Short Arm Of Chromosome 1A Research Articles

Fine mapping and genetic analysis identified a C2H2-type zinc finger as a candidate gene for heading date regulation in wheat.

A minor-effect QTL, Qhd.2AS, that affects heading date in wheat was mapped to a genomic interval of 1.70-Mb on 2AS, and gene analysis indicated that the C2H2-type zinc finger protein gene TraesCS2A02G181200 is the best candidate for Qhd.2AS. Heading date (HD) is a complex quantitative trait that determines the regional adaptability of cereal crops, and identifying the underlying genetic elements with minor effects on HD is important for improving wheat production in diverse environments. In this study, a minor QTL for HD that we named Qhd.2AS was detected on the short arm of chromosome 2A by Bulked Segregant Analysis and validated in a recombinant inbred population. Using a segregating population of 4894 individuals, Qhd.2AS was further delimited to an interval of 0.41cM, corresponding to a genomic region spanning 1.70Mb (from 138.87 to 140.57Mb) that contains 16 high-confidence genes based on IWGSC RefSeq v1.0. Analyses of sequence variations and gene transcription indicated that TraesCS2A02G181200, which encodes a C2H2-type zinc finger protein, is the best candidate gene for Qhd.2AS that influences HD. Screening a TILLING mutant library identified two mutants with premature stop codons in TraesCS2A02G181200, both of which exhibited a delay in HD of 2-4days. Additionally, variations in its putative regulatory sites were widely present in natural accession, and we also identified the allele which was positively selected during wheat breeding. Epistatic analyses indicated that Qhd.2AS-mediated HD variation is independent of VRN-B1 and environmental factors. Phenotypic investigation of homozygous recombinant inbred lines (RILs) and F2:3 families showed that Qhd.2AS has no negative effect on yield-related traits. These results provide important cues for refining HD and therefore improving yield in wheat breeding programs and will deepen our understanding of the genetic regulation of HD in cereal plants.

Genomic location of Gb1, a unique gene conferring wheat resistance to greenbug biotype F

Greenbug (Schizaphis graminum, Rondani) is a serious insect pest in many wheat growing regions and has been infesting cereal crops in the USA for over a century. Continuous occurrence of new greenbug biotypes makes it essential to explore all greenbug resistant sources available to manage this pest. Gb1, a recessive greenbug resistance gene in DS28A, confers resistance to several economically important greenbug biotypes and is the only gene found to be resistant to greenbug biotype F. A set of 174 F2:3 lines from the cross DS28A × Custer was evaluated for resistance to greenbug biotype F in 2020 and 2022. Selective genotyping of the corresponding F2 population using single nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing (GBS) led to the identification of a candidate genomic region for Gb1. Thus, SSR markers previously mapped in this region were used to genotype the entire F2 population, and kompetitive allele specific PCR (KASP) markers were also developed from SNPs in the target region. Gb1 was placed in the terminal region of the short arm of chromosome 1A, and its location was confirmed in a second population derived from the cross DS28A × PI 697274. The combined data analysis from the two mapping populations delimited Gb1 to a < 1 Mb interval between 13,328,200 and 14,241,426 bp on 1AS.

Characterization and Molecular Mapping of a Gene Conferring High-Temperature Adult-Plant Resistance to Stripe Rust Originally from Aegilops ventricosa.

