Near-isogenic Inbred Lines Research Articles

Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel

BackgroundThe teleost medaka (Oryzias latipes) is a well-established vertebrate model system, with a long history of genetic research, and multiple high-quality reference genomes available for several inbred strains. Medaka has a high tolerance to inbreeding from the wild, thus allowing one to establish inbred lines from wild founder individuals.ResultsWe exploit this feature to create an inbred panel resource: the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel. This panel of 80 near-isogenic inbred lines contains a large amount of genetic variation inherited from the original wild population. We use Oxford Nanopore Technologies (ONT) long read data to further investigate the genomic and epigenomic landscapes of a subset of the MIKK panel. Nanopore sequencing allows us to identify a large variety of high-quality structural variants, and we present results and methods using a pan-genome graph representation of 12 individual medaka lines. This graph-based reference MIKK panel genome reveals novel differences between the MIKK panel lines and standard linear reference genomes. We find additional MIKK panel-specific genomic content that would be missing from linear reference alignment approaches. We are also able to identify and quantify the presence of repeat elements in each of the lines. Finally, we investigate line-specific CpG methylation and performed differential DNA methylation analysis across these 12 lines.ConclusionsWe present a detailed analysis of the MIKK panel genomes using long and short read sequence technologies, creating a MIKK panel-specific pan genome reference dataset allowing for investigation of novel variation types that would be elusive using standard approaches.

Genetic diversity analyses of Brassica napus accessions using SRAP molecular markers

Knowledge about genetic diversity among Brassica napus cultivars developed for many growing regions and their possible use as potential inbred lines for hybrid seed production is limited. We studied the genetic diversity and relationships among B. napus accessions using Sequence Related Amplified Polymorphism (SRAP) markers, which preferentially amplify open reading frames. A total of 60 spring-type B. napus accessions were screened using 20 SRAP primers, which revealed 162 polymorphic fragments with an average of eight markers per primer combination. Genetic similarity estimates ranged from 40 to 100, which indicated sufficient diversity among the accessions. The majority of the accessions were uniquely identified by the markers with the exception of near-isogenic inbred lines. Cluster analysis displayed five major groups. The first major cluster comprised 23 accessions mostly of Australian origin, whereas the second cluster included 13 accessions mostly of Canadian origin. The accessions in the first and second clusters were identified as maintainers of cytoplasmic male sterility. The two restorer lines R-111 and R-101 along with their corresponding backcross progeny constituted the third cluster. Scandinavian cultivars made the fourth separate cluster. One cultivar Salam and its respective inbred line were the most divergent lines. Variations in the number of markers between open-pollinated cultivars and their respective selfed inbred lines were also observed. The clustering pattern mostly supported their respective pedigree and characteristic traits. Genetic diversity in genetically distinct groups in the tested maintainer and restorer lines can be exploited for hybrid development in B. napus.

General Resistance in Maize to Southern Rust (Puccinia polysora Underw.)

ABSTRACTSouthern corn rust (Puccinia polysora Underw.) is a major tropical disease that can lead to severe yield losses in the tropics. Occasionally it becomes of concern in temperate regions, as in 2010. We summarize 45 yr of research on the occurrence, genetic basis, and breeding of general resistance. Trials were conducted in Colombia, Hawaii, Nigeria, the Philippines, Texas, and Thailand. Temperate maize proved uniformly susceptible. No racially specific monogenes were effective. Resistance varied continuously among tropical inbreds and many of these showed stable intermediate tolerance. Two diallel populations revealed high correlations of inbred values with hybrid array means and slight heterosis for resistance. Narrow‐sense heritabilities were 51% and 66%, and mean square ratios for general to specific combining ability (GCA:SCA) were 7.8 and 10.7 to 1. Generation mean analyses were performed on six sets of families. Mean and additive effects were significant across families, while significant nonadditive effects were rare. Heritability values ranged from 19% to 49%. A set of recombinant lines segregated a primary susceptibility locus on chromosome 6. Studies of 137 near‐isogenic inbred lines (NILs) of resistant tropical inbred Hi27 revealed a dominant susceptibility quantitative trait locus (QTL) in the NIL for dwarf‐1 locus, but linkage could not be confirmed. Premature senescence was associated with rust infections in many NILs, emphasizing the ubiquity of modifying genes. No correlation existed between resistance to southern and common rusts. Resistant tropical inbreds and populations were bred to serve as sources for future improvement.

