Chromosome Arms 7DS Research Articles

WPA1 encodes a vWA domain protein that regulates wheat plant architecture

Plant height, spike, leaf, stem and grain morphologies are key components of plant architecture and related to wheat yield. A wheat (Triticum aestivum L.) mutant, wpa1, displaying temperature-dependent pleiotropic developmental anomalies, was isolated. The WPA1 gene, encoding a von Willebrand factor type A (vWA) domain protein, was located on chromosome arm 7DS and isolated by map-based cloning. The functionality of WPA1 was validated by multiple independent EMS-induced mutants and gene editing. Phylogenetic analysis revealed that WPA1 is monocotyledon-specific in higher plants. The identification of WPA1 provides opportunity to study the temperature regulated wheat development and grain yield.

Characterization of Quantitative Trait Loci for Leaf Rust Resistance from CI 13227 in Three Winter Wheat Populations.

Leaf rust is a widespread foliar wheat disease causing substantial yield losses worldwide. Slow rusting is "adult plant" resistance that significantly slows epidemic development and thereby reduces yield loss. Wheat accession CI 13227 was previously characterized as having slow-rusting resistance. To validate the quantitative trait loci (QTLs) and develop diagnostic markers for slow rusting resistance in CI 13227, a new population of recombinant inbred lines of CI 13227 × Everest was evaluated for latent period, final severity, area under the disease progress curve, and infection type in greenhouses and genotyped using genotyping-by-sequencing. Four QTLs were identified on chromosome arms 2BL, 2DS, 3BS, and 7BL, explaining 6.82 to 28.45% of the phenotypic variance for these traits. Seven kompetitive allele-specific polymorphism markers previously reported to be linked to the QTLs in two other CI 13227 populations were validated. In addition, the previously reported QLr.hwwg-7AL was remapped to 2BL (renamed QLr.hwwg-2BL) after adding new markers in this study. Phenotypic data showed that the recombinant inbred lines harboring two or three of the QTLs had a significantly longer latent period. QLr.hwwg-2DS on 2DS showed a major effect on all rust resistance traits and was finely mapped to a 2.7-Mb interval by two newly developed flanking markers from exome capture. Three disease-resistance genes and two transporter genes were identified as the putative candidates for QLr.hwwg-2DS. The validated QTLs can be used as slow-rusting resistance resources, and the markers developed in this study will be useful for marker-assisted selection.

Identification and functional analysis of a chromosome 2D fragment harboring TaFPF1 gene with the potential for yield improvement using a late heading wheat mutant.

A chromosome fragment influencing wheat heading and grain size was identified using mapping of m406 mutant. The study of TaFPF1 in this fragment provides more insights into wheat yield improvement. In recent years, wheat production has faced formidable challenges driven by rapid population growth and climate change, emphasizing the importance of improving specific agronomic traits such as heading date, spike length, and grain size. To identify potential genes for improving these traits, we screened a wheat EMS mutant library and identified a mutant, designated m406, which exhibited a significantly delayed heading date compared to the wild-type. Intriguingly, the mutant also displayed significantly longer spike and larger grain size. Genetic analysis revealed that a single recessive gene was responsible for the delayed heading. Surprisingly, a large 46.58 Mb deletion at the terminal region of chromosome arm 2DS in the mutant was identified through fine mapping and fluorescence in situ hybridization. Thus, the phenotypes of the mutant m406 are controlled by a group of linked genes. This deletion encompassed 917 annotated high-confidence genes, including the previously studied wheat genes Ppd1 and TaDA1, which could affect heading date and grain size. Multiple genes in this region probably contribute to the phenotypes of m406. We further investigated the function of TaFPF1 using gene editing. TaFPF1 knockout mutants showed delayed heading and increased grain size. Moreover, we identified the direct upstream gene of TaFPF1 and investigated its relationship with other important flowering genes. Our study not only identified more genes affecting heading and grain development within this deleted region but also highlighted the potential of combining these genes for improvement of wheat traits.

Identification of Two Novel QTL for Fusarium Head Blight Resistance in German Wheat Cultivar Centrum.

