*Recent Advancements in Genetic Improvement of Food Legume Crops DOI: http://dx.doi.org/10.5772/intechopen.106734*

Over the past few decades, to understand the genetics of complex traits has become a major concern. With the progress made in the area of molecular markers as well as in genomics significant number of QTLs have been found in various crops. In legumes also, several genes/ QTL controlling the target traits have been mapped (**Table 2**). The efficiency and accuracy of breeding practices have been improved significantly with the help of molecular marker-assisted selection of important traits. Further, the mapped gene(s) or QTLs can be introduced individually or pyramided in an improved variety.


#### **Table 2.**

*QTL mapping in different legume crops.*

There are two approaches for marker-trait associations identification in plants: (1) Linkage mapping and (2) Association or linkage disequilibrium (LD) mapping. Linkage mapping is a conventional mapping approach based on genetic recombination between two loci, whereas association mapping is a new approach and based on linkage disequilibrium.

Currently, candidate gene and whole-genome association mapping methods are used in crop plants. As a new approach to conventional linkage analysis, association mapping has the advantages of increased mapping resolution, research speed, and greater allele number. Different loci for iron deficiency chlorosis in soybeans have been effectively mapped using the candidate gene-based method [28].

Similarly, Bachalva *et al*. [29] mapped several candidate genes in soybean involved in oleate biosynthesis and examined their co-segregation with oleate, linolenate quantitative trait loci (QTLs). Whole-genome association mapping has been used in several legume crops; for example- Medicago truncatula, common bean, soybean, chickpea, cowpea, peanut etc. In pigeonpea, 292 accessions were characterized using genome-wide association analysis for the purpose of accelerating genetic gains and identifying associations between several candidate genes and agronomically significant traits [13]. In a diversity panel including 96 Middle American genotypes of common bean, Hoyos-Villegas, Song, and Kelly [43] studied the genetic basis of variation for drought tolerance and related traits, and the GWAS analysis enabled identification of important marker-trait associations for traits related to drought tolerance and candidate genes associated with wilting. Salinity stress, which is intensified by changing climatic conditions, has a negative impact on cowpea at the germination and seedling stages. Ravelombola *et al*. [44] conducted research to identify SNP markers linked to salt tolerance through association mapping.

#### **2.3 Pan-genomes of legume crops**

It is clear that a single individual's genome does not adequately represent the diversity of genes in a species. Pangenome assemblies, which capture sequence and structural variation in a species more comprehensively, can be developed as a remedy. Pangenome includes the core complement of genes common to all individuals of the species. The variable genome contributes to species diversity and provides functions that are not essential, but which may. While the availability of reference genomes has significantly supported plant breeding and research, these reference genomes capture only a portion of the species diversity. These reference genomes provide a selective advantage under some circumstances like; biotic and abiotic stress resistance. Tettelin et al. developed the pangenome concept [45] and developed the first-ever pangenome for a bacterial species, Streptococcus agalactiae. The first legume pangenome was generated by sequencing and de novo assembly of seven phylogenetically and geographically representative accessions of the wild relatives of cultivated soybean. The soybean pangenome indicates a faster evolution and greater diversity in dispensable genes than core genes related to adaptation to environmental stresses. Recently, the Pigeonpea pangenome was developed, based on 89 accessions mostly from India and the Philippines. This reveals that in Philippine individuals, there is a substantial genetic variation that is not present in Indian individuals.

Existence of a large number of repeats and several rounds of polyploidy, genome and pangenome assembly in plants is always difficult. The traditional de novo assembly and comparison approach was first used to demonstrate significant genomic differences between individuals. It has the benefit of providing the physical position

of genes. During the breeding of certain crops, a decline in genetic variation has been observed, especially associated with the selection of important characteristics. This approach will help identify genes lost during breeding and selection that can be bread back into elite germplasm.
