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

Abstract

Grain legumes form an important component of the human diet, provide feed for livestock, and replenish soil fertility through biological nitrogen fixation. Globally, the demand for food legumes is increasing as they complement cereals in protein requirements and possess a high percentage of digestible protein. Climate change has enhanced the frequency and intensity of drought stress, posing serious production constraints, especially in rainfed regions where most legumes are produced. Genetic improvement of legumes, like other crops, is mostly based on pedigree and performance-based selection over the past half century. To achieve faster genetic gains in legumes in rainfed conditions, this review proposes the integration of modern genomics approaches, high throughput phenomics, and simulation modelling in support of crop improvement that leads to improved varieties that perform with appropriate agronomy. Selection intensity, generation interval, and improved operational efficiencies in breeding are expected to further enhance the genetic gain in experimental plots. Improved seed access to farmers, combined with appropriate agronomic packages in farmers' fields, will deliver higher genetic gains. Enhanced genetic gains, including not only productivity but also nutritional and market traits, will increase the profitability of farming and the availability of affordable nutritious food especially in developing countries.

Whole‐genome resequencing‐based QTL‐seq identified candidate genes and molecular markers for fresh seed dormancy in groundnut

“…Advent of next‐generation sequencing (NGS) technologies has greatly facilitated development of genome assembly, trait mapping and candidate gene discovery (Varshney et al ., ). Thus, NGS technology has augmented faster and precise trait discovery through rapid detection of linked genomic regions (also gene discovery), trait‐associated polymorphism and identification of diagnostic markers (Varshney et al ., , ,b). There are several sequencing‐based trait‐mapping approaches which provide faster discovery of candidate genes and facilitate marker development; and one of such approach for trait mapping is QTL‐seq (Pandey et al ., ; Takagi et al ., ).…”

“…Many of these efforts facilitated successful development of diagnostic markers which are being deployed in GAB. In coming years, there will be a shift from GAB to sequence-based breeding (Varshney et al, 2018a) and these SNP-based diagnostic markers will be of great use in enhancing the modernization and precision of breeding programmes for achieving higher genetic gains in farmers' field (Varshney et al, 2018b).…”

“…Genomics‐assisted breeding (GAB) can significantly shorten the breeding cycle time for the improvement of elite cultivars with desired traits (Varshney et al ., , ,b). Notably, for the fruitful GAB, primary requirement is identification of marker tightly linked with the desired trait(s).…”

Integrating genomics for chickpea improvement: achievements and opportunities

“…NGS technology has resulted in development and application of a wide variety of molecular markers for chickpea improvement (Thudi et al 2011(Thudi et al , 2014Jaganathan et al 2015;Kale et al 2015;Varshney et al 2018). Over the past decade, more than 2000 simple sequence repeat (SSR) markers, 15,000 features-based diversity array technology (DArT) platform and millions of SNP markers have been developed for chickpea (Varshney 2016).…”

Polyamines and legumes: Joint stories of stress, nitrogen fixation and environment

“…In this scenario, a considerable effort is required to increase production of rainfed legumes, via the adaptation of cropping systems and the design of new plant varieties (Tester and Langridge, 2010;Varshney et al, 2018). The water deficit affects a broad spectrum of plant functions such as transpiration, photosynthesis, leaf and root growth, and reproductive development (Chaves et al, 2003;Fuad-Hassan et al, 2008), impacting on cell division, hydraulics, cell wall mechanics, primary and secondary metabolism and ROS detoxification.…”