Quantitative trait loci for heading date and straw characters in barley

Usefulness of a Multiparent Advanced Generation Intercross Population With a Greatly Reduced Mating Design for Genetic Studies in Winter Wheat

Multiparent advanced generation intercross (MAGIC) populations were recently developed to allow the high-resolution mapping of quantitative traits. We present a genetic linkage map of an elite but highly diverse eight-founder MAGIC population in common wheat (Triticum aestivum L.). Our MAGIC population is composed of 394 F6:8 recombinant inbred lines lacking significant signatures of population structure. The linkage map included 5435 SNP markers distributed over 2804 loci and spanning 5230 cM. The analysis of population parameters, including genetic structure, kinship, founder probabilities, and linkage disequilibrium and congruency to other maps indicated appropriate construction of both the population and the genetic map. It was shown that eight-founder MAGIC populations exhibit a greater number of loci and higher recombination rates, especially in the pericentromeric regions, compared to four-founder MAGIC, and biparental populations. In addition, our greatly simplified eight-parental MAGIC mating design with an additional eight-way intercross step was found to be equivalent to a MAGIC design with all 210 possible four-way crosses regarding the levels of missing founder assignments and the number of recombination events. Furthermore, the MAGIC population captured 71.7% of the allelic diversity available in the German wheat breeding gene pool. As a proof of principle, we demonstrated the application of the resource for quantitative trait loci mapping analyzing seedling resistance to powdery mildew. As wheat is a crop with many breeding objectives, this resource will allow scientists and breeders to carry out genetic studies for a wide range of breeder-relevant parameters in a single genetic background and reveal possible interactions between traits of economic importance.

Genetic Mapping of Quantitative Trait Loci for Yield-Affecting Traits in a Barley Doubled Haploid Population Derived from Clipper × Sahara 3771

Many traits play essential roles in determining crop yield. Wide variation for morphological traits exists in Hordeum vulgare L., but the genetic basis of this morphological variation is largely unknown. To understand genetic basis controlling morphological traits affecting yield, a barley doubled haploid population (146 individuals) derived from Clipper × Sahara 3771 was used to map chromosome regions underlying days to awn appearance, plant height, fertile spike number, flag leaf length, spike length, harvest index, seed number per plant, thousands kernel weight, and grain yield. Twenty-seven QTLs for nine traits were mapped to the barley genome that described 3-69% of phenotypic variations; and some genomic regions harbor a given QTL for more than one trait. Out of 27 QTLs identified, 19 QTLs were novel. Chromosomal regions on 1H, 2H, 4H, and 6H associated with seed grain yield, and chromosome regions on 2H and 6H had major effects on grain yield (GY). One major QTL for seed number per plant was flanked by marker VRS1-KSUF15 on chromosome 2H. This QTL was also associated with GY. Some loci controlling thousands kernel weight (TKW), fertile spike number (FSN), and GY were the same. The major grain yield QTL detected on linkage PSR167 co-localized with TAM10. Two major QTLs controlling TKW and FSN were also mapped at this locus. Eight QTLs on chromosomes 1H, 2H, 3H, 4H, 5H, 6H, and 7H consistently affected spike characteristics. One major QTL (ANIONT1A-TACMD) on 4H affected both spike length (SL) and spike number explained 9 and 5% of the variation of SL and FSN, respectively. In conclusion, this study could cast some light on the genetic basis of the studied pivotal traits. Moreover, fine mapping of the identified major effect markers may facilitate the application of molecular markers in barley breeding programs.

