Browsing by Author "Jaiswal, Vandana"

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Genome-wide association study (GWAS) delineates genomic loci for ten nutritional elements in foxtail millet (Setaria italica L.)
(Elsevier B.V., 2019) Jaiswal, Vandana; Bandyopadhyay, Tirthankar; Gahlaut, Vijay; Gupta, Sarika; Dhaka, Annvi; Ramchiary, Nirala; Prasad, Manoj
Nutritional deficiency is found to be a major threat to human health, especially in low-income countries. Thus it is essential to improve nutritional qualities of important food crops. Foxtail millet is second largest cultivated millet and 2–5 times nutritionally richer than major cereal crops. During the present study, we identified genetic determinants of ten nutritional elements including potassium, nickel, calcium, boron, magnesium, phosphorus, sulphur, zinc, manganese and iron for the first time in foxtail millet. For this purpose, genome-wide association studies (GWAS) were conducted using 93 diverse accessions and 10 K SNPs (distributed across all the nine foxtail millet chromosomes). Altogether, 74 marker-trait associations (MTAs) were identified to be associated with above mentioned ten elements, out of which ten (10) MTAs (associated with B, Mg, Zn and Fe) showed high confidence [-log(p) > 5.78]. Identified desirable SNP alleles and favourable haplotypes may prove useful in foxtail breeding. Also, significant pyramiding effect suggested that associated elements can be substantially enhanced through combining more than one MTA. Candidate genes residing within or near the association signal may be selected for functional characterization. Superior genotypes identified may prove as a potential donor in foxtail millet breeding assisted through the molecular marker.
Genome-wide association study of major agronomic traits in foxtail millet (Setaria italica L.) using ddRAD sequencing
(Springer Nature, 2019) Jaiswal, Vandana; Gupta, Sarika; Gahlaut, Vijay; Muthamilarasan, Mehanathan; Bandyopadhyay, Tirthankar; Ramchiary, Nirala; Prasad, Manoj
Foxtail millet (Setaria italica), the second largest cultivated millet crop after pearl millet, is utilized for food and forage globally. Further, it is also considered as a model crop for studying agronomic, nutritional and biofuel traits. In the present study, a genome-wide association study (GWAS) was performed for ten important agronomic traits in 142 foxtail millet core eco-geographically diverse genotypes using 10 K SNPs developed through GBS-ddRAD approach. Number of SNPs on individual chromosome ranged from 844 (chromosome 5) to 2153 (chromosome 8) with an average SNP frequency of 25.9 per Mb. The pairwise linkage disequilibrium (LD) estimated using the squared-allele frequency correlations was found to decay rapidly with the genetic distance of 177 Kb. However, for individual chromosome, LD decay distance ranged from 76 Kb (chromosome 6) to 357 Kb (chromosome 4). GWAS identified 81 MTAs (marker-trait associations) for ten traits across the genome. High confidence MTAs for three important agronomic traits including FLW (flag leaf width), GY (grain yield) and TGW (thousand-grain weight) were identified. Significant pyramiding effect of identified MTAs further supplemented its importance in breeding programs. Desirable alleles and superior genotypes identified in the present study may prove valuable for foxtail millet improvement through marker-assisted selection.
GWAS identifies genetic loci underlying nitrogen responsiveness in the climate resilient C4 model Setaria italica (L.)
(Elsevier B.V., 2022) Bandyopadhyay, Tirthankar; Swarbreck, Stéphanie M; Jaiswal, Vandana; Maurya, Jyoti; Gupta, Rajeev; Bentley, Alison R.; Griffiths, Howard; Prasad, Manoj
Introduction N responsiveness is the capacity to perceive and induce morpho-physiological adaptation to external and internal Nitrogen (N). Crop productivity is propelled by N fertilizer and requires the breeding/selection of cultivars with intrinsically high N responsiveness. This trait has many advantages in being more meaningful in commercial/environmental context, facilitating in-season N management and not being inversely correlated with N availability over processes regulating NUE. Current lack of its understanding at the physio-genetic basis is an impediment to select for cultivars with a predictably high N response. Objectives To dissect physio-genetic basis of N responsiveness in 142 diverse population of foxtail millet, Setaria italica (L.) by employing contrasting N fertilizer nutrition regimes. Methods We phenotyped S. italica accessions for major yield related traits under low (N10, N25) and optimal (N100) growth conditions and genotyped them to subsequently perform a genome-wide association study to identify genetic loci associated with nitrogen responsiveness trait. Groups of accessions showing contrasting trait performance and allelic forms of specific linked genetic loci (showing haplotypes) were further accessed for N dependent transcript abundances of their proximal genes. Results Our study show that N dependent yield rise in S. italica is driven by grain number whose responsiveness to N availability is genetically underlined. We identify 22 unique SNP loci strongly associated with this trait out of which six exhibit haplotypes and consistent allelic variation between lines with contrasting N dependent grain number response and panicle architectures. Furthermore, differential transcript abundances of specific genes proximally linked to these SNPs in same lines is indicative of their N dependence in a genotype specific manner. Conclusion The study demonstrates the value/ potential of N responsiveness as a selection trait and identifies key genetic components underlying the trait in S. italica. This has major implications for improving crop N sustainability and food security.
