Cleaved Amplified Polymorphic Sequence Markers Research Articles

Cleaved Amplified Polymorphic Sequence Markers in Horticultural Crops: Current Status and Future Perspectives

DNA markers have broad applications, including marker-assisted selection (MAS) for breeding new cultivars. Currently, single nucleotide polymorphisms (SNPs) have become a preferred choice of markers for molecular geneticists and breeders. They offer many advantages, such as high abundance and coverage in the genome, codominant inheritance, locus specificity, and flexibility for high-throughput genotyping/detection formats, and they are relatively inexpensive. The availability of reference genome sequences enables precise identification of candidate genes and SNPs associated with a trait of interest through quantitative trait loci (QTL) mapping and genome-wide association studies (GWAS). Such SNPs can be converted into markers for their application in MAS in crop breeding programs. Cleaved amplified polymorphic sequence (CAPS) markers amplify short genomic sequences around the polymorphic endonuclease restriction site. This review provides insight into the recent advancements made in the development and application of CAPS markers in several horticultural plants. We discussed many new tools that aid faster and more accurate design of CAPS markers from the whole genome resequencing (WGRS) data. The developed CAPS markers offer immense application in germplasm screening and field trials, genomic loci mapping, identifying candidate genes, and MAS of important horticultural traits such as disease resistance, fruit quality and morphology, and genetic purity.

Workflow for development of CAPS markers with one type of restriction enzyme to identify citrus cultivars

Given the ease of propagating fruit tree species through cloning, the economic viability of their breeding programs hinges on protecting breeders' rights. This necessitates the development of highly accurate DNA markers for cultivar identification. Here, we present a methodology for the rapid design of cleaved amplified polymorphic sequence (CAPS) markers to discriminate newly bred Japanese citrus cultivars from genetically related cultivars. We first compared the performance of ddRAD-seq and MIG-seq in citrus germplasm. The ddRAD-seq libraries generated using EcoRI and HindIII restriction enzymes yielded the highest number of polymorphisms. Subsequently, ddRAD-seq with EcoRI and HindIII was employed to analyze 29 citrus cultivars and thus identify 331,801 genome-wide polymorphisms. A semi-automated bioinformatics pipeline was then utilized to identify candidate CAPS markers, resulting in the discovery of 14,072 potential markers. Of these candidates, 52 were chosen for validation based on their recognition by the PstI restriction enzyme. This evaluation resulted in the development of 11 highly discriminative CAPS markers. Remarkably, a combination of only six such markers was sufficient to differentiate newly bred cultivars from their genetically related parents. The single restriction enzyme employed for these markers facilitates straightforward multiplexing. Finally, a combination of one multiplex marker testing two loci and four singleplex markers was successfully selected that completely discriminated the cultivars other than the bud sports used in this study. The pipeline established here extends beyond citrus and has the potential to simplify marker development and cultivar protection in various plant species.

Identification of genetic loci and candidate genes underlying freezing tolerance in wheat seedlings.

Ten stable loci for freezing tolerance (FT) in wheat were detected by genome-wide association analysis. The putative candidate gene TaRPM1-7BL underlying the major locus QFT.ahau-7B.2 was identified and validated. Frost damage restricts wheat growth, development, and geographical distribution. However, the genetic mechanism of freezing tolerance (FT) remains unclear. Here, we evaluated FT phenotypes of 245 wheat varieties and lines, and genotyped them using a Wheat 90K array. The association analysis showed that ten stable loci were significantly associated with FT (P < 1 × 10-4), and explained 6.45-26.33% of the phenotypic variation. In particular, the major locus QFT.ahau-7B.2 was consistently related to all nine sets of FT phenotypic data. Based on five cleaved amplified polymorphic sequence (CAPS) markers closely linked to QFT.ahau-7B.2, we narrowed down the target region to the 570.67-571.16Mb interval (0.49Mb) on chromosome 7B, in which four candidate genes were annotated. Of these, only TaRPM1-7BL exhibited consistent differential expression after low temperature treatment between freezing-tolerant and freezing-sensitive varieties. The results of cloning and whole-exome capture sequencing indicated that there were two main haplotypes for TaRPM1-7BL, including freezing-tolerant Hap1 and freezing-sensitive Hap2. Based on the representative SNP (+1956, A/G), leading to an amino acid change in the NBS domain, a CAPS marker (CAPS-TaRPM1-7BL) was developed and validated in 431 wheat varieties (including the above 245 materials) and 318 F2 lines derived from the cross of 'Annong 9267' (freezing-tolerant) × 'Yumai 9' (freezing-sensitive). Subsequently, the TaRPM1-7BL gene was silenced in 'Yumai 9' by virus-induced gene silencing (VIGS), and these silenced wheat seedlings exhibited enhanced FT phenotypes, suggesting that TaRPM1-7BL negatively regulates FT. These findings are valuable for understanding the complex genetic basis of FT in wheat.

