Elite Breeding Material Research Articles

To be or not to be tetraploid-the impact of marker ploidy on genomic prediction and GWAS of potato.

Cultivated potato, Solanum tuberosum L., is considered an autotetraploid with 12 chromosomes with four homologous phases. However, recent evidence found that, due to frequent large phase deletions in the genome, gene ploidy is not constant across the genome. The elite cultivar "Otava" was found to have an average gene copy number of 3.2 across all loci. Breeding programs for elite potato cultivars rely increasingly on genomic prediction tools for selection breeding and elucidation of quantitative trait loci underpinning trait genetic variance. These are typically based on anonymous single nucleotide polymorphism (SNP) markers, which are usually called from, for example, SNP array or sequencing data using a tetraploid model. In this study, we analyzed the impact of using whole genome markers genotyped as either tetraploid or observed allele frequencies from genotype-by-sequencing data on single-trait additive genomic best linear unbiased prediction (GBLUP) genomic prediction (GP) models and single-marker regression genome-wide association studies of potato to evaluate the implications of capturing varying ploidy on the statistical models employed in genomic breeding. A panel of 762 offspring of a diallel cross of 18 parents of elite breeding material was used for modeling. These were genotyped by sequencing and phenotyped for five key performance traits: chipping quality, length/width ratio, senescence, dry matter content, and yield. We also estimated the read coverage required to confidently discriminate between a heterozygous triploid and tetraploid state from simulated data. It was found that using a tetraploid model neither impaired nor improved genomic predictions compared to using the observed allele frequencies that account for true marker ploidy. In genome-wide associations studies (GWAS), very minor variations of both signal amplitude and number of SNPs supporting both minor and major quantitative trait loci (QTLs) were observed between the two data sets. However, all major QTLs were reproducible using both data sets.

Accelerated breeding strategies for biochemical marker-assisted backcross breeding and mapping population development in bread wheat (Triticum aestivum L.)

In order to rapidly adapt to the evolving climate and sustainably nourish the growing global population, plant breeders are actively investigating more efficient strategies to enhance crop yields. In this study, we present the development of a bread wheat mapping population and backcross breeding program, serving as a valuable genetic resource for mapping the effects of different alleles on trait performance. We employed innovative methodologies to rapidly introgress traits into the bread wheat cultivar. Specifically, we utilized two parents, including Tosunbey x Tahirova2000, in a recombinant inbred line population, in addition, a backcross strategy was applied with line 148 (obtained by crossing Tosunbey x Tahirova2000 with high gluten quality) as the recipient parent of the Nevzatbey cv., known for its awnless feature. The two most important applications of the rapid breeding method are extending the light period and breaking dormancy in early harvested seeds. Both applications were successfully implemented in our study. Our vegetation periods ranging from approximately 50–60 days. Additionally, an early genotype in our developed population was harvested in 40 days. Considering that the genotype underwent a 15-day vernalization period, the generation cycle, including vernalization, drying, and refrigeration, was completed in a total of 64 days. Notably, we employed not only biochemical markers for selection but also incorporated the rapid generation advance technology known as ‘speed breeding’, allowing us to develop BC5F1 within a span of two years. We posit that this approach proves instrumental in swiftly transferring genes for multiple target traits into adapted wheat cultivars or in pyramiding desirable traits within elite breeding material.

