Evaluating the contribution of Yr genes to stripe rust resistance breeding through marker-assisted detection in wheat

Numerous stripe rust resistance genes have been identified from wheat, and new virulent races of Puccinia striiformis f. sp. tritici have also emerged in recent years. Deployment of diverse combinations of resistance genes is an efficient way to combat virulent evolution of strip rust pathogen. In this study, publically available molecular markers were used to identify the distribution of 36 Yr genes in 672 wheat accessions. The effectiveness of Yr genes individually and in combinations was also evaluated in field conditions. The result showed effective resistance of some recently applied genes, such as Yr15 and Yr65. It also showed the lost efficacy of some once widely used genes, such as Yr9 and Yr10. Moreover, significant additive effects were observed in some gene combinations, such as Yr9 + Yr18 and Yr30 + Yr46. Proper deploying of Yr genes and utilizing the positive interactions will be helpful for durable resistance breeding in wheat.     

Chromosomal location of genes for resistance to powdery mildew in <Emphasis Type="Italic">Agropyron cristatum</Emphasis> and mapping of conserved orthologous set molecular markers

Agropyron cristatum exhibits resistance to Blumeria graminis f. sp. tritici. Disomic and ditelosomic chromosome addition lines of A. cristatum in ‘Chinese Spring’ wheat were utilized to determine which A. cristatum chromosomes carry resistance gene(s). Resistance is conferred by gene(s) on chromosome arms 2PL and 6PL. The availability of molecular markers capable of detecting these chromosome arms in a wheat background would be very useful for marker-assisted introgression of 2PL and 6PL chromatin into common wheat. With this aim, 170 wheat conserved orthologous set (COS) markers (92 and 78 from wheat homoeologous groups 2 and 6 respectively) were assessed for their utility in A. cristatum. A total of 116 (68.2%) COS markers successfully amplified product in A. cristatum and 46 (40.0%) of these markers were polymorphic between A. cristatum and common wheat. From marker loci mapping on wheat homoeologous group 2 chromosomes, 23 markers (34.9%) were polymorphic between A. cristatum and common wheat and from them 13 markers were assigned to chromosome arm 2PL and six markers were mapped to chromosome 4P of A. cristatum showing that this chromosome is related to wheat homoeologous group 2. From marker loci mapping on wheat homoeologous group 6 chromosomes, 23 (46.0%) markers were polymorphic between A. cristatum and common wheat and from them 17 markers were located on chromosome 6P, six of them were mapped to chromosome arm 6PS and five to chromosome arm 6PL, respectively. The specific COS markers allocated on the long arms of chromosomes 2P and 6P may have a role in marker-assisted screening in wheat breeding for powdery mildew disease resistance.     

Evaluation of end use quality and root traits in wheat cultivars associated with 1RS.1BL translocation

1RS.1BL translocation in wheat, exploited for its multiple disease resistance (Lr26, Yr9, Sr31 and Pm8), has  maintained significance due to its agronomical advantages. However, this translocation exhibits serious defects in dough quality due to the presence of Sec-1 loci on 1RS arm. In the present investigation micro SDS sedimentation test (MST), high molecular weight glutenin subunits (HMWGS) and bread making analysis of 26 genotypes were studied along with their root phenotyping in the field and under hydroponic culture system. The MST values showed that genotypes having Sec-1 loci had low MST values but in the presence of Glu-D1 (5?+?10) with Glu-B1 (7?+?9) and (7?+?8) they had high MST values, thus overcoming the negative effects of secalin on dough quality. The loaf volume showed positive correlation with MST values of the genotypes. The translocation of 1RS arm led to higher root biomass and longer root length than Pavon 76 without 1RS. Better root traits in recombinant 1RS 44:38 and 1B?+?38 than Pavon 1RS.1BL suggested the role of negative epistatic effects between different QTL regions in 1RS arm. The results suggest that it should be possible to harness the useful alleles associated with good dough quality, better root traits, high yield and stress tolerance with or without secalin.     

