Objectives and Benefits of Molecular Breeding in Forage Species

The amount of resources and information provided by forage crop genomic programs has dramatically increased during the past few years. Trait-based forward genetic procedures such as mapping and expression profiling have successfully provided new candidate genes or genome regions affecting forage quality. Respective information can easily be transferred across related forage species. Since several genes in major biochemical pathways related to forage traits have been isolated, gene-based reverse genetic approaches (transformation, association studies) are promising. Most genetic experiments are conducted under simplified artificial conditions such as on single-spaced plants. Therefore, transferability of respective genetic information to breeding practice needs to be demonstrated

"PolyMin": software for identification of the minimum number of polymorphisms required for haplotype and genotype differentiation

Background Analysis of allelic variation for relevant genes and monitoring chromosome segment transmission during selection are important approaches in plant breeding and ecology. To minimize the number of required molecular markers for this purpose is crucial due to cost and time constraints. To date, software for identification of the minimum number of required markers has been optimized for human genetics and is only partly matching the needs of plant scientists and breeders. In addition, different software packages with insufficient interoperability need to be combined to extract this information from available allele sequence data, resulting in an error-prone multi-step process of data handling. Results PolyMin, a computer program combining the detection of a minimum set of single nucleotide polymorphisms (SNPs) and/or insertions/deletions (INDELs) necessary for allele differentiation with the subsequent genotype differentiation in plant populations has been developed. Its efficiency in finding minimum sets of polymorphisms is comparable to other available program packages. Conclusion A computer program detecting the minimum number of SNPs for haplotype discrimination and subsequent genotype differentiation has been developed, and its performance compared to other relevant software. The main advantages of PolyMin, especially for plant scientists, is the integration of procedures from sequence analysis to polymorphism selection within a single program, including both haplotype and genotype differentiation

Nucleotide diversity and linkage disequilibrium in 11 expressed resistance candidate genes in Lolium perenne

<p>Abstract</p> <p>Background</p> <p>Association analysis is an alternative way for QTL mapping in ryegrass. So far, knowledge on nucleotide diversity and linkage disequilibrium in ryegrass is lacking, which is essential for the efficiency of association analyses.</p> <p>Results</p> <p>11 expressed disease resistance candidate (R) genes including 6 nucleotide binding site and leucine rich repeat (NBS-LRR) like genes and 5 non-NBS-LRR genes were analyzed for nucleotide diversity. For each of the genes about 1 kb genomic fragments were isolated from 20 heterozygous genotypes in ryegrass. The number of haplotypes per gene ranged from 9 to 27. On average, one single nucleotide polymorphism (SNP) was present per 33 bp between two randomly sampled sequences for the 11 genes. NBS-LRR like gene fragments showed a high degree of nucleotide diversity, with one SNP every 22 bp between two randomly sampled sequences. NBS-LRR like gene fragments showed very high non-synonymous mutation rates, leading to altered amino acid sequences. Particularly LRR regions showed very high diversity with on average one SNP every 10 bp between two sequences. In contrast, non-NBS LRR resistance candidate genes showed a lower degree of nucleotide diversity, with one SNP every 112 bp. 78% of haplotypes occurred at low frequency (<5%) within the collection of 20 genotypes. Low intragenic LD was detected for most R genes, and rapid LD decay within 500 bp was detected.</p> <p>Conclusion</p> <p>Substantial LD decay was found within a distance of 500 bp for most resistance candidate genes in this study. Hence, LD based association analysis is feasible and promising for QTL fine mapping of resistance traits in ryegrass.</p

