Bhupender Kumar

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 diversity of early maturing Indian maize (Zea mays L) inbred lines revealed by SSR markers.

A set of 16 popular inbred lines, (8 released and 8 experimental) were analyzed using 24 Simple Sequence Repeats (SSR) markers. In total 71 SSR alleles were identified with a mean of 2.96 alleles per locus. The study revealed 28 rare alleles among the total, out of which 9 were unique to some of the inbred lines. The average Polymorphism Information Content (PIC) and Discrimination Rate (DR) were 0.39 and 0.61, respectively. Genetic similarity expressed as Jaccard’s coefficient varied from 0.23–0.68 with an average of 0.41. Five clusters were obtained by using Unweighted Paired Group Method using Arithmetic Averages (UPGMA). The pattern of grouping did not match well with available pedigree information, which may be attributed to inadequate pedigree information. Inbred lines used in present study revealed heterozygosity ranges from 8.3–33.3% and were clearly distinguished with a minimum set of three markers with high PIC and DR. However, fingerprints obtained using 13 markers with high DR revealed a probability of identical match by chance at 4.06×10−8. In this study we found SSR as a good tool for characterization of maize genotypes along with morphological markers.

Comparative analysis of diversity based on morpho-metric and molecular markers in chickpea over different environments

Ten morpho-agronomic traits and 80 random amplified polymorphic DNA (RAPD) molecular markers were used to survey genetic diversity in 25 chickpea genotypes. Analysis of variance revealed significant variability among different genotypes for morpho-metric traits. The cluster analysis done using morpho-metric traits grouped 25 genotypes into seven and six clusters in Environment I (Env. I) and Environment II (Env. II), respectively. Three genotypes viz., ICCV-96904, HPG-17, ICCV-95503 and L-HR-1 belonging to diverse clusters were identified divergent and may use in heterosis breeding programme. Of 80 random RAPD markers, 25 were found polymorphic. Three major clusters were identified using 25 polymorphic RAPD markers. The genetic similarity coefficient among genotypes ranged from 0.57 to 0.91. The average polymorphic information content (PIC) for 25 RAPD markers ranges from 0.12 to 0.40. D2-statistic, RAPD analysis and study of genotypes performance revealed sufficient genetic diversity among chickpea genotypes which would be useful in future breeding programme.

Biochemical screening for trypsin inhibitor factors and morphomolecular characterization of soybean (Glycine max L. Merr.)

A set of 101 diverse soybean genotypes were biochemically analyzed for trypsin inhibitor (TI) contents, and were characterized with morphological and molecular markers. The TI content in the seeds ranged from 14.65 to 175.52 mg g−1 soymeal. The Indian soybean varieties were found to contain higher amount of TI (58.79–126.78 mg g−1 soymeal) while PI542044, an exotic germplasm was found to contain the least (14.65 mg g−1 soymeal). Morphological characterization with 16 qualitative and quantitative traits revealed significant variations and grouped the genotypes in to three major groups with overall mean dissimilarity value of 0.30. Genetic diversity study conducted with 100 simple sequence repeat (SSR) markers detected higher level of polymorphism (71%). Of the total 221 alleles amplified, 65 were rare (frequency <0.2). The mean polymorphism information content (PIC) of the markers was 0.27 while the value for gene diversity was 0.44. UPGMA-based cluster analysis grouped the genotypes into four major clusters of which I, II and III were occupied by genotypes containing higher and moderate level of TI. PI542044, which was free from Kunitz trypsin inhibitor (KTI), grouped singly. Such genotype would be suitable for use in breeding program directed towards development of varieties with zero KTI.