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Cassava is one of the most important food security crops in tropical countries, and a competitive resource for the starch, food, feed and ethanol industries. However, genomics research in this crop is much less developed compared to other economically important crops such as rice or maize. The International Center for Tropical Agriculture (CIAT) maintains the largest cassava germplasm collection in the world. Unfortunately, the genetic potential of this diversity for breeding programs remains underexploited due to the difficulties in phenotypic screening and lack of deep genomic information about the different accessions. A chromosome-level assembly of the cassava reference genome was released this year and only a handful of studies have been made, mainly to find quantitative trait loci (QTL) on breeding populations with limited variability. This work presents the results of pooled targeted resequencing of more than 1500 cassava accessions from the CIAT germplasm collection to obtain a dataset of more than 2000 variants within genes related to starch functional properties and herbicide tolerance. Results of twelve bioinformatic pipelines for variant detection in pooled samples were compared to ensure the quality of the variant calling process. Predictions of functional impact were performed using two separate methods to prioritize interesting variation for genotyping and cultivar selection. Targeted resequencing, either by pooled samples or by similar approaches such as Ecotilling or capture, emerges as a cost effective alternative to whole genome sequencing to identify interesting alleles of genes related to relevant traits within large germplasm collections. Keywords: Cassava, Pooled targeted resequencing, Herbicide tolerance, Starch biosynthesis, SNP detection

Improvements to massively parallel sequencing have allowed the routine recovery of natural and induced sequence variants. A broad range of biological disciplines have benefited from this, ranging from plant breeding to cancer research. The need for high sequence coverage to accurately recover single nucleotide variants and small insertions and deletions limits the applicability of whole genome approaches. This is especially true in organisms with a large genome size or for applications requiring the screening of thousands of individuals, such as the reverse-genetic technique known as TILLING, where whole genome approaches become cost prohibitive. Using PCR to target and sequence chosen genomic regions provides an attractive alternative as the vast reduction in interrogated bases means that sample size can be dramatically increased through amplicon multiplexing and multidimensional sample pooling while maintaining suitable coverage for recovery of small mutations. Direct sequencing of PCR products is limited, however, due to limitations in read lengths of many next generation sequencers. In the present study we show the optimization and use of ultrasonication for the simultaneous fragmentation of multiplexed PCR amplicons for TILLING highly pooled samples. Thirty-two PCR products were produced from genomic DNA pools representing 265 pooled barley mutant lines. Mutant lines were produced with the chemical mutagen ethyl methanesulfonate. Samples were subjected to 2×300PE illumina sequencing. Evaluation of read coverage and base quality across amplicons suggests this approach is suitable for high-throughput TILLING and other applications employing highly pooled complex sampling schemes. Induced mutations previously identified in a traditional TILLING screen were recovered in this dataset further supporting the efficacy of the approach.

Nucleotide variation, whether induced or natural, is responsible for a vast majority of heritable phenotypic variation. Evaluation of genomic DNA sequence is therefore fundamental for both functional genomics and marker-assisted breeding. The starting point for this is the extraction of high-quality DNA of a suitable quantity for planned downstream applications. A myriad of kits and techniques exists, but not all are suitable for laboratories with limiting infrastructure due to high costs and reliance on toxic chemicals. We describe here a protocol for extraction of high-quality genomic DNA from leaves of a variety of plant species that uses self-prepared buffers and reagents and obviates the need for toxic organic chemicals such as chloroform. We also provide a protocol for using free image analysis software to quantify isolated DNA.

Doubled haploidy is an important tool for plant breeders. It provides a rapid means of developing recombinant populations consisting of individuals that are homozygous and therefore genetically fixed. Homozygosity is also important in plant mutation breeding where many induced mutations are predicted to be recessive and mutant alleles need to be in a homozygous state before new traits are expressed. While production of doubled haploids has been described for many plant species, efficient means to validate that produced materials are indeed homozygous are needed. Polymorphism discovery methods utilizing enzymatic mismatch cleavage are ideally suited for validation of doubled haploid plants. We describe here a low-cost protocol that utilizes self-extracted single-strand-specific nucleases, standard PCR reactions and agarose gel electrophoresis that can be applied to most plant species.