DNAMarkMaker: streamlining ARMS and CAPS marker development from resequencing data with NGS short reads.

DNA markers serve as essential tools in breeding selection and genetic analysis. However, developing DNA markers can be time-consuming and labor-intensive due to the need to identify polymorphisms between cultivars/lines and to design suitable primers. To address these challenges, we have developed DNAMarkMaker, a tool designed to automate the process of primer design for Amplification Refractory Mutation System (ARMS) and Cleaved Amplified Polymorphic Sequences (CAPS) markers, utilizing resequencing data. One key feature of DNAMarkMaker is its user-friendly graphical user interface (GUI), ensuring its accessibility and ease of use, even for researchers not well-versed in bioinformatics. We confirmed DNAMarkMaker's applicability by developing DNA markers for rice, potato, and turnip-each representing distinct genome structures: homozygous diploid, heterozygous autotetraploid, and heterozygous diploid, respectively. DNAMarkMaker will contribute to the rapid and efficient development of DNA markers, accelerating breeding and genetic analysis in various crops.

A Novel PCR-Based Functional Marker of Rice Blast Resistance Gene Pi25

Rice blast is arguably the most devastating fungal disease of rice. Utilization of resistance genes to breed resistant cultivars is one of the most economical and environmentally friendly approaches to combat the disease. Pi25, a major resistance gene conferring broad-spectrum resistance to both leaf and neck blast, is an ideal gene resource to improve the resistance of rice varieties to blast. Recently, several allele-specific markers were developed. However, they were deficiently efficient due to either an additional process of restriction enzyme digestion for cleaved amplified polymorphic sequence (CAPS) markers or the risk of false-positive error in identifying susceptible Tetep allele (Pi25TTP) for PCR-based markers. In this study, based on a conserved single nucleotide polymorphism (SNP) between resistant and susceptible alleles, a tetra-primer amplification refractory mutation system (ARMS)-PCR marker was developed. The new marker, namely Pi25-2687R3, could effectively distinguish the resistant Gumei 2 (GM2) allele (Pi25GM2) and the susceptible allele Pi25TTP. Moreover, a perfect consistency of genotyping was exhibited between Pi25-2687R3 and published CAPS marker CAP3/Hpy 99I. A more accurate genotyping was also displayed compared to the previous PCR-based SNP marker Pi25-2566. Our finding proved that Pi25-2687R3 could achieve the same result as CAP3/Hpy 99I with less workload and cost and could promote the accuracy in the identification of genotypes superior to Pi25-2566. This study provided a quick and reliable functional marker for discriminating Pi25 alleles, which would be a valuable tool for genotypic assay and rice molecular breeding of blast resistance.

