A Proposal Regarding Best Practices for Validating the Identity of Genetic Stocks and the Effects of Genetic Variants

Genotyping Genebank Collections: Strategic Approaches and Considerations for Optimal Collection Management

The maintenance of plant germplasm and its genetic diversity is critical to preserving and making it available for food security, so this invaluable diversity is not permanently lost due to population growth and development, climate change, or changing needs from the growers and/or the marketplace. There are numerous genebanks worldwide that serve to preserve valuable plant germplasm for humankind's future and to serve as a resource for research, breeding, and training. The United States Department of Agriculture (USDA) National Plant Germplasm System (NPGS) and the Consultative Group for International Agricultural Research (CGIAR) both have a network of plant germplasm collections scattered across varying geographical locations preserving genetic resources for the future. Besides the USDA and CGIAR, there are germplasm collections established in many countries across the world that also aim to preserve crop and plant collections. Due to the advancement of technology, genotyping and sequencing whole genomes of plant germplasm collections is now feasible. Data from genotyping can help define genetic diversity within a collection, identify genetic gaps, reveal genetic redundancies and verify uniqueness, enable the comparison of collections of the same crop across genebanks (rationalization), and determine errors or mix-ups in genetic identity that may have occurred in a germplasm collection. Large-scale projects, such as genotyping germplasm collections, require strategic planning and the development of best practices. This article details strategies and best practices to consider when genotyping whole collections, considerations for the identity verification of germplasm and determining genetic replicates, quality management systems (QMS)/QC genotyping, and some use cases.

Promiscuous potato: elucidating genetic identity and the complex genetic relationships of a cultivated potato germplasm collection

A total of 3,860 accessions from the global in trust clonal potato germplasm collection w3ere genotyped with the Illumina Infinium SolCAP V2 12K potato SNP array to evaluate genetic diversity and population structure within the potato germplasm collection. Diploid, triploid, tetraploid, and pentaploid accessions were included representing the cultivated potato taxa. Heterozygosity ranged from 9.7% to 66.6% increasing with ploidy level with an average heterozygosity of 33.5%. Identity, relatedness, and ancestry were evaluated using hierarchal clustering and model-based Bayesian admixture analyses. Errors in genetic identity were revealed in a side-by-side comparison of in vitro clonal material with the original mother plants revealing mistakes putatively occurring during decades of processing and handling. A phylogeny was constructed to evaluate inter- and intraspecific relationships which together with a STRUCTURE analysis supported both commonly used treatments of potato taxonomy. Accessions generally clustered based on taxonomic and ploidy classifications with some exceptions but did not consistently cluster by geographic origin. STRUCTURE analysis identified putative hybrids and suggested six genetic clusters in the cultivated potato collection with extensive gene flow occurring among the potato populations, implying most populations readily shared alleles and that introgression is common in potato. Solanum tuberosum subsp. andigena (ADG) and S. curtilobum (CUR) displayed significant admixture. ADG likely has extensive admixture due to its broad geographic distribution. Solanum phureja (PHU), Solanum chaucha (CHA)/Solanum stenotomum subsp. stenotomum (STN), and Solanum tuberosum subsp. tuberosum (TBR) populations had less admixture from an accession/population perspective relative to the species evaluated. A core and mini core subset from the genebank material was also constructed. SNP genotyping was also carried out on 745 accessions from the Seed Savers potato collection which confirmed no genetic duplication between the two potato collections, suggesting that the collections hold very different genetic resources of potato. The Infinium SNP Potato Array is a powerful tool that can provide diversity assessments, fingerprint genebank accessions for quality management programs, use in research and breeding, and provide insights into the complex genetic structure and hybrid origin of the diversity present in potato genetic resource collections.

