Testcross performance of rye introgression lines developed by marker-assisted backcrossing using an Iranian accession as donor

Introgression libraries facilitate the identification of favorable exotic alleles or genomic regions, which can be exploited for improving elite breeding material. We evaluated the first two introgression libraries in rye (Secale cereale L.) on the phenotypic and molecular level. Our objectives were to detect candidate introgression lines (pre-ILs) with a better testcross performance than the recurrent parent and identify donor chromosome segments (DCS) responsible for the improved performance. We introduced DCS from the self-incompatible heterozygous exotic Iranian primitive rye accession Altevogt 14160 (donor) into the genetic background of the elite inbred line L2053-N (recurrent parent) by marker-assisted backcrossing and developed 40 BC₂S₃ lines in each introgression library. Testcross performance for three agronomic and six quality traits was evaluated in replicated field trials across two testers at five locations over 2 years. The phenotypic effect of the DCS was analyzed for all traits. The pre-ILs had on average a testcross performance comparable to that of the recurrent parent. Significant (P < 0.05) differences between individual pre-ILs and the recurrent parent were detected for all traits except for heading date. For more than 60% of the significant (P < 0.05) differences, the pre-ILs were superior to the recurrent parent. For some pre-ILs, specific DCS were identified containing presumably quantitative trait loci responsible for the superior hybrid performance. Consequently, our study revealed that the development and employment of introgression libraries offers the opportunity for a targeted increase of genetic diversity of elite rye material for hybrid performance of agronomically important traits.     

Identification of quantitative trait loci in rye introgression lines carrying multiple donor chromosome segments

Introgression libraries can be used to make favorable genetic variation of exotic donor genotypes available in the genetic background of elite breeding material. Our objective was to employ a combination of the Dunnett test and a linear model analysis to identify favorable donor alleles in introgression lines (ILs) that carry long or multiple donor chromosome segments (DCS). We reanalyzed a dataset of two rye introgression libraries that consisted of ILs carrying on average about four donor segments. After identifying ILs that had a significantly better per se or testcross performance than the recipient line with the Dunnett test, the linear model analysis was in most instances able to clearly identify the donor regions that were responsible for the superior performance. The precise localization of the favorable DCS allowed a detailed analysis of pleiotropic effects and the study of the consistency of effects for per se and testcross performance. We conclude that in many cases the linear model analysis allows the assignment of donor effects to individual DCS even for ILs with long or multiple donor segments. This may considerably increase the efficiency of producing sub-ILs, because only such segments need to be isolated that are known to have a significant effect on the phenotype.     

Selection strategies for the development of rye introgression libraries

Computer simulations can be employed to find optimal procedures for developing introgression libraries in rye with marker-assisted backcrossing. Our objectives were to investigate the effects of the employed (1) breeding scheme, (2) selection strategy, and (3) population sizes on the donor genome coverage of the library, the number of introgression lines carrying additional donor chromosome segments outside the target regions, and the number of required marker data points. With respect to these target criteria, a BC₃S₂ breeding scheme and increasing population sizes from early to advanced generations were superior to a BC₂S₃ breeding scheme and constant population sizes. The smallest number of donor segments outside the target regions was reached with a three-stage selection strategy, which consists on selection for the target segment, selection for recombination at flanking markers and selection for recurrent parent alleles across the entire genome. Omitting the selection for flanking markers in generation BC₁ reduced considerably the number of required marker data points. A pre-selection of chromosomes consisting completely of donor genome in BC₁ was advantageous, if the effort in the breeding nursery should kept minimum. Adopting the described designs can help rye breeders to successfully develop introgression libraries.     

Optimized breeding strategies for multiple trait integration: I. Minimizing linkage drag in single event introgression