Allelic variation at the gliadin coding loci of improved Ethiopian durum wheat varieties

The objective of this study was to determine gliadin allele compositions of 20 improved Ethiopian durum wheat varieties using acid-polyacrylamide gel electrophoresis (A-PAGE). Each block of co-dominantly inherited polypeptides encoded by gliadin loci were identified and their genetic diversities were estimated using statistical analyses. A total of 30 electrophoretic blocks were identified at five major gliadin loci. In addition, four novel gliadin blocks were identified. Gli-B1 and Gli-A2 loci had higher numbers of gliadin alleles (nine and ten, respectively) compared to other loci. Alleles Gli-A1c on chromosome 1A, Gli-B1c on chromosome 1B, Gli-A2a, and Gli-A2o on chromosome 6A, and Gli-B2h on chromosome 6B had maximal frequencies in their corresponding loci. Varieties were classified into three main clusters and one singleton based on genetic distances of detected gliadin alleles. These results indicate that Ethiopian durum wheat varieties are genetically diverse with unique allele compositions at gliadin-coding loci.     

Conferring resistance to pre-harvest sprouting in durum wheat by a QTL identified in <Emphasis Type="Italic">Triticum spelta</Emphasis>

Pre-harvest sprouting (PHS) causes significant yield loss and degrade the end-use quality of wheat, especially in regions with prolonged wet weather during the harvesting season. Unfortunately, the gene pool of Triticum durum (tetraploid durum wheat) has narrow genetic base for PHS resistance. Therefore, finding out new genetic resources from other wheat species to develop PHS resistance in durum wheat is of importance. A major PHS resistance QTL, Qphs.sicau-3B.1, was mapped on chromosome 3BL in a recombinant inbred line population derived from ‘CSCR6’ (Triticum spelta), a PHS resistant hexaploid wheat and ‘Lang’, a PHS susceptible Australian hexaploid wheat cultivar. This QTL, Qphs.sicau-3B.1, is positioned between DArT marker wPt-3107 and wPt-6785. Two SCAR markers (Ph3B.1 and Ph3B.2) were developed to track this major QTL and were used to assay a BC₂F₈ tetraploid population derived from a cross between the durum wheat ‘Bellaroi’ (PHS susceptible) and ‘CSCR6’ (PHS resistant). Phenotypic assay and marker-assisted selection revealed five stable tetraploid lines were highly PHS resistant. This study has successfully established that PHS-resistance QTL from hexaploid wheat could be efficiently introgressed into tetraploid durum wheat. This tetraploid wheat germplasm could be useful in developing PHS resistant durum cultivars with higher yield and good end-use quality.     

Rapid identification of a major effect QTL conferring adult plant resistance to stripe rust in wheat cultivar Yaco“S”

Stripe rust is a devastating disease in common wheat (Triticum aestivum) worldwide. Growing cultivars with adult-plant resistance (APR) is an environmental friendly approach that provides long-term protection to wheat from this disease. Wheat cultivar Yaco“S” showed a high level of APR to stripe rust in the field from 2008 to 2014. The objective of this study was to detect the major quantitative trait loci (QTL) for APR to stripe rust in Yaco“S”. One hundred and eighty-four F_2:3 lines were developed from a cross between Yaco“S” and susceptible cultivar Mingxian169. Illumina 90K and 660K single nucleotide polymorphism (SNP) chips were implemented to bulked pools and their parents to identify SNPs associated with the major QTL. A high-density linkage map was constructed using simple sequence repeat (SSR) and SNP markers. Inclusive composite interval mapping detected a major effect QTL Qyryac.nwafu-2BS conferring stable resistance to stripe rust in all tested environments. Qyryac.nwafu-2BS were mapped to a 1.3 cm interval and explained 17.3–51.9% of the phenotypic variation. Compared with stripe rust resistance genes previously mapped to chromosome 2B, Qyryac.nwafu-2BS is likely a new APR gene to stripe rust. Combining SNP iSelect assay and kompetitive allele specific PCR technology, we found that the APR gene could be rapidly and accurately mapped and it is useful for improving stripe rust resistance in wheat breeding.     

