Search

Cytoplasmic male sterility(CMS), a maternally inherited trait, provides a promising means to harness yield gains associated with hybrid vigor. In pigeonpea [Cajanus cajan (L.) Huth], nine types of sterility‐inducing cytoplasm have been reported, of which A2 and A4 have been successfully deployed in hybrid breeding. Unfortunately, molecular mechanism of the CMS trait is poorly understood because of limited research invested. More recently, an association between a mitochondrial gene (nad7) and A4‐CMS has been demonstrated in pigeonpea; however, the mechanism underlying A2‐CMS still remains obscure. The current investigation aimed to analyze the differences in A2‐CMS line (ICPL 88039A) and its isogenic maintainer line (ICPL 88039B) at transcriptome level using next‐generation sequencing. Gene expression profiling uncovered a set of 505 genes that showed altered expression in response to CMS, of which, 412 genes were upregulated while 93 were downregulated in the fertile maintainer line vs. the CMS line. Further, gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and protein–protein interaction (PPI) network analyses revealed association of CMS in pigeonpea with four major pathways: glucose and lipid metabolism, ATP production, pollen development and pollen tube growth, and reactive oxygen species (ROS) scavenging. Patterns of digital gene expression were confirmed by quantitative real‐time polymerase chain reaction (qRT‐PCR) of six candidate genes. This study elucidates candidate genes and metabolic pathways having potential associations with pollen development and male sterility in pigeonpea A2‐CMS. New insights on molecular mechanism of CMS trait in pigeonpea will be helpful to accelerate heterosis utilization for enhancing productivity gains in pigeonpea.

The genetic base of 150 pigeonpea varieties released in India during1960 to 2018 was examined. Of these, 89, 57, three, and one variety were developed by pedigree selection, pureline selection, mutation and population improvement, respectively. Examination of pedigree records of 89 pigeonpea varieties developed through pedigree breeding method between 1971 and 2018 traced back to 113 ancestors. The highest mean genetic contribution was recorded for the genotype T 190 (0.051) accompanied by UPAS 120 (0.049) and ICP 8863 (0.043). The ancestor T 190 appeared with highest frequency of 21, directly as one of the parent (male/female) in four varieties and indirectly in the development of 17 varieties. Similarly, the ancestors UPAS 120 and ICP 8863 were more frequently used (in nine varieties) as direct parents followed by T 21 and C 11 (in five varieties). The variety PRG 176 involved the highest number (9) of ancestors during the course of its development followed by the variety VBN (Rg) 3 with eight ancestors. Results indicated that 51.69% (46 of the 89 varieties) of released varieties were developed through bi-parental crossing whereas 48.31% involved multiple parents. The frequent use of a limited number of ancestors has caused the narrow genetic base of released pigeonpea varieties. We recommend large-scale deployment of novel germplasm resources for generating broad-base breeding populations. This will help to obtain improved pigeonpea cultivars with high grain yield, biotic tolerance and climate adaptation.

Seed traits present important breeding targets for enhancing grain yield and quality in various grain legume crops including pigeonpea. The present study reports significant genetic variation for six seed traits including seed length (SL), seed width (SW), seed thickness (ST), seed weight (SWT), electrical conductivity (EC) and water uptake (WU) among Cajanus cajan (L.) Millspaugh acc. ICPL 20340 and Cajanus scarabaeoides (L.) Thouars acc. ICP 15739 and an F2 population derived from this interspecific cross. Maximum phenotypic values recorded for the F2 population were higher than observed in the parent ICPL 20340 [F2 max vs ICPL 20340: SW (7.05 vs 5.38), ST (4.63 vs 4.51), EC (65.17 vs 9.72), WU (213.17 vs 109.5)], which suggested contribution of positive alleles from the wild parent, ICP 15739. Concurrently, to identify the QTL controlling these seed traits, we assayed two parents and 94 F2 individuals with 113 polymorphic simple sequence repeat (SSR) markers. In the F2 population, 98 of the 113 SSRs showed Mendelian segregation ratio 1:2:1, whereas significant deviations were observed for 15 SSRs with their χ(2) values ranging between 6.26 and 20.62. A partial genetic linkage map comprising 83 SSR loci was constructed. QTL analysis identified 15 marker-trait associations (MTAs) for seed traits on four linkage groups i.e. LG01, LG02, LG04 and LG05. Phenotypic variations (PVs) explained by these QTL ranged from 4.4 (WU) to 19.91% (EC). These genomic regions contributing significantly towards observed variability of seed traits would serve as potential candidates for future research that aims to improve seed traits in pigeonpea. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13205-020-02423-x) contains supplementary material, which is available to authorized users.

Chickpea production is seriously challenged by various biotic and abiotic stresses globally. Among the various abiotic stresses, drought, heat, salinity and cold stresses are the major factors that restrict sustainable global chickpea production. Considerable progress has been made in developing drought, heat, cold and salinity stress-tolerant chickpea genotypes through conventional breeding approaches in concert with advanced breeding methods. Concurrently, current progress of molecular marker technology and availability of high-density genetic maps allowed genetic dissection of various abiotic stresses through biparental QTL mapping approach in chickpea. Subsequently, release of draft chickpea genome sequences greatly enriched chickpea genomic repertoire that provided us great opportunity for exploring the novel genetic determinants/haplotypes controlling these stresses across the whole genome level through genome-wide association study (GWAS). In parallel, current efforts of re-sequencing of global chickpea germplasm hold great promise for exploring ‘haplotype assembly’ carrying allelic variations for various abiotic stresses. Likewise, rapid advances in functional genomic approaches have enabled in unfolding the candidate gene(s) underlying the QTLs controlling these abiotic stresses, providing novel insights into the key molecular players participating in the complex mechanisms to acclimatize chickpea against various abiotic stress stimuli. In this chapter, we cover the effects of various abiotic stresses in chickpea, scope of diverse gene pool enabling in tailoring abiotic stress-tolerant chickpea genotypes and the role of rapidly growing genomics and emerging phenomics approaches to measure precise spatio-temporal response of plant under abiotic stresses for bridging genotyping and phenotyping gap. Finally, we conclude the chapter by discussing feasibility and scope of novel breeding techniques including genomic selection, ‘speed breeding’ and genome editing tool that could help in accelerating desired genetic gain to ensure protein-based nutritional food security under the fluctuating global climate scenario.

Key message Given 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. Abstract The 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.