Molecular detection of Lophopyrum chromatin in wheat-Lophopyrum recombinants and their use in the physical mapping of chromosome 7D

Genotyping-by-sequencing uncovers a Thinopyrum 4StS·1JvsS Robertsonian translocation linked to multiple stress tolerances in bread wheat

KEYMESSAGE

GBS read coverage analysis identified a Robertsonian chromosome from two Thinopyrum subgenomes in wheat, conferring leaf and stripe rust resistance, drought tolerance, and maintaining yield stability. Agropyron glael (GLAEL), a Thinopyrum intermedium × Th. ponticum hybrid, serves as a valuable genetic resource for wheat improvement. Despite its potential, limited knowledge of its chromosome structure and homoeologous relationships with hexaploid wheat (Triticum aestivum) has restricted the full exploitation of GLAEL's genetic diversity in breeding programs. Here, we present the development of a 44-chromosome wheat/GLAEL addition line (GLA7). Multicolor genomic in situ hybridization identified one chromosome arm from the St subgenome of Th. intermedium, while the other arm remained unclassified. Genotyping-by-sequencing (GBS) read coverage analysis revealed a unique Robertsonian translocation between two distinct Thinopyrum subgenomes, identified as 4StS·1JvsS. The GLA7 line demonstrated strong adult plant resistance to both leaf rust and stripe rust under natural and artificial infection conditions. Automated phenotyping of shoot morphological parameters together with leaf relative water content and yield components showed that the GLA7 line exhibited elevated drought tolerance compared to parental wheat genotypes. Three years of field trials showed that GLA7 exhibits similar agronomic performance and yield components to the wheat parents. This unique addition line holds promise for enhancing wheat's tolerance to multiple stresses through the introduction of new resistance genes, as well as its ability to mitigate the effects of temporary water limitation during flowering, all without negatively impacting wheat performance.

Genetic mapping of the wheat leaf rust resistance gene Lr19 and development of translocation lines to break its linkage with yellow pigment

KEY MESSAGE

The leaf rust resistance gene Lr19, which is present on the long arm of chromosome 7E1 in Thinopyrum ponticum, was mapped within a 0.3-cM genetic interval, and translocation lines were developed to break its linkage with yellow pigmentation The leaf rust resistance locus Lr19, which was transferred to wheat (Triticum aestivum) from its relative Thinopyrum ponticum in 1966, still confers broad resistance to most known races of the leaf rust pathogen Puccinia triticina (Pt) worldwide. However, this gene has not previously been fine-mapped, and its tight linkage with a gene causing yellow pigmentation has limited its application in bread wheat breeding. In this study, we genetically mapped Lr19 using a bi-parental population from a cross of two wheat-Th. ponticum substitution lines, the Lr19-carrying line 7E1(7D) and the leaf rust-susceptible line 7E2(7D). Genetic analysis of the F2 population and the F2:3 families showed that Lr19 was a single dominant gene. Genetic markers allowed the gene to be mapped within a 0.3-cM interval on the long arm of Th. ponticum chromosome 7E1, flanked by markers XsdauK3734 and XsdauK2839. To reduce the size of the Th. ponticum chromosome segment carrying Lr19, the Chinese Spring Ph1b mutant was employed to promote recombination between the homoeologous chromosomes of the wheat chromosome 7D and the Th. ponticum chromosome 7E1. Two translocation lines with short Th. ponticum chromosome fragments carrying Lr19 were identified using the genetic markers closely linked to Lr19. Both translocation lines were resistant to 16 Pt races collected throughout China. Importantly, the linkage between Lr19 and yellow pigment content was broken in one of the lines. Thus, the Lr19 linked markers and translocation lines developed in this study are valuable resources in marker-assisted selection as part of common wheat breeding programs.

Physical mapping of a new powdery mildew resistance locus from Thinopyrum ponticum chromosome 4AgS

Thinopyrum ponticum (Podp.) Barkworth and D.R. Dewey is a decaploid species that has served as an important genetic resource for improving wheat for the better part of a century. The wheat-Th. ponticum 4Ag (4D) disomic substitution line Blue 58, which was obtained following the distant hybridization between Th. ponticum and common wheat, has been stably resistant to powdery mildew under field conditions for more than 40 years. The transfer of 4Ag into the susceptible wheat cultivar Xiaoyan 81 resulted in powdery mildew resistance, indicating the alien chromosome includes the resistance locus. Irradiated Blue 58 pollen were used for the pollination of the recurrent parent Xiaoyan 81, which led to the development of four stable wheat-Th. ponticum 4Ag translocation lines with diverse alien chromosomal segments. The assessment of powdery mildew resistance showed that translocation line L1 was susceptible, but the other three translocation lines (WTT139, WTT146, and WTT323) were highly resistant. The alignment of 81 specific-locus amplified fragments to the Th. elongatum genome revealed that 4Ag originated from a group 4 chromosome. The corresponding physical positions of every 4Ag-derived fragment were determined according to a cytogenetic analysis, the amplification of specific markers, and a sequence alignment. Considering the results of the evaluation of disease resistance, the Pm locus was mapped to the 3.79-97.12 Mb region of the short arm of chromosome 4Ag. Because of its durability, this newly identified Pm locus from a group 4 chromosome of Th. ponticum may be important for breeding wheat varieties with broad-spectrum disease resistance.