Unveilingsources of stripe rust resistance in diverse wheat (<Emphasis Type="Italic">Triticum Aestivum</Emphasis> L.) germplasm using narrow down methodology: a proof of concept

Stripe rust of wheat caused by the fungal pathogen is a destructive foliar disease of wheat. Thus, it is crucial step to characterize the resistant germplasm for stripe rust in a diverse germplasm pool for their ultimate utilization in efficient crop rust resistance breeding. In the present study, we followed two pronged strategies involving integrated phenotypic and molecular characterization of 440 diverse wheat germplasm lines for rust resistance. The germplasm panel was extensively evaluated in field epiphytotic conditions during two consecutive years. After rigorous screening, 72 accessions were successfully revealed as resistant to moderately resistant to stripe rust. Subsequently, entries were then evaluated for their field agronomicperformances, considering prerequisites for serving as a donor germplasm,particularly for yield and 33 potential rust-resistant accessions were identified. Furthermore, to detect the sources of resistance, accessions were molecular characterized for potential race-specific resistance genes Yr5, Yr10,Yr15, and effective adult plant resistance (APR) gene Lr34/Yr18/pm38. We identified the 22 accessions possessing one or more single resistance genes and two accessions were observed with at least three of them. Moreover, Lr34/Yr18/pm38 was determined to confer resistance when observed along with any of the race-specific genes. Thus, the study not only provides proof of concept methodology to identify candidate resistant sources from large germplasm collections but simultaneouslyconfirmed the contribution of combining race-specific andnon-specific APR genes. The finding could further assist in the potential deployment of resistant genes directly into the stripe rust breeding program by involving marker-assisted approaches.     

Association mapping reveals loci associated with multiple traits that affect grain yield and adaptation in soft winter wheat

Genome-wide association studies (GWAS) are useful to facilitate crop improvement via enhanced knowledge of marker-trait associations (MTA). A GWAS for grain yield (GY), yield components, and agronomic traits was conducted using a diverse panel of 239 soft red winter wheat (Triticum aestivum) genotypes evaluated across two growing seasons and eight site-years. Analysis of variance showed significant environment, genotype, and genotype-by-environment effects for GY and yield components. Narrow sense heritability of GY (h ²  = 0.48) was moderate compared to other traits including plant height (h ²  = 0.81) and kernel weight (h ²  = 0.77). There were 112 significant MTA (p < 0.0005) detected for eight measured traits using compressed mixed linear models and 5715 single nucleotide polymorphism markers. MTA for GY and agronomic traits coincided with previously reported QTL for winter and spring wheat. Highly significant MTA for GY showed an overall negative allelic effect for the minor allele, indicating selection against these alleles by breeders. Markers associated with multiple traits observed on chromosomes 1A, 2D, 3B, and 4B with positive minor effects serve as potential targets for marker assisted breeding to select for improvement of GY and related traits. Following marker validation, these multi-trait loci have the potential to be utilized for MAS to improve GY and adaptation of soft red winter wheat.     

Complementary DNA (cDNA) cloning and functional verification of resistance to head smut disease (<Emphasis Type="Italic">Sphacelotheca reiliana</Emphasis>) of an NBS–LRR gene <Emphasis Type="Italic">ZmNL</Emphasis> in maize (<Emphasis Type="Italic">Zea mays</Emphasis>)

The nucleotide-binding site (NBS)-leucine-rich repeat (LRR) gene family comprises the largest number of known disease resistance (R) genes and is one of the largest gene families in plants. In the present study, the full-length cDNA of ZmNL (GenBank Accession Number KF765443) was isolated using Rapid Amplification of cDNA Ends. The nucleotide sequence of ZmNL contains an open reading frame of 3156 bp that encodes the ZmNL protein, which is comprised of 1051 amino acid residues. This putative protein has high homology to other known resistance proteins (84% to Triticum aestivum LR10) and belongs to the CC–NBS–LRR type R gene family. The ZmNL gene was introduced into the maize inbred line of Huangzao4 which was highly susceptible to head smut under the control of the maize ubiquitin promoter by Agrobacterium-mediated transformation. The head smut disease incidence of 3 T₂ transgenic lines was significantly reduced (by 18.38–29.40%) compared with the wild type, which indicated that the overexpression of ZmNL gene in maize enhanced the resistance to the fungus Sporisorium reilianum (Kühn) Clint of these plants.     