From a breeding standpoint, multiple trait integration (MTI) is a four-step process of converting an elite variety/hybrid for value-added traits (e.g. transgenic events) using backcross breeding, ultimately regaining the performance attributes of the target hybrid along with reliable expression of the value-added traits. In the light of the overarching goal of recovering equivalent performance in the finished conversion, this study focuses on the first step of MTI, single event introgression, exploring the feasibility of marker-aided backcross conversion of a target maize hybrid for 15 transgenic events, incorporating eight events into the female hybrid parent and seven into the male parent. Single event introgression is conducted in parallel streams to convert the recurrent parent (RP) for individual events, with the primary objective of minimizing residual non-recurrent parent (NRP) germplasm, especially in the chromosomal proximity to the event (i.e. linkage drag). In keeping with a defined lower limit of 96.66 % overall RP germplasm recovery (i.e. ≤120 cM NRP germplasm given a genome size of 1,788 cM), a breeding goal for each of the 15 single event conversions was developed: <8 cM of residual NRP germplasm across the genome with ~1 cM in the 20 cM region flanking the event. Using computer simulation, we aimed to identify optimal breeding strategies for single event introgression to achieve this breeding goal, measuring efficiency in terms of number of backcross generations required, marker data points needed, and total population size across generations. Various selection schemes classified as three-stage, modified two-stage, and combined selection conducted from BC1 through BC3, BC4, or BC5 were compared. The breeding goal was achieved with a selection scheme involving five generations of marker-aided backcrossing, with BC1 through BC3 selected for the event of interest and minimal linkage drag at population size of 600, and BC4 and BC5 selected for the event of interest and recovery of the RP germplasm across the genome at population size of 400, with selection intensity of 0.01 for all generations. In addition, strategies for choice of donor parent to facilitate conversion efficiency and quality were evaluated. Two essential criteria for choosing an optimal donor parent for a given RP were established: introgression history showing reduction of linkage drag to ~1 cM in the 20 cM region flanking the event and genetic similarity between the RP and potential donor parents. Computer simulation demonstrated that single event conversions with <8 cM residual NRP germplasm can be accomplished by BC5 with no genetic similarity, by BC4 with 30 % genetic similarity, and by BC3 with 86 % genetic similarity using previously converted RPs as event donors. This study indicates that MTI to produce a ‘quality’ 15-event-stacked hybrid conversion is achievable. Furthermore, it lays the groundwork for a comprehensive approach to MTI by outlining a pathway to produce appropriate starting materials with which to proceed with event pyramiding and trait fixation before version testing.     

Development of candidate introgression lines using an exotic barley accession (<Emphasis Type="Italic">Hordeum vulgare</Emphasis> ssp.<Emphasis Type="Italic"> spontaneum</Emphasis>) as donor

In the present paper, we report on the selection of two sets of candidate introgression lines (pre-ILs) in spring barley. Two BC₂DH populations, S42 and T42, were generated by introgressing an accession of Hordeum vulgare ssp. spontaneum (ISR42-8, from Israel) into two different spring barley cultivars, Scarlett (S) and Thuringia (T). From these BC₂DH populations two sets with 49 (S42) and 43 (T42) pre-ILs were selected, and their genomic architecture as revealed by SSR marker analysis was characterised. The selected pre-ILs cover at least 98.1% (S42) and 93.0% (T42) of the exotic genome in overlapping introgressions and contain on average 2 (S42) and 1.5 (T42) additional non-target introgressions. In order to illustrate a potential application and validation of these pre-ILs, the phenotypic effect of the exotic introgression at the locus of the major photoperiod response gene Ppd-H1 was analysed. Pre-ILs carrying the introgression at the Ppd-H1 locus flowered significantly earlier than the elite parents, and the introgression maintained its effect across the two genetic backgrounds and across four tested environments. The selected pre-ILs represent a first promising step towards the assessment and utilization of genetic variation present in exotic barley. They may promote the breeding progress, serve for the verification of QTL effects and provide a valuable resource for the unravelling of gene function, e.g. by expression profiling or map-based cloning.     

Comparative mapping of DNA sequences in rye (Secale cereale L.) in relation to the rice genome

