Microsatellite-based deletion bin system for the establishment of genetic-physical map relationships in wheat (Triticum aestivum L.)

Molecular Mapping of Yr85 and Comparison with Other Genes for Resistance to Stripe Rust on Wheat Chromosome 1B

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most serious plant diseases worldwide. Resistant cultivars are the most effective way to control the disease. YrTr1 is an important stripe rust resistance gene that has been used in wheat breeding programs and is represented in the host differential set to identify P. striiformis f. sp. tritici races in the United States. To map YrTr1, AvSYrTr1NIL was backcrossed to its recurrent parent Avocet S (AvS). Seedlings of BC7F2, BC7F3, and BC8F1 populations were tested with YrTr1-avirulent races under controlled conditions, and BC7F2 plants were genotyped using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. YrTr1 was mapped to the short arm of chromosome 1B using four SSR and seven SNP markers. The genetic distances of YrTr1 from the nearest flanking markers IWA2583 and IWA7480 were 1.8 and 1.3 centimorgans (cM), respectively. DNA amplification of a set of 21 Chinese Spring (CS) nulli-tetrasomic lines and seven CS 1B deletion lines with three SSR markers confirmed the chromosome arm location and further placed the gene in chromosomal bin region 1BS18 (0.5). The gene was determined to be about 7.4 cM proximal to Yr10. Based on multirace response array and chromosomal location, YrTr1 was determined to be different from other permanently named stripe rust resistance genes in chromosome arm 1BS and was named Yr85.

Cytological and genetic effects of rye chromosomes 1RS and 3R on the wheat-breeding founder parent Chuanmai 42 from southwestern China

Rye (Secale cereale L.) is an important genetic resource for improving the disease resistance of wheat. An increasing number of rye chromosome segments have been transferred into modern wheat cultivars via chromatin insertions. In this study, 185 recombinant inbred lines (RILs) derived from a cross between a wheat accession containing rye chromosomes 1RS and 3R and a wheat-breeding founder parent Chuanmai 42 from southwestern China were used to decipher the cytological and genetic effects of 1RS and 3R via fluorescence/genomic in situ hybridization and quantitative trait locus (QTL) analyses. Chromosome centromere breakage and fusion were detected in the RIL population. Additionally, the recombination of chromosomes 1BS and 3D from Chuanmai 42 was completely suppressed by 1RS and 3R in the RIL population. In contrast to chromosome 3D of Chuanmai 42, rye chromosome 3R was significantly associated with white seed coats and decreased yield-related traits, as revealed by QTL and single marker analyses, whereas it had no effect on stripe rust resistance. Rye chromosome 1RS did not affect yield-related traits and it increased the susceptibility of plants to stripe rust. Most of the detected QTLs that positively affected yield-related traits were from Chuanmai 42. The findings of this study suggest that the negative effects of rye-wheat substitutions or translocations, including the suppression of the pyramiding of favorable QTLs on paired wheat chromosomes from different parents and the transfer of disadvantageous alleles to filial generations, should be considered when selecting alien germplasm to enhance wheat-breeding founder parents or to breed new varieties.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01386-0.

The use of PI 277012-derived Fusarium head blight resistance QTL in winter wheat breeding

Fusarium head blight (FHB) caused by Fusarium graminearum results in substantial grain yield and quality losses in common wheat (Triticum aestivum L.). Genetic resistance is partial but crucial for effective, integrated management of the disease. Host resistance is conditioned by numerous small effect quantitative trait loci (QTL) that are strongly affected by the environment and genetic background. Qfhb.rwg-5A.1 and Qfhb.rwg-5A.2 (PI 277012 is the source for both genes) are two recently discovered FHB resistance QTL that also occur in spring wheat GP80 (PI 277012 derivative). To transfer the PI 277012 resistance from GP80 to hard winter wheat (HWW), GP80 was first crossed with Novus-4. The F₁ hybrid was crossed with SY Monument, following which marker-selected progeny were crossed with, and backcrossed to, ND Noreen. To potential carriers of FHB resistance QTL among the 22 F₁ of the ND Noreen cross, simple sequence repeat (SSR) markers, Illumina 90 K single nucleotide polymorphism (SNP) haplotypes and greenhouse FHB Type II resistance tests were done. Likely homozygotes for Qfhb.rwg.5A.1 and Qfhb.rwg.5A.2, were selected and backcrossed to ND Noreen. In the B₁F₁, 131 plants were evaluated for SNP haplotypes, SSR markers and FHB resistance. Nine B₁F_2:3 lines were derived, and their resistance confirmed in a third greenhouse FHB trial. The results suggested that eight lines had higher resistance and were comparable to GP80 with the Qfhb.rwg-5A.2 markers occurring in all eight and the Qfhb.rwg-5A.1 markers occurring in four lines. The eight selections constitute a valuable HWW resistance breeding resource.

Characterization and identification of the powdery mildew resistance gene in wheat breeding line ShiCG15-009

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a serious fungal disease that critically threatens the yield and quality of wheat. Utilization of host resistance is the most effective and economical method to control this disease. In our study, a wheat breeding line ShiCG15-009, released from Hebei Province, was highly resistant to powdery mildew at all stages. To dissect its genetic basis, ShiCG15-009 was crossed with the susceptible cultivar Yannong 21 to produce F₁, F₂ and F_2:3 progenies. After genetic analysis, a single dominant gene, tentatively designated PmCG15-009, was proved to confer resistance to Bgt isolate E09. Further molecular markers analysis showed that PmCG15-009 was located on chromosome 2BL and flanked by markers XCINAU130 and XCINAU143 with the genetic distances 0.2 and 0.4 cM, respectively, corresponding to a physic interval of 705.14-723.48 Mb referred to the Chinese Spring reference genome sequence v2.1. PmCG15-009 was most likely a new gene differed from the documented Pm genes on chromosome 2BL since its different origin, genetic diversity, and physical position. To analyze and identify the candidate genes, six genes associated with disease resistance in the candidate interval were confirmed to be associated with PmCG15-009 via qRT-PCR analysis using the parents ShiCG15-009 and Yannong 21 and time-course analysis post-inoculation with Bgt isolate E09. To accelerate the transfer of PmCG15-009 using marker-assisted selection (MAS), 18 closely or co-segregated markers were evaluated and confirmed to be suitable for tracing PmCG15-009, when it was transferred into different wheat cultivars.

Haplotype variants of the stripe rust resistance gene Yr28 in Aegilops tauschii

Stripe rust resistance gene YrAet672 from Aegilops tauschii accession CPI110672 encodes a nucleotide-binding and leucine-rich repeat domain containing protein similar to YrAS2388 and both these members were haplotypes of Yr28. New sources of host resistance are required to counter the continued emergence of new pathotypes of the wheat stripe rust pathogen Puccinia striiformis Westend. f. sp. tritici Erikss. (Pst). Here, we show that CPI110672, an Aegilops tauschii accession from Turkmenistan, carries a single Pst resistance gene, YrAet672, that is effective against multiple Pst pathotypes, including the four predominant Pst lineages present in Australia. The YRAet672 locus was fine mapped to the short arm of chromosome 4D, and a nucleotide-binding and leucine-rich repeat gene was identified at the locus. A transgene encoding the YrAet672 genomic sequence, but lacking a copy of a duplicated sequence present in the 3' UTR, was transformed into wheat cultivar Fielder and Avocet S. This transgene conferred a weak resistance response, suggesting that the duplicated 3' UTR region was essential for function. Subsequent analyses demonstrated that YrAet672 is the same as two other Pst resistance genes described in Ae. tauschii, namely YrAS2388 and Yr28. They were identified as haplotypes encoding identical protein sequences but are polymorphic in non-translated regions of the gene. Suppression of resistance conferred by YrAet672 and Yr28 in synthetic hexaploid wheat lines (AABBDD) involving Langdon (AABB) as the tetraploid parent was associated with a reduction in transcript accumulation.