Wheat near-isogenic line AvSYr17NIL carrying Yr17, originally from Aegilops ventricosa for all-stage resistance to Puccinia striiformis f. sp. tritici, also shows nonrace-specific, high-temperature adult-plant (HTAP) resistance to the stripe rust pathogen. To separate and identify the HTAP resistance gene, seeds of AvSYr17NIL were treated with ethyl methanesulfonate. Mutant lines with only HTAP resistance were obtained, and one of the lines, M1225, was crossed with the susceptible recurrent parent Avocet S (AvS). Field responses of the F2 plants and F3 lines, together with the parents, were recorded at the adult-plant stage in Pullman and Mount Vernon, WA under natural P. striiformis f. sp. tritici infection. The parents and the F4 population were phenotyped with a Yr17-virulent P. striiformis f. sp. tritici race in the adult-plant stage under the high-temperature profile in the greenhouse. The phenotypic results were confirmed by testing the F5 population in the field under natural P. striiformis f. sp. tritici infection. The F2 data indicated a single recessive gene, temporarily named YrM1225, for HTAP resistance. The F4 lines were genotyped with Kompetitive allele-specific PCR markers converted from single-nucleotide polymorphism markers polymorphic between M1225 and AvS. The HTAP resistance gene was mapped on the short arm of chromosome 2A in an interval of 7.5 centimorgans using both linkage and quantitative trait locus mapping approaches. The separation of the HTAP resistance gene from Yr17 should improve the understanding and utilization of the different types of resistance.

Genome-wide association mapping of septoria nodorum blotch resistance in Nordic winter and spring wheat collections.

A new QTL for SNB, QSnb.nmbu-2AS, was found in both winter and spring wheat panels that can greatly advance SNB resistance breeding Septoria nodorum blotch (SNB), caused by the necrotrophic fungal pathogen Parastagonospora nodorum, is the dominant leaf blotch pathogen of wheat in Norway. Resistance/susceptibility to SNB is a quantitatively inherited trait, which can be partly explained by the interactions between wheat sensitivity loci (Snn) and corresponding P. nodorum necrotrophic effectors (NEs). Two Nordic wheat association mapping panels were assessed for SNB resistance in the field over three to four years: a spring wheat and a winter wheat panel (n = 296 and 102, respectively). Genome-wide association studies found consistent SNB resistance associated with quantitative trait loci (QTL) on eleven wheat chromosomes, and ten of those QTL were common in the spring and winter wheat panels. One robust QTL on the short arm of chromosome 2A, QSnb.nmbu-2AS, was significantly detected in both the winter and spring wheat panels. For winter wheat, using the four years of SNB field severity data in combination with five years of historical data, the effect of QSnb.nmbu-2AS was confirmed in seven of the nine years, while for spring wheat, the effect was confirmed for all tested years including the historical data from 2014 to 2015. However, lines containing the resistant haplotype are rare in both Nordic spring (4.0%) and winter wheat cultivars (15.7%), indicating the potential of integrating this QTL in SNB resistance breeding programs. In addition, clear and significant additive effects were observed by stacking resistant alleles of the detected QTL, suggesting that marker-assisted selection can greatly facilitate SNB resistance breeding.

Identification and characterization of the novel leaf rust resistance gene Lr81 in wheat.

The novel, leaf rust seedling resistance gene, Lr81, was identified in a Croatian breeding line and mapped to a genomic region of less than 100Kb on chromosome 2AS. Leaf rust, caused by Puccinia triticina, is the most common and widespread rust disease in wheat. Races of Puccinia triticina evolve rapidly in the southern Great Plains of the USA, and leaf rust resistance genes often lose effectiveness shortly after deployment in wheat production. PI 470121, a wheat breeding line developed by the University of Zagreb in Croatia, showed high resistance to Puccinia triticina races collected from Oklahoma, suggesting that PI 470121 could be a leaf rust resistance source for the southern Great Plains of the USA. Genetic analysis based on an F2 population and F2:3 families derived from the cross PI 470121 × Stardust indicated that PI 470121 carries a dominant seedling resistance gene, designated as Lr81. Linkage mapping delimited Lr81 to a genomic region of 96,148bp flanked by newly developed KASP markers Xstars-KASP320 and Xstars-KASP323 on the short arm of chromosome 2A, spanning 67,030,206-67,132,354bp in the Chinese Spring reference assembly (IWGSC RefSeq v1.0). Deletion bin mapping assigned Lr81 to the terminal bin 2AS-0.78-1.00. Allelism tests indicated that Lr81 is a distinctive leaf rust resistance locus with the physical order Lr65-Lr17-Lr81. Marker-assisted selection based on a set of markers closely linked to leaf rust resistance genes in PI 470121 and Stardust enabled identification of a recombinant inbred line RIL92 carrying Lr81 only. Lr81 is a valuable leaf rust resistance source that can be rapidly introgressed into locally adapted cultivars using KASP markers Xstars-KASP320 and Xstars-KASP323.