Identification of novel SNP in promoter sequence of TaGW2-6A associated with grain weight and other agronomic traits in wheat (Triticum aestivum L.)
(PLOS, 2015) Jaiswal, Vandana; Gahlaut, Vijay; Mathur, Saloni; Agarwal, Priyanka; Khandelwal, Manoj Kumar; Khurana, Jitendra Paul; Tyagi, Akhilesh K.; Balyan, Harindra Singh; Gupta, Pushpendra Kumar
TaGW2 is an orthologue of rice gene OsGW2, which encodes E3 RING ubiquitin ligase and controls the grain size in rice. In wheat, three copies of TaGW2 have been identified and mapped on wheat homoeologous group 6 viz. TaGW2-6A, TaGW2-6B and TaGW2-6D. In the present study, using as many as 207 Indian wheat genotypes, we identified four SNPs including two novel SNPs (SNP-988 and SNP-494) in the promoter sequence of TaGW2-6A. All the four SNPs were G/A or A/G substitutions (transitions). Out of the four SNPs, SNP-494 was causal, since it was found associated with grain weight. The mean TGW (41.1 g) of genotypes with the allele SNP-494_A was significantly higher than mean TGW (38.6 g) of genotypes with the allele SNP-494_G. SNP-494 also regulates the expression of TaGW2-6A so that the wheat genotypes with SNP-494_G have higher expression and lower TGW and the genotypes with SNP-494_A have lower expression but higher TGW. Besides, SNP-494 was also found associated with grain length-width ratio, awn length, spike length, grain protein content, peduncle length and plant height. This suggested that gene TaGW2-6A not only controls grain size, but also controls other agronomic traits. In the promoter region, SNP-494 was present in 'CGCG' motif that plays an important role in Ca2+/calmodulin mediated regulation of genes. A user-friendly CAPS marker was also developed to identify the desirable allele of causal SNP (SNP-494) for use in marker-assisted selection for improvement of grain weight in wheat. Using four SNPs, five haplotypes were identified; of these, Hap_5 (G_A_G_A) was found to be a desirable haplotype having significantly higher grain weight (41.13g) relative to other four haplotypes (36.33-39.16 g).
Multi-environment GWAS identifies genomic regions underlying grain nutrient traits in foxtail millet (Setaria italica)
(Springer Nature Publishing AG, 2024) Jaiswal, Vandana; Bandyopadhyay, Tirthankar; Singh, Roshan Kumar; Gahlaut, Vijay; Muthamilarasan, Mehanathan; Prasad, Manoj
A total of 104 foxtail millet accessions were evaluated for 11 nutrients in three environments and 67 high-confidence marker-trait associations (MTAs) were identified. Six SNPs showed pleiotropic effect and associated with two or more nutrients, whereas 24 candidate genes were identified for 28 MTAs involving seven traits. Millets are known for their better nutritional profiles compared to major cereals. Foxtail millet (Setaria italica) is rich in nutrients essential to circumvent malnutrition and hidden hunger. However, the genetic determinants underlying this trait remain elusive. In this context, we evaluated 104 diverse foxtail millet accessions in three different environments (E1, E2, and E3) for 11 nutrients and genotyped with 30K SNPs. The genome-wide association study showed 67 high-confidence (Bonferroni-corrected) marker-trait associations (MTAs) for the nutrients except for phosphorus. Six pleiotropic SNPs were also identified, which were associated with two or more nutrients. Around 24 candidate genes (CGs) were identified for 28 MTAs involving seven nutrients. A total of 17 associated SNPs were present within the gene region, and five (5) were mapped in the exon of the CGs. Significant SNPs, desirable alleles and CGs identified in the present study will be useful in breeding programmes for trait improvement.
Nutrition potential of foxtail millet in comparison to other millets and major cereals
(Springer, 2017) Bandyopadhyay, Tirthankar; Jaiswal, Vandana; Prasad, Manoj
Global population is burgeoning at an alarming rate and is expected to reach 9.7 billion by 2050 and 11.2 billion by the end of this century. This has led to immense pressure on global agriculture, compounded by dwindling productivity of the existing systems and acreage because of climate change, resulting in ever-increasing input costs for the cultivation of most resource-intensive cereal crops such as rice, wheat, and maize. Ironically, the most affected populations are those with least resources to mitigate the problem—those belonging to Asian and Sub-Saharan Africa. It is against this backdrop that there is an ever-increasing need for adopting cereal crops that are easy to cultivate, less resource hungry, climate resilient, and importantly, that meet the major nutritional requirement of the feeding population. Foxtail millet is a perfect cereal crop in this light and stands to help significantly global endeavors toward food security and nutrition. The present chapter provides a comparative nutritional assessment of foxtail millet with other cereal crops, summarizes the major scientific approaches currently being undertaken for its biofortification and highlights potential avenues of crop improvement using conventional breeding, genomics, and other interdisciplinary “omic” tools.