Fine mapping and marker development for the wheat leaf rust resistance gene Lr32

Wheat leaf rust is caused by the fungal pathogen Puccinia triticina and is one of the wheat diseases of concern globally. Among the known leaf rust resistance genes (Lr) genes, Lr32 is a broadly effective gene derived from the diploid species Aegilops tauschii coss. accession RL5497-1 and has been genetically mapped to chromosome arm 3DS. However, Lr32 resistance has not been utilized in current cultivars in part due to the lack of modern, predictive DNA markers. The goals of this study were to fine map the Lr32 region and develop SNP-based kompetitive allele-specific polymerase chain reaction markers. The genomic analysis was conducted by using doubled haploid and F2-derived mapping populations. For marker development, a 90K wheat chip array, 35K and 820K Axiom R SNPs, A. tauschii pseudomolecules v4.0 and International Wheat Genome Sequencing Consortium ReqSeq v2.1 reference genomes were used. Total 28 kompetitive allele-specific polymerase chain reaction and 2 simple sequence repeat markers were developed. The Lr32 region was fine mapped between kompetitive allele-specific polymerase chain reaction markers Kwh142 and Kwh355 that flanked 34-35 Mb of the diploid and hexaploid reference genomes. Leaf rust resistance mapped as a Mendelian trait that cosegregated with 20 markers, recombination restriction limited the further resolution of the Lr32 region. A total of 10-11 candidate genes associated with disease resistance were identified between the flanking regions on both reference genomes, with the majority belonging to the nucleotide-binding domain and leucine-rich repeat gene family. The validation analysis selected 2 kompetitive allele-specific polymerase chain reaction markers, Kwh147 and Kwh722, for marker-assisted selection. The presence of Lr32 along with other Lr genes such as Lr67 and Lr34 would increase the resistance in future wheat breeding lines and have a high impact on controlling wheat leaf rust.

Integrated transcriptional and metabolomics signature pattern of pigmented wheat to insight the seed pigmentation and other associated features

Anthocyanin biosynthesis in plants is complex, especially in a polyploid monocot wheat plant. Using whole-genome sequencing, transcriptomics, and LC-MS/MS, we investigated anthocyanin pigmentation patterns in (black, blue, and purple) colored wheat seeds. According to differential gene expression profiling, 2AS-MYC, 7DL-MYB, and WD40 regulatory genes control purple pericarp coloration, 4DL-MYC, 2AS-MYC, 7DL-MYB, WD40 control blue aleurone coloration, and 4DL-MYC, 7DL-MYB, WD40 controls black aleurone color. We hypothesized that at least one MYC and MYB isoform is sufficient to regulate the anthocyanin synthesis in pericarp or aleurone. Transcriptomics and metabolomics revealed that the purple pericarp trait is associated with acylated anthocyanins compared to blue aleurone. Based upon the reduced expressions of the genes belonging to the 4D, SSR molecular marker mapping, variant calling using genome sequencing, and IGV browser gene structure visualization, it was inferred that the advanced black and blue wheat lines were substitution lines (4E{4D}), with very small recombinations. Pericarp anthocyanin pigmentation is controlled by a mutation in chromosome 2AS of purple wheat, and environmental variations influence pigmented pericarp trait. The expression patterns of anthocyanin structural and other genes varied in different colored wheat, corroborating differences in agronomical metrics. Ovate seed shape trait in black and blue wheat dragged with 4E chromosome.

Identification of QTL for Stem Traits in Wheat (Triticum aestivum L.)

Lodging in wheat (Triticum aestivum L.) is a complicated phenomenon that is influenced by physiological, genetics, and external factors. It causes a great yield loss and reduces grain quality and mechanical harvesting efficiency. Lodging resistance is contributed by various traits, including increased stem strength. The aim of this study was to map quantitative trait loci (QTL) controlling stem strength-related features (the number of big vascular bundles, stem diameter, stem wall thickness) using a doubled haploid (DH) population derived from a cross between Baiqimai and Neixiang 5. Field experiments were conducted during 2020-2022, and glasshouse experiments were conducted during 2021-2022. Significant genetic variations were observed for all measured traits, and they were all highly heritable. Fifteen QTL for stem strength-related traits were identified on chromosomes 2D, 3A, 3B, 3D, 4B, 5A, 6B, 7A, and 7D, respectively, and 7 QTL for grain yield-related traits were identified on chromosomes 2B, 2D, 3D, 4B, 7A, and 7B, respectively. The superior allele of the major QTL for the number of big vascular bundle (VB) was independent of plant height (PH), making it possible to improve stem strength without a trade-off of PH, thus improving lodging resistance. VB also showed positive correlations with some of the yield components. The result will be useful for molecular marker-assisted selection (MAS) for high stem strength and high yield potential.

Identification and Validation of a Major Quantitative Trait Locus for Adult Plant Resistance Against Leaf Rust From the Chinese Wheat Landrace Bai Qimai

Leaf rust caused by Puccinia triticina Eriks. (Pt) is a common disease of wheat worldwide. The Chinese wheat landrace Bai Qimai (BQM) has shown high resistance to leaf rust for a prolonged period of time; the infected leaves of BQM displayed high infection types (ITs), but they showed low disease severities at the adult plant stage. To find quantitative trait loci (QTL) for resistance to leaf rust, 186 recombinant inbred lines from the cross Nugaines × BQM were phenotyped for leaf rust response in multiple field environments under natural Pt infections and genotyped using the 90K wheat single nucleotide polymorphism (SNP) chip and simple sequence repeat (SSR) markers. A total of 2,397 polymorphic markers were used for QTL mapping, and a novel major QTL (QLr.cau-6DL) was detected on chromosome 6DL from BQM. The effectiveness of QLr.cau-6DL was validated using the three additional wheat populations (RL6058 × BQM, Aikang58 × BQM, and Jimai22 × BQM). QLr.cau-6DL could significantly reduce leaf rust severities across all tested environments and different genetic backgrounds, and its resistance was more effective than that of Lr34. Moreover, QLr.cau-6DL acted synergistically with Lr34 to confer strong resistance to leaf rust. We believe that QLr.cau-6DL should have high potential value in the breeding of wheat cultivars with leaf rust resistance.

Origin and genetic analysis of stem rust resistance in wheat line Tr129

Wheat line Tr129 is resistant to stem rust, caused by Puccinia graminis f. sp. tritici (Pgt). The resistance in Tr129 was reportedly derived from Aegilops triuncialis, but the origin and genetics of resistance have not been confirmed. Here, genomic in situ hybridization (GISH) showed that no Ae. triuncialis chromatin was present in Tr129. Genetic and phenotypic analysis was conducted on F₂ and DH populations from the cross RL6071/Tr129. Seedlings were tested with six Pgt races and were genotyped using an Illumina iSelect 90 K SNP array and kompetitive allele specific PCR (KASP) markers. Mapping and phenotyping showed that Tr129 carried four stem rust resistance (Sr) genes on chromosome arms 2BL (Sr9b), 4AL (Sr7b), 6AS (Sr8a), and 6DS (SrTr129). SrTr129 co-segregated with markers for SrCad, however Tr129 has a unique haplotype suggesting the resistance could be new. Analysis of a RL6071/Peace population revealed that like SrTr129, SrCad is ineffective against three North American races. This new understanding of SrCad will guide its use in breeding. Tr129 and the DNA markers reported here are useful resources for improving stem rust resistance in cultivars.

Generation of Deletion Lines in Allohexaploid Bread Wheat

Positional cloning in bread wheat (Triticum aestivum L.) remains a daunting task because of its large genome, high density of repeats, low recombination rate especially in pericentromeric regions and its allopolyploidy. One way to face this challenge is to decrease the size of the interval bearing the gene of interest both genetically and physically, in order to reduce significantly the number of potential candidate genes. In this chapter, we describe a technical approach to produce chromosome-specific deletion lines to locate precisely genes of interest onto wheat chromosomes, a step forward to their cloning.

Characterization and Use in Wheat Breeding of Leaf Rust Resistance Genes from Durable Varieties

Simple Summary

Wheat leaf rust is one of the most significant diseases worldwide, incited by a parasitic fungus which infects leaves, affecting grain yield. This pathogen is spread by the wind over large areas through microscopic spores. This huge number of spores favors the selection of virulent forms; therefore, there is a continuous need for new resistance genes to control this disease without fungicides. These resistant genes are naturally found in resistant wheat varieties and can be introduced by standard crosses. In this work, seven resistant genes were introduced into several commercial susceptible varieties. The selection of resistance genes was assisted by DNA markers that are close to these genes on the chromosome. Additionally, the selection of desirable traits from the commercial variety was also assisted by DNA markers to accelerate the process. In field testing, the varieties developed here were resistant to leaf rust, and suitable for commercial use.