Fusarium head blight (FHB) is a devastating disease that occurs in warm and humid environments. The German wheat 'Centrum' has displayed moderate to high levels of FHB resistance in the field for many years. In this study, an F6:8 recombinant inbred line (RIL) population derived from cross 'Centrum' × 'Xinong 979' was evaluated for FHB response following point inoculation in five environments. The population and parents were genotyped using the GenoBaits Wheat 16 K Panel. Stable quantitative trait loci (QTL) associated with FHB resistance in 'Centrum' were mapped on chromosome arms 2DS and 5BS. The most effective QTL, located in 2DS, was identified as a new chromosome region represented by a 1.4 Mb interval containing 17 candidate genes. Another novel QTL was mapped in chromosome arm 5BS of a 5BS to 7BS translocation chromosome. In addition, two environmentally sensitive QTL were mapped on chromosome arms 2BL from 'Centrum' and 5AS from 'Xinong 979'. Polymorphisms of flanking phenotypic variance explained (PVE) markers (allele-specific quantitative PCR [AQP]) AQP-6 for QFhb.nwafu-2DS and 16K-13073 for QFhb.nwafu-5BS were validated in a panel of 217 cultivars and breeding lines. These markers could be useful for marker-assisted selection (MAS) of FHB resistance and provide a starting point for fine mapping and marker-based cloning of the resistance genes.

Fine mapping of leaf delayed virescence gene dv4 in Triticum aestivum

Wheat (Triticum aestivum L.) is one of the most important crops worldwide, and its yield affects national food security. Wheat leaves are key photosynthetic organs where carbohydrates are synthesized for grain yield. Leaf colour mutants are ideal germplasm resources for molecular genetic studies of wheat chloroplast development, chlorophyll synthesis and photosynthesis. We obtained a wheat mutant delayed virescence 4 (dv4) from cultivar Guomai 301. The leaves of mutant dv4 were pale yellow at the seedling stage, golden yellow at the turning green stage, and they started to turn green at the jointing stage. Genetic analysis demonstrated that the yellow-leaf phenotype was controlled by a single recessive gene named as dv4. Gene dv4 was fine mapped in a 1.46 Mb region on chromosome 7DS by SSR and dCAPS marker assays. Three putative candidate genes were identified in this region. Because no leaf colour genes have been reported on wheat chromosome arm 7DS previously, dv4 is a novel leaf colour gene. The result facilitates map-based cloning of dv4 and provides information for the construction of a high-photosynthetic efficiency ideotype for improving wheat yield.

Introgression of the bread wheat D genome encoded Lr34/Yr18/Sr57/Pm38/Ltn1 adult plant resistance gene into Triticum turgidum (durum wheat)

Key MessageLack of function of a D-genome adult plant resistance gene upon introgression into durum wheat.The wheat Lr34/Yr18/Sr57/Pm38/Ltn1 adult plant resistance gene (Lr34), located on chromosome arm 7DS, provides broad spectrum, partial, adult plant resistance to leaf rust, stripe rust, stem rust and powdery mildew. It has been used extensively in hexaploid bread wheat (AABBDD) and conferred durable resistance for many decades. These same diseases also occur on cultivated tetraploid durum wheat and emmer wheat but transfer of D genome sequences to those subspecies is restricted due to very limited intergenomic recombination. Herein we have introgressed the Lr34 gene into chromosome 7A of durum wheat. Durum chromosome substitution line Langdon 7D(7A) was crossed to Cappelli ph1c, a mutant derivative of durum cultivar Cappelli homozygous for a deletion of the chromosome pairing locus Ph1. Screening of BC1F2 plants and their progeny by KASP and PCR markers, 90 K SNP genotyping and cytology identified 7A chromosomes containing small chromosome 7D fragments encoding Lr34. However, in contrast to previous transgenesis experiments in durum wheat, resistance to wheat stripe rust was not observed in either Cappelli/Langdon 7D(7A) or Bansi durum plants carrying this Lr34 encoding segment due to low levels of Lr34 gene expression. Key message

Genetic architecture of quantitative trait loci (QTL) for FHB resistance and agronomic traits in a hard winter wheat population

