Development of tetra-primer amplicon refractory mutation system (T-ARMS) strategy for identification of the dark green mutant allele in tomato

Development of a tetra-primer ARMS-PCR for identification of sika and red deer and their hybrids

Accurate identification of deer-derived components is significant in food and drug authenticity. Over the years, several methods have been developed to authenticate these products; however, identifying whether female deer products are hybrids is challenging. In this study, the zinc finger protein X-linked (ZFX) gene sequences of sika deer (Cervus nippon), red deer (Cervus elaphus) and their hybrid offspring were amplified and sequenced, the X221 and X428 species-specific single nucleotide polymorphisms (SNP) loci were verified, and a tetra-primer amplification refractory mutation system (T-ARMS-PCR) assay was developed to identify the parent-of-origin of female sika deer, red deer, and their hybrid deer. The T-ARMS-PCR developed based on the X221 locus could identify sika deer, red deer, and their hybrid offspring according to the presence or absence of PCR product sizes of 486 bp, 352 bp, and 179 bp, respectively, just as X428 locus could identify sika deer, red deer, and their hybrid offspring according to the presence or absence of PCR product sizes of 549 bp, 213 bp, and 383 bp, respectively. Forty products labeled deer-derived ingredients randomly purchased were tested using this assay, and the results showed that the identification results based on the two SNP loci were utterly consistent with the actual sources. In addition, this method was found to be accurate, simple, convenient, and with high specificity, thus providing an essential technical reference for deer product species identification. It is also an important supplement to the identification methods of the original ingredients of existing deer products.

Marker assisted early generation identification of root knot disease resistant orange tomato segregants with multiple desirable alleles

Enhanced bioavailability of cis-isomers of lycopene, accumulated in orange-fruited tangerine mutant has broadened the scope of nutritional enrichment in tomato. At the same time, advancements in the field of marker assisted selection (MAS) have made the stacking of multiple desirable alleles through molecular breeding to develop superior tomato genotypes possible. Here we report seedling stage MAS from 146 F2 plants, to identify 3 superior performing, root knot disease resistant orange-fruited segregants. In the selected segregants, fruit weight ranged from 39.2 to 54.6 g, pericarp thickness ranged from 4.56 to 6.05 mm and total soluble solid content ranged from 3.65 to 4.87° Brix. Presence of parental diversity allowed identification of the other desirable alleles of the genes governing late blight and mosaic disease resistance, growth habit (determinate and indeterminate) as well as fruit elongation and firmness. Resistance to root knot disease of the selected 3 segregants was also validated through a unique method employing in vitro rooted stem cuttings subjected to artificial inoculation, where the resistant parent and the selected segregants developed no galls in comparison to ~ 24 galls developed in the susceptible parent. The selected segregants form the base for development of multiple disease resistant, nutritionally enriched orange-fruited determinate/indeterminate tomato lines with superior fruit quality. The study also highlights the utility of early generation MAS for detailed characterization of segregants, through which multiple desirable alleles can be precisely targeted and fixed to develop superior tomato genotypes.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01361-1.

Tetra-Primer Amplification Refractory Mutation System (T-ARMS)

Single-nucleotide polymorphisms (SNPs), the most abundant genetic variation in the population, have become the molecular marker of choice. Generally, the efficient detection of SNPs requires specialized costly equipment. Although there are a few strategies for detecting SNPs through polymerase chain reaction, followed by restriction enzyme digestion and agarose gel electrophoresis, these methods are time-consuming and might be less diagnostic. Interestingly, the tetra primer amplification refractory mutation system (T-ARMS) strategy utilizes a pair of allele-specific primers in a single PCR for the diagnostic detection of SNPs in a codominant manner through standard agarose gel electrophoresis. The simplicity and robustness of the strategy have inspired the researchers to adopt this low-cost method of SNP detection in different crop plants. Here, we have described the principle, methods, and conditions for the T-ARMS strategy. The described methodology starts from the isolation of genomic DNA and ends with the post-PCR analysis of refractory amplicons in standard agarose gel electrophoresis. The limitations and future perspectives are also discussed. Taken together, T-ARMS evolves as a method of choice for low-cost SNP detection in plants.

Development and validation of the OVATE gene-based functional marker to assist fruit shape selection in tomato

Fruit size, shape and colour are important determinants of fruit quality in tomato. Among the different genetic factors, the OVATE gene is a key regulator of fruit elongation in tomato. The loss-of-function recessive ovate allele results from a functional single nucleotide polymorphism (SNP) in the second exon of the gene to produce fruit elongation and variable fruit shapes in different genetic backgrounds. The mutation has also been associated with increased fruit firmness, a desirable trait for processing purpose of tomato. However, the recessive nature of this important mutant allele makes its identification and utilization in breeding programme difficult. Hence, we developed the OVATE gene-based functional marker using the tetra-primer amplification refractory mutation system (T-ARMS) strategy. The developed functional marker was capable of identifying the allelic status at OVATE locus in a co-dominant manner, using routine polymerase chain reaction (PCR) followed by standard agarose gel electrophoresis. Trait-marker association of the developed functional marker was validated in the F₂ segregants bearing elongated and non-elongated fruits. Thus, the functional marker developed and validated in this study will assist the tomato breeders in identification and introgression of the desired allelic version of the OVATE gene in a time-, labour- and cost-effective manner. Moreover, identification of the allelic status at the OVATE locus will help in exploring its interacting partners and modifiers for detailed understanding of the fascinating genetics behind fruit shape variation in tomato.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-03029-7.