The rice genome has proven a valuable resource for comparative approaches to address individual genomic regions in Triticeae species at the molecular level. To exploit this resource for rye genetics and breeding, an inventory was made of EST-derived markers with known genomic positions in rye, which were related with those in rice. As a first inventory set, 92 EST-SSR markers were mapped which had been drawn from a non-redundant rye EST collection representing 5,423 unigenes and 2.2 Mb of DNA. Using a BC1 mapping population which involved an exotic rye accession as donor parent, these EST-SSR markers were arranged in a linkage map together with 25 genomic SSR markers as well as 131 AFLP and four STS markers. This map comprises seven linkage groups corresponding to the seven rye chromosomes and covers 724 cM of the rye genome. For comparative studies, additional inventory sets of EST-based markers were included which originated from the rye-mapping data published by other authors. Altogether, 502 EST-based markers with known chromosomal localizations in rye were used for BlastN search and 334 of them could be in silico mapped in the rice genome. Additionally, 14 markers were included which lacked sequence information but had been genetically mapped in rice. Based on the 348 markers, each of the seven rye chromosomes could be aligned with distinct portions of the rice genome, providing improved insight into the status of the rye–rice genome relationships. Furthermore, the aligned markers provide genomic anchor points between rye and rice, enabling the identification of conserved ortholog set markers for rye. Perspectives of rice as a model for genome analysis in rye are discussed. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Dedicated to Prof. em. Dr. Dr. h.c. Günter Wricke on occasion of his 80th birthday.     

Marker-assisted introgression (MAI) of almond genes into the peach background: a fast method to mine and integrate novel variation from exotic sources in long intergeneration species

This paper proposes a new breeding strategy, marker-assisted introgression (MAI), to obtain lines of perennial species with a single introgressed fragment from a compatible species two generations after the interspecific hybrid. MAI allows enrichment of the genome of a species with genes from a wild or exotic relative in a short timeframe and with an intermediate step that allows a first exploration of genes/QTLs that the donor species can provide to the target crop. This method has three phases: (1) creating a large backcross one (BC1) population to select, with markers, a reduced number of individuals (15–30, called the prIL set) with a low number of introgressions; (2) phenotyping the prIL set for the traits of interest and inferring the inheritance and map position of segregating major genes/QTLs based on the known genotypes of the prILs; and (3) advancing selected lines carrying the traits of interest to a next generation of backcross or selfing to obtain individuals with a single introgression in the background of the elite commercial germplasm. The proof of concept of this strategy was implemented by using peach as the recurrent species and almond as the donor. The whole process can be done in 9–10 years as the identification of the first line with one introgression was after 5 years (2006–2011), and 4–5 additional years are needed for phenotypic evaluation of selected lines. The expansion of this method to other perennial clonally propagated crops and to other species of Prunus compatible with peach is discussed.     

Selecting a set of wild barley introgression lines and verification of QTL effects for resistance to powdery mildew and leaf rust

A set of 59 spring barley introgression lines (ILs) was developed from the advanced backcross population S42. The ILs were generated by three rounds of backcrossing, two to four subsequent selfings, and, in parallel, marker-assisted selection. Each line includes a single marker-defined chromosomal segment of the wild barley accession ISR42-8 (Hordeum vulgare ssp. spontaneum), whereas the remaining part of the genome is derived from the elite barley cultivar Scarlett (H. vulgare ssp. vulgare). Based on a map containing 98 SSR markers, the IL set covers so far 86.6% (1041.5 cM) of the donor genome. Each single line contains an average exotic introgression of 39.2 cM, representing 3.2% of the exotic genome. The utility of the developed IL set is illustrated by verification of QTLs controlling resistance to powdery mildew (Blumeria graminis f. sp. hordei L.) and leaf rust (Puccinia hordei L.) which were previously identified in the advanced backcross population S42. Altogether 57.1 and 75.0% of QTLs conferring resistance to powdery mildew and leaf rust, respectively, were verified by ILs. The strongest favorable effects were mapped to regions 1H, 0–85 cM and 4H, 125–170 cM, where susceptibility to powdery mildew and leaf rust was decreased by 66.1 and 34.7%, respectively, compared to the recurrent parent. In addition, three and one new QTLs were localized, respectively. A co-localization of two favorable QTLs was identified for line S42IL-138, which holds an introgressed segment in region 7H, 166–181. Here, a reduction effect was revealed for powdery mildew as well as for leaf rust severity. This line might be a valuable resource for transferring new resistance alleles into elite cultivars. In future, we aim to cover the complete exotic genome by selecting additional ILs. We intend to conduct further phenotype studies with the IL set in regard to the trait complexes agronomic performance, malting quality, biotic stress, and abiotic stress.     

Genome-wide prediction methods for detecting genetic effects of donor chromosome segments in introgression populations

Background

Introgression populations are used to make the genetic variation of unadapted germplasm or wild relatives of crops available for plant breeding. They consist of introgression lines that carry small chromosome segments from an exotic donor in the genetic background of an elite line. The goal of our study was to investigate the detection of favorable donor chromosome segments in introgression lines with statistical methods developed for genome-wide prediction.

