Akshay Talukdar

Population structure and association mapping studies for important agronomic traits in soybean

The present study was carried out with a set of 96 diverse soybean genotypes with the objectives of analysing the population structure and to identify molecular markers associated with important agronomic traits. Large phenotypic variability was observed for the agronomic traits under study indicating suitability of the genotypes for association studies. The maximum values for plant height, pods per plant, seeds per pod, 100-seed weight and seed yield per plant were approximately two and half to three times more than the minimum values for the genotypes. Seed yield per plant was found to be significantly correlated with pods per plant (r = 0.77), 100-seed weight (r = 0.35) and days to maturity (r = 0.23). The population structure studies depicted the presence of seven subpopulations which nearly corresponded with the source of geographical origin of the genotypes. Linkage disequilibrium (LD) between the linked markers decreased with the increased distance, and a substantial drop in LD decay values was observed between 30 and 35 cM. Genomewide marker-traits association analysis carried out using general linear (GLM) and mixed linear models (MLM) identified six genomic regions (two of them were common in both) on chromosomes 6, 7, 8, 13, 15 and 17, which were found to be significantly associated with various important traits viz., plant height, pods per plant, 100-seed weight, plant growth habit, average number of seeds per pod, days to 50% flowering and days to maturity. The phenotypic variation explained by these loci ranged from 6.09 to 13.18% and 4.25 to 9.01% in the GLM and MLM studies, respectively. In conclusion, association mapping (AM) in soybean could be a viable alternative to conventional QTL mapping approach.

Genetic Variability and Effect of Heat Treatment on Trypsin Inhibitor Content in Soybean [ Glycine max (L.) Merrill.]

Kunitz trypsin inhibitor (KTI), a major anti-nutritional factor present in soybean seed, is a major bottleneck in industrial use of soybean and public acceptance of soybean food products. Biochemical screening for trypsin inhibitor content was carried out in 145 genotypes of soybean comprising exotic collections and released varieties. The trypsin inhibitor content ranged from 14.15 to 186.27 mg g-1 of seed meal. Lowest level of trypsin inhibitor content was observed in genotype PI542044, (14.15 mg g-1 seed meal). Popular Indian soybean varieties viz., JS335, JS9305, NRC37, NRC7, PK1225, DS9712, JS9752, and DS9814 contained higher level of trypsin inhibitor. Heat treatment was able to reduce the TI content but to certain level leaving about 20% residual activity. The study indicated the need for other ways to create genotypes with reduced KTI for use in breeding program.

Genetic elimination of Kunitz trypsin inhibitors (KTI) from DS9712, an Indian soybean variety

In this study, the null allele of Kunitz trypsin inhibitor i.e. kti was transferred from PI542044, a germplasm line free from KTI in to a popular Indian soybean variety DS9712 through marker assisted backcross breeding (MABB) approach. Following foreground selection with 3 SSR markers viz., Satt228, Satt429 and Satt409 that are linked to kti, and background selection with 93 polymorphic SSR markers in BC1F1 and BC2F1 generations, target plants were selected that had 96–98% recovery of the recurrent parent genome (RPG). In BC2F2 generation, plants homozygous the for target allele (kti kti) were identified and harvested individually. In BC2F3 generation, seed proteins of the selected lines were extracted and analyzed through native polyacrylamide gel electrophoresis (PAGE) and confirmed absence of the KTI peptides. Four lines were identified that were free from Kunitz trypsin inhibitor but retained nearly all of the phenotypic features of DS9712. This study exemplified successful elimination of KTI from soybean seeds through MABB approach.

