Genome-wide DNA polymorphism and transcriptome analysis of an early-maturing rice mutant

Physio-biochemical and molecular characterization of a rice drought-insensitive TILLING line 1 (ditl1) mutant

Drought stress is a major abiotic stress that limits rice yield. Therefore, the development of new varieties tolerant to drought stress is a high priority in breeding programs. In this study, 150 rice M₁₀ mutant lines, previously developed using gamma-ray irradiation, were used, and a drought-insensitive rice mutant (ditl1) was selected by drought stress screening. The ditl1 mutant exhibited significantly decreased water loss, leaf curling, and H₂ O₂ accumulation under drought stress. Chlorophyll leaching assay and toluidine blue staining suggested lower cuticle permeability in ditl1 mutants than in wild-type (WT) plants. In addition, transmission electron microscopy revealed that ditl1 plants accumulated more cuticular wax on the epidermal surface. Whole-genome resequencing analysis suggested that the deletion of a single nucleotide on the LOC_Os05g48260 gene, a putative ortholog of WSD1 (wax ester synthase/diacylglycerol O-acyltransferase in Arabidopsis), maybe be the gene responsible for the drought insensitive phenotype of ditl1. The ditl1 mutant will be a valuable breeding resource for developing drought stress tolerant rice cultivar.

Effects of the total dose and duration of γ-irradiation on the growth responses and induced SNPs of a Cymbidium hybrid

Purpose: Ionizing radiation has been used for developing new cultivars of diverse plant species, including Cymbidium orchid species. The effects of the total dose on mutation induction have been investigated; however, there is relatively little research on the influence of the dose rate or irradiation duration.Materials and methods: Thus, we analyzed the effects of the total dose and irradiation duration on the growth of Cymbidium hybrid RB001 protocorm-like bodies (PLBs). We completed a genotyping-by-sequencing analysis to compare the induced SNPs among five γ-irradiated populations with similar growth responses (LD₅₀) to γ-rays.Results: The optimal time to assess the effects of the γ-irradiation was at 6 months after the treatment. On the basis of the survival rate of γ-irradiated PLBs, the optimal doses (LD₅₀) for each irradiation duration were estimated: 1 h, 16.1 Gy; 4 h, 23.6 Gy; 8 h, 37.9 Gy; 16 h, 37.9 Gy; and 24 h, 40.0 Gy. The estimated optimal doses were duration-dependent at irradiation durations shorter than 8 h, but not at irradiation durations exceeding 8 h. A SNP comparison revealed a lack of significant differences among the mutations induced by γ-irradiations.Conclusions: These results indicate the irradiation duration affects PLB growth in response to γ-rays. Moreover, the mutations induced by a short-term treatment may be similar to those induced by a treatment over a longer period.

Identification of candidate genes for leaf scorch in Populus deltoids by the whole genome resequencing analysis

Leaf scorch exists as a common phenomenon in the development of plant, especially when plants encounter various adversities, which leads to great losses in agricultural production. Both Jinhong poplar (JHP) and Caihong poplar (CHP) (Populus deltoids) are obtained from a bud sport on Zhonghong poplar. Compared with CHP, JHP always exhibits leaf scorch, poor growth, premature leaf discoloration, and even death. In this study, the candidate genes associated with leaf scorch between JHP and CHP were identified by the whole genome resequencing using Illumina HiSeqTM. There were 218,880 polymorphic SNPs and 46,933 indels between JHP and CHP, respectively. Among these, the candidate genes carrying non-synonymous SNPs in coding regions were classified into 6 groups. The expression pattern of these candidate genes was also explored in JHP and CHP among different sampling stages. Combined with the qRT-PCR analysis, the results showed that genes associated with transport of various nutritional elements, senescence and MYB transcription factor might play important roles during the process of leaf scorch in Populus deltoids. Four genes belonging to these three groups carried more than three SNPs in their coding sequence, which might play important roles in leaf scorch. The above results provided candidate genes involved in leaf scorch in Populus deltoids, and made us better understand the molecular regulation mechanism of leaf scorch in Populus deltoids.

Identification of candidate genes for the seed coat colour change in a Brachypodium distachyon mutant induced by gamma radiation using whole-genome re-sequencing

Brachypodium distachyon has been proposed as a model plant for agriculturally important cereal crops such as wheat and barley. Seed coat colour change from brown-red to yellow was observed in a mutant line (142-3) of B. distachyon, which was induced by chronic gamma radiation. In addition, dwarf phenotypes were observed in each of the lines 142-3, 421-2, and 1376-1. To identify causal mutations for the seed coat colour change, the three mutant lines and the wild type were subjected to whole-genome re-sequencing. After removing natural variations, 906, 1057, and 978 DNA polymorphisms were detected in 142-3, 421-2, and 1376-1, respectively. A total of 13 high-risk DNA polymorphisms were identified in mutant 142-3. Based on a comparison with DNA polymorphisms in 421-2 and 1376-1, candidate causal mutations for the seed coat colour change in 142-3 were selected. In the two independent Arabidopsis thaliana lines carrying T-DNA insertions in the AtCHI, seed colour change was observed. We propose a frameshift mutation in BdCHI1 as a causal mutation responsible for seed colour change in 142-3. The DNA polymorphism information for these mutant lines can be utilized for functional genomics in B. distachyon and cereal crops.