Single-strand-specific nucleases are used to cleave mismatches in otherwise double-stranded DNA. Assays typically involve PCR amplification followed by a denaturing and annealing step to generate heteroduplexed DNA molecules from PCR products containing nucleotide polymorphisms. This is followed by digestion with nucleases that cleave at the site of the mismatch. The molecular weights of the cleavage products indicate the approximate position of nucleotide polymorphisms in PCR amplicons. Cleaved DNA products are observed by one of several readout platforms such as native gel electrophoresis, denaturing gel electrophoresis, capillary electrophoresis, or denaturing high-performance liquid chromatography (DHPLC). This approach is highly suitable for accurate discovery of natural and induced single-nucleotide polymorphisms (SNPs) and also small insertions and deletions (indels). The use of self-extracted single-strand-specific nucleases, typically prepared from crude extracts of celery (Apium graveolens), is common for reverse-genetics (e.g. Targeting Induced Local Lesions IN Genomes (TILLING)) and studies of natural nucleotide polymorphisms (e.g. Ecotilling). While protocols have been published describing the preparation of single-strand-specific nuclease from plant tissues, many rely on toxic chemicals, dialysis and large-volume preparatory centrifuges and also require steps to be performed at 4 °C. We provide here a streamlined room temperature extraction protocol that uses standard microcentrifuges and eliminates toxic chemicals and traditional dialysis.

Microspore embryogenesis is a method of great importance for plant production in many species. Its practical use in monocotyledonous plants, however, is limited due to the occurrence of albino plants. Molecular examinations of such albino plants showed an aberrant form of plastids and, frequently, deletions in their plastid DNA. Moreover, in our preceding work we found typical deficiencies in plastid transcription and translation. Nevertheless, there are also indications for an involvement of the nuclear genome in albino plant formation. To address these questions, we characterised, on the one hand, a plastid factor, which is possibly involved in the formation of plastid DNA deletions, and investigated, on the other hand, nuclear gene expression in albino plants. The ycf1 gene is present in the plastid genomes of dicots, while monocots only have a truncated pseudogene. The disruption of ycf1 in tobacco showed that it is essential for the survival of dicotyledonous plants. In addition, we replaced the tobacco ycf1 by the pseudogene of rice and found rearrangements in the plastid genomes of the resulting plants indicating that the ycf1 locus plays a role in the stability of plastid DNA. The study on nuclear gene expression showed that there is an extensive alteration of transcript levels in albino plants. We found that the respective genes encode proteins with a broad range of functions in plants. All these findings taken together suggest that albino plant formation is a complex phenomenon in which both, plastid and nuclear factors or their defective interactions are involved.

Of importance to the successful extraction of genomic DNA from plant tissues is the collection of the suitable material and proper storage of the tissues before DNA isolation. If the samples are not properly treated, DNA can be degraded prior to isolation. The rate of sample degradation can vary dramatically from species to species depending on the method of sample collection. Mechanisms of genomic DNA degradation include exposure to endogenous nucleases due to organellar and cellular lysis. To prevent this from occurring, leaf or root tissues are commonly flash frozen in liquid nitrogen and then stored at −80 °C. At these temperatures, nucleases remain inactive and DNA is stable. Thawing of tissue in some species can lead to rapid degradation. Therefore, during the extraction procedure, it may be necessary to grind the tissue to a fine powder in the presence of liquid nitrogen and expose frozen tissue immediately to a lysis buffer containing EDTA, which inhibits nuclease activity. This chapter provides an alternative method for sample collection and storage. Silica gel is used to desiccate tissues at room temperature. This avoids the use of liquid nitrogen and storage at −80 °C.

PCR is used to amplify regions to be interrogated for the presence of mutations (SNP and small indel polymorphisms). While PCR is a common practice and many protocols exist, reaction conditions are provided here that are optimized for TILLING and Ecotilling assays utilizing native agarose gel electrophoresis.