Cytogenetic and genomic characterization of a novel tall wheatgrass-derived Fhb7 allele integrated into wheat B genome

We identified and integrated the novel FHB-resistant Fhb7^The2 allele into wheat B genome and made it usable in both common and durum wheat breeding programs without yellow flour linkage drag. A novel tall wheatgrass-derived (Thinopyrum elongatum, genome EE) Fhb7 allele, designated Fhb7^The2, was identified and integrated into the wheat B genome through a small 7B-7E translocation (7BS·7BL-7EL) involving the terminal regions of the long arms. Fhb7^The2 conditions significant Type II resistance to Fusarium head blight (FHB) in wheat. Integration of Fhb7^The2 into the wheat B genome makes this wild species-derived FHB resistance gene usable for breeding in both common and durum wheat. By contrast, other Fhb7 introgression lines involving wheat chromosome 7D can be utilized only in common wheat breeding programs, not in durum wheat. Additionally, we found that Fhb7^The2 does not have the linkage drag of the yellow flour pigment gene that is tightly linked to the decaploid Th. ponticum-derived Fhb7 allele Fhb7^Thp. This will further improve the utility of Fhb7^The2 in wheat breeding. DNA sequence analysis identified 12 single nucleotide polymorphisms (SNPs) in Fhb7^The2, Fhb7^Thp, and another Th. elongatum-derived Fhb7 allele Fhb7^The1, which led to seven amino acid conversions in Fhb7^The2, Fhb7^Thp, and Fhb7^The1, respectively. However, no significant variation was observed in their predicted protein configuration as a glutathione transferase. Diagnostic DNA markers were developed specifically for Fhb7^The2. The 7EL segment containing Fhb7^The2 in the translocation chromosome 7BS·7BL-7EL exhibited a monogenic inheritance pattern in the wheat genetic background. This will enhance the efficacy of marker-assisted selection for Fhb7^The2 introgression, pyramiding, and deployment in wheat germplasm and varieties.

Genome-Wide Association Studies for Fusarium Head Blight Resistance and Its Trade-Off With Grain Yield in Soft Red Winter Wheat

Identification of quantitative trait loci for Fusarium head blight (FHB) resistance from different sources and pyramiding them into cultivars could provide effective protection against FHB. The objective of this study was to characterize a soft red winter wheat (SRWW) breeding population that has been subjected to intense germplasm introduction and alien introgression for FHB resistance in the past. The population was evaluated under misted FHB nurseries inoculated with Fusarium graminearum-infested corn spawn for two years. Phenotypic data included disease incidence (INC), disease severity (SEV), Fusarium damaged kernels (FDK), FHB index (FHBdx), and deoxynivalenol concentration (DON). Genome-wide association studies using 13,784 SNP markers identified 25 genomic regions at -logP ≥ 4.0 that were associated with five FHB-related traits. Of these 25, the marker trait associations that explained more than 5% phenotypic variation were localized on chromosomes 1A, 2B, 3B, 5A, 7A, 7B, and 7D, and from diverse sources including adapted SRWW lines such as Truman and Bess, and unadapted common wheat lines such as Ning7840 and Fundulea 201R. Furthermore, individuals with favorable alleles at the four loci Fhb1, Qfhb.nc-2B.1 (Q_2B.1), Q_7D.1, and Q_7D.2 showed better FDK and DON scores (but not INC, SEV, and FHBdx) compared with other allelic combinations. Our data also showed while pyramiding multiple loci provides protection against FHB disease, it has a significant trade-off with grain yield.