Dissecting the genetic basis of grain color and pre-harvest sprouting resistance in common wheat by association analysis

Pre-harvest sprouting (PHS) adversely affects wheat quality and yield, and grain color (GC) is associated with PHS resistance. However, the genetic relationship between GC and PHS resistance remains unclear. In this study, 168 wheat varieties (lines) with significant differences in GC and PHS resistance were genotyped using an Illumina 90K iSelect SNP array. Genome-wide association study (GWAS) based on a mixed linear model showed that 67 marker-trait associations (MTAs) assigned to 29 loci, including 17 potentially novel loci, were significantly associated with GC, which explained 1.1–17.0% of the phenotypic variation. In addition, 100 MTAs belonging to 54 loci, including 31 novel loci, were significantly associated with PHS resistance, which accounted for 1.1–14.7% of the phenotypic variation. Subsequently, two cleaved amplified polymorphic sequences (CAPS) markers, 2B-448 on chromosome 2B and 5B-301 on chromosome 5B, were developed from the representative SNPs of the major common loci Qgc.ahau-2B.3/Qphs.ahau-2B.4 controlling GC/PHS resistance and PHS resistance locus Qphs.ahau-5B.4, respectively. Further validation in 171 Chinese mini-core collections confirmed significant correlations of the two CAPS markers with GC and PHS resistance phenotypes under different environments (P<0.05). Furthermore, the wheat public expression database, transcriptomic sequencing, and gene allelic variation analysis identified TraesCS5B02G545100, which encodes glutaredoxin, as a potential candidate gene linked to Qphs.ahau-5B.4. The new CAPS marker CAPS-356 was then developed based on the SNP (T/C) in the coding sequences (CDS) region of TraesCS5B02G545100. The high-density linkage map of the Jing 411/Hongmangchun 21 recombinant inbred lines (RILs) constructed based on specific locus amplified fragment sequencing markers showed that CAPS-356 collocated with a novel QTL for PHS resistance, supporting the role of TraesCS5B02G545100 as the potential candidate gene linked to Qphs.ahau-5B.4. These results provide valuable information for the map-based cloning of Qphs.ahau-5B.4 and breeding of PHS resistant white-grained varieties.

A rapid method for detection of the root-knot nematode resistance gene, Mi-1.2, in tomato cultivars.

Molecular markers have been widely used in plant breeding to improve the accuracy and efficiency of trait selection. In particular, molecular markers are powerful in facilitating the introgression of resistance genes by circumventing costly and time-consuming infection assays. To achieve their practical use, it is important to ensure the tight linkage between the markers and the traits. Here we report a new cleaved amplified polymorphic sequence (CAPS) marker, Mi1713, for the root-knot nematode resistance gene, Mi-1.2, in cultivated tomato. The Mi1713 marker is designed in the conserved region of Mi-1.2 and its homologs in tomato and other nightshade species. Combined with a single-step procedure for preparing PCR templates, the Mi1713 marker enables rapid and reliable screening for the presence of Mi-1.2. The approach described in this study is applicable in designing CAPS markers for various genes or alleles of interest in tomato and other crops.

Phenotypic and genotypic characterization to authenticate and trace a high-quality yellow tomato ecotype through the processing chain

In the last few years considerable interest is growing for high food quality, both for organoleptic and nutritional aspects. As for tomatoes, the yellow fruit varieties are conquering the consumer markets in many Mediterranean countries. Among the great variability of yellow tomatoes, one landrace of “Pomodorino giallo del Vesuvio”, named GiaGiù (E40), differs from the traditional “Pomodorino del Piennolo” for the fruit color and stands out for its quality traits, such as high glutamic acid, pectin content and titratable acidity of fruit, thus increasing its demand for both fresh consumption and cooking purposes. The aim of this work was to phenotypically and genotypically distinguish the GiaGiù landrace through morphological descriptors and molecular markers, in order to provide an effective tool to authenticate this product as fresh and processed tomatoes. Morphological characterization evidenced that the distinctive traits of GiaGiù landrace were the potato leaf morphology and the pyriform shape with a pointed apex of the yellow fruits. The genotypic distinction of E40 was performed by using two Cleaved Amplified Polymorphic Sequence (CAPS) markers designed on a Single Nucleotide Polymorphism (SNP) of the Phytoene synthase 1 (psy1) gene that confers the yellow color to tomato fruit and already known as specific of GiaGiù genotype. Additional CAPS markers were designed on two private mutations of E40 genes derived from data retrieved from a Genotyping-By-Sequencing (GBS) dataset, already available. These findings were confirmed by comparing E40 private mutations with the 360 accessions of the BGI tomato 360 genomes resequencing project. The designed markers allowed to distinguish GiaGiù genotype in all fresh and processed fruit tomato matrices, thus representing a molecular tool able to prevent food fraud and authenticate GiaGiù products.

