Genomic resources in plant breeding for sustainable agriculture

Abstract

Climate change during the last 40 years has had a serious impact on agriculture and threatens global food and nutritional security. From over half a million plant species, cereals and legumes are the most important for food and nutritional security. Although systematic plant breeding has a relatively short history, conventional breeding coupled with advances in technology and crop management strategies has increased crop yields by 56 % globally between 1965−85, referred to as the Green Revolution. Nevertheless, increased demand for food, feed, fiber, and fuel necessitates the need to break existing yield barriers in many crop plants. In the first decade of the 21st century we witnessed rapid discovery, transformative technological development and declining costs of genomics technologies. In the second decade, the field turned towards making sense of the vast amount of genomic information and subsequently moved towards accurately predicting gene-to-phenotype associations and tailoring plants for climate resilience and global food security. In this review we focus on genomic resources, genome and germplasm sequencing, sequencing-based trait mapping, and genomics-assisted breeding approaches aimed at developing biotic stress resistant, abiotic stress tolerant and high nutrition varieties in six major cereals (rice, maize, wheat, barley, sorghum and pearl millet), and six major legumes (soybean, groundnut, cowpea, common bean, chickpea and pigeonpea). We further provide a perspective and way forward to use genomic breeding approaches including marker-assisted selection, marker-assisted backcrossing, haplotype based breeding and genomic prediction approaches coupled with machine learning and artificial intelligence, to speed breeding approaches. The overall goal is to accelerate genetic gains and deliver climate resilient and high nutrition crop varieties for sustainable agriculture.

Systems biology for crop improvement

“…Therefore, a 5G breeding approach for bringing in the much-needed disruptive changes to crop improvement has been proposed by Varshney et al (2020). Unlimited genomics resources, such as SNPs and genome-wide SVs, are made available through sequencing and resequencing of diverse germplasm in different crops (Thudi et al, 2021). These resources would facilitate genotyping the landraces and breeding material for identification of candidate genes and diagnostic markers for the traits of interest in crop species.…”

“…Systematic application of genome‐wide sequence information in support of crop improvement as translational genomics for agriculture will accelerate the precision of crop breeding cycle (Bohra et al., 2020; Varshney et al., 2015). The genomic resources developed in crop species will facilitate the dissection of complex traits and identification and exploitation of SNPs and SVs associated with traits of interest (Thudi et al., 2021). Furthermore, knowledge of resequencing and pangenomes and super‐pangenomes would provide information on an untapped pool of diversity for easy access in breeding resulting in genetic improvement of crop species to meet future food demands.…”

Major QTLs and Potential Candidate Genes for Heat Stress Tolerance Identified in Chickpea (Cicer arietinum L.)

“…Genomic revolution, during the last two decades, simplified understanding of the complex responses to biotic and abiotic stress in several crop plants (Roorkiwal et al, 2020 ; Thudi et al, 2020 ). Chickpea research community has access to genome sequence (Varshney et al, 2013 ), genome-wide variations among diverse germplasm lines at the sequence level (Thudi et al, 2016a , b ; Varshney et al, 2019 ) for trait dissection, and the development of climate-resilient chickpea varieties (Mannur et al, 2019 ; Bharadwaj et al, 2020 ).…”

“…Chickpea research community has access to genome sequence (Varshney et al, 2013 ), genome-wide variations among diverse germplasm lines at the sequence level (Thudi et al, 2016a , b ; Varshney et al, 2019 ) for trait dissection, and the development of climate-resilient chickpea varieties (Mannur et al, 2019 ; Bharadwaj et al, 2020 ). The genotyping-by-sequencing (GBS) approach has been extensively used for single-nucleotide polymorphism (SNP) discovery and mapping traits in several crops for genetic research and breeding applications (Chung et al, 2017 ), including chickpea (Jaganathan et al, 2015 ; Thudi et al, 2020 ). Besides proteomic and metabolomic approaches to understanding the molecular mechanism of heat tolerance (Parankusam et al, 2017 ; Salvi et al, 2018 ), efforts were made to map QTLs and markers associated with heat tolerance in chickpea (Thudi et al, 2014 ; Paul et al, 2018a ; Varshney et al, 2019 ; Roorkiwal et al, 2020 ).…”

MutMap Approach Enables Rapid Identification of Candidate Genes and Development of Markers Associated With Early Flowering and Enhanced Seed Size in Chickpea (Cicer arietinum L.)

“…The majority of the QTL mapping and gene isolation approaches using traditional approaches are time-consuming and low-throughput methods. Nevertheless, for more than a decade, the next-generation sequencing (NGS) technologies facilitated understanding of the genetics of complex traits at a faster pace in cereals and legumes ( Thudi et al, 2020 ; Jaganathan et al, 2020 ). In the case of chickpea, apart from sequencing the genome ( Varshney et al, 2013b ) and several hundred germplasm lines ( Thudi et al, 2016a , b ; Varshney et al, 2019b ), traits were fine-mapped ( Kale et al, 2015 ; Singh et al, 2016 ).…”