Identification of novel mutations in the rice starch branching enzyme I gene via TILLING by sequencing

Kim, Hyun-Jung; Yoon, Min-Ho; Chun, Areum; Tai, Thomas H.

doi:10.1007/s10681-018-2174-7

Cited by 11 publications

(7 citation statements)

References 29 publications

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“…Unfortunately, any kind of genome editing is legally classified as genetic modification especially in the EU which prevents its application in plant breeding. Today, with the availability of advanced bioinformatics and reduced sequencing costs, TILLING by Sequencing (TbyS) can be implemented in every crop in various approaches like whole genome, exome capture or amplicon sequencing (Rigola et al , ; Tsai et al , ; Tsuda et al , ; Krasileva et al , ; Kim et al , ). The selection of a suitable method depends on the size of the genome and on underlying costs for library preparation and sequencing.…”

Section: Introductionmentioning

confidence: 99%

Identification of phytic acid mutants in oilseed rape (Brassica napus) by large‐scale screening of mutant populations through amplicon sequencing

Sashidhar

Harloff

2019

New Phytologist

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Brassica napus (oilseed rape) is an important oil crop in temperate regions, which originated from hybridization of Brassica oleracea and Brassica rapa. Owing to its polyploidy, the functional study of single genes is cumbersome. Phytic acid is considered as an antinutritive compound, and we aimed to knock out the underlying synthesis and transporter genes to identify low phytic acid mutants.We implemented a high-throughput next-generation sequencing screening protocol for an ethylmethane sulfonate population of 7680 plants in six gene families (BnMIPS, BnMIK, Bn2-PGK, BnIPK1, BnIPK2, and BnMRP5) with two paralogues for each gene.A total of 1487 mutations were revealed, and the vast majority (96%) were confirmed by Sanger sequencing. Furthermore, the characterization of double mutants of Bn.2-PGK2 showed a significant reduction of phytic acid contents.We propose to use three-dimensional pooling combined with amplicon stacking and nextgeneration sequencing to identify mutations in polyploid oilseed rape in a fast and cost-effective manner for complex metabolic pathways. Furthermore, the mutants identified in Bn2-PGK2 might be a very valuable resource for industrial production of oilseed rape protein for human consumption.

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Section: Introductionmentioning

confidence: 99%

Identification of phytic acid mutants in oilseed rape (Brassica napus) by large‐scale screening of mutant populations through amplicon sequencing

Sashidhar

Harloff

2019

New Phytologist

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“…SBEI plays a critical role in amylose content, and from these 37 identified mutations, one mutant M-4936 significantly reduced grain width and thickness. Physicochemical analysis revealed significant differences in apparent amylose content (15% vs. 19%) and protein content (9.2% vs. 4.8%) [78].…”

Section: Tilling For Starch Synthesismentioning

confidence: 94%

TILLING in Cereal Crops for Allele Expansion and Mutation Detection by Using Modern Sequencing Technologies

et al. 2020

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A substantial increase in yield of food crops is crucial to feeding the burgeoning global population. There is a need to introduce new breeding strategies that will accelerate the average phenotypic values of crop plants. The use of induced mutations coupled with modern genomics tools is an effective strategy for identifying and manipulating genes for crop improvement. High-throughput TILLING (Targeting Induced local Lesions IN Genomes) methodology, detects mutations in mutagenized populations, and EcoTILLING identifies single nucleotide polymorphisms (SNPs) within a natural population and associates these variations with traits of breeding interest. The main advantage of these techniques as a “reverse genetics” strategy is that they can be applied to any species regardless of genome size and ploidy level. In cereals, several space-induced and EMS-induced mutant populations have been used to identify mutants with important traits including salinity tolerance, grain size, and recombinant crossovers via TILLING by sequencing (TbyS). Genes such as TaSSIV, which plays an important role in starch granule formation, and Pin a and Pin b, which have been associated with kernel hardness in wheat, have been exploited in cereals via the EcoTILLING approach. This review focused on the functions and challenges of TILLING and the relation of TILLING to next-generation sequencing (NGS) technologies which help to exploit the induced mutations and their potential applications in cereal crops.

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“…Over the last few years, higher amylose content in staple crops has gained considerable interest due to its positive correlation with resistant starch (RS; Kim et al, 2018). RS is resistant to enzymatic hydrolysis (i.e., digestion) in the small intestine and is fermented by microorganism in the large intestine to produce short chain fatty acid (Englyst et al, 1982;Yang et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Interaction of starch branching enzyme 3 and granule-bound starch synthase 1 alleles increases amylose content and alters physico-chemical properties in japonica rice (Oryza sativa L.)

et al. 2022

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Four near-isogenic lines (NILs) with different allele combinations of the starch branching enzyme 3 (SBE3) and granule-bound starch synthase 1 (GBSS1) were developed by crossing the japonica rice cultivars “Dodamssal” and “Hwayeong.” The associations between sequence variations in SBE3 and GBSS1, and starch-related traits were investigated. These sequence variations led to changes in seed morphology, starch structure, starch crystallinity, amylopectin chain length distribution, digestibility, apparent amylose content (AAC), and resistant starch content (RS). SBE3 and GBSS1 showed genetic interaction in regulating AAC and RS. Gene expression profiling of panicle tissues revealed significant differences in expression levels of GBSS1, SBE3, and other starch-related genes among the four NILs, indicating that variations in GBSS1 and SBE3 changed the expression level of starch-related genes. These variations contributed to the changes observed in AAC, RS, and physico-chemical characteristics of the rice starch from the NILs.

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Identification of novel mutations in the rice starch branching enzyme I gene via TILLING by sequencing

Cited by 11 publications

References 29 publications

Identification of phytic acid mutants in oilseed rape (Brassica napus) by large‐scale screening of mutant populations through amplicon sequencing

Identification of phytic acid mutants in oilseed rape (Brassica napus) by large‐scale screening of mutant populations through amplicon sequencing

TILLING in Cereal Crops for Allele Expansion and Mutation Detection by Using Modern Sequencing Technologies

Interaction of starch branching enzyme 3 and granule-bound starch synthase 1 alleles increases amylose content and alters physico-chemical properties in japonica rice (Oryza sativa L.)

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