Fine Mapping the Soybean Mosaic Virus Resistance Gene in Soybean Cultivar Heinong 84 and Development of CAPS Markers for Rapid Identification.

Heinong 84 is one of the major soybean varieties growing in Northeast China, and is resistant to the infection of all strains of soybean mosaic virus (SMV) in the region including the most prevalent strain, N3. However, the resistance gene(s) in Heinong 84 and the resistant mechanism are still elusive. In this study, genetic and next-generation sequencing (NGS)-based bulk segregation analysis (BSA) were performed to map the resistance gene using a segregation population from the cross of Heinong 84 and a susceptible cultivar to strain N3, Zhonghuang 13. Results show that the resistance of Heinong 84 is controlled by a dominant gene on chromosome 13. Further analyses suggest that the resistance gene in Heinong 84 is probably an allele of Rsv1. Finally, two pairs of single-nucleotide-polymorphism (SNP)-based primers that are tightly cosegregated with the resistance gene were designed for rapidly identifying resistant progenies in breeding via the cleaved amplified polymorphic sequence (CAPS) assay.

Validation of CAPS marker WR003 for the leaf rust resistance gene Lr1 and the molecular evolution of Lr1 in wheat

The wheat leaf rust resistance gene Lr1 encodes a typical coiled-coil nucleotide-binding site leucine-rich repeat (CC-NBS-LRR) of resistance protein containing 1 344 amino acids. WR003, a cleaved amplified polymorphic sequence (CAPS) marker is derived from the LRR regions of Lr1. In this study, a worldwide collection of 120 Aegilops tauschii accessions and 282 hexaploid wheat varieties was screened for Lr1 alleles using WR003, and the specificity of WR003 for Lr1 was confirmed by pathogenicity tests and genotype analysis. The sequence alignment and phylogenetic tree analysis of 38 Lr1 haplotypes provided a further view of the molecular evolution of Lr1. The results showed that there were very few polymorphisms between the Lr1 alleles from Ae. tauschii and hexaploid wheat with the same resistance phenotype. The polymorphisms of the Lr1 haplotypes were mainly between the different resistance lines, rather than between the different ploidy levels. These results indicate that Lr1 originated from Ae. tauschii and differentiated into resistant and susceptible genotypes before its introgression into hexaploid wheat. Therefore, it is likely that wheat Lr1 has at least two major variants for disease resistance and susceptibility, and except for certain point mutations, few gene conversions and genetic re-combinations occurred during the hexaploid wheat domestication.

Genome-wide association study reveals a NAC transcription factor TaNAC074 linked to pre-harvest sprouting tolerance in wheat.

Twelve QTL associated with pre-harvest sprouting tolerance were identified using association analysis in wheat. Two markers were validated and a candidate gene TaNAC074 for Qgpf.cas-3B.2 was verified using Agrobacterium-mediated transformation. Pre-harvest sprouting (PHS) is a considerable global threat to wheat yield and quality. Due to this threat, breeders must identify quantitative trait loci (QTL) and genes conferring PHS-tolerance (PHST) to reduce the negative effects of PHS caused by low seed dormancy. In this study, we evaluated a panel of 302 diverse wheat genotypes for PHST in four environments and genotyped the panel with a high-density wheat 660K SNP array. By using a genome-wide association study (GWAS), we identified 12 stable loci significantly associated with PHST (P < 0.0001), explaining 3.34 - 9.88% of the phenotypic variances. Seven of these loci co-located with QTL and genes reported previously. Five loci (Qgpf.cas-3B.2, Qgpf.cas-3B.3, Qgpf.cas-3B.4, Qgpf.cas-7B.2, and Qgpf.cas-7B.3), located in genomic regions with no known PHST QTL or genes, are likely to be new QTL conferring PHST. Additionally, two molecular markers were developed for Qgpf.cas-3A and Qgpf.cas-7B.3, and validated using a different set of 233 wheat accessions. Finally, the PHST-related function of candidate gene TaNAC074 for Qgpf.cas-3B.2 was confirmed by CAPS (cleaved amplified polymorphic sequences) marker association analysis in 233 wheat accessions and by expression and phenotypic analysis of transgenic wheat. Overexpression of TaNAC074 significantly reduced seed dormancy in wheat. This study contributes to broaden the genetic basis and molecular marker-assisted breeding of PHST.

