QTLomics in Soybean: A Way Forward for Translational Genomics and Breeding

Abstract

Food legumes play an important role in attaining both food and nutritional security along with sustainable agricultural production for the well-being of humans globally. The various traits of economic importance in legume crops are complex and quantitative in nature, which are governed by quantitative trait loci (QTLs). Mapping of quantitative traits is a tedious and costly process, however, a large number of QTLs has been mapped in soybean for various traits albeit their utilization in breeding programmes is poorly reported. For their effective use in breeding programme it is imperative to narrow down the confidence interval of QTLs, to identify the underlying genes, and most importantly allelic characterization of these genes for identifying superior variants. In the field of functional genomics, especially in the identification and characterization of gene responsible for quantitative traits, soybean is far ahead from other legume crops. The availability of genic information about quantitative traits is more significant because it is easy and effective to identify homologs than identifying shared syntenic regions in other crop species. In soybean, genes underlying QTLs have been identified and functionally characterized for phosphorous efficiency, flowering and maturity, pod dehiscence, hard-seededness, α-Tocopherol content, soybean cyst nematode, sudden death syndrome, and salt tolerance. Candidate genes have also been identified for many other quantitative traits for which functional validation is required. Using the sequence information of identified genes from soybean, comparative genomic analysis of homologs in other legume crops could discover novel structural variants and useful alleles for functional marker development. The functional markers may be very useful for molecular breeding in soybean and harnessing benefit of translational research from soybean to other leguminous crops. Thus, soybean crop can act as a model crop for translational genomics and breeding of quantitative traits in legume crops. In this review, we summarize current status of identification and characterization of genes underlying QTLs for various quantitative traits in soybean and their significance in translational genomics and breeding of other legume crops.

Mutagenic effects of gamma rays on soybean (Glycine max L.) germination and seedlings

“….00 ** GR = gamma rays; GP 1 = germination percentage at the 5 th day (first count); GP 2 = germination percentage at the 8 th day (final count); MGT = mean germination time; FDG = the first day of germination; LDG = last day of germination; CVG = coefficient of velocity of germination; GRI = germination rate index; GI = germination index; TSG = time spread of germination. Data were transformed by arcsine (1) and Log (X+1) (2) prior to analysis; nontransformed data are presented; * significant difference at P ≤ 0.05; ** significant at P ≤ 0.01 The result showed that the maximum germination percentage was observed at the control treatments (0 Gy) ( Table 1). The germination percentage at the first count was significantly decreased with increasing gamma ray doses.…”

“…Soybean can be used as food, feed, functional food and industrial products. Increasing interest in functional food and various soybean by-product is the reason for high demand of soybean [1]. However, soybean yield is decreased because of many stresses such as salinity stress.…”

Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits

“…Whole genome resequencing of different soybean accessions has been reported previously to associate SNPs with numerous traits such as biotic stress, domestication, seed composition, seed size, seed coat, flowering etc. [ 25 ]. The present study centered on whole-genome resequencing of G. max and G. soja to identify variation (SNPs and InDels) present in genes related to seed coat properties with implications on water permeability.…”

Advances in salinity tolerance of soybean: Genetic diversity, heredity, and gene identification contribute to improving salinity tolerance

“…In addition, a 3.8-kb insertion of the Ty1/copia type retrotransposon fragment was identified to be responsible for the loss of function of the salt-tolerant gene Glyma03g23900 (Guan et al 2014b;Qi et al 2014;Do et al 2016;Kumawat et al 2016). Abel (1969) first identified the dominant gene for salt tolerance using the classical genetics approach in soybean; he called it Ncl.…”