Genomic Analysis and Delineation of the Tan Spot Susceptibility Locus Tsc1 in Wheat.

The necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr) causes the foliar disease tan spot in both bread wheat and durum wheat. Wheat lines carrying the tan spot susceptibility gene Tsc1 are sensitive to the Ptr-produced necrotrophic effector (NE) Ptr ToxC. A compatible interaction results in leaf chlorosis, reducing yield by decreasing the photosynthetic area of leaves. Developing genetically resistant cultivars will effectively reduce disease incidence. Toward that goal, the production of chlorosis in response to inoculation with Ptr ToxC-producing isolates was mapped in two low-resolution biparental populations derived from LMPG-6 × PI 626573 (LP) and Louise × Penawawa (LouPen). In total, 58 genetic markers were developed and mapped, delineating the Tsc1 candidate gene region to a 1.4 centiMorgan (cM) genetic interval spanning 184 kb on the short arm of chromosome 1A. A total of nine candidate genes were identified in the Chinese Spring reference genome, seven with protein domains characteristic of resistance genes. Mapping of the chlorotic phenotype, development of genetic markers, both for genetic mapping and marker-assisted selection (MAS), and the identification of Tsc1 candidate genes provide a foundation for map-based cloning of Tsc1.

Genome-wide identification of loci modifying spike-branching in tetraploid wheat

Key messageGenetic modification of spike architecture is essential for improving wheat yield. Newly identified loci for the ‘Miracle wheat’ phenotype on chromosomes 1AS and 2BS have significant effects on spike traits.The wheat (Triticum ssp.) inflorescence, also known as a spike, forms an unbranched inflorescence in which the inflorescence meristem generates axillary spikelet meristems (SMs) destined to become sessile spikelets. Previously, we identified the putatively causative mutation in the branched headt (bht) gene (TtBH-A1) of tetraploid wheat (T. turgidum convar. compositum (L.f.) Filat.) responsible for the loss of SM identity, converting the non-branching spike to a branched wheat spike. In the current study, we performed whole-genome quantitative trait loci (QTL) analysis using 146 recombinant inbred lines (RILs) derived from a cross between spike-branching wheat (‘Miracle wheat’) and an elite durum wheat cultivar showing broad phenotypic variation for spike architecture. Besides the previously found gene at the bht-A1 locus on the short arm of chromosome 2A, we also mapped two new modifier QTL for spike-branching on the short arm of chromosome 1A, termed bht-A2, and 2BS. Using biparental mapping population and GWAS in 302 diverse accessions, the 2BS locus was highly associated with coding sequence variation found at the homoeo-allele of TtBH-B1 (bht-B1). Thus, RILs that combined both bht-A1 and bht-B1 alleles showed additive genetic effects leading to increased penetrance and expressivity of the supernumerary spikelet and/or mini-spike formation.

Genome-wide association analysis uncovers stable QTLs for yield and quality traits of spring bread wheat (Triticum aestivum) across contrasting environments

