Identification of SNPs in crucial starch biosynthesis genes in rice.

Rice is the foremost crop catering to the major calorific requirement of the human population but has the disadvantage of having high glycaemic index (GI). The fine quality rice varieties, BPT and RNR have been recently identified as having low GI in nature and are grown mostly in southern parts of India. Starch (80%) is the major component of rice endosperm attributing to GI. The study aimed to unravel the molecular basis of low GI through targeted pooled amplicon sequencing of major starch biosynthetic genes. A total of 13 candidate genes involved in starch synthesis were amplified and pooled in equimolar proportion for sequencing. Single-nucleotide polymorphisms (SNPs) and insertions/deletions (Indels) were detected in both coding and noncoding regions. Among the genes that are under study, the highest number of variations were identified in starch synthase I (SSI) followed by starch synthase IIIA (SSIIIA) genes. Nonsynonymous SNPs with high probability of effecting gene function were validated by Sanger sequencing and molecular docking. Identified causative SNPs were mapped on 3000 rice genome database and their allele frequencies were obtained. The outcome of this study has a potential to be applied in breeding programmes to obtain low GI rice varieties with added beneficial traits.

Assessment of germination, phytochemicals, and transcriptional responses to ethephon priming in soybean [Glycine max (L.) Merrill].

The present work aims to dissect the underlying signaling pathways associated with soybean [Glycine max (L.) Merrill] seed hormo-priming with ethephon (Eth). Our results demonstrated that soybean germination improved significantly upon Eth priming (Ethp). Phytohormone quantification shows relative enhanced endogenous gibberellin A4 (GA4) levels concomitant with impaired biogenesis and signaling of auxin, viz., indole acetic acid (IAA) and abscisic acid (ABA). Phytochemical analysis revealed relative reduced levels of individual and total raffinose family oligosaccharide (RFO) components, starch, soluble sugars, and sucrose concomitant with enhanced levels of reducing sugars, glucose, cellular ATP, and acetyl-CoA pools. Secondary metabolite analysis revealed the activation of the mevalonate (MVA) pathway with a concomitant suppression of the plastidal 2-methyl-d-erythritol-4-phosphate/1-deoxy-d-xylulose-5-phosphate (MEP/DOX) and phenylpropanoid pathways, substantiated by relative reduced levels of total phenolics, tannins, and proanthocyanidin. Ethp also enhances the in vitro antioxidative activity (viz., 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging ability and ferric reducing antioxidant power (FRAP)) and endogenous antioxidants levels (viz., flavonoids, isoflavones, ß-carotene, vitamin C, and vitamin E). Further quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed transcriptional pattern of representative genes in agreement with these metabolic alterations.

Development of KASP marker for cytoplasmic male sterility in Nicotiana tabacum and utilization in trait introgression.

Cytoplasmic male sterility (CMS) is an important trait for large-scale hybrid seed production which avoids manual emasculation and undesired horizontal spread of pollen. Rearrangements in mitochondrial genome in terms of deletions and insertions are frequent causes leading to CMS. Mitochondrial ATP synthase is a multisubunit molecular machine which is involved in synthesis of ATP. In this study, three mutations in ATPase subunit 6 were identified and their cosegregation with male sterility was established using tobacco male sterile hybrids and Nicotiana suvaolensis. A breeder friendly Kompetitive allele specific polymerase chain reaction (KASP) SNP marker was developed for high throughput and quick genotyping. Introgression of this trait into selected germplasm lines (n = 9) was achieved based on foreground for CMS and background selection for recurrent parent using KASP marker and 50K custom tobacco SNP array, respectively. Analysis of genotyping data from SNP array revealed the presence of 88-99% of recurrent parent genome in BC3F1 plants. The selected BC3F1 plants exhibit CMS and are indistinguishable from the fertile recurrent parent (germplasm) in terms of plant morphology.

Differential response of tomato and tobacco to Agrobacterium mediated transformation with cytokinin independent -1 (CKI-1) gene as influenced by cytokinin levels.

Cytokinin independent-1 (CKI-1) gene was identified through its ability to confer cytokinin independent growth in Arabidopsis which has led to this gene being advocated as a selectable marker in plant transformation. Keeping this in view, CKI-1 gene was assessed as a selectable marker by transformation of tobacco (Nicotiana tabacum) and tomato (Lycopersicon esculentum L.). Overexpression of CKI-1 gene through Agrobacterium mediated transformation in tobacco and tomato conferred cytokinin independent shoot regeneration (in media devoid of cytokinin/plant growth regulators) in tobacco, but not in tomato wherein this ability (cytokinin independence) was conferred to T1 explants of CKI-1 transgenic tomato plant (T0) regenerated on cytokinin medium. Analysis of cytokinin levels revealed that cytokinin independent growth upon transformation with CKI-1 gene in tobacco (T0) and tomato (T1) was achieved through maintaining/regulating higher endogenous cytokinin levels and CKI-1 gene expression. Levels of CKI-1 transcripts assayed through quantitative RT-PCR suggested that there seemed to be a threshold level of endogenous cytokinin level, regulated due to external or internal supply via CKI-1 gene upto which CKI-1 gene expression correlated with endogenous cytokinin content and beyond that, either the gene expression was not induced or it remains same. With the incorporation of CKI-1 gene, it appeared that this threshold level of endogenous cytokinin might be reduced in crops like tomato to support shoot regeneration at lower concentration of cytokinin, but could not be made independent of external supply of cytokinin as in tobacco suggesting that use of CKI-1 gene as an effective alternate selection marker could not be universally applicable across the species. The results of the present study revealed that CKI-1 gene in addition to enhancing cytokinin levels, was also involved in contributing to the sensitivity to cytokinin and thus served as a positive regulator of cytokinin signal transduction.