Diploid and tetraploid progenitors of wheat are valuable sources of resistance to the root lesion nematode <Emphasis Type="Italic">Pratylenchus</Emphasis><Emphasis Type="Italic">thornei</Emphasis>

The root lesion nematode Pratylenchus thornei is widely distributed in Australian wheat (Triticum aestivum) producing regions and can reduce yield by more than 50%, costing the industry AU$50 M/year. Genetic resistance is the most effective form of management but no commercial cultivars are resistant (R) and the best parental lines are only moderately R. The wild relatives of wheat have evolved in P. thornei-infested soil for millennia and may have superior levels of resistance that can be transferred to commercial wheats. To evaluate this hypothesis, a collection of 251 accessions of wheat and related species was tested for resistance to P. thornei under controlled conditions in glasshouse pot experiments over two consecutive years. Diploid accessions were more R than tetraploid accessions which proved more R than hexaploid accessions. Of the diploid accessions, 11 (52%) Aegilops speltoides (S-[B]-genome), 10 (43%) Triticum monococcum (A ^m -genome) and 5 (24%) Triticum urartu (A ^u -genome) accessions were R. One tetraploid accession (Triticum dicoccoides) was R. This establishes for the first time that P. thornei resistance is located on the A-genome and confirms resistance on the B-genome. Since previous research has shown that the moderate levels of P. thornei resistance in hexaploid wheat are dose-dependent, additive and located on the B and D-genomes, it would seem efficient to target A-genome resistance for introduction to hexaploid lines through direct crossing, using durum wheat as a bridging species and/or through the development of amphiploids. This would allow resistances from each genome to be combined to generate a higher level of resistance than is currently available in hexaploid wheat.     

Identification and validation of root length QTLs for water stress resistance in hexaploid wheat (<Emphasis Type="Italic">Titicum aestivum</Emphasis> L.)

Thorough understanding of the genetic mechanisms governing drought adaptive traits can facilitate drought resistance improvement. This study was conducted to identify chromosome regions harbouring QTLs contributing for water stress resistance in wheat. A RIL mapping population derived from a cross between W7984 (Synthetic) and Opata 85 was phenotyped for root length and root dry weight under water stress and non-stress growing conditions. ANOVA showed highly significant (p ≤ 0.01) variation among the RILs for both traits. Root length and root dry weight showed positive and significant (p ≤ 0.01) phenotypic correlation. Broad sense heritability was 86% for root length under stress and 65% for root dry weight under non-stress conditions. A total of eight root length and five root dry weight QTLs were identified under both water conditions. Root length QTLs Qrln.uwa.1BL, Qrln.uwa.2DS, Qrln.uwa.5AL and Qrln.uwa.6AL combined explained 43% of phenotypic variation under non-stress condition. Opata was the source of favourable alleles for root length QTLs under non-stress condition except for Qrln.uwa.6AL. Four stress specific root length QTLs, Qrls.uwa.1AS, Qrls.uwa.3AL, Qrls.uwa.7BL.1 and Qrls.uwa.7BL.2 jointly explained 47% of phenotypic variation. Synthetic wheat contributed favourable alleles for Qrls.uwa.1AS and Qrls.uwa.3AL. Two stable root dry weight QTLs on chromosomes 4AL and 5AL were consistently found in both water conditions. Three validation populations were developed by crossing cultivars Lang, Yitpi, and Chara with Synthetic W7984 to transfer two of the QTLs identified under stress condition. The F_2.3 and F_3.4 validation lines were phenotyped under the same level of water stress as RILs to examine the effect of these QTLs. There were 13.5 and 14.5% increases in average root length due to the inheritance of Qrls.uwa.1AS and Qrls.uwa.3AL, respectively. The result indicated that closely linked SSR markers Xbarc148 (Qrls.uwa.1AS) and Xgwm391 (Qrls.uwa.3AL) can be incorporated into MAS for water stress improvement in wheat.     

Identification of the <Emphasis Type="Italic">S</Emphasis> locus core sequences determining self-incompatibility and <Emphasis Type="Italic">S</Emphasis> multigene family from draft genome sequences of radish (<Emphasis Type="Italic">Raphanus sativus</Emphasis> L.)