DEFECTIVELY ORGANIZED TRIBUTARIES 5 is not required for leaf venation patterning in Arabidopsis thaliana

The search for genetic regulators of leaf venation patterning started over 30 years ago, primarily focused on mutant screens in the eudicotyledon Arabidopsis thaliana. Developmental perturbations in either cotyledons or true leaves led to the identification of transcription factors required to elaborate the characteristic reticulated vein network. An ortholog of one of these, the C2H2 zinc finger protein DEFECTIVELY ORGANIZED TRIBUTARIES 5 (AtDOT5), was recently identified through transcriptomics as a candidate regulator of parallel venation in maize (Zea mays) leaves. To elucidate how AtDOT5 regulates vein patterning, we generated three independent loss-of-function mutations by gene editing in Arabidopsis. Surprisingly, none of them exhibited any obvious phenotypic perturbations. To reconcile our findings with earlier reports, we re-evaluated the original Atdot5-1 and Atdot5-2 alleles. By genome sequencing, we show that reported mutations at the Atdot5-1 locus are actually polymorphisms between Landsberg erecta and Columbia ecotypes, and that other mutations present in the background most likely cause the pleiotropic mutant phenotype observed. We further show that a T-DNA insertion in the Atdot5-2 locus has no impact on leaf venation patterns when segregated from other T-DNA insertions present in the original line. We thus conclude that AtDOT5 plays no role in leaf venation patterning in Arabidopsis.

Genetic Identity, Diversity, and Population Structure of CIP's Sweetpotato (I. batatas) Germplasm Collection

The in trust sweetpotato collection housed by the International Center of Potato (CIP) is one of the largest assemblages of plant material representing the genetic resources of this important staple crop. The collection currently contains almost 6,000 accessions of Ipomoea batatas (cultivated sweetpotato) and over 1,000 accessions of sweetpotato crop wild relatives (CWRs). In this study, the entire cultivated collection (5,979 accessions) was genotyped with a panel of 20 simple sequence repeat (SSR) markers to assess genetic identity, diversity, and population structure. Genotyping and phenotyping of in vitro plantlets and mother plants were conducted simultaneously on 2,711 accessions (45% of the total collection) to identify and correct possible genetic identity errors which could have occurred at any time over the thirty plus years of maintenance in the in vitro collection. Within this group, 533 accessions (19.6%) had errors in identity. Field evaluations of morphological descriptors were carried out to confirm the marker data. A phylogenetic tree was constructed to reveal the intraspecific relationships in the population which uncovered high levels of redundancy in material from Peru and Latin America. These genotypic data were supported by morphological data. Population structure analysis demonstrated support for four ancestral populations with many of the accessions having lower levels of gene flow from the other populations. This was especially true of germplasm derived from Peru, Ecuador, and Africa. The set of 20 SSR markers was subsequently utilized to examine a subset of 189 accessions from the USDA sweetpotato germplasm collection and to identify and reconcile potential errors in the identification of clones shared between these collections. Marker analysis demonstrated that the USDA subset of material had 65 unique accessions that were not found in the larger CIP collection. As far as the authors are aware, this is the first report of genotyping an entire sweetpotato germplasm collection in its entirety.

Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation

The genus Phytophthora comprises many economically and ecologically important plant pathogens. Hybrid species have previously been identified in at least six of the 12 phylogenetic clades. These hybrids can potentially infect a wider host range and display enhanced vigour compared to their progenitors. Phytophthora hybrids therefore pose a serious threat to agriculture as well as to natural ecosystems. Early and correct identification of hybrids is therefore essential for adequate plant protection but this is hampered by the limitations of morphological and traditional molecular methods. Identification of hybrids is also important in evolutionary studies as the positioning of hybrids in a phylogenetic tree can lead to suboptimal topologies. To improve the identification of hybrids we have combined genotyping-by-sequencing (GBS) and genome size estimation on a genus-wide collection of 614 Phytophthora isolates. Analyses based on locus- and allele counts and especially on the combination of species-specific loci and genome size estimations allowed us to confirm and characterize 27 previously described hybrid species and discover 16 new hybrid species. Our method was also valuable for species identification at an unprecedented resolution and further allowed correct naming of misidentified isolates. We used both a concatenation- and a coalescent-based phylogenomic method to construct a reliable phylogeny using the GBS data of 140 non-hybrid Phytophthora isolates. Hybrid species were subsequently connected to their progenitors in this phylogenetic tree. In this study we demonstrate the application of two validated techniques (GBS and flow cytometry) for relatively low cost but high resolution identification of hybrids and their phylogenetic relations.