Abstract

Leaf rust is one of the most significant diseases of wheat worldwide. In Argentina, it is one of the main reasons for variety replacement that becomes susceptible after large-scale use. Some varieties showed durable resistance to this disease, including Buck Manantial and Sinvalocho MA. RILs (Recombinant Inbred Lines) were developed for each of these varieties and used in genetics studies to identify components of resistance, both in greenhouse inoculations using leaf rust races, and in field evaluations under natural population infections. In Buck Manantial, the APR gene LrBMP1 was associated with resistance in field tests. In crosses involving Sinvalocho MA, four genes were previously identified and associated with resistance in field testing: APR (Adult Plant Resistance) gene LrSV1, the APR genetic system LrSV2 + LrcSV2 and the ASR (All Stage Resistance) gene LrG6. Using backcrosses, LrBMP1 was introgressed in four commercial susceptible varieties and LrSV1, LrSV2 + LrcSV2 and LrG6 were simultaneously introgressed in three susceptible commercial varieties. The use of molecular markers for recurrent parent background selection allowed us to select resistant lines with more than 80% similarity to commercial varieties. Additionally, progress towards positional cloning of the genetic system LrSV2 + LrcSV2 for leaf rust APR is reported.

Construction of Consensus Genetic Map With Applications in Gene Mapping of Wheat (Triticum aestivum L.) Using 90K SNP Array

Wheat is one of the most important cereal crops worldwide. A consensus map combines genetic information from multiple populations, providing an effective alternative to improve the genome coverage and marker density. In this study, we constructed a consensus map from three populations of recombinant inbred lines (RILs) of wheat using a 90K single nucleotide polymorphism (SNP) array. Phenotypic data on plant height (PH), spike length (SL), and thousand-kernel weight (TKW) was collected in six, four, and four environments in the three populations, and then used for quantitative trait locus (QTL) mapping. The mapping results obtained using the constructed consensus map were compared with previous results obtained using individual maps and previous studies on other populations. A simulation experiment was also conducted to assess the performance of QTL mapping with the consensus map. The constructed consensus map from the three populations spanned 4558.55 cM in length, with 25,667 SNPs, having high collinearity with physical map and individual maps. Based on the consensus map, 21, 27, and 19 stable QTLs were identified for PH, SL, and TKW, much more than those detected with individual maps. Four PH QTLs and six SL QTLs were likely to be novel. A putative gene called TraesCS4D02G076400 encoding gibberellin-regulated protein was identified to be the candidate gene for one major PH QTL located on 4DS, which may enrich genetic resources in wheat semi-dwarfing breeding. The simulation results indicated that the length of the confidence interval and standard errors of the QTLs detected using the consensus map were much smaller than those detected using individual maps. The consensus map constructed in this study provides the underlying genetic information for systematic mapping, comparison, and clustering of QTL, and gene discovery in wheat genetic study. The QTLs detected in this study had stable effects across environments and can be used to improve the wide adaptation of wheat cultivars through marker-assisted breeding.

The effects of crop attributes, selection, and recombination on Canadian bread wheat molecular variation

Cultivated germplasm provides an opportunity to investigate how crop agronomic traits, selection for major genes, and differences in crossing-over rates drive patterns of allelic variation. To identify how these factors correlated with allelic variation within a collection of cultivated bread wheat (Triticum aestivum L.), we generated genotypes for 388 accessions grown in Canada over the past 170 yr using filtered single nucleotide polymorphism (SNP) calls from an Illumina Wheat iSelect 90K SNP-array. Entries' breeding program, era of release, grain texture, kernel color, and growth habit contributed to allelic differentiation. Allelic diversity and linkage disequilibrium (LD) of markers flanking some major loci known to affect traits such as gluten strength, growth habit, and grain color were consistent with selective sweeps. Nonetheless, some flanking markers of major loci had low LD and high allelic diversity. Positive selection may have acted upon homoeologous genes that had significant enrichment for the gene ontology terms 'response-to-auxin' and 'response-to-wounding.' Long regions of LD, spanning approximately one-third the length of entire chromosomes, were associated with many pericentromeric regions. These regions were also characterized by low diversity. Enhancing recombination across these regions could generate novel allele combinations to accelerate Canadian wheat improvement.

Function and evolution of allelic variations of Sr13 conferring resistance to stem rust in tetraploid wheat (Triticum turgidum L.)

The resistance gene Sr13 is one of the most important genes in durum wheat for controlling stem rust caused by Puccinia graminis f. sp. tritici (Pgt). The Sr13 functional gene CNL13 has haplotypes R1, R2 and R3. The R1/R3 and R2 haplotypes were originally designated as alleles Sr13a and Sr13b, respectively. To detect additional Sr13 alleles, we developed Kompetitive allele specific PCR (KASP™) marker KASPSr13 and four semi-thermal asymmetric reverse PCR markers, rwgsnp37-rwgsnp40, based on the CNL13 sequence. These markers were shown to detect R1, R2 and R3 haplotypes in a panel of diverse tetraploid wheat accessions. We also observed the presence of Sr13 in durum line CAT-A1, although it lacked any of the known haplotypes. Sequence analysis revealed that CNL13 of CAT-A1 differed from the susceptible haplotype S1 by a single nucleotide (C2200T) in the leucine-rich repeat region and differed from the other three R haplotypes by one or two additional nucleotides, confirming that CAT-A1 carries a new (R4) haplotype. Stem rust tests on the monogenic, transgenic and mutant lines showed that R1 differed from R3 in its susceptibility to races TCMJC and THTSC, whereas R4 differed from all other haplotypes for susceptibility to TTKSK, TPPKC and TCCJC. Based on these differences, we designate the R1, R3 and R4 haplotypes as alleles Sr13a, Sr13c and Sr13d, respectively. This study indicates that Sr13d may be the primitive functional allele originating from the S1 haplotype via a point mutation, with the other three R alleles probably being derived from Sr13d through one or two additional point mutations.

Genetic mapping of a novel powdery mildew resistance gene in wild emmer wheat from "Evolution Canyon" in Mt. Carmel Israel

A single dominant powdery mildew resistance gene MlNFS10 was identified in wild emmer wheat and mapped within a 0.3cM genetic interval spanning a 2.1Mb physical interval on chromosome arm 4AL. Wheat powdery mildew caused by Blumeria graminis forma specialis tritici (Bgt) is a globally devastating disease. The use of powdery mildew resistance genes from wild relatives of wheat is an effective method of disease management. Our previous research has shown that disruptive ecological selection has driven the discrete adaptations of the wild emmer wheat population on the south facing slope (SFS) and north facing slope (NFS) at the microsite of "Evolution Canyon" at Mount Carmel, Israel and demonstrated that 16 accessions in the NFS population display high resistance to 11 powdery mildew isolates (collected from different wheat fields in China). Here, we constructed bi-parental population by crossing the accession NFS-10 (resistant to 22 Bgt races collected from China in seedling resistance screen) and the susceptible line SFS2-12. Genetic analysis indicated that NFS-10 carries a single dominant gene, temporarily designated MlNFS10. Ultimately, 13 markers were successfully located within the long arm of chromosome 4A, thereby delineating MlNFS10 to a 0.3 cM interval covering 2.1 Mb (729275816-731365462) in the Chinese Spring reference sequence. We identified disease resistance-associated genes based on the RNA-seq analysis of both parents. The tightly linked InDel marker XWsdau73447 and SSR marker XWsdau72928 were developed and used for marker-assisted selection when MlNFS10 was introgressed into a hexaploid wheat background. Therefore, MlNFS10 can be used for improvement of germplasm in breeding programs for powdery mildew resistant cultivars.

