Molecular characterization and genetic diversity analysis of soybean (Glycine max (L.) Merr.) germplasm accessions in India

Identification and genetic diversity analysis of high-yielding charcoal rot resistant soybean genotypes

Charcoal rot disease caused by Macrophomina phaseolina (Tassi) Goid is one of the most devastating diseases in soybean in India. During 2018, 226 diverse soybean genotypes were evaluated for genetic resistance under hot-spot conditions. Out of them, a subset of 151 genotypes were selected based on Percent Disease Incidence (PDI) and better agronomic performance. Out of these 151 genotypes evaluated during 2019, 43 genotypes were selected based on PDI and superior agronomic performance for further field evaluation and molecular characterization. During 2020 and 2021, these forty-three genotypes, were evaluated for PDI, Area Under Disease Progress Curve (AUDPC), and grain yield. In 2020, genotype JS 20-20 showed least PDI (0.42) and AUDPC (9.37).Highest grain yield was recorded by the genotype JS 21-05 (515.00 g). In 2021, genotype JS 20-20 exhibited least PDI (0.00) and AUDPC (0.00).Highest grain yield was recorded in JS 20-98 (631.66 g). Across both years, JS 20-20 had the least PDI (0.21) and AUDPC (4.68), while grain yield was highest in JS 20-98 (571.67 g). Through MGIDI (multi-trait genotype-ideotype distance) analysis, JS 21-05 (G19), JS 22-01 (G43), JS 20-98 (G28) and JS 20-20 (G21) were identified as the ideotypes with respect to the traits that were evaluated. Two unique alleles, Satt588 (100 bp) on linkage group K (Chromosome no 9) and Sat_218 (200 bp) on linkage group H (Chromosome no 12), were specific for thetwo resistant genotypes JS 21-71and DS 1318, respectively. Through cluster analysis, it was observed that the genotypes bred at Jabalpur were more genetically related.

Genetic diversity and population structure analysis in cultivated soybean (Glycine max [L.] Merr.) using SSR and EST-SSR markers

Soybean (Glycine max) is an important legume that is used to fulfill the need of protein and oil of large number of population across the world. There are large numbers of soybean germplasm present in the USDA germplasm resources. Finding and understanding genetically diverse germplasm is a top priority for crop improvement programs. The current study used 20 functional EST-SSR and 80 SSR markers to characterize 96 soybean accessions from diverse geographic backgrounds. Ninety-six of the 100 markers were polymorphic, with 262 alleles (average 2.79 per locus). The molecular markers had an average polymorphic information content (PIC) value of 0.44, with 28 markers ≥ 0.50. The average major allele frequency was 0.57. The observed heterozygosity of the population ranged from 0-0.184 (average 0.02), while the expected heterozygosity ranged from 0.20-0.73 (average 0.51). The lower value for observed heterozygosity than expected heterozygosity suggests the likelihood of a population structure among the germplasm. The phylogenetic analysis and principal coordinate analysis (PCoA) divided the total population into two major groups (G1 and G2), with G1 comprising most of the USA lines and the Australian and Brazilian lines. Furthermore, the phylogenetic analysis and PCoA divided the USA lines into three major clusters without any specific differentiation, supported by the model-based STRUCTURE analysis. Analysis of molecular variance (AMOVA) showed 94% variation among individuals in the total population, with 2% among the populations. For the USA lines, 93% of the variation occurred among individuals, with only 2% among lines from different US states. Pairwise population distance indicated more similarity between the lines from continental America and Australia (189.371) than Asia (199.518). Overall, the 96 soybean lines had a high degree of genetic diversity.

Molecular Breeding to Overcome Biotic Stresses in Soybean: Update

Soybean (Glycine max (L.) Merr.) is an important leguminous crop and biotic stresses are a global concern for soybean growers. In recent decades, significant development has been carried outtowards identification of the diseases caused by pathogens, sources of resistance and determination of loci conferring resistance to different diseases on linkage maps of soybean. Host-plant resistance is generally accepted as the bestsolution because of its role in the management of environmental and economic conditions of farmers owing to low input in terms of chemicals. The main objectives of soybean crop improvement are based on the identification of sources of resistance or tolerance against various biotic as well as abiotic stresses and utilization of these sources for further hybridization and transgenic processes for development of new cultivars for stress management. The focus of the present review is to summarize genetic aspects of various diseases caused by pathogens in soybean and molecular breeding research work conducted to date.

