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. 2023 Oct 20:14:1274759.
doi: 10.3389/fpls.2023.1274759. eCollection 2023.

High confidence QTLs and key genes identified using Meta-QTL analysis for enhancing heat tolerance in chickpea (Cicer arietinum L.)

Raj Kumar  1   2 , Vinay Kumar Sharma  1 , Sagar Krushnaji Rangari  1   2 , Uday Chand Jha  3 , Aakash Sahu  1 , Pronob J Paul  2   4 , Shreshth Gupta  1 , Sunil S Gangurde  5 , Himabindu Kudapa  2 , Reyazul Rouf Mir  6 , Pooran M Gaur  2 , Rajeev K Varshney  7 , Dinakaran Elango  8 , Mahendar Thudi  1   9
Affiliations

High confidence QTLs and key genes identified using Meta-QTL analysis for enhancing heat tolerance in chickpea (Cicer arietinum L.)

Raj Kumar et al. Front Plant Sci. .

Abstract

The rising global temperatures seriously threaten sustainable crop production, particularly the productivity and production of heat-sensitive crops like chickpeas. Multiple QTLs have been identified to enhance the heat stress tolerance in chickpeas, but their successful use in breeding programs remains limited. Towards this direction, we constructed a high-density genetic map spanning 2233.5 cM with 1069 markers. Using 138 QTLs reported earlier, we identified six Meta-QTL regions for heat tolerance whose confidence interval was reduced by 2.7-folds compared to the reported QTLs. Meta-QTLs identified on CaLG01 and CaLG06 harbor QTLs for important traits, including days to 50% flowering, days to maturity, days to flower initiation, days to pod initiation, number of filled pods, visual score, seed yield per plant, biological yield per plant, chlorophyll content, and harvest index. In addition, key genes identified in Meta-QTL regions like Pollen receptor-like kinase 3 (CaPRK3), Flowering-promoting factor 1 (CaFPF1), Flowering Locus C (CaFLC), Heat stress transcription factor A-5 (CaHsfsA5), and Pollen-specific leucine-rich repeat extensins (CaLRXs) play an important role in regulating the flowering time, pollen germination, and growth. The consensus genomic regions, and the key genes reported in this study can be used in genomics-assisted breeding for enhancing heat tolerance and developing heat-resilient chickpea cultivars.

Keywords: Meta-QTLs; candidate genes; confidence interval; heat stress; recombinant inbred lines.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The reviewer RS declared a shared affiliation with the authors PG, HK to the handling editor at the time of review. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision.

Figures

Figure 1
Figure 1
Comparison of confidence interval (CI) between original QTL and Meta-QTL; CaLG03 shown maximum reduction in CI (four times against original QTL) but CaLG07 shown minimum reduction in CI.
Figure 2
Figure 2
Circos indicating the projected QTLs, Meta-QTLs and genes. From outside to inside , Track 1 representing ideogram of linkage groups and black bands are showing marker density; Track 2 representing the histogram of projected QTLs and width of histogram is showing the confidence interval; Track 3 representing heatmap of identified Meta-QTLs and width of heatmap is indicating the reduction in confidence interval of Meta-QTLs; Track 4 representing magnified view of accepted Meta-QTL regions into the redundant physical interval; Track 5 representing the density map of identified candidate genes.
See this image and copyright information in PMC

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