A null allele of granule bound starch synthase (Wx-B1) may be one of the major genes controlling chapatti softness

Chapatti (unleavened flatbread) is a staple food in northern India and neighboring countries but the genetics behind its processing quality are poorly understood. To understand the genes determining chapatti quality, differentially expressed genes were selected from microarray data of contrasting chapatti cultivars. From the gene and trait association studies, a null allele of granule bound starch synthase (GBSS; Wx-B1) was found to be associated with low amylose content and good chapatti quality. For validation, near-isogenic lines (NILs) of this allele were created by marker assisted backcross (MAB) breeding. Background screening indicated 88.2 to 96.7% background recovery in 16 selected BC3F5 NILs. Processing quality and sensory evaluation of selected NILs indicated improvement in chapatti making quality. Traits that showed improvement were mouthfeel, tearing strength and softness indicating that the Wx-B1 may be one of the major genes controlling chapatti softness.

Molecular Cytogenetic and Agronomic Characterization of the Similarities and Differences Between Wheat-Leymus mollis Trin. and Wheat-Psathyrostachys huashanica Keng 3Ns (3D) Substitution Lines

Psathyrostachys huashanica Keng (2n = 2x = 14, NsNs) and Leymus mollis Trin. (2n = 4x = 28, NsNsXmXm) are valuable resources for wheat breeding improvement as they share the Ns genome, which contains diverse resistance genes. To explore the behaviors and traits of Ns chromosomes from the two species in wheat background, a series of wheat-P. huashanica and wheat-L. mollis substitution lines were developed. In the present study, line DH109 (F₇ progeny of wheat-P. huashanica heptaploid line H8911 × durum wheat Trs-372) and line DM131 (F₈ progeny of wheat-L. mollis octoploid line M842 × durum wheat Trs-372) were selected. Cytological observation combined with genomic in situ hybridization experiments showed that DH109 and DM131 each had 20 pairs of wheat chromosomes plus a pair of alien chromosomes (Ns chromosome), and the pair of alien chromosomes showed stable inheritance. Multiple molecular markers and wheat 55K SNP array demonstrated that a pair of wheat 3D chromosome in DH109 and in DM131 was substituted by a pair of P. huashanica 3Ns chromosome and a pair of L. mollis 3Ns chromosome, respectively. Fluorescence in situ hybridization (FISH) analysis confirmed that wheat 3D chromosomes were absent from DH109 and DM131, and chromosomal FISH karyotypes of wheat 3D, P. huashanica 3Ns, and L. mollis 3Ns were different. Moreover, the two lines had many differences in agronomic traits. Comparing with their wheat parents, DH109 expressed superior resistance to powdery mildew and fusarium head blight, whereas DM131 had powdery mildew resistance, longer spike, and more tiller number. Therefore, Ns genome from P. huashanica and L. mollis might have some different effects. The two novel wheat-alien substitution lines provide new ideas and resources for disease resistance and high-yield breeding on further utilization of 3Ns chromosomes of P. huashanica or L. mollis.

Molecular mapping of a new recessive wheat leaf rust resistance gene originating from Triticum spelta

TSD276-2, a wheat genetic stock derived from the cross Agra Local/T. spelta 276 showed broad spectrum resistance against leaf rust pathogen. Genetic analysis was undertaken using F₁, F₂, F_2:3 and BC₁F₁ generations derived from the cross TSD276-2/Agra Local. The results revealed a single recessive gene for leaf rust resistance, tentatively named as LrTs_276-2, in TSD276-2. Molecular mapping of leaf rust resistance gene LrTs_276-2 in TSD276-2 was done using SNP-based PCR and SSR markers. For Bulked Segregant Analysis (BSA), two bulks viz. resistant bulk and susceptible bulk, and the parents TSD276-2 and Agra Local were genotyped for SNPs using AFFYMETRIX 35K Wheat Breeders' AXIOM array. T. spelta 276 was also genotyped and used as a check. BSA indicated that the gene for leaf rust resistance in TSD276-2 is located on chromosome arm 1DS. Putatively linked SNPs on chromosome arm 1DS were converted into PCR-based markers. Polymorphic SSR markers on chromosome arm 1DS were also identified. Final linkage map was constructed using one SNP-based PCR and three SSR markers. The rust reaction and chromosomal location suggest that LrTs_276-2 is a new leaf rust resistance gene which may be useful in broadening the genetic base of leaf rust resistance in wheat.

Dissection and physical mapping of wheat chromosome 7B by inducing meiotic recombination with its homoeologues in Aegilops speltoides and Thinopyrum elongatum

We constructed a homoeologous recombination-based bin map of wheat chromosome 7B, providing a unique physical framework for further study of chromosome 7B and its homoeologues in wheat and its relatives. Homoeologous recombination leads to the dissection and diversification of the wheat genome. Advances in genome sequencing and genotyping have dramatically improved the efficacy and throughput of homoeologous recombination-based genome studies and alien introgression in wheat and its relatives. In this study, we aimed to physically dissect and map wheat chromosome 7B by inducing meiotic recombination of chromosome 7B with its homoeologues 7E in Thinopyrum elongatum and 7S in Aegilops speltoides. The special genotypes, which were double monosomic for chromosomes 7B' + 7E' or 7B' + 7S' and homozygous for the ph1b mutant, were produced to enhance 7B - 7E and 7B - 7S recombination. Chromosome-specific DNA markers were developed and used to pre-screen the large recombination populations for 7B - 7E and 7B - 7S recombinants. The DNA marker-mediated preselections were verified by fluorescent genomic in situ hybridization (GISH). In total, 29 7B - 7E and 61 7B - 7S recombinants and multiple chromosome aberrations were recovered and delineated by GISH and the wheat 90 K SNP assay. Integrated GISH and SNP analysis of the recombinants physically mapped the recombination breakpoints and partitioned wheat chromosome 7B into 44 bins with 523 SNPs assigned within. A composite bin map was constructed for chromosome 7B, showing the bin size and physical distribution of SNPs. This provides a unique physical framework for further study of chromosome 7B and its homoeologues. In addition, the 7B - 7E and 7B - 7S recombinants extend the genetic variability of wheat chromosome 7B and represent useful germplasm for wheat breeding. Thereby, this genomics-enabled chromosome engineering approach facilitates wheat genome study and enriches the gene pool of wheat improvement.

Evaluation of leaf rust resistance in the Chinese wheat cultivar ‘Een1’

Wheat cultivar Een1, 34 near isogenic lines (NILs), and two cultivars were used as plant materials to evaluate the resistance of Een1 to leaf rust disease. Infection type identification and gene postulation were carried out by inoculation of 12 Chinese Puccinia triticina (Pt) pathotypes. Based on the unique phenotype of Een1, we speculated that Een1 might carry Lr gene(s) different from the tested ones. The chromosomal locations for resistance gene to leaf rust disease was employed using SSR primers mapping the populations derived from the cross between Een1 and susceptible Thatcher. A total of 285 plants in the F2 population were tested by inoculating Pt pathotype FHNQ during the seedling stage. Results from the segregation analysis fits a ratio of 3:1 (${\chi }_{3:1}^{2}=2.37$, P = 0.12), indicating the presence of a single dominant gene in Een1 conferring resistance to FHNQ. A total of 1,255 simple sequence repeat (SSR) primers were first used to identify the likely linked markers based on bulk segregation analysis (BSA), and then those likely linked markers were further genotyped in the F2 population for linkage analysis. Our linkage analysis found that the resistance gene (LrE1) was distal to seven SSR loci on the long arm of chromosome 7B, with distances from 2.6 cM (Xgwm344) to 27.1 cM (Xgwm131). The closest marker Xgwm344 was further verified with F3 lines.

