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Development of transcriptome-wide SSR markers for genetic diversity and structure analysis in Macrotyloma uniflorum (Lam.) Verdc.

ABSTRACT: Horsegram is an important drought resistant pulse crop from Fabaceae and can be easily grown in dry lands with no irrigation facilities. However, it remained neglected since long and has been considered as orphan legume which requires immediate attention for its improvement and for the development of new promising varieties in future. In the present study, 7352 simple sequence repeat (SSR) markers were developed from the transcriptome data and 150 SSR were randomly synthesized for validation and diversity analysis in a panel of 58 horsegram genotypes. The synthesized primers included all types of repeats spanning direpeats to hexarepeats. Of the validated SSR markers, 33 markers were polymorphic and produced 40 loci which were used to analyze the genetic diversity and structure of horsegram. In total, 130 alleles were produced in a range of 2-9 alleles with maximum alleles produced by primer HTSSR 155. Expected heterozygosity (He) ranged from 0.03 to 1.00 and observed heterozygosity (Ho) ranged from 0.13 to 0.81. Polymorphism information content value ranged from 0.065 to 0.78. Dendrogram based on UPGMA and principal component analysis showed four groups of the 58 genotypes of horsegram. Structure analysis showed three genetic stocks for the analyzed germplasm. Thus, the developed SSRs can be useful in future population genetics analysis, molecular breeding studies and mapping works in horsegram germplasm as well as in related legume species.

SUBMITTER: Kumar R

PROVIDER: S-EPMC7688872 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:The agronomic stability and nutritional importance of 30 (Test genotypes: 29 + Check: 1 = 30) promising horse gram mutants were evaluated in this multi-environment-based experiment (MEE). Attempts were made to (i) identify stable mutants for agronomic traits through AMMI and GGE biplot models, (ii) quantify nutritional traits, (iii) understand the linkage between yield and nutritional traits, and (iv) estimate physical (PP) and cooking properties (CP) of selected genotypes to fix their food-chain usability. The ANOVA of the pooled data exhibited significant differences among environments (E), genotypes (G), and GxE interaction. The combined AMMI and GGE results helped to identify a few good-yielding and stable genotypes (GYSM) (G1, G25, G3, and G27). The yield advantages of these GYSMs over the parent PAIYUR 2 are 42.99%, 34.63%, 28.68%, and 30.59% respectively. The nutrient profiling of mutants revealed (i) a significant coefficient of variation for macronutrients (fat: 29.98%; fibre: 20.72%, and protein: 5.01%), (ii) a good range of variation for micronutrients, and (iii) helped to identify macro (MaNSM) and micro nutrient-specific mutants (MiNSM). The relationship analysis between yield and nutrient traits ascertained that yield had (i) positivity with protein (r2 = 0.69) and negativity for micronutrients except for Mn (r2 = 0.63), Cu (r2 = 0.46), and B (r2 = 0.01) in GYSM, (ii) positivity with protein and fibre in MaNSM, and (iii) negativity with micronutrients in MiNSM. Of the GYSM, G1 and G25 offer scope for commercial exploitation, and their PP and CP analyses revealed that G1 can be used for pastry and baked product preparation while G25 for weaning foods. Cooking time exhibited positivity with seed size parameters and negativity with water absorption capacity (r2 = - 0.53). An LC-MS-MS-based amino acid (AA) fractionation study showed the effect of induced mutagenesis on the contents of amino acids and also revealed the significance of horse gram for its lysine and methionine contents.

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Development of transcriptome-wide SSR markers for genetic diversity and structure analysis in Macrotyloma uniflorum (Lam.) Verdc.

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