Heat and drought are the foremost abiotic stress factors that significantly diminish both grain yield and quality parameters of bread wheat. Genetic improvement of varieties withstanding such stresses and able to give sufficient grain yield with appropriate quality is very essential. A Genome-wide association study was conducted with 15 K wheat SNP assay for grain yield and quality traits of 189 spring bread wheat genotypes from ICARDA tested at two heat-stressed locations of Dongula and Wad Medani (Sudan) and the drought-stressed location at Marchouch (Morocco). Analysis of variance revealed a significant variation among genotypes for grain yield and quality traits. GWAS with a mixed linear model (MLM) revealed 192 marker-trait associations (MTAs) across the three environments on 17 chromosomes. Highest MTAs were scored for grain yield (50) followed by zeleny sedimentation test (39) and grain protein content (37). Gluten content and alveograph strength scored 29 and 25 MTAs, respectively. The SNP markers RAC875_c24504_119 and BS00063946_51 on chromosome 3B exhibited highly significant and stable MTAs for zeleny sedimentation test across the three environments. The BS00063624_51 marker on chromosome 3B had also revealed a robust and stable MTA for both zeleny sedimentation test and alveograph strength. Highly significant multi-MTAs were detected for grain yield on chromosome 5A and for both grain protein content and gluten content on the short arm of chromosome 1A across the three contrasting environments. The high confidence gene models identified for SNP markers with significant MTAs were involved in encoding genes for various functions including regulating plant growth, development and resistance to both biotic and abiotic stresses. The identified SNP markers with strong MTAs for grain yield and quality traits could potentially applicable for marker-assisted breeding.

Genetic analysis revealed a quantitative trait loci (QTL2A.K) on short arm of chromosome 2A associated with yellow rust resistance in wheat (Triticum aestivum L.)

Yellow rust, caused by Puccinia striiformis, is one of the most devastating diseases in wheat. A synthetic by elite recombinant inbred line (RIL) population derived from a cross, Botnol/Aegilops squarrosa (666)//Kachu was evaluated for yellow rust resistance in two different environments in Mexico. The population was subjected to DArT-seq analysis for an in-depth genetic characterization. A major effect rust resistance QTL (QTL2A.K) explaining up to 45% phenotypic variance was found to be contributed by Kachee, an elite line of International Maize and Wheat Improvement Center (CIMMYT) Mexico. The QTL2A.K was found to be contributed by a segment of 2NS Chromosome of Triticum ventricosum translocated into the short arm of bread wheat chromosome 2A (QTL2A.K). The position of QTL2A.K was confirmed using T. ventricosum specific primer VENTRIUP-LN2. Identified genomic regions are being introgressed in to the popular but susceptible wheat varieties through marker-assisted breeding for enhancing yellow rust resistance.

The Hessian fly recessive resistance gene h4 mapped to chromosome 1A of the wheat cultivar 'Java' using genotyping-by-sequencing.

The recessive Hessian fly resistance gene h4 and flanking SNP markers were located to a 642kb region in chromosome 1A of the wheat cultivar 'Java.' Hessian fly (HF), Mayetiola destructor, is one of the most destructive insect pests in wheat worldwide. The wheat cultivar 'Java' was reported to carry a recessive gene (h4) for HF resistance; however, its chromosome location has not been determined. To map the HF resistance gene in Java, two populations of recombinant inbred lines (RILs) were developed from 'Bobwhite' × Java and 'Overley' × Java, respectively, and were phenotyped for responses to infestation of HF Great Plains biotype. Analysis of phenotypic data from the F1 and the RIL populations confirmed that one recessive gene conditioned HF resistance in Java. Two linkage maps were constructed using single-nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing (GBS). The h4 gene was mapped to the distal end of the short arm of chromosome 1A, which explained 60.4 to 70.5% of the phenotypic variation for HF resistance in the two populations. The GBS-SNPs in the h4 candidate interval were converted into Kompetitive Allele-Specific Polymerase Chain Reaction (KASP) markers to eliminate the missing data points in GBS-SNPs. Using the revised maps with KASP markers, h4 was further located to a 642kb interval (6,635,984-7,277,935bp). The two flanking KASP markers, KASP3299 and KASP1871, as well as four other closely linked KASP markers, may be useful for pyramiding h4 with other HF resistance genes in breeding.

Development of self-fertile deletion homozygous and ditelosomic lines for the long arm of chromosome 2A in common wheat.