Natural variations in the promoter of Awn Length Inhibitor 1 (ALI-1) are associated with awn elongation and grain length in common wheat

Wheat awn plays a vital role in photosynthesis, grain production, and drought tolerance. However, the systematic identification or cloning of genes controlling wheat awn development is seldom reported. Here, we conducted a genome-wide association study (GWAS) with 364 wheat accessions and identified 26 loci involved in awn length development, including previously characterized B1, B2, Hd, and several rice homologs. The dominant awn suppressor B1 was fine mapped to a 125-kb physical interval, and a C₂ H₂ zinc finger protein Awn Length Inhibitor 1 (ALI-1) was confirmed to be the underlying gene of the B1 locus through the functional complimentary test with native awnless allele. ALI-1 expresses predominantly in the developing spike of awnless individuals, transcriptionally suppressing downstream genes. ALI-1 reduces cytokinin content and simultaneously restrains cytokinin signal transduction, leading to a stagnation of cell proliferation and reduction of cell numbers during awn development. Polymorphisms of four single nucleotide polymorphisms (SNPs) located in ALI-1 promoter region are diagnostic for the B1/b1 genotypes, and these SNPs are associated with awn length (AL), grain length (GL) and thousand-grain weight (TGW). More importantly, ali-1 was observed to increase grain length in wheat, which is a valuable attribute of awn on grain weight, aside from photosynthesis. Therefore, ALI-1 pleiotropically regulates awn and grain development, providing an alternative for grain yield improvement and addressing future climate changes.

Stay-Green Trait: A Prospective Approach for Yield Potential, and Drought and Heat Stress Adaptation in Globally Important Cereals

The yield losses in cereal crops because of abiotic stress and the expected huge losses from climate change indicate our urgent need for useful traits to achieve food security. The stay-green (SG) is a secondary trait that enables crop plants to maintain their green leaves and photosynthesis capacity for a longer time after anthesis, especially under drought and heat stress conditions. Thus, SG plants have longer grain-filling period and subsequently higher yield than non-SG. SG trait was recognized as a superior characteristic for commercially bred cereal selection to overcome the current yield stagnation in alliance with yield adaptability and stability. Breeding for functional SG has contributed in improving crop yields, particularly when it is combined with other useful traits. Thus, elucidating the molecular and physiological mechanisms associated with SG trait is maybe the key to defeating the stagnation in productivity associated with adaptation to environmental stress. This review discusses the recent advances in SG as a crucial trait for genetic improvement of the five major cereal crops, sorghum, wheat, rice, maize, and barley with particular emphasis on the physiological consequences of SG trait. Finally, we provided perspectives on future directions for SG research that addresses present and future global challenges.

Rapid identification and characterization of genetic loci for defective kernel in bread wheat

BACKGROUND

Wheat is a momentous crop and feeds billions of people in the world. The improvement of wheat yield is very important to ensure world food security. Normal development of grain is the essential guarantee for wheat yield formation. The genetic study of grain phenotype and identification of key genes for grain filling are of great significance upon dissecting the molecular mechanism of wheat grain morphogenesis and yield potential.

RESULTS

Here we identified a pair of defective kernel (Dek) isogenic lines, BL31 and BL33, with plump and shrunken mature grains, respectively, and constructed a genetic population from the BL31/BL33 cross. Ten chromosomes had higher frequency of polymorphic single nucleotide polymorphism (SNP) markers between BL31 and BL33 using Wheat660K chip. Totally 783 simple sequence repeat (SSR) markers were chosen from the above chromosomes and 15 of these were integrated into two linkage groups using the genetic population. Genetic mapping identified three QTL, QDek.caas-3BS.1, QDek.caas-3BS.2 and QDek.caas-4AL, explaining 14.78-18.17%, 16.61-21.83% and 19.08-28.19% of phenotypic variances, respectively. Additionally, five polymorphic SNPs from Wheat660K were successfully converted into cleaved amplified polymorphic sequence (CAPS) markers and enriched the target regions of the above QTL. Biochemical analyses revealed that BL33 has significantly higher grain sucrose contents at filling stages and lower mature grain starch contents than BL31, indicating that the Dek QTL may be involved in carbohydrate metabolism. As such, the candidate genes for each QTL were predicated according to International Wheat Genome Sequence Consortium (IWGSC) RefSeq v1.0.

CONCLUSIONS

Three major QTL for Dek were identified and their causal genes were predicted, laying a foundation to conduct fine mapping and dissect the regulatory mechanism underlying Dek trait in wheat.

Genome-Wide Linkage Mapping Reveals Stripe Rust Resistance in Common Wheat (Triticum aestivum) Xinong1376

Stripe rust, also known as yellow rust, is a significant threat to wheat yield worldwide. Adult plant resistance (APR) is the preferred way to obtain durable protection. Chinese winter wheat cultivar Xinong1376 has maintained acceptable APR to stripe rust in field environments. To characterize APR in this cultivar, 190 F₁₀ recombinant inbred lines (RILs) developed from Xiaoyan81 × Xinong1376 were evaluated for infection type and disease severity in fields either artificially or naturally inoculated. The population along with parents were genotyped using the Illumina 90K single-nucleotide polymorphism arrays. Six quantitative trait loci (QTL) were detected using the inclusive composite interval mapping method. QYr.nwafu-4AL and QYr.nwafu-6BL.3 conferred stable resistance in all environments, and likely corresponded to a gene-rich region on the long arm of chromosomes 4A and 6B. QYr.nwafu-5AL, QYr.nwafu-5BL, QYr.nwafu-3BL.1, and QYr.nwafu-3BL.2 were detected only in some environments but enhanced the level of resistance conferred by QYr.nwafu-4AL and QYr.nwafu-6BL.3. Kompetitive allele-specific PCR (KASP) markers developed for QYr.nwafu-4AL and QYr.nwafu-6BL.3 were confirmed in a subset of RILs and 133 wheat genotypes. The QTL on 4AL and 6BL with their linked KASP markers would be useful for marker-assisted selection to improve stripe rust resistance in breeding programs.

Deletion mapping and verification of an enhanced-grain number per spike locus from the 6PL chromosome arm of Agropyron cristatum in common wheat

An enhanced-grain number per spike locus from Agropyron cristatum 6PL was mapped onto 6PL (0.27-0.51) via deletion mapping, and its effect was further verified by evaluating a newly created translocation line. Agropyron cristatum (2n = 4x = 28, PPPP) is an important wild relative of common wheat and carries many desirable yield-related traits. The wheat-A. cristatum 6P disomic addition line 4844-12 exhibited high grain number per spike (GNS), high spikelet number per spike (SNS), and high kernel number per spikelet (KNS). In this study, five A. cristatum 6P deletion lines, five wheat-A. cristatum 6P translocation lines, and genetic populations of these lines were used to map the enhanced-GNS locus from A. cristatum chromosome 6P, which were genotyped via genomic in situ hybridization, fluorescence in situ hybridization, or molecular markers. According to the evaluation of the agronomic traits in four growing seasons (2014-2015, 2015-2016, 2016-2017, and 2017-2018), we found that the deletion lines and the translocation lines carrying the long arm of A. cristatum chromosome 6P (6PL) exhibited high GNS, SNS, and KNS, and the enhanced-GNS locus was ultimately mapped onto 6PL (0.27-0.51). To verify the localization results, we created a new translocation line WAT650a (T5BL•5BS-6PL) that carried 6PL (0.35-0.42); this line exhibited higher GNS and SNS than the recipient parent Fukuhokomugi (Fukuho). Collectively, the enhanced-GNS locus of A. cristatum 6PL can be important for improving yield traits in common wheat; the translocation lines with the enhanced-GNS locus can serve as novel and valuable germplasm resources for wheat breeding.

Mapping a Resistance Gene to Puccinia graminis f. sp. tritici in the Bread Wheat Cultivar 'Matlabas'

Puccinia graminis f. sp. tritici race TTKSF+ was collected from the South African wheat cultivar 'Matlabas' in 2010. F₂ and F₃ populations derived from a Matlabas × Line 37-07 cross segregated for a single resistance gene to race TTKSF that is avirulent to Matlabas. In screening genomic DNA bulks of susceptible or resistant F₂ plants with simple sequence repeat (SSR) markers, three chromosome arm 2BS markers and one multilocus marker amplified alleles present only in the resistant bulks and Matlabas. Additional 2B-specific SSR markers, incorporating markers spanning regions containing Sr9h, SrWLR, Sr28, and Sr47, were screened in the parental lines and mapped in the F₂ population. Linkage and QTL mapping showed that the gene is located between Xbarc160 in the centromeric region and Xgwm47 on the long arm of chromosome 2B. When 2B-specific SNP markers were mapped, the area of interest was delimited to a 15.3 cM region on chromosome arm 2BL, with XIWA543-HRM and Xgwm47 as flanking loci. Matlabas, Webster, and related Sr9h lines all produced a similar, low infection type to race TTKSF, but were susceptible to race TTKSF+. Phenotypic data and allelic studies suggested that stem rust resistance in Matlabas was derived from an Sr9h source.