Intergeneric hybridization of marguerite (Argyranthemum frutescens (L.) Sch. Bip.) and Roman chamomile (Chamaemelum nobile (L.) All.) using ovule culture and confirmation of hybridity.

To introduce useful characteristics such as fragrance into Argyranthemum frutescens (L.) and to expand the variation, we conducted crosses using A. frutescens as the seed parent and Chamaemelum nobile (L.) All. as the pollen parent. All the tested cross combinations between the three strains of A. frutescens and one strain of C. nobile produced embryos, and healthy plants were obtained by ovule culture. The obtained plantlets had a white ray floret, and the leaf shape was intermediate to those of the parents. The individuals obtained from this cross were subjected to two methods to determine hybridity: flow cytometry analyses and cleaved amplified polymorphic sequence (CAPS) markers. For the CAPS marker, we selected the internal transcribed spacer (ITS) region, which is highly variable among the genera, as the region to be amplified. We selected restriction enzymes BmgT120 I and Afl II, which selectively cut common sequences in the genus Argyranthemum, based on the sequence analysis of one parent strain each of A. frutescens and C. nobile and alignment with known sequences of related species. Flow cytometry analyses and CAPS markers revealed that the individuals obtained from the cross between A. frutescens and C. nobile are intergeneric hybrids. In addition, these established methods were capable of quickly and reliably identifying hybrids between A. frutescens and C. nobile. This report shows for the first time that crossbreeding between A. frutescens (seed parent) and C. nobile (pollen parent) is possible, and further development of Argyranthemum breeding, such as the expansion of variation by intergeneric crosses, is expected.

Cultivar-specific markers, mutations, and chimerisim of Cavendish banana somaclonal variants resistant to Fusarium oxysporum f. sp. cubense tropical race 4

BackgroundThe selection of tissue culture–derived somaclonal variants of Giant Cavendish banana (Musa spp., Cavendish sub-group AAA) by the Taiwan Banana Research Institute (TBRI) has resulted in several cultivars resistant to Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4), a destructive fungus threatening global banana production. However, the mutations in these somaclonal variants have not yet been determined. We performed an RNA-sequencing (RNA-seq) analysis of three TBRI Foc TR4–resistant cultivars: ‘Tai-Chiao No. 5’ (TC5), ‘Tai-Chiao No. 7’ (TC7), and ‘Formosana’ (FM), as well as their susceptible progenitor ‘Pei-Chiao’ (PC), to investigate the sequence variations among them and develop cultivar-specific markers.ResultsA group of single-nucleotide variants (SNVs) specific to one cultivar were identified from the analysis of RNA-seq data and validated using Sanger sequencing from genomic DNA. Several SNVs were further converted into cleaved amplified polymorphic sequence (CAPS) markers or derived CAPS markers that could identify the three Foc TR4–resistant cultivars among 6 local and 5 international Cavendish cultivars. Compared with PC, the three resistant cultivars showed a loss or alteration of heterozygosity in some chromosomal regions, which appears to be a consequence of single-copy chromosomal deletions. Notably, TC7 and FM shared a common deletion region on chromosome 5; however, different TC7 tissues displayed varying degrees of allele ratios in this region, suggesting the presence of chimerism in TC7.ConclusionsThis work demonstrates that reliable SNV markers of tissue culture–derived and propagated banana cultivars with a triploid genome can be developed through RNA-seq data analysis. Moreover, the analysis of sequence heterozygosity can uncover chromosomal deletions and chimerism in banana somaclonal variants. The markers obtained from this study will assist with the identification of TBRI Cavendish somaclonal variants for the quality control of tissue culture propagation, and the protection of breeders’ rights.

