the rust pathogen and contemporary wheat varieties, and how these research strategies galvanized to control the wheat killer genus Puccinia. It will also highlight the outcome and research impact of cost-effective NGS technologies and cloning of rust resistance genes amid the public availability of common and tetraploid wheat reference genomes.

High-Resolution Mapping of the Novel Early Leaf Senescence Gene Els2 in Common Wheat

Early leaf senescence negatively impacts the grain yield in wheat (Triticum aestivum L.). Induced mutants provide an important resource for mapping and cloning of genes for early leaf senescence. In our previous study, Els2, a single incomplete dominance gene, that caused early leaf senescence phenotype in the wheat mutant LF2099, had been mapped on the long arm of chromosome 2B. The objective of this study was to develop molecular markers tightly linked to the Els2 gene and construct a high-resolution map surrounding the Els2 gene. Three tightly linked single-nucleotide polymorphism (SNP) markers were obtained from the Illumina Wheat 90K iSelect SNP genotyping array and converted to Kompetitive allele-specific polymerase chain reaction (KASP) markers. To saturate the Els2 region, the Axiom® Wheat 660K SNP array was used to screen bulked extreme phenotype DNA pools, and 9 KASP markers were developed. For fine mapping of the Els2 gene, these KASP markers and previously identified polymorphic markers were analyzed in a large F₂ population of the LF2099 × Chinese Spring cross. The Els2 gene was located in a 0.24-cM genetic region flanked by the KASP markers AX-111643885 and AX-111128667, which corresponded to a physical interval of 1.61 Mb in the Chinese Spring chromosome 2BL containing 27 predicted genes with high confidence. The study laid a foundation for a map-based clone of the Els2 gene controlling the mutation phenotype and revealing the molecular regulatory mechanism of wheat leaf senescence.

Molecular cytogenetic characterization of wheat-Elymus repens chromosomal translocation lines with resistance to Fusarium head blight and stripe rust

BACKGROUND

Fusarium head blight (FHB) caused by the fungus Fusarium graminearum Schwabe and stripe rust caused by Puccinia striiformis f. sp. tritici are devastating diseases that affect wheat production worldwide. The use of disease-resistant genes and cultivars is the most effective means of reducing fungicide applications to combat these diseases. Elymus repens (2n = 6x = 42, StStStStHH) is a potentially useful germplasm of FHB and stripe rust resistance for wheat improvement.

RESULTS

Here, we report the development and characterization of two wheat-E. repens lines derived from the progeny of common wheat-E. repens hybrids. Cytological studies indicated that the mean chromosome configuration of K15-1192-2 and K15-1194-2 at meiosis were 2n = 42 = 0.86 I + 17.46 II (ring) + 3.11 II (rod) and 2n = 42 = 2.45 I + 14.17 II (ring) + 5.50 II (rod) + 0.07 III, respectively. Genomic and fluorescence in situ hybridization karyotyping and simple sequence repeats markers revealed that K15-1192-2 was a wheat-E. repens 3D/?St double terminal chromosomal translocation line. Line K15-1194-2 was identified as harboring a pair of 7DS/?StL Robertsonian translocations and one 3D/?St double terminal translocational chromosome. Further analyses using specific expressed sequence tag-SSR markers confirmed that the wheat-E. repens translocations involved the 3St chromatin in both lines. Furthermore, compared with the wheat parent Chuannong16, K15-1192-2 and K15-1194-2 expressed high levels of resistance to FHB and stripe rust pathogens prevalent in China.

CONCLUSIONS

Thus, this study has determined that the chromosome 3St of E. repens harbors gene(s) highly resistant to FHB and stripe rust, and chromatin of 3St introgressed into wheat chromosomes completely presented the resistance, indicating the feasibility of using these translocation lines as novel material for breeding resistant wheat cultivars and alien gene mining.

