Unravelling consensus genomic regions associated with quality traits in wheat (Triticum aestivum L.) using meta-analysis of quantitative trait loci

Abstract

A meta-analysis of quantitative trait loci (QTLs) associated with following six major quality traits (i) arabinoxylan, (ii) dough rheology properties, (iii) nutritional traits, (iv) polyphenol content, (v) processing quality traits, and (vi) sedimentation volume was conducted in wheat. For this purpose, as many as 2458 QTLs were collected from the 50 mapping studies published during 2013-20. Of the total QTLs, 1126 QTLs were projected on to the consensus map saturated with 2,50,077 markers resulting into the identification of 110 meta-QTLs (MQTLs) with average confidence interval (CI) of 5.6 cM. These MQTLs had 18.84 times reduced CI compared to CI of initial QTLs. Fifty-one (51) MQTLs were also verified with the marker-trait associations (MTAs) detected in earlier genome-wide association studies (GWAS). Physical region occupied by a single MQTL ranged from 0.12 to 749.71 Mb with an average of 130.25 Mb. Candidate gene mining allowed the identification of 2533 unique gene models from the MQTL regions. In-silico expression analysis discovered 439 differentially expressed gene models with >2 transcripts per million (TPM) expression in grains and related tissues which also included 44 high-confidence candidate genes known to be involved in the various cellular and biochemical processes related to quality traits. Further, nine functionally characterized wheat genes associated with grain protein content, high molecular weight glutenin and starch synthase enzymes were also found to be co-localized with some of the MQTLs. In addition, synteny analysis between wheat and rice MQTL regions identified 23 wheat MQTLs syntenic to 16 rice MQTLs. Furthermore, 64 wheat orthologues of 30 known rice genes were detected in 44 MQTL regions. These genes encoded proteins mainly belonging to the following families: starch synthase, glycosyl transferase, aldehyde dehydrogenase, SWEET sugar transporter, alpha amylase, glycoside hydrolase, glycogen debranching enzyme, protein kinase, peptidase, legumain and seed storage protein enzyme.

Consensus genomic regions associated with multiple abiotic stress tolerance in wheat and implications for wheat breeding

“…These ortho-MQTL regions were identified by integrating the two different approaches utilized by Saini et al 26 and Sandhu et al 20 , respectively. Ortho-MQTL analyses have recently been conducted in wheat for different traits including quality traits 28 , HS 33 , SS 30 , nitrogen use efficiency 24 , grain yield and component traits 22 . The discovery of ortho-MQTLs in closely related species shows their relevance and stability, as well as the reliability of associated genes 56 .…”

Consensus genomic regions associated with multiple abiotic stress tolerance in wheat and implications for wheat breeding

“…These ortho-MQTL regions were identified by integrating the two different approaches utilized by Saini et al 26 and Sandhu et al 20 , respectively. Ortho-MQTLs have recently been conducted in wheat for different traits including quality traits 28 , thermotolerance 33 , salinity stress tolerance 30 , nitrogen use efficiency 24 , grain yield and component traits 22 . The discovery of ortho-MQTLs in closely related species shows their relevance and stability, as well as the reliability of associated genes 54 .…”

“…The decrease of confidence intervals (CIs) in MQTLs, which leads to increased genetic resolution for marker-assisted breeding (MAB) and the identification of high-confidence candidate genes (CGs), is another advantage of this approach. For instance, meta-analysis of QTLs associated with several traits has already been conducted in wheat, for instance, disease resistance 21,22.23 , nitrogen use efficiency and root related traits 24,25 , yield and associated traits 26,27 , and quality traits 28,29 . In addition, meta-analysis of QTLs associated with some of the individual abiotic stresses has also been conducted previously, for instance, (i) salinity stress 30 , (ii) drought stress 31,32 , heat stress 31,33 and pre-harvest sprouting 72 .…”