Identification of fruit firmness QTL ff2.1 by SLAF-BSA and QTL mapping in melon

Fruit firmness is an important target of melon breeding, as it is associated with shelf life and economic value; however, the precise mechanism that determines fruit firmness during fruit ripening remains elusive. In the present study, one hundred forty-four F2 plants and F2–3 families derived from the high-firmness melon line M2–10 and the low-firmness melon line ZT091 were used to identify major quantitative trait loci by specific-locus amplified fragment sequencing with bulked segregant analysis. Simple sequence repeat (SSR) and cleaved amplified polymorphic sequence (CAPS) markers based on the resequencing of parental lines were also used to narrow the associated region to identify candidate genes. Two regions associated with fruit firmness were investigated, including a 4.87 Mb region on chr. 2 and a 28.7 Mb region on chr. 5 of the melon genome. SSR and CAPS markers were used to construct a genetic map of the associated regions: QTL ff5.1 was located between CmSSR13509 and CmSSR13423 and explained 38.44% of the observed variation, with an LOD threshold of 17.44; ff2.1 was located between CmSSR07709 and SNP22228 and explained 28.14% of the variation, with an LOD threshold of 3.8, and this region included 106 Kb and 10 candidate genes. Quantitative real-time PCR was performed to investigated the investigate candidate gene expression at 15, 20 and 25 days after pollination in the parental lines, and significant expression levels were detected for most of the genes, including four genes of unknown function and MELO3C017519, MELO3C017520, MELO3C017522, MELO3C029506, and MELO3C029520. These results revealed a new QTL, ff2.1, for melon fruit firmness-related gene identification.

Development of a CAPS Marker and a LAMP Assay for Rapid Detection of Xylella fastidiosa Subsp. multiplex and Differentiation from X. fastidiosa Subsp. fastidiosa on Blueberry.

Bacterial leaf scorch (BLS), caused by Xylella fastidiosa (Xf), is a prevalent disease of blueberries in the southeastern United States. Initially, this disease was reported to be caused by X. fastidiosa subsp. multiplex (Xfm). However, a recent survey revealed the presence of another subspecies, X. fastidiosa subsp. fastidiosa (Xff), within naturally infected blueberry plantings in Georgia. Since knowledge regarding the origins of isolates causing Xf outbreaks can impact management recommendations, a routine method for identifying the pathogen at the subspecies level can be beneficial. Several detection strategies are available to identify Xf infection at the subspecies level. However, none of these have been developed for the routine and rapid differentiation of the blueberry-infecting Xf subspecies. Here, we developed two separate straightforward and rapid detection techniques, a cleaved amplified polymorphic sequence (CAPS) marker, and a loop-mediated isothermal amplification (LAMP) assay, targeting the RNA polymerase sigma-70 factor (rpoD) gene sequence of Xfm to discriminate between the two Xf subspecies infecting blueberry. With the CAPS marker, specific detection of Xfm isolates was possible from pure cultures, inoculated greenhouse-grown plant samples, and field infected blueberry samples by restriction digestion of the rpoD gene PCR product (amplified with primers RST31 and RST33) using the BtsI enzyme. The LAMP assay allowed for specific real-time amplification of a 204-bp portion of the Xfm rpoD gene from both pure bacterial cultures and infected plant material using the Genie® III system, a result further affirmed by gel electrophoresis and SYBR™ Green I DNA staining for visual observation. These detection strategies have the potential to greatly aid existing diagnostic methods for determining the distribution and prevalence of these Xf subspecies causing bacterial leaf scorch (BLS) in blueberries in the southeastern United States.