SNP-based high density genetic map and mapping of btwd1 dwarfing gene in barley

A high-density linkage map is a valuable tool for functional genomics and breeding. A newly developed sequence-based marker technology, restriction site associated DNA (RAD) sequencing, has been proven to be powerful for the rapid discovery and genotyping of genome-wide single nucleotide polymorphism (SNP) markers and for the high-density genetic map construction. The objective of this research was to construct a high-density genetic map of barley using RAD sequencing. 1894 high-quality SNP markers were developed and mapped onto all seven chromosomes together with 68 SSR markers. These 1962 markers constituted a total genetic length of 1375.8 cM and an average of 0.7 cM between adjacent loci. The number of markers within each linkage group ranged from 209 to 396. The new recessive dwarfing gene btwd1 in Huaai 11 was mapped onto the high density linkage maps. The result showed that the btwd1 is positioned between SNP marks 7HL_6335336 and 7_249275418 with a genetic distance of 0.9 cM and 0.7 cM on chromosome 7H, respectively. The SNP-based high-density genetic map developed and the dwarfing gene btwd1 mapped in this study provide critical information for position cloning of the btwd1 gene and molecular breeding of barley.

Mapping a major QTL for malt extract of barley from a cross between TX9425 × Naso Nijo

One major QTL-controlling malt extract was identified on 2H, based on the data from four different environments and a large number of DH lines, determining 48% of phenotypic variation. This QTL is of a high value for marker-assisted selection. Improving malting quality traits is one of the major breeding objectives for barley breeding programmes. Among different quality traits, malt extract is one of the most important, determining the yield of beer production. The use of molecular markers linked to loci affecting the quality traits can greatly improve selection efficiency. However, the discovery of closely linked markers relies on not only the availability of the loci, but the accuracy of phenotyping. In this experiment, 188 doubled-haploid lines derived from the cross between a Japanese malting barley and a Chinese feed barley were grown in four different environments (two sites × 2 years). Different quality traits were determined and used to map QTL for these traits. Several QTLs were identified for different quality traits. One major QTL-controlling malt extract was identified on 2H and determined 48% of phenotypic variation with the closest marker of GBM1121. This QTL was consistently expressed in all four environments and is of a high value for marker-assisted selection in malting barley breeding.

Characterization of powdery mildew resistance and linkage studies involving the Pm3 locus on chromosome 1A of common wheat (Triticum aestivum L.)

Genetic characterization of a new powdery mildew resistance gene in a common wheat line ATRI3004/79 was conducted by employing a set of Blumeria graminis tritici isolates collected from Europe. Monosomic analysis revealed that a major resistance gene is located on chromosome 1A. Allelism tests of the F2 and F3 populations with other previously known genes on 1A showed that the resistance gene in ATRI3004/79 is closely linked to the Pm3d resistance gene in the German cultivar Syros, whereas it segregated independently from Pm25. Based on its distinct disease response pattern and close linkage to the Pm3 locus, this new resistance gene is tentatively designated PmH1A. A genetic linkage map was constructed for the powdery mildew gene Pm3d, the red glume color gene Rg3, and the gliadin gene Gli-A1 on chromosome 1A, based on data from a F3 population of 120 families derived from the cross Kolibri (Pm3/Gli-A1a/rg3) × F10 Strela (pm3/Gli-A1f/Rg3). Close linkage to an easily visualized morphological character such as red glume color may facilitate the selection of the resistance gene PmH1A.

A new QTL for plant height in barley (Hordeum vulgare L.) showing no negative effects on grain yield

INTRODUCTION

Reducing plant height has played an important role in improving crop yields. The success of a breeding program relies on the source of dwarfing genes. For a dwarfing or semi-dwarfing gene to be successfully used in a breeding program, the gene should have minimal negative effects on yield and perform consistently in different environments.

METHODS

In this study, 182 doubled haploid lines, generated from a cross between TX9425 and Naso Nijo, were grown in six different environments to identify quantitative trait loci (QTL) controlling plant height and investigate QTL × environments interaction.

RESULTS

A QTL for plant was identified on 7H. This QTL showed no significant effects on other agronomic traits and yield components and consistently expressed in the six environments. A sufficient allelic effect makes it possible for this QTL to be successfully used in breeding programs.

