Genomics-assisted breeding in four major pulse crops of developing countries: present status and prospects

Abstract

Key messageGiven recent advances in pulse molecular biology, genomics-driven breeding has emerged as a promising approach to address the issues of limited genetic gain and low productivity in various pulse crops.AbstractThe global population is continuously increasing and is expected to reach nine billion by 2050. This huge population pressure will lead to severe shortage of food, natural resources and arable land. Such an alarming situation is most likely to arise in developing countries due to increase in the proportion of people suffering from protein and micronutrient malnutrition. Pulses being a primary and affordable source of proteins and minerals play a key role in alleviating the protein calorie malnutrition, micronutrient deficiencies and other undernourishment-related issues. Additionally, pulses are a vital source of livelihood generation for millions of resource-poor farmers practising agriculture in the semi-arid and sub-tropical regions. Limited success achieved through conventional breeding so far in most of the pulse crops will not be enough to feed the ever increasing population. In this context, genomics-assisted breeding (GAB) holds promise in enhancing the genetic gains. Though pulses have long been considered as orphan crops, recent advances in the area of pulse genomics are noteworthy, e.g. discovery of genome-wide genetic markers, high-throughput genotyping and sequencing platforms, high-density genetic linkage/QTL maps and, more importantly, the availability of whole-genome sequence. With genome sequence in hand, there is a great scope to apply genome-wide methods for trait mapping using association studies and to choose desirable genotypes via genomic selection. It is anticipated that GAB will speed up the progress of genetic improvement of pulses, leading to the rapid development of cultivars with higher yield, enhanced stress tolerance and wider adaptability.

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

“…Efforts are underway to sequence the remaining legume genomes. The past decade has witnessed an exponential increase in availability of genomic resources and their deployment in trait discovery and breeding (see Bohra et al, 2014;Varshney et al, 2015;Pandey et al, 2016). As a result, several of these legume crops have genomic resources and associated phenotypic data to support genomics-based discovery and breeding approaches to develop superior legume varieties.…”

Characterisation of Faba Bean (Vicia faba L.) Transcriptome Using RNA-Seq: Sequencing, De Novo Assembly, Annotation, and Expression Analysis

“…Faba bean (Vicia faba L.) is a cool-season legume species, producing protein-rich grain not only for human production (particularly in Western Asia and Northern Africa), but also for livestock feed in developed regions, such as Europe and Australia [1,2]. Global cultivation on 2.4 Mha in 2012 produced circa 4 Mt [3], the primary production countries being China, Ethiopia, Morocco, and Australia.…”

“…), and downy mildew (caused by Peronospora viciae [Berk.] Caspary) [1,4,5]. Constraints due to environmental stresses, such as drought [6], salinity [7], and of the respective transcriptome assemblies have been made to the gene complements of several related species.…”

Perspectives on the Application of Next-generation Sequencing to the Improvement of Africa’s Staple Food Crops

“…The genome sequences of many major world crops have been completed in the past decade, as well as a few crops of specific importance to the developing world, including cassava, yam, tef, pigeon pea, and peanut, while many still remain to be sequenced [11][12][13]. A drive to sequence more crop plants, particularly orphan crops of Africa, is in progress.…”

“…These approaches are being adopted in crops of importance in developing countries such as in maize and wheat [121], rice [124], pulses (legumes) [11], cassava [118,120], cowpea [125], lentil [126], soybean [127,128], and pigeon pea [129]. With respect to the best practice for GS, various models are being put forward [113].…”