Identification of resistance sources in common bean (

Context Among biotic factors, bean anthracnose caused by Colletotrichum lindemuthianum (Sacc. &amp; Magnus) Briosi &amp; Cavara is one of the most destructive diseases of common bean (Phaseolus vulgaris L.). Resistance in common bean genotypes is controlled by anthracnose resistance loci (designated Co). Aims The objective of this study was to evaluate the presence of Co resistance genes in common bean genotypes from Turkey and to examine promising genotypes as candidates for parent plants in breeding studies. Methods The presence of Co resistance genes in 693 common bean genotypes from 35 provinces of Turkey was determined by 12 SCAR (sequence characterised amplified region), RAPD (random amplified polymorphic DNA), STS (sequence-tagged site) and CAPS (cleaved amplified polymorphic sequence) markers. The disease reaction of 40 agronomically promising genotypes to different pathogen isolates was evaluated in a pot study. Key results The results indicated the presence of Co-1, Co-14, Co-15, Co-2, Co-33, Co-4, Co-42, Co-6, Co-10, Co-11 and Co-13 resistance genes, alone or in combination; Co-5 was not detected in any of the genotypes. Among the genotypes, Co-15 was the most frequent resistance source, followed by Co-4, Co-6 and Co-11, respectively. Common bean genotypes carrying Co-14, Co-2, Co-33, Co-11 and Co-13 have been identified for the first time in Turkish germplasm. Five genotypes carrying the various combinations of Co-1, Co-15, Co-4, Co-6, Co-10, Co-11 and Co-13 were resistant to all isolates in pathogenicity tests. Conclusions This study is the most comprehensive to date on Co genes linked to the resistance of common bean genotypes throughout Turkey and provides an important gene pool for breeding studies into bean anthracnose. Resistant genotypes identified will be useful as parent plants in resistance breeding studies. Implications Resistance genotypes carrying different Co genes to bean anthracnose will contribute significantly to the disease management strategy.

Whole-Genome Resequencing of Near-Isogenic Lines Reveals a Genomic Region Associated with High Trans-Lycopene Contents in Watermelon.

Trans-lycopene is a functional phytochemical abundant in red-fleshed watermelons, and its contents vary among cultivars. In this study, the genetic basis of high trans-lycopene contents in scarlet red flesh was evaluated. Three near-isogenic lines (NILs) with high trans-lycopene contents were derived from the scarlet red-fleshed donor parent DRD and three coral red-fleshed (low trans-lycopene contents) recurrent parents. The lycopene contents of DRD (589.4 ± 71.8 µg/g) were two times higher than that of the recurrent parents, and values for NILs were intermediate between those of the parents. Coral red-fleshed lines and F1 cultivars showed low trans-lycopene contents (135.7 ± 18.0 µg/g to 213.7 ± 39.5 µg/g). Whole-genome resequencing of two NILs and their parents and an analysis of genome-wide single-nucleotide polymorphisms revealed three common introgressed regions (CIRs) on chromosomes 6, 9, and 10. Twenty-eight gene-based cleaved amplified polymorphic sequence (CAPS) markers were developed from the CIRs. The CAPS markers derived from CIR6 on chromosome 6, spanning approximately 1 Mb, were associated (R2 = 0.45–0.72) with the trans-lycopene contents, particularly CIR6-M1 and CIR6-M4. Our results imply that CIR6 is a major genomic region associated with variation in the trans-lycopene contents in red-fleshed watermelon, and CIR6-M1 and CIR6-M4 may be useful for marker-assisted selection.

Loss of chromatin remodeler DDM1 causes segregation distortion in Arabidopsis thaliana.

In ddm1 mutants, the DNA methylation is primarily affected in the heterochromatic region of the chromosomes, which is associated with the segregation distortion of SNPs in the F2 progenies. Segregation distortion (SD) is common in most genetic mapping experiments and a valuable resource to determine how gene loci induce deviation. Meiotic DNA crossing over and SD are under the control of several types of epigenetic modifications. DNA methylation is an important regulatory epigenetic modification that is inherited across generations. In the present study, we investigated the relationship between SD and DNA methylation. The ecotypes Col-0/C24 and chromatin remodeler mutants ddm1-10/Col and ddm1-15/C24 were reciprocally crossed to obtain F2 generations. A total of 300 plants for each reciprocally crossed plant in the F2 generations were subjected to next-generation sequencing to detect the single-nucleotide polymorphisms (SNPs) as DNA markers. All SNPs were analyzed using the Chi-square test method to determine their segregation ratio in F2 generations. Through the segregation ratio, whole-genome SNPs were classified into 16 classes. In class 10, the SNPs in the reciprocal crosses of wild type showed the expected Mendelian ratio of 1:2:1, while those in the reciprocal crosses of ddm1 mutants showed distortion. In contrast, all SNPs in class 16 displayed a normal 1:2:1 ratio, and class 1 showed SD, regardless of wild type or mutants, as assessed using CAPS (cleaved amplified polymorphic sequences) marker analysis to confirm the next-generation sequencing. In ddm1 mutants, the DNA methylation is highly reduced throughout the whole genome and more significantly in the heterochromatic regions of chromosomes. Our results showed that the ddm1 mutants exhibit low levels of DNA methylation, which facilitates the SD of SNPs primarily located in the heterochromatic region of chromosomes by reducing the heterozygous ratio. The present study will provide a strong base for future research focusing on the impact of DNA methylation on trait segregation and plant evolution.

