Emerging Genomic Tools for Legume Breeding: Current Status and Future Prospects

Abstract

Legumes play a vital role in ensuring global nutritional food security and improving soil quality through nitrogen fixation. Accelerated higher genetic gains is required to meet the demand of ever increasing global population. In recent years, speedy developments have been witnessed in legume genomics due to advancements in next-generation sequencing (NGS) and high-throughput genotyping technologies. Reference genome sequences for many legume crops have been reported in the last 5 years. The availability of the draft genome sequences and re-sequencing of elite genotypes for several important legume crops have made it possible to identify structural variations at large scale. Availability of large-scale genomic resources and low-cost and high-throughput genotyping technologies are enhancing the efficiency and resolution of genetic mapping and marker-trait association studies. Most importantly, deployment of molecular breeding approaches has resulted in development of improved lines in some legume crops such as chickpea and groundnut. In order to support genomics-driven crop improvement at a fast pace, the deployment of breeder-friendly genomics and decision support tools seems appear to be critical in breeding programs in developing countries. This review provides an overview of emerging genomics and informatics tools/approaches that will be the key driving force for accelerating genomics-assisted breeding and ultimately ensuring nutritional and food security in developing countries.

Genome-Wide Discovery and Deployment of Insertions and Deletions Markers Provided Greater Insights on Species, Genomes, and Sections Relationships in the Genus Arachis

“…Among different marker types, SSRs have dominated genetic studies in groundnut due to multiple advantages of SSR markers but lacked amenability for high throughput genotyping (Gupta and Varshney, 2000). Therefore, the current emphasis is now on developing single-nucleotide polymorphism (SNP) markers in groundnut due to their high preponderance throughout the genome and their amenability for high throughput genotyping for genome-wide breeding applications (Varshney et al, 2009; Pandey et al, 2016). Surprisingly, both SSRs and SNPs have their own drawbacks in spite of usefulness.…”

Accelerating genetic gains in legumes for the development of prosperous smallholder agriculture: integrating genomics, phenotyping, systems modelling and agronomy

“…Efforts are underway to sequence the remaining legume genomes. The past decade has witnessed an exponential increase in availability of genomic resources and their deployment in trait discovery and breeding (see Bohra et al, 2014;Varshney et al, 2015;Pandey et al, 2016). As a result, several of these legume crops have genomic resources and associated phenotypic data to support genomics-based discovery and breeding approaches to develop superior legume varieties.…”

“…Several of these improved lines have either been released or are in the release pipeline in different countries. In addition to the above, the gene/QTL pyramiding efforts are at an advanced stage for several legume traits such as in groundnut (leaf rust resistance+late leaf spot+high oleic acid), chickpea (fusarium wilt resistance+ascochyta blight resistance+drought tolerance; see Pandey et al, 2016), and cowpea (resistance to Striga+aphid+macrophomina root rot; see Boukar et al, 2016). The majority of the legume crops now enjoy the availability of genomic resources and such examples are seen more frequently in grain legumes.…”

“…The legume community has been successful in developing several molecular breeding products despite the late arrival of genomic resources and trait-associated markers (Varshney et al, 2013a,b;Pandey et al, 2016;Varshney, 2016). Some key examples include resistance to Fusarium wilt and ascochyta blight (Varshney et al, 2013b) and improved drought tolerance (Varshney et al, 2013a) in chickpea; resistance to nematode and high oleic acid (Chu et al, 2011), resistance to leaf rust , and resistance to high oleic acid (Janila et al, 2016) in groundnut; resistance to rust disease (Khanh et al, 2013), soybean mosaic virus (Saghai-Maroof et al, 2008;Shi et al, 2009;Parhe et al, 2017), and low phytate (Landau-Ellis and Pantalone, 2009) in soybean; Striga resistance and seed size in cowpea (Lucas et al, 2015; see Boukar et al, 2016); pyramid genes for resistance to ascochyta blight and anthracnose in lentil (Taran et al, 2003); powdery mildew resistance (Ghafoor and McPhee 2012), lodging resistance (Zhang et al, 2006), frost tolerance (see Tayeh et al, 2015b), and Aphanomyces root rot resistance (Lavaud et al, 2015) in pea; and resistance to common bacterial blight disease (Miklas et al, 2000(Miklas et al, , 2006Mutlu et al, 2005;O'Boyle and Kelly, 2007), rust and viruses (Stavely, 2000), rust, anthracnose, and angular leaf spot (Oliveira et al, 2008), rust (Feleiro et al, 2001), and anthracnose (Alzate-Marin et al, 1999) in common bean.…”

Simultaneous selection model based evaluation of arsenic tolerance in black gram (Vigna mungo L.) using morphological parameters

“…Pulses are cultivated on 28,635 thousand hectares and produces 17,647 thousand tonnes each year in India (FAO, 2014). Among the food grains pulses are rich sources of protein, minerals, vitamins and omega-3-fatty acid as well as ultimate source of protein for vegetarian person (Pandey et al, 2016). Black gram (Vigna mungo L.) also known as Urd bean or mash belongs to the family Fabaceae is a self-pollinated diploid pulse crop (2n= 22) (Jayamani and Sathya, 2013;Arumuganthan and Earle, 1991).…”