Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase further due to global warming. This situation has compelled plant scientists to develop climate change-resilient crops, which can withstand broad-spectrum stresses such as drought, heat, cold, salinity, flood, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful in enhancing the stress adaptation of crop plants, and recent advances in high-throughput sequencing and phenotyping platforms have transformed molecular breeding to genomics-assisted breeding (GAB). In view of this, the present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security.

Root and tuber crops are a major food source in tropical Africa. Among these crops are several species in the monocotyledonous genus Dioscorea collectively known as yam, a staple tuber crop that contributes enormously to the subsistence and socio-cultural lives of millions of people, principally in West and Central Africa. Yam cultivation is constrained by several factors, and yam can be considered a neglected “orphan” crop that would benefit from crop improvement efforts. However, the lack of genetic and genomic tools has impeded the improvement of this staple crop. To accelerate marker-assisted breeding of yam, we performed genome analysis of white Guinea yam (Dioscorea rotundata) and assembled a 594-Mb genome, 76.4% of which was distributed among 21 linkage groups. In total, we predicted 26,198 genes. Phylogenetic analyses with 2381 conserved genes revealed that Dioscorea is a unique lineage of monocotyledons distinct from the Poales (rice), Arecales (palm), and Zingiberales (banana). The entire Dioscorea genus is characterized by the occurrence of separate male and female plants (dioecy), a feature that has limited efficient yam breeding. To infer the genetics of sex determination, we performed whole-genome resequencing of bulked segregants (quantitative trait locus sequencing [QTL-seq]) in F1 progeny segregating for male and female plants and identified a genomic region associated with female heterogametic (male = ZZ, female = ZW) sex determination. We further delineated the W locus and used it to develop a molecular marker for sex identification of Guinea yam plants at the seedling stage. Guinea yam belongs to a unique and highly differentiated clade of monocotyledons. The genome analyses and sex-linked marker development performed in this study should greatly accelerate marker-assisted breeding of Guinea yam. In addition, our QTL-seq approach can be utilized in genetic studies of other outcrossing crops and organisms with highly heterozygous genomes. Genomic analysis of orphan crops such as yam promotes efforts to improve food security and the sustainability of tropical agriculture.

Red clover (Trifolium pratense L.) is a versatile forage crop legume, which can tolerate a variety of soils and is suitable for silage production for winter feed and for grazing. It is one of the most important forage legumes in temperate livestock agriculture. Its beneficial attributes include ability to fix nitrogen, improve soil and provide protein rich animal feed. It is however, a short-lived perennial providing good biomass yield for two or three years. Improved persistency is thus a major breeding target. Better water-stress tolerance is one of the key factors influencing persistency, but little is known about how red clover tolerates water stress. Plants from a full sib mapping family were used in a drought experiment, in which the growth rate and relative water content (RWC) identified two pools of ten plants contrasting in their tolerance to drought. Key metabolites were measured and RNA-Seq analysis was carried out on four bulked samples: the two pools sampled before and after drought. Massively parallel sequencing was used to analyse the bulked RNA samples. A de novo transcriptome reconstruction based on the RNA-Seq data was made, resulting in 45181 contigs, representing ‘transcript tags’. These transcript tags were annotated with gene ontology (GO) terms. One of the most striking results from the expression analysis was that the drought sensitive plants were characterised by having approximately twice the number of differentially expressed transcript tags than the tolerant plants after drought. This difference was evident in most of the major GO terms. Before onset of drought the sensitive plants overexpressed a number of genes annotated as senescence-related. Furthermore, the concentration of three metabolites, particularly pinitol, but also proline and malate increased in leaves after drought stress. This de novo assembly of a red clover transcriptome from leaf material of droughted and non-droughted plants provides a rich source for gene identification, single nucleotide polymorphisms (SNP) and short sequence repeats (SSR). Comparison of gene expression levels between pools and treatments identified candidate genes for further analysis of the genetic basis of drought tolerance in red clover.

In plant breeding and agricultural research, biplot analysis has become an important statistical technique. The goal of this study was to find the winning genotype(s) for the test settings in a part of the Southwest region of Nigeria, as well as to investigate the nature and extent of genotype × environment interaction (GEI) effects on Bambara groundnut (BGN) production. The experiment was carried out in four environments (two separate sites, Ibadan and Ikenne, for two consecutive years, 2018 and 2019) with ninety-five BGN accessions. According to the combined analysis of variance over environments, genotypes and GEI both had a substantial (p < 0.001) impact on BGN yield. The results revealed that BGN accessions performed differently in different test conditions, indicating that the interaction was crossover in nature. The results revealed that BGN accessions performed differently in different test conditions, indicating that the interaction was crossover in nature. To examine and show the pattern of the interaction components, biplots with the genotype main effect and genotype × environment interaction (GEI) were used. The first two PCs explained 80% of the total variation of the GGE model (i.e., G + GE) (PC1 = 48.59%, PC2 = 31.41%). The accessions that performed best in each environment based on the “which-won-where” polygon were TVSu-2031, TVSu-1724, TVSu-1742, TVSu-2022, TVSu-1943, TVSu-1892, TVSu-1557, TVSu-2060, and TVSu-2017. Among these accessions, TVSu-2017, TVSu-1557, TVSu-2060, TVSu-1892, and TVSu-1943 were among the highest-yielding accessions on the field. The adaptable accessions were TVSu-1763, TVSu-1899, TVSu-2019, TVSu-1898, TVSu-1957, TVSu-2021, and TVSu-1850, and the stable accessions were TVSu-1589, TVSu-1905, and TVSu-2048. In terms of discriminating and representativeness for the environments, Ibadan 2019 is deemed to be a superior environment. The selected accessions are recommended as parental lines in breeding programs for grain yield improvement in Ibadan or Ikenne or similar agro-ecological zones.

Adopting underutilized legumes in tackling food security is essential, especially in this era of climate change. Underutilized legumes are embedded with inherent potentials such as the ability to survive in extreme conditions (such as temperature, drought, pH, saline, etc.), high nitrogen-fixing potential, weed and disease control ability, and high nutrient status. Underutilized legumes can improve the yield of companion crops in an intercropping system and as a subsequent crop (due to their residual effects). They possess symbiotic and non-symbiotic organisms in their nodules, and also have different organisms in their bulk soil, rhizoplanes and rhizosphere, which can fix nitrogen, solubilize phosphorus or produce exudates which help in improving plant growth. Also, they contain some phytochemicals, including alkaloids, saponin, amino acids, organic and inorganic minerals, and compounds that help improve human health and prevent diseases. Hence, this review discusses the current status, role, challenges and the prospects of underutilized legumes in food security.

Constant production of quality food should be a norm in any community, but climate change, increasing population, and unavailability of land for farming affect food production. As a result, food scarcity is affecting some communities, especially in the developing world. Finding a stable solution to this problem is a major cause of concern for researchers. Synergistic application of molecular marker techniques with next generation sequencing (NGS) technologies can unlock the potentials hidden in most crop genomes for improving yield and food availability. Most crops such as Bambara groundnut (BGN), Winged bean, and African yam bean are underutilized. These underutilized crops can compete with the major crops such as cowpea, soybean, maize, and rice, in areas of nutrition, ability to withstand drought stress, economic importance, and food production. One of these underutilized crops, BGN [Vigna subterranea(L.), Verdc.], is an indigenous African legume and can survive in tropical climates and marginal soils. In this review, we focus on the roles of BGN and the opportunities it possesses in tackling food insecurity and its benefits to local farmers. We will discuss BGN’s potential impact on global food production and how the advances in NGS technologies can enhance its production.