Characterization of a QTL affecting spike morphology on the long arm of chromosome 3H in barley (Hordeum vulgare L.) based on near isogenic lines and a NIL-derived population

Traits related to spike morphology (SM), including grain density (GD), spike length (SL) and awn length (AL), are of central importance in cereal improvement. A recent study based on a two-row landrace of barley, TX9425, detected QTL controlling all of the three traits in a similar region on the long arm of chromosome 3H. To further characterize this chromosomal region, 12 pairs of near isogenic lines (NILs) for GD were generated from two populations between TX9425 and two different commercial cultivars. A population consisting of 1,028 lines segregating primarily for the target region was also developed using materials generated during the production of these NILs. Results from the analysis of the NILs and the NIL-derived population showed that these three traits were likely controlled by a single-locus which was mapped to a 2.84 cM interval between two SSR markers, GBM1495 and HVM33. Across the 12 pairs of NILs, the presence of the 3HL locus increased GD by 53.4 %, reduced SL and AL by 38.8 % and 62.7 %, respectively. In the NIL-derived population, the presence of the 3HL locus increased GD by 64.6 %, reduced SL and AL by 33.7 % and 62.6 %, respectively. An interesting question arising from this research is why some loci such as the one reported here affect several SM-related traits while others appear to affect one of these traits only. The NILs and the NIL-derived population generated in this study will help answer such questions by providing the germplasm to enable cloning and comparative analysis of the genes responsible for these SM-related traits.

Molecular mapping of powdery mildew resistance gene Eg-3 in cultivated oat (Avena sativa L. cv. Rollo)

Powdery mildew is a prevalent fungal disease affecting oat (Avena sativa L.) production in Europe. Common oat cultivar Rollo was previously shown to carry the powdery mildew resistance gene Eg-3 in common with cultivar Mostyn. The resistance gene was mapped with restriction fragment length polymorphism (RFLP) markers from Triticeae group-1 chromosomes using a population of F(3) lines from a cross between A. byzantina cv. Kanota and A. sativa cv. Rollo. This comparative mapping approach positioned Eg-3 between cDNA-RFLP marker loci cmwg706 and cmwg733. Since both marker loci were derived from the long arm of barley chromosome 1H, the subchromosomal location of Eg-3 was assumed to be on the long arm of oat chromosome 17. Amplified fragment length polymorphism (AFLP) marker technology featured as an efficient means for obtaining markers closely linked to Eg-3.

Cross-genome map based dissection of a nitrogen use efficiency ortho-metaQTL in bread wheat unravels concerted cereal genome evolution

Monitoring nitrogen use efficiency (NUE) in plants is becoming essential to maintain yield while reducing fertilizer usage. Optimized NUE application in major crops is essential for long-term sustainability of agriculture production. Here, we report the precise identification of 11 major chromosomal regions controlling NUE in wheat that co-localise with key developmental genes such as Ppd (photoperiod sensitivity), Vrn (vernalization requirement), Rht (reduced height) and can be considered as robust markers from a molecular breeding perspective. Physical mapping, sequencing, annotation and candidate gene validation of an NUE metaQTL on wheat chromosome 3B allowed us to propose that a glutamate synthase (GoGAT) gene that is conserved structurally and functionally at orthologous positions in rice, sorghum and maize genomes may contribute to NUE in wheat and other cereals. We propose an evolutionary model for the NUE locus in cereals from a common ancestral region, involving species specific shuffling events such as gene deletion, inversion, transposition and the invasion of repetitive elements.

A quantitative trait locus for reduced culm internode length in barley segregates as a Mendelian gene

Yield losses caused by lodging in cereals can be partially controlled by reducing plant height. A progeny of recombinant inbred lines from a cross of two Japanese barley varieties was used to study the inheritance of culm and culm internode lengths. An unexpected QTL for reduced culm length (qCUL), which affected mainly the length of the third and fourth culm internodes, was contributed by 'Kanto Nakate Gold'. This QTL was also associated with reduced lodging in two experiments. A near-isogenic line (culm length 62.9-73.4 cm) in an 'Azumamugi' background, carrying a chromosome segment containing the qCUL allele from Kanto Nakate Gold, was significantly shorter than its recurrent parent (82.9-89.4 cm). The F(2) generation from the next backcross segregated for plant height in a Mendelian monogenic ratio. The qCUL locus was shown to be tightly linked (1.2 cM) with the codominant STS marker ABG608.