Genetic mapping of a major QTL promoting homoeologous chromosome pairing in a wheat landrace

Common wheat landrace Kaixian-luohanmai carries a gene(s) that promotes homoeologous chromosome pairing. A major QTL responsible for this effect was mapped to chromosome arm 3AL. Polyhaploid hybrids of a Chinese common wheat landrace Kaixian-luohanmai (KL) and related species show increased levels of chromosome pairing. Over 90% of that pairing is between homoeologous arms of wheat chromosomes, with a very strong preference for pairing between homoeologs from genomes A and D. Wheat-rye pairing was also observed at low frequency. Two mapping populations were created from the hybrids of KL with two wheat genotypes top crossed to rye. Mean chiasmata numbers per plant were used as phenotypic data. Wheat 660 K and 15 K SNP arrays, DArT markers and SSR markers were used for genotyping of the top-cross ABDR hybrids. One major QTL, named QPh.sicau-3A, for increased homoeologous pairing was detected on chromosome arm 3AL, and it was responsible for ca. 16% of the total variation. This QTL was located in the interval 696-725 Mb in the Chinese Spring reference genome. SNP markers closely linked with QPh.sicau-3A were converted to KASP markers and validated for marker-assisted selection.

Genome-wide mapping of adult plant stripe rust resistance in wheat cultivar Toni

Two adult plant stripe rust resistance QTL, QYrto.swust-3AS and QYrto.swust-3BS, were identified and mapped in common wheat cultivar Toni. The two QTL were located to corresponding positions in the wheat physical map position based on flanking SNP markers. Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important foliar diseases of wheat. Characterization and utilization of resistance genes are the most effective, economic and environmental-friendly way to control the disease. The wheat cultivar Toni resistant at the adult plant stage to predominant Chinese Pst races was crossed with the susceptible genotype Mingxian 169. A recombinant inbred line population comprising 171 lines was tested in the field at three locations in the 2016 and 2017 crop seasons. The Affymetrix Axiom^® 35 K single-nucleotide polymorphism (SNP) Wheat Breeder's Genotyping Array was used to map quantitative trait loci (QTL) for adult plant resistance to stripe rust. Inclusive composite interval mapping identified stable QTL QYrto.swust-3AS and QYrto.swust-3BS that explained 31.6-48.2% and 21.9-56.3% of the variation in stripe rust severity and infection type, respectively. The two QTL regions were anchored to the wheat IWGSC Ref Seq v1.0 sequence. QYrto.swust-3AS was localized to a 2.22-Mb interval flanked by SNP markers AX-95240191 and AX-94828890. Among 65 HC (high confidence) annotated genes in this region, 11 (16.9%) contained NB-ARC domains and 9 (13.8%) contained protein kinase domains and thus could contribute to disease resistance. QYrto.swust-3BS was localized to a 4.77-Mb interval flanked by SNP markers AX-94509749 and AX-94998050. One hundred and thirty three HC genes are annotated in this region. Among them, 14 (10.5%) protein kinase domain genes may contribute to disease resistance. The linked markers should be useful for marker-assisted selection in breeding for resistance.

QTL analysis of durable stripe rust resistance in the North American winter wheat cultivar Skiles

This study determined the effects of growth stage and temperature on expression of high-temperature adult-plant resistance to stripe rust, mapped six QTL for durable resistance in winter wheat Skiles using a doubled haploid population, and selected breeding lines with different combinations of the QTL using marker-assisted selection. The winter wheat cultivar Skiles has a high level of high-temperature adult-plant (HTAP) resistance to stripe rust caused by Puccinia striiformis f. sp. tritici (Pst). The Skiles HTAP resistance was highly effective at the adult-plant stage even under low temperatures, but high temperatures induced earlier expression and increased levels of resistance. To map resistance genes, Skiles was crossed with the susceptible cultivar Avocet S and a doubled haploid (DH) population was developed. The DH population was tested in fields at Pullman, WA, in 2016, 2017 and 2018, Mount Vernon, WA, in 2017 and 2018 under natural infection, and an environmentally controlled greenhouse at the adult-plant stage with the currently predominant race PSTv-37. The population was genotyped using the 90 K Illumina iSelect wheat SNP chip and selected SSR markers on specific chromosomes. In total, 2526 polymorphic markers were used for QTL mapping and six QTL were detected. Two of the six QTL had major effects across all environments, with one mapped on chromosome 3BS, explaining up to 28.2% of the phenotypic variation and the other on chromosome 4BL, explaining up to 41.8%. Minor QTL were mapped on chromosomes 1BL, 5AL, 6B and 7DL. Genotyping 140 wheat cultivars from the US Pacific Northwest revealed high polymorphism of markers for five of the QTL, and five highly resistant lines with the five QTL were selected from Skiles-derived breeding lines using the markers. This study demonstrated that multiple QTL with mostly additive effects contributed to the high-level HTAP resistance in Skiles.

Genome-wide Mapping for Stripe Rust Resistance Loci in Common Wheat Cultivar Qinnong 142

Stripe rust caused by Puccinia striiformis f. sp. tritici threatens worldwide wheat production. Growing resistant cultivars is the best way to control this disease. Chinese wheat cultivar Qinnong 142 (QN142) has a high level of adult-plant resistance to stripe rust. To identify quantitative trait loci (QTLs) related to stripe rust resistance, we developed a recombinant inbred line (RIL) population from a cross between QN142 and susceptible cultivar Avocet S. The parents and 165 F₆ RILs were evaluated in terms of their stripe rust infection type and disease severity in replicated field tests with six site-year environments. The parents and RILs were genotyped with single-nucleotide polymorphism (SNP) markers. Four stable QTLs were identified in QN142 and mapped to chromosome arms 1BL, 2AL, 2BL, and 6BS. The 1BL QTL was probably the known resistance gene Yr29, the 2BL QTL was in a resistance gene-rich region, and the 2AL and 6BS QTLs might be new. Kompetitive allele specific polymerase chain reaction markers developed from the SNP markers flanking these QTLs were highly polymorphic in a panel of 150 wheat cultivars and breeding lines. These markers could be used in marker-assisted selection for incorporating the stripe rust resistance QTL into new wheat cultivars.

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.

Identification of a major QTL on chromosome arm 2AL for reducing yellow rust severity from a Chinese wheat landrace with evidence for durable resistance

A QTL on 2AL for reducing yellow rust severity was identified from a Chinese wheat landrace, being more effective than Yr18, with evidence for durable resistance from field observations. Utilization of wheat resistance is an important strategy to control yellow rust. The Chinese wheat landrace Hong Qimai (HQM) and the advanced breeding line AQ24788-83 (AQ; a progeny of HQM) can significantly reduce disease severity at the adult-plant growth stage. HQM has maintained adult-plant resistance for a prolonged period of time. To study the inheritance of the resistance, 126 recombinant inbred lines (RILs) derived from the cross Thatcher (TC) × HQM and 138 RILs from Luke × AQ were assessed for disease severity in six field trials. A genetic map of TC × HQM was constructed by genotyping these RILs using the 90 K wheat single-nucleotide polymorphism chip. Luke × AQ map was previously constructed for another disease study and also utilized here. Based on these maps and disease data, a quantitative trait locus (QTL) was detected on the chromosome arm 2AL from both TC × HQM and Luke × AQ and designated as QYr.cau-2AL. The resistance allele at QYr.cau-2AL came from HQM and AQ. QYr.cau-2AL was significantly effective across all the test environments and different genetic backgrounds, with its effect magnitude being higher than that of Yr18. QYr.cau-2AL synergistically acted with Yr18 and a QTL for high-temperature adult-plant resistance on 2BS, resulting in an elevated resistance from the juvenile plant growth stage onward, although QYr.cau-2AL alone displayed no substantial resistance at juvenile stage. Evidence indicates that QYr.cau-2AL is novel and confers durable resistance, and thus, should have high potential value for practical breeding.