Origin of current intermediate wheatgrass germplasm being developed for Kernza grain production

AbstractIntermediate wheatgrass (IWG, Thinopyrum intermedium [Host] Barkworth & D. R. Dewey) has been developed as a perennial grain crop for human consumption along with providing environmental benefits and ecosystem services. Grain and products derived from IWG cultivars improved for food production have been marketed under the registered trademark, Kernza. Development of IWG as a perennial grain crop began in 1980s with a phenotypic recurrent selection program as the Rodale Institute (RI) and the Big Flats Plant Material Center (BFPMC) used IWG plant introductions (PI) from the National Plant Germplasm System (NPGS) to improve populations of IWG. Initial selections were provided to The Land Institute (TLI) where they were subsequently improved for grain production, yet the identity of the founder material of improved, food-grade IWG has not been publicly documented. Recently recovered original documents have been used to reconstruct the early breeding program to identify the most likely 20 PIs that form the founders of modern food-grade IWG. Molecular data using genotyping-by-sequencing in current elite breeding material, and remnant seed and plant material from the initial RI selections have provided supporting evidence for the historical records. The genetic origin for food-grade IWG is focused between the Black Sea and Caspian Sea in the Stavropol region of Russia, with smaller contributions likely from collections as distant as Kazakhstan in the east to Turkey in the west. This work connects the flow of germplasm and utility of NPGS PIs to present day IWG grain cultivars being developed in multiple breeding programs around the world.

Variability of high dry matter orange‐fleshed sweetpotato [Ipomoea batatas (L.) Lam.] in later breeding stages and allocation of breeding resources in the humid tropics of Peru

AbstractOrange‐fleshed sweetpotato (OFSP) [Ipomoea batatas (L.) Lam] often lacks high dry matter (DM) in elite breeding material. The objectives were to examine the potential to combine yield with high root DM and high root β‐carotene (BC) content by variance‐covariance analysis and optimization of breeding scenarios for “OFSP dry and starchy,” which was exemplarily shown for the humid tropics of Peru. The trial series across seasons suggested a good chance to combine yield and quality (high DM and high BC). The unique data were used to estimate variance components and correlations among four yield traits and four quality traits. For the optimization of selections in our breeding program, we used the selection response by Cochran's approach and developed a small R script. Responses to selection were predicted for storage root yield and a modified Elston index aggregating eight traits. The differences between two‐ and three‐stage selection scenarios were small. For storage root yield, the recommended optimized two‐stage selection increased the response relative to the standard (one‐stage selection 100%) to 141.6% for 2268 plots and to 189.1% for 540 plots; the corresponding optimized three‐stage selection increased the response to 144.3% for 2268 plots and to 190.5% for 540 plots. A two‐stage selection is recommended with two to three locations at the first stage and 6–12 locations at the second stage, according to low‐ or high‐test capacity, respectively. Optimization of breeding schemes is much more important for smaller breeding programs than those with larger test capacity, and this allows testing even larger numbers of genotypes in a small breeding program.

Morphological, cytogenetic and molecular characterization of new somaclonal variants in four caladium (<i>Caladium</i> × <i>hortulanum</i>) cultivars

The discovery of triploids in caladium has raised strong interest in their use in cultivar development. For triploid production, tetraploids must first be generated from elite breeding material without the introduction of deleterious alleles like has been seen with chemical agents like colchicine and 2,4-D. To meet this new demand, virus eradicated, meristem-tip caladium cultures were grown on auxin-free media and used for generation and evaluation of new somaclonal variants. Over 12,000 micropropagated caladiums were visually screened <italic>ex vitro</italic> for sports varying from the wild-type phenotype. Eight variants from four cultivars were discovered and characterized for morphological, cytological, and molecular changes. Genome duplication occurred in seven of the variants with an average nuclear DNA content of 18.76 pg·2C⁻¹. The tetraploid variant of cultivar ‘White Wing’ had eight more chromosomes (2<italic>n</italic> = 4<italic>x</italic> = 68) than the other tetraploids and exactly double that of its wildtype. All other diploids had the expected 2<italic>n</italic> = 2<italic>x</italic> = 30 chromosomes and tetraploids recorded 2<italic>n</italic> = 4<italic>x</italic> = 60. Tetraploids had 19% rounder leaves and 44% thicker leaves than the diploids in the study. Tetraploids also had a 49% and 31% increase in stomata length and width, respectively. Molecular marker analysis only revealed two polymorphisms with both occurring in the 'White Wing' variant. Few changes in molecular marker banding could indicate that the tetraploids discovered have a clean duplication of the genome and might effectively be used for new triploid cultivar development.