Genetic architecture of quantitative trait loci associated with morphological and agronomic trait differences in a wild by cultivated barley cross

Hordeum vulgare subsp. spontaneum is the progenitor of cultivated barley (Hordeum vulgare L.). Domestication combined with plant breeding has led to the morphological and agronomic characteristics of modern barley cultivars. The objective of this study was to map the genetic factors that morphologically and agronomically differentiate wild barley from modern barley cultivars. To address this objective, we identified quantitative trait loci (QTLs) associated with plant height, flag leaf width, spike length, spike width, glume length in relation to seed length, awn length, fragility of ear rachis, endosperm width and groove depth, heading date, flag leaf length, number of tillers per plant, and kernel color in a Harrington/OUH602 advanced backcross (BC2F8) population. This population was genotyped with 113 simple sequence repeat markers. Thirty QTLs were identified, of which 16 were newly identified in this study. One to 4 QTLs were identified for each of the traits except glume length, for which no QTL was detected. The portion of phenotypic variation accounted for by individual QTLs ranged from about 9% to 54%. For traits with more than one QTL, the phenotypic variation explained ranged from 25% to 71%. Taken together, our results reveal the genetic architecture of morphological and agronomic traits that differentiate wild from cultivated barley.

Genome relationships in polyploid Poa pratensis and other Poa species inferred from phylogenetic analysis of nuclear and chloroplast DNA sequences

The genus Poa comprises approximately 500 species that occur throughout the world, including the widely grown Kentucky bluegrass (P. pratensis L.). Hybridization and polyploidization have played a prominent role in the evolution of this complex genus, but limited information is available regarding genome relationships in Poa. Thus, we amplified, cloned, and compared the DNA sequences of 2 nuclear genes (CDO504 and thioredoxin-like protein) and 2 chloroplast genome loci (ndhF and trnT-trnF) from 22 Poa species. Four distinct classes of sequences corresponding to 4 putative homoeologous loci from each nuclear gene were found within polyploid P. pratensis. Nuclear sequences from 15 other Poa species were found to group with at least 1 P. pratensis homoeolog, whereas 6 species displayed sequences not present in P. pratensis. The nuclear genome phylogenies presented here show the first evidence of diverse and related genomes in the genus Poa.

Development of candidate introgression lines using an exotic barley accession ( Hordeum vulgare ssp. spontaneum) 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.

Mapping quantitative trait loci for a common bean (Phaseolus vulgaris L.) ideotype

Breeding a model plant that encompasses individual traits thought to enhance yield potential, known as ideotype breeding, has traditionally focused on phenotypic selection of plants with desirable morphological traits. Broadening this breeding method to the molecular level through the use of molecular markers would avoid the environmental interactions associated with phenotypic selection. A population of 110 F5 recombinant inbred lines (RILs), derived from the cross between WO3391 and 'OAC Speedvale', was used to develop a genetic linkage map consisting of 105 random amplified polymorphic DNA (RAPD), simple sequence repeat (SSR), and sequence-tagged site (STS) markers. The map has a total length of 641 cM distributed across 8 linkage groups (LGs). Five of them were aligned on the core linkage map of bean. Twenty-one quantitative trait loci (QTLs) were identified over three environments for eight agronomic and architectural traits previously defined for a bean (Phaseolus vulgaris L.) ideotype. The QTLs were mapped to seven LGs with several regions containing QTLs for multiple traits. At least one QTL was located for each trait and a maximum of four were associated with lodging. Total explained phenotypic variance ranged from 10.6% for hypocotyl diameter to 45.4% for maturity. Some of the QTLs identified will be useful for early generation selection of tall, upright, high-yielding lines in a breeding program.