Most deletions for the short arm of chromosome 2A (2AS), and the telocentric chromosome for the long arm of chromosome 2A (2AL), are available only in the heterozygous condition in 'Chinese Spring' hexaploid wheat. This is due to the female sterility, and therefore self-sterility, of their homozygotes, caused by the partial or entire loss of the 2AS chromosome arm on which genes for normal synapsis and female fertility are located. On the other hand, a D-genome disomic substitution line 2D(2A) of 'Langdon' tetraploid wheat, in which chromosome 2D is disomically substituted for chromosome 2A, is available (i.e., self-fertile) despite chromosome 2A being missing in this line. This fact indicates that another gene for female fertility must be present in Langdon 2D(2A). We attempted to develop self-fertile 2AS homozygous deletion and ditelosomic 2AL lines by transferring this female fertility gene, through a series of crosses and cytological screening, from Langdon 2D(2A) to the two aneuploid lines. We finally obtained self-fertile 2AS homozygous deletion and ditelosomic 2AL lines. These lines displayed normal meiotic chromosome pairing and lacked all 12 of the 2AS markers used for PCR analysis.

Isolation of wheat mutants with higher grain phenolics to enhance anti-oxidant potential

Present in many plant foods, biogenic phenolic compounds are important bioactive phytonutrients with high anti-oxidant activity and thereby are praised for their health-promoting properties. However, current food nutrient improvement by high phenolic content in staples is limited by the shortage of genetic resources rich in phenolic compounds. To resolve this obstacle, we developed a non-destructive massive analytical approach to screen wheat phenolic mutants. In grains, multiple mutant lines showed significantly higher contents of flavonoids or cell wall-bound phenolic esters. Moreover, five mutants showed higher anti-oxidant potentials in wall-bound phenolic compounds ranging from 15% to 20%, with the maximal close to natural black wheat. In contrast to black wheat, two mutants accumulated higher phenolic compounds in the endosperm. lrf4 was mapped by BSR to a concentrated genomic region in the short arm of chromosome 1A. The present work represents an efficient high-throughput strategy to increase wheat anti-oxidant potential through traditional mutagenesis.

Pm223899, a new recessive powdery mildew resistance gene identified in Afghanistan landrace PI 223899.

A new recessive powdery mildew resistance gene, Pm223899, was identified in Afghanistan wheat landrace PI 223899 and mapped to an interval of about 831Kb in the terminal region of the short arm of chromosome 1A. Wheat powdery mildew, a globally important disease caused by the biotrophic fungus Blumeria graminis f.sp. tritici (Bgt), has occurred with increased frequency and severity in recent years, and some widely deployed resistance genes have lost effectiveness. PI 223899 is an Afghanistan landrace exhibiting high resistance to Bgt isolates collected from the Great Plains. An F2 population and F2:3 lines derived from a cross between PI 223899 and OK1059060-126135-3 were evaluated for response to Bgt isolate OKS(14)-B-3-1, and the bulked segregant analysis (BSA) approach was used to map the powdery mildew resistance gene. Genetic analysis indicated that a recessive gene, designated Pm223899, conferred powdery mildew resistance in PI 223899. Linkage analysis placed Pm223899 to an interval of about 831Kb in the terminal region of chromosome 1AS, spanning 4,504,697-5,336,062bp of the Chinese Spring reference sequence. Eight genes were predicted in this genomic region, including TraesCS1AG008300 encoding a putative disease resistance protein RGA4. Pm223899 was flanked proximally by a SSR marker STARS333 (1.4cM) and distally by the Pm3 locus (0.3cM). One F2 recombinant was identified between Pm3 and Pm223899 using a Pm3b-specific marker, indicating that Pm223899 is most likely a new gene, rather than an allele of the Pm3 locus. Pm223389 confers a high level of resistance to Bgt isolates collected from Pennsylvania, Oklahoma, Nebraska, and Montana. Therefore, Pm223389 can be used to enhance powdery mildew resistance in these states. Pm3b-1 and STARS333 have the potential to tag Pm223389 in wheat breeding.

Combination of all-stage and high-temperature adult-plant resistance QTL confers high-level, durable resistance to stripe rust in winter wheat cultivar Madsen.