Chromosomal composition analysis and molecular marker development for the novel Ug99-resistant wheat-Thinopyrum ponticum translocation line WTT34

A novel Ug99-resistant wheat-Thinopyrum ponticum translocation line was produced, its chromosomal composition was analyzed and specific markers were developed. Stem rust caused by Puccinia graminis f. sp. tritici Eriks. & E. Henn (Pgt) has seriously threatened global wheat production since Ug99 race TTKSK was first detected in Uganda in 1998. Thinopyrum ponticum is near immune to Ug99 races and may be useful for enhancing wheat disease resistance. Therefore, developing new wheat-Th. ponticum translocation lines that are resistant to Ug99 is crucial. In this study, a novel wheat-Th. ponticum translocation line, WTT34, was produced. Seedling and field evaluation revealed that WTT34 is resistant to Ug99 race PTKST. The resistance was derived from the alien parent Th. ponticum. Screening WTT34 with markers linked to Sr24, Sr25, Sr26, Sr43, and SrB resulted in the amplification of different DNA fragments from Th. ponticum, implying WTT34 carries at least one novel stem rust resistance gene. Genomic in situ hybridization (GISH), multicolor fluorescence in situ hybridization (mc-FISH), and multi-color GISH (mc-GISH) analyses indicated that WTT34 carries a T5DS·5DL-Th translocation, which was consistent with wheat660K single-nucleotide polymorphism (SNP) array results. The SNP array also uncovered a deletion event in the terminal region of chromosome 1D. Additionally, the homeology between alien segments and the wheat chromosomes 2A and 5D was confirmed. Furthermore, 51 PCR-based markers derived from the alien segments of WTT34 were developed based on specific-locus amplified fragment sequencing (SLAF-seq). These markers may enable wheat breeders to rapidly trace Th. ponticum chromosomal segments carrying Ug99 resistance gene(s).

Cytogenetic mapping of a major locus for resistance to Fusarium head blight and crown rot of wheat on Thinopyrum elongatum 7EL and its pyramiding with valuable genes from a Th. ponticum homoeologous arm onto bread wheat 7DL

A major locus for resistance to different Fusarium diseases was mapped to the most distal end of Th. elongatum 7EL and pyramided with Th. ponticum beneficial genes onto wheat 7DL. Perennial Triticeae species of the Thinopyrum genus are among the richest sources of valuable genes/QTL for wheat improvement. One notable and yet unexploited attribute is the exceptionally effective resistance to a major wheat disease worldwide, Fusarium head blight, associated with the long arm of Thinopyrum elongatum chromosome 7E (7EL). We targeted the transfer of the temporarily designated Fhb-7EL locus into bread wheat, pyramiding it with a Th. ponticum 7el₁L segment stably inserted into the 7DL arm of wheat line T4. Desirable genes/QTL mapped along the T4 7el₁L segment determine resistance to wheat rusts (Lr19, Sr25) and enhancement of yield-related traits. Mapping of the Fhb-7EL QTL, prerequisite for successful pyramiding, was established here on the basis of a bioassay with Fusarium graminearum of different 7EL-7el₁L bread wheat recombinant lines. These were obtained without resorting to any genetic pairing promotion, but relying on the close 7EL-7el₁L homoeology, resulting in 20% pairing frequency between the two arms. Fhb-7EL resided in the telomeric portion and resistant recombinants could be isolated with useful combinations of more proximally located 7el₁L genes/QTL. The transferred Fhb-7EL locus was shown to reduce disease severity and fungal biomass in grains of infected recombinants by over 95%. The same Fhb-7EL was, for the first time, proved to be effective also against F. culmorum and F. pseudograminearum, predominant agents of crown rot. Prebreeding lines possessing a suitable 7EL-7el₁L gene/QTL assembly showed very promising yield performance in preliminary field tests.

McGISH identification and phenotypic description of leaf rust and yellow rust resistant partial amphiploids originating from a wheat × Thinopyrum synthetic hybrid cross

A Thinopyrum intermedium × Thinopyrum ponticum synthetic hybrid wheatgrass is an excellent source of leaf and stem rust resistance produced by N.V.Tsitsin. Wheat line Mv9kr1 was crossed with this hybrid (Agropyron glael) in Hungary in order to transfer its advantageous agronomic traits into wheat. As the wheat parent was susceptible to leaf rust, the transfer of resistance was easily recognizable in the progenies. Three different partial amphiploid lines with leaf rust resistance were selected from the wheat/Thinopyrum hybrid derivatives by multicolour genomic in situ hybridization. Chromosome counting on the partial amphiploids revealed 58 chromosomes (18 wheatgrass) in line 194, 56 (14 wheatgrass) in line 195 and 54 (12 wheatgrass) in line 196. The wheat chromosomes present in these lines were identified and the wheatgrass chromosomes were characterized by fluorescence in situ hybridization using the repetitive DNA probes Afa-family, pSc119.2 and pTa71. The 3D wheat chromosome was missing from the lines. Molecular marker analysis showed the presence of the Lr24 leaf rust resistance gene in lines 195 and 196. The morphological traits were evaluated in the field during two consecutive seasons in two different locations.