Identification of candidate genes for an early-maturing soybean mutant by genome resequencing analysis

Flowering is indicative of the transition from vegetative to reproductive phase, a critical event in the life cycle of plants. In this study, we performed whole genome resequencing by Illumina HiSeq to identify changes in flowering genes using an early-flowering phenotype of soybean mutant line Josaengserori (JS) derived from Korean landrace, Seoritae (SR), and we obtained mapped reads of 131,769,690 and 167,669,640 bp in JS and SR, respectively. From the whole genome sequencing results between JS and SR, we identified 332,821 polymorphic SNPs and 65,178 indels, respectively. Among these, 30 flowering genes were in SNPs and 25 were in indels. Among 30 flowering genes detected in SNPs, Glyma02g33040, Glyma06g22650, Glyma10g36600, Glyma13g01290, Glyma14g10530, Glyma16g01980, Glyma17g11040, Glyma18g53690, and Glyma20g29300 were non-synonymous substitutions between JS and SR. Changes in Glyma10g36600 (GI), Glya02g33040 (AGL18), Glyma17g11040 (TOC1), and Glyma14g10530 (ELF3) in JS affected the expression of GmFT2a and resulted in early flowering. These results provide insight into the regulatory pathways of flowering in soybean mutants and help to improve our knowledge of soybean mutation breeding.

Identification of altered metabolic pathways of γ-irradiated rice mutant via network-based transcriptome analysis

In order to develop rice mutants for crop improvement, we applied γ-irradiation mutagenesis and selected a rice seed color mutant (MT) in the M14 targeting-induced local lesions in genome lines. This mutant exhibited differences in germination rate, plant height, and root length in seedlings compared to the wild-type plants. We found 1645 different expressed probes of MT by microarray hybridization. To identify the modified metabolic pathways, we conducted integrated genomic analysis such as weighted correlation network analysis with a module detection method of differentially expressed genes (DEGs) in MT on the basis of large-scale microarray transcriptional profiling. These modules are largely divided into three subnetworks and mainly exhibit overrepresented gene ontology functions such as oxidation-related function, ion-binding, and kinase activity (phosphorylation), and the expressional coherences of module genes mainly exhibited in vegetative and maturation stages. Through a metabolic pathway analysis, we detected the significant DEGs involved in the major carbohydrate metabolism (starch degradation), protein degradation (aspartate protease), and signaling in sugars and nutrients. Furthermore, the accumulation of amino acids (asparagine and glutamic acid), sucrose, and starch in MT were affected by gamma rays. Our results provide an effective approach for identification of metabolic pathways associated with useful agronomic traits in mutation breeding.

Whole genome sequencing and analysis of Swarna, a widely cultivated indica rice variety with low glycemic index

Swarna is a popular cultivated indica rice variety with low glycemic index (GI) but its genetic basis is not known. The whole genome of Swarna was sequenced using Illumina’s paired-end technology, and the reads were mapped to the Nipponbare reference genome. Overall, 65,984 non-synonymous SNPs were identified in 20,350 genes, and in silico analysis predicted that 4,847 of them in 2,214 genes may have deleterious effect on protein functions. Polymorphisms were found in all the starch biosynthesis genes, except the gene for branching enzyme IIa. It was found that T/G SNP at position 246, ‘A’ at position 2,386, and ‘C’ at position 3,378 in the granule bound starch synthase I gene, and C/T SNP at position 1,188 in the glucose-6-phosphate translocator gene may contribute to the low GI phenotype in Swarna. All these variants were also found in the genome of another low GI indica rice variety from Columbia, Fedearroz 50. The whole genome analysis of Swarna helped to understand the genetic basis of GI in rice, which is a complex trait involving multiple factors.

Rapid identification and recovery of ENU-induced mutations with next-generation sequencing and Paired-End Low-Error analysis

BACKGROUND

Targeting Induced Local Lesions IN Genomes (TILLING) is a reverse genetics approach to directly identify point mutations in specific genes of interest in genomic DNA from a large chemically mutagenized population. Classical TILLING processes, based on enzymatic detection of mutations in heteroduplex PCR amplicons, are slow and labor intensive.

RESULTS

Here we describe a new TILLING strategy in zebrafish using direct next generation sequencing (NGS) of 250 bp amplicons followed by Paired-End Low-Error (PELE) sequence analysis. By pooling a genomic DNA library made from over 9,000 N-ethyl-N-nitrosourea (ENU) mutagenized F1 fish into 32 equal pools of 288 fish, each with a unique Illumina barcode, we reduce the complexity of the template to a level at which we can detect mutations that occur in a single heterozygous fish in the entire library. MiSeq sequencing generates 250 base-pair overlapping paired-end reads, and PELE analysis aligns the overlapping sequences to each other and filters out any imperfect matches, thereby eliminating variants introduced during the sequencing process. We find that this filtering step reduces the number of false positive calls 50-fold without loss of true variant calls. After PELE we were able to validate 61.5% of the mutant calls that occurred at a frequency between 1 mutant call:100 wildtype calls and 1 mutant call:1000 wildtype calls in a pool of 288 fish. We then use high-resolution melt analysis to identify the single heterozygous mutation carrier in the 288-fish pool in which the mutation was identified.

CONCLUSIONS

Using this NGS-TILLING protocol we validated 28 nonsense or splice site mutations in 20 genes, at a two-fold higher efficiency than using traditional Cel1 screening. We conclude that this approach significantly increases screening efficiency and accuracy at reduced cost and can be applied in a wide range of organisms.