Molecular characterization and genetic diversity studies of Indian soybean (Glycine max (L.) Merr.) cultivars using SSR markers

BACKGROUND

The genetic base of soybean cultivars in India has been reported to be extremely narrow, due to repeated use of few selected and elite genotypes as parents in the breeding programmes. This ultimately led to the reduction of genetic variability among existing soybean cultivars and stagnation in crop yield. Thus in order to enhance production and productivity of soybean, broadening of genetic base and exploring untapped valuable genetic diversity has become quite indispensable. This could be successfully accomplished through molecular characterization of soybean genotypes using various DNA based markers. Hence, an attempt was made to study the molecular divergence and relatedness among 29 genotypes of soybean using SSR markers.

METHODS AND RESULTS

A total of 35 SSR primers were deployed to study the genetic divergence among 29 genotypes of soybean. Among them, 14 primer pairs were found to be polymorphic producing a total of 34 polymorphic alleles; and the allele number for each locus ranged from two to four with an average of 2.43 alleles per primer pair. Polymorphic information content (PIC) values of SSRs ranged from 0.064 to 0.689 with an average of 0.331. The dendrogram constructed based on dissimilarity indices clustered the 29 genotypes into two major groups and four sub-groups. Similarly, principal coordinate analysis grouped the genotypes into four major groups that exactly corresponded to the clustering of genotypes among four sub-groups of dendrogram. Besides, the study has reported eight unique and two rare alleles that could be potentially utilized for genetic purity analysis and cultivar identification in soybean.

CONCLUSION

In the present investigation, two major clusters were reported and grouping of large number of genotypes in each cluster indicated high degree of genetic resemblance and narrow genetic base among the genotypes used in the study. With respect to the primers used in the study, the values of PIC and other related parameters revealed that the selected SSR markers are moderately informative and could be potentially utilized for diversity analysis of soybean. The clustering pattern of dendrogram constructed based on SSR loci profile displayed good agreement with the cultivar's pedigree information. High level of genetic similarity observed among the genotypes from the present study necessitates the inclusion of wild relatives, land races and traditional cultivars in future soybean breeding programmes to widen the crop gene pool. Thus, hybridization among diverse gene pool could result in more heterotic combinations ultimately enhancing genetic gain, crop yield and resistance to various stress factors.

Genetics and mapping of seed coat impermeability in soybean using inter-specific populations

Seed coat impermeability (SCI) in soybean is associated with seed viability under storage and quality of processed products. Understanding genetics and identification of linked molecular markers would facilitate need-based utilization of seed coat impermeability. Two impermeable wild type (G. soja Sieb. and Zucc.) accessions viz. PI 424079 and PI 136620 were crossed with a permeable cultivated (G. max) variety JS335 to generate the mapping populations. Genetic analysis of the F_1:2 and F_2:3 seeds of the crosses indicated that SCI is controlled by a single gene/major QTL, and impermeability is dominant over permeability. Presence of seeds with intermediate permeability indicated role of some minor genes/QTLs. A set of 204 inter-specific recombinant inbred line (RILs) (F₇) was used to map SCI with 207 SSR markers. Phenotyping through rapid imbibition approach (seed imbibition for 6 h), seven QTLs were mapped on chromosomes (Chrs.) 2, 5, 12, 13 and 16 in the seeds stored for 1-3 years, while through slow imbibition method (seed imbibition for 7 days), five QTLs were mapped on Chrs. 2, 9, 10 and 20. Phenotypic variation explained (PVE) by the QTLs ranged from 5.96 to 39.67%. Two major and stable QTLs viz., qScI-h2-1 and qScI-h2-2 that mapped in tandem on Chr.2 jointly explained 43.09-62.92% of the variations in impermeability. Seven minor QTLs identified here were novel and two (qScI-h5, and qScI-h16) were consistent. It is the first report of mapping impermeability using two imbibition approaches together in 200 plus inter-specific RILs in soybean. The study will pave the way for developing genotypes with restricted permeability, enhanced seed viability, and improved seeds quality.

Exploring the genetic base of the soybean germplasm from Africa, America and Asia as well as mining of beneficial allele for flowering and seed weight