slim shady is a novel allele of PHYTOCHROME B present in the T-DNA line SALK_015201

Auxin is a hormone that is required for hypocotyl elongation during seedling development. In response to auxin, rapid changes in transcript and protein abundance occur in hypocotyls, and some auxin responsive gene expression is linked to hypocotyl growth. To functionally validate proteomic studies, a reverse genetics screen was performed on mutants in auxin-regulated proteins to identify novel regulators of plant growth. This uncovered a long hypocotyl mutant, which we called slim shady, in an annotated insertion line in IMMUNOREGULATORY RNA-BINDING PROTEIN (IRR). Overexpression of the IRR gene failed to rescue the slim shady phenotype and characterization of a second T-DNA allele of IRR found that it had a wild-type (WT) hypocotyl length. The slim shady mutant has an elevated expression of numerous genes associated with the brassinosteroid-auxin-phytochrome (BAP) regulatory module compared to WT, including transcription factors that regulate brassinosteroid, auxin, and phytochrome pathways. Additionally, slim shady seedlings fail to exhibit a strong transcriptional response to auxin. Using whole genome sequence data and genetic complementation analysis with SALK_015201C, we determined that a novel single nucleotide polymorphism in PHYTOCHROME B was responsible for the slim shady phenotype. This is predicted to induce a frameshift and premature stop codon at leucine 1125, within the histidine kinase-related domain of the carboxy terminus of PHYB, which is required for phytochrome signaling and function. Genetic complementation analyses with phyb-9 confirmed that slim shady is a mutant allele of PHYB. This study advances our understanding of the molecular mechanisms in seedling development, by furthering our understanding of how light signaling is linked to auxin-dependent cell elongation. Furthermore, this study highlights the importance of confirming the genetic identity of research material before attributing phenotypes to known mutations sourced from T-DNA stocks.

Development and screening of EMS mutants with altered seed oil content or fatty acid composition in Brassica napus

Brassica napus is an important oilseed crop in the world, and the mechanism of seed oil biosynthesis in B. napus remains unclear. In order to study the mechanism of oil biosynthesis and generate germplasms for breeding, an ethyl methanesulfonate (EMS) mutant population with ~100 000 M2 lines was generated using Zhongshuang 11 as the parent line. The EMS-induced genome-wide mutations in M2-M4 plants were assessed. The average number of mutations including single nucleotide polymorphisms and insertion/deletion in M2-M4 was 21 177, 28 675 and 17 915, respectively. The effects of the mutations on gene function were predicted in M2-M4 mutants, respectively. We screened the seeds from 98 113 M2 lines, and 9415 seed oil content and fatty acid mutants were identified. We further confirmed 686 mutants with altered seed oil content and fatty acid in advanced generation (M4 seeds). Five representative M4 mutants with increased oleic acid were re-sequenced, and the potential causal variations in FAD2 and ROD1 genes were identified. This study generated and screened a large scale of B. napus EMS mutant population, and the identified mutants could provide useful genetic resources for the study of oil biosynthesis and genetic improvement of seed oil content and fatty acid composition of B. napus in the future.

An ethyl methanesulfonate-induced neutral mutant-bridging method efficiently identifies spontaneously mutated genes in rice