Powdery mildew resistance gene Pm22 in cultivar Virest is a member of the complex Pm1 locus in common wheat ( Triticum aestivum L. em Thell.)

The powdery mildew resistance gene Pm22, identified in the Italian wheat cultivar Virest and originally assigned to wheat chromosome 1D, was mapped to chromosome 7A with the aid of molecular markers. Mapping of common AFLP and SSR markers in two wheat crosses segregating for Pm22 and Pm1c, respectively, indicated that Pm22 is a member of the complex Pm1 locus. Pm22 also showed a pattern of resistance reaction to a differential set of Blumeria graminis f. sp. tritici isolates that was distinguishable from those from other Pm1 alleles in lines Axminster/8*Cc ( Pm1a), MocZlatka ( Pm1b), Weihenstephan Stamm M1N ( Pm1c) and Triticum spelta var. duhamelianum TRI 2258 ( Pm1d). Based on these results, the gene symbol Pm1e is proposed for the powdery mildew resistance gene in cv. Virest.

Detection of QTLs for heading time and photoperiod response in wheat using a doubled-haploid population

The genetic basis of heading time in wheat (Triticum aestivum L.) was investigated through the study of flowering under normal autumn sown field conditions as well as photoperiod responses under a controlled environment. Quantitative trait loci (QTLs) for these traits were mapped in a doubled-haploid (DH) population derived from a cross between the wheat cultivars 'Courtot' and 'Chinese Spring'. A molecular marker linkage map of this cross that was previously constructed based on 187 DH lines and 380 markers was used for QTL mapping. The genome was well covered (85%) except for chromosomes 1D and 4D, and a set of anchor loci regularly spaced over the genome (one marker each 15.5 cM) was chosen for marker regression analysis. The presence of a QTL was declared at a significance threshold of alpha = 0.005. The population was grown under field conditions in Clermont-Ferrand, France during two years (1994-1995), in Norwich, U.K. over one year (1998), and also under controlled environments in Norwich. For each trait, between 2 and 4 QTLs were identified with individual effects ranging between 6.3% and 44.4% of the total phenotypic variation. Two QTLs were detected that simultaneously affected heading time and photoperiod response. For heading time, these two QTLs were detected in more than one year. One QTL located on chromosome arm 2BS near the locus Xfbb121-2B, co-segregated with the gene Ppd-B1 known to be involved in photoperiod response. This chromosome region explained a large part of the variation (23.4-44.4% depending on the years or the traits). Another region located on chromosome arm 7BS between the loci Xfbb324-7B and Xfbb53-7B also had a strong effect (7.3-15.3%). This region may correspond to a QTL for earliness per se.Key words: molecular markers, Triticum aestivum, Ppd, Vrn.

An AFLP-based procedure for the efficient mapping of mutations and DNA probes in barley

A strategy based upon AFLP markers for high-efficiency mapping of morphological mutations and DNA probes to linkage groups in barley is presented. First, 511 AFLP markers were placed on the linkage map derived from the cross Proctor x Nudinka. Second, loci controlling phenotypic traits were assigned to linkage groups by AFLP analysis, using F2 populations consisting of 30-50 mutant plants derived from crosses of the type "mutant x Proctor" and "mutant x Nudinka." To map DNA probes, 67 different wild-type barley lines were selected to generate F2 populations by crossing with Proctor and Nudinka. F2 plants that were polymorphic for a given RFLP fragment were classified into genotypic classes. Linkage of the RFLP polymorphism to 1 of the 511 AFLP loci was indicated by cosegregation. The use of the strategy is exemplified by the mapping of the mutation branched-5 to chromosome 2 and of the DNA probes Bkn2 and BM-7 to chromosomes 5 and 1, respectively. Map expansion and marker order in map regions with dense clustering of markers represented a particular problem. A discussion considering the effect of noncanonical recombinant products on these two parameters is provided.