Development of Deletion Lines for Chromosome 3D of Bread Wheat

The identification of genes of agronomic interest in bread wheat (Triticum aestivum L.) is hampered by its allopolyploid nature (2n = 6x = 42; AABBDD) and its very large genome, which is largely covered by transposable elements. However, owing to this complex structure, aneuploid stocks can be developed in which fragments or entire chromosomes are missing, sometimes resulting in visible phenotypes that help in the cloning of affected genes. In this study, the 2C gametocidal chromosome from Aegilops cylindrica was used to develop a set of 113 deletion lines for chromosome 3D in the reference cultivar Chinese Spring. Eighty-four markers were used to show that the deletions evenly covered chromosome 3D and ranged from 6.5 to 357 Mb. Cytogenetic analyses confirmed that the physical size of the deletions correlated well with the known molecular size deduced from the reference sequence. This new genetic stock will be useful for positional cloning of genes on chromosome 3D, especially for Ph2 affecting homoeologous pairing in bread wheat.

Detection and validation of a novel major QTL for resistance to Fusarium head blight from Triticum aestivum in the terminal region of chromosome 7DL

A novel QTL for FHB resistance was mapped on wheat 7DL, being effective in multiple genetic backgrounds and environments, and comparable to Fhb1 in effect magnitude. Fusarium head blight (FHB) is one of the major fungal diseases affecting wheat production in many countries. The wheat line AQ24788-83 (AQ) possesses FHB resistance. The American wheat cultivar Luke is FHB susceptible. A Luke × AQ population consisting of 1652 advanced recombinant inbred lines (RILs) was developed, from which 272 RILs were randomly sampled and used to construct a linkage map. Another 154 RILs were selected for homogeneity in plant height (PH) and flowering date (FD). This selection strategy was adopted to reduce possible confounding effects on FHB assessment due to variation in PH and FD. The 272 and 154 RILs were genotyped applying simple sequence repeat (SSR), diversity arrays technology (DArT) and single-nucleotide polymorphism (SNP) markers. The two sets of RILs were evaluated for FHB resistance applying point inoculation in greenhouses; the 154 RILs were also evaluated applying spray inoculation in multiple field environments. The linkage map consisted of 2088 SSR, DArT, and SNP markers. A FHB resistance quantitative trait locus (QTL), designated as QFhb.cau-7DL, was detected on chromosome arm 7DL; this QTL was closely linked to the SSR marker gwm428 ( http://www.wheat.pw.usda.gov/ggpages/SSR/ ). QFhb.cau-7DL was significantly effective (α = 0.01) in every test trial, and its effectiveness was validated using three additional wheat crosses. Sumai 3 (donor wheat of the FHB resistance gene Fhb1) was used in one of these crosses. QFhb.cau-7DL was comparable to Fhb1 in effect magnitude, providing a great potential for improving FHB resistance.

Mapping a gene on wheat chromosome 4BL involved in a complementary interaction with adult plant leaf rust resistance gene LrSV2

A complementary gene to LrSV2 for specific adult plant leaf rust resistance in wheat was mapped on chromosome 4BL, tightly linked to Lr12 / 31. LrSV2 is a race-specific adult plant leaf rust (Puccinia triticina) resistance gene on subdistal chromosome 3BS detected in the cross of the traditional Argentinean wheat (Triticum aestivum) variety Sinvalocho MA and the experimental line Gama6. The analysis of the cross of R46 [recombinant inbred line (RIL) derived from Sinvalocho MA carrying LrSV2 gene and the complementary gene Lrc-SV2 identified in the current paper] and the commercial variety Relmo Siriri (not carrying neither of these two genes) allowed the detection of the unlinked complementary gene Lrc-SV2 because the presence of one dominant allele of both is necessary to express the LrSV2-specific adult plant resistance. Lrc-SV2 was mapped within a 1-cM interval on chromosome 4BL using 100 RILs from the cross Sinvalocho MA × Purple Straw. This genetic system resembles the Lr27+31 seedling resistance reported in the Australian varieties Gatcher and Timgalen where interacting genes map at similar chromosomal positions. However, in high-resolution maps, Lr27 and LrSV2 were already mapped to adjacent intervals on 3BS and Lrc-SV2 map position on 4BL is distal to the reported Lr12/31-flanking microsatellites.

Characterisation and mapping of adult plant stripe rust resistance in wheat accession Aus27284

A new adult plant stripe rust resistance gene, Yr80, was identified in a common wheat landrace Aus27284. Linked markers were developed and validated for their utility in marker-assisted selection. Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is among the most important constraints to global wheat production. The identification and characterisation of new sources of host plant resistance enrich the gene pool and underpin deployment of resistance gene pyramids in new cultivars. Aus27284 exhibited resistance at the adult plant stage against predominant Pst pathotypes and was crossed with a susceptible genotype Avocet S. A recombinant inbred line (RIL) population comprising 121 lines was developed and tested in the field at three locations in 2016 and two in 2017 crop seasons. Monogenic segregation for adult plant stripe rust response was observed among the Aus27284/Avocet S RIL population and the underlying locus was temporarily designated YrAW11. Bulked-segregant analysis using the Infinium iSelect 90K SNP wheat array placed YrAW11 in chromosome 3B. Kompetitive allele specific PCR (KASP) primers were designed for the linked SNPs and YrAW11 was flanked by KASP_65624 and KASP_53292 (3 cM) proximally and KASP_53113 (4.9 cM) distally. A partial linkage map of the genomic region carrying YrAW11 comprised nine KASP and two SSR markers. The physical position of KASP markers in the pseudomolecule of chromosome 3B placed YrAW11 in the long arm and the location of markers gwm108 and gwm376 in the deletion bin 3BL2-0.22 supported this conclusion. As no other stripe rust resistance locus has been reported in chromosome 3BL, YrAW11 was formally designated Yr80. Marker KASP_ 53113 was polymorphic among 94% of 81 Australian wheat cultivars used for validation.

Characterization of Novel Gene Yr79 and Four Additional Quantitative Trait Loci for All-Stage and High-Temperature Adult-Plant Resistance to Stripe Rust in Spring Wheat PI 182103

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is an important disease of wheat worldwide. Exploring new resistance genes is essential for breeding resistant wheat cultivars. PI 182103, a spring wheat landrace originally from Pakistan, has shown a high level of resistance to stripe rust in fields for many years, but genes for resistance to stripe rust in the variety have not been studied. To map the resistance gene(s) in PI 182103, 185 recombinant inbred lines (RILs) were developed from a cross with Avocet Susceptible (AvS). The RIL population was genotyped with simple sequence repeat (SSR) and single nucleotide polymorphism markers and tested with races PST-100 and PST-114 at the seedling stage under controlled greenhouse conditions and at the adult-plant stage in fields at Pullman and Mt. Vernon, Washington under natural infection by the stripe rust pathogen in 2011, 2012, and 2013. A total of five quantitative trait loci (QTL) were detected. QyrPI182103.wgp-2AS and QyrPI182103.wgp-3AL were detected at the seedling stage, QyrPI182103.wgp-4DL was detected only in Mt. Vernon field tests, and QyrPI182103.wgp-5BS was detected in both seedling and field tests. QyrPI182103.wgp-7BL was identified as a high-temperature adult-plant resistance gene and detected in all field tests. Interactions among the QTL were mostly additive, but some negative interactions were detected. The 7BL QTL was mapped in chromosomal bin 7BL 0.40 to 0.45 and identified as a new gene, permanently designated as Yr79. SSR markers Xbarc72 and Xwmc335 flanking the Yr79 locus were highly polymorphic in various wheat genotypes, indicating that the molecular markers are useful for incorporating the new gene for potentially durable stripe rust resistance into new wheat cultivars.