Spontaneous mutants are mainly obtained from tissue culture or natural occurrences in plants. The traditional strategy for identifying spontaneously mutated genes is to continuously backcross these mutants to another variety and develop a near-isogenic F₂ population for map-based cloning or bulked segregant analysis. However, this strategy is time-consuming. Here, we have developed a new method to efficiently accelerate the identification process. The chemical mutagen ethyl methanesulfonate was first used to treat the wild type of the spontaneous mutants to induce thousands of neutral mutations. An induced individual without any statistically significant phenotypic changes which was compared with the wild type was chosen as the neutral mutant. The spontaneous mutant was then crossed with the neutral mutant to develop a pseudo-near-isogenic F₂ population in which only the induced neutral mutations and the causal mutation were segregated in the genome. This population ensures that the variation of the mutated trait is controlled only by the spontaneously mutated gene. Finally, after sequencing the neutral mutant and the mutant-type DNA pool of the F₂ population the spontaneous mutation will be identified quickly by bioinformatics analysis. Using this method, two spontaneously mutated genes were identified successfully. Therefore, the neutral mutant-bridging method efficiently identifies spontaneously mutated genes in rice, and its value in other plants is discussed.

Diversity of genetic lesions characterizes new Arabidopsis flavonoid pigment mutant alleles from T-DNA collections

The visual phenotypes afforded by flavonoid pigments have provided invaluable tools for modern genetics. Many Arabidopsis transparent testa (tt) mutants lacking the characteristic proanthocyanidin (PA) seed coat pigmentation and often failing to accumulate anthocyanins in vegetative tissues have been characterized. These mutants have significantly contributed to our understanding of flavonoid biosynthesis, regulation, and transport. A comprehensive screening for tt mutants in available large T-DNA collection lines resulted in the identification of 16 independent lines lacking PAs and anthocyanins, or with seed coat pigmentation clearly distinct from wild type. Segregation analyses and the characterization of second alleles in the genes disrupted by the indexed T-DNA insertions demonstrated that all the lines contained at least one additional mutation responsible for the tt phenotypes. Using a combination of RNA-Seq and whole genome re-sequencing and confirmed through complementation, we show here that these mutations correspond to novel alleles of ttg1 (two alleles), tt3 (two alleles), tt5 (two alleles), ban (two alleles), tt1 (two alleles), and tt8 (six alleles), which harbored additional T-DNA insertions, indels, missense mutations, and large genomic deletion. Several of the identified alleles offer interesting perspectives on flavonoid biosynthesis and regulation.

Construction and comparison of three reference-quality genome assemblies for soybean

We report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G. max. The G. max assemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G. soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single-nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines and G. soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan-gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40-42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G. soja and the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species.

Arabidopsis research requires a critical re-evaluation of genetic tools

An increasing number of reports question conclusions based on loss-of-function lines that have unexpected genetic backgrounds. In this opinion paper, we urge researchers to meticulously (re)investigate phenotypes retrieved from various genetic backgrounds and be critical regarding some previously drawn conclusions. As an example, we provide new evidence that acr4-2 mutant phenotypes with respect to columella stem cells are due to the lack of ACR4 and not - at least not as a major contributor - to a mutation in QRT1. In addition, we take the opportunity to alert the scientific community about the qrt1-2 background of a large number of Syngenta Arabidopsis Insertion Library (SAIL) T-DNA lines, a feature that is not commonly recognized by Arabidopsis researchers. This qrt1-2 background might have an important impact on the interpretation of the results obtained using these research tools, now and in the past. In conclusion, as a community, we should continuously assess and - if necessary - correct our conclusions based on the large number of (genetic) tools our work is built on. In addition, the positive or negative results of this self-criticism should be made available to the scientific community.

The importance of genotype identity, genetic heterogeneity, and bioinformatic handling for properly assessing genomic variation in transgenic plants

BACKGROUND

The advent of -omics technologies has enabled the resolution of fine molecular differences among individuals within a species. DNA sequence variations, such as single nucleotide polymorphisms or small deletions, can be tabulated for many kinds of genotype comparisons. However, experimental designs and analytical approaches are replete with ways to overestimate the level of variation present within a given sample. Analytical pipelines that do not apply proper thresholds nor assess reproducibility among samples are susceptible to calling false-positive variants. Furthermore, issues with sample genotype identity or failing to account for heterogeneity in reference genotypes may lead to misinterpretations of standing variants as polymorphisms derived de novo.