Efficiency and utility of pollination without emasculation (PWE) method in intra-and inter-specific hybridization in soybean

Efficiency and applicability of a new method of hybridization called ‘pollination without emasculation’ was evaluated in a set of crosses involving Glycine max and Glycine soja genotypes. The genotypes were crossed in various combinations to develop MAGIC (multiparent advanced generation intercross) and NAM (nested association mapping) population as well as to widen the genetic base of soybean through wide hybridization. Success of hybridization ranged from 33% to 77% during kharif season. Number of false crossed seeds as measured through hybridity testing was negligible (0–15%). Rate of crossing success was more during kharif than rabi (17.33%) season. The PWE appeared to be highly efficient and applicable equally to intra-specific and inter-specific crosses in soybean.

Emerging Concepts and Strategies for Genomics and Breeding

To feed the ever-increasing population on earth, production of food crops must increase at an unprecedented pace with limited inputs and little or no harm to the environment. The target is more challenging in the face of a changing climate scenario. The main focus should be on developing technologies and crop genotypes suitable for the input-poor and low-yielding areas that represent the lion’s share of the cultivable areas of the world. Plant breeding is evolving; more so with the advancement of molecular biological sciences. Emerging concepts of structural and functional genomics, transcriptomics, proteomics, and metabolomics approaches contribute towards identification of target genes and eQTL (expression-quantitative trait loci) for effective deployment. The genome editing technologies creating site-directed mutation can facilitate development of nontransgenic designer crop genotypes having wider adaptation. Plant breeding approaches should focus on the natural resources to identify and deploy useful gene(s)/alleles to develop genotypes with enhanced yield potential, better stress tolerance and, quality end products. Improvement in mapping efforts like genomic selection (GS), marker-assisted recurrent selection (MARS), and next-generation mapping, viz. NAM (nested association mapping), MAGIC (multiparent advanced generation intercross) would accelerate breeding progress with improved genotyping and phenotyping facilities. Plant biotechnology and genetic engineering techniques would continue to play a pivotal role in making a crop widely adaptable to the changed climate. Improving crop efficiencies in utilization of solar radiation, inorganic nitrogen, water and other inputs would render crops suitable for climate-resilient agriculture. Policies should be in place to make technologies accessible and affordable by all sections of users globally.

Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits

BackgroundWater permeability governed by seed coat is a major facet of seed crops, especially soybean, whose seeds lack physiological dormancy and experience rapid deterioration in seed viability under prolonged storage. Moreover, the physiological and chemical characteristics of soybean seeds are known to vary with seed coat color. Thus, to underpin the genes controlling water permeability in soybean seeds, we carried out an in-depth characterization of the associated genomic variation.ResultsIn the present study, we have analyzed genomic variation between cultivated soybean and its wild progenitor with implications on seed permeability, a trait related to seed storability. Whole genome resequencing of G.max and G. soja, identified SNPs and InDels which were further characterized on the basis of their genomic location and impact on gene expression. Chromosomal density distribution of the variation was assessed across the genome and genes carrying SNPs and InDels were characterized into different metabolic pathways. Seed hardiness is a complex trait that is affected by the allelic constitution of a genetic locus as well as by a tricky web of plant hormone interactions. Seven genes that hold a probable role in the determination of seed permeability were selected and their expression differences at different stages of water imbibition were analyzed. Variant interaction network derived 205 downstream interacting partners of 7 genes confirmed their role in seed related traits. Interestingly, genes encoding for Type I- Inositol polyphosphate 5 phosphatase1 and E3 Ubiquitin ligase could differentiate parental genotypes, revealed protein conformational deformations and were found to segregate among RILs in coherence with their permeability scores. The 2 identified genes, thus showed a preliminary association with the desirable permeability characteristics.ConclusionIn the light of above outcomes, 2 genes were identified that revealed preliminary, but a relevant association with soybean seed permeability trait and hence could serve as a primary material for understanding the molecular pathways controlling seed permeability traits in soybean.