High-density mapping of the major FHB resistance gene Fhb7 derived from Thinopyrum ponticum and its pyramiding with Fhb1 by marker-assisted selection

Wheat lines with shortened Th. ponticum chromatin carrying Fhb7 and molecular markers linked to Fhb7 will accelerate the transfer of Fhb7 to breeding lines and provide an important resource for future map-based cloning of this gene. Fusarium head blight is a major wheat disease globally. A major FHB resistance gene, designated as Fhb7, derived from Thinopyrum ponticum, was earlier transferred to common wheat, but was not used in wheat breeding due to linkage drag. The aims of this study were to (1) saturate this FHB resistance gene region; (2) develop and characterize secondary translocation lines with shortened Thinopyrum segments carrying Fhb7 using ph1b; (3) pyramid Fhb7 and Fhb1 by marker-assisted selection. Fhb7 was mapped in a 1.7 cM interval that was flanked by molecular markers XsdauK66 and Xcfa2240 with SSR, diversity arrays technology, EST-derived and conserved markers. KS24-2 carrying Fhb7 was analyzed with molecular markers and genomic in situ hybridization, confirming it was a 7DS.7el2L Robertsonian translocation. To reduce the Thinopyrum chromatin segments carrying Fhb7, a BC1F2 population (Chinese Spring ph1bph1b*2/KS24-2) was developed and genotyped with the markers linked to Fhb7. Two new translocation lines (SDAU1881 and SDAU1886) carrying Fhb7 on shortened alien segments (approximately 16.1 and 17.3% of the translocation chromosome, respectively) were developed. Furthermore, four wheat lines (SDAU1902, SDAU1903, SDAU1904, and SDAU1906) with the pyramided markers flanking Fhb1 and Fhb7 were developed and the FHB responses indicated lines with mean NDS ranging from 1.3 to 1.6 had successfully combined Fhb7 and Fhb1. Three new molecular markers associated with Fhb7 were identified and validated in 35 common wheat varieties. The translocation lines with shortened alien segments carrying Fhb7 (and Fhb1) and the markers closely linked to Fhb7 will be useful for improving wheat scab resistance.

Resistance to the Ug99 Race Group of Puccinia graminis f. sp. tritici in Wheat-Intra/intergeneric Hybrid Derivatives

New races of Puccinia graminis f. sp. tritici, the causal agent of stem rust, threaten global wheat production. In particular, races belonging to the Ug99 race group significantly contribute to yield loss in several African nations. Genetic resistance remains the most effective means of controlling this disease. A collection of 546 wheat-intra- and intergeneric hybrids developed by W. J. Sando (United States Department of Agriculture, Beltsville, MD) was screened with eight races of P. graminis f. sp. tritici, including races TTKSK, TTKST, TTTSK, TRTTF, TTTTF, TPMKC, RKQQC, and QTHJC. There were 152 accessions resistant to one or more races and 29 accessions resistant to TTKSK, TTKST, and TTTSK. Of these 29 accessions, 9 were resistant to all races, 14 had infection type patterns that were indistinguishable from cultivars possessing Sr9h and Sr42, 2 were indistinguishable from accessions with SrTmp, and 4 did not display resistant patterns of accessions with any known Sr gene. Three accessions (604981, 605286, and 611932) characterized cytogenetically were disomic substitution lines, each with a single Thinopyrum ponticum chromosome pair. One accession (606057) was a disomic substitution or addition line with two pairs of T. ponticum chromosomes. In total, seven accessions are postulated to contain novel stem rust resistance genes. This research indicates the value of extant collections of wheat-intergeneric hybrids as sources of disease resistance genes.

Molecular and Cytological Comparisons of Chromosomes 7el₁, 7el₂, 7E(e), and 7E ⁱ Derived from Thinopyrum

Thinopyrum chromosomes 7el1, 7el2, 7E(e), and 7E(i), homoeologous to group 7 chromosomes of common wheat (Triticum aestivum), were determined to have many useful agronomical traits for wheat improvement. To analyze the genetic relationships among the 4 Thinopyrum 7E chromosomes, the conserved orthologous set markers, genomic in situ hybridization (GISH), and meiotic chromosome pairing were used in this study. The unweighted pair-group method with arithmetical averages (UPGMA) analysis indicated that 7el1, derived from T. ponticum, and 7E(i), derived from T. intermedium, were the most closely related. 7el2, derived from T. ponticum, was relatively distant from the 7el1-7E(i) complex. While 7E(e), derived from T. elongatum, was more distantly related to 7el1, 7el2, and 7E(i). This is the first report showing that 7el1 and 7E(i) may be similar, which could be explained by the similar chromosome signal distribution revealed by GISH as well as UPGMA analysis revealed by both molecular markers and the highest frequency of meiotic pairing. The newly developed genome-specific molecular markers may be useful for marker-assisted selection of Lr19, Bdv3, and Fhblop.