Adaptation of super-sweet maize to cold conditions: mutant×genotype interaction

SUMMARYSuper-sweet maize (shrunken2,sh2) has a longer post-harvest life than standard sweetcorn (sugary1,su1), but is less well-adapted to cold conditions. The objective of the present work was to determine if the replacement ofsu1bysh2alters the combining abilities of sweetcorn inbreds for adaptation to early planting under cold conditions. Two diallel sets ofsu1andsh2near-isogenic inbred lines were evaluated in a cold chamber and by early field planting. For most of the traits related to adaptation, except silking date, there were significant mutant×genotype interactions and the estimates of general combining ability (GCA) of each version of the same inbred were different, probably due to epistasis. Therefore, to widen the genetic base of the super-sweet germplasm for adaptation, conversion of the earliestsu1inbreds tosh2, ignoring other characteristics such as emergence or early vigour in early planting or cold tests, is proposed.

How does arbuscular mycorrhizal colonization vary with host plant genotype? An example based on maize (Zea mays) germplasms

Colonization of plant roots by arbuscular mycorrhizal (AM) fungi is a primary factor determining mycorrhizal associations. This study aimed to investigate the variation in AM colonization among maize genotypes and in response to plant breeding programs. Three types of maize (Zea mays) germplasms composed of 141 inbred lines, 38 hybrids, and 76 landraces were grown in replicated field experiments in Sapporo, Japan, for two cropping years to evaluate the percentage of root length colonized by indigenous AM fungi. The percent colonization varied greatly and continuously among maize genotypes. Inbred lines that originated (released) in particular locations (e.g., Tokachi, Japan) and years (e.g., 1960s) showed significantly larger values than other lines. Inter-location differences were also observed for landraces. The direction of the year-of-release effect on colonization depended on the origin. No significant differences were observed between leaf-blight-disease-resistant near-isogenic inbred lines and their parents. Modern hybrids showed significantly greater values than inbred lines and older landraces. Evaluating numerous, diverse genotypes demonstrated that AM colonization of maize plants varies with germplasm type, origin (country and location), and year of release, and that modern plant breeding programs do not necessarily lead to the suppression of colonization.

Considerations Regarding the Use of Hyperspectral Imaging Data in Classifications of Food Products, Exemplified by Analysis of Maize Kernels

Development of robust analytical procedures is critical when using hyperspectral imaging technology in food technology and agriculture. This study used near-isogenic inbred corn lines to address two basic questions: (1) To what extent is classification accuracy increased by grinding maize kernels? (2) Can the classification accuracy of two near-isogenic inbred lines be increased by using a spectral filter to classify only certain hyperspectral profiles from each image cube? Whole kernels and ground kernels in two particle intervals, 0.250-0.354 mm (size 1) and 0.354-0.841 mm (size 2), were examined. Spectral profiles acquired from ground kernels had higher spectral repeatability than data collected from whole kernels. The classification error of discriminant functions from whole kernels was >3 times lower than that of size 1 ground particles. Applying a spectral filter to input data had negligible effect on classifications of hyperspectral profiles from whole kernels and size 2 ground particles, but for size 1 ground particles a considerable increase in accuracy was observed. Independent validation confirmed that distinction between wild type and mutant inbred maize lines could be conducted with >80% accuracy after the proposed spectral filter had been applied to hyperspectral profiles of size 1 ground particles. A combination of discriminant analysis and regression analysis could be used to accurately predict mixture ratios of the two inbred lines. The use of spectral filtering to increase the level of spectral repeatability and the use of hyperspectral imaging technology in large-scale commercial operations are discussed.