RESULTS

A recent publication that featured the analysis of RNA-sequencing data in three transgenic soybean event series appeared to overestimate the number of sequence variants identified in plants that were exposed to a tissue culture based transformation process. We reanalyzed these data with a stringent set of criteria and demonstrate three different factors that lead to variant overestimation, including issues related to the genetic identity of the background genotype, unaccounted genetic heterogeneity in the reference genome, and insufficient bioinformatics filtering.

CONCLUSIONS

This study serves as a cautionary tale to users of genomic and transcriptomic data that wish to assess the molecular variation attributable to tissue culture and transformation processes. Moreover, accounting for the factors that lead to sequence variant overestimation is equally applicable to samples derived from other germplasm sources, including chemical or irradiation mutagenesis and genome engineering (e.g., CRISPR) processes.

Genetic identity in genebanks: application of the SolCAP 12K SNP array in fingerprinting and diversity analysis in the global in trust potato collection

Breeders rely on genetic integrity of material from genebanks; however, admixture, mislabeling, and errors in original data can occur and be detrimental. Two hundred and fifty accessions, representing paired samples consisting of original mother plants and their in vitro counterparts from the cultivated potato collection at the International Potato Center (CIP) were fingerprinted using the Infinium 12K V2 Potato Array to confirm genetic identity of the accessions and evaluate genetic diversity of the potato collection. Diploid, triploid, and tetraploid accessions were included, representing seven cultivated potato taxa (based on Hawkes, 1990). Fingerprints between voucher mother plants maintained in the field and in vitro clones of the same accession were used to evaluate identity, relatedness, and ancestry using hierarchal clustering and model-based Bayesian admixture analyses. Generally, in vitro and field clones of the same accession grouped together; however, 11 (4.4%) accessions were mismatches genetically, and in some cases the SNP data revealed the identity of the mixed accession. SNP genotypes were used to assess genetic diversity and to evaluate inter- and intraspecific relationships along with determining population structure and hybrid origins. Phylogenetic analyses suggest that the triploids included in this study are genetically similar. Further, some genetic redundancies among individual accessions were also identified along with some putative misclassified accessions. Accessions generally clustered together based on taxonomic classification and ploidy level with some deviations. STRUCTURE analysis identified six populations with significant gene flow among the populations, as well as revealed hybrid taxa and accessions. Overall, the Infinium 12K V2 Potato Array proved useful in confirming identity and highlighting the diversity in this subset of the CIP collection, providing new insights into the accessions evaluated. This study provides a model for genetic identity of plant genetic resources collections as mistakes in conservation of these collections and in genebanks is a reality. For breeders and other users of these collections, confirmed identity is critical, as well as for quality management programs and to provide insights into the accessions evaluated.

Arabidopsis mutants may represent recombinant introgression lines

OBJECTIVES

It is a common practice in Arabidopsis to transfer a mutation generated in one genetic background to other genetic background via crossing. However, the drawback of this methodology is unavoidable presence of genomic fragments from the donor parent being often replacing desirable genomic fragments of the recurrent parent. Here, we highlighted problem of Arabidopsis mutants being recombinant introgression lines that can lead to unreliable and misinterpreted results.

RESULTS

We studied the regulation of low copy number transposable elements Tag1 and Evelknievel (EK), located at the end of the bottom arm of chromosome 1 and both are present in the Arabidopsis Landsberg erecta (Ler) but not in Columbia (Col) ecotype. Using various epigenetic mutants (cmt3, ddm1, kyp2, ago4, rdr2 hen1 etc.), we found that certain mutants in the Ler background are deficient of Tag1 or EK or both and represent recombinant introgression lines whereby chromosomal regions from Col have been recombined into the Ler genome. Our data support a recent proposal calling for formulating standards for authentication of plant lines that are used in plant research. Most important is to verify that a given trait or genomic locus under study is correctly identified, particularly when using mutants generated by crossing.