Development and characterization of wheat lines carrying stem rust resistance gene Sr43 derived from Thinopyrum ponticum

Wheat lines carrying Ug99-effective stem rust resistance gene Sr43 on shortened alien chromosome segments were produced using chromosome engineering, and molecular markers linked to Sr43 were identified for marker-assisted selection. Stem rust resistance gene Sr43, transferred into common wheat (Triticum aestivum) from Thinopyrum ponticum, is an effective gene against stem rust Ug99 races. However, this gene has not been used in wheat breeding because it is located on a large Th. ponticum 7el(2) chromosome segment, which also harbors genes for undesirable traits. The objective of this study was to eliminate excessive Th. ponticum chromatin surrounding Sr43 to make it usable in wheat breeding. The two original translocation lines KS10-2 and KS24-1 carrying Sr43 were first analyzed using simple sequence repeat (SSR) markers and florescent genomic in situ hybridization. Six SSR markers located on wheat chromosome arm 7DL were identified to be associated with the Th. ponticum chromatin in KS10-2 and KS24-1. The results confirmed that KS24-1 is a 7DS·7el(2)L Robertsonian translocation as previously reported. However, KS10-2, which was previously designated as a 7el(2)S·7el(2)L-7DL translocation, was identified as a 7DS-7el(2)S·7el(2)L translocation. To reduce the Th. ponticum chromatin carrying Sr43, a BC(2)F(1) population (Chinese Spring//Chinese Spring ph1bph1b*2/KS10-2) containing ph1b-induced homoeologous recombinants was developed, tested with stem rust, and genotyped with the six SSR markers identified above. Two new wheat lines (RWG33 and RWG34) carrying Sr43 on shortened alien chromosome segments (about 17.5 and 13.7 % of the translocation chromosomes, respectively) were obtained, and two molecular markers linked to Sr43 in these lines were identified. The new wheat lines with Sr43 and the closely linked markers provide new resources for improving resistance to Ug99 and other races of stem rust in wheat.

A physical map of the Thinopyrum-derived Lr19 translocation

Twenty-nine lines with deletions in the Lr19 ('Indis') translocated chromosome segment were used to physically map three Thinopyrum RFLP loci as well as the Sr25 and Sd1 loci. From the data, the relative locations of marker loci on the translocation were determined as: Sd1, Xpsr165, Xpsr105, Xps129, Lr19, Wsp-D1, Sr25/Y. The data confirmed the reported homoeology between the Lr19 segment and chromosome arm 7DL of wheat. Also, it seems that the Lr19 translocation in 'Indis' is very similar to the Lr19 segment in the T4 source and that the former may not derive from Thinopyrum distichum. Key words : deletion mapping, leaf rust resistance.

Molecular markers for four leaf rust resistance genes introgressed into wheat from wild relatives

Near-isolines carrying four different genes for resistance to leaf rust were used to find linked molecular markers for these genes. Clones used to detect polymorphism were selected on the basis of the reported chromosomal location of the resistance genes. Both Lophopyron-derived resistance genes, Lr19 and Lr24, cosegregated with eight molecular markers assigned to chromosomes 7DL and 3DL, respectively. One clone cosegregated with Lr9 and two closely linked RFLP markers were found for Lr32, mapping at 3.3 +/- 2.6 and 6.9 +/- 3.6 cM from the resistance gene. The Lophopyron-chromatin segment in isolines carrying chromosomes 7E (Lr19) and 3E (Lr24) replaced a large portion of chromosome 7D and the distal portion of chromosome 3D, respectively. Clones assigned to these chromosomes on the basis of aneuploid analysis hybridized to 7E and 3E segments, thus confirming cytological results that these introgressed segments represent homoeologous chromosomes. The linked RFLP markers could be used to identify the resistance genes and generate new combinations in breeding populations, especially in the absence of disease in the environment or when virulence is lacking.