Results

Computer simulations showed that genome-wide prediction employing heteroscedastic marker variances had a greater power and a lower false positive rate compared with homoscedastic marker variances when the phenotypic difference between the donor and recipient lines was controlled by few genes. The simulations helped to interpret the analyses of glycosinolate and linolenic acid content in a rapeseed introgression population and plant height in a rye introgression population. These analyses support the superiority of genome-wide prediction approaches that use heteroscedastic marker variances.

Conclusions

We conclude that genome-wide prediction methods in combination with permutation tests can be employed for analysis of introgression populations. They are particularly useful when introgression lines carry several donor segments or when the donor segments of different introgression lines are overlapping.     

Development, utilization of introgression lines using a synthetic wheat as donor

A series of introgression lines (ILs) were generated from repeated backcrossing between the exotic hexaploid wheat genotype Am3 and the common wheat genotype Laizhou953. Am3 was synthesized by crossing Triticum carthlicum with Aegilops tauschii and was used as the donor parent in this study, and Laizhou953 was used as the recurrent parent. Two hundred and five SSR markers showing polymorphism between the two parents were used to identify the introgressed Am3 chromosome segments in 97 BC4F3 ILs. The introgressed segments in each line and the length of the introgressed segments were estimated according to the wheat SSR consensus map. The introgressed segments from Am3 in the 97 lines covers 37.7% of the donor genome. The introgressed segments were most found on 2D, 3B, 6B, and 1D with coverage of 59.8, 59.5, 59.1, and 59% of the chromosomes, respectively. None of the 97 lines tested contained chromosome 4D segments introgressed from Am3. Introgressed segments for each of the chromosomes were mapped using the consensus wheat linkage map. Nine agronomic traits from BC4F3 lines were evaluated and the phenotype showed most lines have the tendency to be more similar to the recurrent parent. There were lines showing better agronomic traits than the recurrent parent, which indicated the introgression of favorable alleles from the exotic hexaploid wheat into the elite cultivar Laizhou953. Marker and phenotype data were used to identify quantitative trait loci (QTLs) controlling these nine traits. In total, 38, 33, and 28 putative QTLs were detected for seven of the nine traits in 2003, 2004, and 2005, respectively. Some of these agronomic important QTLs were detected in more than one season. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Development of PCR-based markers linked to dominant genes for male-fertility restoration in Pampa CMS of rye (<Emphasis Type="Italic">Secale cereale</Emphasis> L.)

Cytoplasmatic male sterility (CMS) is the basis for commercial hybrid seed production of rye. Nuclear restorer genes are indispensable for a complete restoration of fertility of the CMS lines. The drawbacks of current European restorer lines require the utilisation of new genetic resources that have been recently detected in an Iranian primitive rye population (IRAN IX) and an Argentinean landrace (Pico Gentario). The introgression of these effective restorer genes (Rfp1 and Rfp2, respectively) into breeding material can be facilitated by marker-assisted selection. Using two F(2) populations based on crosses between the non-restorer inbred line Lo6 and the restorer IRAN IX, as well as Pico Gentario, RAPDs and AFLPs were screened and led to a closely linked marker set for each of these genes. The conversion of the closest markers into fragment-specific sequence-characterised amplified region (SCAR) markers resulted in flanking ranges of 2.9 cM (Rfp1) and 5.2 cM (Rfp2). The application of these markers in backcross programmes is discussed.     

Molecular tagging of genes for brown planthopper resistance and earliness introgressed from Oryza australiensis into cultivated rice, O. sativa.

