Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.)

Physical map of chickpea was developed for the reference chickpea genotype (ICC 4958) using bacterial artificial chromosome (BAC) libraries targeting 71,094 clones (~12× coverage). High information content fingerprinting (HICF) of these clones gave high-quality fingerprinting data for 67,483 clones, and 1,174 contigs comprising 46,112 clones and 3,256 singletons were defined. In brief, 574 Mb genome size was assembled in 1,174 contigs with an average of 0.49 Mb per contig and 3,256 singletons represent 407 Mb genome. The physical map was linked with two genetic maps with the help of 245 BAC-end sequence (BES)-derived simple sequence repeat (SSR) markers. This allowed locating some of the BACs in the vicinity of some important quantitative trait loci (QTLs) for drought tolerance and reistance to Fusarium wilt and Ascochyta blight. In addition, fingerprinted contig (FPC) assembly was also integrated with the draft genome sequence of chickpea. As a result, ~965 BACs including 163 minimum tilling path (MTP) clones could be mapped on eight pseudo-molecules of chickpea forming 491 hypothetical contigs representing 54,013,992 bp (~54 Mb) of the draft genome. Comprehensive analysis of markers in abiotic and biotic stress tolerance QTL regions led to identification of 654, 306 and 23 genes in drought tolerance “QTL-hotspot” region, Ascochyta blight resistance QTL region and Fusarium wilt resistance QTL region, respectively. Integrated physical, genetic and genome map should provide a foundation for cloning and isolation of QTLs/genes for molecular dissection of traits as well as markers for molecular breeding for chickpea improvement

Chickpea

The narrow genetic base of cultivated chickpea warrants systematic collection, documentation and evaluation of chickpea germplasm and particularly wild Cicer species for effective and efficient use in chickpea breeding programmes. Limiting factors to crop production, possible solutions and ways to overcome them, importance of wild relatives and barriers to alien gene introgression and strategies to overcome them and traits for base broadening have been discussed. It has been clearly demonstrated that resistance to major biotic and abiotic stresses can be successfully introgressed from the primary gene pool comprising progenitor species. However, many desirable traits including high degree of resistance to multiple stresses that are present in the species belonging to secondary and tertiary gene pools can also be introgressed by using special techniques to overcome pre- and post-fertilization barriers. Besides resistance to various biotic and abiotic stresses, the yield QTLs have also been introgressed from wild Cicer species to cultivated varieties. Status and importance of molecular markers, genome mapping and genomic tools for chickpea improvement are elaborated. Because of major genes for various biotic and abiotic stresses, the transfer of agronomically important traits into elite cultivars has been made easy and practical through marker-assisted selection and marker-assisted backcross. The usefulness of molecular markers such as SSR and SNP for the construction of high-density genetic maps of chickpea and for the identification of genes/QTLs for stress resistance, quality and yield contributing traits has also been discussed

Abiotic and Biotic Stresses Interaction in Fabaceae Plants. Contributions from the Grain Legumes/Soilborne Vascular Diseases/Drought Stress Triangle

Editors: Mirza Hasanuzzaman, Susana Araújo, Sarvajeet Singh Gill.As sessile organisms, plants are constantly exposed to simultaneously abiotic and biotic stresses that impact growth thus resulting in significant yield losses. An example is drought and root infecting pathogens, which combined cause greater damage to plants than the stresses individually. Substantial information is available on the physiological, molecular, and metabolic changes in Fabaceae plants exposed to individual stresses, but little is known about how plants respond to multiple stresses. This is of primary importance for the development of breeding approaches based on the trade-off between plant defense response mechanisms, and high and consistent yield under field conditions. A better knowledge of the mechanisms by which legume plants perceive and transduce simultaneous or sequential combination of stress signals to initiate diverse adaptive responses is essential for breeding multiple stress-tolerant crop cultivars. In this chapter, we assess the relevance of understanding legume combined responses to abiotic and biotic stresses for production and breeding, focusing on soilborne vascular diseases and drought interaction in grain legumes. Particular attention is given to the crosstalk between signaling pathways of the “stress triangle” pathogen/host/environment interactions and to the application of integrated breeding methods aiming at multiple stress-resistant legume crops better adapted to climate change.Financial support by Fundação para a Ciência e Tecnologia (FCT), Portugal, is acknowledged through grant SFRH/BD/92160/2013 (STL), DL57 PhD holder contract (SA), IF/01337/2014 FCT Investigator contract (MCVP), research project BeGeQA (PTDC/AGR-TEC/3555/2012) and research unit GREEN-IT “Bioresources for Sustainability” (UID/Multi/04551/2019)