Diagnostics in Plant Breeding

“Diagnostics in Plant Breeding” is systematically organizing cutting-edge research reviews on the development and application of molecular tools for the prediction of plant performance. Given its significance for mankind and the available research resources, medical sciences are leading the area of molecular diagnostics, where DNA-based risk assessments for various diseases and biomarkers to determine their onset become increasingly available. So far, most research in plant genomics has been directed towards understanding the molecular basis of biological processes or phenotypic traits. From a plant breeding perspective, however, the main interest is in predicting optimal genotypes based on molecular information for more time- and cost-efficient breeding schemes. It is anticipated that progress in plant genomics and in particular sequence technology made recently will shift the focus from “explanatory” to “predictive” in crop science. This book assembles chapters on all areas relevant to development and application of predictive molecular tools in plant breeding by leading authorties in the respective areas

Frequency, type, and distribution of EST-SSRs from three genotypes of Lolium perenne, and their conservation across orthologous sequences of Festuca arundinacea, Brachypodium distachyon, and Oryza sativa

<p>Abstract</p> <p>Background</p> <p>Simple sequence repeat (SSR) markers are highly informative and widely used for genetic and breeding studies in several plant species. They are used for cultivar identification, variety protection, as anchor markers in genetic mapping, and in marker-assisted breeding. Currently, a limited number of SSR markers are publicly available for perennial ryegrass (<it>Lolium perenne</it>). We report on the exploitation of a comprehensive EST collection in <it>L. perenne </it>for SSR identification. The objectives of this study were 1) to analyse the frequency, type, and distribution of SSR motifs in ESTs derived from three genotypes of <it>L. perenne</it>, 2) to perform a comparative analysis of SSR motif polymorphisms between allelic sequences, 3) to conduct a comparative analysis of SSR motif polymorphisms between orthologous sequences of <it>L. perenne</it>, <it>Festuca arundinacea, Brachypodium distachyon</it>, and <it>O. sativa</it>, 4) to identify functionally associated EST-SSR markers for application in comparative genomics and breeding.</p> <p>Results</p> <p>From 25,744 ESTs, representing 8.53 megabases of nucleotide information from three genotypes of <it>L. perenne</it>, 1,458 ESTs (5.7%) contained one or more SSRs. Of these SSRs, 955 (3.7%) were non-redundant. Tri-nucleotide repeats were the most abundant type of repeats followed by di- and tetra-nucleotide repeats. The EST-SSRs from the three genotypes were analysed for allelic- and/or genotypic SSR motif polymorphisms. Most of the SSR motifs (97.7%) showed no polymorphisms, whereas 22 EST-SSRs showed allelic- and/or genotypic polymorphisms. All polymorphisms identified were changes in the number of repeat units. Comparative analysis of the <it>L. perenne </it>EST-SSRs with sequences of <it>Festuca arundinacea</it>, <it>Brachypodium distachyon</it>, and <it>Oryza sativa </it>identified 19 clusters of orthologous sequences between these four species. Analysis of the clusters showed that the SSR motif generally is conserved in the closely related species <it>F. arundinacea</it>, but often differs in length of the SSR motif. In contrast, SSR motifs are often lost in the more distant related species <it>B. distachyon </it>and <it>O. sativa</it>.</p> <p>Conclusion</p> <p>The results indicate that the <it>L. perenne </it>EST-SSR markers are a valuable resource for genetic mapping, as well as evaluation of co-location between QTLs and functionally associated markers.</p

Selection of Haploid Maize Kernels from Hybrid Kernels for Plant Breeding Using Near-Infrared Spectroscopy and SIMCA Analysis

Samples of haploid and hybrid seed from three different maize donor genotypes after maternal haploid induction were used to test the capability of automated near-infrared transmission spectroscopy to individually differentiate haploid from hybrid seeds. Using a two-step chemometric analysis in which the seeds were first classified according to genotype and then the haploid or hybrid status was determined proved to be the most successful approach. This approach allowed 11 of 13 haploid and 25 of 25 hybrid kernels to be correctly identified from a mixture that included seeds of all the genotypes

Quantitative trait loci mapping of forage agronomic traits in six mapping populations derived from European elite maize germplasm

