Whole Genome Characterization of a Few EMS-Induced Mutants of Upland Rice Variety Nagina 22 Reveals a Staggeringly High Frequency of SNPs Which Show High Phenotypic Plasticity Towards the Wild-Type

Abstract

The Indian initiative, in creating mutant resources for the functional genomics in rice, has been instrumental in the development of 87,000 ethylmethanesulfonate (EMS)-induced mutants, of which 7,000 are in advanced generations. The mutants have been created in the background of Nagina 22, a popular drought- and heat-tolerant upland cultivar. As it is a pregreen revolution cultivar, as many as 573 dwarf mutants identified from this resource could be useful as an alternate source of dwarfing. A total of 541 mutants, including the macromutants and the trait-specific ones, obtained after appropriate screening, are being maintained in the mutant garden. Here, we report on the detailed characterizations of the 541 mutants based on the distinctness, uniformity, and stability (DUS) descriptors at two different locations. About 90% of the mutants were found to be similar to the wild type (WT) with high similarity index (>0.6) at both the locations. All 541 mutants were characterized for chlorophyll and epicuticular wax contents, while a subset of 84 mutants were characterized for their ionomes, namely, phosphorous, silicon, and chloride contents. Genotyping of these mutants with 54 genomewide simple sequence repeat (SSR) markers revealed 93% of the mutants to be either completely identical to WT or nearly identical with just one polymorphic locus. Whole genome resequencing (WGS) of four mutants, which have minimal differences in the SSR fingerprint pattern and DUS characters from the WT, revealed a staggeringly high number of single nucleotide polymorphisms (SNPs) on an average (16,453 per mutant) in the genic sequences. Of these, nearly 50% of the SNPs led to non-synonymous codons, while 30% resulted in synonymous codons. The number of insertions and deletions (InDels) varied from 898 to 2,595, with more than 80% of them being 1–2 bp long. Such a high number of SNPs could pose a serious challenge in identifying gene(s) governing the mutant phenotype by next generation sequencing-based mapping approaches such as Mutmap. From the WGS data of the WT and the mutants, we developed a genic resource of the WT with a novel analysis pipeline. The entire information about this resource along with the panicle architecture of the 493 mutants is made available in a mutant database EMSgardeN22 (http://14.139.229.201/EMSgardeN22).

Fast Neutron Mutagenesis in Plants: Advances, Applicability and Challenges

“…However larger deletions and chromosomal rearrangements as usually observed with the FN mutagenesis have very less chances to occur spontaneously. The whole genome sequencing of fast neutron mediated mutant lines provides opportunity to develop a genomic resource that can be used for forward and reverse genetic applications [51].…”

Ethyl methanesulfonate mutant library construction in Gossypium hirsutum L. for allotetraploid functional genomics and germplasm innovation

“…Therefore, it is necessary to select appropriate technical means for artificial mutagenesis. Chemical and physical mutagens induction are the better choices to create mutants (Sevanthi et al, 2018). And time consuming and costly in cotton species renders physical mutagens impractical.…”

Increased Catalase Activity and Maintenance of Photosystem II Distinguishes High-Yield Mutants From Low-Yield Mutants of Rice var. Nagina22 Under Low-Phosphorus Stress

“…For characterization, 85,000 EMS-induced mutants were generated and maintained under a multi-institutional program ( Mithra et al, 2016 ). Mutants for abiotic stresses such as heat, drought, low-P tolerance, and herbicide resistance were identified ( Poli et al, 2013 , 2017a , b ; Mohapatra et al, 2014 ; Panigrahy et al, 2014 ; Lima et al, 2015 ; Talla et al, 2016 ; Shoba et al, 2017 ; Yugandhar et al, 2018a ).…”