Wheat cultivar Madsen has a new gene on the short arm of chromosome 1A and two QTL for all-stage resistance and three QTL for high-temperature adult-plant resistance that in combination confer high-level, durable resistance to stripe rust. Wheat cultivar Madsen has maintained a high-level resistance to stripe rust over 30years. To map quantitative trait loci (QTL) underlying the high-level, durable resistance, 156 recombinant inbred lines (RILs) developed from cross Avocet S × Madsen were phenotyped with selected races of Puccinia striiformis f. sp. tritici in the greenhouse seedling tests, and in naturally infected fields during 2015-2017. The RILs were genotyped by SSR and SNP markers from genotyping by sequencing and the 90K wheat SNP chip. Three QTL for all-stage resistance were mapped on chromosomes 1AS, 1BS and 2AS, and two QTL for high-temperature adult-plant (HTAP) resistance were mapped on 3BS and 6BS. The most effective QTL on 2AS, explaining 8.97-23.10% of the phenotypic variation in seedling tests and 8.60-71.23% in field tests, contained Yr17 for all-stage resistance and an additional gene for HTAP resistance. The 6BS QTL, detected in all field tests, was identified as Yr78. The 1AS QTL, conferring all-stage resistance, was identified as a new gene, which explained 20.45 and 30.23% of variation in resistance to races PSTv-37 and PSTv-40, respectively, and contributed significantly to field resistance at Pullman in 2015-2017, but was not detected at Mount Vernon. The interactions among QTL were mostly additive, and RILs with all five QTL had the highest level of resistance in the field, similar to Madsen. Genotyping 148 US Pacific Northwest wheat cultivars with markers for the 1AS, 2AS and 6BS QTL validated the genes and markers, and indicated their usefulness for marker-assisted selection.

Novel and favorable genomic regions for spike related traits in a wheat germplasm Pubing 3504 with high grain number per spike under varying environments

Grain number per spike (GNPS) is a major factor in wheat yield breeding. A new wheat germplasm Pubing 3504 shows superior features in spike traits. To elucidate the genetic basis of spike and yield related traits in Pubing 3504, 282 F2:3 families were generated from the cross Pubing 3504×Jing 4839, and seven spike and yield related traits, including GNPS, spike length (SL), kernel number per spikelet (KPS), spikelet number per spike (SNS), thousand-grain weight (TGW), spike number per plant (SNP), and plant height (HT) were investigated. Correlation analysis indicated significant positive correlations between GNPS and spike-related traits, including KPS, SNS, and SL, especially KPS. A genetic map was constructed using 190 polymorphic simple sequence repeat (SSR), expressed sequence tag (EST)-SSR, and sequence-tagged-site (STS) markers. For the seven traits measured, a total of 37 quantitative trait loci (QTLs) in a single-environment analysis and 25 QTLs in a joint-environment analysis were detected. Additive effects of 70.3% (in a single environment) and 57.6% (in a joint environment) of the QTLs were positively contributed by Pubing 3504 alleles. Five important genomic regions on chromosomes 1A, 4A, 4B, 2D, and 4D could be stably detected in different environments. Among these regions, the marker interval Xmag834–Xbarc83 on the short arm of chromosome 1A was a novel important genomic region that included QTLs controlling GNPS, KPS, SNS, TGW, and SNP with stable environmental repeatability. This genomic region can improve the spike trait and may play a key role in improving wheat yield in the future. We deduced that this genomic region was vital to the high GNPS of Pubing 3504.

Microsatellite mapping of the loci for false glume and semi-compact spike in Triticum L.