Wheat resistance to Fusarium head blight (FHB) has often been associated with some undesirable agronomic traits. To study the relationship between wheat FHB resistance and agronomic traits, we constructed a linkage map of single nucleotide polymorphisms (SNPs) using an F6:8 population from G97252W × G97380A. The two hard winter wheat parents showed contrasts in FHB resistance, plant height (HT), heading date (HD), spike length (SL), spike compactness (SC), kernel number per spike (KNS), spikelet number per spike (SNS), thousand-grain weight (TGW) and grain size (length and width). Quantitative trait locus (QTL) mapping identified one major QTL (QFhb.hwwg-2DS) on chromosome arm 2DS for the percentage of symptomatic spikelets (PSS) in the spike, deoxynivalenol (DON) content and Fusarium damaged kernel (FDK). This QTL explained up to 71.8% of the phenotypic variation for the three FHB-related traits and overlapped with the major QTL for HT, HD, SL, KNS, SNS, TGW, and grain size. QTL on chromosome arms 2AL, 2DS, 3AL and 4BS were significant for the spike and grain traits measured. G97252W contributed FHB resistance and high SNS alleles at QFhb.hwwg-2DS, high KNS alleles at the QTL on 2AL and 2DS, and high TGW and grain size alleles at QTL on 3AL; whereas G97380A contributed high TGW and grain size alleles at the QTL on 2AL and 2DS, respectively, and the high KNS allele at the 4BS QTL. Combining QFhb.hwwg-2DS with positive alleles for spike and grain traits from other chromosomes may simultaneously improve FHB resistance and grain yield in new cultivars.

QTL mapping reveals both all-stage and adult-plant resistance to powdery mildew in Chinese elite wheat cultivars.

Powdery mildew caused by Blumeria graminis f. sp. tritici (Bgt) is a threat to wheat production in China. Mapping quantitative trait loci (QTL) for resistance to powdery mildew and developing breeder-friendly markers are important initial steps in breeding resistant cultivars. An all-stage resistance gene and several QTL were identified using a population of 254 recombinant inbred lines (RILs) developed from a Jingdong 8/Aikang 58 cross. The population was evaluated for powdery mildew resistance across six field environments over three consecutive growing seasons utilizing two different mixtures of Bgt isolates, named #Bgt-HB and #Bgt-BJ. Using genotypic data obtained from the Wheat TraitBreed 50K SNP array, seven stable QTL were identified on chromosome arms 1DL, 2AL, 2DS, 4DL, 5AL, 6BL.1 and 6BL.2. The QTL on 2AL conferred all-stage resistance to Bgt race E20 in greenhouse tests and explained up to 52% of the phenotypic variance in field trials but was resistant only against #Bgt-HB. The gene involved in this QTL was predicted to be Pm4a based on genome location and gene sequence. QPmja.caas-1DL, QPmja.caas-4DL and QPmja.caas-6BL.1 were identified as potentially new QTL for powdery mildew resistance. QPmja.caas-2DS and QPmja.caas-6BL.1 were effective against both Bgt mixtures indicating their probable broad-spectrum resistance. A Kompetitive Allele-Specific PCR (KASP) marker closely linked to QPmja.caas-2DS was developed and validated in a panel of 286 wheat cultivars. Since both Jingdong 8 and Aikang 58 have been leading cultivars and breeding parents, the QTL and marker reported represent valuable resources for wheat researchers and breeders.

Genetic mapping of the wheat leaf rust resistance gene Lr2a and its importance in Canadian wheat cultivars.

Leaf rust resistance gene Lr2a was located to chromosome arm 2DS in three mapping populations, which will facilitate map-based cloning and marker-assisted selection of Lr2a in wheat breeding programs. Incorporating effective leaf rust resistance (Lr) genes into high-yielding wheat cultivars has been an efficient method of disease control. One of the most widely used genes in Canada is the multi-allelic resistance gene Lr2, with alleles Lr2a, Lr2b, Lr2c, and Lr2d. The Lr2a allele confers complete resistance to a large portion of the Puccinia triticina (Pt) population in Canada. In this study, Lr2a was genetically mapped in two doubled haploid populations developed from the crosses Superb/BW278 and Superb/86ISMN 2137, and an F2 population developed from the cross Chinese Spring/RL6016. Seedlings were tested with the Lr2a avirulent Pt races 74-2 MGBJ (Superb/BW278) and 12-3 MBDS (Superb/86ISMN 2137 and Chinese Spring/RL6016) in greenhouse assays and were genotyped with 90K wheat Infinium SNP and kompetitive allele-specific PCR (KASP) markers. Lr2a was mapped to a collinear position on chromosome arm 2DS in all three populations, within a 1.00cM genetic interval between KASP markers kwm1620 and kwm1623. This corresponded to a 305kb genomic region of chromosome 2D in Chinese Spring RefSeq v2.1. The KASP marker kwh740 was predictive of Lr2a in all mapping populations. A panel of 260 wheats were tested with three Pt isolates, which revealed that Lr2a is common in Canadian wheats. The KASP markers kwh740 and kwm1584 were highly associated with resistance at the Lr2 locus, while kwm1622 was slightly less correlated. Genetic mapping of the leaf rust resistance gene Lr2a and DNA markers developed here will facilitate its use in wheat breeding programs.