Comparison of genetic impact on growth and wood traits between seedlings and clones from the same plus trees of Pinus koraiensis

To evaluate the relationships among clones and open pollinated families from the same plus trees and to select elite breeding materials, growth, and wood characteristics of 33-year-old Pinus koraiensis clones and families were measured and analyzed. The results show that growth and wood characters varied significantly. The variation due to clonal effects was higher than that of family effects. The ratio of genetic to phenotypic coefficient of variation of clones in growth and wood traits was above 90%, and the repeatability of these characteristics was more than 0.8, whereas the ratio of genetic to phenotypic coefficient of variation of families was above 90%. The broad-sense heritability of all characteristics exceeded 0.4, and the narrow-sense family heritability of growth traits was less than 0.3. Growth characteristics were positively correlated with each other, but most wood properties were weakly correlated in both clones and families. Fiber length and width were positively correlated between clones and families. Using the membership function method, eleven clones and four families were selected as superior material for improved diameter growth and wood production, and two families from clonal and open-pollinated trees showed consistently better performance. Generally, selection of the best clones is an effective alternative to deployment of families as the repeatability estimates from clonal trees were higher than narrow-sense heritability estimates from open pollinated families. The results provide valuable insight for improving P. koraiensis breeding programs and subsequent genetic improvement.

Virus Yellows in sugar beet – possibilities to achieve virus resistance

Virus yellows in sugar beet is caused by different virus species. Monitoring has shown that Beet yellows virus (BYV), Beet mild yellowing virus (BMYV), Beet chlorosis virus (BChV) are common and widespread, while Beet mosaic virus (BtMV) is less prevalent. The green peach aphid (Myzus persicae) is considered the main vector of these viruses. Sugar beet varieties with resistance or tolerance traits are currently not available to practical growers, therefore it is imperative to support breeding efforts with improved strategies to achieve virus resistance. For this purpose, a field test was established in which yield differences between susceptible and tolerant varieties can be generated by a 3% inoculation with BMYV-carrying aphids. A greenhouse bioassay has also been developed to distinguish susceptible and tolerant genotypes following BYV infection. Both assays pave the way for future use of natural resources such as wild forms and other breeding material to screen for virus resistance. In addition, molecular biology approaches are used to identify plant susceptibility factors of the plant-virus interaction, which will be knocked out via modern precision breeding methods to generate recessive virus resistance. Consequently, genotypes with naturally occurring mutations in the appropriate factors can be used for crossbreeding processes into elite breeding material.

Technological quality traits phenotyping of Camelina across multienvironment trials

ABSTRACT Camelina (Camelina sativa [L.] Crtz.) is an oilseed crop of the Brassicaceae family. It represents revived crops, which was reintroduced to contribute in diversification of the used crops. Field trials were set in a total of five different locations across four years in which in Serbia (2015/2016, 2016/2017, 2017/2018, 2018/2019) and in Austria (2016/2017). In all samples, 12 different environments were processed. Analysis of the distributions of environments for oil content, which mirrored protein content, using the PCA analysis, shows a statistical significance of the first two main components, which participated in the phenotypic variation with a larger amount to additive component and with both axes having a statistically significant effect on the interaction. The first two main components jointly explained more than 80% of the variation in two traits. The statistical significance of the remainder is a consequence of an agronomically explicable variation. The genotypes NS Zlatka and NS Slatka, used in this study, come from elite breeding material that is engineered to provide a consistent return to the producer regardless of the amount of money invested in primary agricultural production. Incorporating these varieties into the crop rotation would broaden the range of species available in Balkan agriculture.