The “false glume” is an extra glume between the glume and lemma of the outer florets of each spikelet. The “false glume” phenotype was found in tetraploid wheat Triticum durum Desf. (2n = 4x = 28, genome BBAuAu) ‘Sharik’ and a Chernobyl radio mutant (‘UKR-1’) of hexaploid wheat T. aestivum L. (2n = 6x = 42, genome BBAuAuDD). The spikes of Sharik and UKR-1 were semi-compact; suggesting homoeoallelism or allelism at the false glume and semi-compact spike loci, which are specific to diploid wheat T. sinskajae A. Filat. et Kurkiev (2n = 2x = 14, genome AmAm). The objective of this study was to map the novel mutant genes for false glume and semi-compact spike in T. aestivum, T. durum and T. sinskajae, and to assess homoeologous relationship in genus Triticum L. by using molecular markers. It was evident that the gene false glume (fg) and semi-compact spike genes were linked in the F2 of UKR-1/T. aestivum ‘Novosibirskaya 67’, F2 of Sharik/T. durum ‘LD222’ and F2 of T. sinskajae k-48993/T. monococcum L. (2n = 2x = 14, genome AmAm) CItr 13962. The segregation analyses confirmed that the semi-compact spike locus (sc1) in Sharik was allelic to the sc1 locus in UKR-1, whereas neither loci were allelic to the C locus on chromosome 2D or the Cp locus on chromosome 5A. The sc1 gene and fg gene were bracketed by Xgwm372 and Xgwm312 in the F2 of Sharik/LD222, and by Xgwm372 and Xwmc644 in the F2 of UKR-1/N67. The sog gene for semi-compact spike of T. sinskajae, and fg genes were bracketed by Xgwm558 and Xwmc644 in the F2 of k-48993/CItr 13962. It was concluded that the semi-compact and spike false glume genes in T. sinskajae, T. durum and T. aestivum were determined by homoeoalleles in the short arm of chromosome 2A.

Molecular mapping of stripe rust resistance gene YrHu derived from Psathyrostachys huashanica

Wheat stripe rust is a destructive disease that affects most wheat-growing areas worldwide. Resistance genes from related species and genera add to the genetic diversity available to wheat breeding programs. The stripe rust-resistant introgression line H9020-17-25-6-4 was developed from a cross of resistant Psathyrostachys huashanica with the susceptible wheat cultivar 7182. H9020-17-25-6-4 is resistant to all existing Chinese stripe rust races, including the three most widely virulent races, CYR32, CYR33, and V26. We attempted to characterize this new line by genomic in situ hybridization (GISH) and genetic analysis. GISH using P. huashanica genomic DNA as a probe indicated that the translocated segment was too small to be detected. Genetic analysis involving F1, F2, and F2:3 materials derived from a cross of Mingxian 169 and H9020-17-25-6-4 indicated that a single dominant gene from H9020-17-25-6-4, temporarily designated YrHu, conferred resistance to CYR29 and CYR33. A genetic map consisting of four simple sequence repeat, two sequence-tagged site (STS), and two sequence-related amplified polymorphism markers was constructed. YrHu was located on the short arm of chromosome 3A and was about 0.7 and 1.5 cM proximal to EST-STS markers BG604577 and BE489244, respectively. Both the gene and the closely linked markers could be used in marker-assisted selection.

Genetic analysis of glume hairiness (Hg) gene in bread wheat (Triticum aestivum L.)

Hairiness is a common character in planta. Glume hairiness (Hg) is present in the full spectrum of bread wheat and its close relatives and was mainly studied in phenotypic diversity, species evolution, and mapping as a morphological marker. Previous studies indicated that Hg was controlled by a single dominant gene Hg on the short arm of chromosome 1A. However, to date, systematic and comprehensive study of Hg is not available; and markers flanking Hg were rather limited as well, hindering the fine mapping and even cloning of this gene. In the study reported here, aiming at genetically analyze Hg gene systematically, a linkage map of a recombinant inbred line (RIL) generated from the cross between the Tibetan semi-wild wheat (Triticum aestivum subsp. tibetanum Shao) Q1028 and a cultivated wheat Zhengmai 9023 (ZM9023) was constructed using diversity array technology (DArT) and reported simple sequence repeat (SSR) markers. Five SSR markers (saufc2, saufc9, saufc17, saufc25, saufc90) were further developed to accurately locate Hg in this study. Of these five SSR markers all linked to Hg, saufc2 was genetically most closed to Hg with a distance of 1.6 cM. The effectiveness of the five newly developed SSR markers were validated in another RIL derived from Q1028 and a cultivated line 99E18. To our knowledge, this is the first report on fine mapping of Hg in bread wheat. The accurate localization of the Hg and the development of the markers flanked it should facilitate the cloning of this gene and further the study of its possible physiological function in bread wheat.

