Mapping and identification of a Cicer arietinum NSP2 gene involved in nodulation pathway

Abstract

For the first time the putative NSP2 gene in chickpea has been identified using pairs of NILs differing for the Rn1 / rn1 nodulation gene that was located in LG5 of chickpea genetic map. An intraspecific cross between the mutant non-nodulating genotype PM233, carrying the recessive gene rn1, and the wild-type CA2139 was used to develop two pairs of near-isogenic lines (NILs) for nodulation in chickpea. These pairs of NILs were characterized using sequence tagged microsatellite site (STMS) markers distributed across different linkage groups (LGs) of the chickpea genetic map leading to the detection of polymorphic markers located in LG5. Using this information, together with the genome annotation in Medicago truncatula, a candidate gene (NSP2) known to be involved in nodulation pathway was selected for mapping in chickpea. The full length sequence obtained in chickpea wild-type (CaNSP2) was 1,503 bp. Linkage analysis in an F3 population of 118 plants derived from the cross between the pair of NILS NIL7-2A (nod) × NIL7-2B (non-nod) revealed a co-localization between CaNSP2 and Rn1 gene. These data implicate the CaNSP2 gene as a candidate for identity to Rn1, and suggest that it could act in the nodulation signaling transduction pathway similarly to that in other legumes species.

Advances in Host Plant and Rhizobium Genomics to Enhance Symbiotic Nitrogen Fixation in Grain Legumes

“…The former is associated with differences in growth and possibly yield and N accumulation between climbing and bush beans, while the latter with total amount of symbiotic nitrogen fixed. Further, the extensive conservation of gene order between chickpea and a model plant M. truncatula (Seres et al, 2007) have allowed researchers identify a candidate gene, CaNSP2, involved in nodulation pathway in chickpea, which had shown 85-86% sequence similarity to that reported for NSP2 genes in pea and M. truncatula (Ali et al, 2014). In pea, 7 root QTL and 11 nodule QTL were detected in region of LG I close to Af gene (LG I-Af), with several QTL for root or nodule traits and seed N accumulation QTL mapped in similar regions that highlight the possibility of breeding new pea cultivars with increased root system size, sustained nodule number, and improved N nutrition (Bourion et al, 2010).…”

Deploying QTL-seq for rapid delineation of a potential candidate gene underlying major trait-associated QTL in chickpea

“…3 – 27 However, only limited number of these QTLs alongside the QTLs regulating seed weight, nodulation, drought tolerance, and Fusarium wilt and Ascochyta blight resistance traits have been fine mapped till date and subsequently utilized for marker-assisted genetic improvement of chickpea. 23 , 24 , 26 – 29 To drive the fine mapping of trait-regulating QTLs, the large-scale genotyping of simple sequence repeat (SSR) and prior discovered single-nucleotide polymorphism (SNP) markers in individuals of inter-/intra-specific mapping populations employing multiple high-throughput genotyping assays are found to be fairly suitable in chickpea. 30 – 32 , 24 This includes SSR markers-based genotyping assay like fluorescent dye-labelled automated fragment analyzer and array-based genotyping platforms, including Illumina GoldenGate/Infinium and Competitive Allele Specific PCR (KASPar) assays and MALDI-TOF (matrix-assisted laser desorption ionization-time of flight) mass array for large-scale genotyping of SNP markers.…”

Comparative transcriptome analysis of nodules of two Mesorhizobium–chickpea associations with differential symbiotic efficiency under phosphate deficiency

“…In addition to genes involved in hormone metabolism, the XM_004492427 . 2 gene that putatively encodes a nodulation signalling pathway 2‐like (NSP2), which is required for initiating transcription of the early nodulin ( ENOD ) gene and cell division events in the root cortex and consequently nodulation (Ali et al ., ; Ferguson et al ., ), was up‐regulated in Mm SWRI9‐Pd/ Mm SWRI9‐Ps by 2.44‐fold, but not in Mc CP‐31‐Pd/ Mc CP‐31‐Ps (Table ). Thus, up‐regulation of the NSP2 gene may also be another factor contributing to the production of more nodules in Mm SWRI9‐inoculated plants (Nasr Esfahani et al ., ).…”