Discovery of mutations in Chenopodium quinoa Willd through EMS mutagenesis and mutation screening using pre-selection phenotypic data and next-generation sequencing

Mestanza, Camilo; Riegel, Ricardo; Vásquez, Santiago C.; Veliz, Diana; Rosero, Nicolás Cruz; Canchignia, Hayron; Silva, Herman

doi:10.1017/s0021859619000182

Cited by 10 publications

(9 citation statements)

References 59 publications

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“…For the chemical mutagen ethyl methyl sulfone (EMS), a genome-wide analysis of induced mutations has been performed in rice [7] and a number of other plant species, e.g., wheat [8][9][10], foxtail millet [11], Chenopodium quinoa Willd. [12], sorghum [13], tomato [14], Cucurbita pepo [15], peach [16], Lotus japonicus [17] and Jatropha curcas [18]. Similar studies have also been performed for physical mutagens, such as γ ray mutagenesis in rice [19,20] and poplar [21], fast neutron mutagenesis in Arabidopsis thaliana [22] and rice [23], and ion beams in Arabidopsis thaliana [24][25][26][27][28].…”

Section: Introductionmentioning

confidence: 91%

Mutagenic Effect of Three Ion Beams on Rice and Identification of Heritable Mutations by Whole Genome Sequencing

Zheng

Huang

et al. 2020

Plants

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High-energy ion beams are known to be an effective and unique type of physical mutagen in plants. However, no study on the mutagenic effect of argon (Ar) ion beam radiation on rice has been reported. Genome-wide studies on induced mutations are important to comprehend their characteristics for establishing knowledge-based protocols for mutation induction and breeding, which are still very limited in rice. The present study aimed to investigate the mutagenic effect of three ion beams, i.e., Ar, carbon (C) and neon (Ne) on rice and identify and characterize heritable induced mutations by the whole genome sequencing of six M4 plants. Dose-dependent damage effects were observed on M1 plants, which were developed from ion beam irradiated dry seeds of two indica (LH15, T23) and two japonica (DS551, DS48) rice lines. High frequencies of chlorophyll-deficient seedlings and male-sterile plants were observed in all M2 populations (up to ~30% on M1 plant basis); plants from the seeds of different panicles of a common M1 plant appeared to have different mutations; the whole genome-sequencing demonstrated that there were 236–453 mutations in each of the six M4 plants, including single base substitutions (SBSs) and small insertion/deletions (InDels), with the number of SBSs ~ 4–8 times greater than that of InDels; SBS and InDel mutations were distributed across different genomic regions of all 12 chromosomes, however, only a small number of mutations (0–6) were present in exonic regions that might have an impact on gene function. In summary, the present study demonstrates that Ar, C and Ne ion beam radiation are all effective for mutation induction in rice and has revealed at the genome level the characteristics of the mutations induced by the three ion beams. The findings are of importance to the efficient use of ion beam radiation for the generation and utilization of mutants in rice.

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Section: Introductionmentioning

confidence: 91%

Mutagenic Effect of Three Ion Beams on Rice and Identification of Heritable Mutations by Whole Genome Sequencing

Zheng

Huang

et al. 2020

Plants

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“…As an alternative to genome editing, TILLING (Targeting Induced Local Lesions IN Genomes) methods may soon prove as effective and fast as gene editing technologies for the identification of induced genetic variants in any gene ( Holme et al , 2019 ). Present quinoa TILLING libraries typically contain up to 3000 highly mutagenized individuals ( Mestanza et al , 2018 ). However, the advent of advanced genetic screens now enables the establishment and screening of much larger libraries derived from fewer mutagenized individuals ( Wendt et al , 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Prospects for the accelerated improvement of the resilient crop quinoa

