Maneet Rana

Development of genome-wide SSR markers in horsegram and their use for genetic diversity and cross-transferability analysis

Horsegram [Macrotyloma uniflorum (Lam.) Verdc.] commonly known as kulthi or Madras gram is an important drought tolerant legume crop used as food and fodder in India and across the globe. Horsegram is tolerant to many biotic and abiotic stresses and considered a potential future food legume. Despite being a multiutility crop, insufficient genomic information is available in this species, which is otherwise required for genetic improvement. Hence, in the present work we used next-generation sequencing (NGS) technology for genome-wide development and characterization of novel simple sequence repeat (SSR) markers in horsegram. In all, 2458 SSR primer pairs were designed from NGS data and 117 SSRs were characterized in 48 diverse lines of horsegram. Cross-transferability of these markers was also checked in nine related legume species. The polymorphic SSRs revealed high diversity measures such as mean values of expected heterozygosity (He; 0.54), observed heterozygosity (Ho; 0.64), and polymorphism information content (PIC; 0.46). Analysis of molecular variance (AMOVA) revealed high degree of genetic variance within the populations. Dendrogram based on Jaccard’s similarity coefficient and principal component analysis (PCA) revealed two groups in the analyzed accessions. This observation was further confirmed by Bayesian genetic STRUCTURE analysis. The SSR markers developed herein can be used in diverse genetic analysis including association mapping in this crop and also in related legume crops with limited marker resources. Hence, this new SSR dataset can be useful for molecular breeding research in this underutilized pulse crop. In addition, genetic diversity estimates of analyzed germplasm can be important for devising future breeding programmes in horsegram.

Gene Pyramiding and Multiple Character Breeding

Abstract Plant breeders are often interested in improving several quantitative traits including yield, quality, and resistance to both biotic and abiotic stresses simultaneously. However, breeding for multiple traits together is challenging and largely depends on the choice of germplasm, and the genetics and genetic relationships among the traits under selection. Both conventional and molecular breeding approaches have been used to breed for multiple traits simultaneously. Several selection schemes including independent culling levels, tandem selection, and index selection have been developed and used to improve and integrate traits simultaneously. Of these, selection index was preferred in the past and has been used to improve the overall genotypic performance based simultaneously on several quantitative traits, even for traits with unfavorable associations. With the recent development and advancement in molecular marker technologies, molecular breeding has become preferred for targeted breeding and product development. Molecular breeding technologies including marker-assisted selection, marker-assisted backcrossing, marker-assisted recurrent selection, gene pyramiding, marker-assisted backcross gene pyramiding, and genomic selection have been used to introgress single or multiple genes. Multiple trait selection using selection indices based on information from both phenotypes and markers distributed across the whole genome has recently been practiced in various crops. Multiple trait selection is a realistic approach that can be exploited in lentil breeding programs to simultaneously improve multiple traits. In this chapter, we discuss various conventional and molecular approaches to breeding, improving, and integrating multiple traits into a single genetic background with relevance to lentil crops.

A Comprehensive Study of Variation in Selected QPM and Non-QPM Maize Inbred Lines

To enhance the nutritional value of maize (Zea mays L.), genetic characterization and conversion of common maize into crop enriched with quality protein maize may be beneficial. With the hope of producing a superior maize cultivar, the pattern of relationship among 40 maize inbred lines (QPM and non-QPM) adapted to hills was examined using molecular, biochemical and morphological characteristics. Among the non-QPM set, early maturing lines BAJIM-08-26 and KI-30 were found superior for grain yield, and among QPM set, CML189 line was found superior for high tryptophan content. Phenotypic performance-based clustering using Mahalanobis distance revealed seven clusters. Genotypes were grouped on the basis of flowering and yield traits. Two major clusters were defined, one consisting of all QPM lines and other have all non-QPM lines. This distinction is well observed in the plot generated by principal component analysis. This information may be used in selecting genetically divergent lines for ongoing breeding programs for quality enhancement. The selected QPM line(s) could be used as donor and the well-adapted agronomically superior lines as recurrent parent for conversion of non-QPM to QPM lines.