Vegetative Phase Transition and Corn Borer Resistance of shrunken2 versus sugary1 Sweet Corn Near-isogenic Inbred Lines

The genes sugary1 (su1) and shrunken2 (sh2) are commonly used to produce sweet and super-sweet corn (Zea mays L.), respectively. In this work we compare corn borer [european corn borer (ECB) (Ostrinia nubilalis Hbn.) and pink stem borer (PSB) (Sesamia nonagrioides Lef.)] susceptibility in seven pairs of su1 and sh2 near-isogenic sweet corn inbreds (101t, C23, C40, C68, Ia453, Ia5125, and P39) and the relationship between corn borer resistance and vegetative phase transition. The seven pairs of near-isogenic inbreds were evaluated under corn borer infestation during 3 years in northwestern Spain. Differences among inbreds were significant for most of the traits, although resistance was partial. Ia5125su1 and C40su1 were the most resistant inbreds. Differences between a few pairs of near-isogenic su1 and sh2 strains were significant for some vegetative phase change and corn borer damage-related traits. Generally su1 strains flowered earlier, had a shorter juvenile phase, fewer PSB, and more ECB larvae than sh2 strains. However su1 and sh2 strains did not differ significantly for most traits related to phase transition and corn borer damage; notably ear damage was not significantly different between su1 and sh2 strains. These results suggest that theoretical and practical results of sweet corn (sugary1) breeding for corn borer resistance could be capitalized for super-sweet corn (shrunken2) breeding.

Effects of the Dt 2 and S Alleles on Agronomic Traits of F 1 Hybrid Soybean

Agronomic evaluation of F1 hybrid soybean [Glycine max (L) Merr.] will be useful for germplasm evaluation, recurrent selection, and estimating heterosis. We anticipated that vegetative heterosis, commonly observed in soybean, could increase early lodging and pod abortion, reducing grain yield. Under these circumstances, observed hybrid grain yield would not reflect the true potential of the hybrid as expressed in later generations. The Dt2 (semideterminate stem type) and S (short internode stem type) alleles have been shown to reduce excessive vegetative growth and lodging in narrow-row production of inbred soybean. Our objectives were (i) to determine the per se effects and effects on heterosis, for agronomic traits, of the semideterminate (Dt2_) and short (S_) stem types in hybrid soybean, (ii) to assess their potential in facilitating germplasm evaluation and recurrent selection, and (iii) to determine if either stem type would be agronomically desirable in commercial hybrid soybean production. Near-isogenic inbred lines and hybrid (F1) lines were evaluated replicated three-row plots. The Dt2 and S alleles affected agronomic traits of hybrids and inbreds similarly. The Dt2 and S alleles hastened maturity, decreased plant height and lodging, and increased harvest index per se values. The Dt2 allele decreased seed weight and protein content. Both the per se and heterosis data suggest that the Dt2 and S alleles would not be consistently beneficial to germplasm evaluation or recurrent selection. The per se data suggest that the S allele might be useful for both inbred and commercial hybrid soybean.

Maize leaf β-1,3-glucanase activity in relation to resistance to Exserohilum turcicum

β-1,3-Glucanase activity was assayed over a 14-day period in leaves of three maize (Zea mays L.) near-isogenic inbred lines with differing susceptibilities to the fungal pathogen Exserohilum turcicum (Pass.) Leonard and Suggs. Crude leaf extracts of β-1,3-glucanase activity had a pH optimum of 4.5 and required a sulfhydryl reagent for maximal activity. One half of the plants of each inbred line were inoculated with race 2 of E. turcicum at the beginning of the experiment. β-1,3-Glucanase activity increased with inoculation in all isolines, but was highest 14 days after inoculation in line B37Ht2, with an allele conferring specific resistance to race 2. Isoline B37HtN, with a nonspecific allele for resistance, displayed an intermediate increase in β-1,3-glucanase activity. Susceptible line B37 had the lowest β-1,3-glucanase activity. β-1,3-Glucanase activity appeared to be induced in maize and was not a result of increased enzyme activity in the pathogen.