Restriction fragment length polymorphism analysis was carried out to tag the alien genes for brown planthopper (BPH) resistance and earliness introgressed from wild species Oryza australiensis into cultivated rice, O. sativa L. One introgression line (IR65482-4-136-2-2), resistant to biotypes 1, 2, and 3 of BPH and early in flowering, was selected from BC2F4 of the cross between O. sativa (IR31917-45-3-2) and O. australiensis (accession 100882). Recurrent parent, O. australiensis, and introgression line were surveyed for RFLP using probes of chromosomes 10 and 12. Two probes, RG457 and CDO98, detected introgression from O. australiensis. Cosegregation between introgressed characters and molecular markers was studied in F2 derived from the cross between the introgression line and recurrent parent. The gene for BPH resistance is linked with RG457 of chromosome 12 at a distance of 3.68 +/- 1.29 cM, and the gene for earliness is linked with CDO98 of chromosome 10 at a distance of 9.96 +/- 3.28 cM. Such close linkage is useful in marker-based selection while transferring BPH resistance from introgression line into other elite breeding lines. Introgression at the molecular level indicates that the mechanism of alien gene transfer is probably genetic recombination through crossing over rather than substitution of whole or large segment of chromosomes of wild species.     

Improvement of two traditional Basmati rice varieties for bacterial blight resistance and plant stature through morphological and marker-assisted selection

Bacterial blight (BB) is a major production threat to Basmati, the aromatic rice prized for its unique quality. In order to improve the BB resistance of two elite, traditional BB-susceptible Basmati varieties (Taraori Basmati and Basmati 386), we utilized the strategy of limited marker-assisted backcrossing for introgression of two major BB resistance genes, Xa21 and xa13, coupled with phenotype-based selection for improvement of their plant type and yield. Improved Samba Mahsuri, an elite high-yielding, fine-grain-type BB-resistant rice variety served as donor for BB resistance. Backcross-derived improved Basmati lines at BC1F5 possessing a single resistance gene (i.e. either Xa21 or xa13) displayed moderate resistance to BB, while lines possessing both Xa21 and xa13 showed significantly higher levels of resistance. Two-gene pyramid lines (Xa21 + xa13) possessing good grain and cooking quality similar to their respective traditional Basmati parents, short plant stature (<110 cm plant height) and higher grain yield than the recurrent parent(s) were identified and advanced. This work demonstrates the successful application of marker-assisted selection in conjunction with phenotype-based selection for targeted introgression of multiple resistance genes into traditional Basmati varieties along with improvement of their plant stature and yield.     

Discovery of quantitative trait loci for crossability from a synthetic wheat genotype

Crossability between wheat and rye is an important trait for wheat improvement.No quantitative trait loci (QTLs) were detected from wheat ancestors previously.The objectives of this study were to dissect the QTLs for crossability using 111 introgression lines (ILs) derived from synthetic hexaploid wheat.A total of 1275 SSR markers were screened for polymorphism between the two parents,and 552 markers of them displayed polymorphism,of which 64 were selected for genotyping the 111 BC5F6 ILs.Field trials were performed in a Latinized α-lattice design in Luoyang and Jiaozuo of Henan Province of China in 2007-2008 and 2008-2009 cropping seasons.One-way ANOVA and interval mapping (IM) analysis were used to detect QTL for crossability between wheat and rye.A total of 13 putative QTLs were detected.Five of them,QCa.caas.1A,QCa.caas.2D,QCa.caas.4B,QCa.caas.5B and QCa.caas.6A,were detected in both trials and three of them,QCa.caas.2D,QCa.caas.4B and QCa.caas.6A,were novel.The positive effect allele of the four QTLs came from the donor parent Am3 except QCa.caas.6A that came from the recurrent parent Laizhou953.ILs with both higher positive effect alleles and favorable agronomic traits developed in present study are elite germplasm for wide crossing in wheat.Results from the current study suggest that wheat ancestors can be rich in new sources of crossability genes.     

Genotypic and phenotypic characterization of isogenic doubled haploid exotic introgression lines in maize

We characterized the genotypic and phenotypic variation in cell wall digestibility (CWD) and other agronomic traits of 50 backcross 1 generation doubled haploid (BC1DH) lines developed from the Germplasm Enhancement of Maize project. These lines were generated by introgressing 31 exotic unadapted maize races into PHZ51 and PHB47, temperate inbred lines with expired Plant Variety Protection. The 50 BC1DH lines and five check lines were genotyped with 199 single nucleotide polymorphism markers distributed across the genome. We identified, on average, 11.8% of markers with exotic donor parent alleles. This likely underestimates the proportion of donor introgressions, since we cannot discriminate monomorphic alleles from donor and recurrent parents. The potential roles of natural selection and the doubled haploid process in favouring selection of the recurrent genome are discussed. Although the proportion of donor parent genome was underestimated, donor fragments evaluated across the 50 BC1DH lines covered 92.9% of the recurrent parent genome. The evaluation of BC1DH lines for CWD revealed promising lines with CWD not differing significantly (???=?0.05) from forage quality lines used as checks. The introgression of exotic genome segments, however, was generally associated with higher ears, lodging, and late flowering. Even with limited power, our association analysis revealed quantitative trait polymorphisms associated with CWD, flowering date, and lodging.     

