Meta-QTLs, ortho-MQTLs and candidate genes for the traits contributing to salinity stress tolerance in common wheat (Triticum aestivum L.)

• Published in: Physiology and molecular biology of plants Vol. 27; no. 12; pp. 2767 - 2786
• Main Authors: Pal, Neeraj, Saini, Dinesh Kumar, Kumar, Sundip
• Format: Journal Article
• Language: English
• Published: New Delhi Springer India 01.12.2021; Springer Nature B.V
• Subjects: Acyltransferase; Biological and Medical Physics; Biomarkers; Biomedical and Life Sciences; Biophysics; Cell Biology; Cereals; Confidence intervals; Cytochrome; Cytochrome P450; Cytochromes P450; F-box protein; Gene mapping; Genes; Genome-wide association studies; Genomes; Glucosyltransferase; Glutathione; Glutathione transferase; Glycerol; Life Sciences; Meta-analysis; Phospholipids; Plant Physiology; Plant Sciences; Proteins; Quantitative trait loci; Research Article; Salinity; Salinity effects; Salinity tolerance; Synteny; Triticum aestivum; Wheat; Zinc finger proteins; MQTLs; QTLs; Wheat; Ortho-MQTLs; Salinity
• ISSN: 0971-5894; 0974-0430
• DOI: 10.1007/s12298-021-01112-0

A meta-analysis of QTLs associated with the traits contributing to salinity tolerance was undertaken in wheat to detect consensus and robust meta-QTLs (MQTLs) using 844 known QTLs retrieved from 26 earlier studies. A consensus map with a total length of 4621.56 cM including 7710 markers was constructed using 21 individual linkage maps and three previously published integrated genetic maps. Out of 844 QTLs, 571 QTLs were projected on the consensus map which gave origin to 100 MQTLs. Interestingly, 49 MQTLs were co-located with marker-trait associations reported in wheat genome-wide association studies for the traits contributing to salinity stress tolerance. Five potential MQTLs associated with the major salinity-responsive traits were also identified to be utilized in the breeding programme. In the resulted MQTLs, the average confidence interval (CI, 3.58 cM) was reduced up to 4.16 folds compared to the mean CI of the initial QTLs. Furthermore, as many as 617 gene models including 81 most likely candidate genes (CGs) were identified in the high confidence MQTL regions. These most likely CGs encoded proteins mainly belonging to the following families: B-box-type zinc finger, cytochrome P450 protein, pentatricopeptide repeat, phospholipid/glycerol acyltransferase, F-box protein, small auxin-up RNA, UDP-glucosyltransferase, glutathione S-transferase protein, etc. In addition, ortho-MQTL analysis based on synteny among wheat, rice and barley was also performed which permitted the identification of six ortho-MQTLs among these three cereals. This meta-analysis defines a genome-wide landscape on the most stable and consistent loci associated with reliable molecular markers and candidate genes for salinity tolerance in wheat.