Genetic and Physical Mapping of a Putative Leymus mollis-Derived Stripe Rust Resistance Gene on Wheat Chromosome 4A

Wheat stripe rust is one of the most damaging diseases of wheat worldwide. The wheat-Leymus mollis introgression line M8664-3 exhibits all-stage resistance to Chinese stripe rust races. Genetic analysis of stripe rust resistance was performed by crossing M8664-3 with the susceptible line Mingxian169. Analysis of the disease resistance of F₂ and F_2:3 populations revealed that its resistance to Chinese stripe rust race 33 (CYR33) is controlled by a single dominant gene, temporarily designated as YrM8664-3. Genetic and physical mapping showed that YrM8664-3 is located in bin 4AL13-0.59-0.66 close to 4AL12-0.43-0.59 on chromosome 4AL and is flanked by single-nucleotide polymorphism markers AX111655681 and AX109496237 with genetic distances of 5.3 and 2.3 centimorgans, respectively. Resistance spectrum and position analyses indicated that YrM8664-3 may be a novel gene. Molecular detection using the markers linked to YrM8664-3 with wheat varieties commonly cultivated and wheat-L. mollis-derived lines showed that YrM8664-3 is also present in other wheat-L. mollis introgression lines but absent in commercial common wheat cultivars. Thus, YrM8664-3 is a potentially valuable source of stripe rust resistance for breeding.

Mapping and validation of a new QTL for adult-plant resistance to powdery mildew in Chinese elite bread wheat line Zhou8425B

Four QTLs for adult-plant resistance to powdery mildew were mapped in the Zhou8425B/Chinese Spring population, and a new QTL on chromosome 3B was validated in 103 wheat cultivars derived from Zhou8425B. Zhou8425B is an elite wheat (Triticum aestivum L.) line widely used as a parent in Chinese wheat breeding programs. Identification of genes for adult-plant resistance (APR) to powdery mildew in Zhou8425B is of high importance for continued controlling the disease. In the current study, the high-density Illumina iSelect 90K single-nucleotide polymorphism (SNP) array was used to map quantitative trait loci (QTL) for APR to powdery mildew in 244 recombinant inbred lines derived from the cross Zhou8425B/Chinese Spring. Inclusive composite interval mapping identified QTL on chromosomes 1B, 3B, 4B, and 7D, designated as QPm.caas-1BL.1, QPm.caas-3BS, QPm.caas-4BL.2, and QPm.caas-7DS, respectively. Resistance alleles at the QPm.caas-1BL.1, QPm.caas-3BS, and QPm.caas-4BL.2 loci were contributed by Zhou8425B, whereas that at QPm.caas-7DS was from Chinese Spring. QPm.caas-3BS, likely to be a new APR gene for powdery mildew resistance, was detected in all four environments. One SNP marker closely linked to QPm.caas-3BS was transferred into a semi-thermal asymmetric reverse PCR (STARP) marker and tested on 103 commercial wheat cultivars derived from Zhou8425B. Cultivars with the resistance allele at the QPm.caas-3BS locus had averaged maximum disease severity reduced by 5.3%. This STARP marker can be used for marker-assisted selection in improvement of the level of powdery mildew resistance in wheat breeding.

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

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most devastating diseases of wheat worldwide. Growing resistant cultivars is considered the best approach to manage this disease. In order to identify the resistance gene(s) in wheat line 03031-1-5 H62, which displayed high resistance to stripe rust at adult plant stage, a cross was made between 03031-1-5 H62 and susceptible cultivar Avocet S. The mapping population was tested with Chinese P. striiformis f. sp. tritici race CYR32 through artificial inoculation in a field in Yangling, Shaanxi Province and under natural infection in Tianshui, Gansu Province. The segregation ratios indicated that the resistance was conferred by a single dominant gene, temporarily designated as YrH62. A combination of bulked segregant analysis (BSA) with wheat 90K single nucleotide polymorphism (SNP) array was used to identify molecular markers linked to YrH62. A total of 376 polymorphic SNP loci identified from the BSA analysis were located on chromosome 1B, from which 35 kompetitive allele-specific PCR (KASP) markers selected together with 84 simple sequence repeat (SSR) markers on 1B were used to screen polymorphism and a chromosome region associated with rust resistance was identified. To saturate the chromosomal region covering the YrH62 locus, a 660K SNP array was used to identify more SNP markers. To develop tightly linked markers for marker-assisted selection of YrH62 in wheat breeding, 18 SNPs were converted into KASP markers. A final linkage map consisting of 15 KASP and 3 SSR markers was constructed with KASP markers AX-109352427 and AX-109862469 flanking the YrH62 locus in a 1.0 cM interval. YrH62 explained 63.8 and 69.3% of the phenotypic variation for disease severity and infection type, respectively. YrH62 was located near the centromeric region of chromosome 1BS based on the positions of the SSR markers in 1B deletion bins. Based on the origin, responses to P. striiformis f. sp. tritici races, and marker distances, YrH62 is likely different from the other reported stripe rust resistance genes/quantitative trait loci on 1B. The gene and tightly linked KASP markers will be useful for breeding wheat cultivars with resistance to stripe rust.

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.

Development and Validation of KASP-SNP Markers for QTL Underlying Resistance to Stripe Rust in Common Wheat Cultivar P10057

Stripe rust (Puccinia striiformis f. sp. tritici) is among the most important diseases of wheat (Triticum aestivum L.) globally. Utilization of adult plant resistance (APR) constitutes a key tool for maintaining protection against this disease. The CIMMYT wheat cultivar P10057 displayed a high level of APR to stripe rust in germplasm evaluation in field environments. To clarify the genetic basis and identify quantitative trait loci (QTLs) involved in stripe rust resistance in P10057, three wheat populations were used: 150 F_5:6 recombinant inbred lines (RILs) derived from the cross Mingxian 169 × P10057, and 161 and 140 F_2:3 lines from Avocet S × P10057 and Zhengmai 9023 × P10057, respectively. These three populations were evaluated for infection type (IT) and disease severity (DS) in Shaanxi, Gansu, and Sichuan during the 2014-15 and 2015-16 cropping seasons. Genotyping was performed with Kompetitive Allelic Specific PCR (KASP) and simple sequence repeat (SSR) markers linked to the resistance loci. Using QTL analysis, two genomic regions associated with resistance were found on chromosome arms 2BS and 3BS, respectively. These two stable QTLs, designated Qyrlov.nwafu-2BS and Qyrlov.nwafu-3BS, were detected across all environments and explained average 22.6 to 31.6% and 21.3 to 32.3% of stripe rust severity phenotypic variation, respectively. Qyrlov.nwafu-2BS may be the resistance allele derived from CIMMYT germplasm and Qyrlov.nwafu-3BS likely corresponds to the locus Sr2/Lr27/Yr30/Pbc. The KASP markers IWA5377, IWA2674, and IWA5830 linked to QYrlov.nwafu-2BS and IWB57990 and IWB6491 linked to Qyrlov.nwafu-3BS were reliable for marker-assisted selection (MAS) in the Zhengmai 9023 × P10057 population. These QTLs with KASP markers are expected to contribute in developing wheat cultivars with improved stripe rust resistance.

Gametocidal genes of Aegilops: segregation distorters in wheat-Aegilops wide hybridization

Aegilops is a genus belonging to the family Poaceace, which have played an indispensible role in the evolution of bread wheat and continues to do so by transferring genes by wide hybridization. Being the secondary gene pool of wheat, gene transfer from Aegilops poses difficulties and segregation distortion is common. Gametocidal genes are the most well characterized class of segregation distorters reported in interspecific crosses of wheat with Aegilops. These "selfish" genetic elements ensure their preferential transmission to progeny at the cost of gametes lacking them without providing any phenotypic benefits to the plant, thereby causing a proportional reduction in fertility. Gametocidal genes (Gc) have been reported in different species of Aegilops belonging to the sections Aegilops (Ae. geniculata and Ae. triuncialis), Cylindropyrum (Ae. caudata and Ae. cylindrica), and Sitopsis (Ae. longissima, Ae. sharonensis, and Ae. speltoides). Gametocidal activity is mostly confined to 2, 3, and 4 homeologous groups of C, S, S¹, S^sh, and M^g genomes. Removal of such genes is necessary for successful alien gene introgression and can be achieved by mutagenesis or allosyndetic pairing. However, there are some instances where Gc genes are constructively utilized for development of deletion stocks in wheat, improving genetic variability and chromosome engineering.