Meta-QTLs, ortho-meta QTLs and related candidate genes for yield and its component traits under water stress in wheat (Triticum aestivum L.)

Anuj Kumar; Dinesh Kumar Saini; Gautam Saripalli; P K Sharma; H S Balyan; P K Gupta

doi:10.1007/s12298-023-01301-z

Meta-QTLs, ortho-meta QTLs and related candidate genes for yield and its component traits under water stress in wheat (Triticum aestivum L.)

Physiol Mol Biol Plants. 2023 Apr;29(4):525-542. doi: 10.1007/s12298-023-01301-z. Epub 2023 Apr 11.

Authors

Anuj Kumar¹, Dinesh Kumar Saini², Gautam Saripalli³, P K Sharma¹, H S Balyan¹, P K Gupta¹

Affiliations

¹ Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India.
² Punjab Agricultural University, Ludhiana, Punjab India.
³ Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742 USA.

Abstract

Meta-QTLs (MQTLs), ortho-MQTLs, and related candidate genes (CGs) for yield and its seven component traits evaluated under water deficit conditions were identified in wheat. For this purpose, a high density consensus map and 318 known QTLs were used for identification of 56 MQTLs. Confidence intervals (CIs) of the MQTLs were narrower (0.7-21 cM; mean = 5.95 cM) than the CIs of the known QTLs (0.4-66.6 cM; mean = 12.72 cM). Forty-seven MQTLs were co-located with marker trait associations reported in previous genome-wide association studies. Nine selected MQTLs were declared as 'breeders MQTLs' for use in marker-assisted breeding (MAB). Utilizing known MQTLs and synteny/collinearity among wheat, rice and maize, 12 ortho-MQTLs were also identified. A total of 1497 CGs underlying MQTLs were also identified, which were subjected to in-silico expression analysis, leading to identification of 64 differentially expressed CGs (DECGs) under normal and water deficit conditions. These DECGs encoded a variety of proteins, including the following: zinc finger, cytochrome P450, AP2/ERF domain-containing proteins, plant peroxidase, glycosyl transferase, glycoside hydrolase. The expression of 12 CGs at seedling stage (3 h stress) was validated using qRT-PCR in two wheat genotypes, namely Excalibur (drought tolerant) and PBW343 (drought sensitive). Nine of the 12 CGs were up-regulated and three down-regulated in Excalibur. The results of the present study should prove useful for MAB, for fine mapping of promising MQTLs and for cloning of genes across the three cereals studied.

Supplementary information: The online version contains supplementary material available at 10.1007/s12298-023-01301-z.

Keywords: Candidate genes; MQTLs; Ortho-MQTLs; QTL; Water stress/drought; Wheat.

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