Verification of Arabidopsis stock collections using SNPmatch, a tool for genotyping high-plexed samples

Large-scale studies such as the Arabidopsis thaliana ‘1,001 Genomes’ Project require routine genotyping of stocks to avoid sample contamination. To genotype samples efficiently and economically, sequencing must be inexpensive and data processing simple. Here we present SNPmatch, a tool that identifies strains (or inbred lines, or accessions) by matching them to a SNP database. We tested the tool by performing low-coverage resequencing of over 2,000 strains from our lab seed stock collection. SNPmatch correctly genotyped samples from 1-fold coverage sequencing data, and could also identify the parents of F1 or F2 individuals. SNPmatch can be run either on the command line or through AraGeno (https://arageno.gmi.oeaw.ac.at), a web interface that permits sample genotyping from a user-uploaded VCF or BED file.

Extracting genotype information of Arabidopsis thaliana recombinant inbred lines from transcript profiles established with high-density oligonucleotide arrays

Polymorphic probes identified via a sequence-based approach are suitable to infer the genotypes of recombinant inbred lines from hybridisation intensities of GeneChip ^® transcript profiling experiments. The sequences of the probes of the ATH1 GeneChip^® exactly match transcript sequences of the Arabidopsis thaliana reference genome Col-0, whereas nucleotide differences and/or insertions/deletions may be observed for transcripts of other A. thaliana accessions. Individual probes of the GeneChip^® that show sequence polymorphisms between different A. thaliana accessions may serve as single-feature polymorphism (SFP) markers, provided that the sequence changes cause differences in hybridisation intensity for the accessions of interest. A sequence-based approach identified features on the high-density oligonucleotide array that showed sequence polymorphisms between A. thaliana accessions Col-0 and C24. Hybridisation intensities of polymorphic probes were extracted from genome-wide transcript profiles of Col-0/C24 and C24/Col-0 recombinant inbred lines and assessed after standardisation via sliding window analyses to identify SFP markers. The genotypes of the recombinant inbred lines were determined with the SFP markers and the resulting data were integrated with information, which had been established previously with single nucleotide polymorphism and insertion/deletion markers, to enrich the linkage map of the Col-0/C24 and C24/Col-0 recombinant inbred populations. Congruence between the molecular marker map and the sequence maps of the A. thaliana Col-0 chromosomes proved the reliability of the genotype information which was deduced from the transcript profiles of the Col-0/C24 and C24/Col-0 recombinant inbred lines.

kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity

Modern genomics techniques generate overwhelming quantities of data. Extracting population genetic variation demands computationally efficient methods to determine genetic relatedness between individuals (or "samples") in an unbiased manner, preferably de novo. Rapid estimation of genetic relatedness directly from sequencing data has the potential to overcome reference genome bias, and to verify that individuals belong to the correct genetic lineage before conclusions are drawn using mislabelled, or misidentified samples. We present the k-mer Weighted Inner Product (kWIP), an assembly-, and alignment-free estimator of genetic similarity. kWIP combines a probabilistic data structure with a novel metric, the weighted inner product (WIP), to efficiently calculate pairwise similarity between sequencing runs from their k-mer counts. It produces a distance matrix, which can then be further analysed and visualised. Our method does not require prior knowledge of the underlying genomes and applications include establishing sample identity and detecting mix-up, non-obvious genomic variation, and population structure. We show that kWIP can reconstruct the true relatedness between samples from simulated populations. By re-analysing several published datasets we show that our results are consistent with marker-based analyses. kWIP is written in C++, licensed under the GNU GPL, and is available from https://github.com/kdmurray91/kwip.

Safeguarding Our Genetic Resources with Libraries of Doubled-Haploid Lines

Thousands of landraces are stored in seed banks as "gold reserves" for future use in plant breeding. In many crops, their utilization is hampered because they represent heterogeneous populations of heterozygous genotypes, which harbor a high genetic load. We show, with high-density genotyping in five landraces of maize, that libraries of doubled-haploid (DH) lines capture the allelic diversity of genetic resources in an unbiased way. By comparing allelic differentiation between heterozygous plants from the original landraces and 266 derived DH lines, we find conclusive evidence that, in the DH production process, sampling of alleles is random across the entire allele frequency spectrum, and purging of landraces from their genetic load does not act on specific genomic regions. Based on overall process efficiency, we show that generating DH lines is feasible for genetic material that has never been selected for inbreeding tolerance. We conclude that libraries of DH lines will make genetic resources accessible to crop improvement by linking molecular inventories of seed banks with meaningful phenotypes.