Identification, mapping, and application of polymorphic DNA associated with resistance gene Pm21 of wheat

A new powdery mildew resistance gene designated Pm21, from Haynaldia villosa, a relative of wheat, has been identified and incorporated into wheat through an alien translocation line. Cytogenetic and biochemical analyses showed that chromosome arms 6VS and 6AL were involved in this translocation. Random amplified polymorphic DNA (RAPD) analysis was performed on recipient wheat cultivar Yangmai 5, the translocation line, and H. villosa with 180 random primers. Eight of the 180 primers amplified polymorphic DNA in the translocation line, and the same results were obtained in four replications. Furthermore, RAPD analysis was reported for substitution line 6V, seven addition lines (1V-7V), and the F1, as well as F2 plants of (translocation line x 'Yangmai 5'), using two of the eight random primers. One RAPD marker, specific to chromosome arm 6VS, OPH17-1900, could be used as a molecular marker for the detection of gene Pm21 in breeding materials with powdery mildew resistance introduced from H. villosa. Key words : RAPD analysis, 6VS-specific marker, Pm21, Erysiphe graminis f.sp. tritici, Triticum aestivum - Haynaldia villosa translocation.

Molecular cytogenetic analysis of Agropyron chromatin specifying resistance to barley yellow dwarf virus in wheat

Nine families of bread wheat (TC5, TC6, TC7, TC8, TC9, TC10, TC14, 5395-(243AA), and 5395) with resistance to barley yellow dwarf virus and containing putative translocations between wheat and a group 7 chromosome of Agropyron intermedium (L1 disomic addition line, 7Ai#1 chromosome) induced by homoeologous pairing or tissue culture were analyzed. C-banding, genomic in situ hybridization (GISH), and restriction fragment length polymorphism (RFLP) in combination with repetitive Agropyron-specific sequences and deletion mapping in wheat were used to determine the relative locations of the translocation breakpoints and the size of the transferred alien chromatin segments in hexaploid wheat-Agropyron translocation lines. All homoeologous compensating lines had complete 7Ai#1 or translocated 7Ai#1-7D chromosomes that substitute for chromosome 7D. Two complete 7Ai#1 (7D) substitution lines (5395-(243AA) and 5395), one T1BS-7Ai#1S∙7Ai#1L addition line (TC7), and two different translocation types, T7DS-7Ai#1S∙7Ai#1L (TC5, TC6, TC8, TC9, and TC10) and T7DS∙7DL-7Ai#1L (TC14), substituting for chromosome 7D were identified. The substitution line 5395-(243AA) had a reciprocal T1BS∙1BL-4BS/T1BL-4BS∙4BL translocation. TC14 has a 6G (6B) substitution. The RFLP data from deletion mapping studies in wheat using 37 group 7 clones provided 10 molecular tagged chromosome regions for homoeologous and syntenic group 7 wheat or Agropyron chromosomes. Together with GISH we identified three different sizes of the transferred Agropyron chromosome segments with approximate breakpoints at fraction length (FL) 0.33 in the short arm of chromosome T7DS-7Ai#1S∙7Ai#1L (TC5, TC6, TC8, TC9, and TC10) and another at FL 0.37 of the nonhomoeologous translocated chromosome T1BS-7Ai#1S∙7Ai#1L (TC7). One breakpoint was identified in the long arm of chromosome T7DS∙7DL-7Ai#1L (TC14) at FL 0.56. We detected some nonreciprocal translocations for the most proximal region of the chromosome arm of 7DL, which resulted in small duplications. Key words : C-banding, genomic in situ hybridization (GISH), physical mapping, translocation mapping, RFLP analysis.

Genetic characterization of a reciprocal translocation present in a widely grown barley variety

Artificially induced translocation stocks have been used to physically map the barley genome; however, natural translocations are extremely uncommon in cultivated genotypes. Albacete is a barley variety widely grown in recent decades in Spain and carrying a reciprocal translocation which obviously does not affect its agronomical fitness. This translocation has been characterized by a combination of cytological and molecular genetic approaches. Firstly, recombination frequencies between markers on chromosomes 1H and 3H were estimated to determine the boundaries of the reciprocal interchange. Secondly, 1H-3H wheat barley telosome addition lines were used to assign selected markers to chromosome arms. Thirdly, fluorescence in situ hybridization (FISH) with rDNA probes (5S and 18S-5.8S-26S) and microsatellite probes [(ACT)(5), (AAG)(5) and (CAG)(5)] was used to determine the locations of the translocation breakpoints more precisely. Fourthly, fine-mapping of the regions around the translocation breakpoints was used to increase the marker density for comparative genomics. The results obtained in this study indicate that the translocation is quite large with breakpoints located on the long arms of chromosomes 1H and 3H, between the pericentromeric (AAG)(5) bands and above the (ACT)(5) interstitial distal bands, resulting in the reciprocal translocation 1HS.1HL-3HL and 3HS.3HL-1HL. The gene content around the translocation breakpoints could be inferred from syntenic relationships observed among different species from the grass family Poaceae (rice, Sorghum and Brachypodium) and was estimated at approximately 1,100 and 710 gene models for 1H and 3H, respectively. Duplicated segments between chromosomes Os01 and Os05 in rice derived from ancestral duplications within the grass family overlap with the translocation breakpoints on chromosomes 1H and 3H in the barley variety Albacete.