Molecular and phenotypic evaluation for heading date and panicle length on F2 selected aromatic rice progenies derived from gene pyramiding effort

Gene pyramiding, an attempt to combine many favourable genes from many parents into one single genotype, has been applied in recent years. Through hybridization of many rice genotypes including cv. Pandanwangi (fragrance rice), PTB33 (brown planthopper resistant), Ciapus (high yield and moderate amylose content) and KA (early maturity), some promising genotypes have been obtained. Thus, in order to select the best genotypes among the F2 progenies derived from gene pyramiding effort, both phenotypic and molecular evaluations have to be done. These pyramided genotypes were evaluated with IFAP and ESP (fgr gene), RM19414 (Hd3), RM7601 (Hd2), and RM3600 (LP1) for molecular assessment, meanwhile morpho-agronomic traits were done to assess their performance. Aromatic trait was detected by 1.7% KOH. Meanwhile heading date and panicle length were measured phenotypically. Data obtained from molecular markers were scanned by visualizing DNA bands and calculating PIC (Polymorphism Information Content). Data from phenotypic markers were categorized based on IBPGR (International Board for Plant Genetic Resources) standards. Genotype #131 was supposed to have high yield potential, early maturity, aromatic, and intermediate amylose content. The selected will be recommended as promising genotype and continued as elite breeding materials and will be evaluated for their benefit.

Determination of genetic divergence in some bread wheat varieties by IRAP and ISSR analyses

In this study, it was aimed to detect the differences of genotypes through the measurement of genetic distance in bread wheat genotypes and to show the usability of chromosome mapping for different aims such as breeding programs, elite seed productions. The genetic diversity of 12 bread wheat genotypes bread wheat genotypes (Bozkır, Harmankaya 99, Altay 2000, Yıldırım, Bezostaja 1, Ahmetağa, Müfitbey, Aldane, Es 26, Alperbey, Atay 85 ad Eraybey) was examined through ISSR and IRAP techniques. As fast molecular techniques, ISSR and IRAP methods can be effectively included in breeding programs both for genetic exploration and evaluation and for the protection of elite breeding and production materials. 12 genotypes were classified into two main clusters in the dendrogram produced by using the ISSR and IRAP markers. While Cluster I included Bozkır, Harmankaya 99, Altay 2000, Yıldırım, Bezostaja 1, Ahmetağa and Müfitbey, cluster II included Aldane, Es 26, Alperbey, Atay 85 and Eraybey. Furthermore, the results obtained in this study indicated that ISSR and IRAP methods were effective for the definition of bread wheat genotypes.

Characterization of tomato accessions for morphological, agronomic, fruit quality, and virus resistance traits

Characterization of local germplasm is an effective way to identify elite breeding material and develop improved varieties. This study was aimed to assess 52 tomato accessions comprised of local varieties (28), landraces (8), breeding lines (14), and wild relatives (2), and their characterization for 30 morphological/agronomic, four fruit quality, and tomato mosaic virus (ToMV) resistance traits. Morphological, quality, and ToMV traits were evaluated using phenotyping, biochemical assays, and molecular markers, respectively. Fruit shape and size showed appreciable variation, with fruits varying from rounded to heart shaped and small to big size. Significant variation was observed for fruit weight (1.6–564.8 g), fruits per plant (6.0–174.7), productivity (130.5–5146.5 g), soluble solids (4.1%–8.4%), vitamin C (9.5–46.4 mg·100 g−1), antioxidant activity (2.5–9.6 μmol Fe2+·g−1fresh weight), and total polyphenols (23.9–124.2 GAE·100 g−1fresh weight). All accessions were phenotypically screened for the virus resistance in the growth chamber, and CAPS molecular markers were used to identify accessions with ToMV Tm-22resistant alleles, and accessions LYC-13, LYC-15, LYC-17, LYC-26, and LYC-52 were identified as resistant. Multivariate analysis of morphological and quality traits showed that 35 principal components contributed to the total variation and the first two and 12 principal components explained 47.2% and 90% of the variation, respectively. The evaluated tomato collection appears to have breeding potential, and around 20% of the accessions in the collection (LYC-6, LYC-17, LYC-18, LYC-26 to LYC-31, and LYC 33) are promising genetic resources for variety development that are enriched with enhanced fruit quality and high yield.