The S core and its flanking sequences were identified from two independent draft genome sequences of radish (Raphanus sativus L.). After gap-filling with PCR, the S core regions and full-length S receptor kinase (SRK) genes from two radish genomes were obtained. Phylogenetic analysis of the SRK genes clearly showed that one S core region belonged to the class I S haplotypes, but the other was included in the class II S haplotypes. Three sequences showing homology with known transposable elements were identified in the core regions, and one intact copia-type long terminal repeat (LTR)-retrotransposon containing a 4125-bp open reading frame (ORF) was identified in the class I S haplotype. A total of 61 genes showing homology with the SRK genes were identified from two draft genome sequences. Among them, the RsKD1 showed the highest homology with the SRK genes. There was 90% nucleotide sequence identity between the RsKD1 and RsSRK1 genes in the kinase domains. The phylogenetic tree of SRK genes and 13 most closely related homologs showed that all homologs were more closely related to the class II SRK genes than to the class I SRKs. Physical mapping of radish SRK-homologous genes and their B. rapa orthologs showed that two radish homologs and their B. rapa orthologs were tightly linked to the SRK genes in radish and B. rapa genomes. Sequence information about multiple SRK-homologs identified in this study would be helpful for designing reliable primer pairs for faithful PCR amplification of the SRK alleles, leading to improvement of the S haplotyping system in radish breeding programs.     

QTL for flag leaf size and their influence on yield-related traits in wheat

Flag leaf-related traits (FLRTs) are determinant traits affecting plant architecture and yield potential in wheat (Triticum aestivum L.). In this study, three related recombinant inbred line (RIL) populations with a common female parent were developed to identify quantitative trait loci (QTL) for flag leaf width (FLW), length (FLL), and area (FLA) in four environments. A total of 31 QTL were detected in four environments. Two QTL for FLL on chromosomes 3B and 4A (QFll-3B and QFll-4A) and one for FLW on chromosome 2A (QFlw-2A) were major stable QTL. Ten QTL clusters (C1–C10) simultaneously controlling FLRTs and yield-related traits (YRTs) were identified. To investigate the genetic relationship between FLRTs and YRTs, correlation analysis was conducted. FLRTs were found to be positively correlated with YRTs especially with kernel weight per spike and kernel number per spike in all the three RIL populations and negatively correlated with spike number per plant. Appropriate flag leaf size could benefit the formation of high yield potential. This study laid a genetic foundation for improving yield potential in wheat molecular breeding programs.     

Allelic composition and associated quality traits of the <Emphasis Type="Italic">Glu-1</Emphasis> and <Emphasis Type="Italic">Glu-3</Emphasis> loci in selected modern Ethiopian durum wheat varieties

Gluten protein determines the processing quality of both durum wheat and bread wheat. The glutenin subunits compositions and associated quality traits of 20 Ethiopian durum wheat varieties were systematically analyzed using SDS-PAGE and Payne numbers. A total of 16 glutenin patterns were identified. At the Glu-A1 locus, all varieties scored the null allele. The predominant glutenin alleles at the Glu-B1 locus were Glu-B1b (7+8) and Glu-B1e (20). In Glu-3, the most abundant glutenin subunits were Glu-A3a and Glu-B3c. Based on the Payne scores, the varieties Yerer, Ginchi, Candate, and Foka were identified to have allelic composition suitable for pasta making. The cluster analysis using agglomerative hierarchical clustering (AHC) method classified the varieties into four similarity classes. Based on the findings of this experiment, suggestions were made for allelic composition improvement through introgression of superior alleles from known Glu-1 and Glu-3 sources.     

Developing and validating microsatellite markers in elephant grass (<Emphasis Type="Italic">Pennisetum purpureum</Emphasis> S.)