Utilization of the Genomewide Wheat 55K SNP Array for Genetic Analysis of Stripe Rust Resistance in Common Wheat Line P9936

Breeding for resistance to stripe rust (caused by Puccinia striiformis f. tritici) is essential for reducing losses in yield and quality in wheat. To identify genes for use in breeding, a biparental population of 186 recombinant inbred lines (RILs) from a cross of the Chinese landrace Mingxian 169 and CIMMYT-derived line P9936 was evaluated in field nurseries either artificially or naturally inoculated in two crop seasons. Each of the RILs and parents was genotyped with the wheat 55K single-nucleotide polymorphism (SNP) 'Breeders' array and a genetic linkage map with 8,225 polymorphic SNP markers spanning 3,593.37 centimorgans was constructed. Two major quantitative trait loci (QTL) and two minor QTL were identified. The major QTL QYr.nwafu-3BS.2 and QYr.nwafu-7BL on chromosomes arms 3BS and 7BL were detected in all field locations and explained an average 20.4 and 38.9% of phenotypic variation stripe rust severity, respectively. QYr.nwafu-3BS.2 likely corresponds to the locus Yr30/Sr2 and QYr.nwafu-7BL may be a resistance allele identified previously in CIMMYT germplasm. The other minor QTL had limited individual effects but increased resistance when in combinations with other QTL. Markers linked to QYr.nwafu-7BL were converted to kompetitive allele-specific polymerase chain reaction markers and validated in a panel of wheat accessions. Wheat accessions carrying the same haplotype as P9936 at the identified SNP loci had lower average stripe rust severity than the average severity of all other haplotypes.

Identification and validation of a novel major QTL for all-stage stripe rust resistance on 1BL in the winter wheat line 20828

A major, likely novel stripe rust resistance QTL for all-stage resistance on chromosome arm 1BL identified in a 1.76-cM interval using a saturated linkage map was validated in four populations with different genetic backgrounds. Stripe rust is a globally important disease of wheat. Identification and utilization of new resistance genes are essential for breeding resistant cultivars. Wheat line 20828 has exhibited high levels of stripe rust resistance for over a decade. However, the genetics of stripe rust resistance in this line has not been studied. A set of 199 recombinant inbred lines (RILs) were developed from a cross between 20828 and a susceptible cultivar Chuannong 16. The RIL population was genotyped with the Wheat55K SNP (single nucleotide polymorphism) array and SSR (simple sequence repeat) markers and evaluated in four environments with current predominant Puccinia striiformis f. sp. tritici t races including CYR32, CYR33 and CYR34. Four stable QTL were located on chromosomes 1B (2 QTL), 4A and 6A. Among them, the major QTL, QYr.sicau-1B.1 (LOD = 23-28, PVE = 16-39%), was localized to a 1.76-cM interval flanked by SSR markers Xwmc216 and Xwmc156 on chromosome 1BL. Eight resistance genes were previously identified in the physical interval of QYr.sicau-1B.1. Compared with previous studies, QYr.sicau-1B.1 is a new gene for resistant to stripe rust. It was further verified by analysis of the closely linked SSR markers Xwmc216 and Xwmc156 in four other populations with different genetic backgrounds. QYr.sicau-1B.1 reduced the stripe rust disease index by up to 82.8%. Three minor stable QTL (located on chromosomes 1B, 4A and 6A, respectively) also added to the resistance level of QYr.sicau-1B.1. Our results provide valuable information for further fine mapping and cloning as well as molecular-assisted breeding with QYr.sicau-1B.1.

A major QTL co-localized on chromosome 6BL and its epistatic interaction for enhanced wheat stripe rust resistance