Detection of Quantitative Trait Loci (QTL) Associated with the Fruit Morphology of Tomato.

Tomato (Solanum lycopersicum L.) is the second most-consumed vegetable in the world. The market value and culinary purpose of tomato are often determined by fruit size and shape, which makes the genetic improvement of these traits a priority for tomato breeders. The main objective of the study was to detect quantitative trait loci (QTL) associated with the tomato fruit shape and size. The use of elite breeding materials in the genetic mapping studies will facilitate the detection of genetic loci of direct relevance to breeders. We performed QTL analysis in an intra-specific population of tomato developed from a cross between two elite breeding lines NC 30P × NC-22L-1(2008) consisting of 110 recombinant inbred lines (RIL). The precision software Tomato Analyzer (TA) was used to measure fruit morphology attributes associated with fruit shape and size traits. The RIL population was genotyped with the SolCAP 7720 SNP array. We identified novel QTL controlling elongated fruit shape on chromosome 10, explaining up to 24% of the phenotypic variance. This information will be useful in improving tomato fruit morphology traits.

The Dawn of the Age of Multi-Parent MAGIC Populations in Plant Breeding: Novel Powerful Next-Generation Resources for Genetic Analysis and Selection of Recombinant Elite Material.

The compelling need to increase global agricultural production requires new breeding approaches that facilitate exploiting the diversity available in the plant genetic resources. Multi-parent advanced generation inter-cross (MAGIC) populations are large sets of recombinant inbred lines (RILs) that are a genetic mosaic of multiple founder parents. MAGIC populations display emerging features over experimental bi-parental and germplasm populations in combining significant levels of genetic recombination, a lack of genetic structure, and high genetic and phenotypic diversity. The development of MAGIC populations can be performed using “funnel” or “diallel” cross-designs, which are of great relevance choosing appropriate parents and defining optimal population sizes. Significant advances in specific software development are facilitating the genetic analysis of the complex genetic constitutions of MAGIC populations. Despite the complexity and the resources required in their development, due to their potential and interest for breeding, the number of MAGIC populations available and under development is continuously growing, with 45 MAGIC populations in different crops being reported here. Though cereals are by far the crop group where more MAGIC populations have been developed, MAGIC populations have also started to become available in other crop groups. The results obtained so far demonstrate that MAGIC populations are a very powerful tool for the dissection of complex traits, as well as a resource for the selection of recombinant elite breeding material and cultivars. In addition, some new MAGIC approaches that can make significant contributions to breeding, such as the development of inter-specific MAGIC populations, the development of MAGIC-like populations in crops where pure lines are not available, and the establishment of strategies for the straightforward incorporation of MAGIC materials in breeding pipelines, have barely been explored. The evidence that is already available indicates that MAGIC populations will play a major role in the coming years in allowing for impressive gains in plant breeding for developing new generations of dramatically improved cultivars.

Genetic Resources, Breeding Programs in China, and Gene Mining of Peach: A Review

ABSTRACT Research on peach genetic resources and breeding has achieved remarkable progress in recent decades, especially in China. In this review, we first described the geographic distribution, ecology, phenotypes, and genetic diversity of peach landraces and wild relatives in China. We also discussed the almond. Subsequently, breeding programs of peaches in China are summarized, including breeding history, breeding targets, breeding institutes, elite breeding materials, breeding solutions, and domestically bred representative cultivars. Furthermore, we reviewed the genes or loci that have been mined using both linkage mapping and genome wide association study (GWAS) as well as the evolutionary genetics and domestication history of the peach. Finally, we gave our perspectives and suggestions for future breeding in terms of breeding material selection and breeding technology innovation.