Elephant grass [Pennisetum purpureum S.; syn. Cenchrus purpureus (Schumach.) Morrone] is an important global forage crop and is recognized for high yields of herbage with good nutritive value. It also has high biomass potential to be utilized as a biofuel feedstock. Whereas several previous genetic studies adapted simple sequence repeat (SSR) markers from pearl millet [Pennisetum glaucum (L.) R.Br.] for investigations in elephant grass, the present study developed SSR markers from 3536 DNA sequences derived from 16 elephant grass entries. A total of 3866 SSRs were identified including 1028 monomeric, 2019 dimeric, 735 trimeric, 49 tetrameric, 20 pentameric and 15 hexameric repeat motifs. Three hundred and seven sequences contained more than one repeated motif, and 154 SSRs were present in compound formation. Susequenctly,  four elephant grass and two pearl millet genotypes were chosen to validate 727 SSR markers. Of these, 628 markers produced visually detectable amplification products, including 73 (11.6%) polymorphic ones across all six genotypes. Polymorphism between the four elephant grass genotypes was revealed by 316 (50.6%) markers with diversity index values ranging from 0.75 to 0.38. Dimeric SSRs had the highest polymorphic rate (48.7%). These validated SSR markers had 58.6% (368 of 628) transferability rate to pearl millet. The availability of these polymorphic SSR markers will support advanced genetic studies in P. purpureum and its relatives.     

Source of Variation in Flour Protein Quantity and Quality of a Top-Yielding Korean Wheat Cultivar, <Emphasis Type="Italic">Baegjoong</Emphasis> Grown from Different Regions

Korea mainly imports wheat because a relatively little amount (<1.0% of total usage) is produced domestically. Quality variation in domestic wheats is a major challenge for expanding domestic wheat production and end-use applications. Flour is mainly consumed for noodle making in Korea. Baegjoong is one of the most prevalent domestic wheat cultivars. To reduce quality variation of Baegjoong, a baseline data on the current status of Baegjoong quality is required. Therefore, the effect of growing a single cultivar of Korean domestic wheat, Baegjoong grown in different areas on flour quality was explored, mainly focusing on protein properties, which are known more sensitively influenced by growing environments as well as affecting noodle quality. Twenty Baegjoong flour samples milled from wheat grown in Gwangju, Naju, and Chilgok were subjected to proximate analysis, sedimentation volume, glutenin macropolymer, solvent retention capacity (SRC), and mixograph. Flour sample quality variations within each growing region and among growing regions were compared. Protein content, sedimentation volume, SRC value, and mixograph mid-line peak time, value, and width of flour samples showed significant variation among growing regions but much larger variation within growing regions. Although Gwangju and Naju are close, notable flour quality variations existed between the two city groups. Overall, variations in flour quality were larger within regions, compared to those between regions, possibly due to different farming practices. To identify the main cause of quality variations within growing regions and reduce them, a survey of farming practices needs to be conducted.     

Phenotypic variation in root architecture traits and their relationship with eco-geographical and agronomic features in a core collection of tetraploid wheat landraces (<Emphasis Type="Italic">Triticum turgidum</Emphasis> L.)

To obtain varieties with root systems adapted to marginal environments it is necessary to search for new genotypes in genetically diverse materials, such as landraces that are more likely to carry novel alleles for different root features. A core collection of ‘durum’ wheat, including three subspecies (dicoccon, turgidum and durum) from contrasting eco-geographical zones, was evaluated for root traits and shoot weight at the seminal root stage. Distinctive rooting phenotypes were characterized within each subspecies, mainly in subsp. durum. Contrasting rooting types, including large roots with shallow distributions, and others with high root numbers were identified. Correlations with climatic traits showed that root shape is more relevant in adaptation to eco-geographical zones in subsp. dicoccon, whereas in subsp. turgidum and durum, which come from warmer and drier areas, both size and shape of roots could have adaptive roles. Root traits with the largest positive effects on certain yield components under limited water conditions included root diameter in subsp. dicoccon, root size in turgidum, and root number in durum. Additionally, shoot weight at the seedling stage had important effects in subsp. turgidum and durum. Twenty-eight marker–trait associations (MTAs) previously identified in this collection for agronomic or quality traits were associated with seminal root traits. Some markers were associated with only one root trait, but others were associated with up to six traits. These MTAs and the genetic variability characterized for root traits in this collection can be exploited in further work to improve drought tolerance and resource capture in wheat.