Genetic and correlation analysis of silique-traits in Brassica napus L. by quantitative trait locus mapping

Rapeseed yield is directly and indirectly influenced by the silique-traits, such as silique length (SL), seeds per silique (SS), seed weight (SW), because the silique is an organ which produced yield and a major photosynthesis organ as well. In this study, a linkage map comprising 150 simple sequence repeat and 195 amplified fragment length polymorphism markers covering 1,759.6 cM was constructed in a doubled haploid population from a cross between two genotypes of 'HZ396' and 'Y106'. In field experiments across three seasons and two locations in China 140 doubled haploid lines and their corresponding parents were evaluated for silique-traits. In total, 26 quantitative trait loci (QTL) were detected, of which 15 were clustered and integrated into 5 pleiotropic unique QTL by meta-analysis. These unique QTL, which in a certain sense reflected the significant positive correlation between SS and SL and the significant negative correlation between SW and SS by the genomic location and effects of QTL detected, were mapped on linkage groups N7, N8 and N13. A trait-by-trait meta-analysis revealed 5, 2 and 3 consensus QTL for SL, SS and SW, respectively. Epistatic effects varied according to the specific traits performed. All the epistatic interactions showed significant additive by additive effects while no significant epistasis by environment effect was identified. These findings provided a better understanding of the genetic factors controlling silique-traits and gained insights into the gene networks affecting silique-traits at QTL level in rapeseed.

Characterization of Thinopyrum distichum chromosomes using double fluorescence in situ hybridization, RFLP analysis of 5S and 26S rRNA, and C-banding of parents and addition lines

Diagnostic markers for eight Thinopyrum distichum addition chromosomes in Triticum turgidum were established using C-banding, in situ hybridization, and restriction fragment length polymorphism analysis. The C-band karyotype conclusively identified individual Th. distichum chromosomes and distinguished them from chromosomes of T. turgidum. Also, TaqI and BamHI restriction fragments containing 5S and 18S-5.8S-26S rRNA sequences were identified as positive markers specific to Th. distichum chromosomes. Simultaneous fluorescence in situ hybridization showed both 5S and 18S-5.8S-26S ribosomal RNA genes to be located on chromosome IV. Thinopyrum distichum chromosome VII carried only a 18S-5.8S-26S rRNA locus and chromosome pair II carried only a 5S rRNA locus. The arrangement of these loci on Th. distichum chromosome IV was different from that on wheat chromosome pair 1B. Two other unidentified Th. distichum chromosome pairs also carried 5S rRNA loci. The homoeologous relationship between Th. distichum chromosomes IV and VII and chromosomes of other members of the Triticeae was discussed by comparing results obtained using these physical and molecular markers.

Identification and validation of molecular markers linked to the leaf rust resistance gene Lr19 in wheat

A leaf rust resistance gene Lr19 on the chromosome 7DL of wheat derived from Agropyron elongatum was tagged with random amplified polymorphic DNA (RAPD) and microsatellite markers. The F(2) population of 340 plants derived from a cross between the leaf rust resistant near-isogenic line (NIL) of Thatcher (Tc + Lr19) and leaf rust susceptible line Agra Local that segregated for dominant monogenic leaf rust resistance was utilized for generating the mapping population. The molecular markers were mapped in the F(2) derived F(3) homozygous population of 140 seedlings. Sixteen RAPD markers were identified as linked to the alien gene Lr19 among which eight were in a coupling phase linkage. Twelve RAPD markers co-segregated with Lr19 locus. Nine microsatellite markers located on the long arm of chromosome 7D were also mapped as linked to the gene Lr19, including 7 markers which co-segregated with Lr19 locus, thus generating a saturated region carrying 25 molecular markers linked to the gene Lr19 within 10.2 +/- 0.062 cM on either side of the locus. Two RAPD markers S265(512) and S253(737) which flanked the locus Lr19 were converted to sequence characterized amplified region markers SCS265(512) and SCS253(736), respectively. The marker SCS265(512) was linked with Lr19 in a coupling phase and the marker SCS253(736) was linked in a repulsion phase, which when used together mimicked one co-dominant marker capable of distinguishing the heterozygous resistant seedlings from the homozygous resistant. The molecular markers were validated on NILs mostly in Thatcher background isogenic for 44 different Lr genes belonging to both native and alien origin. The validation for polymorphism in common leaf rust susceptible cultivars also confirmed the utility of these tightly linked markers to the gene Lr19 in marker-assisted selection.