Genetic mapping of the common and dwarf bunt resistance gene Bt12 descending from the wheat landrace PI119333

Common bunt (CB), caused by Tilletia caries and T. foetida, and dwarf bunt (DB), caused by T. controversa, are particularly destructive diseases of wheat grown under organic (low-input) production conditions and negatively affect both grain yield and quality. A total of 16 race specific bunt resistance genes have been proposed to date. Thereof, only Bt9 and Bt10 have been mapped so far. A mapping and two validation populations comprising 176 recombinant inbred lines were evaluated for CB and DB in artificially inoculated field trials. The mapping population was derived from the cross of the Bt12 carrier PI119333 and the susceptible cultivar ‘Rainer’. The population was genotyped with the Illumina 15 K SNP chip and the major QTL QBt.ifa-7DS representing Bt12 was identified on chromosome 7DS, explaining 39% and 14% of the phenotypic variation for CB and DB resistance, respectively. Selected SNP markers were turned into Kompetitive Allele-Specific (KASP) markers and used to validate Bt12 in two independent validation populations. These markers can be used for introgressing Bt12 into regionally adapted elite breeding material.

Rapid Isolation of Loss‐of‐Function Mutations for Dominant Traits: A Case Study Using Photoperiod Sensitivity Trait in Pima Cotton

In its natural state, cotton (Gossypium spp.) is a perennial that flowers only under short‐day conditions. Early selection efforts eliminated this photoperiod requirement, allowing cotton cultivation to shift predominantly to annual growth under long summer daylengths throughout the world. Photoperiod sensitivity persists in many wild cottons and remains a major barrier to the introgression of beneficial alleles into elite breeding material. Identification of the variation and genetic factors underlying photoperiod response in cotton is needed to fully harness the genetic diversity of wild cotton and broaden the cultivated germplasm pool. Genetic variants, especially loss‐of‐function mutations in dominant genes conferring photoperiod sensitivity, would be highly valuable in this regard. After mutagenizing pima cotton (G. barbadense L.) seeds heterozygous for the major photoperiod response gene Gb_Ppd1 with γ rays, we identified plants no longer sensitive to photoperiod. Genetic analysis of BC1F1 plants derived from backcrossing the mutants with their photoperiod‐insensitive parent confirmed the loss‐of‐function mutations were allelic with Gb_Ppd1. Characterization of the mutants with molecular markers confirmed that all but one were deletions of Gb_Ppd1. Further, genotyping localized Gb_Ppd1 to a 12‐Mb region on chromosome D10. The newly identified genomic region and loss‐of‐function mutants may help assist with the identification and functional validation of candidate genes for photoperiod response in cotton, facilitating the valuable introgression of genetic diversity into cotton breeding programs.

Genetic dissection of grain elements predicted by hyperspectral imaging associated with yield-related traits in a wild barley NAM population

Enhancing the accumulation of essential mineral elements in cereal grains is of prime importance for combating human malnutrition. Biofortification by breeding holds great potential for improving nutrient accumulation in grains. However, conventional breeding approaches require element analysis of many grain samples, which causes high costs. Here we applied hyperspectral imaging to estimate the concentration of 15 grain elements (C, B, Ca, Cd, Cu, Fe, K, Mg, Mn, Mo, N, Na, P, S, Zn) in high-throughput in the wild barley nested association mapping (NAM) population HEB-25, comprising 1,420 BC1S3 lines derived from crossing 25 wild barley accessions with the cultivar ‘Barke’. Nutrient concentrations varied largely with a multitude of lines having higher micronutrient concentration than ‘Barke’. In a genome-wide association study (GWAS), we located 75 quantitative trait locus (QTL) hotspots, whereof many could be explained by major genes such as NO APICAL MERISTEM-1 (NAM-1) and PHOTOPERIOD 1 (Ppd-H1). The GWAS approach revealed exotic alleles that were able to increase grain element concentrations. Remarkably, a QTL linked to GIBBERELLIN 20 OXIDASE 2 (HvGA20ox2) significantly increased several grain elements without yield loss. We conclude that introgressing promising exotic alleles into elite breeding material can assist in improving the nutritional value of barley grains.