Mapping and characterization of the recessive leaf rust resistance gene Lr83 on wheat chromosome arm 1DS

The leaf rust resistance gene in Thatcher wheat derivative 78-1 was mapped to chromosome 1DS with SNP markers and designated as Lr83. 'Thatcher' wheat near isogenic line RL6149, a putative derivative of Triticum dicoccoides, was previously determined to carry leaf rust resistance gene Lr64 on chromosome arm 6AL and a second gene temporarily named LrX on chromosome arm 1DS. The objective of this study was to map and characterize LrX in a population of recombinant inbred lines (RILs) that segregated for a single gene. Thatcher line 78-1 with LrX was crossed with Thatcher and individual F2 seedlings and F6 RILs were evaluated for leaf rust response. The 208 F2 plants segregated for a single recessive gene and 148 F6 lines for a single gene. The RILs and parents were characterized by genotyping by sequencing (GBS). Six GBS markers and five Kompetitive Allele-Specific PCR (KASP) markers were used to map LrX on the distal region of chromosome arm 1DS. LrX was 1 centiMorgan (cM) proximal to marker K-IWB38437 and 0.4cM distal to GBS marker 1D_9037138. Line 78-1 was crossed with Thatcher wheat lines with Lr21, Lr42, and Lr60 for allelism tests. LrX mapped 19.49cM from Lr21 and 11.93cM from Lr42. In the cross of line 78-1 with the Thatcher line with Lr60, one recombinant in 1,003 F2 plants was found. LrX and Lr60 are at tightly linked loci on the distal region of chromosome arm 1DS. The gene in line 78-1 was designated as Lr83. Cytological examination of RL6149 provided no evidence of transfer of a chromosome segment of an A- or B-genome chromosome to chromosome 1D.

Haplotype variants of Sr46 in Aegilops tauschii, the diploid D genome progenitor of wheat.

Stem rust resistance genes, SrRL5271 and Sr672.1 as well as SrCPI110651, from Aegilops tauschii, the diploid D genome progenitor of wheat, are sequence variants of Sr46 differing by 1-2 nucleotides leading to non-synonymous amino acid substitutions. The Aegilops tauschii (wheat D-genome progenitor) accessions RL 5271 and CPI110672 were identified as resistant to multiple races (including the Ug99) of the wheat stem rust pathogen Puccinia graminis f. sp. tritici (Pgt). This study was conducted to identify the stem rust resistance (Sr) gene(s) in both accessions. Genetic analysis of the resistance in RL 5271 identified a single dominant allele (SrRL5271) controlling resistance, whereas resistance segregated at two loci (SR672.1 and SR672.2) for a cross of CPI110672. Bulked segregant analysis placed SrRL5271 and Sr672.1 in a region on chromosome arm 2DS that encodes Sr46. Molecular marker screening, mapping and genomic sequence analysis demonstrated SrRL5271 and Sr672.1 are alleles of Sr46. The amino acid sequence of SrRL5271 and Sr672.1 is identical but differs from Sr46 (hereafter referred to as Sr46_h1 by following the gene nomenclature in wheat) by a single amino acid (N763K) and is thus designated Sr46_h2. Screening of a panel of Ae. tauschii accessions identified an additional allelic variant that differed from Sr46_h2 by a different amino acid (A648V) and was designated Sr46_h3. By contrast, the protein encoded by the susceptible allele of Ae. tauschii accession AL8/78 differed from these resistance proteins by 54 amino acid substitutions (94% nucleotide sequence gene identity). Cloning and complementation tests of the three resistance haplotypes confirmed their resistance to Pgt race 98-1,2,3,5,6 and partial resistance to Pgt race TTRTF in bread wheat. The three Sr46 haplotypes, with no virulent races detected yet, represent a valuable source for improving stem resistance in wheat.