VCF2CAPS-A high-throughput CAPS marker design from VCF files and its test-use on a genotyping-by-sequencing (GBS) dataset.

Next-generation sequencing (NGS) is a powerful tool for massive detection of DNA sequence variants such as single nucleotide polymorphisms (SNPs), multi-nucleotide polymorphisms (MNPs) and insertions/deletions (indels). For routine screening of numerous samples, these variants are often converted into cleaved amplified polymorphic sequence (CAPS) markers which are based on the presence versus absence of restriction sites within PCR products. Current computational tools for SNP to CAPS conversion are limited and usually infeasible to use for large datasets as those generated with NGS. Moreover, there is no available tool for massive conversion of MNPs and indels into CAPS markers. Here, we present VCF2CAPS–a new software for identification of restriction endonucleases that recognize SNP/MNP/indel-containing sequences from NGS experiments. Additionally, the program contains filtration utilities not available in other SNP to CAPS converters–selection of markers with a single polymorphic cut site within a user-specified sequence length, and selection of markers that differentiate up to three user-defined groups of individuals from the analyzed population. Performance of VCF2CAPS was tested on a thoroughly analyzed dataset from a genotyping-by-sequencing (GBS) experiment. A selection of CAPS markers picked by the program was subjected to experimental verification. CAPS markers, also referred to as PCR-RFLPs, belong to basic tools exploited in plant, animal and human genetics. Our new software–VCF2CAPS–fills the gap in the current inventory of genetic software by high-throughput CAPS marker design from next-generation sequencing (NGS) data. The program should be of interest to geneticists involved in molecular diagnostics. In this paper we show a successful exemplary application of VCF2CAPS and we believe that its usefulness is guaranteed by the growing availability of NGS services.

Study for salt tolerance using CAPS markers in key DNA regulation se-quences in durum wheat (Triticum turgidum L. var. durum) as new alternative

In arid and semi-arid regions, particularly around the Mediterranean basin, soil salinization is one of the abiotic factors that reduces the agricultural yield of several crops and especially the cereal species. Molecular genetics, as an alternative method, makes it possible to select eligible plants for desi-rable traits at an earlier age. Selection based on markers such as CAPS (cleaved amplified polymorphic sequence) can lead to increased accuracy and selection responses in plants. A simple method for detecting polymor-phism of the WRKY candidate gene was performed on nine varieties of du-rum wheat (Triticum turgidum L. var. durum) for the identification of tolerant varieties. The DNA was amplified with a pair of primers, and digested with a restriction endonuclease that recognizes the SNP sequence. The electropho-retic analysis revealed the amplification of 7 bands of different sizes per pro-file in all individuals tested. The analysis of profiles after digestion shows that out of a total of seven bands, five bands do not change size. While, the two fast bands of 130 and 144 bp disappear and two other bands of 122 and 118 bp appear only after digestion, in all individuals studied. In our work, we were unable to demonstrate restriction variation in the DNA binding domain sequences of the transcription factor WRKY1, On the other hand, we show that the CAPS technique can be an easily used alternative, for the detection of variation in key DNA sequences, such as those of the transcription factor binding domains or their cis-acting elements sequences.