Toward a better understanding of the genomic region harboring Fusarium head blight resistance QTL Qfhs.ndsu-3AS in durum wheat.

New molecular markers were developed and mapped to the FHB resistance QTL region in high resolution. Micro-collinearity of the QTL region with rice and Brachypodium was revealed for a better understanding of the genomic region. The wild emmer wheat (Triticum dicoccoides)-derived Fusarium head blight (FHB) resistance quantitative trait locus (QTL) Qfhs.ndsu-3AS previously mapped to the short arm of chromosome 3A (3AS) in a population of recombinant inbred chromosome lines (RICLs). This study aimed to attain a better understanding of the genomic region harboring Qfhs.ndsu-3AS and to improve the utility of the QTL in wheat breeding. Micro-collinearity of the QTL region with rice chromosome 1 and Brachypodium chromosome 2 was identified and used for marker development in saturation mapping. A total of 42 new EST-derived sequence tagged site (STS) and simple sequence repeat (SSR) markers were developed and mapped to the QTL and nearby regions on 3AS. Further comparative analysis revealed a complex collinearity of the 3AS genomic region with their collinear counterparts of rice and Brachypodium. Fine mapping of the QTL region resolved five co-segregating markers (Xwgc1186/Xwgc716/Xwgc1143/Xwgc501/Xwgc1204) into three distinct loci proximal to Xgwm2, a marker previously reported to be closely linked to the QTL. Four other markers (Xwgc1226, Xwgc510, Xwgc1296, and Xwgc1301) mapped farther proximal to the above markers in the QTL region with a higher resolution. Five homozygous recombinants with shortened T. dicoccoides chromosomal segments in the QTL region were recovered by molecular marker analysis and evaluated for FHB resistance. Qfhs.ndsu-3AS was positioned to a 5.2cM interval flanked by the marker Xwgc501 and Xwgc510. The recombinants containing Qfhs.ndsu-3AS and new markers defining the QTL will facilitate utilization of this resistance source in wheat breeding.

Genome-Wide Mapping of Spike-Related and Agronomic Traits in a Common Wheat Population Derived from a Supernumerary Spikelet Parent and an Elite Parent.

In wheat, exotic genotypes harbor a broad range of spike-related traits, and can be used as a source of new genes for germplasm enhancement in wheat breeding programs. In the present study, a population of 163 recombinant inbred lines was derived from a cross between an elite line (WCB414) and an exotic line (WCB617) with branched spike (supernumerary spikelet; SS) head morphology. The population was evaluated over four to six environments to identify quantitative trait loci (QTL) associated with nine spike-related traits and 10 agronomic traits. A genetic map consisting of 939 diversity arrays technology (DArT) markers was constructed. Composite interval mapping identified a total of 143 QTL located on 17 different wheat chromosomes and included 33 consistent and definitive QTL. The amount of phenotype variation explained (PVE) by individual QTL ranged from 0.61 to 91.8%. One major QTL for glume pubescence was located in a QTL-rich region on the short arm of chromosome 1A, where loci for other traits such as for kernels per spike (KS) and spike length (SL) were also identified. Similarly, a cluster of QTL associated with yield-related, agronomic and spike-related traits contributing up to 40.3% of PVE was found on the short arm of chromosome 2D, in the vicinity of a major QTL for SS-related traits. Consistent and major QTL identified in the present study may be useful in marker-assisted breeding programs to facilitate transfer of desirable alleles into other germplasm. Desirable QTL alleles were also contributed by the exotic line, suggesting the possibility of enriching the breeding germplasm with alleles from SS genotypes.