Fine mapping of Pm58 from Aegilops tauschii conferring powdery mildew resistance.

The powdery mildew resistance gene Pm58 was traced to a 141.3-kb interval with the co-segregating marker Xkasp68500 in wheat breeding. Pm58 is a powdery mildew resistance gene identified in Aegilops tauschii accession TA1662 and effective in a common wheat background. To finely map Pm58, an F2 population of 676 plants derived from the cross T093 × TA1662 was used for recombinant screening. We obtained 13 recombinants that occurred between the flanking markers Xhnu670 and Xhnu186. Genotyping and phenotyping these recombinant F2:3 families delimited Pm58 to a 0.22-cM interval (Xsts20220-Xkasp61553) on chromosome arm 2DS. The region carrying the Pm58 locus was approximately 141.3-kb, which contained eight annotated genes according to the reference genome sequence of Ae. tauschii AL8/78. Haplotype analysis of 178 Ae. tauschii accessions using the candidate gene-specific markers identified a disease resistance gene AET2Gv20068500 as a candidate for Pm58. Comparative mapping of the Pm58-containing interval revealed two presence/absence variations (PAVs) between AL8/78 and common wheat Chinese Spring. PAV-1 resides in the 3'-end of AET2Gv20068500. The majority of 158 common wheat cultivars (84.8%) displayed the absence of a 14.1-kb fragment in the PAV-1 region, which was confirmed by aligning the targeted genome sequences of the other sequenced Ae. tauschii accessions and common wheat cultivars. A co-segregating marker Xkasp68500 developed from AET2Gv20068500 can distinguish TA1662 from all randomly selected common wheat cultivars and will be instrumental for tracking Pm58 in breeding programs.

Development of single nucleotide polymorphism‐based functional molecular markers from the Lr22a gene sequence in wheat (Triticum aestivum)

AbstractThe adult‐plant leaf rust resistant gene Lr22a confers broadly effective resistance against the fungal pathogen Puccinia triticina Eriks. (Pt) in wheat that has not been extensively utilized in wheat cultivars. The objective of this study was to develop robust functional molecular markers using the Lr22a gene sequence to facilitate integration of Lr22a in breeding programmes. The Lr22a coding sequence was used to identify isolated SNPs and four kompetitive allele specific polymerase chain reaction (PCR) (KASP) markers were developed. For marker testing, a F2:3 population was developed by crossing a near‐isogenic line RL4495 (Lr22a carrier) with Thatcher and phenotyped with Pt race TDBJ and genotyped with a 90K iSelect SNP array, four KASP markers and two SSR markers. A linkage map of chromosome arm 2DS that included Lr22a was constructed. The KASP markers co‐segregated with Lr22a and were validated for cross‐applicability on a panel of wheat lines. KASP markers Kwh636, Kwh637 and Kwh638 reliably detected the presence or absence of Lr22a. The markers developed in this study will facilitate Lr22a selection in breeding programmes.

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

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

Enhanced stripe rust resistance obtained by combining Yr30 with a widely dispersed, consistent QTL on chromosome arm 4BL.