Controlling for genetic identity of varieties, pollen contamination and stigma receptivity is essential to characterize the self-incompatibility system of Olea europaea L

Bervillé et al. express concern about the existence of the diallelic self‐incompatibility (DSI) system in Olea europaea, mainly because our model does not account for results from previous studies from their group that claimed to have documented asymmetry of the incompatibility response in reciprocal crosses. In this answer to their comment, we present original results based on reciprocal stigma tests that contradict conclusions from these studies. We show that, in our hands, not a single case of asymmetry was confirmed, endorsing that symmetry of incompatibility reactions seems to be the rule in Olive. We discuss three important aspects that were not taken into account in the studies cited in their comments and that can explain the discrepancy: (i) the vast uncertainty around the actual genetic identity of vernacular varieties, (ii) the risk of massive contamination associated with the pollination protocols that they used and (iii) the importance of checking for stigma receptivity in controlled crosses. These studies were thus poorly genetically controlled, and we stand by our original conclusion that Olive tree exhibits DSI.

Time dependent genetic analysis links field and controlled environment phenotypes in the model C4 grass Setaria

Vertical growth of plants is a dynamic process that is influenced by genetic and environmental factors and has a pronounced effect on overall plant architecture and biomass composition. We have performed six controlled growth trials of an interspecific Setaria italica x Setaria viridis recombinant inbred line population to assess how the genetic architecture of plant height is influenced by developmental queues, water availability and planting density. The non-destructive nature of plant height measurements has enabled us to monitor height throughout the plant life cycle in both field and controlled environments. We find that plant height is reduced under water limitation and high density planting and affected by growth environment (field vs. growth chamber). The results support a model where plant height is a heritable, polygenic trait and that the major genetic loci that influence plant height function independent of growth environment. The identity and contribution of loci that influence height changes dynamically throughout development and the reduction of growth observed in water limited environments is a consequence of delayed progression through the genetic program which establishes plant height in Setaria. In this population, alleles inherited from the weedy S. viridis parent act to increase plant height early, whereas a larger number of small effect alleles inherited from the domesticated S. italica parent collectively act to increase plant height later in development.

Growth is a dynamic process that responds to a changing environment. Most of the methods that we have for measuring are static and collecting information throughout an organisms lifecycle is labor and cost prohibitive. Advances in imaging and robotics technology have enabled novel approaches to understanding how plants adapt to the environment. Using the model grass Setaria and new methods for measuring parameters from images, we investigate the genetic architecture of plant height in response to water availability and planting density. Height is one of the most influential components of plant architecture, determining tradeoffs between competition and resource allocation and is an important trait for boosting yields. The non-destructive nature of plant height measurements has enabled us to monitor growth throughout the plant life cycle in both field and controlled environments. We identified several loci controlling height in a population derived from a wild strain of Setaria viridis and its domesticated relative Setaria italica, as well as the developmental time in which these loci act. In this population, alleles inherited from the wild parent act to increase plant height early, whereas a larger number of small effect alleles inherited from the domesticated parent collectively act to increase plant height later in development.

The challenges faced by living stock collections in the USA

Many discoveries in the life sciences have been made using material from living stock collections. These collections provide a uniform and stable supply of living organisms and related materials that enhance the reproducibility of research and minimize the need for repetitive calibration. While collections differ in many ways, they all require expertise in maintaining living organisms and good logistical systems for keeping track of stocks and fulfilling requests for specimens. Here, we review some of the contributions made by living stock collections to research across all branches of the tree of life, and outline the challenges they face.