López‐Marqués

Nørrevang

Ache

et al. 2020

Journal of Experimental Botany

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Abstract Crops tolerant to drought and salt stress may be developed by two approaches. First, major crops may be improved by introducing genes from tolerant plants. For example, many major crops have wild relatives that are more tolerant to drought and high salinity than the cultivated crops, and, once deciphered, the underlying resilience mechanisms could be genetically manipulated to produce crops with improved tolerance. Secondly, some minor (orphan) crops cultivated in marginal areas are already drought and salt tolerant. Improving the agronomic performance of these crops may be an effective way to increase crop and food diversity, and an alternative to engineering tolerance in major crops. Quinoa (Chenopodium quinoa Willd.), a nutritious minor crop that tolerates drought and salinity better than most other crops, is an ideal candidate for both of these approaches. Although quinoa has yet to reach its potential as a fully domesticated crop, breeding efforts to improve the plant have been limited. Molecular and genetic techniques combined with traditional breeding are likely to change this picture. Here we analyse protein-coding sequences in the quinoa genome that are orthologous to domestication genes in established crops. Mutating only a limited number of such genes by targeted mutagenesis appears to be a promising route for accelerating the improvement of quinoa and generating a nutritious high-yielding crop that can meet the future demand for food production in a changing climate.

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“…Another new genome editing method is TILLING (Targeting Induced Local Lesions in Genomes), which proved to be the most effective and fast technology for identifying induced mutations in any gene ( 274 ). At present, large TILLING libraries typically contain up to 3,000 highly mutagenized individuals of quinoa ( 275 ). Advanced genetic screens enable the establishment and screening of much larger libraries derived from mutagenized populations ( 276 ).…”

Section: Breeding Behavior and Approachesmentioning

confidence: 99%

Genetic resources and breeding approaches for improvement of amaranth (Amaranthus spp.) and quinoa (Chenopodium quinoa)

Anuradha¹,

Kumari²,

Zinta³

et al. 2023

Front. Nutr.

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Nowadays, the human population is more concerned about their diet and very specific in choosing their food sources to ensure a healthy lifestyle and avoid diseases. So people are shifting to more smart nutritious food choices other than regular cereals and staple foods they have been eating for a long time. Pseudocereals, especially, amaranth and quinoa, are important alternatives to traditional cereals due to comparatively higher nutrition, essential minerals, amino acids, and zero gluten. Both Amaranchaceae crops are low-input demanding and hardy plants tolerant to stress, drought, and salinity conditions. Thus, these crops may benefit developing countries that follow subsistence agriculture and have limited farming resources. However, these are underutilized orphan crops, and the efforts to improve them by reducing their saponin content remain ignored for a long time. Furthermore, these crops have very rich variability, but the progress of their genetic gain for getting high-yielding genotypes is slow. Realizing problems in traditional cereals and opting for crop diversification to tackle climate change, research should be focused on the genetic improvement for low saponin, nutritionally rich, tolerant to biotic and abiotic stresses, location-specific photoperiod, and high yielding varietal development of amaranth and quinoa to expand their commercial cultivation. The latest technologies that can accelerate the breeding to improve yield and quality in these crops are much behind and slower than the already established major crops of the world. We could learn from past mistakes and utilize the latest trends such as CRISPR/Cas, TILLING, and RNA interference (RNAi) technology to improve these pseudocereals genetically. Hence, the study reviewed important nutrition quality traits, morphological descriptors, their breeding behavior, available genetic resources, and breeding approaches for these crops to shed light on future breeding strategies to develop superior genotypes.

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Discovery of mutations in Chenopodium quinoa Willd through EMS mutagenesis and mutation screening using pre-selection phenotypic data and next-generation sequencing

Cited by 10 publications

References 59 publications

Mutagenic Effect of Three Ion Beams on Rice and Identification of Heritable Mutations by Whole Genome Sequencing

Mutagenic Effect of Three Ion Beams on Rice and Identification of Heritable Mutations by Whole Genome Sequencing

Prospects for the accelerated improvement of the resilient crop quinoa

Genetic resources and breeding approaches for improvement of amaranth (Amaranthus spp.) and quinoa (Chenopodium quinoa)

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