Co-localization of a major QTL for wheat stripe rust resistance to a 3.9-cM interval on chromosome 6BL across both populations and another QTL on chromosome 2B with epistatic interaction. Cultivars with diverse resistance are the optimal strategy to minimize yield losses caused by wheat stripe rust (Puccinia striiformis f. sp. tritici). Two wheat populations involving resistant wheat lines P10078 and Snb"S" from CIMMYT were evaluated for stripe rust response in multiple environments. Pool analysis by Wheat660K SNP array showed that the overlapping interval on chromosome 6B likely harbored a major QTL between two populations. Then, linkage maps were constructed using KASP markers, and a co-localized locus with large effect on chromosome 6BL was detected using QTL analysis in both populations. The coincident QTL, named QYr.nwafu-6BL.2, explained 59.7% of the phenotypic maximum variation in the Mingxian 169 × P10078 and 52.5% in the Zhengmai 9023 × Snb"S" populations, respectively. This co-localization interval spanning 3.9 cM corresponds to ~ 30.5-Mb genomic region of the newest common wheat reference genome (IWGSC RefSeq v.1.0). In addition, another QTL was also detected on chromosome 2B in Zhengmai 9023 × Snb"S" population and it can accelerate expression of QYr.nwafu-6BL.2 to enhance resistance with epistatic interaction. Allowing for Pst response, marker genotypes, pedigree analysis and relative genetic distance, QYr.nwafu-6BL.2 is likely to be a distinct adult plant resistance QTL. Haplotype analysis of QYr.nwafu-6BL.2 revealed specific SNPs or alleles in the target region from a diversity panel of 176 unrelated wheat accessions. This QTL region provides opportunity for further map-based cloning, and haplotypes analysis enables pyramiding favorable alleles into commercial cultivars by marker-assisted selection.

Genetic architecture of wheat stripe rust resistance revealed by combining QTL mapping using SNP-based genetic maps and bulked segregant analysis

A major stripe rust resistance QTL was mapped to a 0.4 centimorgan (cM) genetic region on the long arm of chromosome 7B, using combined genome-wide linkage mapping and bulk segregant analysis. The German winter wheat cv. Centrum has displayed high levels of adult plant stripe rust resistance (APR) in field environments for many years. Here, we used the combined genome-wide linkage mapping and pool-extreme genotyping to characterize the APR resistance. One hundred and fifty-one F_2:7 recombinant inbred lines derived from a cross between susceptible landrace Mingxian 169 and Centrum were evaluated for stripe rust resistance in multiple environments and genotyped by the wheat 35K single nucleotide polymorphism (SNP) array. Three stable quantitative trait loci (QTL) were identified using QTL analysis across five field environments. To saturate the major QTL, the wheat 660K SNP array was also used to genotype bulked extremes. A major QTL named QYrcen.nwafu-7BL from Centrum was mapped in a 0.4 cM genetic interval flanking by AX-94556751 and AX-110366788 across a 2 Mb physical genomic region, explaining 19.39-42.81% of the total phenotypic variation. It is likely a previously uncharacterized QTL based on pedigree analysis, reaction response, genotyping data and map comparison. The SNP markers closely linked with QYrcen.nwafu-7BL were converted to KASP markers and validated in a subset of 120 wheat lines. A 211 F₂ breeding population from a cross of an elite cultivar Xinong 979 with Centrum were developed for marker-based selection. Three selected lines with desirable agronomic traits and the positive alleles of both KASP markers showed acceptable resistance which should be used as resistance donors in wheat breeding programs. The other QTL QYrcen.nwafu-1AL and QYrcen.nwafu-4AL with additive effects could enhance the level of resistance conferred by QYrcen.nwafu-7BL.

QTL Mapping and Validation of Adult Plant Resistance to Stripe Rust in Chinese Wheat Landrace Humai 15

Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is a devastating foliar disease that affects common wheat and barley throughout the world. The reasonable deployment of adult plant resistance (APR) wheat varieties is one of the best methods for controlling this disease. Wheat landraces are valuable resources for identifying the genes/QTLs responsible for disease resistance. Humai 15 is a Chinese spring wheat landrace and it has exhibited adequate levels of APR to the prevalent Pst races in field environments for many years. In this study, a population of 177 recombinant inbred lines (RILs) was derived from Humai 15 × Mingxian 169. After screening based on a 90K chip array using 45 RILs and Kompetitive Allelic Specific PCR marker genotyping for the population of RILs, a major effect QTL in Humai 15 was located on the centromere of chromosome 2B, where it accounted for up to 47.2% of the phenotypic variation. Two other minor QTL genes from Humai 15 were located on chromosome arms 3BS and 4BL. The Yr18 gene was identified on chromosome arm 7DS in Mingxian 169.

