Consensus genomic regions associated with grain protein content in hexaploid and tetraploid wheat

Pooja Saini; Imran Sheikh; Dinesh Kumar Saini; Reyazul Rouf Mir; Harcharan Singh Dhaliwal; Vikrant Tyagi

doi:10.3389/fgene.2022.1021180

Consensus genomic regions associated with grain protein content in hexaploid and tetraploid wheat

Front Genet. 2022 Sep 28:13:1021180. doi: 10.3389/fgene.2022.1021180. eCollection 2022.

Authors

Pooja Saini¹, Imran Sheikh¹, Dinesh Kumar Saini², Reyazul Rouf Mir³, Harcharan Singh Dhaliwal¹, Vikrant Tyagi¹

Affiliations

¹ Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, India.
² Department of Plant Breeding and Genetics, Punajb Agricultural University, Ludhiana, India.
³ Division of Genetics and Plant Breeding, Faculty of Agriculture SKUAST-Kashmir, Srinagar, India.

Abstract

A meta-analysis of QTLs associated with grain protein content (GPC) was conducted in hexaploid and tetraploid wheat to identify robust and stable meta-QTLs (MQTLs). For this purpose, as many as 459 GPC-related QTLs retrieved from 48 linkage-based QTL mapping studies were projected onto the newly developed wheat consensus map. The analysis resulted in the prediction of 57 MQTLs and 7 QTL hotspots located on all wheat chromosomes (except chromosomes 1D and 4D) and the average confidence interval reduced 2.71-fold in the MQTLs and QTL hotspots compared to the initial QTLs. The physical regions occupied by the MQTLs ranged from 140 bp to 224.02 Mb with an average of 15.2 Mb, whereas the physical regions occupied by QTL hotspots ranged from 1.81 Mb to 36.03 Mb with a mean of 8.82 Mb. Nineteen MQTLs and two QTL hotspots were also found to be co-localized with 45 significant SNPs identified in 16 previously published genome-wide association studies in wheat. Candidate gene (CG) investigation within some selected MQTLs led to the identification of 705 gene models which also included 96 high-confidence CGs showing significant expressions in different grain-related tissues and having probable roles in GPC regulation. These significantly expressed CGs mainly involved the genes/gene families encoding for the following proteins: aminotransferases, early nodulin 93, glutamine synthetases, invertase/pectin methylesterase inhibitors, protein BIG GRAIN 1-like, cytochrome P450, glycosyl transferases, hexokinases, small GTPases, UDP-glucuronosyl/UDP-glucosyltransferases, and EamA, SANT/Myb, GNAT, thioredoxin, phytocyanin, and homeobox domains containing proteins. Further, eight genes including GPC-B1, Glu-B1-1b, Glu-1By9, TaBiP1, GSr, TaNAC019-A, TaNAC019-D, and bZIP-TF SPA already known to be associated with GPC were also detected within some of the MQTL regions confirming the efficacy of MQTLs predicted during the current study.

Keywords: QTL hotspots; candidate gene; expression analysis; mQTLs; wheat.