Development of PCR-based codominant markers flanking the Alt3 gene in rye.

Aluminum (Al) toxicity is considered to be a major problem for crop growth and production on acid soils. The ability of crops to overcome Al toxicity varies among crop species and cultivars. Rye (Secale cereale L.) is the most Al-tolerant species among the Triticeae. Our previous study showed that Al tolerance in a rye F6 recombinant inbred line (RIL) population was controlled by a single gene designated as the aluminum tolerance (Alt3) gene on chromosome 4RL. Based on the DNA sequence of a rice (Oryza sativa L.) BAC clone suspected to be syntenic to the Alt3 gene region, we developed two PCR-based codominant markers flanking the gene. These two markers, a sequence-tagged site (STS) marker and a cleaved amplified polymorphic sequence (CAPS) marker, each flanked the Alt3 gene at an approximate distance of 0.4 cM and can be used to facilitate high-resolution mapping of the gene. The markers might also be used for marker-assisted selection in rye or wheat (Triticum aestivum L.) breeding programs to obtain Al-tolerant lines and (or) cultivars.     

Marker-assisted introgression of Trypanotolerance QTL in mice

A marker-assisted introgression (MAI) experiment was conducted to use genetic markers to transfer each of the three trypanotolerance QTL from a donor mouse strain, C57BL/6, into a recipient mouse strain, A/J. We used a backcross strategy that consisted of selecting two lines, each carrying two of the donor QTL alleles through the backcross (BC) phase. At the fourth BC generation, single-carrier animals were selected for the production of homozygous animal in the intercross phase. The QTL regions (QTLR) were located on chromosomes MMU1, MMU5, and MMU17. Groups of mice with different genotypes and the parental lines were subjected to a challenge with Trypanosoma congolense. The results show that trypanotolerance QTL was successfully moved into the recipient background genotype, yielding a longer survival time. The mean estimated survival time was 57.9, 49.5, and 46.8 days for groups of mice carrying the donor QTL on MMU1, MMU5, and MMU17 on A/J background. The mean estimated survival time was 29.7 days for the susceptible A/J line and 68.8 days for the resistant C57BL/6 line. The estimated QTLR effects are close to 30% smaller than those in the original mapping population which was likely caused by the difference in the background on which the effects of QTLR are tested. This is the first report of successful marker-assisted introgression of QTL in animals. It is experimental proof of the use of genetic markers for marker-assisted introgression in animal breeding.Institut National des Recherches Agricoles du Bénin, 01 BP 884 COTONOU, République du Bénin     

Development of resistance gene analog polymorphism markers for the Yr9 gene resistance to wheat stripe rust.

The Yr9 gene, which confers resistance to stripe rust caused by Puccinia striiformis f.sp. tritici (P. s. tritici) and originated from rye, is present in many wheat cultivars. To develop molecular markers for Yr9, a Yr9 near-isogenic line, near-isogenic lines with nine other Yr genes, and the recurrent wheat parent 'Avocet Susceptible' were evaluated for resistance in the seedling stage to North American P s. tritici races under controlled temperature in the greenhouse. The resistance gene analog polymorphism (RGAP) technique was used to identify molecular markers for Yr9. The BC7:F, and BC7:F3 progeny, which were developed by backcrossing the Yr9 donor wheat cultivar Clement with 'Avocet Susceptible', were evaluated for resistance to stripe rust races. Genomic DNA was extracted from 203 BC7:F2 plants and used for cosegregation analysis. Of 16 RGAP markers confirmed by cosegregation analysis, 4 were coincident with Yr9 and 12 were closely linked to Yr9 with a genetic distance ranging from 1 to 18 cM. Analyses of nullitetrasomic 'Chinese Spring' lines with the codominant RGAP marker Xwgp13 confirmed that the markers and Yr9 were located on chromosome 1B. Six wheat cultivars reported to have 1B/1R wheat-rye translocations and, presumably, Yr9, and two rye cultivars were inoculated with four races of P. s. tritici and tested with 9 of the 16 RGAP markers. Results of these tests indicate that 'Clement', 'Aurora', 'Lovrin 10', 'Lovrin 13', and 'Riebesel 47/51' have Yr9 and that 'Weique' does not have Yr9. The genetic information and molecular markers obtained from this study should be useful in cloning Yr9, in identifying germplasm that may have Yr9, and in using marker-assisted selection for combining Yr9 with other stripe rust resistance genes.     