SNP-based pool genotyping and haplotype analysis accelerate fine-mapping of the wheat genomic region containing stripe rust resistance gene Yr26

NGS-assisted super pooling emerging as powerful tool to accelerate gene mapping and haplotype association analysis within target region uncovering specific linkage SNPs or alleles for marker-assisted gene pyramiding. Conventional gene mapping methods to identify genes associated with important agronomic traits require significant amounts of financial support and time. Here, a single nucleotide polymorphism (SNP)-based mapping approach, RNA-Seq and SNP array assisted super pooling analysis, was used for rapid mining of a candidate genomic region for stripe rust resistance gene Yr26 that has been widely used in wheat breeding programs in China. Large DNA and RNA super-pools were genotyped by Wheat SNP Array and sequenced by Illumina HiSeq, respectively. Hundreds of thousands of SNPs were identified and then filtered by multiple filtering criteria. Among selected SNPs, over 900 were found within an overlapping interval of less than 30 Mb as the Yr26 candidate genomic region in the centromeric region of chromosome arm 1BL. The 235 chromosome-specific SNPs were converted into KASP assays to validate the Yr26 interval in different genetic populations. Using a high-resolution mapping population (> 30,000 gametes), we confined Yr26 to a 0.003-cM interval. The Yr26 target region was anchored to the common wheat IWGSC RefSeq v1.0 and wild emmer WEWSeq v.1.0 sequences, from which 488 and 454 kb fragments were obtained. Several candidate genes were identified in the target genomic region, but there was no typical resistance gene in either genome region. Haplotype analysis identified specific SNPs linked to Yr26 and developed robust and breeder-friendly KASP markers. This integration strategy can be applied to accelerate generating many markers closely linked to target genes/QTL for a trait of interest in wheat and other polyploid species.

Rapid identification of an adult plant stripe rust resistance gene in hexaploid wheat by high-throughput SNP array genotyping of pooled extremes

High-throughput SNP array analysis of pooled extreme phenotypes in a segregating population by KASP marker genotyping permitted rapid, cost-effective location of a stripe rust resistance QTL in wheat. German wheat cultivar "Friedrichswerther" has exhibited high levels of adult plant resistance (APR) to stripe rust in field environments for many years. F_2:3 lines and F₆ recombinant inbred line (RILs) populations derived from a cross between Friedrichswerther and susceptible landrace Mingxian 169 were evaluated in the field in 2013, 2016 and 2017. Illumina 90K iSelect SNP arrays were used to genotype bulked extreme pools and parents; 286 of 1135 polymorphic SNPs were identified on chromosome 6B. Kompetitive Allele-Specific PCR (KASP) markers were used to verify the chromosome region associated with the resistance locus. A linkage map was constructed with 18 KASP-SNP markers, and a major effect QTL was identified within a 1.4 cM interval flanked by KASP markers IWB71602 and IWB55937 in the region 6BL3-0-0.36. The QTL, named QYr.nwafu-6BL, was stable across environments, and explained average 54.4 and 47.8% of the total phenotypic variation in F_2:3 lines and F₆ RILs, respectively. On the basis of marker genotypes, pedigree analysis and relative genetic distance QYr.nwafu-6BL is likely to be a new APR QTL. Combined high-throughput SNP array genotyping of pooled extremes and validation by KASP assays lowers sequencing costs compared to genome-wide association studies with SNP arrays, and more importantly, permits rapid isolation of major effect QTL in hexaploid wheat as well as improving accuracy of mapping in the QTL region. QYr.nwafu-6BL with flanking KASP markers developed and verified in a subset of 236 diverse lines can be used in marker-assisted selection to improve stripe rust resistance in breeding programs.