Genetic diversity is the foundation for any breeding program. The present study analyzed the genetic base of 163 soybean genotypes from three continents viz. Africa, America and Asia using 68 trait-linked simple sequence repeats (SSR) markers. The average number of alleles among the germplasm from the three continents followed the trend as Asia (9) > America (8) > Africa (7). Similar trends were observed for gene diversity (0.76 > 0.74 > 0.71) and polymorphism information content (PIC) (0.73 > 0.71 > 0.68). These findings revealed that soybean germplasm from Asia has wider genetic base followed by America, and least in Africa. The 163 genotypes were grouped into 4 clusters by phylogenetic analysis, whereas model-based population structure analysis also divided them into 4 subpopulations comprising 80.61% pure lines and 19.39% admixtures. The genotypes from Africa were easily distinguished from those of other two continents using phylogenetic analysis, indicating important role of geographyical differentiation for this genetic variability. Our results indicated that soybean germplasm has moved from Asia to America, and from America to Africa. Analysis of molecular variance (AMOVA) showed 8.41% variation among the four subpopulations, whereas 63.12% and 28.47% variation existed among and within individuals in the four subpopulations, respectively. Based on the association mapping, a total of 21 SSR markers showed significant association with days to flowering (DoF) and 100-seed weight (HSW). Two markers Satt365 and Satt581 on chromosome 6 and 10, respectively, showed pleiotropic effect or linkage on both traits. Genotype A50 (Gakuran Daizu/PI 506679) from Japan has 8 out of the 13 beneficial alleles for increased HSW. The diverse genotypes, polymorphic SSR markers and desirable alleles identified for DoF and HSW will be used in future breeding programs to improve reproductive, yield and quality traits.

Genetic relationship, population structure analysis and allelic characterization of flowering and maturity genes E1, E2, E3 and E4 among 90 Indian soybean landraces

A set of 90 Indian soybean landraces were analysed for polymorphism at 43 SSRs and five allele specific markers of four major genes involved in regulating flowering and photoperiod response. A total of 42 polymorphic SSRs had amplified 126 alleles which served as raw data for estimation of genetic relationship and population structure among 90 accessions. Rare alleles of four and three SSRs were detected in accessions IC18768 and IC15089, respectively. Gene diversity in the population ranges from 0.065 to 0.717 with a mean value of 0.411. The polymorphism information content of 42 SSRs varied from 0.063 to 0.668. Hierarchical clustering based on neighbour-joining method identified three major clusters among 90 soybean accessions. Model based population structure analysis divided the 90 soybean accessions into four populations (K = 4). Mean value of Fst for different populations ranged between 0.4143 and 0.7239. Genotyping of 90 accessions with allele specific markers had identified accession IC15089 as triple recessive mutant of flowering genes E1, E2 and photoperiod sensitivity gene E3. The triple mutant IC15089 (e1, e3, e3) had been characterized phenotypically and identified as early maturing (88 days) and photoperiod insensitive genotype under extended photoperiod. The present study characterized genetic relationship among 90 Indian soybean landraces and had identified a few diverse and unique genotypes for utilization in soybean breeding programmes targeting development of short duration and photoperiod insensitive varieties through marker assisted selection.

LC-ESI-MS based characterisation of isoflavones in soybean (Glycine max (L.) Merr.) from India

A total of twenty-one soybean varieties were screened for their morphological characteristics followed by isoflavone content analysis by HPLC. The total isoflavone (TI) content was found within a wide range of 140.9-1048.6 μg/g of soy in different varieties. The highest isoflavone content was found in MAUS-2 followed by DS_2613 and lowest in Karunae (140.9 μg/g of soy). Various isoflavone forms were identified by LC-ESI⁺ MS. Significant differences in the isoflavone content were observed for all the aglycones and their glucoside conjugates as well as total daidzein, total genistein, total glycitein, and TI. A positive correlation between TI content and growth stages was found during the progression of seed development. An increase of 5.4-fold and 5.3-fold of TI concentration was observed for JS 335 and MAUS-2 respectively, from early to green mature (R5-R8) stage of bean development.

Physiological and molecular genetic studies on two elicitors for improving the tolerance of six Egyptian soybean cultivars to cotton leaf worm

Cotton leaf worm (Spodoptera littoralis) is considered one of the most destructive agricultural pests in Egypt. Six soybean cultivars (Giza-21, Giza-22, Giza-35, Giza-82, Giza-83 and Giza-111) were grown under natural infection with cotton leaf worm. The effect of two elicitors, methyl jasmonate and sodium nitroprusside on enhancing the ability of susceptible cultivars to tolerate (Spodoptera littoralis) was studied. Giza-35 and Giza-111 showed tolerance performance under natural infection compared to Giza-22 and Giza-82 as sensitive ones, while Giza-83 and Giza-21 showed moderate tolerance. Both treatments positively affected seed yield and its components and fatty acid composition. Extracted fatty acids showed variable changes in treated plants compared with the untreated controls. Plants treated with the two elicitors showed an increase in Linoleic acid and Linolenic acid fatty acids and decrease in Palmitic acid and Palmitolic acid content. Treatment with methyl jasmonate was found to be more effective than sodium nitroprusside and enhanced resistance of the susceptible cultivars. Eight IRAP and iPBS retrotransposon-based markers were used to detect genetic differences among studied soybean cultivars and to develop molecular genetic markers for cotton leaf worm infestation. The technique successfully identified soybean genotypes in addition to nineteen molecular markers related to soybean tolerance.