A crude celery extract containing the single-strand-specific nuclease CEL I, has been widely used in TILLING and Ecotilling projects around the world. Yet, celery is hard to come by in some countries. Sequences homologous to CEL I can be found in different plant species. Previous work showed that similar mismatch cleavage activities could be found in crude extracts of mung bean (Till BJ, Burtner C, Comai L, Henikoff S. Nucleic Acids Res 32:2632–2641, 2004). It is likely that the same activity can be recovered in many different plant species. Therefore, a protocol for the extraction of active enzyme was developed that uses plants common across the world, namely weeds. Monocotyledenous and dicotyledenous weedy plants from the grassland, field and waste grounds around crop fields are suitable for this protocol. Due to lower recovery of enzymatic activity compared to celery-based extractions, a centrifuge-based filter method is applied to concentrate the enzyme extract.

The methods described in this chapter were developed to avoid toxic organic phase separation utilized in many low-cost DNA extraction protocols such as the CTAB method. The steps involve: (1) lysis of the plant material, (2) binding of DNA to silica powder under chaotropic conditions, (3) washing the bound DNA, and (4) elution of DNA from the silica powder. This method has been tested in several plant species and the applicability of such DNA preparations for molecular marker studies in barley is shown in Chap. 8.

All laboratories should have standardized health and safety rules and practices. These can vary from region to region due to differences in legislation. Before beginning new experiments, please consult your local safety guidelines. Failure to follow these rules could result in accidents, fines, or a closure of the laboratory. Consider the following guidelines in this chapter applicable to all laboratories.

This book offers low-cost and rapid molecular assays for the characterization of mutant plant germplasm. Detailed protocols are provided for the desiccation of plant tissues; the extraction of high-quality DNA for downstream applications; the extraction of single-strand-specific nucleases for single nucleotide polymorphism; and small insertion/deletion discovery using standard agarose gel electrophoresis. The methods described can be applied in any laboratory equipped for basic molecular biology and do away with the need for expensive freezers and toxic organic compounds. With the appropriate validation of sample quality and longevity, they can provide sufficient DNA for a variety of molecular applications, such as marker studies and TILLING, at approximately one tenth of the cost per sample when compared to commercial kits

Denaturation and annealing of PCR products allows DNA strands with small sequence differences to hybridize together. The result is heteroduplexed molecules that are single stranded in polymorphic sequence locations, but double stranded elsewhere. These molecules are the substrates for cleavage by single-strand-specific nucleases such as CEL I, crude Celery Juice Extract (CJE) containing CEL I, and other plant extracts containing single-strand-specific nucleases [Till et al. (Nucleic Acids Res, 32:2632–2641, 2004)]. Enzymatic cleavage initiates on a single strand and can result in double strand breaks. The products of cleavage can therefore be observed using native gel electrophoresis.

In barley, the eukaryotic translation initiation factor 4E (eIF4E) gene situated on chromosome 3H is recognized as an important source of resistance to the bymoviruses Barley yellow mosaic virus and Barley mild mosaic virus. In modern barley cultivars, two recessive eIF4E alleles, rym4 and rym5, confer different isolate-specific resistances. In this study, the sequence of eIF4E was analysed in 1090 barley landraces and noncurrent cultivars originating from 84 countries. An exceptionally high nucleotide diversity was evident in the coding sequence of eIF4E but not in either the adjacent MCT-1 gene or the sequence-related eIF(iso)4E gene situated on chromosome 1H. Surprisingly, all nucleotide polymorphisms detected in the coding sequence of eIF4E resulted in amino acid changes. A total of 47 eIF4E haplotypes were identified, and phylogenetic analysis using maximum likelihood provided evidence of strong positive selection acting on this barley gene. The majority of eIF4E haplotypes were found to be specific to distinct geographic regions. Furthermore, the eI4FE haplotype diversity (uh) was found to be considerably higher in East Asia, whereas SNP genotyping identified a comparatively low degree of genome-wide genetic diversity in 16 of 17 tested accessions (each carrying a different eIF4E haplotype) from this same region. In addition, selection statistic calculations using coalescent simulations showed evidence of non-neutral variation for eIF4E in several geographic regions, including East Asia, the region with a long history of the bymovirus-induced yellow mosaic disease. Together these findings suggest that eIF4E may play a role in barley adaptation to local habitats.