Physiological and biochemical response of thermo-sensitive and tolerant tomato genotypes to high temperature stress

High temperature stress induces considerable biochemical and physiological changes in the plants. The aim of the present investigation was to evaluate the physiological response of some selected tomato genotypes to high temperature stress. Twenty one diverse tomato genotypes collected from different sources were field evaluated at the Experimental Farm, Division of Vegetable Science, ICAR-IARI, New Delhi (2013 and 2014). Analysis of variance revealed substantial amount of genetic variability in the genotypes for all the traits. Relative water content (RWC) and membrane stability index (MSI) was recorded maximum in Pusa Sadabahar (83 and 86%, respectively) under heat stress condition. Highest proline content was recorded in wild genotypes, like SPM (S. pimpinellifolium) followed by SPR-1 (S. peruvianum). Tolerant genotypes like SPR-1 and SPM-2 showed the high value of chlorophyll b under heat stress condition as compared to sensitive genotypes. The highest phenotypic coefficient of variation (PCV) and genotypic coefficient of variation (GCV) were recorded for yield per plant followed by chlorophyll b, chlorophyll a, lycopene contents and total chlorophyll. High heritability coupled with high genetic advance as per cent over mean was recorded in yield per plant (98.84 and 79.30, respectively) followed by chlorophyll a, chlorophyll b and total chlorophyll content. This indicated the scope for improvement through simple selection for these traits.

Identification of functions of DWnt4 gene in ventral epidermis of embryos and abdomen of adult Drosophila during development

Wnt protein forms a multigenic family secreting signaling molecules important for various key developmental events in animals. Wingless (wg) is the prototype member of Wnt gene family, while DWnt4 has been identified recently from a clonal library of proteins associated in vivo with Ubx protein. DWnt4 has been reported to function in embryo epidermis patterning, female gonade development, motor neuron axon guidance. In this study, validation was done for some reported functions of DWnt4 with ectopic expression and identified some novel functions using RNA interference. Knockdown of DWnt4 caused in ventral ectoderm reduced denticles with loss of one or two rows or entire denticle belt. Loss of DWnt4 also loss of polarity of wing hairs, loss of wing veins and notched wing phenotype. All the bristles from adult abdomen were lost when DWnt4 was driven with ubiquitous driver actineGal4. Tissue specific drivers enGal4 caused loss of polarity of dorsal tergite bristles and patches of tergites from adult abdomen. Thus, the DWnt4 seems to function in the cuticular differentiation of adult abdomen polarity of tergites bristles in Drosophila.

Screening of soybean [Glycine max (L.) Merrill] genotypes for somatic embryogenesis and plant regeneration potential

Twenty two soybean genotypes were evaluated for the capacity of embryo initiation, differentiation, maturation and plantlet regeneration using standardized protocols. Among the genotypes, Bragg was to have high response to induction with 91.11% and average 38.40 embryos/callus mass), proliferation (89.47%) and differentiation (78.95%) however, SL 688 gave the highest maturation frequency (91.57%). Highest somatic embryogenesis germination was recorded in SL 525 (85.67%) whereas, highest survival was observed in JS 335 (82.22%). Genotype Pusa 37 gave the poor response. Fifteen genotypes which were identified as responsive were Bragg, Bragg-Palampur, Pusa 5, Pusa 12, Pusa 14, Pusa 16, Pusa 24, Pusa 40, Pusa 9814, SL 688, SL 525, SL 979, SL 958, DS 2706 and DS 2708. The study thus open up vistas for efficient transgenic plant development in soybean.

Screening and identification of resistant sources against Cowpea mild mottle virus (CPMMV) disease in soybean

A distinct strain of Cowpea mild mottle virus (CPMMV) infecting soybean was reported from India in 2013. Until now there are no resistant sources against CPMMV disease. In the present study 133 genotypes were screened and three sources of resistance against CPMMV in soybean were identified. The resistance was confirmed by sap inoculation and the presence of the virus was also confirmed through RT-PCR by designing primer specific to coat protein gene and NaBp region of CPMMV genome. The lines which were found to be resistant were further used to develop mapping population.