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.

Keywords: Genomic breeding; Genomic selection; Genomics; Genomics-assisted breeding; Genotyping platforms; Sequence-based trait mapping; Sequencing.

Fig. 1

Genotyping platforms and key sequencing-based trait mapping approaches. (a) Molecular markers and genotyping platforms, during the last there decades, have evolved significantly. While throughput has been increasing and cost-per-marker datapoint has been decreasing over the years. (b) Availability of reference genome sequences, the cost-effective genotyping platforms, and a range of genetic populations have provided new faster sequencing-based trait mapping approaches [like geotyping by sequencing (GBS), whole genome resequencing (WGRS), restriction site associated DNA Seq (RAD-seq), bulked segregant analysis-sequencing (BSA-seq) MutMap, MutMap+, MutMap-Gap, QTL-seq, Specific locus amplified fragment sequencing (SLAF-seq), resistance gene enrichment sequencing (RenSeq)]. With these platforms and trait mapping approaches, it has been possible to map target traits for breeding programmes in time- and cost- effective manner in recent years.

Fig. 2

An integrated framework for using genomic resources for developing climate resilient and high nutrition crop varieties. During the last two decades ample genomic resources have been developed. The availability of draft genomes as well as sequence information from germplasm sets and specialized genetic populations bestowed the research community with millions of genome wide variations (SNPs, Indels, SVs, CNVs and PAVs) and pangenomes. Using high-throughput genotyping and high-throughput precise phenotyping approach, complex traits can be simplified at the genetic/ genome level by using sequencing-based trait mapping approaches, as mentioned in Fig. 1b. The genes, haplotypes, marker-trait association (MTA) and GEBVs can be used in genomic breeding or gene editing approaches. Genomic breeding approaches including MABC/ MAS, haplotype based breeding, and genomic prediction. We have shown four genomic prediction approaches namely global GEBVs, local GEBVs, WhoGEM and optimal contribution selection. The genomic breeding or gene editing approach can be combined with ‘speed breeding’ approach to reduce time in tailoring climate resilient and high nutrition crops.