Just Accepted

This article has been peer reviewed and accepted for publication. It is in production and has not been edited, so may differ from the final published form.

Insight into a region of chickpea chromosome 2 revealed potential candidate genes linked to Foc4 Fusarium wilt resistance

Karma Bhutia , Anima Kisku, Bharati Lap, Sangita Sahni, Madhuri Arya, Nangsol Bhutia, Mahtab Ahmad, Rashmi Chaturvedi, Vinay Sharma

Abstract

The region in chromosome 2 of chickpea flanked by markers TA59 and TR19 have been reported to be associated with race4 (Foc4) Fusarium wilt resistance and these two markers are frequently utilized in marker assisted breeding of chickpeas against Foc4 wilt. However, this region in chromosome 2 is significantly large and remains unexplored for the identification of potential candidate genes that is actually conferring resistance to Foc4 wilt. Thus, the current experiment was carried out to investigate and characterize the genes present in this region utilizing in silico as well as a marker trait association analysis (MTA) approach. NCBI customized nucleotide search tool based exploration of region on chickpea chromosome 2 flanked by TA59 and TR19 markers revealed a total of 225 proteins encoding genes were present in the targeted region. Their expression pattern was retrieved from shoot transcriptome data of two contrasting chickpea genotypes under Foc4 wilt from NCBI SRA database and statistical analysis was performed to identify genes showing significant differential expression in terms of log fold change (LogFC). Among 225 genes, 51 of them showed significant differential expressions under Foc4 wilt. Further In silico analysis such as identification of cis-acting elements in 5’UTR, protein-protein interactions revealed their potential involvement in stress responses. For MTA, 244 diverse set of chickpea genotypes were phenotyped for Fusarium wilt disease incidence % (DI %) under a designated Fusarium wilt sick plot. Simultaneously, the single nucleotide polymorphism (SNPs) specific to 51 potential candidate genes present in 244 chickpea genotypes were retrieved from CicerSeq database. Genotyping of 244 chickpea genotypes was done first with TA59 and TR19 markers and based on the amplification pattern of TA59 marker and DI% observed, 40 highly resistant and 40 highly susceptible bulks of genotypes were selected. Subsequently, the selected contrasting set of 80 genotypes as well as whole population of 244 chickpea genotypes were further genotyped with1238 SNPs specific to 51 different genes. The SNPs based genotypic data and DI % phenotypic data of chickpea genotypes was then used in an MTA analysis first in contrasting set of 80 genotypes (40 resistant and 40 highly susceptible) followed by 244 diverse sets of chickpeas genotypes to determine SNPs association with the DI% using TASSEL software and simple linear regression model in MS excel. The results showed that out of 1238 SNPs, only 7 SNPs were significantly correlated with DI %. The regression analysis revealed that the SNP Ca2_24099002, specific to LOC101498008 (Transmembrane protein 87A) gene, accounted for 16.30 % of the highest phenotypic variance for DI %, while SNPs Ca2_25166118 and Ca2_27029215, specific to LOC101494644 (β-glucosidase BoGH3B-like) and LOC101505289 (Putative tRNA pseudouridine synthase) genes, explained 10.51 % and 10.50 % of the variation, respectively in selected set of contrasting population. These SNPs can be effectively utilized together with the TA59 and TR19 markers in a chickpea breeding scheme to develop Foc4 wilt resistance.

FP24068  Accepted 16 July 2024

© CSIRO 2024