Fusarium head blight resistance in hexaploid wheat (Triticum aestivum)-Lophopyrum genetic lines and tagging of the alien chromatin by PCR markers

The objective of this research was to identify Fusarium head blight (FHB) resistance in wheat ( Triticum aestivum)- Lophopyrum genetic lines that might complement FHB resistance in common wheat; and to identify DNA markers that can be used to tag the resistance gene in the alien chromatin (E or el(2) genome) for the development of improved wheat cultivars. FHB resistance was evaluated in 19 Chinese Spring- Lophopyrum elongatum (EE) substitution lines, two Thatcher -L. ponticum (el(1) and el(2)) substitution lines, and four Thatcher- L. ponticum translocation lines. Significant resistance was identified in the substitution lines 7E(7A), 7E(7B), and 7E(7D). The homoeologous chromosome, 7el(2),()also showed resistance in the Thatcher genetic background. Both the Thatcher-7el(1) substitution and translocation lines were susceptible, like Thatcher, indicating that there is no resistance gene on the 7el(1) chromosome. Simple sequence repeat (SSR) and cleaved amplified polymorphic sequences (CAPS) in homoeologous group 7 chromosomes were used to identify DNA markers located on 7E and 7el(2). As expected, the transferability of wheat SSR markers to Lophopyrum is low. Of the 52 SSR markers that we tested, only five were found to be co-dominant on 7E of L. elongatum versus 7A, 7B, and 7D, one of which is also positive on 7el(2). A CAPS marker, derived from the RFLP probe PSR129, can serve as a dominant marker for 7el(2) chromatin.

Molecular aids for integration of alien chromatin through wide crosses

Wide crosses in wheat have now been performed for over 100 years. In that time, approximately 100 genes have been transferred for numerous traits, including biotic and abiotic stresses and value-added traits. Resistance genes from alien sources do become defeated with time, so the search for additional variability must continue. Recent screening of alien species has identified accessions with multiple pest resistance plus combinations of pest resistance and value-added traits. The majority of existing induced recombinants are of a noncompensating type with considerable linkage drag, so sequential useage of Ph mutants is recommended to produce smaller interstitial recombinants. Molecular methods, including GISH, RAPD, RFLP, AFLP, and microsatellites, are being widely used to identify integrated alien chromosomes, chromosome segments, and genes.Key words: Triticum aestivium, molecular markers, disease resistance, gene introgression, interspecific hybrids.

Inheritance and chromosomal locations of male fertility restoring gene transferred from Aegilops umbellulata Zhuk. to Triticum aestivum L

Restriction fragment length polymorphism (RFLP) markers were used to map male fertility restoring gene that was transferred from chromosome 6U of Aegilops umbellulata Zhuk. to wheat. Segments of chromosome 6U bearing the gene that restore fertility to T. timopheevi Zhuk. male sterile cytoplasm were identified in all four translocation lines by two probes, BCD21 and BCD342. Lines 040-5, 061-1 and 061-4 are T6BL.6BS-6U translocations, while line 2114 is a T6AL.6AS-6U translocation. Line 2114 has a much larger 6U chromosomal segment and lower frequency of transmission of male gametes with the alien segment than the other three lines. The restoring gene carried by the 6U segment in 2114 showed high expressivity and complete penetrance. This restoring gene is designated Rf6. A homoeologous chromosome recombination mechanism is discussed for the alien gene transfer.

Comparison of genetic and physical maps of group 7 chromosomes from Triticum aestivum L

We present a high density physical map of homoeologous group 7 chromosomes from Triticum aestivum L. using a series of 54 deletion lines, 6 random amplified polymorphic DNA (RAPD) markers and 91 cDNA or genomic DNA clones from wheat, barley and oat. So far, 51 chromosome segments have been distinguished by molecular markers, and 54 homoeoloci have been allocated among chromosomes 7A, 7B and 7D. The linear order of molecular markers along the chromosomes is almost identical in the A- B- and D-genome of wheat. In addition, there is colinearity between the physical and genetic maps of chromosomes 7A, 7B and 7D from T. aestivum, indicating gene synteny among the Triticeae. However, comparison of the physical map of chromosome 7D from T. aestivum with the genetic map from Triticum tauschii some markers have been shown to be physically allocated with distortion in more distal chromosome regions. The integration of genetic and physical maps could assist in estimating the frequency and distribution of recombination in defined regions along the chromosome. Physical distance did not correlate with genetic distance. A dense map facilitates the detection of multiple rearrangements. We present the first evidence for an interstitial inversion either on chromosome arm 7AS or 7DS of Chinese Spring. Molecularly tagged chromosome regions (MTCRs) provide landmarks for long-range mapping of DNA fragments.