AB-QTL analysis in winter wheat: I. Synthetic hexaploid wheat (<Emphasis Type="Italic">T. turgidum</Emphasis> ssp. <Emphasis Type="Italic">dicoccoides </Emphasis> × <Emphasis Type="Italic">T. tauschii</Emphasis>) as a source of favourable alleles for milling and baking quality traits

The advanced backcross QTL (AB-QTL) strategy was utilised to locate quantitative trait loci (QTLs) for baking quality traits in two BC₂F₃ populations of winter wheat. The backcrosses are derived from two German winter wheat cultivars, Batis and Zentos, and two synthetic, hexaploid wheat accessions, Syn022 and Syn086. The synthetics originate from hybridisations of wild emmer (T. turgidum spp. dicoccoides) and T. tauschii, rather than from durum wheat and T. tauschii and thus allowed for the first time to test for exotic QTL effects on wheat genomes A and B in addition to genome D. The investigated quality traits comprised hectolitre weight, grain hardness, flour yield Type 550, falling number, grain protein content, sedimentation volume and baking volume. One hundred and forty-nine SSR markers were applied to genotype a total of 400 BC₂F₃ lines. For QTL detection, a mixed-model ANOVA was conducted, including the effects DNA marker, BC₂F₃ line, environment and marker × environment interaction. Overall 38 QTLs significant for a marker main effect were detected. The exotic allele improved trait performance at 14 QTLs (36.8%), while the elite genotype contributed the favourable effect at 24 QTLs (63.2%). The favourable exotic alleles were mainly associated with grain protein content, though the greatest improvement of trait performance due to the exotic alleles was achieved for the traits falling number and sedimentation volume. At the QTL on chromosome 4B the exotic allele increased the falling number by 19.6% and at the QTL on chromosome 6D the exotic allele led to an increase of the sedimentation volume by 21.7%. The results indicate that synthetic wheat derived from wild emmer × T. tauschii carries favourable QTL alleles for baking quality traits, which might be useful for breeding improved wheat varieties by marker-assisted selection.     

Improvement of hybrid yield by advanced backcross QTL analysis in elite maize

We applied an advanced backcross breeding strategy to identify quantitative trait loci (QTLs) of agronomic importance in a cross between two elite inbreds of maize, RD6502 (Mo17-type recurrent parent) and RD3013 (Iodent donor parent). Two hundred and four BC(2) families were scored at 106 SSR, 15 AFLP, and 38 Heartbreaker (MITE) loci. BC(2) testcrosses (TC) with B73 were phenotyped at six locations in the Midwest and N.Y. We detected four grain yield, six grain moisture, and three plant height QTLs at which the RD3013 allele had a favorable effect ( p < 0.05). All four yield QTLs were selected as target introgressions in the development of BC(3)TC families. As predicted by BC(2)TC analysis, BC(3)TC entries containing introgressions at yld3.1 and yld10.1 significantly outperformed non-carrier entries by 11.1% (15.6 bu/A at one location) and 6.7% (7.1 bu/A averaged across two locations), respectively, in replicated Midwestern trials ( p < 0.05). Detection of yld10.1 effects in the BC(2)TC by spatial analysis (i.e., incomplete block, response surface, autoregressive, moving average or autoregressive moving average), but not by conventional single point analysis or interval mapping, indicated the utility of local environmental control for QTL mapping in unreplicated maize progeny. This work demonstrated that the advanced backcross QTL method can be applied to identify and manipulate useful QTLs in heterotic inbreds of elite maize. Genetic gains by this approach can be coupled with the maintenance and selection of favorable epistatic gene complexes by traditional hybrid breeding for maize improvement.