DOI:http://dx.doi.org/10.7554/eLife.24611.001

Mutations in the Arabidopsis AtMRS2-11/AtMGT10/VAR5 Gene Cause Leaf Reticulation

In higher plants, the development of functional chloroplasts is essential for photosynthesis and many other physiological processes. With a long-term goal of elucidating the genetic regulation of chloroplast development, we identified two allelic leaf variegation mutants, variegated5-1 (var5-1) and var5-2. Both mutants showed a distinct leaf reticulation phenotype of yellow paraveinal regions and green interveinal regions, and the leaf reticulation phenotype correlated with photosynthetic defects. Through the identification of mutation sites in the two mutant alleles and the molecular complementation, we confirmed that VAR5 encodes a CorA family of Mg²⁺ transporters also known as AtMRS2-11/AtMGT10. Using protoplast transient expression and biochemical fractionation assays, we demonstrated that AtMRS2-11/AtMGT10/VAR5 likely localizes to the chloroplast envelope. Moreover, we established that AtMRS2-11/AtMGT10/VAR5 forms large molecular weight complexes in the chloroplast and the sizes of these complexes clearly exceed those of their bacterial counterparts, suggesting the compositions of CorA Mg²⁺ transporter complex is different between the chloroplast and bacteria. Our findings indicate that AtMRS2-11/AtMGT10/VAR5 plays an important role in the tissue specific regulation of chloroplast development.

Analysis of Arabidopsis Accessions Hypersensitive to a Loss of Chloroplast Translation

Natural accessions of Arabidopsis (Arabidopsis thaliana) differ in their ability to tolerate a loss of chloroplast translation. These differences can be attributed in part to variation in a duplicated nuclear gene (ACC2) that targets homomeric acetyl-coenzyme A carboxylase (ACCase) to plastids. This functional redundancy allows limited fatty acid biosynthesis to occur in the absence of heteromeric ACCase, which is encoded in part by the plastid genome. In the presence of functional ACC2, tolerant alleles of several nuclear genes, not yet identified, enhance the growth of seedlings and embryos disrupted in chloroplast translation. ACC2 knockout mutants, by contrast, are hypersensitive. Here we describe an expanded search for hypersensitive accessions of Arabidopsis, evaluate whether all of these accessions are defective in ACC2, and characterize genotype-to-phenotype relationships for homomeric ACCase variants identified among 855 accessions with sequenced genomes. Null alleles with ACC2 nonsense mutations, frameshift mutations, small deletions, genomic rearrangements, and defects in RNA splicing are included among the most sensitive accessions examined. By contrast, most missense mutations affecting highly conserved residues failed to eliminate ACC2 function. Several accessions were identified where sensitivity could not be attributed to a defect in either ACC2 or Tic20-IV, the chloroplast membrane channel required for ACC2 uptake. Overall, these results underscore the central role of ACC2 in mediating Arabidopsis response to a loss of chloroplast translation, highlight future applications of this system to analyzing chloroplast protein import, and provide valuable insights into the mutational landscape of an important metabolic enzyme that is highly conserved throughout eukaryotes.

RNA-Seq Based Analysis of Population Structure within the Maize Inbred B73

Recent reports have shown than many identically named genetic lines used in research around the world actually contain large amounts of uncharacterized genetic variation as a result of cross contamination of stocks, unintentional crossing, residual heterozygosity within original stocks, or de novo mutation. 27 public, large scale, RNA-seq datasets from 20 independent research groups around the world were used to assess variation within the maize (Zea mays ssp. mays) inbred B73, a four decade old variety which served as the reference genotype for the original maize genome sequencing project and is widely used in genetic, genomic, and phenotypic research. Several clearly distinct clades were identified among putatively B73 samples. A number of these clades were defined by the presence of clearly defined genomic blocks containing a haplotype which did not match the published B73 reference genome. The overall proportion of the maize genotype where multiple distinct haplotypes were observed across different research groups was approximately 2.3%. In some cases the relationship among B73 samples generated by different research groups recapitulated mentor/mentee relationships within the maize genetics community.