YrFDC12 and PbcFDC, co-segregated in chromosome 4BL, and significantly interacted with Yr30/Pbc1 to enhance stripe rust resistance and to promote pseudo-black chaff development. Cultivars with durable resistance are the most popular means to control wheat stripe rust. Durable resistance can be achieved by stacking multiple adult plant resistance (APR) genes that individually have relatively small effect. Chinese wheat cultivars Ruihua 520 (RH520) and Fengdecun 12 (FDC12) confer partial APR to stripe rust across environments. One hundred and seventy recombinant inbred lines from the cross RH520 × FDC12 were used to determine the genetic basis of resistance and identify genomic regions associated with stripe rust resistance. Genotyping was carried out using 55K SNP array, and eight quantitative trait loci (QTL) were detected on chromosome arms 2AL, 2DS, 3BS, 4BL, 5BL (2), and 7BL (2) by inclusive composite interval mapping. Only QYr.nwafu-3BS from RH520 and QYr.nwafu-4BL.2 (named YrFDC12 for convenience) from FDC12 were consistent across the four testing environments. QYr.nwafu-3BS is likely the pleiotropic resistance gene Sr2/Yr30. YrFDC12 was mapped in a 2.1-cM interval corresponding to 12Mb and flanked by SNP markers AX-111121224 and AX-89518393. Lines harboring both Yr30 and YrFDC12 displayed higher resistance than the parents and expressed pseudo-black chaff (PBC) controlled by loci Pbc1 and PbcFDC12, which co-segregated with Yr30 and YrFDC12, respectively. Both marker-based and pedigree-based kinship analyses revealed that YrFDC12 was inherited from founder parent Zhou 8425B. Fifty-four other wheat cultivars shared the YrFDC12 haplotype. These results suggest an effective pyramiding strategy to acquire highly effective, durable stripe rust resistance in breeding.

The Haplotype-Based Analysis of Aegilops tauschii Introgression Into Hard Red Winter Wheat and Its Impact on Productivity Traits.

The introgression from wild relatives have a great potential to broaden the availability of beneficial allelic diversity for crop improvement in breeding programs. Here, we assessed the impact of the introgression from 21 diverse accessions of Aegilops tauschii, the diploid ancestor of the wheat D genome, into 6 hard red winter wheat cultivars on yield and yield component traits. We used 5.2 million imputed D genome SNPs identified by the whole-genome sequencing of parental lines and the sequence-based genotyping of introgression population, including 351 BC1F3:5 lines. Phenotyping data collected from the irrigated and non-irrigated field trials revealed that up to 23% of the introgression lines (ILs) produce more grain than the parents and check cultivars. Based on 16 yield stability statistics, the yield of 12 ILs (3.4%) was stable across treatments, years, and locations; 5 of these lines were also high yielding lines, producing 9.8% more grain than the average yield of check cultivars. The most significant SNP- and haplotype-trait associations were identified on chromosome arms 2DS and 6DL for the spikelet number per spike (SNS), on chromosome arms 2DS, 3DS, 5DS, and 7DS for grain length (GL) and on chromosome arms 1DL, 2DS, 6DL, and 7DS for grain width (GW). The introgression of haplotypes from A. tauschii parents was associated with an increase in SNS, which was positively correlated with a heading date (HD), whereas the haplotypes from hexaploid wheat parents were associated with an increase in GW. We show that the haplotypes on 2DS associated with an increase in the spikelet number and HD are linked with multiple introgressed alleles of Ppd-D1 identified by the whole-genome sequencing of A. tauschii parents. Meanwhile, some introgressed haplotypes exhibited significant pleiotropic effects with the direction of effects on the yield component traits being largely consistent with the previously reported trade-offs, there were haplotype combinations associated with the positive trends in yield. The characterized repertoire of the introgressed haplotypes derived from A. tauschii accessions with the combined positive effects on yield and yield component traits in elite germplasm provides a valuable source of alleles for improving the productivity of winter wheat by optimizing the contribution of component traits to yield.

A robust KASP marker for selection of four pairs of linked leaf rust and stripe rust resistance genes introgressed on chromosome arm 5DS from different wheat genomes.