Four agronomic traits were analysed including dry matter concentration (DMC) and dry matter yield (DMY) for stover, plant height (PHT) and days from planting to silking (DPS). We mapped quantitative trait loci (QTL) in three populations with doubled haploid lines (DHL), one RIL population and two testcross (TC) populations derived from crosses between two of the four populations mentioned above to elite tester lines, based on field phenotyping at multiple locations and years for each; 146–168 SSRs were used for genotyping of the four mapping populations. Significant high phenotypic and genotypic correlations were found for all traits at two locations, while DMC was negatively correlated with the other traits. A total of 42, 41, 54, and 45 QTL were identified for DMC, DMY, PHT, and DPS, respectively, with 9, 7, 12, and 7 major QTL for each trait. Most detected QTL displayed significant interactions with environment. Major QTL detected in more than two populations will contribute to marker‐assisted breeding and also to fine mapping candidate genes associated with maize agronomic traits

Characterization of phenylpropanoid pathway genes within European maize (Zea mays L.) inbreds

<p>Abstract</p> <p>Background</p> <p>Forage quality of maize is influenced by both the content and structure of lignins in the cell wall. Biosynthesis of monolignols, constituting the complex structure of lignins, is catalyzed by enzymes in the phenylpropanoid pathway.</p> <p>Results</p> <p>In the present study we have amplified partial genomic fragments of six putative phenylpropanoid pathway genes in a panel of elite European inbred lines of maize (<it>Zea mays </it>L.) contrasting in forage quality traits. Six loci, encoding C4H, 4CL1, 4CL2, C3H, F5H, and CAD, displayed different levels of nucleotide diversity and linkage disequilibrium (LD) possibly reflecting different levels of selection. Associations with forage quality traits were identified for several individual polymorphisms within the <it>4CL1</it>, <it>C3H</it>, and <it>F5H </it>genomic fragments when controlling for both overall population structure and relative kinship. A 1-bp indel in <it>4CL1 </it>was associated with <it>in vitro </it>digestibility of organic matter (IVDOM), a non-synonymous SNP in <it>C3H </it>was associated with IVDOM, and an intron SNP in <it>F5H </it>was associated with neutral detergent fiber. However, the <it>C3H </it>and <it>F5H </it>associations did not remain significant when controlling for multiple testing.</p> <p>Conclusion</p> <p>While the number of lines included in this study limit the power of the association analysis, our results imply that genetic variation for forage quality traits can be mined in phenylpropanoid pathway genes of elite breeding lines of maize.</p

Fine-mapping and comparative genomic analysis reveal the gene composition at the S and Z self-incompatibility loci in grasses

Self-incompatibility (SI) is a genetic mechanism of hermaphroditic plants to prevent inbreeding after self-pollination. Allogamous Poaceae species exhibit a unique gametophytic SI system controlled by two multi-allelic and independent loci, S and Z. Despite intense research efforts in the last decades, the genes that determine the initial recognition mechanism are yet to be identified. Here, we report the fine-mapping of the Z-locus in perennial ryegrass (Lolium perenne L.) and provide evidence that the pollen and stigma components are determined by two genes encoding DUF247 domain proteins (ZDUF247-I and ZDUF247-II) and the gene sZ, respectively. The pollen and stigma determinants are located side-by-side and were genetically linked in 10,245 individuals of two independent mapping populations segregating for Z. Moreover, they exhibited high allelic diversity as well as tissue-specific gene expression, matching the expected characteristics of SI determinants known from other systems. Revisiting the S-locus using the latest high-quality whole-genome assemblies revealed a similar gene composition and structure as found for Z, supporting the hypothesis of a duplicated origin of the two-locus SI system of grasses. Ultimately, comparative genomic analyses across a wide range of self-compatible and self-incompatible Poaceae species revealed that the absence of a functional copy of at least one of the six putative SI determinants is accompanied by a self-compatible phenotype. Our study provides new insights into the origin and evolution of the unique gametophytic SI system in one of the largest and economically most important plant families.Open access articleThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]