Use of genetic resources to develop new commercial Rhododendron simsii hybrids

Rhododendron simsii Planch. hybrid or pot azalea is the most important ornamental plant in Belgium. At least four different species (R. simsii, Rhododendron indicum, Rhododendron scabrum and Rhododendron mucronatum) have contributed to modern hybrids. These species are found in parts of China and Japan. R. simsii introduced the early flowering trait and the ability to produce flower sports. The other species contributed to the diversification of flower color (purple, carmine red), large flowers and specific plant habitus. The Instituut voor Landbouw-, Visserij- en Voedingsonderzoek (ILVO) holds a large gene bank of pot azalea accessions and their wild relatives. To safeguard this gene bank, the core collection is also partly kept in cryopreservation. Gene bank accessions are used for both genetic studies and breeding. In recent years, we have specifically focused on introgression of traits such as new flower and growth forms, fragrance, and disease resistance. The introduction of such specific traits from a wild species into elite breeding material is time consuming, as several backcrosses are necessary. For some characteristics, i.e., disease resistance, adapted screening methods have been developed that enable us to select more adequately.

Rice Galaxy: an open resource for plant science.

BackgroundRice molecular genetics, breeding, genetic diversity, and allied research (such as rice-pathogen interaction) have adopted sequencing technologies and high-density genotyping platforms for genome variation analysis and gene discovery. Germplasm collections representing rice diversity, improved varieties, and elite breeding materials are accessible through rice gene banks for use in research and breeding, with many having genome sequences and high-density genotype data available. Combining phenotypic and genotypic information on these accessions enables genome-wide association analysis, which is driving quantitative trait loci discovery and molecular marker development. Comparative sequence analyses across quantitative trait loci regions facilitate the discovery of novel alleles. Analyses involving DNA sequences and large genotyping matrices for thousands of samples, however, pose a challenge to non−computer savvy rice researchers.FindingsThe Rice Galaxy resource has shared datasets that include high-density genotypes from the 3,000 Rice Genomes project and sequences with corresponding annotations from 9 published rice genomes. The Rice Galaxy web server and deployment installer includes tools for designing single-nucleotide polymorphism assays, analyzing genome-wide association studies, population diversity, rice−bacterial pathogen diagnostics, and a suite of published genomic prediction methods. A prototype Rice Galaxy compliant to Open Access, Open Data, and Findable, Accessible, Interoperable, and Reproducible principles is also presented.ConclusionsRice Galaxy is a freely available resource that empowers the plant research community to perform state-of-the-art analyses and utilize publicly available big datasets for both fundamental and applied science.

Genetic Diversity among Tropical Provitamin A Maize Inbred Lines and Implications for a Biofortification Program

Insights into the diversity and relationships among elite breeding materials are an important component in maize improvement programs. We genotyped 63 inbred lines bred for high levels of provitamin A using 137 single nucleotide polymorphism markers. A total of 272 alleles were detected with gene diversity of 0.36. Average genetic distance was 0.36 with 56% of the pairs of lines having between 0.30 and 0.40. Eighty-six percent of the pairs of lines showed relative kinship values <0.50, which indicated that the majority of these provitamin A inbred lines were unique. Relationship pattern and population structure analysis revealed presence of seven major groups with good agreement with Neighbour Joining clustering and somewhat correlated with pedigree and breeding origin. Utilization of this set of provitamin A lines in a new biofortification program will be aided by information from both molecular-based grouping and pedigree analysis. The results should guide breeders in selecting parents for hybrid formation and testing as a short-term objective, and parents with diverse alleles for new breeding starts as a long-term objective in a provitamin A breeding program.