Genomics-Assisted Germplasm Characterization and Trait Mapping in Rice Bean (Vigna umbellata)

Rice bean is an important legume food crop cultivated in Asia, with considerable implications for sustainable crop production and food security under changing climate conditions. It is an underutilized crop with limited genetic and genomic research data. Although it remains unknown when and where rice bean was domesticated, the cultivated form of rice bean is currently considered to be a “semidomesticated” crop. There is an urgent need for rice bean (Vigna umbellata (Thunb.) Ohwi and Ohashi) germplasm characterization and genetic improvement, which can transform this semidomesticated crop into a fully domesticated and mainstream crop. In addition, the relatively high genetic diversity of rice bean can be exploited for the genetic improvement of other Vigna crop species. Genomics-assisted breeding and gene editing are promising approaches for the efficient and rapid development of new crop cultivars with improved architecture, phenology, yield, quality, and resistance to biotic and abiotic stresses. Rice bean genome research was initiated 30 years ago, but significant progress in terms of genomic resource development (e.g., DNA markers, genetic linkage maps, and reference genome sequences), germplasm characterization at the molecular level, and QTL/gene discovery occurred relatively recently. More specifically, two chromosome-scale rice bean reference genomes were constructed using advanced sequencing technology and then used to develop DNA markers and identify candidate genes for complex traits. In this chapter, we provide an overview of the progress and current status of rice bean genomics research. We also summarize and discuss results from studies conducted to clarify rice bean genetic diversity and the genetic basis of agronomic- and yield-related traits as well as biotic and abiotic stress resistance.