Stripe rust and leaf rust are among the most devastating diseases of wheat, limiting its production globally. Wheat wild relatives harbour genetic diversity for new genes and alleles for all major wheat diseases. However, the use of this genetic variation from wild progenitor and non-progenitor species has been limited in the breeding programs. Reasons include limited recombination of donor and recipient genomes and the lack of tertiary gene pool markers. Here, we describe the development of a SNP based marker from the flow-sorted and sequenced Aegilops umbellulata chromosome 5U which can be used for marker assisted selection of four pair of alien leaf rust and stripe rust resistance genes. Lr57-Yr40_CAPS16 marker was reported earlier to be linked with alien leaf and stripe rust resistance genes introgressed on wheat chromosome 5DS. Due to its dominant nature and laborious to work with, a new SNP-based KASP marker, XTa5DS-2754099_kasp23, was developed from the same CAPS marker contig. XTa5DS-2754099_kasp23 was tested in Aegilops umbellulata, Ae. geniculata, Ae. peregrina and Ae. caudata derived alien introgression lines, which harbour four pairs of linked leaf and stripe rust genes; Lr76-Yr70, Lr57-Yr40, LrP- YrP, LrAc-YrAc, respectively. This KASP marker was found to be effective for the selection of the aforesaid four pairs of leaf rust and stripe rust resistance genes. Further, we tested and validated XTa5DS-2754099_kasp23 on commercial varieties and advanced breeding lines from four countries (India, Egypt, Australia and UK) including hexaploid and durum wheat. Our results provide evidence that KASP marker, XTa5DS-2754099_kasp23 can be used in marker-assisted selection of the four pairs of rust resistance alien genes in wheat breeding programmes.

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, F2:3 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 LrTs276-2, in TSD276-2. Molecular mapping of leaf rust resistance gene LrTs276-2 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 LrTs276-2 is a new leaf rust resistance gene which may be useful in broadening the genetic base of leaf rust resistance in wheat.

Sequence analysis of wheat subtelomeres reveals a high polymorphism among homoeologous chromosomes.

Bread wheat, Triticum aestivum L., is one of the most important crops in the world. Understanding its genome organization (allohexaploid; AABBDD; 2n=6x=42) is essential for geneticists and plant breeders. Particularly, the knowledge of how homologous chromosomes (equivalent chromosomes from the same genome) specifically recognize each other to pair at the beginning of meiosis, the cellular process to generate gametes in sexually reproducing organisms, is fundamental for plant breeding and has a big influence on the fertility of wheat plants. Initial homologous chromosome interactions contribute to specific recognition and pairing between homologues at the onset of meiosis. Understanding the molecular basis of these critical processes can help to develop genetic tools in a breeding context to promote interspecific chromosome associations in hybrids or interspecific genetic crosses to facilitate the transfer of desirable agronomic traits from related species into a crop like wheat. The terminal regions of chromosomes, which include telomeres and subtelomeres, participate in chromosome recognition and pairing. We present a detailed molecular analysis of subtelomeres of wheat chromosome arms 1AS, 4AS, 7AS, 7BS and 7DS. Results showed a high polymorphism in the subtelomeric region among homoeologues (equivalent chromosomes from related genomes) for all the features analyzed, including genes, transposable elements, repeats, GC content, predicted CpG islands, recombination hotspots and targeted sequence motifs for relevant DNA-binding proteins. These polymorphisms might be the molecular basis for the specificity of homologous recognition and pairing in initial chromosome interactions at the beginning of meiosis in wheat.

Genome-Wide Association Analysis of Fusarium Head Blight Resistance in Chinese Elite Wheat Lines.

Fusarium head blight (FHB) is a devastating wheat disease worldwide. To decipher the genetic architecture of FHB resistance in Chinese germplasm, a Wheat Association Panel for Scab Research (WAPS) consisting of 240 leading Chinese wheat cultivars and elite lines was genotyped using the 90K single nucleotide polymorphism (SNP) arrays. The FHB response was evaluated in the field nurseries in Wuhan in Hubei Province over four consecutive years from 2014 to 2017. Five quantitative trait loci (QTL) were consistently identified on chromosome arms 1AS, 2DL, 5AS, 5AL, and 7DS using a mixed linear model (MLM), explaining 5.6, 10.3, 5.7, 5.4, and 5.6% of phenotypic variation, respectively. The QTL on 5AS, 5AL, and 7DS QTL are probably novel. The allelic frequency analysis indicated that cultivars from the Middle and Lower Yangtze River Valleys harbored more favorable alleles and were therefore more resistant than those from other regions. To facilitate in-house germplasm screening and marker-assisted selection (MAS), SNP-derived PCR markers were developed for the QTL regions on 1AS, 5AS, and 5AL QTL. In addition to the above five QTL, the WAPS population had a very low frequency of Fhb1, confirming that the gene is not widely used in Chinese wheat breeding programs. The resistant lines and molecular markers developed in this study are resources and information for enhancing FHB resistance in breeding populations by marker-assisted recurrent selection and gene stacking.